35 results found
Chaban B, Coleman I, Beeby M, 2018, Evolution of higher torque in Campylobacter-type bacterial flagellar motors, SCIENTIFIC REPORTS, Vol: 8, ISSN: 2045-2322
Henderson LD, Beeby M, 2018, High-Throughput Electron Cryo-tomography of Protein Complexes and Their Assembly., Methods Mol Biol, Vol: 1764, Pages: 29-44
Electron cryo-tomography and subtomogram averaging enable visualization of protein complexes in situ, in three dimensions, in a near-native frozen-hydrated state to nanometer resolutions. To achieve this, intact cells are vitrified and imaged over a range of tilts within an electron microscope. These images can subsequently be reconstructed into a three-dimensional volume representation of the sample cell. Because complexes are visualized in situ, crucial insights into their mechanism, assembly process, and dynamic interactions with other proteins become possible. To illustrate the electron cryo-tomography workflow for visualizing protein complexes in situ, we describe our workflow of preparing samples, imaging, and image processing using Leginon for data collection, IMOD for image reconstruction, and PEET for subtomogram averaging.
Asmar AT, Ferreira JL, Cohen EJ, et al., 2017, Communication across the bacterial cell envelope depends on the size of the periplasm, PLOS BIOLOGY, Vol: 15, ISSN: 1545-7885
Cohen EJ, Ferreira JL, Ladinsky MS, et al., 2017, Nanoscale-length control of the flagellar driveshaft requires hitting the tethered outer membrane, SCIENCE, Vol: 356, Pages: 197-200, ISSN: 0036-8075
Ferreira J, Matthews-Palmer T, Beeby M, 2017, Electron cryo-tomography, Cellular Imaging Electron Tomography and Related Techniques, Editors: Hanssen, Publisher: Springer, ISBN: 9783319689975
This book highlights important techniques for cellular imaging and covers the basics and applications of electron tomography and related techniques.
Haurat MF, Figueiredo AS, Hoffmann L, et al., 2017, ArnS, a kinase involved in starvation-induced archaellum expression, MOLECULAR MICROBIOLOGY, Vol: 103, Pages: 181-194, ISSN: 0950-382X
Hoffmann L, Schummer A, Reimann J, et al., 2017, Expanding the archaellum regulatory network - the eukaryotic protein kinases ArnC and ArnD influence motility of Sulfolobus acidocaldarius, MICROBIOLOGYOPEN, Vol: 6, ISSN: 2045-8827
The bacterial flagellum is the principal organelle of motility in bacteria. Here, we address the question of size when applied to the chief flagellar protein flagellin and the flagellar filament. Surprisingly, nature furnishes multiple examples of 'giant flagellins' greater than a thousand amino acids in length, with large surface-exposed hypervariable domains. We review the contexts in which these giant flagellins occur, speculate as to their functions, and highlight the potential for biotechnology to build on what nature provides.
Yao Q, Jewett AI, Chang Y-W, et al., 2017, Short FtsZ filaments can drive asymmetric cell envelope constriction at the onset of bacterial cytokinesis, EMBO JOURNAL, Vol: 36, Pages: 1577-1589, ISSN: 0261-4189
Beeby M, Ribardo DA, Brennan CA, et al., 2016, Diverse high-torque bacterial flagellar motors assemble wider stator rings using a conserved protein scaffold, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol: 113, Pages: E1917-E1926, ISSN: 0027-8424
Nguyen LT, Swulius M, Gumbart JC, et al., 2016, Coarse-Grained Simulations Reveal Mechanisms of Bacterial Morphogenesis, 60th Annual Meeting of the Biophysical-Society, Publisher: CELL PRESS, Pages: 468A-468A, ISSN: 0006-3495
Taylor WR, Matthews-Palmer TRS, Beeby M, 2016, Molecular Models for the Core Components of the Flagellar Type-III Secretion Complex, PLOS ONE, Vol: 11, ISSN: 1932-6203
Beeby M, 2015, Motility in the epsilon-proteobacteria, CURRENT OPINION IN MICROBIOLOGY, Vol: 28, Pages: 115-121, ISSN: 1369-5274
Chaban B, Hughes HV, Beeby M, 2015, The flagellum in bacterial pathogens: For motility and a whole lot more, SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY, Vol: 46, Pages: 91-103, ISSN: 1084-9521
Nguyen LT, Gumbart JC, Beeby M, et al., 2015, Coarse-grained simulations of bacterial cell wall growth reveal that local coordination alone can be sufficient to maintain rod shape, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol: 112, Pages: E3689-E3698, ISSN: 0027-8424
Beeby M, 2014, Evolution of Novel Components of the Bacterial Flagellar Motor, 28th Annual Symposium of the Protein-Society, Publisher: WILEY-BLACKWELL, Pages: 61-61, ISSN: 0961-8368
Gumbart JC, Beeby M, Jensen GJ, et al., 2014, Escherichia coli Peptidoglycan Structure and Mechanics as Predicted by Atomic-Scale Simulations, PLOS COMPUTATIONAL BIOLOGY, Vol: 10, ISSN: 1553-734X
Mueller A, Beeby M, McDowall AW, et al., 2014, Ultrastructure and complex polar architecture of the human pathogen Campylobacter jejuni, MICROBIOLOGYOPEN, Vol: 3, Pages: 702-710, ISSN: 2045-8827
Abrusci P, Vergara-Irigaray M, Johnson S, et al., 2013, Architecture of the major component of the type III secretion system export apparatus, NATURE STRUCTURAL & MOLECULAR BIOLOGY, Vol: 20, Pages: 99-U126, ISSN: 1545-9993
Beeby M, Gumbart JC, Roux B, et al., 2013, Architecture and assembly of the Gram-positive cell wall, MOLECULAR MICROBIOLOGY, Vol: 88, Pages: 664-672, ISSN: 0950-382X
Jensen G, Briegel A, Beeby M, 2013, Visualizing large macromolecular assemblies in vivo with electron cryotomography, 245th National Spring Meeting of the American-Chemical-Society (ACS), Publisher: AMER CHEMICAL SOC, ISSN: 0065-7727
Beeby M, Cho M, Stubbe J, et al., 2012, Growth and Localization of Polyhydroxybutyrate Granules in Ralstonia eutropha, JOURNAL OF BACTERIOLOGY, Vol: 194, Pages: 1092-1099, ISSN: 0021-9193
Briegel A, Beeby M, Thanbichler M, et al., 2011, Activated chemoreceptor arrays remain intact and hexagonally packed, MOLECULAR MICROBIOLOGY, Vol: 82, Pages: 748-757, ISSN: 0950-382X
Chen S, Beeby M, Murphy GE, et al., 2011, Structural diversity of bacterial flagellar motors, EMBO JOURNAL, Vol: 30, Pages: 2972-2981, ISSN: 0261-4189
While much is already known about the basic metabolism of bacterial cells, many fundamental questions are still surprisingly unanswered, including for instance how they generate and maintain specific cell shapes, establish polarity, segregate their genomes, and divide. In order to understand these phenomena, imaging technologies are needed that bridge the resolution gap between fluorescence light microscopy and higher-resolution methods such as X-ray crystallography and NMR spectroscopy. Electron cryotomography (ECT) is an emerging technology that does just this, allowing the ultrastructure of cells to be visualized in a near-native state, in three dimensions (3D), with "macromolecular" resolution (approximately 4nm).(1, 2) In ECT, cells are imaged in a vitreous, "frozen-hydrated" state in a cryo transmission electron microscope (cryoTEM) at low temperature (< -180 degrees C). For slender cells (up to approximately 500 nm in thickness(3)), intact cells are plunge-frozen within media across EM grids in cryogens such as ethane or ethane/propane mixtures. Thicker cells and biofilms can also be imaged in a vitreous state by first "high-pressure freezing" and then, "cryo-sectioning" them. A series of two-dimensional projection images are then collected through the sample as it is incrementally tilted along one or two axes. A three-dimensional reconstruction, or "tomogram" can then be calculated from the images. While ECT requires expensive instrumentation, in recent years, it has been used in a few labs to reveal the structures of various external appendages, the structures of different cell envelopes, the positions and structures of cytoskeletal filaments, and the locations and architectures of large macromolecular assemblies such as flagellar motors, internal compartments and chemoreceptor arrays.(1, 2) In this video article we illustrate how to image cells with ECT, including the processes of sample preparation, dat
Beeby M, Bobik TA, Yeates TO, 2009, Exploiting genomic patterns to discover new supramolecular protein assemblies, PROTEIN SCIENCE, Vol: 18, Pages: 69-79, ISSN: 0961-8368
Chim N, McMath LM, Beeby M, et al., 2009, Advances in Mycobacterium tuberculosis structural genomics: investigating potential chinks in the armor of a deadly pathogen, Infect Disord Drug Targets, Vol: 9, Pages: 475-492
Yeates TO, Beeby M, 2006, Biochemistry. Proteins in a small world, Science, Vol: 314, Pages: 1882-1883
Yeates TO, Beeby M, 2006, Proteins in a small world, SCIENCE, Vol: 314, Pages: 1882-1883, ISSN: 0036-8075
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