AtlasBibTeX.bib

@article{albers2018,
  title = {The Archaellum: {{An}} Update on the Unique Archaeal Motility Structure},
  shorttitle = {The {{Archaellum}}},
  author = {Albers, Sonja-Verena and Jarrell, Ken F.},
  year = {2018},
  month = apr,
  volume = {26},
  pages = {351--362},
  issn = {1878-4380},
  doi = {10.1016/j.tim.2018.01.004},
  abstract = {Each of the three domains of life exhibits a unique motility structure: while Bacteria use flagella, Eukarya employ cilia, and Archaea swim using archaella. Since the new name for the archaeal motility structure was proposed, in 2012, a significant amount of new data on the regulation of transcription of archaella operons, the structure and function of archaellum subunits, their interactions, and cryo-EM data on in situ archaellum complexes in whole cells have been obtained. These data support the notion that the archaellum is evolutionary and structurally unrelated to the flagellum, but instead is related to archaeal and bacterial type IV pili and emphasize that it is a motility structure unique to the Archaea.},
  journal = {Trends Microbiol},
  keywords = {archaea,Archaea,archaeal flagellum,cryo-EM,Cytoskeleton,Fimbriae Proteins,Flagella,KaiC,Locomotion,Peptide Fragments,type IV pili},
  language = {eng},
  number = {4},
  pmid = {29452953}
}

@article{alberts1998,
  title = {The Cell as a Collection of Protein Machines: {{Preparing}} the next Generation of Molecular Biologists},
  shorttitle = {The Cell as a Collection of Protein Machines: Preparing the next Generation of Molecular Biologists},
  author = {Alberts, B.},
  year = {1998},
  month = feb,
  volume = {92},
  pages = {291--4},
  issn = {0092-8674 (Print) 0092-8674 (Linking)},
  doi = {10.1016/s0092-8674(00)80922-8},
  file = {/Users/coiko/Zotero/storage/T4HBMZGL/Alberts-1998-The cell as a collection of prote.pdf},
  journal = {Cell},
  keywords = {*Molecular Biology,Cells/*chemistry,Macromolecular Substances,Proteins/*chemistry},
  number = {3}
}

@article{armbruster2012,
  title = {Merging Mythology and Morphology: The Multifaceted Lifestyle of {{Proteus}} Mirabilis},
  shorttitle = {Merging Mythology and Morphology},
  author = {Armbruster, Chelsie E. and Mobley, Harry L. T.},
  year = {2012},
  month = nov,
  volume = {10},
  pages = {743--754},
  issn = {1740-1526, 1740-1534},
  doi = {10.1038/nrmicro2890},
  abstract = {Proteus mirabilis, named for the Greek god who changed shape to avoid capture, has fascinated microbiologists for more than a century with its unique swarming differentiation, Dienes line formation and potent urease activity. Transcriptome profiling during both host infection and swarming motility, coupled with the availability of the complete genome sequence for P. mirabilis, has revealed the occurrence of interbacterial competition and killing through a type VI secretion system, and the reciprocal regulation of adhesion and motility, as well as the intimate connections between metabolism, swarming and virulence. This Review addresses some of the unique and recently described aspects of P. mirabilis biology and pathogenesis, and emphasizes the potential role of this bacterium in single- species and polymicrobial urinary tract infections.},
  file = {/Users/coiko/Zotero/storage/ZB42AETU/Armbruster and Mobley - 2012 - Merging mythology and morphology the multifaceted.pdf},
  journal = {Nat Rev Microbiol},
  language = {en},
  number = {11}
}

@article{badrinarayanan2015,
  title = {Bacterial Chromosome Organization and Segregation},
  shorttitle = {Bacterial Chromosome Organization and Segregation},
  author = {Badrinarayanan, A. and Le, T. B. and Laub, M. T.},
  year = {2015},
  volume = {31},
  pages = {171--99},
  issn = {1530-8995 (Electronic) 1081-0706 (Linking)},
  doi = {10.1146/annurev-cellbio-100814-125211},
  abstract = {If fully stretched out, a typical bacterial chromosome would be nearly 1 mm long, approximately 1,000 times the length of a cell. Not only must cells massively compact their genetic material, but they must also organize their DNA in a manner that is compatible with a range of cellular processes, including DNA replication, DNA repair, homologous recombination, and horizontal gene transfer. Recent work, driven in part by technological advances, has begun to reveal the general principles of chromosome organization in bacteria. Here, drawing on studies of many different organisms, we review the emerging picture of how bacterial chromosomes are structured at multiple length scales, highlighting the functions of various DNA-binding proteins and the impact of physical forces. Additionally, we discuss the spatial dynamics of chromosomes, particularly during their segregation to daughter cells. Although there has been tremendous progress, we also highlight gaps that remain in understanding chromosome organization and segregation.},
  file = {/Users/coiko/Zotero/storage/RSLHH42X/Badrinarayanan-2015-Bacterial chromosome organ.pdf},
  journal = {Annu Rev Cell Dev Biol},
  keywords = {Animals,Bacteria/*genetics,Bacterial Proteins/genetics,Chromosome Segregation/*genetics,Chromosomes; Bacterial/*genetics,DNA Repair/genetics,DNA Replication/genetics,DNA-Binding Proteins/genetics,Hi-C,macrodomains,nucleoid-associated proteins,ParA-ParB-parS,supercoiling,transcription}
}

@article{barry2011,
  title = {Self-Assembling Enzymes and the Origins of the Cytoskeleton},
  shorttitle = {Self-Assembling Enzymes and the Origins of the Cytoskeleton},
  author = {Barry, R. M. and Gitai, Z.},
  year = {2011},
  month = dec,
  volume = {14},
  pages = {704--11},
  issn = {1879-0364 (Electronic) 1369-5274 (Linking)},
  doi = {10.1016/j.mib.2011.09.015},
  abstract = {The bacterial cytoskeleton is composed of a complex and diverse group of proteins that self-assemble into linear filaments. These filaments support and organize cellular architecture and provide a dynamic network controlling transport and localization within the cell. Here, we review recent discoveries related to a newly appreciated class of self-assembling proteins that expand our view of the bacterial cytoskeleton and provide potential explanations for its evolutionary origins. Specifically, several types of metabolic enzymes can form structures similar to established cytoskeletal filaments and, in some cases, these structures have been repurposed for structural uses independent of their normal roles. The behaviors of these enzymes suggest that some modern cytoskeletal proteins may have evolved from dual-role proteins with catalytic and structural functions.},
  file = {/Users/coiko/Zotero/storage/5CUGDF7D/Barry-2011-Self-assembling enzy.pdf;/Users/coiko/Zotero/storage/BEZ4TCVY/Barry-2011-Self-assembling enzy.pdf;/Users/coiko/Zotero/storage/PQ3JBTAU/Barry-2011-Self-assembling enzy.pdf},
  journal = {Curr Opin Microbiol},
  keywords = {*Protein Multimerization,Bacteria/*enzymology,Bacterial Proteins/*metabolism,Cytoskeletal Proteins/*metabolism,Cytoskeleton/*metabolism,Enzymes/*metabolism,Metabolic Networks and Pathways,Models; Biological,Protein Binding},
  number = {6}
}

@article{beeby2016,
  title = {Diverse High-Torque Bacterial Flagellar Motors Assemble Wider Stator Rings Using a Conserved Protein Scaffold},
  shorttitle = {Diverse High-Torque Bacterial Flagellar Motors Assemble Wider Stator Rings Using a Conserved Protein Scaffold},
  author = {Beeby, M. and Ribardo, D. A. and Brennan, C. A. and Ruby, E. G. and Jensen, G. J. and Hendrixson, D. R.},
  year = {2016},
  month = mar,
  volume = {113},
  pages = {E1917-26},
  issn = {1091-6490 (Electronic) 0027-8424 (Linking)},
  doi = {10.1073/pnas.1518952113},
  abstract = {Although it is known that diverse bacterial flagellar motors produce different torques, the mechanism underlying torque variation is unknown. To understand this difference better, we combined genetic analyses with electron cryo-tomography subtomogram averaging to determine in situ structures of flagellar motors that produce different torques, fromCampylobacterandVibriospecies. For the first time, to our knowledge, our results unambiguously locate the torque-generating stator complexes and show that diverse high-torque motors use variants of an ancestrally related family of structures to scaffold incorporation of additional stator complexes at wider radii from the axial driveshaft than in the model enteric motor. We identify the protein components of these additional scaffold structures and elucidate their sequential assembly, demonstrating that they are required for stator-complex incorporation. These proteins are widespread, suggesting that different bacteria have tailored torques to specific environments by scaffolding alternative stator placement and number. Our results quantitatively account for different motor torques, complete the assignment of the locations of the major flagellar components, and provide crucial constraints for understanding mechanisms of torque generation and the evolution of multiprotein complexes.},
  file = {/Users/coiko/Zotero/storage/6RSDAV2Y/Beeby et al. - 2016 - Diverse high-torque bacterial flagellar motors ass.pdf;/Users/coiko/Zotero/storage/AF2KNTWP/Beeby-2016-Diverse high-torque bacterial flage.pdf;/Users/coiko/Zotero/storage/D2KEW579/Beeby-2016-Diverse high-torque bacterial flage.pdf;/Users/coiko/Zotero/storage/F8YVVYNC/Beeby-2016-Diverse high-torque bacterial flage.pdf;/Users/coiko/Zotero/storage/KMP5ZHEB/Beeby-2016-Diverse high-torque bacterial flage.pdf;/Users/coiko/Zotero/storage/TMSI9GTR/Beeby-2016-Diverse high-torque bacterial flage.pdf},
  journal = {Proc Natl Acad Sci U S A},
  keywords = {bacterial flagellar motors,Bacterial Proteins,Bacterial Proteins/*chemistry/genetics/metabolism,Campylobacter,Campylobacter jejuni,Campylobacter jejuni/chemistry/cytology/genetics,electron cryo-tomography,Electron Microscope Tomography,Electron Microscope Tomography/methods,Flagella,Flagella/*chemistry,macromolecular evolution,Molecular Motor Proteins,Molecular Motor Proteins/*chemistry/metabolism,Multiprotein Complexes,Multiprotein Complexes/chemistry/metabolism,Protein Conformation,Salmonella,Salmonella/chemistry/cytology,torque,Torque,Vibrio,Vibrio/chemistry/cytology},
  number = {13},
  pmcid = {PMC4822576},
  pmid = {26976588}
}

@article{berg1988,
  title = {A Physicist Looks at Bacterial Chemotaxis},
  shorttitle = {A Physicist Looks at Bacterial Chemotaxis},
  author = {Berg, H. C.},
  year = {1988},
  volume = {53 Pt 1},
  pages = {1--9},
  issn = {0091-7451 (Print) 0091-7451 (Linking)},
  doi = {10.1101/sqb.1988.053.01.003},
  abstract = {What is distinctive about bacterial chemotaxis, as compared to, for example, taste in the elephant, is the time over which decisions must be made. The lower limit is set by diffusion of chemicals to and from the cell surface, which demands long times for statistically significant counts. The upper limit is set by diffusion of the cell itself, which demands short times for well-defined swimming paths. For an organism the size of E. coli, temporal comparisons of the concentrations of chemicals in the environment must be made within a few seconds. Although such short time spans might be difficult for the biochemist, they are not so difficult for E. coli, because diffusion can carry a small molecule across the cell in about 1 msec. E. coli has the opposite problem: How does it integrate inputs from many receptors over periods 1000 times as long? The mechanisms for this signal processing are beginning to be understood. We know how most chemical attractants are identified, how temporal comparisons might be made, and how the behavioral output is effected. We know less about how sensory information crosses the cytoplasmic membrane, how the reactions that link the receptors to the flagella generate such high gain, and what actually controls the direction of flagellar rotation. One thing is quite clear: E. coli demands our admiration and respect.},
  file = {/Users/coiko/Zotero/storage/T8PNU9KB/Berg-1988-A physicist looks at bacterial chemo.pdf},
  journal = {Cold Spring Harb Symp Quant Biol},
  keywords = {*Chemotaxis,Escherichia coli/genetics/*physiology,Flagella/physiology,Humans,Models; Biological,Signal Transduction}
}

@article{berg2003,
  ids = {bergRotaryMotorBacterial2003},
  title = {The Rotary Motor of Bacterial Flagella},
  author = {Berg, Howard C.},
  year = {2003},
  month = jun,
  volume = {72},
  pages = {19--54},
  publisher = {{Annual Reviews}},
  issn = {0066-4154},
  doi = {10.1146/annurev.biochem.72.121801.161737},
  abstract = {Flagellated bacteria, such as Escherichia coli, swim by rotating thin helical filaments, each driven at its base by a reversible rotary motor, powered by an ion flux. A motor is about 45 nm in diameter and is assembled from about 20 different kinds of parts. It develops maximum torque at stall but can spin several hundred Hz. Its direction of rotation is controlled by a sensory system that enables cells to accumulate in regions deemed more favorable. We know a great deal about motor structure, genetics, assembly, and function, but we do not really understand how it works. We need more crystal structures. All of this is reviewed, but the emphasis is on function.},
  file = {/Users/coiko/Zotero/storage/55DG9MBN/Berg - 2003 - The Rotary Motor of Bacterial Flagella.pdf;/Users/coiko/Zotero/storage/QDJY9R2Q/Berg-2003-The rotary motor of bacterial flagel.pdf;/Users/coiko/Zotero/storage/MCFWXPCD/annurev.biochem.72.121801.html},
  journal = {Annu Rev Biochem},
  keywords = {*Bacterial Physiological Phenomena,Escherichia coli/physiology,Flagella/*physiology,Molecular Motor Proteins/chemistry/*physiology,Torque},
  number = {1}
}

@article{bergeron2017,
  title = {Structure of the Magnetosome-Associated Actin-like {{MamK}} Filament at Subnanometer Resolution},
  shorttitle = {Structure of the Magnetosome-Associated Actin-like {{MamK}} Filament at Subnanometer Resolution},
  author = {Bergeron, J. R. and Hutto, R. and Ozyamak, E. and Hom, N. and Hansen, J. and Draper, O. and Byrne, M. E. and Keyhani, S. and Komeili, A. and Kollman, J. M.},
  year = {2017},
  month = jan,
  volume = {26},
  pages = {93--102},
  issn = {1469-896X (Electronic) 0961-8368 (Linking)},
  doi = {10.1002/pro.2979},
  abstract = {Magnetotactic bacteria possess cellular compartments called magnetosomes that sense magnetic fields. Alignment of magnetosomes in the bacterial cell is necessary for their function, and this is achieved through anchoring of magnetosomes to filaments composed of the protein MamK. MamK is an actin homolog that polymerizes upon ATP binding. Here, we report the structure of the MamK filament at approximately 6.5 A, obtained by cryo-Electron Microscopy. This structure confirms our previously reported double-stranded, nonstaggered architecture, and reveals the molecular basis for filament formation. While MamK is closest in sequence to the bacterial actin MreB, the longitudinal contacts along each MamK strand most closely resemble those of eukaryotic actin. In contrast, the cross-strand interface, with a surprisingly limited set of contacts, is novel among actin homologs and gives rise to the nonstaggered architecture.},
  file = {/Users/coiko/Zotero/storage/H43I3QBX/Bergeron-2017-Structure of the magnetosome-ass.pdf},
  journal = {Protein Sci},
  keywords = {actin,Cryo-EM,filaments,magnetosome},
  number = {1}
}

@misc{bergInternet,
  title = {Swimming {{Escherichia}} Coli},
  author = {Berg, H. C.},
  year = {Internet},
  url = {http://www.rowland.harvard.edu/labs/bacteria/movies/ecoli.php},
  urldate = {2020-06-10},
  journal = {Bacterial motility and behavior}
}

@article{bharat2017,
  title = {Structure of the Hexagonal Surface Layer on {{Caulobacter}} Crescentus Cells},
  shorttitle = {Structure of the Hexagonal Surface Layer on {{Caulobacter}} Crescentus Cells},
  author = {Bharat, T. A. M. and {Kureisaite-Ciziene}, D. and Hardy, G. G. and Yu, E. W. and Devant, J. M. and Hagen, W. J. H. and Brun, Y. V. and Briggs, J. A. G. and Lowe, J.},
  year = {2017},
  month = apr,
  volume = {2},
  pages = {17059},
  issn = {2058-5276 (Electronic) 2058-5276 (Linking)},
  doi = {10.1038/nmicrobiol.2017.59},
  abstract = {Many prokaryotic cells are encapsulated by a surface layer (S-layer) consisting of repeating units of S-layer proteins. S-layer proteins are a diverse class of molecules found in Gram-positive and Gram-negative bacteria and most archaea1-5. S-layers protect cells from the outside, provide mechanical stability and also play roles in pathogenicity. In situ structural information about this highly abundant class of proteins is scarce, so atomic details of how S-layers are arranged on the surface of cells have remained elusive. Here, using purified Caulobacter crescentus' sole S-layer protein RsaA, we obtained a 2.7 A X-ray structure that shows the hexameric S-layer lattice. We also solved a 7.4 A structure of the S-layer through electron cryotomography and sub-tomogram averaging of cell stalks. The X-ray structure was docked unambiguously into the electron cryotomography map, resulting in a pseudo-atomic-level description of the in vivo S-layer, which agrees completely with the atomic X-ray lattice model. The cellular S-layer atomic structure shows that the S-layer is porous, with a largest gap dimension of 27 A, and is stabilized by multiple Ca2+ ions bound near the interfaces. This study spans different spatial scales from atoms to cells by combining X-ray crystallography with electron cryotomography and sub-nanometre-resolution sub-tomogram averaging.},
  file = {/Users/coiko/Zotero/storage/L9JDBICV/Bharat et al. - 2017 - Structure of the hexagonal surface layer on Caulob.pdf;/Users/coiko/Zotero/storage/QC37D7XI/Bharat-2017-Structure of the hexagonal surface.pdf;/Users/coiko/Zotero/storage/WMMBZYNQ/Bharat-2017-Structure of the hexagonal surface.pdf},
  journal = {Nat Microbiol},
  keywords = {Bacterial Outer Membrane Proteins,Bacterial Outer Membrane Proteins/*chemistry,Bacterial Proteins,Bacterial Proteins/chemistry,Caulobacter crescentus,Caulobacter crescentus/*chemistry,Crystallography; X-Ray,Electron Microscope Tomography,Membrane Glycoproteins,Membrane Glycoproteins/*chemistry/isolation \& purification/ultrastructure,Surface Properties},
  pmcid = {PMC5699643},
  pmid = {28418382}
}

@article{bulieris2017,
  title = {Structure of {{FlgK}} Reveals the Divergence of the Bacterial {{Hook}}-{{Filament Junction}} of {{Campylobacter}}},
  author = {Bulieris, Paula V. and Shaikh, Nausad H. and Freddolino, Peter L. and Samatey, Fadel A.},
  year = {2017},
  month = nov,
  volume = {7},
  pages = {15743},
  publisher = {{Nature Publishing Group}},
  issn = {2045-2322},
  doi = {10.1038/s41598-017-15837-0},
  abstract = {Evolution of a nano-machine consisting of multiple parts, each with a specific function, is a complex process. A change in one part should eventually result in changes in other parts, if the overall function is to be conserved. In bacterial flagella, the filament and the hook have distinct functions and their respective proteins, FliC and FlgE, have different three-dimensional structures. The filament functions as a helical propeller and the hook as a flexible universal joint. Two proteins, FlgK and FlgL, assure a~smooth connectivity between the hook and the filament. Here we show that, in Campylobacter, the 3D structure of FlgK differs from that of its orthologs in Salmonella and Burkholderia, whose structures have previously been solved. Docking the model of the FlgK junction onto the structure of the Campylobacter hook provides some clues about its divergence. These data suggest how evolutionary pressure to adapt to structural constraints, due to the structure of Campylobacter hook, causes divergence of one element of a supra-molecular complex in order to maintain the function of the entire flagellar assembly.},
  copyright = {2017 The Author(s)},
  file = {/Users/coiko/Zotero/storage/3URGWQSB/Bulieris et al. - 2017 - Structure of FlgK reveals the divergence of the ba.pdf;/Users/coiko/Zotero/storage/W9WZKTRC/s41598-017-15837-0.html},
  journal = {Sci Rep},
  language = {en},
  number = {1}
}

@article{cassidy2020,
  title = {Structure and Dynamics of the {{E}}. Coli Chemotaxis Core Signaling Complex by Cryo-Electron Tomography and Molecular Simulations},
  author = {Cassidy, C. Keith and Himes, Benjamin A. and Sun, Dapeng and Ma, Jun and Zhao, Gongpu and Parkinson, John S. and Stansfeld, Phillip J. and {Luthey-Schulten}, Zaida and Zhang, Peijun},
  year = {2020},
  month = jan,
  volume = {3},
  pages = {1--10},
  publisher = {{Nature Publishing Group}},
  issn = {2399-3642},
  doi = {10.1038/s42003-019-0748-0},
  abstract = {To enable the processing of chemical gradients, chemotactic bacteria possess large arrays of transmembrane chemoreceptors, the histidine kinase CheA, and the adaptor protein CheW, organized as coupled core-signaling units (CSU). Despite decades of study, important questions surrounding the molecular mechanisms of sensory signal transduction remain unresolved, owing especially to the lack of a high-resolution CSU structure. Here, we use cryo-electron tomography and sub-tomogram averaging to determine a structure of the Escherichia coli CSU at sub-nanometer resolution. Based on our experimental data, we use molecular simulations to construct an atomistic model of the CSU, enabling a detailed characterization of CheA conformational dynamics in its native structural context. We identify multiple, distinct conformations of the critical P4 domain as well as asymmetries in the localization of the P3 bundle, offering several novel insights into the CheA signaling mechanism.},
  copyright = {2020 The Author(s)},
  file = {/Users/coiko/Zotero/storage/PHHMAN5V/Cassidy et al. - 2020 - Structure and dynamics of the E. coli chemotaxis c.pdf;/Users/coiko/Zotero/storage/VR7SLJSA/s42003-019-0748-0.html},
  journal = {Commun Biol},
  language = {en},
  number = {1}
}

@article{chaban2018,
  title = {Evolution of Higher Torque in {{Campylobacter}}- Type Bacterial Flagellar Motors},
  author = {Chaban, Bonnie and Coleman, Izaak and Beeby, Morgan},
  year = {2018},
  month = jan,
  volume = {8},
  pages = {97},
  publisher = {{Nature Publishing Group}},
  issn = {2045-2322},
  doi = {10.1038/s41598-017-18115-1},
  abstract = {Understanding the evolution of molecular machines underpins our understanding of the development of life on earth. A well-studied case are bacterial flagellar motors that spin helical propellers for bacterial motility. Diverse motors produce different torques, but how this diversity evolved remains unknown. To gain insights into evolution of the high-torque {$\epsilon$}-proteobacterial motor exemplified by the Campylobacter jejuni motor, we inferred ancestral states by combining phylogenetics, electron cryotomography, and motility assays to characterize motors from Wolinella succinogenes, Arcobacter butzleri and Bdellovibrio bacteriovorus. Observation of \textasciitilde{}12 stator complexes in many proteobacteria, yet \textasciitilde{}17 in {$\epsilon$}-proteobacteria suggest a ``quantum leap'' evolutionary event. Campylobacter-type motors have high stator occupancy in wider rings of additional stator complexes that are scaffolded by large proteinaceous periplasmic rings. We propose a model for motor evolution wherein independent inner- and outer-membrane structures fused to form a scaffold for additional stator complexes. Significantly, inner- and outer-membrane associated structures have evolved independently multiple times, suggesting that evolution of such structures is facile and poised the {$\epsilon$}-proteobacteria to fuse them to form the high-torque Campylobacter-type motor.},
  copyright = {2017 The Author(s)},
  file = {/Users/coiko/Zotero/storage/ZWG7X5AF/Chaban et al. - 2018 - Evolution of higher torque in Campylobacter- type .pdf;/Users/coiko/Zotero/storage/UD83HSNE/s41598-017-18115-1.html},
  journal = {Sci Rep},
  language = {en},
  number = {1}
}

@article{chalfie1994,
  title = {Green Fluorescent Protein as a Marker for Gene Expression},
  shorttitle = {Green Fluorescent Protein as a Marker for Gene Expression},
  author = {Chalfie, M. and Tu, Y. and Euskirchen, G. and Ward, W. W. and Prasher, D. C.},
  year = {1994},
  month = feb,
  volume = {263},
  pages = {802--5},
  issn = {0036-8075 (Print) 0036-8075 (Linking)},
  doi = {10.1126/science.8303295},
  abstract = {A complementary DNA for the Aequorea victoria green fluorescent protein (GFP) produces a fluorescent product when expressed in prokaryotic (Escherichia coli) or eukaryotic (Caenorhabditis elegans) cells. Because exogenous substrates and cofactors are not required for this fluorescence, GFP expression can be used to monitor gene expression and protein localization in living organisms.},
  file = {/Users/coiko/Zotero/storage/H3P837PG/Chalfie.pdf;/Users/coiko/Zotero/storage/HP7JRQVW/Chalfie-1994-Green fluorescent protein as a ma.pdf},
  journal = {Science},
  keywords = {*Gene Expression,Animals,Base Sequence,Caenorhabditis elegans/*genetics/growth \& development,Cell Division,Cell Separation,Escherichia coli/*genetics,Fluorescence,Green Fluorescent Proteins,Luminescent Proteins/*analysis/genetics,Microscopy; Fluorescence,Molecular Sequence Data,Neurons/*chemistry,Oligodeoxyribonucleotides,Recombinant Proteins,Spectrometry; Fluorescence,Transformation; Genetic},
  number = {5148}
}

@article{chang2014,
  title = {Correlated Cryogenic Photoactivated Localization Microscopy and Cryo-Electron Tomography},
  shorttitle = {Correlated Cryogenic Photoactivated Localization Microscopy and Cryo-Electron Tomography},
  author = {Chang, Y. W. and Chen, S. and Tocheva, E. I. and {Treuner-Lange}, A. and Lobach, S. and {Sogaard-Andersen}, L. and Jensen, G. J.},
  year = {2014},
  month = jul,
  volume = {11},
  pages = {737--9},
  issn = {1548-7105 (Electronic) 1548-7091 (Linking)},
  doi = {10.1038/nmeth.2961},
  abstract = {Cryo-electron tomography (CET) produces three-dimensional images of cells in a near-native state at macromolecular resolution, but identifying structures of interest can be challenging. Here we describe a correlated cryo-PALM (photoactivated localization microscopy)-CET method for localizing objects within cryo-tomograms to beyond the diffraction limit of the light microscope. Using cryo-PALM-CET, we identified multiple and new conformations of the dynamic type VI secretion system in the crowded interior of Myxococcus xanthus.},
  file = {/Users/coiko/Zotero/storage/2HDS6VUP/Chang-2014-Correlated cryogenic photoactivated.pdf;/Users/coiko/Zotero/storage/48F4ICUN/Chang-2014-Correlated cryogenic photoactivated.pdf;/Users/coiko/Zotero/storage/8MH9S42K/Chang-2014-Correlated cryogenic.pdf;/Users/coiko/Zotero/storage/A4M2FDNE/Chang-2014-Correlated cryogenic photoactivated.pdf;/Users/coiko/Zotero/storage/AS4SI4AL/Chang-2014-Correlated cryogenic photoactivated.pdf;/Users/coiko/Zotero/storage/ASCQ3WRL/Chang et al. - 2014 - Correlated cryogenic photoactivated localization m.pdf;/Users/coiko/Zotero/storage/FMB67Y2F/Chang-2014-Correlated cryogenic.pdf;/Users/coiko/Zotero/storage/HTDH3UGI/Chang-2014-Correlated cryogenic photoactivated.pdf;/Users/coiko/Zotero/storage/M9L52DGV/Chang-2014-Correlated cryogenic photoactivated.pdf;/Users/coiko/Zotero/storage/SN5XZL4G/Chang-2014-Correlated cryogenic photoactivated.pdf;/Users/coiko/Zotero/storage/V5ZH4PYK/Chang-2014-Correlated cryogenic photoactivated.pdf;/Users/coiko/Zotero/storage/VUFDRNNV/Chang-2014-Correlated cryogenic photoactivated.pdf},
  journal = {Nat Methods},
  keywords = {*Bacterial Secretion Systems,Bacterial Secretion Systems,Cryoelectron Microscopy,Cryoelectron Microscopy/*methods,Electron Microscope Tomography,Electron Microscope Tomography/*methods,Imaging; Three-Dimensional,Imaging; Three-Dimensional/methods,Myxococcus xanthus,Myxococcus xanthus/chemistry/*ultrastructure},
  number = {7},
  pmcid = {PMC4081473},
  pmid = {24813625}
}

@article{chang2016,
  title = {Architecture of the Type {{IVa}} Pilus Machine},
  shorttitle = {Architecture of the Type {{IVa}} Pilus Machine},
  author = {Chang, Y. W. and Rettberg, L. A. and {Treuner-Lange}, A. and Iwasa, J. and {Sogaard-Andersen}, L. and Jensen, G. J.},
  year = {2016},
  month = mar,
  volume = {351},
  pages = {aad2001},
  issn = {1095-9203 (Electronic) 0036-8075 (Linking)},
  doi = {10.1126/science.aad2001},
  abstract = {Type IVa pili are filamentous cell surface structures observed in many bacteria. They pull cells forward by extending, adhering to surfaces, and then retracting. We used cryo-electron tomography of intact Myxococcus xanthus cells to visualize type IVa pili and the protein machine that assembles and retracts them (the type IVa pilus machine, or T4PM) in situ, in both the piliated and nonpiliated states, at a resolution of 3 to 4 nanometers. We found that T4PM comprises an outer membrane pore, four interconnected ring structures in the periplasm and cytoplasm, a cytoplasmic disc and dome, and a periplasmic stem. By systematically imaging mutants lacking defined T4PM proteins or with individual proteins fused to tags, we mapped the locations of all 10 T4PM core components and the minor pilins, thereby providing insights into pilus assembly, structure, and function.},
  file = {/Users/coiko/Zotero/storage/4P5TBKCR/Chang-2016-Architecture of the type IVa pilus.pdf;/Users/coiko/Zotero/storage/CCWBXHHC/Chang-2016-Architecture of the type IVa pilus.pdf;/Users/coiko/Zotero/storage/ENLAYRP7/Chang-2016-Architecture of the type IVa pilus.pdf;/Users/coiko/Zotero/storage/GVILU67H/Chang et al. - 2016 - Architecture of the type IVa pilus machine.pdf;/Users/coiko/Zotero/storage/I2X2WT3D/Chang-2016-Architecture of the type IVa pilus.pdf;/Users/coiko/Zotero/storage/JKLGDVIR/Chang-2016-Architecture of the type IVa pilus.pdf;/Users/coiko/Zotero/storage/MF2N3MLJ/Chang-2016-Architecture of the type IVa pilus.pdf;/Users/coiko/Zotero/storage/N7K54ELU/aad2001.full.pdf;/Users/coiko/Zotero/storage/N9VJGNKC/Chang-2016-Architecture of the type IVa pilus.pdf;/Users/coiko/Zotero/storage/SV6AV6M3/Chang-2016-Architecture of the type IVa pilus.pdf;/Users/coiko/Zotero/storage/ZAGTEQD7/Chang-2016-Architecture of the type IVa pilus.pdf},
  journal = {Science},
  keywords = {Bacterial Adhesion,Cryoelectron Microscopy,Fimbriae; Bacterial,Fimbriae; Bacterial/genetics/*ultrastructure,Microscopy; Electron; Transmission,Models; Molecular,Mutation,Myxococcus xanthus,Myxococcus xanthus/genetics/physiology/*ultrastructure},
  number = {6278},
  pmcid = {PMC5929464},
  pmid = {26965631}
}

@article{chang2017,
  title = {In Vivo Structures of an Intact Type {{VI}} Secretion System Revealed by Electron Cryotomography},
  shorttitle = {In Vivo Structures of an Intact Type {{VI}} Secretion System Revealed by Electron Cryotomography},
  author = {Chang, Y. W. and Rettberg, L. A. and Ortega, D. R. and Jensen, G. J.},
  year = {2017},
  month = jul,
  volume = {18},
  pages = {1090--1099},
  issn = {1469-3178 (Electronic) 1469-221X (Linking)},
  doi = {10.15252/embr.201744072},
  abstract = {The type VI secretion system (T6SS) is a versatile molecular weapon used by many bacteria against eukaryotic hosts or prokaryotic competitors. It consists of a cytoplasmic bacteriophage tail-like structure anchored in the bacterial cell envelope via a cytoplasmic baseplate and a periplasmic membrane complex. Rapid contraction of the sheath in the bacteriophage tail-like structure propels an inner tube/spike complex through the target cell envelope to deliver effectors. While structures of purified contracted sheath and purified membrane complex have been solved, because sheaths contract upon cell lysis and purification, no structure is available for the extended sheath. Structural information about the baseplate is also lacking. Here, we use electron cryotomography to directly visualize intact T6SS structures inside Myxococcus xanthus cells. Using sub-tomogram averaging, we resolve the structure of the extended sheath and membrane-associated components including the baseplate. Moreover, we identify novel extracellular bacteriophage tail fiber-like antennae. These results provide new structural insights into how the extended sheath prevents premature disassembly and how this sophisticated machine may recognize targets.},
  file = {/Users/coiko/Zotero/storage/3K5QQSAS/Chang-2017-In vivo structures of an intact typ.pdf;/Users/coiko/Zotero/storage/6N9RSFUN/Chang-2017-In vivo structures of an intact typ.pdf;/Users/coiko/Zotero/storage/AUIHDBQ7/Chang-2017-In vivo structures of an intact typ.pdf;/Users/coiko/Zotero/storage/CIG268JK/Chang et al. - 2017 - In vivo structures of an intact type VI secretion .pdf;/Users/coiko/Zotero/storage/DIRVJ9K4/Chang-2017-In vivo structures of an intact typ.pdf;/Users/coiko/Zotero/storage/G6UKH6VB/Chang et al. - 2017 - In vivo structures of an intact type VI secretion .pdf;/Users/coiko/Zotero/storage/HPGMHWU8/Chang-2017-In vivo structures of an intact typ.pdf;/Users/coiko/Zotero/storage/N5C4R8SZ/Chang-2017-In vivo structures of an intact typ.pdf;/Users/coiko/Zotero/storage/X42F85TA/Chang-2017-In vivo structures of an intact typ.pdf},
  journal = {EMBO Rep},
  keywords = {*bacterial molecular weapon,*contractile bacteriophage tail,*electron cryotomography,*sub-tomogram averaging,*type VI secretion system,bacterial molecular weapon,Bacteriophages,Bacteriophages/ultrastructure,contractile bacteriophage tail,Cryoelectron Microscopy,Cryoelectron Microscopy/instrumentation/methods,electron cryotomography,Intravital Microscopy,Intravital Microscopy/instrumentation/methods,Molecular Structure,Myxococcus xanthus,Myxococcus xanthus/chemistry/cytology/*ultrastructure,Protein Binding,Protein Multimerization,sub-tomogram averaging,sub‐tomogram averaging,type VI secretion system,Type VI Secretion Systems,Type VI Secretion Systems/chemistry/*ultrastructure},
  number = {7},
  pmcid = {PMC5494534},
  pmid = {28487352}
}

@article{chang2019,
  title = {Structural Insights into Flagellar Stator-Rotor Interactions},
  author = {Chang, Yunjie and Moon, Ki Hwan and Zhao, Xiaowei and Norris, Steven J and Motaleb, MD A and Liu, Jun},
  editor = {Egelman, Edward H and Kuriyan, John and Egelman, Edward H and Ito, Masahiro},
  year = {2019},
  month = jul,
  volume = {8},
  pages = {e48979},
  publisher = {{eLife Sciences Publications, Ltd}},
  issn = {2050-084X},
  doi = {10.7554/eLife.48979},
  abstract = {The bacterial flagellar motor is a molecular machine that can rotate the flagellar filament at high speed. The rotation is generated by the stator-rotor interaction, coupled with an ion flux through the torque-generating stator. Here we employed cryo-electron tomography to visualize the intact flagellar motor in the Lyme disease spirochete, Borrelia burgdorferi. By analyzing the motor structures of wild-type and stator-deletion mutants, we not only localized the stator complex in situ, but also revealed the stator-rotor interaction at an unprecedented detail. Importantly, the stator-rotor interaction induces a conformational change in the flagella C-ring. Given our observation that a non-motile mutant, in which proton flux is blocked, cannot generate the similar conformational change, we propose that the proton-driven torque is responsible for the conformational change required for flagellar rotation.},
  file = {/Users/coiko/Zotero/storage/JJJCMT74/Chang et al. - 2019 - Structural insights into flagellar stator–rotor in.pdf},
  journal = {eLife},
  keywords = {bacterial flagella,motility,nanomachine,protein-protein interaction,spirochete}
}

@article{chen2011,
  title = {Structural Diversity of Bacterial Flagellar Motors},
  shorttitle = {Structural Diversity of Bacterial Flagellar Motors},
  author = {Chen, S. and Beeby, M. and Murphy, G. E. and Leadbetter, J. R. and Hendrixson, D. R. and Briegel, A. and Li, Z. and Shi, J. and Tocheva, E. I. and Muller, A. and Dobro, M. J. and Jensen, G. J.},
  year = {2011},
  month = jul,
  volume = {30},
  pages = {2972--81},
  issn = {1460-2075 (Electronic) 0261-4189 (Linking)},
  doi = {10.1038/emboj.2011.186},
  abstract = {The bacterial flagellum is one of nature's most amazing and well-studied nanomachines. Its cell-wall-anchored motor uses chemical energy to rotate a microns-long filament and propel the bacterium towards nutrients and away from toxins. While much is known about flagellar motors from certain model organisms, their diversity across the bacterial kingdom is less well characterized, allowing the occasional misrepresentation of the motor as an invariant, ideal machine. Here, we present an electron cryotomographical survey of flagellar motor architectures throughout the Bacteria. While a conserved structural core was observed in all 11 bacteria imaged, surprisingly novel and divergent structures as well as different symmetries were observed surrounding the core. Correlating the motor structures with the presence and absence of particular motor genes in each organism suggested the locations of five proteins involved in the export apparatus including FliI, whose position below the C-ring was confirmed by imaging a deletion strain. The combination of conserved and specially-adapted structures seen here sheds light on how this complex protein nanomachine has evolved to meet the needs of different species.},
  file = {/Users/coiko/Zotero/storage/74V3YT2S/Chen-2011-Structural diversity.pdf;/Users/coiko/Zotero/storage/7VF892E8/Chen-2011-Structural diversity of bacterial fl.pdf;/Users/coiko/Zotero/storage/A7ATNN7W/Chen-2011-Structural diversity.pdf;/Users/coiko/Zotero/storage/DDCJ2K4D/Chen-2011-Structural diversity of bacterial fl.pdf;/Users/coiko/Zotero/storage/EXHN3DHX/Chen-2011-Structural diversity.pdf;/Users/coiko/Zotero/storage/H9FYQH8J/Chen et al. - 2011 - Structural diversity of bacterial flagellar motors.pdf;/Users/coiko/Zotero/storage/HAZ26Z9Z/Chen-2011-Structural diversity of bacterial fl.pdf;/Users/coiko/Zotero/storage/LLXDCUI4/Chen-2011-Structural diversity.pdf;/Users/coiko/Zotero/storage/USYVLEFR/Chen-2011-Structural diversity.pdf;/Users/coiko/Zotero/storage/UUTD6X54/Chen-2011-Structural diversity.pdf},
  journal = {EMBO J},
  keywords = {Bacteria,Bacteria/*chemistry/*metabolism,Cell Movement,Flagella,Flagella/*chemistry/metabolism,Models; Molecular,Molecular Motor Proteins,Molecular Motor Proteins/*chemistry/*metabolism},
  number = {14},
  pmcid = {PMC3160247},
  pmid = {21673657}
}

@article{christie2019,
  title = {The {{Rich Tapestry}} of {{Bacterial Protein Translocation Systems}}},
  author = {Christie, Peter J.},
  year = {2019},
  month = aug,
  volume = {38},
  pages = {389--408},
  issn = {1573-4943},
  doi = {10.1007/s10930-019-09862-3},
  abstract = {The translocation of proteins across membranes is a fundamental cellular function. Bacteria have evolved a striking array of pathways for delivering proteins into or across cytoplasmic membranes and, when present, outer membranes. Translocated proteins can form part of the membrane landscape, reside in the periplasmic space situated between the inner and outer membranes of Gram-negative bacteria, deposit on the cell surface, or be released to the extracellular milieu or injected directly into target cells. One protein translocation system, the general secretory pathway, is conserved in all domains of life. A second, the twin-arginine translocation pathway, is also phylogenetically distributed among most bacteria and plant chloroplasts. While all cell types have evolved additional systems dedicated to the translocation of protein cargoes, the number of such systems in bacteria is now known to exceed nine. These dedicated protein translocation systems, which include the types 1 through 9 secretion systems (T1SSs-T9SSs), the chaperone-usher pathway, and type IV pilus system, are the subject of this review. Most of these systems were originally identified and have been extensively characterized in Gram-negative or diderm (two-membrane) species. It is now known that several of these systems also have been adapted to function in Gram-positive or monoderm (single-membrane) species, and at least one pathway is found only in monoderms. This review briefly summarizes the distinctive mechanistic and structural features of each dedicated pathway, as well as the shared properties, that together account for the broad biological diversity of protein translocation in bacteria.},
  journal = {Protein J},
  language = {en},
  number = {4}
}

@article{claude1974,
  title = {Nobel {{Lecture}}},
  author = {Claude, A},
  year = {1974},
  url = {https://nobelprize.org/prizes/medicine/1974/claude/lecture/},
  urldate = {2020-05-07}
}

@article{collins2014,
  title = {Internal Sense of Direction: {{Sensing}} and Signaling from Cytoplasmic Chemoreceptors},
  shorttitle = {Internal {{Sense}} of {{Direction}}},
  author = {Collins, Kieran D. and Lacal, Jesus and Ottemann, Karen M.},
  year = {2014},
  month = dec,
  volume = {78},
  pages = {672--684},
  publisher = {{American Society for Microbiology}},
  issn = {1092-2172, 1098-5557},
  doi = {10.1128/MMBR.00033-14},
  abstract = {Chemoreceptors sense environmental signals and drive chemotactic responses in Bacteria and Archaea. There are two main classes of chemoreceptors: integral inner membrane and soluble cytoplasmic proteins. The latter were identified more recently than integral membrane chemoreceptors and have been studied much less thoroughly. These cytoplasmic chemoreceptors are the subject of this review. Our analysis determined that 14\% of bacterial and 43\% of archaeal chemoreceptors are cytoplasmic, based on currently sequenced genomes. Cytoplasmic chemoreceptors appear to share the same key structural features as integral membrane chemoreceptors, including the formations of homodimers, trimers of dimers, and 12-nm hexagonal arrays within the cell. Cytoplasmic chemoreceptors exhibit varied subcellular locations, with some localizing to the poles and others appearing both cytoplasmic and polar. Some cytoplasmic chemoreceptors adopt more exotic locations, including the formations of exclusively internal clusters or moving dynamic clusters that coalesce at points of contact with other cells. Cytoplasmic chemoreceptors presumably sense signals within the cytoplasm and bear diverse signal input domains that are mostly N terminal to the domain that defines chemoreceptors, the so-called MA domain. Similar to the case for transmembrane receptors, our analysis suggests that the most common signal input domain is the PAS (Per-Arnt-Sim) domain, but a variety of other N-terminal domains exist. It is also common, however, for cytoplasmic chemoreceptors to have C-terminal domains that may function for signal input. The most common of these is the recently identified chemoreceptor zinc binding (CZB) domain, found in 8\% of all cytoplasmic chemoreceptors. The widespread nature and diverse signal input domains suggest that these chemoreceptors can monitor a variety of cytoplasmically based signals, most of which remain to be determined.},
  copyright = {Copyright \textcopyright{} 2014, American Society for Microbiology. All Rights Reserved.},
  file = {/Users/coiko/Zotero/storage/FUJGEELR/Collins et al. - 2014 - Internal Sense of Direction Sensing and Signaling.pdf;/Users/coiko/Zotero/storage/SRCAZ5N5/672.html},
  journal = {Microbiol Mol Biol Rev},
  language = {en},
  number = {4},
  pmid = {25428939}
}

@book{darwin1888,
  title = {The {{Life}} and {{Letters}} of {{Charles Darwin}}, {{Including An Autobiographical Chapter}}},
  author = {Darwin, C},
  year = {1888},
  volume = {1},
  publisher = {{D. Appleton}},
  address = {{New York}}
}

@article{deng2019,
  title = {The Structure of Bactofilin Filaments Reveals Their Mode of Membrane Binding and Lack of Polarity},
  author = {Deng, Xian and Gonzalez Llamazares, Andres and Wagstaff, James M. and Hale, Victoria L. and Cannone, Giuseppe and McLaughlin, Stephen H. and {Kureisaite-Ciziene}, Danguole and L{\"o}we, Jan},
  year = {2019},
  month = dec,
  volume = {4},
  pages = {2357--2368},
  publisher = {{Nature Publishing Group}},
  issn = {2058-5276},
  doi = {10.1038/s41564-019-0544-0},
  abstract = {Bactofilins are small {$\beta$}-helical proteins that form cytoskeletal filaments in a range of bacteria. Bactofilins have diverse functions, from cell stalk formation in Caulobacter crescentus to chromosome segregation and motility in Myxococcus xanthus. However, the precise molecular architecture of bactofilin filaments has remained unclear. Here, sequence analysis and electron microscopy results reveal that, in addition to being widely distributed across bacteria and archaea, bactofilins are also present in a few eukaryotic lineages such as the Oomycetes. Electron cryomicroscopy analysis demonstrated that the sole bactofilin from Thermus thermophilus (TtBac) forms constitutive filaments that polymerize through end-to-end association of the {$\beta$}-helical domains. Using a nanobody, we determined the near-atomic filament structure, showing that the filaments are non-polar. A polymerization-impairing mutation enabled crystallization and structure determination, while reaffirming the lack of polarity and the strength of the {$\beta$}-stacking interface. To confirm the generality of the lack of polarity, we performed coevolutionary analysis on a large set of sequences. Finally, we determined that the widely conserved N-terminal disordered tail of TtBac is responsible for direct binding to lipid membranes, both on liposomes and in Escherichia coli cells. Membrane binding is probably a common feature of these widespread but only recently discovered filaments of the prokaryotic cytoskeleton.},
  copyright = {2019 The Author(s), under exclusive licence to Springer Nature Limited},
  file = {/Users/coiko/Zotero/storage/PGXS9SBY/Deng et al. - 2019 - The structure of bactofilin filaments reveals thei.pdf;/Users/coiko/Zotero/storage/FELNKEYE/s41564-019-0544-0.html},
  journal = {Nat Microbiol},
  language = {en},
  number = {12}
}

@article{dobro2017,
  title = {Uncharacterized {{Bacterial Structures Revealed}} by {{Electron Cryotomography}}},
  author = {Dobro, Megan J. and Oikonomou, Catherine M. and Piper, Aidan and Cohen, John and Guo, Kylie and Jensen, Taylor and Tadayon, Jahan and Donermeyer, Joseph and Park, Yeram and Solis, Benjamin A. and Kj{\ae}r, Andreas and Jewett, Andrew I. and McDowall, Alasdair W. and Chen, Songye and Chang, Yi-Wei and Shi, Jian and Subramanian, Poorna and Iancu, Cristina V. and Li, Zhuo and Briegel, Ariane and Tocheva, Elitza I. and Pilhofer, Martin and Jensen, Grant J.},
  year = {2017},
  month = sep,
  volume = {199},
  publisher = {{American Society for Microbiology Journals}},
  issn = {0021-9193, 1098-5530},
  doi = {10.1128/JB.00100-17},
  abstract = {Electron cryotomography (ECT) can reveal the native structure and arrangement of macromolecular complexes inside intact cells. This technique has greatly advanced our understanding of the ultrastructure of bacterial cells. We now view bacteria as structurally complex assemblies of macromolecular machines rather than as undifferentiated bags of enzymes. To date, our group has applied ECT to nearly 90 different bacterial species, collecting more than 15,000 cryotomograms. In addition to known structures, we have observed, to our knowledge, several uncharacterized features in these tomograms. Some are completely novel structures; others expand the features or species range of known structure types. Here, we present a survey of these uncharacterized bacterial structures in the hopes of accelerating their identification and study, and furthering our understanding of the structural complexity of bacterial cells.
IMPORTANCE Bacteria are more structurally complex than is commonly appreciated. Here we present a survey of previously uncharacterized structures that we observed in bacterial cells by electron cryotomography, structures that will initiate new lines of research investigating their identities and roles.},
  copyright = {Copyright \textcopyright{} 2017 American Society for Microbiology..  All Rights Reserved .},
  file = {/Users/coiko/Zotero/storage/RDHN48NY/Dobro et al. - 2017 - Uncharacterized Bacterial Structures Revealed by E.pdf;/Users/coiko/Zotero/storage/P9WKBIYZ/e00100-17.html},
  journal = {J Bacteriol},
  language = {en},
  number = {17},
  pmid = {28607161}
}

@book{dodge1968,
  title = {An {{Atlas}} of {{Biological Ultrastructure}}},
  author = {Dodge, J. D.},
  year = {1968},
  publisher = {{Edward Arnold}},
  address = {{London}}
}

@article{errington2013,
  title = {L-Form Bacteria, Cell Walls and the Origins of Life},
  shorttitle = {L-Form Bacteria, Cell Walls and the Origins of Life},
  author = {Errington, J.},
  year = {2013},
  month = jan,
  volume = {3},
  pages = {120143},
  issn = {2046-2441 (Electronic) 2046-2441 (Linking)},
  doi = {10.1098/rsob.120143},
  abstract = {The peptidoglycan wall is a defining feature of bacterial cells and was probably already present in their last common ancestor. L-forms are bacterial variants that lack a cell wall and divide by a variety of processes involving membrane blebbing, tubulation, vesiculation and fission. Their unusual mode of proliferation provides a model for primitive cells and is reminiscent of recently developed in vitro vesicle reproduction processes. Invention of the cell wall may have underpinned the explosion of bacterial life on the Earth. Later innovations in cell envelope structure, particularly the emergence of the outer membrane of Gram-negative bacteria, possibly in an early endospore former, seem to have spurned further major evolutionary radiations. Comparative studies of bacterial cell envelope structure may help to resolve the early key steps in evolutionary development of the bacterial domain of life.},
  file = {/Users/coiko/Zotero/storage/XH2KYEKV/Errington-2013-L-form bacteria, cell walls and.pdf},
  journal = {Open Biol},
  keywords = {*Origin of Life,Bacillus subtilis/metabolism,Bacteria/classification/*metabolism,Cell Wall/*metabolism,L Forms/*metabolism,Phylogeny},
  number = {1}
}

@book{fawcett1966,
  title = {An {{Atlas}} of {{Fine Structure}}: {{The Cell}}, {{Its Organelles}}, and {{Inclusions}}},
  author = {Fawcett, D. W.},
  year = {1966},
  publisher = {{W. B. Saunders Company}},
  address = {{Philadelphia}}
}

@article{fendrihan2006,
  title = {Extremely Halophilic Archaea and the Issue of Long-Term Microbial Survival},
  shorttitle = {Extremely Halophilic Archaea and the Issue of Long-Term Microbial Survival},
  author = {Fendrihan, S. and Legat, A. and Pfaffenhuemer, M. and Gruber, C. and Weidler, G. and Gerbl, F. and {Stan-Lotter}, H.},
  year = {2006},
  month = aug,
  volume = {5},
  pages = {203--218},
  issn = {1572-9826 (Print) 1569-1705 (Linking)},
  doi = {10.1007/s11157-006-0007-y},
  abstract = {Halophilic archaebacteria (haloarchaea) thrive in environments with salt concentrations approaching saturation, such as natural brines, the Dead Sea, alkaline salt lakes and marine solar salterns; they have also been isolated from rock salt of great geological age (195-250 million years). An overview of their taxonomy, including novel isolates from rock salt, is presented here; in addition, some of their unique characteristics and physiological adaptations to environments of low water activity are reviewed. The issue of extreme long-term microbial survival is considered and its implications for the search for extraterrestrial life. The development of detection methods for subterranean haloarchaea, which might also be applicable to samples from future missions to space, is presented.},
  file = {/Users/coiko/Zotero/storage/W94LC5GL/Fendrihan-2006-Extremely halophilic archaea an.pdf},
  journal = {Rev Environ Sci Biotechnol},
  number = {2-3}
}

@article{ferreira2019,
  title = {{$\gamma$}-Proteobacteria Eject Their Polar Flagella under Nutrient Depletion, Retaining Flagellar Motor Relic Structures},
  author = {Ferreira, Josie L. and Gao, Forson Z. and Rossmann, Florian M. and Nans, Andrea and Brenzinger, Susanne and Hosseini, Rohola and Wilson, Amanda and Briegel, Ariane and Thormann, Kai M. and Rosenthal, Peter B. and Beeby, Morgan},
  year = {2019},
  month = mar,
  volume = {17},
  pages = {e3000165},
  publisher = {{Public Library of Science}},
  issn = {1545-7885},
  doi = {10.1371/journal.pbio.3000165},
  abstract = {Bacteria switch only intermittently to motile planktonic lifestyles under favorable conditions. Under chronic nutrient deprivation, however, bacteria orchestrate a switch to stationary phase, conserving energy by altering metabolism and stopping motility. About two-thirds of bacteria use flagella to swim, but how bacteria deactivate this large molecular machine remains unclear. Here, we describe the previously unreported ejection of polar motors by {$\gamma$}-proteobacteria. We show that these bacteria eject their flagella at the base of the flagellar hook when nutrients are depleted, leaving a relic of a former flagellar motor in the outer membrane. Subtomogram averages of the full motor and relic reveal that this is an active process, as a plug protein appears in the relic, likely to prevent leakage across their outer membrane; furthermore, we show that ejection is triggered only under nutritional depletion and is independent of the filament as a possible mechanosensor. We show that filament ejection is a widespread phenomenon demonstrated by the appearance of relic structures in diverse {$\gamma$}-proteobacteria including Plesiomonas shigelloides, Vibrio cholerae, Vibrio fischeri, Shewanella putrefaciens, and Pseudomonas aeruginosa. While the molecular details remain to be determined, our results demonstrate a novel mechanism for bacteria to halt costly motility when nutrients become scarce.},
  file = {/Users/coiko/Zotero/storage/IDVWSP5K/Ferreira et al. - 2019 - γ-proteobacteria eject their polar flagella under .pdf;/Users/coiko/Zotero/storage/GKVRKULQ/article.html},
  journal = {PLoS Biol},
  keywords = {Cell polarity,Flagella,Flagellar motility,Motor proteins,Pathogen motility,Salmonella,Shigella,Swimming},
  language = {en},
  number = {3}
}

@article{feynman1960,
  title = {There's Plenty of Room at the Bottom: {{An}} Invitation to Enter a New Field of Physics},
  shorttitle = {There's Plenty of Room at the Bottom: {{An}} Invitation to Enter a New Field of Physics},
  author = {Feynman, R.},
  year = {1960},
  volume = {23},
  pages = {22--36},
  url = {https://resolver.caltech.edu/CaltechES:23.5.1960Bottom},
  file = {/Users/coiko/Zotero/storage/AL2IB6GW/1960Bottom.pdf;/Users/coiko/Zotero/storage/LJ5BPWDT/1960Bottom.pdf},
  journal = {Caltech Eng Sci},
  number = {5}
}

@article{flemming2016,
  title = {Biofilms: An Emergent Form of Bacterial Life},
  shorttitle = {Biofilms: An Emergent Form of Bacterial Life},
  author = {Flemming, H. C. and Wingender, J. and Szewzyk, U. and Steinberg, P. and Rice, S. A. and Kjelleberg, S.},
  year = {2016},
  month = aug,
  volume = {14},
  pages = {563--75},
  issn = {1740-1534 (Electronic) 1740-1526 (Linking)},
  doi = {10.1038/nrmicro.2016.94},
  abstract = {Bacterial biofilms are formed by communities that are embedded in a self-produced matrix of extracellular polymeric substances (EPS). Importantly, bacteria in biofilms exhibit a set of 'emergent properties' that differ substantially from free-living bacterial cells. In this Review, we consider the fundamental role of the biofilm matrix in establishing the emergent properties of biofilms, describing how the characteristic features of biofilms - such as social cooperation, resource capture and enhanced survival of exposure to antimicrobials - all rely on the structural and functional properties of the matrix. Finally, we highlight the value of an ecological perspective in the study of the emergent properties of biofilms, which enables an appreciation of the ecological success of biofilms as habitat formers and, more generally, as a bacterial lifestyle.},
  file = {/Users/coiko/Zotero/storage/M7XBSHYQ/Flemming-2016-Biofilms_ an emergent form of ba.pdf},
  journal = {Nat Rev Microbiol},
  keywords = {*Bacterial Physiological Phenomena,*Biofilms,*Microbial Consortia,Anti-Bacterial Agents/pharmacology,Bacteria/*metabolism,Bacterial Adhesion,Polymers/metabolism,Polysaccharides; Bacterial/chemistry/*physiology},
  number = {9}
}

@article{ghosal2019,
  ids = {ghosalVivoStructureLegionella2019a},
  title = {In Vivo Structure of the {{Legionella}} Type {{II}} Secretion System by Electron Cryotomography},
  author = {Ghosal, Debnath and Kim, Ki Woo and Zheng, Huaixin and Kaplan, Mohammed and Truchan, Hilary K. and Lopez, Alberto E. and McIntire, Ian E. and Vogel, Joseph P. and Cianciotto, Nicholas P. and Jensen, Grant J.},
  year = {2019},
  month = dec,
  volume = {4},
  pages = {2101--2108},
  issn = {2058-5276},
  doi = {10.1038/s41564-019-0603-6},
  abstract = {The in vivo structure of a T2SS from Legionella pneumophila elucidates the structure and function of the different components of this macromolecular complex that exports a wide range of virulence factors.},
  copyright = {2019 This is a U.S. government work and not under copyright protection in the U.S.; foreign copyright protection may apply},
  file = {/Users/coiko/Zotero/storage/DM2432G9/Ghosal et al. - 2019 - In vivo structure of the Legionella type II secret.pdf;/Users/coiko/Zotero/storage/MKMJK2Y7/Ghosal et al. - 2019 - In vivo structure of the Legionella type II secret.pdf;/Users/coiko/Zotero/storage/ML42D8QF/Ghosal et al. - 2019 - In vivo structure of the Legionella type II secret.pdf;/Users/coiko/Zotero/storage/Q8AA3WC3/Ghosal et al. - 2019 - In vivo structure of the Legionella type II secret.pdf;/Users/coiko/Zotero/storage/S33YBCNF/Ghosal et al. - 2019 - In vivo structure of the Legionella type II secret.pdf;/Users/coiko/Zotero/storage/BIPG8BQH/s41564-019-0603-6.html;/Users/coiko/Zotero/storage/HAYQFD5A/s41564-019-0603-6.html;/Users/coiko/Zotero/storage/WDKAQH9V/s41564-019-0603-6.html},
  journal = {Nat Microbiol},
  language = {en},
  number = {12},
  pmcid = {PMC6879910},
  pmid = {31754273}
}

@article{ghosal2019a,
  title = {Molecular Architecture, Polar Targeting and Biogenesis of the {{Legionella Dot}}/{{Icm T4SS}}},
  author = {Ghosal, Debnath and Jeong, Kwangcheol C. and Chang, Yi-Wei and Gyore, Jacob and Teng, Lin and Gardner, Adam and Vogel, Joseph P. and Jensen, Grant J.},
  year = {2019},
  month = jul,
  volume = {4},
  pages = {1173--1182},
  issn = {2058-5276},
  doi = {10.1038/s41564-019-0427-4},
  abstract = {A combination of electron cryotomography and immunofluorescence microscopy reveals the structure of the core transmembrane subcomplex of the Legionella defective in organelle trafficking (Dot)/intracellular multiplication (Icm) type IVB secretion system (T4BSS) and an early-stage assembly process by which T4BSS components are targeted to the bacterial poles by DotU and IcmF.},
  copyright = {2019 The Author(s), under exclusive licence to Springer Nature Limited},
  file = {/Users/coiko/Zotero/storage/CDPJ22CF/Ghosal et al. - 2019 - Molecular architecture, polar targeting and biogen.pdf;/Users/coiko/Zotero/storage/KEC6XYBJ/Ghosal et al. - 2019 - Molecular architecture, polar targeting and biogen.pdf;/Users/coiko/Zotero/storage/STZTZYI9/Ghosal et al. - 2019 - Molecular architecture, polar targeting and biogen.pdf;/Users/coiko/Zotero/storage/TBJID273/Ghosal-2019-Molecular architecture, polar targ.pdf;/Users/coiko/Zotero/storage/5PJPAJ8L/s41564-019-0427-4.html},
  journal = {Nat Microbiol},
  keywords = {Bacterial Proteins,Cell Membrane,Cell Polarity,Electron Microscope Tomography,Legionella pneumophila,Microscopy; Fluorescence,Mutation,Periplasm,Protein Multimerization,Type IV Secretion Systems},
  language = {en},
  number = {7},
  pmcid = {PMC6588468},
  pmid = {31011165}
}

@article{goodsell2009,
  title = {Escherichia Coli},
  shorttitle = {Escherichia Coli},
  author = {Goodsell, D. S.},
  year = {2009},
  month = nov,
  volume = {37},
  pages = {325--32},
  issn = {1539-3429 (Electronic) 1470-8175 (Linking)},
  doi = {10.1002/bmb.20345},
  abstract = {Diverse biological data may be used to create illustrations of molecules in their cellular context. I describe the scientific results that support a recent textbook illustration of an Escherichia coli cell. The image magnifies a portion of the bacterium at one million times, showing the location and form of individual macromolecules. Results from biochemistry, electron microscopy, and X-ray crystallography were used to create the image.},
  file = {/Users/coiko/Zotero/storage/6TJLH32G/Goodsell-2009-Escherichia coli.pdf;/Users/coiko/Zotero/storage/YMKUD4S5/Goodsell-2009-Escherichia coli.pdf},
  journal = {Biochem Mol Biol Educ},
  number = {6}
}

@article{hazelbauer2008,
  title = {Bacterial Chemoreceptors: {{High}}-Performance Signaling in Networked Arrays},
  shorttitle = {Bacterial Chemoreceptors},
  author = {Hazelbauer, Gerald L. and Falke, Joseph J. and Parkinson, John S.},
  year = {2008},
  month = jan,
  volume = {33},
  pages = {9--19},
  issn = {0968-0004},
  doi = {10.1016/j.tibs.2007.09.014},
  abstract = {Chemoreceptors are crucial components in the bacterial sensory systems that mediate chemotaxis. Chemotactic responses exhibit exquisite sensitivity, extensive dynamic range and precise adaptation. The mechanisms that mediate these high-performance functions involve not only actions of individual proteins but also interactions among clusters of components, localized in extensive patches of thousands of molecules. Recently, these patches have been imaged in native cells, important features of chemoreceptor structure and on-off switching have been identified, and new insights have been gained into the structural basis and functional consequences of higher order interactions among sensory components. These new data suggest multiple levels of molecular interactions, each of which contribute specific functional features and together create a sophisticated signaling device.},
  file = {/Users/coiko/Zotero/storage/2G2KK4LB/Hazelbauer et al. - 2008 - Bacterial chemoreceptors high-performance signali.pdf;/Users/coiko/Zotero/storage/5CCLGT84/S0968000407002903.html},
  journal = {Trends Biochem Sci},
  language = {en},
  number = {1}
}

@article{henderson2020,
  title = {Diversification of {{Campylobacter}} Jejuni {{Flagellar C}}-{{Ring Composition Impacts Its Structure}} and {{Function}} in {{Motility}}, {{Flagellar Assembly}}, and {{Cellular Processes}}},
  author = {Henderson, Louie D. and {Matthews-Palmer}, Teige R. S. and Gulbronson, Connor J. and Ribardo, Deborah A. and Beeby, Morgan and Hendrixson, David R.},
  year = {2020},
  month = feb,
  volume = {11},
  publisher = {{American Society for Microbiology}},
  issn = {2150-7511},
  doi = {10.1128/mBio.02286-19},
  abstract = {Bacterial flagella are reversible rotary motors that rotate external filaments for bacterial propulsion. Some flagellar motors have diversified by recruiting additional components that influence torque and rotation, but little is known about the possible diversification and evolution of core motor components. The mechanistic core of flagella is the cytoplasmic C ring, which functions as a rotor, directional switch, and assembly platform for the flagellar type III secretion system (fT3SS) ATPase. The C ring is composed of a ring of FliG proteins and a helical ring of surface presentation of antigen (SPOA) domains from the switch proteins FliM and one of two usually mutually exclusive paralogs, FliN or FliY. We investigated the composition, architecture, and function of the C ring of Campylobacter jejuni, which encodes FliG, FliM, and both FliY and FliN by a variety of interrogative approaches. We discovered a diversified C. jejuni C ring containing FliG, FliM, and both FliY, which functions as a classical FliN-like protein for flagellar assembly, and FliN, which has neofunctionalized into a structural role. Specific protein interactions drive the formation of a more complex heterooligomeric C. jejuni C-ring structure. We discovered that this complex C ring has additional cellular functions in polarly localizing FlhG for numerical regulation of flagellar biogenesis and spatial regulation of division. Furthermore, mutation of the C. jejuni C ring revealed a T3SS that was less dependent on its ATPase complex for assembly than were other systems. Our results highlight considerable evolved flagellar diversity that impacts motor output, biogenesis, and cellular processes in different species.
IMPORTANCE The conserved core of bacterial flagellar motors reflects a shared evolutionary history that preserves the mechanisms essential for flagellar assembly, rotation, and directional switching. In this work, we describe an expanded and diversified set of core components in the Campylobacter jejuni flagellar C ring, the mechanistic core of the motor. Our work provides insight into how usually conserved core components may have diversified by gene duplication, enabling a division of labor of the ancestral protein between the two new proteins, acquisition of new roles in flagellar assembly and motility, and expansion of the function of the flagellum beyond motility, including spatial regulation of cell division and numerical control of flagellar biogenesis in C. jejuni. Our results highlight that relatively small changes, such as gene duplications, can have substantial ramifications on the cellular roles of a molecular machine.},
  copyright = {Copyright \textcopyright{} 2020 Henderson et al.. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.},
  file = {/Users/coiko/Zotero/storage/3ID66PCR/Henderson et al. - 2020 - Diversification of Campylobacter jejuni Flagellar .pdf;/Users/coiko/Zotero/storage/53U6SIH6/e02286-19.html},
  journal = {mBio},
  language = {en},
  number = {1},
  pmid = {31911488}
}

@misc{hillInternet,
  title = {Movie - {{Neutrophil}} Chasing Bacteria},
  author = {Hill, M. A.},
  year = {Internet},
  url = {https://embryology.med.unsw.edu.au/embryology/index.php/Movie_-_Neutrophil_chasing_bacteria},
  urldate = {2020-06-09},
  journal = {Embryology}
}

@article{hirsch1974,
  title = {Budding Bacteria},
  shorttitle = {Budding Bacteria},
  author = {Hirsch, P.},
  year = {1974},
  volume = {28},
  pages = {391--444},
  issn = {0066-4227 (Print) 0066-4227 (Linking)},
  doi = {10.1146/annurev.mi.28.100174.002135},
  file = {/Users/coiko/Zotero/storage/RH7WCIEY/annurev.mi.28.100174.002135.pdf;/Users/coiko/Zotero/storage/V4WCGXVK/Hirsch-1974-Budding bacteria.pdf},
  journal = {Annu Rev Microbiol},
  keywords = {Bacteria/analysis/classification/*growth \& development/metabolism/ultrastructure,Cell Nucleus/metabolism,Cell Wall/growth \& development,Cytosine/analysis,DNA; Bacterial/analysis/biosynthesis,Ecology,Genes,Guanine/analysis,Microscopy; Electron,Models; Biological,Molecular Weight,Morphogenesis,Species Specificity},
  number = {0}
}

@article{hoppert1999,
  title = {Principles of Macromolecular Organization and Cell Function in Bacteria and Archaea},
  author = {Hoppert, Michael and Mayer, Frank},
  year = {1999},
  month = oct,
  volume = {31},
  pages = {247--284},
  issn = {1085-9195, 1559-0283},
  doi = {10.1007/BF02738242},
  abstract = {Structural organization of the cytoplasm by compartmentation is a well established fact for the eukaryotic cell. In prokaryotes, compartmentation is less obvious. Most prokaryotes do not need intracytoplasmic membranes to maintain their vital functions. This review, especially dealing with prokaryotes, will point out that compartmentation in prokaryotes is present, but not only achieved by membranes. Besides membranes, the nucleoid, multienzyme complexes and metabolons, storage granules, and cytoskeletal elements are involved in compartmentation. In this respect, the organization of the cytoplasm of prokaryotes is similar to that in the eukaryotic cell. Compartmentation influences properties of water in cells.},
  file = {/Users/coiko/Zotero/storage/SQQYHCVC/Hoppert and Mayer - 1999 - Principles of macromolecular organization and cell.pdf},
  journal = {Cell Biochem Biophys},
  language = {en},
  number = {3}
}

@article{hu2018,
  title = {Cryo-{{EM}} Analysis of the {{T3S}} Injectisome Reveals the Structure of the Needle and Open Secretin},
  author = {Hu, J. and Worrall, L. J. and Hong, C. and Vuckovic, M. and Atkinson, C. E. and Caveney, N. and Yu, Z. and Strynadka, N. C. J.},
  year = {2018},
  month = sep,
  volume = {9},
  pages = {3840},
  publisher = {{Nature Publishing Group}},
  issn = {2041-1723},
  doi = {10.1038/s41467-018-06298-8},
  abstract = {The bacterial type III secretion system, or injectisome, is a syringe shaped nanomachine essential for the virulence of many disease causing Gram-negative bacteria. At the core of the injectisome structure is the needle complex, a continuous channel formed by the highly oligomerized inner and outer membrane hollow rings and a polymerized helical needle filament which spans through and projects into the infected host cell. Here we present the near-atomic resolution structure of a needle complex from the prototypical Salmonella Typhimurium SPI-1 type III secretion system, with local masking protocols allowing for model building and refinement of the major membrane spanning components of the needle complex~base in addition to an isolated needle filament. This work provides significant insight into injectisome structure and assembly and importantly captures the molecular basis for substrate induced gating in the giant outer membrane secretin portal family.},
  copyright = {2018 The Author(s)},
  file = {/Users/coiko/Zotero/storage/EBNR8THV/Hu et al. - 2018 - Cryo-EM analysis of the T3S injectisome reveals th.pdf;/Users/coiko/Zotero/storage/WN9IZMXD/s41467-018-06298-8.html},
  journal = {Nature Communications},
  language = {en},
  number = {1}
}

@incollection{jacob2002a,
  title = {Inaugural Lecture, {{Chair}} of {{Cellular Genetics}}, {{Coll{\'e}ge}} de {{France}}, Delivered {{Friday May}} 7, 1965},
  booktitle = {Travaux {{Scientifiques}} de {{Fran{\c c}ois Jacob}}},
  author = {Jacob, Fran{\c c}ois},
  year = {2002},
  publisher = {{{\'E}ditions Odile Jacob}},
  address = {{Paris}}
}

@article{jarrell2008,
  title = {The Surprisingly Diverse Ways That Prokaryotes Move},
  shorttitle = {The Surprisingly Diverse Ways That Prokaryotes Move},
  author = {Jarrell, K. F. and McBride, M. J.},
  year = {2008},
  month = jun,
  volume = {6},
  pages = {466--76},
  issn = {1740-1534 (Electronic) 1740-1526 (Linking)},
  doi = {10.1038/nrmicro1900},
  abstract = {Prokaryotic cells move through liquids or over moist surfaces by swimming, swarming, gliding, twitching or floating. An impressive diversity of motility mechanisms has evolved in prokaryotes. Movement can involve surface appendages, such as flagella that spin, pili that pull and Mycoplasma 'legs' that walk. Internal structures, such as the cytoskeleton and gas vesicles, are involved in some types of motility, whereas the mechanisms of some other types of movement remain mysterious. Regardless of the type of motility machinery that is employed, most motile microorganisms use complex sensory systems to control their movements in response to stimuli, which allows them to migrate to optimal environments.},
  file = {/Users/coiko/Zotero/storage/PREJR4AQ/Jarrell-2008-The surprisingly diverse ways tha.pdf},
  journal = {Nat Rev Microbiol},
  keywords = {Adhesins; Bacterial/physiology,Archaea/physiology,Bacteria/genetics,Bacterial Physiological Phenomena,Fimbriae; Bacterial/physiology,Flagella/physiology,Focal Adhesions/physiology,Models; Biological,Movement,Mycoplasma/physiology,Prokaryotic Cells/*physiology},
  number = {6}
}

@misc{jensenInternet,
  title = {Getting {{Started}} in {{Cryo}}-{{EM}}},
  author = {Jensen, G},
  year = {Internet},
  url = {cryo-em-course.caltech.edu},
  urldate = {2020-05-11},
  journal = {Video Lectures}
}

@article{johnson2020a,
  title = {Symmetry Mismatch in the {{MS}}-Ring of the Bacterial Flagellar Rotor Explains the Structural Coordination of Secretion and Rotation},
  author = {Johnson, Steven and Fong, Yu Hang and Deme, Justin C. and Furlong, Emily J. and Kuhlen, Lucas and Lea, Susan M.},
  year = {2020},
  month = jul,
  volume = {5},
  pages = {966--975},
  publisher = {{Nature Publishing Group}},
  issn = {2058-5276},
  doi = {10.1038/s41564-020-0703-3},
  abstract = {The bacterial flagellum is a complex self-assembling nanomachine that confers motility to the cell. Despite great variation across species, all flagella are ultimately constructed from a helical propeller that is attached to a motor embedded in the inner membrane. The motor consists of a series of stator units surrounding a central rotor made up of two ring complexes, the MS-ring and the C-ring. Despite many studies, high-resolution structural information is still lacking for the MS-ring of the rotor, and proposed mismatches in stoichiometry between the two rings have long provided a source of confusion for the field. Here, we present structures of the Salmonella MS-ring, revealing a high level of variation in inter- and intrachain symmetry that provides a structural explanation for the ability of the MS-ring to function as a complex and elegant interface between the two main functions of the flagellum\textemdash{}protein secretion and rotation.},
  copyright = {2020 The Author(s), under exclusive licence to Springer Nature Limited},
  file = {/Users/coiko/Zotero/storage/TRN3LLUC/Johnson et al. - 2020 - Symmetry mismatch in the MS-ring of the bacterial .pdf;/Users/coiko/Zotero/storage/6ZH5DDN3/s41564-020-0703-3.html},
  journal = {Nat Microbiol},
  language = {en},
  number = {7}
}

@article{jordan2001,
  title = {Three-Dimensional Structure of Cyanobacterial Photosystem {{I}} at 2.5 {{{\AA}}} Resolution},
  author = {Jordan, Patrick and Fromme, Petra and Witt, Horst Tobias and Klukas, Olaf and Saenger, Wolfram and Krau{\ss}, Norbert},
  year = {2001},
  month = jun,
  volume = {411},
  pages = {909--917},
  publisher = {{Nature Publishing Group}},
  issn = {1476-4687},
  doi = {10.1038/35082000},
  abstract = {Life on Earth depends on photosynthesis, the conversion of light energy from the Sun to chemical energy. In plants, green algae and cyanobacteria, this process is driven by the cooperation of two large protein-cofactor complexes, photosystems I and II, which are located in the thylakoid photosynthetic membranes. The crystal structure of photosystem I from the thermophilic cyanobacterium Synechococcus elongatus described here provides a picture at atomic detail of 12 protein subunits and 127 cofactors comprising 96 chlorophylls, 2 phylloquinones, 3 Fe4S4 clusters, 22 carotenoids, 4 lipids, a putative Ca2+ ion and 201 water molecules. The structural information on the proteins and cofactors and their interactions provides a basis for understanding how the high efficiency of photosystem I in light capturing and electron transfer is achieved.},
  copyright = {2001 Macmillan Magazines Ltd.},
  file = {/Users/coiko/Zotero/storage/5T6PVQ6T/Jordan et al. - 2001 - Three-dimensional structure of cyanobacterial phot.pdf;/Users/coiko/Zotero/storage/7CBJJ3NT/35082000.html},
  journal = {Nature},
  language = {en},
  number = {6840}
}

@article{kaledhonkar2019,
  title = {Late Steps in Bacterial Translation Initiation Visualized Using Time-Resolved Cryo-{{EM}}},
  author = {Kaledhonkar, Sandip and Fu, Ziao and Caban, Kelvin and Li, Wen and Chen, Bo and Sun, Ming and Gonzalez, Ruben L. and Frank, Joachim},
  year = {2019},
  month = jun,
  volume = {570},
  pages = {400--404},
  publisher = {{Nature Publishing Group}},
  issn = {1476-4687},
  doi = {10.1038/s41586-019-1249-5},
  abstract = {The initiation of bacterial translation involves the tightly regulated joining of the 50S ribosomal subunit to an initiator transfer RNA (fMet-tRNAfMet)-containing 30S ribosomal initiation complex to form a 70S initiation complex, which subsequently matures into a 70S elongation-competent complex. Rapid and accurate formation of the 70S initiation complex is promoted by initiation factors, which must dissociate from the 30S initiation complex before the resulting 70S elongation-competent complex can begin the elongation of translation1. Although comparisons of the structures of the 30S2-5 and 70S4,6-8 initiation complexes have revealed that the ribosome, initiation factors and fMet-tRNAfMet can acquire different conformations in these complexes, the timing of conformational changes during formation of the 70S initiation complex, the structures of any intermediates formed during these rearrangements, and the contributions that these dynamics might make to the mechanism and regulation of initiation remain unknown. Moreover, the absence of a structure of the 70S elongation-competent complex formed via an initiation-factor-catalysed reaction has precluded an understanding of the rearrangements to the ribosome, initiation factors and fMet-tRNAfMet that occur during maturation of a 70S initiation complex into a 70S elongation-competent complex. Here, using time-resolved cryogenic electron microscopy9, we report the near-atomic-resolution view of how a time-ordered series of conformational changes drive and regulate subunit joining, initiation factor dissociation and fMet-tRNAfMet positioning during formation of the 70S elongation-competent complex. Our results demonstrate the power of time-resolved cryogenic electron microscopy to determine how a time-ordered series of conformational changes contribute to the mechanism and regulation of one of the most fundamental processes in biology.},
  copyright = {2019 The Author(s), under exclusive licence to Springer Nature Limited},
  file = {/Users/coiko/Zotero/storage/6N9IP7MB/Kaledhonkar et al. - 2019 - Late steps in bacterial translation initiation vis.pdf;/Users/coiko/Zotero/storage/G82W52U9/s41586-019-1249-5.html},
  journal = {Nature},
  language = {en},
  number = {7761}
}

@article{kaplan2019,
  title = {The Presence and Absence of Periplasmic Rings in Bacterial Flagellar Motors Correlates with Stator Type},
  author = {Kaplan, Mohammed and Ghosal, Debnath and Subramanian, Poorna and Oikonomou, Catherine M and Kjaer, Andreas and Pirbadian, Sahand and Ortega, Davi R and Briegel, Ariane and {El-Naggar}, Mohamed Y and Jensen, Grant J},
  editor = {Egelman, Edward H and Storz, Gisela and Egelman, Edward H and Ito, Masahiro and Stahlberg, Henning},
  year = {2019},
  month = jan,
  volume = {8},
  pages = {e43487},
  publisher = {{eLife Sciences Publications, Ltd}},
  issn = {2050-084X},
  doi = {10.7554/eLife.43487},
  abstract = {The bacterial flagellar motor, a cell-envelope-embedded macromolecular machine that functions as a cellular propeller, exhibits significant structural variability between species. Different torque-generating stator modules allow motors to operate in different pH, salt or viscosity levels. How such diversity evolved is unknown. Here, we use electron cryo-tomography to determine the in situ macromolecular structures of three Gammaproteobacteria motors: Legionella pneumophila, Pseudomonas aeruginosa, and Shewanella oneidensis, providing the first views of intact motors with dual stator systems. Complementing our imaging with bioinformatics analysis, we find a correlation between the motor's stator system and its structural elaboration. Motors with a single H+-driven stator have only the core periplasmic P- and L-rings; those with dual H+-driven stators have an elaborated P-ring; and motors with Na+ or Na+/H+-driven stators have both their P- and L-rings embellished. Our results suggest an evolution of structural elaboration that may have enabled pathogenic bacteria to colonize higher-viscosity environments in animal hosts.},
  file = {/Users/coiko/Zotero/storage/5JQIZ6AR/Kaplan et al. - 2019 - The presence and absence of periplasmic rings in b.pdf},
  journal = {eLife},
  keywords = {bacterial flagellar motor,electron cryo-tomography,evolution,Legionella pneumophila,Pseudomonas aeruginosa,Shewanella oneidensis MR-1}
}

@article{keen2015,
  title = {A Century of Phage Research: {{Bacteriophages}} and the Shaping of Modern Biology},
  shorttitle = {A Century of Phage Research: Bacteriophages and the Shaping of Modern Biology},
  author = {Keen, E. C.},
  year = {2015},
  month = jan,
  volume = {37},
  pages = {6--9},
  issn = {1521-1878 (Electronic) 0265-9247 (Linking)},
  doi = {10.1002/bies.201400152},
  abstract = {2015 marks the centennial of the discovery of bacteriophages, viruses that infect bacteria. Phages have been central to some of biology's most meaningful advances over the past hundred years (shown here); they greatly influence the workings of the biosphere, and are poised to play expanded roles in biomedicine, biotechnology, and ecology.},
  file = {/Users/coiko/Zotero/storage/ZITUZKUE/Keen-2015-A century of phage research_ bacteri.pdf},
  journal = {Bioessays},
  keywords = {bacteriophage,Bacteriophages/*physiology,Biology/*history,history of science,History; 20th Century,model organism,molecular biology,phage group,phage therapy,Research/*history,virology},
  number = {1}
}

@article{kerfeld2018,
  ids = {kerfeldBacterialMicrocompartments2018a},
  title = {Bacterial Microcompartments},
  shorttitle = {Bacterial Microcompartments},
  author = {Kerfeld, C. A. and Aussignargues, C. and Zarzycki, J. and Cai, F. and Sutter, M.},
  year = {2018},
  month = mar,
  issn = {1740-1534 (Electronic) 1740-1526 (Linking)},
  doi = {10.1038/nrmicro.2018.10},
  abstract = {Bacterial microcompartments (BMCs) are self-assembling organelles that consist of an enzymatic core that is encapsulated by a selectively permeable protein shell. The potential to form BMCs is widespread and found across the kingdom Bacteria. BMCs have crucial roles in carbon dioxide fixation in autotrophs and the catabolism of organic substrates in heterotrophs. They contribute to the metabolic versatility of bacteria, providing a competitive advantage in specific environmental niches. Although BMCs were first visualized more than 60 years ago, it is mainly in the past decade that progress has been made in understanding their metabolic diversity and the structural basis of their assembly and function. This progress has not only heightened our understanding of their role in microbial metabolism but is also beginning to enable their use in a variety of applications in synthetic biology. In this Review, we focus on recent insights into the structure, assembly, diversity and function of BMCs.},
  file = {/Users/coiko/Zotero/storage/6WQJ5QZA/Kerfeld et al. - 2018 - Bacterial microcompartments.pdf;/Users/coiko/Zotero/storage/7D63GRWB/Kerfeld-2018-Bacterial microcompartments.pdf},
  journal = {Nat Rev Microbiol},
  keywords = {Bacteria,Bacterial Proteins,Carbon Cycle,Carbon Dioxide,Gene Expression Regulation; Bacterial,Organelles},
  pmcid = {PMC6022854},
  pmid = {29503457}
}

@article{laloux2014,
  title = {How Do Bacteria Localize Proteins to the Cell Pole?},
  shorttitle = {How Do Bacteria Localize Proteins to the Cell Pole?},
  author = {Laloux, G. and {Jacobs-Wagner}, C.},
  year = {2014},
  month = jan,
  volume = {127},
  pages = {11--9},
  issn = {1477-9137 (Electronic) 0021-9533 (Linking)},
  doi = {10.1242/jcs.138628},
  abstract = {It is now well appreciated that bacterial cells are highly organized, which is far from the initial concept that they are merely bags of randomly distributed macromolecules and chemicals. Central to their spatial organization is the precise positioning of certain proteins in subcellular domains of the cell. In particular, the cell poles - the ends of rod-shaped cells - constitute important platforms for cellular regulation that underlie processes as essential as cell cycle progression, cellular differentiation, virulence, chemotaxis and growth of appendages. Thus, understanding how the polar localization of specific proteins is achieved and regulated is a crucial question in bacterial cell biology. Often, polarly localized proteins are recruited to the poles through their interaction with other proteins or protein complexes that were already located there, in a so-called diffusion-and-capture mechanism. Bacteria are also starting to reveal their secrets on how the initial pole 'recognition' can occur and how this event can be regulated to generate dynamic, reproducible patterns in time (for example, during the cell cycle) and space (for example, at a specific cell pole). Here, we review the major mechanisms that have been described in the literature, with an emphasis on the self-organizing principles. We also present regulation strategies adopted by bacterial cells to obtain complex spatiotemporal patterns of protein localization.},
  file = {/Users/coiko/Zotero/storage/BPP7P6LM/Laloux-2014-How do bacteria localize proteins.pdf;/Users/coiko/Zotero/storage/E8WJ8AL6/Laloux-2014-How do bacteria localize proteins.pdf},
  journal = {J Cell Sci},
  keywords = {Bacterial cell cycle,Bacterial Proteins/chemistry/*metabolism,Caulobacter crescentus/*physiology/ultrastructure,Cell Compartmentation,Cell Cycle,Cell Division,Cell Polarity,Chemotaxis/physiology,Escherichia coli/*physiology/ultrastructure,Hydrophobic and Hydrophilic Interactions,Mycobacterium tuberculosis/*physiology/ultrastructure,Polar localization,Protein Binding,Spatial organization},
  number = {Pt 1}
}

@article{letunic2019,
  title = {Interactive {{Tree Of Life}} ({{iTOL}}) v4: Recent Updates and New Developments},
  shorttitle = {Interactive {{Tree Of Life}} ({{iTOL}}) V4},
  author = {Letunic, Ivica and Bork, Peer},
  year = {2019},
  month = jul,
  volume = {47},
  pages = {W256-W259},
  publisher = {{Oxford Academic}},
  issn = {0305-1048},
  doi = {10.1093/nar/gkz239},
  abstract = {Abstract.  The Interactive Tree Of Life (https://itol.embl.de) is an online tool for the display, manipulation and annotation of phylogenetic and other trees. I},
  file = {/Users/coiko/Zotero/storage/F9TRBYVG/Letunic and Bork - 2019 - Interactive Tree Of Life (iTOL) v4 recent updates.pdf;/Users/coiko/Zotero/storage/QQCMFAEM/5424068.html},
  journal = {Nucleic Acids Res},
  language = {en},
  number = {W1}
}

@article{lopez-castilla2017,
  title = {Structure of the Calcium-Dependent Type 2 Secretion Pseudopilus},
  author = {{L{\'o}pez-Castilla}, Aracelys and Thomassin, Jenny-Lee and Bardiaux, Benjamin and Zheng, Weili and Nivaskumar, Mangayarkarasi and Yu, Xiong and Nilges, Michael and Egelman, Edward H. and {Izadi-Pruneyre}, Nadia and Francetic, Olivera},
  year = {2017},
  month = dec,
  volume = {2},
  pages = {1686--1695},
  publisher = {{Nature Publishing Group}},
  issn = {2058-5276},
  doi = {10.1038/s41564-017-0041-2},
  abstract = {Many Gram-negative bacteria use type 2 secretion systems (T2SSs) to secrete proteins involved in virulence and adaptation. Transport of folded proteins via T2SS nanomachines requires the assembly of inner membrane-anchored fibres called pseudopili. Although efficient pseudopilus assembly is essential for protein secretion, structure-based functional analyses are required to unravel the mechanistic link between these processes. Here, we report an atomic model for a T2SS pseudopilus from Klebsiella oxytoca, obtained by fitting the NMR structure of its calcium-bound subunit PulG into the \textasciitilde{}5-{\AA}-resolution cryo-electron microscopy reconstruction of assembled fibres. This structure reveals the comprehensive network of inter-subunit contacts and unexpected features, including a disordered central region of the PulG helical stem, and highly flexible C-terminal residues on the fibre surface. NMR, mutagenesis and functional analyses highlight the key role of calcium in PulG folding and stability. Fibre disassembly in the absence of calcium provides a basis for pseudopilus length control, essential for protein secretion, and supports the Archimedes screw model for the type 2 secretion mechanism.},
  copyright = {2017 The Author(s)},
  file = {/Users/coiko/Zotero/storage/3SV76DTR/López-Castilla et al. - 2017 - Structure of the calcium-dependent type 2 secretio.pdf;/Users/coiko/Zotero/storage/6WEBTG8E/s41564-017-0041-2.html},
  journal = {Nature Microbiology},
  language = {en},
  number = {12}
}

@article{lower2013,
  title = {The Bacterial Magnetosome: {{A}} Unique Prokaryotic Organelle},
  shorttitle = {The {{Bacterial Magnetosome}}},
  author = {Lower, Brian H. and Bazylinski, Dennis A.},
  year = {2013},
  volume = {23},
  pages = {63--80},
  publisher = {{Karger Publishers}},
  issn = {1464-1801, 1660-2412},
  doi = {10.1159/000346543},
  abstract = {The bacterial magnetosome is a unique prokaryotic organelle comprising magnetic mineral crystals surrounded by a phospholipid bilayer. These inclusions are biomineralized by the magnetotactic bacteria which are ubiquitous, aquatic, motile microorganisms. Magnetosomes cause cells of magnetotactic bacteria to passively align and swim along the Earth's magnetic field lines, as miniature motile compass needles. These specialized compartments consist of a phospholipid bilayer membrane surrounding magnetic crystals of magnetite (Fe\textsubscript{3}O\textsubscript{4}) or greigite (Fe\textsubscript{3}S\textsubscript{4}). The morphology of these membrane-bound crystals varies by species with a nominal magnetic domain size between 35 and 120 nm. Almost all magnetotactic bacteria arrange their magnetosomes in a chain within the cell there by maximizing the magnetic dipole moment of the cell. It is presumed that magnetotactic bacteria use magnetotaxis in conjunction with chemotaxis to locate and maintain an optimum position for growth and survival based on chemistry, redox and physiology in aquatic habitats with vertical chemical concentration and redox gradients. The biosynthesis of magnetosomes is a complex process that involves several distinct steps including cytoplasmic membrane modifications, iron uptake and transport, initiation of crystallization, crystal maturation and magnetosome chain formation. While many mechanistic details remain unresolved, magnetotactic bacteria appear to contain the genetic determinants for magnetosome biomineralization within their genomes in clusters of genes that make up what is referred to as the magnetosome gene island in some species. In addition, magnetosomes contain a unique set of proteins, not present in other cellular fractions, which control the biomineralization process. Through the development of genetic systems, proteomic and genomic work, and the use of molecular and biochemical tools, the functions of a number of magnetosome membrane proteins have been demonstrated and the molecular mechanism for the biomineralization of magnetosomes in these organisms is beginning to be revealed.},
  file = {/Users/coiko/Zotero/storage/J7CGLBEH/346543.html},
  journal = {J Mol Microb Biotech},
  language = {english},
  number = {1-2},
  pmid = {23615196}
}

@article{lynch2017,
  title = {Human {{CTP}} Synthase Filament Structure Reveals the Active Enzyme Conformation},
  author = {Lynch, Eric M. and Hicks, Derrick R. and Shepherd, Matthew and Endrizzi, James A. and Maker, Allison and Hansen, Jesse M. and Barry, Rachael M. and Gitai, Zemer and Baldwin, Enoch P. and Kollman, Justin M.},
  year = {2017},
  month = jun,
  volume = {24},
  pages = {507--514},
  publisher = {{Nature Publishing Group}},
  issn = {1545-9985},
  doi = {10.1038/nsmb.3407},
  abstract = {The human enzyme CTP synthase forms polymeric filaments with increased catalytic activity, in contrast to the inactive filaments formed by bacterial CTP synthase. Cryo-EM and crystallographic analyses explain the structural bases for those different behaviors.},
  copyright = {2017 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
  file = {/Users/coiko/Zotero/storage/BM2JL5W6/Lynch et al. - 2017 - Human CTP synthase filament structure reveals the .pdf;/Users/coiko/Zotero/storage/QCUEG36Z/nsmb.html},
  journal = {Nat Struct Mol Biol},
  language = {en},
  number = {6}
}

@article{ma2020,
  title = {Structural Basis of Energy Transfer in {{Porphyridium}} Purpureum Phycobilisome},
  author = {Ma, Jianfei and You, Xin and Sun, Shan and Wang, Xiaoxiao and Qin, Song and Sui, Sen-Fang},
  year = {2020},
  month = mar,
  volume = {579},
  pages = {146--151},
  publisher = {{Nature Publishing Group}},
  issn = {1476-4687},
  doi = {10.1038/s41586-020-2020-7},
  abstract = {Photosynthetic organisms have developed various light-harvesting systems to adapt to their environments1. Phycobilisomes are large light-harvesting protein complexes found in cyanobacteria and red algae2-4, although how the energies of the chromophores within these complexes are modulated by their environment is unclear. Here we report the cryo-electron microscopy structure of a 14.7-megadalton phycobilisome with a hemiellipsoidal shape from the red alga Porphyridium purpureum. Within this complex we determine the structures of 706 protein subunits, including 528 phycoerythrin, 72 phycocyanin, 46 allophycocyanin and 60 linker proteins. In addition, 1,598 chromophores are resolved comprising 1,430 phycoerythrobilin, 48 phycourobilin and 120 phycocyanobilin molecules. The markedly improved resolution of our structure compared with that of the phycobilisome of Griffithsia pacifica5 enabled us to build an accurate atomic model of the P. purpureum phycobilisome system. The model reveals how the linker proteins affect the microenvironment of the chromophores, and suggests that interactions of the aromatic amino acids of the linker proteins with the chromophores may be a key factor in fine-tuning the energy states of the chromophores to ensure the efficient unidirectional transfer of energy.},
  copyright = {2020 The Author(s), under exclusive licence to Springer Nature Limited},
  file = {/Users/coiko/Zotero/storage/EGAJ8K3J/Ma et al. - 2020 - Structural basis of energy transfer in Porphyridiu.pdf;/Users/coiko/Zotero/storage/5FVKQMJQ/s41586-020-2020-7.html},
  journal = {Nature},
  language = {en},
  number = {7797}
}

@article{matsunami2016,
  title = {Complete Structure of the Bacterial Flagellar Hook Reveals Extensive Set of Stabilizing Interactions},
  author = {Matsunami, Hideyuki and Barker, Clive S. and Yoon, Young-Ho and Wolf, Matthias and Samatey, Fadel A.},
  year = {2016},
  month = nov,
  volume = {7},
  pages = {13425},
  publisher = {{Nature Publishing Group}},
  issn = {2041-1723},
  doi = {10.1038/ncomms13425},
  abstract = {The bacterial flagellar hook is a tubular helical structure made by the polymerization of multiple copies of a protein, FlgE. Here we report the structure of the hook from Campylobacter jejuni by cryo-electron microscopy at a resolution of 3.5\,{\AA}. On the basis of this structure, we show that the hook is stabilized by intricate inter-molecular interactions between FlgE molecules. Extra domains in FlgE, found only in Campylobacter and in related bacteria, bring more stability and robustness to the hook. Functional experiments suggest that Campylobacter requires an unusually strong hook to swim without its flagella being torn off. This structure reveals details of the quaternary organization of the hook that consists of 11 protofilaments. Previous study of the flagellar filament of Campylobacter by electron microscopy showed its quaternary structure made of seven protofilaments. Therefore, this study puts in evidence the difference between the quaternary structures of a bacterial filament and its hook.},
  copyright = {2016 The Author(s)},
  file = {/Users/coiko/Zotero/storage/MUYPL3CA/Matsunami et al. - 2016 - Complete structure of the bacterial flagellar hook.pdf;/Users/coiko/Zotero/storage/MIY4GH4V/ncomms13425.html},
  journal = {Nat Commun},
  language = {en},
  number = {1}
}

@article{munoz-dorado2016,
  ids = {munoz-doradoMyxobacteriaMovingKilling2016},
  title = {Myxobacteria: {{Moving}}, Killing, Feeding, and Surviving Together},
  shorttitle = {Myxobacteria},
  author = {{Mu{\~n}oz-Dorado}, Jos{\'e} and {Marcos-Torres}, Francisco J. and {Garc{\'i}a-Bravo}, Elena and {Moraleda-Mu{\~n}oz}, Aurelio and P{\'e}rez, Juana},
  year = {2016},
  volume = {7},
  pages = {781},
  issn = {1664-302X},
  doi = {10.3389/fmicb.2016.00781},
  abstract = {Myxococcus xanthus, like other myxobacteria, is a social bacterium that moves and feeds cooperatively in predatory groups. On surfaces, rod-shaped vegetative cells move in search of the prey in a coordinated manner, forming dynamic multicellular groups referred to as swarms. Within the swarms, cells interact with one another and use two separate locomotion systems. Adventurous motility, which drives the movement of individual cells, is associated with the secretion of slime that forms trails at the leading edge of the swarms. It has been proposed that cellular traffic along these trails contributes to M. xanthus social behavior via stigmergic regulation. However, most of the cells travel in groups by using social motility, which is cell contact-dependent and requires a large number of individuals. Exopolysaccharides and the retraction of type IV pili at alternate poles of the cells are the engines associated with social motility. When the swarms encounter prey, the population of M. xanthus lyses and takes up nutrients from nearby cells. This cooperative and highly density-dependent feeding behavior has the advantage that the pool of hydrolytic enzymes and other secondary metabolites secreted by the entire group is shared by the community to optimize the use of the degradation products. This multicellular behavior is especially observed in the absence of nutrients. In this condition, M. xanthus swarms have the ability to organize the gliding movements of 1000s of rods, synchronizing rippling waves of oscillating cells, to form macroscopic fruiting bodies, with three subpopulations of cells showing division of labor. A small fraction of cells either develop into resistant myxospores or remain as peripheral rods, while the majority of cells die, probably to provide nutrients to allow aggregation and spore differentiation. Sporulation within multicellular fruiting bodies has the benefit of enabling survival in hostile environments, and increases germination and growth rates when cells encounter favorable conditions. Herein, we review how these social bacteria cooperate and review the main cell-cell signaling systems used for communication to maintain multicellularity.},
  file = {/Users/coiko/Zotero/storage/4NMQAASX/Muñoz-Dorado et al. - 2016 - Myxobacteria Moving, Killing, Feeding, and Surviv.pdf;/Users/coiko/Zotero/storage/KT8RGCCG/Munoz-Dorado-2016-Myxobacteria_ Moving, Killin.pdf},
  journal = {Front Microbiol},
  keywords = {motility,multicellularity,Myxococcus xanthus,predation,prokaryotic development},
  language = {eng},
  pmcid = {PMC4880591},
  pmid = {27303375}
}

@article{murphy2006,
  title = {In Situ Structure of the Complete {{Treponema}} Primitia Flagellar Motor},
  shorttitle = {In Situ Structure of the Complete {{Treponema}} Primitia Flagellar Motor},
  author = {Murphy, G. E. and Leadbetter, J. R. and Jensen, G. J.},
  year = {2006},
  month = aug,
  volume = {442},
  pages = {1062--4},
  issn = {1476-4687 (Electronic) 0028-0836 (Linking)},
  doi = {10.1038/nature05015},
  abstract = {The bacterial flagellar motor is an amazing nanomachine: built from approximately 25 different proteins, it uses an electrochemical ion gradient to drive rotation at speeds of up to 300 Hz (refs 1, 2). The flagellar motor consists of a fixed, membrane-embedded, torque-generating stator and a typically bidirectional, spinning rotor that changes direction in response to chemotactic signals. Most structural analyses so far have targeted the purified rotor, and hence little is known about the stator and its interactions. Here we show, using electron cryotomography of whole cells, the in situ structure of the complete flagellar motor from the spirochaete Treponema primitia at 7 nm resolution. Twenty individual motor particles were computationally extracted from the reconstructions, aligned and then averaged. The stator assembly, revealed for the first time, possessed 16-fold symmetry and was connected directly to the rotor, C ring and a novel P-ring-like structure. The unusually large size of the motor suggested mechanisms for increasing torque and supported models wherein critical interactions occur atop the C ring, where our data suggest that both the carboxy-terminal and middle domains of FliG are found.},
  file = {/Users/coiko/Zotero/storage/54DUWQEY/Murphy-2006-In situ structure of the complete.pdf;/Users/coiko/Zotero/storage/69FKCEI8/Murphy-2006-In situ structure of.pdf;/Users/coiko/Zotero/storage/8J6IPCX4/Murphy-2006-In situ structure of.pdf;/Users/coiko/Zotero/storage/AJCKI85Y/Murphy-2006-In situ structure of.pdf;/Users/coiko/Zotero/storage/ATSBEWDF/Murphy-2006-In situ structure of the complete.pdf;/Users/coiko/Zotero/storage/BCC9WUTC/Murphy-2006-In situ structure of the complete.pdf;/Users/coiko/Zotero/storage/C7LHLNHS/Murphy-2006-In situ structure of.pdf;/Users/coiko/Zotero/storage/PYT4DSU7/Murphy et al. - 2006 - In situ structure of the complete Treponema primit.pdf;/Users/coiko/Zotero/storage/U96CRWX4/Murphy-2006-In situ structure of.pdf;/Users/coiko/Zotero/storage/UBSLM52D/Murphy-2006-In situ structure of.pdf;/Users/coiko/Zotero/storage/V6Z6Z4GY/Murphy-2006-In situ structure of.pdf;/Users/coiko/Zotero/storage/WMWQWD8P/Murphy-2006-In situ structure of.pdf;/Users/coiko/Zotero/storage/X2N2UN73/Murphy-2006-In situ structure of the complete.pdf},
  journal = {Nature},
  keywords = {Cryoelectron Microscopy,Flagella,Flagella/*chemistry/*ultrastructure,Molecular Motor Proteins,Molecular Motor Proteins/*chemistry/*ultrastructure,Salmonella,Salmonella/chemistry/cytology,Tomography,Torque,Treponema,Treponema/chemistry/*cytology/*ultrastructure},
  number = {7106},
  pmid = {16885937}
}

@article{nguyen2015,
  title = {Coarse-Grained Simulations of Bacterial Cell Wall Growth Reveal That Local Coordination Alone Can Be Sufficient to Maintain Rod Shape},
  shorttitle = {Coarse-Grained Simulations of Bacterial Cell Wall Growth Reveal That Local Coordination Alone Can Be Sufficient to Maintain Rod Shape},
  author = {Nguyen, L. T. and Gumbart, J. C. and Beeby, M. and Jensen, G. J.},
  year = {2015},
  month = jul,
  volume = {112},
  pages = {E3689-98},
  issn = {1091-6490 (Electronic) 0027-8424 (Linking)},
  doi = {10.1073/pnas.1504281112},
  abstract = {Bacteria are surrounded by a peptidoglycan (PG) cell wall that must be remodeled to allow cell growth. While many structural details and properties of PG and the individual enzymes involved are known, how the process is coordinated to maintain cell integrity and rod shape is not understood. We have developed a coarse-grained method to simulate how individual transglycosylases, transpeptidases, and endopeptidases could introduce new material into an existing unilayer PG network. We find that a simple model with no enzyme coordination fails to maintain cell wall integrity and rod shape. We then iteratively analyze failure modes and explore different mechanistic hypotheses about how each problem might be overcome by the macromolecules involved. In contrast to a current theory, which posits that long MreB filaments are needed to coordinate PG insertion sites, we find that local coordination of enzyme activities in individual complexes can be sufficient to maintain cell integrity and rod shape. We also present possible molecular explanations for the existence of monofunctional transpeptidases and glycosidases (glycoside hydrolases), trimeric peptide crosslinks, cell twisting during growth, and synthesis of new strands in pairs.},
  file = {/Users/coiko/Zotero/storage/5JGMUKLY/Nguyen-2015-Coarse-grained simulations of bact.pdf;/Users/coiko/Zotero/storage/EQFY5LZY/Nguyen-2015-Coarse-grained simulations of bact.pdf;/Users/coiko/Zotero/storage/SI2KWN6H/Nguyen-2015-Coarse-grained simulations of bact.pdf;/Users/coiko/Zotero/storage/XITPTH6P/Nguyen-2015-Coarse-grained simulations of bact.pdf},
  journal = {Proc Natl Acad Sci U S A},
  keywords = {*Cell Shape,Bacteria/enzymology/*growth \& development,cell wall synthesis,Cell Wall/*physiology,coarse-grained modeling,Glycosylation,Hydrolysis,morphogenesis,Peptide Hydrolases/metabolism,Peptidoglycan Glycosyltransferase/metabolism},
  number = {28}
}

@article{oikonomou2017,
  title = {Cellular Electron Cryotomography: {{Toward}} Structural Biology in Situ},
  shorttitle = {Cellular {{Electron Cryotomography}}: {{Toward Structural Biology In Situ}}},
  author = {Oikonomou, C. M. and Jensen, G. J.},
  year = {2017},
  month = jun,
  volume = {86},
  pages = {873--896},
  issn = {1545-4509 (Electronic) 0066-4154 (Linking)},
  doi = {10.1146/annurev-biochem-061516-044741},
  abstract = {Electron cryotomography (ECT) provides three-dimensional views of macromolecular complexes inside cells in a native frozen-hydrated state. Over the last two decades, ECT has revealed the ultrastructure of cells in unprecedented detail. It has also allowed us to visualize the structures of macromolecular machines in their native context inside intact cells. In many cases, such machines cannot be purified intact for in vitro study. In other cases, the function of a structure is lost outside the cell, so that the mechanism can be understood only by observation in situ. In this review, we describe the technique and its history and provide examples of its power when applied to cell biology. We also discuss the integration of ECT with other techniques, including lower-resolution fluorescence imaging and higher-resolution atomic structure determination, to cover the full scale of cellular processes.},
  file = {/Users/coiko/Zotero/storage/8C9X33FJ/Oikonomou-2017-Cellular Electron Cryotomograph.pdf;/Users/coiko/Zotero/storage/BQT3MJGC/Oikonomou-2017-Cellular Electron Cryotomograph.pdf;/Users/coiko/Zotero/storage/JG8NJCP8/Oikonomou-2017-Cellular Electron Cryotomograph.pdf;/Users/coiko/Zotero/storage/QVFLZD9F/Oikonomou-2017-Cellular Electron Cryotomograph.pdf;/Users/coiko/Zotero/storage/T56AB92A/Oikonomou-2017-Cellular Electron Cryotomograph.pdf;/Users/coiko/Zotero/storage/WTY7B897/Oikonomou-2017-Cellular Electron Cryotomograph.pdf},
  journal = {Annu Rev Biochem},
  keywords = {*cilia,*Clem,*cryo-electron microscopy,*cryo-electron tomography,*electron cryotomography,*flagella,*hybrid methods,*nuclear pore complex,*type IV pili,*type VI secretion,Archaea,Archaea/metabolism/ultrastructure,Bacteria,Bacteria/metabolism/ultrastructure,Bacterial Secretion Systems,Bacterial Secretion Systems/metabolism/ultrastructure,cilia,Clem,CLEM,cryo-electron microscopy,cryo-electron tomography,cryo–electron microscopy,cryo–electron tomography,Cryoelectron Microscopy,Cryoelectron Microscopy/history/instrumentation/*methods,electron cryotomography,Electron Microscope Tomography,Electron Microscope Tomography/history/instrumentation/*methods,Fimbriae; Bacterial,Fimbriae; Bacterial/metabolism/*ultrastructure,flagella,Flagella,Flagella/metabolism/ultrastructure,History; 20th Century,History; 21st Century,hybrid methods,Models; Molecular,Nuclear Pore,nuclear pore complex,Nuclear Pore/*chemistry/metabolism/ultrastructure,Optical Imaging,Optical Imaging/history/instrumentation/*methods,Prokaryotic Cells,Prokaryotic Cells/metabolism/*ultrastructure,Protein Domains,Protein Structure; Secondary,type IV pili,type VI secretion},
  pmid = {28426242}
}

@article{oltrogge2020,
  title = {Multivalent Interactions between {{CsoS2}} and {{Rubisco}} Mediate {$\alpha$}-Carboxysome Formation},
  author = {Oltrogge, Luke M. and Chaijarasphong, Thawatchai and Chen, Allen W. and Bolin, Eric R. and Marqusee, Susan and Savage, David F.},
  year = {2020},
  month = mar,
  volume = {27},
  pages = {281--287},
  publisher = {{Nature Publishing Group}},
  issn = {1545-9985},
  doi = {10.1038/s41594-020-0387-7},
  abstract = {Carboxysomes are bacterial microcompartments that function as the centerpiece of the bacterial CO2-concentrating mechanism by facilitating high CO2 concentrations near the carboxylase Rubisco. The carboxysome self-assembles from thousands of individual proteins into icosahedral-like particles with a dense enzyme cargo encapsulated within a proteinaceous shell. In the case of the {$\alpha$}-carboxysome, there is little molecular insight into protein-protein interactions that drive the assembly process. Here, studies on the {$\alpha$}-carboxysome from Halothiobacillus neapolitanus demonstrate that Rubisco interacts with the N terminus of CsoS2, a multivalent, intrinsically disordered protein. X-ray structural analysis of the CsoS2 interaction motif bound to Rubisco reveals a series of conserved electrostatic interactions that are only made with properly assembled hexadecameric Rubisco. Although biophysical measurements indicate that this single interaction is weak, its implicit multivalency induces high-affinity binding through avidity. Taken together, our results indicate that CsoS2 acts as an interaction hub to condense Rubisco and enable efficient {$\alpha$}-carboxysome formation.},
  copyright = {2020 The Author(s), under exclusive licence to Springer Nature America, Inc.},
  file = {/Users/coiko/Zotero/storage/I85EKGKU/Oltrogge et al. - 2020 - Multivalent interactions between CsoS2 and Rubisco.pdf;/Users/coiko/Zotero/storage/3Q4MT3QD/s41594-020-0387-7.html},
  journal = {Nat Struct Mol Biol},
  language = {en},
  number = {3}
}

@article{oostergetel2010,
  title = {The Chlorosome: A Prototype for Efficient Light Harvesting in Photosynthesis},
  shorttitle = {The Chlorosome: A Prototype for Efficient Light Harvesting in Photosynthesis},
  author = {Oostergetel, G. T. and {van Amerongen}, H. and Boekema, E. J.},
  year = {2010},
  month = jun,
  volume = {104},
  pages = {245--55},
  issn = {1573-5079 (Electronic) 0166-8595 (Linking)},
  doi = {10.1007/s11120-010-9533-0},
  abstract = {Three phyla of bacteria include phototrophs that contain unique antenna systems, chlorosomes, as the principal light-harvesting apparatus. Chlorosomes are the largest known supramolecular antenna systems and contain hundreds of thousands of BChl c/d/e molecules enclosed by a single membrane leaflet and a baseplate. The BChl pigments are organized via self-assembly and do not require proteins to provide a scaffold for efficient light harvesting. Their excitation energy flows via a small protein, CsmA embedded in the baseplate to the photosynthetic reaction centres. Chlorosomes allow for photosynthesis at very low light intensities by ultra-rapid transfer of excitations to reaction centres and enable organisms with chlorosomes to live at extraordinarily low light intensities under which no other phototrophic organisms can grow. This article reviews several aspects of chlorosomes: the supramolecular and molecular organizations and the light-harvesting and spectroscopic properties. In addition, it provides some novel information about the organization of the baseplate.},
  file = {/Users/coiko/Zotero/storage/DVBTJQBJ/Oostergetel-2010-The chlorosome_ a prototype f.pdf},
  journal = {Photosynth Res},
  keywords = {*Photosynthesis,Chlorophyll/chemistry,Light-Harvesting Protein Complexes/*metabolism,Models; Molecular,Organelles/*metabolism/ultrastructure,Spectrum Analysis},
  number = {2-3}
}

@article{park2006,
  title = {Reconstruction of the Chemotaxis Receptor-Kinase Assembly},
  author = {Park, Sang-Youn and Borbat, Peter P. and {Gonzalez-Bonet}, Gabriela and Bhatnagar, Jaya and Pollard, Abiola M. and Freed, Jack H. and Bilwes, Alexandrine M. and Crane, Brian R.},
  year = {2006},
  month = may,
  volume = {13},
  pages = {400--407},
  publisher = {{Nature Publishing Group}},
  issn = {1545-9985},
  doi = {10.1038/nsmb1085},
  abstract = {In bacterial chemotaxis, an assembly of transmembrane receptors, the CheA histidine kinase and the adaptor protein CheW processes environmental stimuli to regulate motility. The structure of a Thermotoga maritima receptor cytoplasmic domain defines CheA interaction regions and metal ion-coordinating charge centers that undergo chemical modification to tune receptor response. Dimeric CheA-CheW, defined by crystallography and pulsed ESR, positions two CheWs to form a cleft that is lined with residues important for receptor interactions and sized to clamp one receptor dimer. CheW residues involved in kinase activation map to interfaces that orient the CheW clamps. CheA regulatory domains associate in crystals through conserved hydrophobic surfaces. Such CheA self-contacts align the CheW receptor clamps for binding receptor tips. Linking layers of ternary complexes with close-packed receptors generates a lattice with reasonable component ratios, cooperative interactions among receptors and accessible sites for modification enzymes.},
  copyright = {2006 Nature Publishing Group},
  file = {/Users/coiko/Zotero/storage/MC9GFHLT/Park et al. - 2006 - Reconstruction of the chemotaxis receptor–kinase a.pdf;/Users/coiko/Zotero/storage/S7SD83D8/nsmb1085.html},
  journal = {Nat Struct Mol Biol},
  language = {en},
  number = {5}
}

@article{patz2019,
  title = {Phage Tail-like Particles Are Versatile Bacterial Nanomachines},
  author = {Patz, Sascha and Becker, Yvonne and {Richert-P{\"o}ggeler}, Katja R. and Berger, Beatrice and Ruppel, Silke and Huson, Daniel H. and Becker, Matthias},
  year = {2019},
  month = sep,
  volume = {19},
  pages = {75--84},
  issn = {2090-1232},
  doi = {10.1016/j.jare.2019.04.003},
  abstract = {Type VI secretion systems and tailocins, two bacterial phage tail-like particles, have been reported to foster interbacterial competition. Both nanostructures enable their producer to kill other bacteria competing for the same ecological niche. Previously, type VI secretion systems and particularly R-type tailocins were considered highly specific, attacking a rather small range of competitors. Their specificity is conferred by cell surface receptors of the target bacterium and receptor-binding proteins on tailocin tail fibers and tail fiber-like appendages of T6SS. Since many R-type tailocin gene clusters contain only one tail fiber gene it was appropriate to expect small R-type tailocin target ranges. However, recently up to three tail fiber genes and broader target ranges have been reported for one plant-associated Pseudomonas strain. Here, we show that having three tail fiber genes per R-type tailocin gene cluster is a common feature of several strains of Gram-negative (often plant-associated) bacteria of the genus Kosakonia. Knowledge about the specificity of type VI secretion systems binding to target bacteria is even lower than in R-type tailocins. Although the mode of operation implicated specific binding, it was only published recently that type VI secretion systems develop tail fiber-like appendages. Here again Kosakonia, exhibiting up to three different type VI secretion systems, may provide valuable insights into the antagonistic potential of plant-associated bacteria. Current understanding of the diversity and potential of phage tail-like particles is fragmentary due to various synonyms and misleading terminology. Consistency in technical terms is a precondition for concerted and purposeful research, which precedes a comprehensive understanding of the specific interaction between bacteria producing phage tail-like particles and their targets. This knowledge is fundamental for selecting and applying tailored, and possibly engineered, producer bacteria for antagonizing plant pathogenic microorganisms.},
  file = {/Users/coiko/Zotero/storage/5FI7SVW6/Patz et al. - 2019 - Phage tail-like particles are versatile bacterial .pdf;/Users/coiko/Zotero/storage/CS9LS7GC/S2090123219300815.html},
  journal = {J Adv Res},
  keywords = {Contractile phage tail-like particle,Interbacterial competition,Kosakonicin,R-type tailocin,Type VI secretion system},
  language = {en},
  series = {Special {{Issue}} on {{Plant Microbiome}}}
}

@article{pfeifer2012,
  title = {Distribution, Formation and Regulation of Gas Vesicles},
  shorttitle = {Distribution, Formation and Regulation of Gas Vesicles},
  author = {Pfeifer, F.},
  year = {2012},
  month = oct,
  volume = {10},
  pages = {705--15},
  issn = {1740-1534 (Electronic) 1740-1526 (Linking)},
  doi = {10.1038/nrmicro2834},
  abstract = {A range of bacteria and archaea produce intracellular gas-filled proteinaceous structures that function as flotation devices in order to maintain a suitable depth in the aqueous environment. The wall of these gas vesicles is freely permeable to gas molecules and is composed of a small hydrophobic protein, GvpA, which forms a single-layer wall. In addition, several minor structural, accessory or regulatory proteins are required for gas vesicle formation. In different organisms, 8-14 genes encoding gas vesicle proteins have been identified, and their expression has been shown to be regulated by environmental factors. In this Review, I describe the basic properties of gas vesicles, the genes that encode them and how their production is regulated. I also discuss the function of these vesicles and the initial attempts to exploit them for biotechnological purposes.},
  file = {/Users/coiko/Zotero/storage/S779K8LP/Pfeifer-2012-Distribution, formation and regul.pdf},
  journal = {Nat Rev Microbiol},
  keywords = {Amino Acid Sequence,Bacterial Proteins/genetics/*metabolism,Cytoplasmic Vesicles/*metabolism,Halobacterium/genetics/*metabolism,Molecular Sequence Data,Multigene Family,Proteins/genetics/*metabolism,Sequence Alignment},
  number = {10}
}

@article{pilhofer2013,
  title = {The Bacterial Cytoskeleton: {{More}} than Twisted Filaments},
  shorttitle = {The Bacterial Cytoskeleton: More than Twisted Filaments},
  author = {Pilhofer, M. and Jensen, G. J.},
  year = {2013},
  month = feb,
  volume = {25},
  pages = {125--33},
  issn = {1879-0410 (Electronic) 0955-0674 (Linking)},
  doi = {10.1016/j.ceb.2012.10.019},
  abstract = {Far from being simple 'bags' of enzymes, bacteria are richly endowed with ultrastructures that challenge and expand standard definitions of the cytoskeleton. Here we review rods, rings, twisted pairs, tubes, sheets, spirals, moving patches, meshes and composites, and suggest defining the term 'bacterial cytoskeleton' as all cytoplasmic protein filaments and their superstructures that move or scaffold (stabilize/position/recruit) other cellular materials. The evolution of each superstructure has been driven by specific functional requirements. As a result, while homologous proteins with different functions have evolved to form surprisingly divergent superstructures, those of unrelated proteins with similar functions have converged.},
  file = {/Users/coiko/Zotero/storage/5W7S9C53/Pilhofer-2013-The bacterial cytosk.pdf;/Users/coiko/Zotero/storage/8SMXJUGZ/Pilhofer-2013-The bacterial cytosk.pdf;/Users/coiko/Zotero/storage/E8THIC6U/Pilhofer and Jensen - 2013 - The bacterial cytoskeleton more than twisted fila.pdf;/Users/coiko/Zotero/storage/JKJVN2DB/Pilhofer-2013-The bacterial cytoskeleton_ more.pdf;/Users/coiko/Zotero/storage/YWBCEH6Z/Pilhofer-2013-The bacterial cytosk.pdf},
  journal = {Curr Opin Cell Biol},
  keywords = {Bacteria,Bacteria/chemistry/*cytology/*metabolism/ultrastructure,Cytoskeleton,Cytoskeleton/chemistry/*metabolism/ultrastructure,Humans,Microtubules,Microtubules/metabolism},
  number = {1},
  pmcid = {PMC3597445},
  pmid = {23183140}
}

@article{pletnev2015,
  title = {Survival Guide: {{Escherichia}} Coli in the Stationary Phase},
  shorttitle = {Survival Guide: {{Escherichia}} Coli in the Stationary Phase},
  author = {Pletnev, P. and Osterman, I. and Sergiev, P. and Bogdanov, A. and Dontsova, O.},
  year = {2015},
  month = oct,
  volume = {7},
  pages = {22--33},
  issn = {2075-8251 (Print) 2075-8251 (Linking)},
  url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4717247/},
  abstract = {This review centers on the stationary phase of bacterial culture. The basic processes specific to the stationary phase, as well as the regulatory mechanisms that allow the bacteria to survive in conditions of stress, are described.},
  file = {/Users/coiko/Zotero/storage/G6FSQFYI/Pletnev-2015-Survival guide_ Escherichia coli.pdf},
  journal = {Acta Naturae},
  keywords = {Escherichia coli,starvation,stationary phase,stress,survival},
  number = {4}
}

@article{pony2020,
  title = {Filamentation of the Bacterial Bi-Functional Alcohol/Aldehyde Dehydrogenase {{AdhE}} Is Essential for Substrate Channeling and Enzymatic Regulation},
  author = {Pony, Pauline and Rapisarda, Chiara and Terradot, Laurent and Marza, Esther and Fronzes, R{\'e}mi},
  year = {2020},
  month = mar,
  volume = {11},
  pages = {1426},
  publisher = {{Nature Publishing Group}},
  issn = {2041-1723},
  doi = {10.1038/s41467-020-15214-y},
  abstract = {Acetaldehyde-alcohol dehydrogenase (AdhE) enzymes are a key metabolic enzyme in bacterial physiology and pathogenicity. They convert acetyl-CoA to ethanol via an acetaldehyde intermediate during ethanol fermentation in an anaerobic environment. This two-step reaction is associated to NAD+ regeneration, essential for glycolysis. The bifunctional AdhE enzyme is conserved in all bacterial kingdoms but also in more phylogenetically distant microorganisms such as green microalgae. It is found as an oligomeric form called spirosomes, for which the function remains elusive. Here, we use cryo-electron microscopy to obtain structures of Escherichia coli spirosomes in different conformational states. We show that spirosomes contain active AdhE monomers, and that AdhE filamentation is essential for its activity in vitro and function in vivo. The detailed analysis of these structures provides insight showing that AdhE filamentation is essential for substrate channeling within the filament and for the regulation of enzyme activity.},
  copyright = {2020 The Author(s)},
  file = {/Users/coiko/Zotero/storage/LZLK4YVY/Pony et al. - 2020 - Filamentation of the bacterial bi-functional alcoh.pdf;/Users/coiko/Zotero/storage/FP55HN8L/s41467-020-15214-y.html},
  journal = {Nat Commun},
  language = {en},
  number = {1}
}

@book{postgate1994,
  title = {The {{Outer Reaches}} of {{Life}}},
  shorttitle = {The {{Outer Reaches}} of {{Life}}},
  author = {Postgate, J. R.},
  year = {1994},
  publisher = {{Cambridge University Press}},
  address = {{Cambridge}}
}

@article{poweleit2016,
  title = {{{CryoEM}} Structure of the {{Methanospirillum}} Hungatei Archaellum Reveals Structural Features Distinct from the Bacterial Flagellum and Type {{IV}} Pilus},
  author = {Poweleit, Nicole and Ge, Peng and Nguyen, Hong H. and Loo, Rachel R. Ogorzalek and Gunsalus, Robert P. and Zhou, Z. Hong},
  year = {2016},
  month = dec,
  volume = {2},
  pages = {1--12},
  publisher = {{Nature Publishing Group}},
  issn = {2058-5276},
  doi = {10.1038/nmicrobiol.2016.222},
  abstract = {Archaea use flagella known as archaella\textemdash{}distinct both in protein composition and structure from bacterial flagella\textemdash{}to drive cell motility, but the structural basis of this function is unknown. Here, we report an atomic model of the archaella, based on the cryo electron microscopy (cryoEM) structure of the Methanospirillum hungatei archaellum at 3.4\hspace{0.25em}{\AA} resolution. Each archaellum contains {$\sim$}61,500 archaellin subunits organized into a curved helix with a diameter of 10\hspace{0.25em}nm and average length of 10,000\hspace{0.25em}nm. The tadpole-shaped archaellin monomer has two domains, a {$\beta$}-barrel domain and a long, mildly kinked {$\alpha$}-helix tail. Our structure reveals multiple post-translational modifications to the archaella, including six O-linked glycans and an unusual N-linked modification. The extensive interactions among neighbouring archaellins explain how the long but thin archaellum maintains the structural integrity required for motility-driving rotation. These extensive inter-subunit interactions and the absence of a central pore in the archaellum distinguish it from both the bacterial flagellum and type IV pili.},
  copyright = {2016 Macmillan Publishers Limited},
  file = {/Users/coiko/Zotero/storage/VT6APAAB/Poweleit et al. - 2016 - CryoEM structure of the Methanospirillum hungatei .pdf;/Users/coiko/Zotero/storage/FUQ2ESJD/nmicrobiol2016222.html},
  journal = {Nat Microbiol},
  language = {en},
  number = {3}
}

@article{prangishvili2017,
  title = {The Enigmatic Archaeal Virosphere},
  shorttitle = {The Enigmatic Archaeal Virosphere},
  author = {Prangishvili, D. and Bamford, D. H. and Forterre, P. and Iranzo, J. and Koonin, E. V. and Krupovic, M.},
  year = {2017},
  month = nov,
  volume = {15},
  pages = {724--739},
  issn = {1740-1534 (Electronic) 1740-1526 (Linking)},
  doi = {10.1038/nrmicro.2017.125},
  abstract = {One of the most prominent features of archaea is the extraordinary diversity of their DNA viruses. Many archaeal viruses differ substantially in morphology from bacterial and eukaryotic viruses and represent unique virus families. The distinct nature of archaeal viruses also extends to the gene composition and architectures of their genomes and the properties of the proteins that they encode. Environmental research has revealed prominent roles of archaeal viruses in influencing microbial communities in ocean ecosystems, and recent metagenomic studies have uncovered new groups of archaeal viruses that infect extremophiles and mesophiles in diverse habitats. In this Review, we summarize recent advances in our understanding of the genomic and morphological diversity of archaeal viruses and the molecular biology of their life cycles and virus-host interactions, including interactions with archaeal CRISPR-Cas systems. We also examine the potential origins and evolution of archaeal viruses and discuss their place in the global virosphere.},
  file = {/Users/coiko/Zotero/storage/9GQCYYYE/Prangishvili-2017-The enigmatic archaeal viros.pdf},
  journal = {Nat Rev Microbiol},
  number = {12}
}

@article{ptacin2013,
  title = {Chromosome Architecture Is a Key Element of Bacterial Cellular Organization},
  shorttitle = {Chromosome Architecture Is a Key Element of Bacterial Cellular Organization},
  author = {Ptacin, J. L. and Shapiro, L.},
  year = {2013},
  month = jan,
  volume = {15},
  pages = {45--52},
  issn = {1462-5822 (Electronic) 1462-5814 (Linking)},
  doi = {10.1111/cmi.12049},
  abstract = {The bacterial chromosome encodes information at multiple levels. Beyond direct protein coding, genomes encode regulatory information required to orchestrate the proper timing and levels of gene expression and protein synthesis, and contain binding sites and regulatory sequences to co-ordinate the activities of proteins involved in chromosome repair and maintenance. In addition, it is becoming increasingly clear that yet another level of information is encoded by the bacterial chromosome - the three-dimensional packaging of the chromosomal DNA molecule itself and its positioning relative to the cell. This vast structural blueprint of specific positional information is manifested in various ways, directing chromosome compaction, accessibility, attachment to the cell envelope, supercoiling, and general architecture and arrangement of the chromosome relative to the cell body. Recent studies have begun to identify and characterize novel systems that utilize the three-dimensional spatial information encoded by chromosomal architecture to co-ordinate and direct fundamental cellular processes within the cytoplasm, providing large-scale order within the complex clutter of the cytoplasmic compartment.},
  file = {/Users/coiko/Zotero/storage/6VD4TL8D/Ptacin-2013-Chromosome architecture is a key e.pdf},
  journal = {Cell Microbiol},
  keywords = {*Bacterial Physiological Phenomena,Bacteria/*genetics/*metabolism,Chromosomes; Bacterial/*metabolism/*ultrastructure,DNA; Bacterial/*chemistry/*metabolism,Models; Biological},
  number = {1}
}

@article{qin2017,
  title = {Imaging the Motility and Chemotaxis Machineries in {{Helicobacter}} Pylori by Cryo-Electron Tomography},
  author = {Qin, Zhuan and Lin, Wei-ting and Zhu, Shiwei and Franco, Aime T. and Liu, Jun},
  year = {2017},
  month = feb,
  volume = {199},
  publisher = {{American Society for Microbiology Journals}},
  issn = {0021-9193, 1098-5530},
  doi = {10.1128/JB.00695-16},
  abstract = {Helicobacter pylori is a bacterial pathogen that can cause many gastrointestinal diseases, including ulcers and gastric cancer. A unique chemotaxis-mediated motility is critical for H. pylori to colonize in the human stomach and to establish chronic infection, but the underlying molecular mechanisms are not well understood. Here, we employ cryo-electron tomography (cryo-ET) to reveal detailed structures of the H. pylori cell envelope, including the sheathed flagella and chemotaxis arrays. Notably, H. pylori possesses a distinctive periplasmic cage-like structure with 18-fold symmetry. We propose that this structure forms a robust platform for recruiting 18 torque generators, which likely provide the higher torque needed for swimming in high-viscosity environments. We also reveal a series of key flagellar assembly intermediates, providing structural evidence that flagellar assembly is tightly coupled with the biogenesis of the membrane sheath. Finally, we determine the structure of putative chemotaxis arrays at the flagellar pole, which have implications for how the direction of flagellar rotation is regulated. Together, our pilot cryo-ET studies provide novel structural insights into the unipolar flagella of H. pylori and lay a foundation for a better understanding of the unique motility of this organism.
IMPORTANCE Helicobacter pylori is a highly motile bacterial pathogen that colonizes approximately 50\% of the world's population. H. pylori can move readily within the viscous mucosal layer of the stomach. It has become increasingly clear that its unique flagella-driven motility is essential for successful gastric colonization and pathogenesis. Here, we use advanced imaging techniques to visualize novel in situ structures with unprecedented detail in intact H. pylori cells. Remarkably, H. pylori possesses multiple unipolar flagella, which are driven by one of the largest flagellar motors found in bacteria. These large motors presumably provide the higher torque needed by the bacterial pathogens to navigate in the viscous environment of the human stomach.},
  copyright = {Copyright \textcopyright{} 2017 American Society for Microbiology..  All Rights Reserved .},
  file = {/Users/coiko/Zotero/storage/JBX8CCCD/Qin et al. - 2017 - Imaging the Motility and Chemotaxis Machineries in.pdf;/Users/coiko/Zotero/storage/NGHDBIWE/e00695-16.html},
  journal = {J Bacteriol},
  language = {en},
  number = {3},
  pmid = {27849173}
}

@article{reyes-lamothe2012,
  title = {Chromosome Replication and Segregation in Bacteria},
  shorttitle = {Chromosome Replication and Segregation in Bacteria},
  author = {{Reyes-Lamothe}, R. and Nicolas, E. and Sherratt, D. J.},
  year = {2012},
  volume = {46},
  pages = {121--43},
  issn = {1545-2948 (Electronic) 0066-4197 (Linking)},
  doi = {10.1146/annurev-genet-110711-155421},
  abstract = {In dividing cells, chromosome duplication once per generation must be coordinated with faithful segregation of newly replicated chromosomes and with cell growth and division. Many of the mechanistic details of bacterial replication elongation are well established. However, an understanding of the complexities of how replication initiation is controlled and coordinated with other cellular processes is emerging only slowly. In contrast to eukaryotes, in which replication and segregation are separate in time, the segregation of most newly replicated bacterial genetic loci occurs sequentially soon after replication. We compare the strategies used by chromosomes and plasmids to ensure their accurate duplication and segregation and discuss how these processes are coordinated spatially and temporally with growth and cell division. We also describe what is known about the three conserved families of ATP-binding proteins that contribute to chromosome segregation and discuss their inter-relationships in a range of disparate bacteria.},
  file = {/Users/coiko/Zotero/storage/5WWSHY5Y/annurev-genet-110711-155421.pdf;/Users/coiko/Zotero/storage/UCVWDBS3/Reyes-Lamothe-2012-Chromosome replication and.pdf},
  journal = {Annu Rev Genet},
  keywords = {*Chromosome Segregation,*DNA Replication,Bacterial Proteins/genetics/metabolism,Cell Division,Chromosomes; Bacterial/*genetics/metabolism,DNA Primase,DNA-Binding Proteins/genetics/metabolism,DNA; Bacterial/*genetics/metabolism,Endodeoxyribonucleases/genetics/metabolism,Escherichia coli Proteins/genetics/metabolism,Escherichia coli/*genetics/metabolism,Exodeoxyribonucleases/genetics/metabolism,Membrane Proteins/genetics/metabolism,Plasmids/genetics/metabolism,Transcription; Genetic,Translocation; Genetic}
}

@book{rohwer2014,
  title = {Life in {{Our Phage World}}},
  shorttitle = {Life in {{Our Phage World}}},
  author = {Rohwer, F. and Youle, M. and Maughan, H. and Hisakawa, N.},
  year = {2014},
  publisher = {{Wholon}},
  address = {{San Diego, CA}},
  url = {http://2015phage.org/art.php},
  file = {/Users/coiko/Zotero/storage/Q7YLJLLB/Life_In_Our_Phage_World_Max.pdf}
}

@article{ruhe2018,
  title = {Programmed Secretion Arrest and Receptor-Triggered Toxin Export during Antibacterial Contact-Dependent Growth Inhibition},
  author = {Ruhe, Zachary C. and Subramanian, Poorna and Song, Kiho and Nguyen, Josephine Y. and Stevens, Taylor A. and Low, David A. and Jensen, Grant J. and Hayes, Christopher S.},
  year = {2018},
  month = nov,
  volume = {175},
  pages = {921-933.e14},
  publisher = {{Elsevier}},
  issn = {0092-8674, 1097-4172},
  doi = {10.1016/j.cell.2018.10.033},
  abstract = {{$<$}h2{$>$}Summary{$<$}/h2{$><$}p{$>$}Contact-dependent growth inhibition (CDI) entails receptor-mediated delivery of CdiA-derived toxins into Gram-negative target bacteria. Using electron cryotomography, we show that each CdiA effector protein forms a filament extending {$\sim$}33 nm from the cell surface. Remarkably, the extracellular filament represents only the N-terminal half of the effector. A programmed secretion arrest sequesters the C-terminal half of CdiA, including the toxin domain, in the periplasm prior to target-cell recognition. Upon binding receptor, CdiA secretion resumes, and the periplasmic FHA-2 domain is transferred to the target-cell outer membrane. The C-terminal toxin region of CdiA then penetrates into the target-cell periplasm, where it is cleaved for subsequent translocation into the cytoplasm. Our findings suggest that the FHA-2 domain assembles into a transmembrane conduit for toxin transport into the periplasm of target bacteria. We propose that receptor-triggered secretion ensures that FHA-2 export is closely coordinated with integration into the target-cell outer membrane.{$<$}/p{$><$}h3{$>$}Video Abstract{$<$}/h3{$>$}},
  file = {/Users/coiko/Zotero/storage/D7UPGU86/Ruhe et al. - 2018 - Programmed Secretion Arrest and Receptor-Triggered.pdf;/Users/coiko/Zotero/storage/M5P4Y8TI/S0092-8674(18)31386-2.html},
  journal = {Cell},
  language = {English},
  number = {4},
  pmid = {30388452}
}

@article{ruska1987,
  title = {Nobel Lecture. {{The}} Development of the Electron Microscope and of Electron Microscopy},
  shorttitle = {Nobel Lecture. {{The}} Development of the Electron Microscope and of Electron Microscopy},
  author = {Ruska, E.},
  year = {1987},
  month = aug,
  volume = {7},
  pages = {607--29},
  issn = {0144-8463 (Print) 0144-8463 (Linking)},
  doi = {10.1007/bf01127674},
  file = {/Users/coiko/Zotero/storage/3FEVVYF8/Ruska-1987-Nobel lecture. The development of t.pdf;/Users/coiko/Zotero/storage/NCML6YHS/Ruska-1987-Nobel lecture. The development of t.pdf;/Users/coiko/Zotero/storage/NVERHCVK/Ruska-1987-Nobel lecture. The development of t.pdf},
  journal = {Biosci Rep},
  keywords = {Berlin,History; 20th Century,Microscopy; Electron/*history/instrumentation},
  number = {8}
}

@article{schlimpert2012,
  title = {General Protein Diffusion Barriers Create Compartments within Bacterial Cells},
  shorttitle = {General Protein Diffusion Barriers Create Compartments within Bacterial Cells},
  author = {Schlimpert, S. and Klein, E. A. and Briegel, A. and Hughes, V. and Kahnt, J. and Bolte, K. and Maier, U. G. and Brun, Y. V. and Jensen, G. J. and Gitai, Z. and Thanbichler, M.},
  year = {2012},
  month = dec,
  volume = {151},
  pages = {1270--82},
  issn = {1097-4172 (Electronic) 0092-8674 (Linking)},
  doi = {10.1016/j.cell.2012.10.046},
  abstract = {In eukaryotes, the differentiation of cellular extensions such as cilia or neuronal axons depends on the partitioning of proteins to distinct plasma membrane domains by specialized diffusion barriers. However, examples of this compartmentalization strategy are still missing for prokaryotes, although complex cellular architectures are also widespread among this group of organisms. This study reveals the existence of a protein-mediated membrane diffusion barrier in the stalked bacterium Caulobacter crescentus. We show that the Caulobacter cell envelope is compartmentalized by macromolecular complexes that prevent the exchange of both membrane and soluble proteins between the polar stalk extension and the cell body. The barrier structures span the cross-sectional area of the stalk and comprise at least four proteins that assemble in a cell-cycle-dependent manner. Their presence is critical for cellular fitness because they minimize the effective cell volume, allowing faster adaptation to environmental changes that require de novo synthesis of envelope proteins.},
  file = {/Users/coiko/Zotero/storage/2TD677IG/Schlimpert-2012-General protein diff.pdf;/Users/coiko/Zotero/storage/5QZJ8MRT/Schlimpert-2012-General protein diff.pdf;/Users/coiko/Zotero/storage/ALKQHGKG/Schlimpert-2012-General protein diff.pdf;/Users/coiko/Zotero/storage/CKCZD2CA/Schlimpert-2012-General protein diff.pdf;/Users/coiko/Zotero/storage/CUZX67Q5/Schlimpert-2012-General protein diff.pdf;/Users/coiko/Zotero/storage/E4WXPUCT/Schlimpert et al. - 2012 - General protein diffusion barriers create compartm.pdf;/Users/coiko/Zotero/storage/QU6JUQT7/Schlimpert-2012-General protein diff.pdf},
  journal = {Cell},
  keywords = {Bacterial Proteins,Bacterial Proteins/*metabolism,Caulobacter crescentus,Caulobacter crescentus/*cytology/*metabolism,Cell Membrane,Cell Membrane/metabolism,Diffusion,Multiprotein Complexes,Multiprotein Complexes/metabolism},
  number = {6},
  pmcid = {PMC3542395},
  pmid = {23201141}
}

@article{schuergers2016,
  title = {Cyanobacteria Use Micro-Optics to Sense Light Direction},
  shorttitle = {Cyanobacteria Use Micro-Optics to Sense Light Direction},
  author = {Schuergers, N. and Lenn, T. and Kampmann, R. and Meissner, M. V. and Esteves, T. and {Temerinac-Ott}, M. and Korvink, J. G. and Lowe, A. R. and Mullineaux, C. W. and Wilde, A.},
  year = {2016},
  month = feb,
  volume = {5},
  issn = {2050-084X (Electronic) 2050-084X (Linking)},
  doi = {10.7554/eLife.12620},
  abstract = {Bacterial phototaxis was first recognized over a century ago, but the method by which such small cells can sense the direction of illumination has remained puzzling. The unicellular cyanobacterium Synechocystis sp. PCC 6803 moves with Type IV pili and measures light intensity and color with a range of photoreceptors. Here, we show that individual Synechocystis cells do not respond to a spatiotemporal gradient in light intensity, but rather they directly and accurately sense the position of a light source. We show that directional light sensing is possible because Synechocystis cells act as spherical microlenses, allowing the cell to see a light source and move towards it. A high-resolution image of the light source is focused on the edge of the cell opposite to the source, triggering movement away from the focused spot. Spherical cyanobacteria are probably the world's smallest and oldest example of a camera eye.},
  file = {/Users/coiko/Zotero/storage/IH6DYKZ2/Schuergers-2016-Cyanobacteria use micro-optics.pdf},
  journal = {Elife},
  keywords = {*Light,*Locomotion,biophysics,Cyanobacteria,infectious disease,Micro-optics,microbiology,Phototaxis,Signal transduction,structural biology,Synechocystis sp PCC6803,Synechocystis/*physiology/*radiation effects,Thermosynechococcus elongatus}
}

@article{shapiro2009,
  title = {Why and How Bacteria Localize Proteins},
  shorttitle = {Why and How Bacteria Localize Proteins},
  author = {Shapiro, L. and McAdams, H. H. and Losick, R.},
  year = {2009},
  month = nov,
  volume = {326},
  pages = {1225--8},
  issn = {1095-9203 (Electronic) 0036-8075 (Linking)},
  doi = {10.1126/science.1175685},
  abstract = {Despite their small size, bacteria have a remarkably intricate internal organization. Bacteria deploy proteins and protein complexes to particular locations and do so in a dynamic manner in lockstep with the organized deployment of their chromosome. The dynamic subcellular localization of protein complexes is an integral feature of regulatory processes of bacterial cells.},
  file = {/Users/coiko/Zotero/storage/CPVSXXQM/Shapiro-2009-Why and how bacteria localize pro.pdf},
  journal = {Science},
  keywords = {Bacteria/cytology/*metabolism/ultrastructure,Bacterial Proteins/*metabolism,Cell Division,Cell Membrane/physiology/ultrastructure,Chemotaxis,Chromosomes; Bacterial/physiology,Diffusion,Intracellular Space/metabolism,Protein Binding},
  number = {5957}
}

@article{shikuma2014,
  title = {Marine Tubeworm Metamorphosis Induced by Arrays of Bacterial Phage Tail-like Structures},
  shorttitle = {Marine Tubeworm Metamorphosis Induced by Arrays of Bacterial Phage Tail-like Structures},
  author = {Shikuma, N. J. and Pilhofer, M. and Weiss, G. L. and Hadfield, M. G. and Jensen, G. J. and Newman, D. K.},
  year = {2014},
  month = jan,
  volume = {343},
  pages = {529--33},
  issn = {1095-9203 (Electronic) 0036-8075 (Linking)},
  doi = {10.1126/science.1246794},
  abstract = {Many benthic marine animal populations are established and maintained by free-swimming larvae that recognize cues from surface-bound bacteria to settle and metamorphose. Larvae of the tubeworm Hydroides elegans, an important biofouling agent, require contact with surface-bound bacteria to undergo metamorphosis; however, the mechanisms that underpin this microbially mediated developmental transition have been enigmatic. Here, we show that a marine bacterium, Pseudoalteromonas luteoviolacea, produces arrays of phage tail-like structures that trigger metamorphosis of H. elegans. These arrays comprise about 100 contractile structures with outward-facing baseplates, linked by tail fibers and a dynamic hexagonal net. Not only do these arrays suggest a novel form of bacterium-animal interaction, they provide an entry point to understanding how marine biofilms can trigger animal development.},
  file = {/Users/coiko/Zotero/storage/4EDQZTEN/Shikuma-2014-Marine tubeworm meta.pdf;/Users/coiko/Zotero/storage/5V2ZMGJD/Shikuma-2014-Marine tubeworm meta.pdf;/Users/coiko/Zotero/storage/C4KVI58Q/Shikuma et al. - 2014 - Marine tubeworm metamorphosis induced by arrays of.pdf;/Users/coiko/Zotero/storage/C7WPAEE7/Shikuma-2014-Marine tubeworm meta.pdf;/Users/coiko/Zotero/storage/EQ7W9KBT/Shikuma et al. - 2014 - Marine tubeworm metamorphosis induced by arrays of.pdf;/Users/coiko/Zotero/storage/IDZWNYTA/Shikuma-2014-Marine tubeworm meta.pdf;/Users/coiko/Zotero/storage/K8BFDCMZ/Shikuma-2014-Marine tubeworm metamorphosis ind.pdf;/Users/coiko/Zotero/storage/KIH4GMUJ/Shikuma-2014-Marine tubeworm metamorphosis ind.pdf;/Users/coiko/Zotero/storage/WKVV77BZ/Shikuma-2014-Marine tubeworm meta.pdf;/Users/coiko/Zotero/storage/X7PEND7E/Shikuma-2014-Marine tubeworm metamorphosis ind.pdf},
  journal = {Science},
  keywords = {*Biofilms,*Metamorphosis; Biological,Animals,Aquatic Organisms,Aquatic Organisms/growth \& development/microbiology,Bacteriocins,Bacteriocins/genetics/*metabolism,Bacteriophages,Bacteriophages/ultrastructure,Biofilms,Genes; Bacterial,Genes; Bacterial/physiology,Larva,Larva/growth \& development/microbiology,Metamorphosis; Biological,Molecular Sequence Data,Open Reading Frames,Polychaeta,Polychaeta/*growth \& development/*microbiology,Pseudoalteromonas,Pseudoalteromonas/genetics/*physiology/*virology,Viral Tail Proteins,Viral Tail Proteins/genetics/*physiology},
  number = {6170},
  pmcid = {PMC4949041},
  pmid = {24407482}
}

@article{shrivastava2015,
  title = {Towards a Model for {{Flavobacterium}} Gliding},
  author = {Shrivastava, Abhishek and Berg, Howard C},
  year = {2015},
  month = dec,
  volume = {28},
  pages = {93--97},
  issn = {1369-5274},
  doi = {10.1016/j.mib.2015.07.018},
  abstract = {Cells of Flavobacterium johnsoniae, a rod-shaped bacterium about 6{$\mu$}m long, do not have flagella or pili, yet they move over surfaces at speeds of about 2{$\mu$}m/s. This motion is called gliding. Recent advances in F. johnsoniae research include the discovery of mobile cell-surface adhesins and rotary motors. The puzzle is how rotary motion leads to linear motion. We suggest a possible mechanism, inspired by the snowmobile.},
  file = {/Users/coiko/Zotero/storage/X4AZS7VK/Shrivastava and Berg - 2015 - Towards a model for Flavobacterium gliding.pdf;/Users/coiko/Zotero/storage/KLRYPSBM/S136952741500140X.html},
  journal = {Curr Opin Microbiol},
  language = {en},
  series = {Growth and Development: Eukaryotes and Prokaryotes}
}

@article{shu2000,
  title = {Core Structure of the Outer Membrane Lipoprotein from {{Escherichia}} Coli at 1.9 {{{\AA}}} Resolution},
  author = {Shu, Wei and Liu, Jie and Ji, Hong and Lu, Min},
  year = {2000},
  month = jun,
  volume = {299},
  pages = {1101--1112},
  issn = {0022-2836},
  doi = {10.1006/jmbi.2000.3776},
  abstract = {The outer membrane lipoprotein of the Escherichia coli cell envelope has characteristic lipid modifications at an amino-terminal cysteine and can exist in a form bound covalently to the peptidoglycan through a carboxyl-terminal lysine. The 56-residue polypeptide moiety of the lipoprotein, designated Lpp-56, folds into a stable, trimeric helical structure in aqueous solution. The 1.9 {\AA} resolution crystal structure of Lpp-56 comprises a parallel three-stranded coiled coil including a novel alanine-zipper unit and two helix-capping motifs. The amino-terminal motif forms a hydrogen-bonding network anchoring an umbrella-shaped fold. The carboxyl-terminal motif uses puckering of the tyrosine side-chains as a unique docking arrangement in helix termination. The structure provides an explanation for assembly and insertion of the lipoprotein molecules into the outer membrane of gram-negative bacteria and suggests a molecular target for antibacterial drug discovery.},
  file = {/Users/coiko/Zotero/storage/VV35ELQC/Shu et al. - 2000 - Core structure of the outer membrane lipoprotein f.pdf;/Users/coiko/Zotero/storage/J5T88GCH/S0022283600937768.html},
  journal = {J Mol Biol},
  keywords = {coiled coil,helix capping,lipoprotein,outer membrane,protein folding},
  language = {en},
  number = {4}
}

@article{sleytr1999,
  title = {Bacterial {{S}}-Layers},
  shorttitle = {Bacterial {{S}}-Layers},
  author = {Sleytr, U. B. and Beveridge, T. J.},
  year = {1999},
  month = jun,
  volume = {7},
  pages = {253--60},
  issn = {0966-842X (Print) 0966-842X (Linking)},
  doi = {10.1016/s0966-842x(99)01513-9},
  abstract = {S-layers are produced by the self assembly of proteinaceous subunits on the surfaces of prokaryotes, so that planar, monomolecular-thick crystalline lattices are formed. Some archaeal and eubacterial S-layer proteins are glycosylated. These lattices typically have center-to-center spacings of less than 25 nm, which makes them attractive for biomimetic or nanotechnological applications.},
  file = {/Users/coiko/Zotero/storage/MPYEL2SW/Sleytr-1999-Bacterial S-layers.pdf},
  journal = {Trends Microbiol},
  keywords = {Bacillus thuringiensis/chemistry,Bacteria/*ultrastructure,Bacterial Proteins/*chemistry,Clostridium/chemistry,Geobacillus stearothermophilus/chemistry,Image Processing; Computer-Assisted,Lactobacillus/chemistry,Microscopy; Electron,Sulfolobus/chemistry,Surface Properties},
  number = {6}
}

@article{sobti2016,
  ids = {sobtiCryoEMStructuresAutoinhibited2016},
  title = {Cryo-{{EM}} Structures of the Autoinhibited {{E}}. Coli {{ATP}} Synthase in Three Rotational States},
  author = {Sobti, Meghna and Smits, Callum and Wong, Andrew SW and Ishmukhametov, Robert and Stock, Daniela and Sandin, Sara and Stewart, Alastair G},
  editor = {K{\"u}hlbrandt, Werner},
  year = {2016},
  month = dec,
  volume = {5},
  pages = {e21598},
  publisher = {{eLife Sciences Publications, Ltd}},
  issn = {2050-084X},
  doi = {10.7554/eLife.21598},
  abstract = {A molecular model that provides a framework for interpreting the wealth of functional information obtained on the E. coli F-ATP synthase has been generated using cryo-electron microscopy. Three different states that relate to rotation of the enzyme were observed, with the central stalk's {$\epsilon$} subunit in an extended autoinhibitory conformation in all three states. The Fo motor comprises of seven transmembrane helices and a decameric c-ring and invaginations on either side of the membrane indicate the entry and exit channels for protons. The proton translocating subunit contains near parallel helices inclined by \textasciitilde{}30\textdegree{} to the membrane, a feature now synonymous with rotary ATPases. For the first time in this rotary ATPase subtype, the peripheral stalk is resolved over its entire length of the complex, revealing the F1 attachment points and a coiled-coil that bifurcates toward the membrane with its helices separating to embrace subunit a from two sides.},
  file = {/Users/coiko/Zotero/storage/FFHMZPVK/Sobti et al. - 2016 - Cryo-EM structures of the autoinhibited E. coli AT.pdf;/Users/coiko/Zotero/storage/Q5SP4QJG/Sobti-2016-Cryo-EM structures of the autoinhib.pdf;/Users/coiko/Zotero/storage/QJ3FPXAE/Sobti-2016-Cryo-EM structures of the autoinhib.pdf},
  journal = {eLife},
  keywords = {*Cryoelectron Microscopy,ATP synthase,Bacterial Proton-Translocating ATPases/*ultrastructure,bioenergetics,biophysics,cryoEM,E. coli,Escherichia coli/*enzymology,membrane protein,rotary ATPase,structural biology}
}

@article{sockett2009,
  title = {Predatory Lifestyle of {{Bdellovibrio}} Bacteriovorus},
  shorttitle = {Predatory Lifestyle of {{Bdellovibrio}} Bacteriovorus},
  author = {Sockett, R. E.},
  year = {2009},
  volume = {63},
  pages = {523--39},
  issn = {1545-3251 (Electronic) 0066-4227 (Linking)},
  doi = {10.1146/annurev.micro.091208.073346},
  abstract = {Bdellovibrio species are naturally predatory, small, motile, Deltaproteobacteria that invade the periplasm of other larger gram-negative bacteria, killing and digesting them. Bdellovibrio grows and divides inside the prey cell, in a structure called a bdelloplast, which then lyses, releasing the Bdellovibrio to prey upon more bacteria. This capability makes Bdellovibrio a potential therapeutic agent, but since its discovery in the 1960s it has not been applied in this way. This review considers what is known postgenomically about Bdellovibrio and its predatory lifestyle, drawing also from what was learned by the excellent microbial physiology work of the early Bdellovibrio researchers. Recent work on the diversity and evolution of predatory bdellovibrios, the role of surface structures in predation, and the ongoing questions about how Bdellovibrio switches between axenic and predatory growth and how its predatory activities may be tempered in the wild, as well as suggestions for future research priorities, are discussed.},
  file = {/Users/coiko/Zotero/storage/U8KZVLJF/Sockett-2009-Predatory lifestyle of Bdellovibr.pdf},
  journal = {Annu Rev Microbiol},
  keywords = {Bdellovibrio/genetics/*physiology,Gene Expression Regulation; Bacterial,Genome; Bacterial}
}

@article{strahl2017,
  title = {Bacterial Membranes: {{Structure}}, Domains, and Function},
  shorttitle = {Bacterial {{Membranes}}: {{Structure}}, {{Domains}}, and {{Function}}},
  author = {Strahl, H. and Errington, J.},
  year = {2017},
  month = jul,
  issn = {1545-3251 (Electronic) 0066-4227 (Linking)},
  doi = {10.1146/annurev-micro-102215-095630},
  abstract = {The bacterial cytoplasmic membrane is composed of roughly equal proportions of lipids and proteins. The main lipid components are phospholipids, which vary in acyl chain length, saturation, and branching and carry head groups that vary in size and charge. Phospholipid variants determine membrane properties such as fluidity and charge that in turn modulate interactions with membrane-associated proteins. We summarize recent advances in understanding bacterial membrane structure and function, focusing particularly on the possible existence and significance of specialized membrane domains. We review the role of membrane curvature as a spatial cue for recruitment and regulation of proteins involved in morphogenic functions, especially elongation and division. Finally, we examine the role of the membrane, especially regulation of synthesis and fluid properties, in the life cycle of cell wall-deficient L-form bacteria. Expected final online publication date for the Annual Review of Microbiology Volume 71 is September 8, 2017. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.},
  file = {/Users/coiko/Zotero/storage/6IIGGWT7/Strahl-2017-Bacterial Membranes_ Structure, Do.pdf},
  journal = {Annu Rev Microbiol}
}

@article{sutter2008,
  title = {Structural Basis of Enzyme Encapsulation into a Bacterial Nanocompartment},
  shorttitle = {Structural Basis of Enzyme Encapsulation into a Bacterial Nanocompartment},
  author = {Sutter, M. and Boehringer, D. and Gutmann, S. and Gunther, S. and Prangishvili, D. and Loessner, M. J. and Stetter, K. O. and {Weber-Ban}, E. and Ban, N.},
  year = {2008},
  month = sep,
  volume = {15},
  pages = {939--47},
  issn = {1545-9993 (Print) 1545-9985 (Linking)},
  doi = {10.1038/nsmb.1473},
  abstract = {Compartmentalization is an important organizational feature of life. It occurs at varying levels of complexity ranging from eukaryotic organelles and the bacterial microcompartments, to the molecular reaction chambers formed by enzyme assemblies. The structural basis of enzyme encapsulation in molecular compartments is poorly understood. Here we show, using X-ray crystallographic, biochemical and EM experiments, that a widespread family of conserved bacterial proteins, the linocin-like proteins, form large assemblies that function as a minimal compartment to package enzymes. We refer to this shell-forming protein as 'encapsulin'. The crystal structure of such a particle from Thermotoga maritima determined at 3.1-angstroms resolution reveals that 60 copies of the monomer assemble into a thin, icosahedral shell with a diameter of 240 angstroms. The interior of this nanocompartment is lined with conserved binding sites for short polypeptide tags present as C-terminal extensions of enzymes involved in oxidative-stress response.},
  file = {/Users/coiko/Zotero/storage/UUNT2RRB/Sutter-2008-Structural basis of enzyme encapsu.pdf},
  journal = {Nat Struct Mol Biol},
  keywords = {Amino Acid Sequence,Bacterial Proteins/chemistry/genetics,Binding Sites,Brevibacterium/enzymology/genetics/ultrastructure,Crystallography; X-Ray,Models; Molecular,Molecular Sequence Data,Multiprotein Complexes/chemistry,Organelles/enzymology/ultrastructure,Recombinant Proteins/chemistry/genetics,Sequence Homology; Amino Acid,Thermotoga maritima/*enzymology/genetics/*ultrastructure},
  number = {9}
}

@article{tachiyama2019,
  title = {The Cytoplasmic Domain of {{MxiG}} Interacts with {{MxiK}} and Directs Assembly of the Sorting Platform in the {{Shigella}} Type {{III}} Secretion System},
  author = {Tachiyama, Shoichi and Chang, Yunjie and Muthuramalingam, Meenakumari and Hu, Bo and Barta, Michael L. and Picking, Wendy L. and Liu, Jun and Picking, William D.},
  year = {2019},
  month = dec,
  volume = {294},
  pages = {19184--19196},
  publisher = {{American Society for Biochemistry and Molecular Biology}},
  issn = {0021-9258, 1083-351X},
  doi = {10.1074/jbc.RA119.009125},
  abstract = {Many Gram-negative bacteria use type III secretion systems (T3SSs) to inject virulence effector proteins into eukaryotic cells. The T3SS apparatus (T3SA) is structurally conserved among diverse bacterial pathogens and consists of a cytoplasmic sorting platform, an envelope-spanning basal body, and an extracellular needle with tip complex. The sorting platform is essential for effector recognition and powering secretion. Studies using bacterial ``minicells'' have revealed an unprecedented level of structural detail of the sorting platform; however, many of the structure-function relationships within this complex remain enigmatic. Here, we report on improved cryo-electron tomographic approaches to enhance the resolution of the Shigella T3SA sorting platform (at {$\leq$}2 nm resolution) done in concert with biochemical and genetic methods to define the sorting platform interactome and interactions with the T3SA inner membrane ring (IR). We observed that the sorting platform consists of ``pods'' with 6-fold symmetry that interact with the Spa47 ATPase via radial extensions comprising MxiN. Most importantly, MxiK maintained an interaction with the IR via specific interactions with the cytoplasmic domain of the IR protein MxiG (MxiGC), which is a noncanonical forkhead-associated domain, and MxiK has an elongated structure that interacts with the IR via MxiGC. T4 lysozyme-mediated insertional mutagenesis of MxiK revealed its orientation within the sorting platform and enabled disruption of interactions with its binding partners, which abolished sorting platform assembly. Finally, a comparison with the homologous interactions in the Salmonella T3SS sorting platform revealed clear differences in their IR-sorting platform interfaces that have possible mechanistic implications.},
  file = {/Users/coiko/Zotero/storage/SPDRN3C5/19184.html},
  journal = {J Biol Chem},
  keywords = {bacteria,cryo-electron tomography,effector protein,MxiG,MxiK,protein complex,protein-protein interaction,secretion,Shigella,sorting platform,type III secretion system (T3SS),virulence factor},
  language = {en},
  number = {50},
  pmid = {31699894}
}

@article{tang2019,
  title = {Cryo-{{EM}} Structures of Lipopolysaccharide Transporter {{LptB}} 2 {{FGC}} in Lipopolysaccharide or {{AMP}}-{{PNP}}-Bound States Reveal Its Transport Mechanism},
  author = {Tang, Xiaodi and Chang, Shenghai and Luo, Qinghua and Zhang, Zhengyu and Qiao, Wen and Xu, Caihuang and Zhang, Changbin and Niu, Yang and Yang, Wenxian and Wang, Ting and Zhang, Zhibo and Zhu, Xiaofeng and Wei, Xiawei and Dong, Changjiang and Zhang, Xing and Dong, Haohao},
  year = {2019},
  month = sep,
  volume = {10},
  pages = {4175},
  publisher = {{Nature Publishing Group}},
  issn = {2041-1723},
  doi = {10.1038/s41467-019-11977-1},
  abstract = {Lipopolysaccharides (LPS) of Gram-negative bacteria are critical for the defence against cytotoxic substances and must be transported from the inner membrane (IM) to the outer membrane (OM) through a bridge formed by seven membrane proteins (LptBFGCADE). The IM component LptB2FG powers the process through a yet unclarified mechanism. Here we report three high-resolution cryo-EM structures of LptB2FG alone and complexed with LptC (LptB2FGC), trapped in either the LPS- or AMP-PNP-bound state. The structures reveal conformational changes between these states and substrate binding with or without LptC. We identify two functional transmembrane arginine-containing loops interacting with the bound AMP-PNP and elucidate allosteric communications between the domains. AMP-PNP binding induces an inward rotation and shift of the transmembrane helices of LptFG and LptC to tighten the cavity, with the closure of two lateral gates, to eventually expel LPS into the bridge. Functional assays reveal the functionality of the LptF and LptG periplasmic domains. Our findings shed light on the LPS transport mechanism.},
  copyright = {2019 The Author(s)},
  file = {/Users/coiko/Zotero/storage/NPXI2DH9/Tang et al. - 2019 - Cryo-EM structures of lipopolysaccharide transport.pdf;/Users/coiko/Zotero/storage/WBYKD9LL/s41467-019-11977-1.html},
  journal = {Nat Commun},
  language = {en},
  number = {1}
}

@book{thomas1974,
  title = {The {{Lives}} of a {{Cell}}},
  shorttitle = {The {{Lives}} of a {{Cell}}},
  author = {Thomas, L.},
  year = {1974},
  publisher = {{The Viking Press}},
  address = {{New York}}
}

@book{thomas1990,
  title = {A {{Long Line}} of {{Cells}}: {{Collected Essays}}},
  author = {Thomas, Lewis},
  year = {1990},
  publisher = {{Book-of-the-Month-Club}},
  address = {{New York}}
}

@article{tocheva2016,
  title = {Sporulation, Bacterial Cell Envelopes and the Origin of Life},
  shorttitle = {Sporulation, Bacterial Cell Envelopes and the Origin of Life},
  author = {Tocheva, E. I. and Ortega, D. R. and Jensen, G. J.},
  year = {2016},
  month = aug,
  volume = {14},
  pages = {535--542},
  issn = {1740-1534 (Electronic) 1740-1526 (Linking)},
  doi = {10.1038/nrmicro.2016.85},
  abstract = {Electron cryotomography (ECT) enables the 3D reconstruction of intact cells in a near-native state. Images produced by ECT have led to the proposal that an ancient sporulation-like event gave rise to the second membrane in diderm bacteria. Tomograms of sporulating monoderm and diderm bacterial cells show how sporulation can lead to the generation of diderm cells. Tomograms of Gram-negative and Gram-positive cell walls and purified sacculi suggest that they are more closely related than previously thought and support the hypothesis that they share a common origin. Mapping the distribution of cell envelope architectures onto a recent phylogenetic tree of life indicates that the diderm cell plan, and therefore the sporulation-like event that gave rise to it, must be very ancient. One explanation for this model is that during the cataclysmic transitions of the early Earth, cellular evolution may have gone through a bottleneck in which only spores survived, which implies that the last bacterial common ancestor was a spore.},
  file = {/Users/coiko/Zotero/storage/GAJH2SID/Tocheva-2016-Sporulation, bacterial cell envel.pdf;/Users/coiko/Zotero/storage/RV7BBXBA/Tocheva-2016-Sporulation, bacterial cell envel.pdf},
  journal = {Nat Rev Microbiol},
  keywords = {*Biological Evolution,Cell Membrane/*chemistry/ultrastructure,Cell Wall/*chemistry/ultrastructure,Gram-Negative Bacteria/ultrastructure,Gram-Positive Bacteria/*physiology/ultrastructure,Peptidoglycan/chemistry,Phylogeny,Spores; Bacterial/*physiology/ultrastructure},
  number = {8}
}

@incollection{tsien2005,
  title = {Breeding Molecules to Spy on Cells},
  booktitle = {The {{Harvey Lectures}}: {{Series}} 99, 2003-2004},
  author = {Tsien, R. Y.},
  year = {2005},
  publisher = {{Harvey Society}},
  url = {http://tsienlab.ucsd.edu/Publications/Tsien%202006%20Harvey%20Lectures%20-%20Breeding%20Molecules%20to%20Spy.pdf},
  file = {/Users/coiko/Zotero/storage/73FX6ZA5/Tsien - 2005 - Breeding molecules to spy on cells.pdf}
}

@article{turner2000,
  ids = {turnerRealtimeImagingFluorescent2000},
  title = {Real-Time Imaging of Fluorescent Flagellar Filaments},
  author = {Turner, Linda and Ryu, William S. and Berg, Howard C.},
  year = {2000},
  month = may,
  volume = {182},
  pages = {2793--2801},
  publisher = {{American Society for Microbiology Journals}},
  issn = {0021-9193, 1098-5530},
  doi = {10.1128/JB.182.10.2793-2801.2000},
  abstract = {Bacteria swim by rotating flagellar filaments that are several micrometers long, but only about 20 nm in diameter. The filaments can exist in different polymorphic forms, having distinct values of curvature and twist. Rotation rates are on the order of 100 Hz. In the past, the motion of individual filaments has been visualized by dark-field or differential-interference-contrast microscopy, methods hampered by intense scattering from the cell body or shallow depth of field, respectively. We have found a simple procedure for fluorescently labeling cells and filaments that allows recording their motion in real time with an inexpensive video camera and an ordinary fluorescence microscope with mercury-arc or strobed laser illumination. We report our initial findings with cells of Escherichia coli. Tumbles (events that enable swimming cells to alter course) are remarkably varied. Not every filament on a cell needs to change its direction of rotation: different filaments can change directions at different times, and a tumble can result from the change in direction of only one. Polymorphic transformations tend to occur in the sequence normal, semicoiled, curly 1, with changes in the direction of movement of the cell body correlated with transformations to the semicoiled form.},
  copyright = {Copyright \textcopyright{} 2000 American Society for Microbiology},
  file = {/Users/coiko/Zotero/storage/BRSXMGCQ/Turner et al. - 2000 - Real-Time Imaging of Fluorescent Flagellar Filamen.pdf;/Users/coiko/Zotero/storage/YANSN63T/Turner-2000-Real-time imaging of fluorescent f.pdf;/Users/coiko/Zotero/storage/F786C94B/2793.html},
  journal = {J Bacteriol},
  keywords = {Escherichia coli/*ultrastructure,Flagella/*ultrastructure,Microscopy; Fluorescence/methods},
  language = {en},
  number = {10},
  pmid = {10781548}
}

@article{veesler2013,
  title = {Atomic Structure of the 75 {{MDa}} Extremophile {{Sulfolobus}} Turreted Icosahedral Virus Determined by {{CryoEM}} and {{X}}-Ray Crystallography},
  author = {Veesler, David and Ng, Thiam-Seng and Sendamarai, Anoop K. and Eilers, Brian J. and Lawrence, C. Martin and Lok, Shee-Mei and Young, Mark J. and Johnson, John E. and Fu, Chi-yu},
  year = {2013},
  month = apr,
  volume = {110},
  pages = {5504--5509},
  publisher = {{National Academy of Sciences}},
  issn = {0027-8424, 1091-6490},
  doi = {10.1073/pnas.1300601110},
  abstract = {Sulfolobus turreted icosahedral virus (STIV) was isolated in acidic hot springs where it infects the archeon Sulfolobus solfataricus. We determined the STIV structure using near-atomic resolution electron microscopy and X-ray crystallography allowing tracing of structural polypeptide chains and visualization of transmembrane proteins embedded in the viral membrane. We propose that the vertex complexes orchestrate virion assembly by coordinating interactions of the membrane and various protein components involved. STIV shares the same coat subunit and penton base protein folds as some eukaryotic and bacterial viruses, suggesting that they derive from a common ancestor predating the divergence of the three kingdoms of life. One architectural motif ({$\beta$}-jelly roll fold) forms virtually the entire capsid (distributed in three different gene products), indicating that a single ancestral protein module may have been at the origin of its evolution.},
  file = {/Users/coiko/Zotero/storage/MUYTDARG/Veesler et al. - 2013 - Atomic structure of the 75 MDa extremophile Sulfol.pdf;/Users/coiko/Zotero/storage/GGZJYMRY/5504.html},
  journal = {Proc Natl Acad Sci USA},
  keywords = {Archaea,electron microscopy,PRD1-Adeno viral lineage,single-particle reconstruction,virus assembly},
  language = {en},
  number = {14},
  pmid = {23520050}
}

@article{vreeland2000,
  title = {Isolation of a 250 Million-Year-Old Halotolerant Bacterium from a Primary Salt Crystal},
  shorttitle = {Isolation of a 250 Million-Year-Old Halotolerant Bacterium from a Primary Salt Crystal},
  author = {Vreeland, R. H. and Rosenzweig, W. D. and Powers, D. W.},
  year = {2000},
  month = oct,
  volume = {407},
  pages = {897--900},
  issn = {0028-0836 (Print) 0028-0836 (Linking)},
  doi = {10.1038/35038060},
  abstract = {Bacteria have been found associated with a variety of ancient samples, however few studies are generally accepted due to questions about sample quality and contamination. When Cano and Borucki isolated a strain of Bacillus sphaericus from an extinct bee trapped in 25-30 million-year-old amber, careful sample selection and stringent sterilization techniques were the keys to acceptance. Here we report the isolation and growth of a previously unrecognized spore-forming bacterium (Bacillus species, designated 2-9-3) from a brine inclusion within a 250 million-year-old salt crystal from the Permian Salado Formation. Complete gene sequences of the 16S ribosomal DNA show that the organism is part of the lineage of Bacillus marismortui and Virgibacillus pantothenticus. Delicate crystal structures and sedimentary features indicate the salt has not recrystallized since formation. Samples were rejected if brine inclusions showed physical signs of possible contamination. Surfaces of salt crystal samples were sterilized with strong alkali and acid before extracting brines from inclusions. Sterilization procedures reduce the probability of contamination to less than 1 in 10(9).},
  file = {/Users/coiko/Zotero/storage/7SILT7K9/Vreeland-2000-Isolation of a 250 million-year-.pdf},
  journal = {Nature},
  keywords = {Bacillus/classification/growth \& development/*isolation \& purification,Crystallization,Molecular Sequence Data,Phylogeny,RNA; Ribosomal; 16S/genetics,Sequence Analysis; DNA,Sodium Chloride,Spores; Bacterial/isolation \& purification,Time},
  number = {6806}
}

@article{wagstaff2017,
  title = {A Polymerization-Associated Structural Switch in {{FtsZ}} That Enables Treadmilling of Model Filaments},
  author = {Wagstaff, James M. and Tsim, Matthew and Oliva, Mar{\'i}a A. and {Garc{\'i}a-Sanchez}, Alba and {Kureisaite-Ciziene}, Danguole and Andreu, Jos{\'e} Manuel and L{\"o}we, Jan},
  year = {2017},
  month = jul,
  volume = {8},
  publisher = {{American Society for Microbiology}},
  issn = {2150-7511},
  doi = {10.1128/mBio.00254-17},
  abstract = {Bacterial cell division in many organisms involves a constricting cytokinetic ring that is orchestrated by the tubulin-like protein FtsZ. FtsZ forms dynamic filaments close to the membrane at the site of division that have recently been shown to treadmill around the division ring, guiding septal wall synthesis. Here, using X-ray crystallography of Staphylococcus aureus FtsZ (SaFtsZ), we reveal how an FtsZ can adopt two functionally distinct conformations, open and closed. The open form is found in SaFtsZ filaments formed in crystals and also in soluble filaments of Escherichia coli FtsZ as deduced by electron cryomicroscopy. The closed form is found within several crystal forms of two nonpolymerizing SaFtsZ mutants and corresponds to many previous FtsZ structures from other organisms. We argue that FtsZ's conformational switch is polymerization-associated, driven by the formation of the longitudinal intersubunit interfaces along the filament. We show that such a switch provides explanations for both how treadmilling may occur within a single-stranded filament and why filament assembly is cooperative.
IMPORTANCE The FtsZ protein is a key molecule during bacterial cell division. FtsZ forms filaments that organize cell membrane constriction, as well as remodeling of the cell wall, to divide cells. FtsZ functions through nucleotide-driven filament dynamics that are poorly understood at the molecular level. In particular, mechanisms for cooperative assembly (nonlinear dependency on concentration) and treadmilling (preferential growth at one filament end and loss at the other) have remained elusive. Here, we show that most likely all FtsZ proteins have two distinct conformations, a ``closed'' form in monomeric FtsZ and an ``open'' form in filaments. The conformational switch that occurs upon polymerization explains cooperativity and, in concert with polymerization-dependent nucleotide hydrolysis, efficient treadmilling of FtsZ polymers.},
  copyright = {Copyright \textcopyright{} 2017 Wagstaff et al.. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license .},
  file = {/Users/coiko/Zotero/storage/B9GJIEIW/Wagstaff et al. - 2017 - A Polymerization-Associated Structural Switch in F.pdf;/Users/coiko/Zotero/storage/GXMUK7MM/e00254-17.html},
  journal = {mBio},
  language = {en},
  number = {3},
  pmid = {28465423}
}

@article{wang2017,
  title = {A Structural Model of Flagellar Filament Switching across Multiple Bacterial Species},
  shorttitle = {A Structural Model of Flagellar Filament Switching across Multiple Bacterial Species},
  author = {Wang, F. and Burrage, A. M. and Postel, S. and Clark, R. E. and Orlova, A. and Sundberg, E. J. and Kearns, D. B. and Egelman, E. H.},
  year = {2017},
  month = oct,
  volume = {8},
  pages = {960},
  issn = {2041-1723 (Electronic) 2041-1723 (Linking)},
  doi = {10.1038/s41467-017-01075-5},
  abstract = {The bacterial flagellar filament has long been studied to understand how a polymer composed of a single protein can switch between different supercoiled states with high cooperativity. Here we present near-atomic resolution cryo-EM structures for flagellar filaments from both Gram-positive Bacillus subtilis and Gram-negative Pseudomonas aeruginosa. Seven mutant flagellar filaments in B. subtilis and two in P. aeruginosa capture two different states of the filament. These reliable atomic models of both states reveal conserved molecular interactions in the interior of the filament among B. subtilis, P. aeruginosa and Salmonella enterica. Using the detailed information about the molecular interactions in two filament states, we successfully predict point mutations that shift the equilibrium between those two states. Further, we observe the dimerization of P. aeruginosa outer domains without any perturbation of the conserved interior of the filament. Our results give new insights into how the flagellin sequence has been "tuned" over evolution.Bacterial flagellar filaments are composed almost entirely of a single protein-flagellin-which can switch between different supercoiled states in a highly cooperative manner. Here the authors present near-atomic resolution cryo-EM structures of nine flagellar filaments, and begin to shed light on the molecular basis of filament switching.},
  file = {/Users/coiko/Zotero/storage/7E25RQYI/Wang-2017-A structural model of flagellar fila.pdf},
  journal = {Nat Commun},
  number = {1}
}

@article{woese2002,
  title = {On the Evolution of Cells},
  shorttitle = {On the Evolution of Cells},
  author = {Woese, C. R.},
  year = {2002},
  month = jun,
  volume = {99},
  pages = {8742--7},
  issn = {0027-8424 (Print) 0027-8424 (Linking)},
  doi = {10.1073/pnas.132266999},
  abstract = {A theory for the evolution of cellular organization is presented. The model is based on the (data supported) conjecture that the dynamic of horizontal gene transfer (HGT) is primarily determined by the organization of the recipient cell. Aboriginal cell designs are taken to be simple and loosely organized enough that all cellular componentry can be altered and/or displaced through HGT, making HGT the principal driving force in early cellular evolution. Primitive cells did not carry a stable organismal genealogical trace. Primitive cellular evolution is basically communal. The high level of novelty required to evolve cell designs is a product of communal invention, of the universal HGT field, not intralineage variation. It is the community as a whole, the ecosystem, which evolves. The individual cell designs that evolved in this way are nevertheless fundamentally distinct, because the initial conditions in each case are somewhat different. As a cell design becomes more complex and interconnected a critical point is reached where a more integrated cellular organization emerges, and vertically generated novelty can and does assume greater importance. This critical point is called the "Darwinian Threshold" for the reasons given.},
  file = {/Users/coiko/Zotero/storage/92DPYAKQ/Woese-2002-On the evolution of cells.pdf},
  journal = {Proc Natl Acad Sci U S A},
  keywords = {*Biological Evolution,*Cells,Gene Transfer; Horizontal,Protein Biosynthesis},
  number = {13}
}

@article{worrall2016,
  title = {Near-Atomic-Resolution Cryo-{{EM}} Analysis of the {{Salmonella T3S}} Injectisome Basal Body},
  author = {Worrall, L. J. and Hong, C. and Vuckovic, M. and Deng, W. and Bergeron, J. R. C. and Majewski, D. D. and Huang, R. K. and Spreter, T. and Finlay, B. B. and Yu, Z. and Strynadka, N. C. J.},
  year = {2016},
  month = dec,
  volume = {540},
  pages = {597--601},
  publisher = {{Nature Publishing Group}},
  issn = {1476-4687},
  doi = {10.1038/nature20576},
  abstract = {The authors report the structure of the assembled membrane spanning ring forming proteins of the Salmonella Typhimurium injectisome basal body, including the first atomic structure of a member of the secretin family of outer-membrane pores.},
  copyright = {2016 Macmillan Publishers Limited, part of Springer Nature. All rights reserved.},
  file = {/Users/coiko/Zotero/storage/PL6Q3HTZ/Worrall et al. - 2016 - Near-atomic-resolution cryo-EM analysis of the Sal.pdf;/Users/coiko/Zotero/storage/2WQ6PYSK/nature20576.html},
  journal = {Nature},
  language = {en},
  number = {7634}
}

@book{xie2016,
  title = {Bookdown: {{Authoring Books}} and {{Technical Documents}} with {{R Markdown}}},
  author = {Xie, Y},
  year = {2016},
  url = {https://github.com/rstudio/bookdown},
  urldate = {2020-05-07}
}

@article{xue2018,
  title = {Crystal Structure of the {{FliF}}\textendash{{FliG}} Complex from {{Helicobacter}} Pylori Yields Insight into the Assembly of the Motor {{MS}}\textendash{{C}} Ring in the Bacterial Flagellum},
  author = {Xue, Chaolun and Lam, Kwok Ho and Zhang, Huawei and Sun, Kailei and Lee, Sai Hang and Chen, Xin and Au, Shannon Wing Ngor},
  year = {2018},
  month = sep,
  volume = {293},
  pages = {2066--2078},
  publisher = {{American Society for Biochemistry and Molecular Biology}},
  issn = {0021-9258, 1083-351X},
  doi = {10.1074/jbc.M117.797936},
  abstract = {The bacterial flagellar motor is a self-assembling supramolecular nanodevice. Its spontaneous biosynthesis is initiated by the insertion of the MS ring protein FliF into the inner membrane, followed by attachment of the switch protein FliG. Assembly of this multiprotein complex is tightly regulated to avoid nonspecific aggregation, but the molecular mechanisms governing flagellar assembly are unclear. Here, we present the crystal structure of the cytoplasmic domain of FliF complexed with the N-terminal domain of FliG (FliFC-FliGN) from the bacterium Helicobacter pylori. Within this complex, FliFC interacted with FliGN through extensive hydrophobic contacts similar to those observed in the FliFC-FliGN structure from the thermophile Thermotoga maritima, indicating conservation of the FliFC-FliGN interaction across bacterial species. Analysis of the crystal lattice revealed that the heterodimeric complex packs as a linear superhelix via stacking of the armadillo repeat-like motifs (ARM) of FliGN. Notably, this linear helix was similar to that observed for the assembly of the FliG middle domain. We validated the in vivo relevance of the FliGN stacking by complementation studies in Escherichia coli. Furthermore, structural comparison with apo FliG from the thermophile Aquifex aeolicus indicated that FliF regulates the conformational transition of FliG and exposes the complementary ARM-like motifs of FliGN, containing conserved hydrophobic residues. FliF apparently both provides a template for FliG polymerization and spatiotemporally controls subunit interactions within FliG. Our findings reveal that a small protein fold can serve as a versatile building block to assemble into a multiprotein machinery of distinct shapes for specific functions.},
  file = {/Users/coiko/Zotero/storage/SL2YZMF2/Xue et al. - 2018 - Crystal structure of the FliF–FliG complex from He.pdf;/Users/coiko/Zotero/storage/SE5F6SKR/2066.html},
  journal = {J. Biol. Chem.},
  keywords = {bacterial motility,conformational change,flagellar motor,Helicobacter pylori,molecular motor,protein assembly,protein structure},
  language = {en},
  number = {6},
  pmid = {29229777}
}

@article{yan2017a,
  title = {Structural Insights into the Secretin Translocation Channel in the Type {{II}} Secretion System},
  author = {Yan, Zhaofeng and Yin, Meng and Xu, Dandan and Zhu, Yongqun and Li, Xueming},
  year = {2017},
  month = feb,
  volume = {24},
  pages = {177--183},
  publisher = {{Nature Publishing Group}},
  issn = {1545-9985},
  doi = {10.1038/nsmb.3350},
  abstract = {Cryo-EM structures of secretin GspD in type II secretion systems from Escherichia coli and Vibrio cholera reveal a pentadecameric architecture, with three rings in the periplasm and {$\beta$}-strand-enriched gates on the outer membrane.},
  copyright = {2017 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
  file = {/Users/coiko/Zotero/storage/AYKXD7WM/Yan et al. - 2017 - Structural insights into the secretin translocatio.pdf;/Users/coiko/Zotero/storage/32NLI3FB/nsmb.html},
  journal = {Nat Struct Mol Biol},
  language = {en},
  number = {2}
}

@article{young2006,
  title = {The Selective Value of Bacterial Shape},
  shorttitle = {The Selective Value of Bacterial Shape},
  author = {Young, K. D.},
  year = {2006},
  month = sep,
  volume = {70},
  pages = {660--703},
  issn = {1092-2172 (Print) 1092-2172 (Linking)},
  doi = {10.1128/MMBR.00001-06},
  abstract = {Why do bacteria have shape? Is morphology valuable or just a trivial secondary characteristic? Why should bacteria have one shape instead of another? Three broad considerations suggest that bacterial shapes are not accidental but are biologically important: cells adopt uniform morphologies from among a wide variety of possibilities, some cells modify their shape as conditions demand, and morphology can be tracked through evolutionary lineages. All of these imply that shape is a selectable feature that aids survival. The aim of this review is to spell out the physical, environmental, and biological forces that favor different bacterial morphologies and which, therefore, contribute to natural selection. Specifically, cell shape is driven by eight general considerations: nutrient access, cell division and segregation, attachment to surfaces, passive dispersal, active motility, polar differentiation, the need to escape predators, and the advantages of cellular differentiation. Bacteria respond to these forces by performing a type of calculus, integrating over a number of environmental and behavioral factors to produce a size and shape that are optimal for the circumstances in which they live. Just as we are beginning to answer how bacteria create their shapes, it seems reasonable and essential that we expand our efforts to understand why they do so.},
  file = {/Users/coiko/Zotero/storage/YYPLGQKK/Young-2006-The selective value.pdf},
  journal = {Microbiol Mol Biol Rev},
  keywords = {*Bacterial Physiological Phenomena,Bacteria/*cytology,Bacterial Adhesion/physiology,Cell Division/physiology,Models; Biological},
  number = {3}
}

@article{zhao2014,
  title = {Molecular Architecture of the Bacterial Flagellar Motor in Cells},
  shorttitle = {Molecular Architecture of the Bacterial Flagellar Motor in Cells},
  author = {Zhao, X. and Norris, S. J. and Liu, J.},
  year = {2014},
  month = jul,
  volume = {53},
  pages = {4323--33},
  issn = {1520-4995 (Electronic) 0006-2960 (Linking)},
  doi = {10.1021/bi500059y},
  abstract = {The flagellum is one of the most sophisticated self-assembling molecular machines in bacteria. Powered by the proton-motive force, the flagellum rapidly rotates in either a clockwise or counterclockwise direction, which ultimately controls bacterial motility and behavior. Escherichia coli and Salmonella enterica have served as important model systems for extensive genetic, biochemical, and structural analysis of the flagellum, providing unparalleled insights into its structure, function, and gene regulation. Despite these advances, our understanding of flagellar assembly and rotational mechanisms remains incomplete, in part because of the limited structural information available regarding the intact rotor-stator complex and secretion apparatus. Cryo-electron tomography (cryo-ET) has become a valuable imaging technique capable of visualizing the intact flagellar motor in cells at molecular resolution. Because the resolution that can be achieved by cryo-ET with large bacteria (such as E. coli and S. enterica) is limited, analysis of small-diameter bacteria (including Borrelia burgdorferi and Campylobacter jejuni) can provide additional insights into the in situ structure of the flagellar motor and other cellular components. This review is focused on the application of cryo-ET, in combination with genetic and biophysical approaches, to the study of flagellar structures and its potential for improving the understanding of rotor-stator interactions, the rotational switching mechanism, and the secretion and assembly of flagellar components.},
  file = {/Users/coiko/Zotero/storage/F89ZXWRS/Zhao-2014-Molecular architecture of the bacter.pdf;/Users/coiko/Zotero/storage/GEV2WC94/Zhao-2014-Molecular architecture of the bacter.pdf;/Users/coiko/Zotero/storage/U2XURA52/Zhao-2014-Molecular architecture of the bacter.pdf},
  journal = {Biochemistry},
  keywords = {Bacteria/cytology/*metabolism,Bacterial Physiological Phenomena,Bacterial Proteins/metabolism,Cryoelectron Microscopy,Electron Microscope Tomography,Flagella/*physiology/ultrastructure,Protein Conformation,Species Specificity,Spirochaetales/cytology/metabolism},
  number = {27}
}