Functional Interaction of the Tona/Tonb Receptor System in Escherichia Coli K
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Structural Comparison of Tonb-Dependent Receptors in Bradyrhizobium Japonicum Allie R
James Madison University JMU Scholarly Commons Senior Honors Projects, 2010-current Honors College Fall 2015 Structural comparison of TonB-dependent receptors in bradyrhizobium japonicum Allie R. Casto James Madison University Follow this and additional works at: https://commons.lib.jmu.edu/honors201019 Part of the Bioinformatics Commons, and the Biology Commons Recommended Citation Casto, Allie R., "Structural comparison of TonB-dependent receptors in bradyrhizobium japonicum" (2015). Senior Honors Projects, 2010-current. 126. https://commons.lib.jmu.edu/honors201019/126 This Thesis is brought to you for free and open access by the Honors College at JMU Scholarly Commons. It has been accepted for inclusion in Senior Honors Projects, 2010-current by an authorized administrator of JMU Scholarly Commons. For more information, please contact [email protected]. Structural Comparison of TonB-Dependent Receptors in Bradyrhizobium japonicum _______________________ An Honors Program Project Presented to the Faculty of the Undergraduate College of Sciences and Mathematics James Madison University _______________________ by Allie Renee Casto December 2015 Accepted by the faculty of the Department of Integrated Science and Technology, James Madison University, in partial fulfillment of the requirements for the Honors Program. FACULTY COMMITTEE: HONORS PROGRAM APPROVAL: Project Advisor: Stephanie Stockwell, Ph. D. Bradley R. Newcomer, Ph.D., Professor, Integrated Science and Technology Director, Honors Program Reader: Jonathan Monroe, Ph. D. Professor, -
Structural Engineering of a Phage Lysin That Targets Gram-Negative Pathogens
Structural engineering of a phage lysin that targets Gram-negative pathogens Petra Lukacika, Travis J. Barnarda, Paul W. Kellerb, Kaveri S. Chaturvedic, Nadir Seddikia,JamesW.Fairmana, Nicholas Noinaja, Tara L. Kirbya, Jeffrey P. Hendersonc, Alasdair C. Stevenb, B. Joseph Hinnebuschd, and Susan K. Buchanana,1 aLaboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892; bLaboratory of Structural Biology, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda,MD 20892; cCenter for Women’s Infectious Diseases Research, Washington University School of Medicine, St. Louis, MO 63110; and dLaboratory of Zoonotic Pathogens, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840 Edited by* Brian W. Matthews, University of Oregon, Eugene, OR, and approved April 18, 2012 (received for review February 27, 2012) Bacterial pathogens are becoming increasingly resistant to antibio- ∼10 kb plasmid called pPCP1 (7). Pla facilitates invasion in bu- tics. As an alternative therapeutic strategy, phage therapy reagents bonic plague and, as such, is an important virulence factor (8, 9). containing purified viral lysins have been developed against Gram- When strains lose the pPCP1 plasmid, they are killed by pesticin positive organisms but not against Gram-negative organisms due thus ensuring maximal virulence in the bacterial population. to the inability of these types of drugs to cross the bacterial outer Bacteriocins belong to two classes. Type A bacteriocins depend membrane. We solved the crystal structures of a Yersinia pestis on the Tolsystem to traverse the outer membrane, whereas type B outer membrane transporter called FyuA and a bacterial toxin bacteriocins require the Ton system. -
Organic Matter Processing by Microbial Communities Throughout
Organic matter processing by microbial communities PNAS PLUS throughout the Atlantic water column as revealed by metaproteomics Kristin Bergauera,1, Antonio Fernandez-Guerrab,c, Juan A. L. Garciaa, Richard R. Sprengerd, Ramunas Stepanauskase, Maria G. Pachiadakie, Ole N. Jensend, and Gerhard J. Herndla,f,g aDepartment of Limnology and Bio-Oceanography, University of Vienna, A-1090 Vienna, Austria; bMicrobial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, D-28359 Bremen, Germany; cOxford e-Research Centre, University of Oxford, Oxford OX1 3QG, United Kingdom; dDepartment of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, DK-5230 Odense M, Denmark; eBigelow Laboratory for Ocean Sciences, East Boothbay, ME 04544; fDepartment of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Utrecht University, 1790 AB Den Burg, The Netherlands; and gVienna Metabolomics Center, University of Vienna, A-1090 Vienna, Austria Edited by David M. Karl, University of Hawaii, Honolulu, HI, and approved November 21, 2017 (received for review May 26, 2017) The phylogenetic composition of the heterotrophic microbial demand in the mesopelagic and bathypelagic waters (7, 8). Despite community is depth stratified in the oceanic water column down this apparent low contribution of DOM compared with POM in to abyssopelagic layers. In the layers below the euphotic zone, it has supporting heterotrophic microbial metabolism in the deep ocean, been suggested that heterotrophic microbes rely largely on solubi- DOM quantity and quality decreases with depth (9). The decrease in lized particulate organic matter as a carbon and energy source the overall nutritional quality of the DOM with depth might reflect rather than on dissolved organic matter. -
Escherichia Coli and Other Gram-Negative Bacteria
Biochimica et Biophysica A cta, 737 (1983) 51 - 115 51 Elsevier Biomedical Press BBA 85241 MOLECULAR ARCHITECTURE AND FUNCTIONING OF THE OUTER MEMBRANE OF ESCHERICHIA COLI AND OTHER GRAM-NEGATIVE BACTERIA BEN LUGTENBERG a,, and LOEK VAN ALPHEN h " Department of Molecular Cell Biology' and Institute for Molecular Biology', State University, Transitorium 3, Padualaan 8, 3584 CH Utrecht and h Laboratorium voor de Gezondheidsleer, University of Amsterdam, Mauritskade 57, 1092 AD Amsterdam (The Netherlands) (Received July 26th, 1982) Contents Introduction ............................................................................. 52 A. Scope of this review ...................................................................... 52 B. Ecological considerations relevant to structure and functioning of the outer membrane of Enterobacteriaceae ........ 53 C. General description of the cell envelope of Gram-negative bacteria ..................................... 53 II. Methods for the isolation of outer membranes ...................................................... 58 A. E. coli and S. typhimurium ................................................................. 58 1. Isolation of peptidoglycan-less outer membranes after spheroplast formation ............................ 58 2. Isolation of outer membrane-peptidoglycan complexes ........................................... 58 3. Differential membrane solubilization using detergents ............................................ 59 4. Membrane separation based on charge differences of vesicles ...................................... -
Analysis of the Genome and Outer Membrane Proteome
pathogens Article How Bacteria Change after Exposure to Silver Nanoformulations: Analysis of the Genome and Outer Membrane Proteome Anna K˛edziora 1,* , Mateusz Speruda 1, Maciej Wernecki 1 , Bartłomiej Dudek 1, Katarzyna Kapczynska 2 , Eva Krzyzewska˙ 2 , Jacek Rybka 2 and Gabriela Bugla-Płosko ´nska 1,* 1 Department of Microbiology, Faculty of Biological Sciences, University of Wroclaw, 51-148 Wroclaw, Poland; [email protected] (M.S.); [email protected] (M.W.); [email protected] (B.D.) 2 Department of Immunology of Infectious Diseases, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wroclaw, Poland; [email protected] (K.K.); [email protected] (E.K.); [email protected] (J.R.) * Correspondence: [email protected] (A.K.); [email protected] (G.B.-P.); Tel.: +487-1375-6323 (A.K.) Abstract: Objective: the main purpose of this work was to compare the genetic and phenotypic changes of E. coli treated with silver nanoformulations (E. coli BW25113 wt, E. coli BW25113 AgR, E. coli J53, E. coli ATCC 11229 wt, E. coli ATCC 11229 var. S2 and E. coli ATCC 11229 var. S7). Silver, as the metal with promising antibacterial properties, is currently widely used in medicine and the biomedical industry, in both ionic and nanoparticles forms. Silver nanoformulations are usually Citation: K˛edziora,A.; Speruda, M.; considered as one type of antibacterial agent, but their physical and chemical properties determine Wernecki, M.; Dudek, B.; Kapczynska, the way of interactions with the bacterial cell, the mode of action, and the bacterial cell response K.; Krzyzewska,˙ E.; Rybka, J.; Bugla-Płosko´nska,G. -
Tonb-Dependent Transporters in Sphingomonads: Unraveling Their Distribution and Function in Environmental Adaptation
microorganisms Review TonB-Dependent Transporters in Sphingomonads: Unraveling Their Distribution and Function in Environmental Adaptation Devyani Samantarrai y, Annapoorni Lakshman Sagar y, Ramurthy Gudla and Dayananda Siddavattam * Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad 500 046, India; [email protected] (D.S.); [email protected] (A.L.S.); [email protected] (R.G.) * Correspondence: [email protected]; Tel.: +91-040-66794578 These authors contributed equally to this work. y Received: 30 November 2019; Accepted: 7 January 2020; Published: 3 March 2020 Abstract: TonB-dependent transport system plays a critical role in the transport of nutrients across the energy-deprived outer membrane of Gram-negative bacteria. It contains a specialized outer membrane TonB-dependent transporter (TBDT) and energy generating (ExbB/ExbD) and transducing (TonB) inner membrane multi-protein complex, called TonB complex. Very few TonB complex protein-coding sequences exist in the genomes of Gram-negative bacteria. Interestingly, the TBDT coding alleles are phenomenally high, especially in the genomes of bacteria surviving in complex and stressful environments. Sphingomonads are known to survive in highly polluted environments using rare, recalcitrant, and toxic substances as their sole source of carbon. Naturally, they also contain a huge number of TBDTs in the outer membrane. Out of them, only a few align with the well-characterized TBDTs. The functions of the remaining TBDTs are not known. Predictions made based on genome context and expression pattern suggest their involvement in the transport of xenobiotic compounds across the outer membrane. Keywords: TonB-dependent transporter (TBDT); sphingomonads; xenobiotics 1. Introduction The outer membrane of Gram-negative bacteria performs several important functions. -
The DUF560 Family Outer Membrane Protein Superfamily SPAM Has Distinct
bioRxiv preprint doi: https://doi.org/10.1101/2020.01.20.912956; this version posted January 21, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Beyond Slam: the DUF560 family outer membrane protein superfamily SPAM has distinct network subclusters that suggest a role in non-lipidated substrate transport and bacterial environmental adaptation Terra J. Mauer1 ¶, Alex S. Grossman2¶, Katrina T. Forest1, and Heidi Goodrich-Blair1,2* 1University of Wisconsin-Madison, Department of Bacteriology, Madison, WI 2University of Tennessee-Knoxville, Department of Microbiology, Knoxville, TN ¶These authors contributed equally to this work. *To whom correspondence should be addressed: [email protected], https://orcid.org/0000-0003- 1934-2636 Short title: Bacterial Surface/Secreted Protein Associated Outer Membrane Proteins (SPAMs) Abstract In host-associated bacteria, surface and secreted proteins mediate acquisition of nutrients, interactions with host cells, and specificity of host-range and tissue-localization. In Gram- negative bacteria, the mechanism by which many proteins cross, become embedded within, or become tethered to the outer membrane remains unclear. The domain of unknown function (DUF)560 occurs in outer membrane proteins found throughout and beyond the proteobacteria. Functionally characterized DUF560 representatives include NilB, a host-range specificity determinant of the nematode-mutualist Xenorhabdus nematophila and the surface lipoprotein assembly modulators (Slam), Slam1 and Slam2 which facilitate surface exposure of lipoproteins in the human pathogen Neisseria meningitidis. Through network analysis of protein sequence similarity we show that DUF560 subclusters exist and correspond with organism lifestyle rather than with taxonomy, suggesting a role for these proteins in environmental adaptation. -
A Comparative Genomics Approach. the ISME
The ISME Journal (2013) 7, 1026–1037 & 2013 International Society for Microbial Ecology All rights reserved 1751-7362/13 www.nature.com/ismej ORIGINAL ARTICLE Ecology of marine Bacteroidetes: a comparative genomics approach Beatriz Ferna´ndez-Go´mez1, Michael Richter2, Margarete Schu¨ ler3, Jarone Pinhassi4, Silvia G Acinas1, Jose´ M Gonza´lez5 and Carlos Pedro´s-Alio´ 1 1Department of Marine Biology and Oceanography, Institut de Cie`ncies del Mar, Consejo Superior de Investigaciones Cientı´ficas (CSIC), Barcelona, Spain; 2Microbial Genomics and Bioinformatics Research Group, Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany; 3Department of Molecular Structural Biology, Max Planck Institute for Biochemistry, Martinsried, Germany; 4Centre for Ecology and Evolution in Microbial model Systems, Linnaeus University, Kalmar, Sweden and 5Department of Microbiology, University of La Laguna, La Laguna, Spain Bacteroidetes are commonly assumed to be specialized in degrading high molecular weight (HMW) compounds and to have a preference for growth attached to particles, surfaces or algal cells. The first sequenced genomes of marine Bacteroidetes seemed to confirm this assumption. Many more genomes have been sequenced recently. Here, a comparative analysis of marine Bacteroidetes genomes revealed a life strategy different from those of other important phyla of marine bacterioplankton such as Cyanobacteria and Proteobacteria. Bacteroidetes have many adaptations to grow attached to particles, have the capacity to degrade polymers, including a large number of peptidases, glycoside hydrolases (GHs), glycosyl transferases, adhesion proteins, as well as the genes for gliding motility. Several of the polymer degradation genes are located in close association with genes for TonB-dependent receptors and transducers, suggesting an integrated regulation of adhesion and degradation of polymers. -
Expression of Hypothetical Genes and Improved Functional Annotations
Global profiling of Shewanella oneidensis MR-1: Expression of hypothetical genes and improved functional annotations Eugene Kolkera,b, Alex F. Piconea, Michael Y. Galperinc, Margaret F. Romined, Roger Higdona, Kira S. Makarovac, Natali Kolkera, Gordon A. Andersone, Xiaoyun Qiuf, Kenneth J. Auberrye, Gyorgy Babniggg, Alex S. Beliaevd, Paul Edlefsena, Dwayne A. Eliasd,e, Yuri A. Gorbyd, Ted Holzmana, Joel A. Klappenbachf, Konstantinos T. Konstantinidisf, Miriam L. Landh, Mary S. Liptond,e, Lee-Ann McCuei, Matthew Monroee, Ljiljana Pasa-Tolice, Grigoriy Pinchukd, Samuel Purvinea,e, Margrethe H. Serresj, Sasha Tsapink, Brian A. Zakrajsekd, Wenhong Zhul, Jizhong Zhoum, Frank W. Larimerh, Charles E. Lawrencei, Monica Rileyj, Frank R. Collartg, John R. Yates, IIIl, Richard D. Smithe, Carol S. Giomettig, Kenneth H. Nealsonk, James K. Fredricksond, and James M. Tiedjef aBIATECH, 19310 North Creek Parkway, Suite 115, Bothell, WA 98011; cNational Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20894; dBiological Sciences Division and eEnvironmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352; fCenter for Microbial Ecology, Michigan State University, East Lansing, MI 48824; gBiosciences Division, Argonne National Laboratory, Argonne, IL 60439; hGenome Analysis Group and mEnvironmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831; iWadsworth Center, Albany, NY 12201; jCenter for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543; kDepartment of Earth Sciences, University of Southern California, Los Angeles, CA 90089; and lDepartment of Cell Biology, The Scripps Research Institute, La Jolla, CA 92037 Contributed by James M. Tiedje, December 17, 2004 The ␥-proteobacterium Shewanella oneidensis strain MR-1 is a the predicted genes and analysis of genes designated as hypothetical metabolically versatile organism that can reduce a wide range of (4–6). -
The Outer Membranes of Pseudomonads
19 THE OUTER MEMBRANES OF PSEUDOMONADS Sandeep Tamber and Robert E.W. Hancock Department ofMicrobiology and Immunology University ofBritish Columbia, Vancouver British Columbia, Canada 1. INTRODUCTION The study of bacterial cell surfaces began in 1675 when Leeuwenhoek peering through his microscope wondered what "held [bacteria] together, or what contained them,,92. Since that time, our knowledge of cell surfaces, namely the Gram-negative outer membrane, has grown considerably. In addi tion to containing the bacteria, the outer membrane mediates a myriad offunc tions including other structural roles such as maintaining bacterial shape and providing a scaffold for fimbriae and flagella. Another key function ofthe outer membrane is to mediate the interactions between Gram-negative bacteria and their environment, primarily by determining which compounds enter and exit the cell. This complex task involves the integration of lipidic components involved in the barrier function ofthe outer membrane and proteins involved in the uptake and efflux of the various compounds able to traverse this barrier. Pseudomonads are intrinsically resistant to a large variety of toxic com pounds including antibiotics, organic solvents, dyes, detergents, and heavy metals". Yet, at the same time, these organisms are able to take up an astoni shing array of metabolites . Therefore the Pseudomonas outer membrane has emerged as a prototype to study the intricacies ofthis dynamic organelle. This chapter covers the structural basis ofPseudomonas outer membrane imperme ability. The current status ofPseudomonas porins (upto April 2003) involved in Pseudomonas, Volume 1, edited by Juan-Luis Ramos Kluwer Academic / Plenum Publishers, New York, 2004. 575 576 Sandeep Tamber and Robert E.W.Hancock uptake is also discussed. -
Molecular Mechanism of Ferricsiderophore Transport Via the Outer Membrane Receptor Fhua in Escherichia Coli
East Tennessee State University Digital Commons @ East Tennessee State University Electronic Theses and Dissertations Student Works 5-2009 Molecular Mechanism of Ferricsiderophore Transport via the Outer Membrane Receptor FhuA in Escherichia coli. Jennifer K. Cooke East Tennessee State University Follow this and additional works at: https://dc.etsu.edu/etd Part of the Bacteriology Commons Recommended Citation Cooke, Jennifer K., "Molecular Mechanism of Ferricsiderophore Transport via the Outer Membrane Receptor FhuA in Escherichia coli." (2009). Electronic Theses and Dissertations. Paper 1792. https://dc.etsu.edu/etd/1792 This Thesis - Open Access is brought to you for free and open access by the Student Works at Digital Commons @ East Tennessee State University. It has been accepted for inclusion in Electronic Theses and Dissertations by an authorized administrator of Digital Commons @ East Tennessee State University. For more information, please contact [email protected]. Molecular Mechanism of Ferricsiderophore Transport via the Outer Membrane Receptor FhuA in Escherichia coli _________________ A thesis presented to the faculty of the Department of Health Sciences East Tennessee State University ________________ In partial fulfillment of the requirements for the degree Master of Science in Biology Concentration in Microbiology ________________ by Jennifer K. Cooke May 2009 Ranjan Chakraborty, Committee Chair Bert Lampson, Committee Member Cecilia McIntosh, Committee Member Keywords: FhuA, Ferrichrome, Iron Transport ABSTRACT Molecular Mechanism of Ferricsiderophore Transport via the Outer Membrane Receptor FhuA in Escherichia coli by Jennifer K Cooke Iron is essential for life and growth in most organisms. Although it is abundant, iron exists mostly as insoluble iron-oxyhydroxide. Bacteria secrete siderophores to chelate iron and transport it into the cell via specific outer membrane receptors. -
Colicin Occlusion of Ompf and Tolc Channels: Outer Membrane Translocons for Colicin Import
Biophysical Journal Volume 87 December 2004 3901–3911 3901 Colicin Occlusion of OmpF and TolC Channels: Outer Membrane Translocons for Colicin Import Stanislav D. Zakharov,*y Veronika Y. Eroukova,z Tatyana I. Rokitskaya,z Mariya V. Zhalnina,* Onkar Sharma,* Patrick J. Loll,{ Helen I. Zgurskaya,§ Yuri N. Antonenko,z and William A. Cramer* *Department of Biological Sciences, Purdue University, West Lafayette, Indiana; yInstitute of Basic Biological Problems, Russian Academy of Sciences, Puschino, Russian Federation; zBelozersky Institute, Moscow State University, Moscow, Russian Federation; {Department of Biochemistry, Drexel University College of Medicine, Philadelphia, Pennsylvania; and §Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma ABSTRACT The interaction of colicins with target cells is a paradigm for protein import. To enter cells, bactericidal colicins parasitize Escherichia coli outer membrane receptors whose physiological purpose is the import of essential metabolites. Colicins E1 and E3 initially bind to the BtuB receptor, whose b-barrel pore is occluded by an N-terminal globular ‘‘plug’’. The x-ray structure of a complex of BtuB with the coiled-coil BtuB-binding domain of colicin E3 did not reveal displacement of the BtuB plug that would allow passage of the colicin (Kurisu, G., S. D. Zakharov, M. V. Zhalnina, S. Bano, V. Y. Eroukova, T. I. Rokitskaya, Y. N. Antonenko, M. C. Wiener, and W. A. Cramer. 2003. Nat. Struct. Biol. 10:948–954). This correlates with the inability of BtuB to form ion channels in planar bilayers, shown in this work, suggesting that an additional outer membrane protein(s) is required for colicin import across the outer membrane.