Two Component Regulatory Systems and Antibiotic Resistance in Gram-Negative Pathogens
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Decoupling Hamp from Tm2 in the Eschericha Coli
DECOUPLING HAMP FROM TM2 IN THE ESCHERICHA COLI ASPARTATE CHEMORECEPTOR A Senior Scholars Thesis by RACHEL LEANN CROWDER Submitted to the Office of Undergraduate Research Texas A&M University in partial fulfillment of the requirements for the designation as UNDERGRADUATE RESEARCH SCHOLAR April 2009 Major: Biology DECOUPLING HAMP FROM TM2 IN THE ESCHERICHA COLI ASPARTATE CHEMORECEPTOR A Senior Scholars Thesis by RACHEL LEANN CROWDER Submitted to the Office of Undergraduate Research Texas A&M University in partial fulfillment of the requirements for the designation as UNDERGRADUATE RESEARCH SCHOLAR Approved by: Research Advisor: Michael D. Manson Associate Dean for Undergraduate Research: Robert C. Webb April 2009 Major: Biology iii ABSTRACT Decoupling HAMP from TM2 in the Escherichia coli Aspartate Chemoreceptor. (April 2009) Rachel Leann Crowder Department of Biology Texas A&M University Research Advisor: Dr. Michael D. Manson Department of Biology The HAMP (often found in Histidine kinases, Adenylate cyclases, Methyl-accepting chemotaxis proteins, and Phosphatases) domain is a widely conserved motif often found in transmembrane signaling proteins in many prokaryotes and lower eukaryotes. It consists of a pair of two amphipathic helices connected by a flexible linker. Recently, the solution structure of the Archeoglobus fulgidis Af1503 HAMP domain was isolated and resolved using NMR. The Af1503 HAMP domain forms a stable four helix bundle with parallel helices that pack into a non-canonical knob-on-knob conformation. Several models have been proposed in methyl-accepting chemotaxis proteins (MCPs) to explain how the four-helix bundle transmits the downward piston movement of transmembrane 2 (TM2) into the signaling domain, inhibiting kinase activity. -
Structural Basis for C-Di-GMP-Mediated Inside- out Signaling Controlling Periplasmic Proteolysis
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Biblioteca Digital da Produção Intelectual da Universidade de São Paulo (BDPI/USP) Universidade de São Paulo Biblioteca Digital da Produção Intelectual - BDPI Departamento de Física e Ciência Interdisciplinar - IFSC/FCI Artigos e Materiais de Revistas Científicas - IFSC/FCI 2011-02 Structural basis for c-di-GMP-mediated inside- out signaling controlling periplasmic proteolysis PLoS Biology, San Francisco : Public Library Science, v. 9, n. 2, p. e1000588-1-e1000588-21, Feb. 2011 http://www.producao.usp.br/handle/BDPI/50077 Downloaded from: Biblioteca Digital da Produção Intelectual - BDPI, Universidade de São Paulo Structural Basis for c-di-GMP-Mediated Inside-Out Signaling Controlling Periplasmic Proteolysis Marcos V. A. S. Navarro1.¤, Peter D. Newell2., Petya V. Krasteva1., Debashree Chatterjee1., Dean R. Madden3, George A. O’Toole2, Holger Sondermann1* 1 Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America, 2 Department of Microbiology and Immunology, Dartmouth Medical School, Hanover, New Hampshire, United States of America, 3 Department of Biochemistry, Dartmouth Medical School, Hanover, New Hampshire, United States of America Abstract The bacterial second messenger bis-(39–59) cyclic dimeric guanosine monophosphate (c-di-GMP) has emerged as a central regulator for biofilm formation. Increased cellular c-di-GMP levels lead to stable cell attachment, which in Pseudomonas fluorescens requires the transmembrane receptor LapD. LapD exhibits a conserved and widely used modular architecture containing a HAMP domain and degenerate diguanylate cyclase and phosphodiesterase domains. c-di-GMP binding to the LapD degenerate phosphodiesterase domain is communicated via the HAMP relay to the periplasmic domain, triggering sequestration of the protease LapG, thus preventing cleavage of the surface adhesin LapA. -
Genome-Wide Identification, Classification, and Analysis of Two-Component Signal System Genes in Maize
Genome-wide identification, classification, and analysis of two-component signal system genes in maize Z.X. Chu*, Q. Ma*, Y.X. Lin, X.L. Tang, Y.Q. Zhou, S.W. Zhu, J. Fan and B.J. Cheng Anhui Province Key Laboratory of Crop Biology, School of Life Science, Anhui Agricultural University, Hefei, China *These authors contributed equally to this study. Corresponding authors: B.J. Cheng / J. Fan E-mail: [email protected] / [email protected] Genet. Mol. Res. 10 (4): 3316-3330 (2011) Received March 23, 2011 Accepted August 31, 2011 Published December 8, 2011 DOI http://dx.doi.org/10.4238/2011.December.8.3 ABSTRACT. Cytokinins play many vital roles in plant development and physiology. In plants, cytokinin signals are sensed and transduced by the two-component signal system. This signaling cascade is typically com- posed of three proteins: a sensory histidine kinase, a histidine phosphotrans- fer protein, and a response regulator. Through a comprehensive genome- wide analysis of the maize (Zea mays) genome, 48 genes were identified, including 11 ZmHKs, 9 ZmHPs, and 28 ZmRRs (21 A-type ZmRRs and 7 B-type ZmRRs). Using maize genome sequence databases, we analyzed conserved protein motifs and established phylogenetic relationships based on gene structure, homology, and chromosomal location. The duplication of these two-component system genes in the maize genome corresponded to the clusters of these genes in the phylogenetic trees. Sequence analysis of the duplicate genes demonstrated that one gene may be in gene duplica- tion, and that there was significant variation in the evolutionary history of the different gene families. -
Structure and Function of the Archaeal Response Regulator Chey
Structure and function of the archaeal response PNAS PLUS regulator CheY Tessa E. F. Quaxa, Florian Altegoerb, Fernando Rossia, Zhengqun Lia, Marta Rodriguez-Francoc, Florian Krausd, Gert Bangeb,1, and Sonja-Verena Albersa,1 aMolecular Biology of Archaea, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany; bLandes-Offensive zur Entwicklung Wissenschaftlich- ökonomischer Exzellenz Center for Synthetic Microbiology & Faculty of Chemistry, Philipps-University-Marburg, 35043 Marburg, Germany; cCell Biology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany; and dFaculty of Chemistry, Philipps-University-Marburg, 35043 Marburg, Germany Edited by Norman R. Pace, University of Colorado at Boulder, Boulder, CO, and approved December 13, 2017 (received for review October 2, 2017) Motility is a central feature of many microorganisms and provides display different swimming mechanisms. Counterclockwise ro- an efficient strategy to respond to environmental changes. Bacteria tation results in smooth swimming in well-characterized peritri- and archaea have developed fundamentally different rotary motors chously flagellated bacteria such as Escherichia coli, whereas enabling their motility, termed flagellum and archaellum, respec- rotation in the opposite direction results in tumbling. In contrast, tively. Bacterial motility along chemical gradients, called chemo- in other bacteria (i.e., Vibrio alginolyticus) and haloarchaea, taxis, critically relies on the response regulator CheY, which, when clockwise rotation results -
Crosstalk and the Evolution of Specificity in Two-Component Signaling
Corrections BIOPHYSICS AND COMPUTATIONAL BIOLOGY PLANT BIOLOGY Correction for “Crosstalk and the evolution of specificity in two- Correction for “Differential processing of Arabidopsis ubiquitin- component signaling,” by Michael A. Rowland and Eric J. Deeds, like Atg8 autophagy proteins by Atg4 cysteine proteases,” by which appeared in issue 15, April 15, 2014, of Proc Natl Acad Sci Jongchan Woo, Eunsook Park, and S. P. Dinesh-Kumar, which USA (111:5550–5555; first published March 31, 2014; 10.1073/ appeared in issue 2, January 14, 2014, of Proc Natl Acad Sci pnas.1317178111). USA (111:863–868; first published December 30, 2013; 10.1073/ The authors note that ref. 4, “Huynh TN, Stewart V (2011) pnas.1318207111). Negative control in two-component signal transduction by trans- The authors note that the following statement should be mitter phosphatase activity. Mol Microbiol 82(2):275–286.” should added to the Acknowledgments: “National Science Foundation instead appear as “Ray JC, Igoshin OA (2010) Adaptable func- Grant NSF-IOS-1258135 funded to Dr. Georgia Drakakaki sup- tionality of transcriptional feedback in bacterial two-component ported Eunsook Park.” systems. PLoS Comput Biol 6(2):e1000676.” www.pnas.org/cgi/doi/10.1073/pnas.1409947111 www.pnas.org/cgi/doi/10.1073/pnas.1408294111 CORRECTIONS www.pnas.org PNAS | June 24, 2014 | vol. 111 | no. 25 | 9325 Downloaded by guest on September 29, 2021 Crosstalk and the evolution of specificity in two-component signaling Michael A. Rowlanda and Eric J. Deedsa,b,1 aCenter for Bioinformatics and bDepartment of Molecular Biosciences, University of Kansas, Lawrence, KS 66047 Edited by Thomas J. -
Response Regulators Implicated in His-To-Asp Phosphotransfer Signaling in Arabidopsis (Escherichia Coli)
Proc. Natl. Acad. Sci. USA Vol. 95, pp. 2691–2696, March 1998 Plant Biology Response regulators implicated in His-to-Asp phosphotransfer signaling in Arabidopsis (Escherichia coli) AYA IMAMURA,NAOTO HANAKI,HIROYUKI UMEDA,AYAKO NAKAMURA,TOMOMI SUZUKI,CHIHARU UEGUCHI, AND TAKESHI MIZUNO† Laboratory of Molecular Microbiology, School of Agriculture, Nagoya University, Chikusa-ku, Nagoya 464, Japan Communicated by Robert Haselkorn, University of Chicago, Chicago, IL, December 29, 1997 (received for review November 7, 1997) ABSTRACT The His to Asp phosphotransfer signal as a mediator of phosphotransfer by acquiringytransferring a transduction mechanism involves three common signaling phosphoryl group fromyto another component (8–12). domains: the transmitter (or His-kinase), the receiver, and the Instances of His-Asp phosphotransfer systems have been histidine-containing phototransfer (HPt) domain. Typically, a found in a large number of bacterial species (3). Inspection of sensor kinase has a His-kinase domain and a response the nucleotide sequence of Escherichia coli reveals at least regulator has a receiver domain containing a phosphoaccept- thirty different sensor-regulator pairs in this single species ing aspartate, whereas a histidine-containing phototransfer (13). This mechanism was once thought to be restricted to domain serves as a mediator of the histidine-to-aspartate prokaryotes. However, many instances have been discovered phosphotransfer. This signal transduction mechanism was in diverse eukaryotic species including higher plants (14–23). thought to be restricted to prokaryotes. However, many ex- The most striking example is the yeast osmo-responsive system amples have been discovered in diverse eukaryotic species (23). Three components, Sln1p (sensor kinase)-Ypd1p (HPt including higher plants. -
Subcellular Localization in Bacteria: from Envz/Ompr to Transertion
University of Pennsylvania ScholarlyCommons Publicly Accessible Penn Dissertations Summer 2011 Subcellular Localization in Bacteria: From EnvZ/OmpR to Transertion Elizabeth Libby University of Pennsylvania, [email protected] Follow this and additional works at: https://repository.upenn.edu/edissertations Part of the Biological and Chemical Physics Commons, and the Microbiology Commons Recommended Citation Libby, Elizabeth, "Subcellular Localization in Bacteria: From EnvZ/OmpR to Transertion" (2011). Publicly Accessible Penn Dissertations. 974. https://repository.upenn.edu/edissertations/974 This paper is posted at ScholarlyCommons. https://repository.upenn.edu/edissertations/974 For more information, please contact [email protected]. Subcellular Localization in Bacteria: From EnvZ/OmpR to Transertion Abstract The internal structures of the bacterial cell and the associated dynamic changes as a function of physiological state have only recently begun to be characterized. Here we explore two aspects of subcellular localization in E. coli cells: the cytoplasmic distribution of the response regulator OmpR and its regulated chromosomal genes, and the subcellular repositioning of chromosomal loci encoding membrane proteins upon induction. To address these questions by quantitative fluorescence microscopy, we developed a simple system to tag virtually any chromosomal location with arrays of lacO or tetO by extending and modifying existing tools. An unexplained subcellular localization was reported for a functional fluorescent protein fusion to the response regulator OmpR in Escherichia coli. The pronounced regions of increased fluorescence, or foci, are dependent on OmpR phosphorylation, and do not occupy fixed, easily identifiable positions, such as the poles or midcell. Here we show that the foci are due to OmpR-YFP binding specific sites in the chromosome. -
Making Informed Decisions: Regulatory Interactions Between Two-Component Systems
Review TRENDS in Microbiology Vol.11 No.8 August 2003 359 Making informed decisions: regulatory interactions between two-component systems Jetta J.E. Bijlsma and Eduardo A. Groisman Department of Molecular Microbiology, Howard Hughes Medical Institute, Washington University School of Medicine, Campus Box 8230, 660 S. Euclid Avenue, St Louis, MO 63110, USA Bacteria experience a multitude of stresses in the com- phosphorylate from small molecular weight phosphoryl plex niches they inhabit. These stresses are denoted by donors, such as acetyl phosphate and carbamoyl phos- specific signals that typically alter the activity of individ- phate [3,4]. In addition, the vast majority of sensor kinases ual two-component regulatory systems. Processing of exhibit phosphatase activity towards their cognate multiple signals by different two-component systems response regulators. Although most two-component sys- occurs when multiple sensors interact with a single tems entail a single His-to-Asp phosphotransfer event response regulator, by phosphatases interrupting phos- between a histidine kinase and a response regulator, there phoryl transfer in phosphorelays and through transcrip- is a subset that consists of a three-step His-Asp-His-Asp tional and post-transcriptional mechanisms. Gaining phosphorelay (Fig. 1b) [1,2]. The extra phosphorylatable insight into these mechanisms provides an understand- domains in a phosphorelay can be present in separate ing at the molecular level of bacterial adaptation to ever proteins or be part of multi-domain (i.e. -
Mutations Affecting HVO 1357 Or HVO 2248 Cause Hypermotility in Haloferax Volcanii, Suggesting Roles in Motility Regulation
G C A T T A C G G C A T genes Article Mutations Affecting HVO_1357 or HVO_2248 Cause Hypermotility in Haloferax volcanii, Suggesting Roles in Motility Regulation Michiyah Collins 1 , Simisola Afolayan 1, Aime B. Igiraneza 1, Heather Schiller 1 , Elise Krespan 2, Daniel P. Beiting 2, Mike Dyall-Smith 3,4 , Friedhelm Pfeiffer 4 and Mechthild Pohlschroder 1,* 1 Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA; [email protected] (M.C.); [email protected] (S.A.); [email protected] (A.B.I.); [email protected] (H.S.) 2 Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; [email protected] (E.K.); [email protected] (D.P.B.) 3 Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville 3010, Australia; [email protected] 4 Computational Biology Group, Max-Planck-Institute of Biochemistry, 82152 Martinsried, Germany; [email protected] * Correspondence: [email protected]; Tel.: +1-215-573-2283 Abstract: Motility regulation plays a key role in prokaryotic responses to environmental stimuli. Here, we used a motility screen and selection to isolate hypermotile Haloferax volcanii mutants from a transposon insertion library. Whole genome sequencing revealed that hypermotile mutants were predominantly affected in two genes that encode HVO_1357 and HVO_2248. Alterations of these genes comprised not only transposon insertions but also secondary genome alterations. HVO_1357 Citation: Collins, M.; Afolayan, S.; Igiraneza, A.B.; Schiller, H.; contains a domain that was previously identified in the regulation of bacteriorhodopsin transcription, Krespan, E.; Beiting, D.P.; as well as other domains frequently found in two-component regulatory systems. -
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View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Structure Article Structure and Proposed Mechanism for the pH-Sensing Helicobacter pylori Chemoreceptor TlpB Emily Goers Sweeney,1 J. Nathan Henderson,1,5 John Goers,4 Christopher Wreden,1 Kevin G. Hicks,1,6 Jeneva K. Foster,1 Raghuveer Parthasarathy,1,2,3 S. James Remington,1,3 and Karen Guillemin1,* 1Institute of Molecular Biology 2Materials Science Institute 3Department of Physics University of Oregon, Eugene, OR 97403, USA 4Department of Chemistry, California Polytechnic State University, San Luis Obispo, CA 93407, USA 5Present address: Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA 6Present address: Department of Microbiology, University of Washington, Seattle, WA 98195, USA *Correspondence: [email protected] DOI 10.1016/j.str.2012.04.021 SUMMARY Candidate molecular moieties for pH sensing by a protein receptor include titratable side chains such as aspartate, gluta- pH sensing is crucial for survival of most organisms, mate, and histidine that have pKa values near neutrality. The yet the molecular basis of such sensing is poorly pKa for a sensor can be tuned over a wide range by the imme- understood. Here, we present an atomic resolution diate environment of the protonatable residue. Protonation of structure of the periplasmic portion of the acid- critical residues is generally thought to lead to conformational sensing chemoreceptor, TlpB, from the gastric path- changes that confer signaling states. Examples of bacterial pH ogen Helicobacter pylori. The structure reveals sensors relevant to our studies include the histidine kinase HP165 (ArsS) of H. -
Biological Circuits with Small RNA Switches
Downloaded from genesdev.cshlp.org on September 24, 2021 - Published by Cold Spring Harbor Laboratory Press REVIEW Stealth regulation: biological circuits with small RNA switches Susan Gottesman Laboratory of Molecular Biology, National Cancer Institute, Bethesda, Maryland 20892, USA So you thinkyou finally understand the regulation of temporal RNAs (stRNAs) or microRNAs, and that these your favorite gene? The transcriptional regulators have RNAs are processed by some of the same protein cofac- been identified; the signaling cascades that regulate syn- tors as is RNAi, have put regulatory RNAs in the spot- thesis and activity of the regulators have been found. light in eukaryotes as well. Recent searches have con- Possibly you have found that the regulator is itself un- firmed that flies, worms, plants, and humans all harbor stable, and that instability is necessary for proper regu- significant numbers of small RNAs likely to play regu- lation. Time to lookfor a new project, or retire and rest latory roles. on your laurels? Not so fast—there’s more. It is rapidly Along with the rapid expansion in RNAs doing inter- becoming apparent that another whole level of regula- esting things, has come a proliferation of nomenclature. tion lurks, unsuspected, in both prokaryotic and eukary- Noncoding RNAs (ncRNA) has been used recently, as otic cells, hidden from our notice in part by the tran- the most general term (Storz 2002). Among the noncod- scription-based approaches that we usually use to study ing RNAs, the subclass of relatively small RNAs that gene regulation, and in part because these regulators are frequently act as regulators have been called stRNAs very small targets for mutagenesis and are not easily (small temporal RNAs, eukaryotes) and sRNAs (small found from genome sequences alone. -
Fur Is the Master Regulator of the Extraintestinal Pathogenic
Downloaded from RESEARCH ARTICLE crossmark Fur Is the Master Regulator of the Extraintestinal Pathogenic mbio.asm.org Escherichia coli Response to Serum on August 3, 2015 - Published by Sagi Huja,a Yaara Oren,a Dvora Biran,a Susann Meyer,b Ulrich Dobrindt,c Joerg Bernhard,b Doerte Becher,b Michael Hecker,b Rotem Sorek,d Eliora Z. Rona,e Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israela; Institute for Microbiology, Ernst-Moritz-Arndt-Universität, Greifswald, Germanyb; Institute of Hygiene, Westfälische Wilhelms-Universität, Münster, Germanyc; Department of Molecular Genetics Weizmann Institute of Science, Rehovot, Israeld; MIGAL, Galilee Research Center, Kiriat Shmona, Israele ABSTRACT Drug-resistant extraintestinal pathogenic Escherichia coli (ExPEC) strains are the major cause of colisepticemia (coli- bacillosis), a condition that has become an increasing public health problem in recent years. ExPEC strains are characterized by high resistance to serum, which is otherwise highly toxic to most bacteria. To understand how these bacteria survive and grow in serum, we performed system-wide analyses of their response to serum, making a clear distinction between the responses to nu- tritional immunity and innate immunity. Thus, mild heat inactivation of serum destroys the immune complement and abolishes mbio.asm.org the bactericidal effect of serum (inactive serum), making it possible to examine nutritional immunity. We used a combination of deep RNA sequencing and proteomics in order to characterize ExPEC genes whose expression is affected by the nutritional stress of serum and by the immune complement. The major change in gene expression induced by serum—active and inactive—in- volved metabolic genes.