Stationary Phase in Gramnegative Bacteria
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Interplay Between Ompa and Rpon Regulates Flagellar Synthesis in Stenotrophomonas Maltophilia
microorganisms Article Interplay between OmpA and RpoN Regulates Flagellar Synthesis in Stenotrophomonas maltophilia Chun-Hsing Liao 1,2,†, Chia-Lun Chang 3,†, Hsin-Hui Huang 3, Yi-Tsung Lin 2,4, Li-Hua Li 5,6 and Tsuey-Ching Yang 3,* 1 Division of Infectious Disease, Far Eastern Memorial Hospital, New Taipei City 220, Taiwan; [email protected] 2 Department of Medicine, National Yang Ming Chiao Tung University, Taipei 112, Taiwan; [email protected] 3 Department of Biotechnology and Laboratory Science in Medicine, National Yang Ming Chiao Tung University, Taipei 112, Taiwan; [email protected] (C.-L.C.); [email protected] (H.-H.H.) 4 Division of Infectious Diseases, Department of Medicine, Taipei Veterans General Hospital, Taipei 112, Taiwan 5 Department of Pathology and Laboratory Medicine, Taipei Veterans General Hosiptal, Taipei 112, Taiwan; [email protected] 6 Ph.D. Program in Medical Biotechnology, Taipei Medical University, Taipei 110, Taiwan * Correspondence: [email protected] † Liao, C.-H. and Chang, C.-L. contributed equally to this work. Abstract: OmpA, which encodes outer membrane protein A (OmpA), is the most abundant transcript in Stenotrophomonas maltophilia based on transcriptome analyses. The functions of OmpA, including adhesion, biofilm formation, drug resistance, and immune response targets, have been reported in some microorganisms, but few functions are known in S. maltophilia. This study aimed to elucidate the relationship between OmpA and swimming motility in S. maltophilia. KJDOmpA, an ompA mutant, Citation: Liao, C.-H.; Chang, C.-L.; displayed compromised swimming and failure of conjugation-mediated plasmid transportation. The Huang, H.-H.; Lin, Y.-T.; Li, L.-H.; hierarchical organization of flagella synthesis genes in S. -
Subunit of RNA Polymerase and the Transcriptional Regulators Rsd from Escherichia Coli and Algq from Pseudomonas Aeruginosa
Bacterial two-hybrid analysis of interactions between region 4 of the sigma(70) subunit of RNA polymerase and the transcriptional regulators Rsd from Escherichia coli and AlgQ from Pseudomonas aeruginosa. The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Dove, S. L., and A. Hochschild. 2001. “Bacterial Two-Hybrid Analysis of Interactions between Region 4 of the 70 Subunit of RNA Polymerase and the Transcriptional Regulators Rsd from Escherichia Coli and AlgQ from Pseudomonas Aeruginosa.” Journal of Bacteriology 183 (21): 6413–21. https://doi.org/10.1128/ jb.183.21.6413-6421.2001. Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:41483172 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Other Posted Material, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#LAA JOURNAL OF BACTERIOLOGY, Nov. 2001, p. 6413–6421 Vol. 183, No. 21 0021-9193/01/$04.00ϩ0 DOI: 10.1128/JB.183.21.6413–6421.2001 Copyright © 2001, American Society for Microbiology. All Rights Reserved. Bacterial Two-Hybrid Analysis of Interactions between Region 4 of the 70 Subunit of RNA Polymerase and the Transcriptional Regulators Rsd from Escherichia coli and AlgQ from Pseudomonas aeruginosa SIMON L. DOVE AND ANN HOCHSCHILD* Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, Massachusetts 02115 Received 3 May 2001/Accepted 6 August 2001 A number of transcriptional regulators mediate their effects through direct contact with the 70 subunit of Escherichia coli RNA polymerase (RNAP). -
Chapter 3. the Beginnings of Genomic Biology – Molecular
Chapter 3. The Beginnings of Genomic Biology – Molecular Genetics Contents 3. The beginnings of Genomic Biology – molecular genetics 3.1. DNA is the Genetic Material 3.6.5. Translation initiation, elongation, and termnation 3.2. Watson & Crick – The structure of DNA 3.6.6. Protein Sorting in Eukaryotes 3.3. Chromosome structure 3.7. Regulation of Eukaryotic Gene Expression 3.3.1. Prokaryotic chromosome structure 3.7.1. Transcriptional Control 3.3.2. Eukaryotic chromosome structure 3.7.2. Pre-mRNA Processing Control 3.3.3. Heterochromatin & Euchromatin 3.4. DNA Replication 3.7.3. mRNA Transport from the Nucleus 3.4.1. DNA replication is semiconservative 3.7.4. Translational Control 3.4.2. DNA polymerases 3.7.5. Protein Processing Control 3.4.3. Initiation of replication 3.7.6. Degradation of mRNA Control 3.4.4. DNA replication is semidiscontinuous 3.7.7. Protein Degradation Control 3.4.5. DNA replication in Eukaryotes. 3.8. Signaling and Signal Transduction 3.4.6. Replicating ends of chromosomes 3.8.1. Types of Cellular Signals 3.5. Transcription 3.8.2. Signal Recognition – Sensing the Environment 3.5.1. Cellular RNAs are transcribed from DNA 3.8.3. Signal transduction – Responding to the Environment 3.5.2. RNA polymerases catalyze transcription 3.5.3. Transcription in Prokaryotes 3.5.4. Transcription in Prokaryotes - Polycistronic mRNAs are produced from operons 3.5.5. Beyond Operons – Modification of expression in Prokaryotes 3.5.6. Transcriptions in Eukaryotes 3.5.7. Processing primary transcripts into mature mRNA 3.6. Translation 3.6.1. -
Mechanism to Control the Cell Lysis and the Cell Survival Strategy in Stationary Phase Under Heat Stress Rashed Noor*
Noor SpringerPlus (2015) 4:599 DOI 10.1186/s40064-015-1415-7 REVIEW Open Access Mechanism to control the cell lysis and the cell survival strategy in stationary phase under heat stress Rashed Noor* Abstract An array of stress signals triggering the bacterial cellular stress response is well known in Escherichia coli and other bacteria. Heat stress is usually sensed through the misfolded outer membrane porin (OMP) precursors in the peri- plasm, resulting in the activation of σE (encoded by rpoE), which binds to RNA polymerase to start the transcription of genes required for responding against the heat stress signal. At the elevated temperatures, σE also serves as the transcription factor for σH (the main heat shock sigma factor, encoded by rpoH), which is involved in the expression of several genes whose products deal with the cytoplasmic unfolded proteins. Besides, oxidative stress in form of the reactive oxygen species (ROS) that accumulate due to heat stress, has been found to give rise to viable but non- culturable (VBNC) cells at the early stationary phase, which is in turn lysed by the σE-dependent process. Such lysis of the defective cells may generate nutrients for the remaining population to survive with the capacity of formation of colony forming units (CFUs). σH is also known to regulate the transcription of the major heat shock proteins (HSPs) required for heat shock response (HSR) resulting in cellular survival. Present review concentrated on the cellular sur- vival against heat stress employing the harmonized impact of σE and σH regulons and the HSPs as well as their inter connectivity towards the maintenance of cellular survival. -
Identification of Small Regulatory Rnas and Their Targets in Bacteria
Identification of Small Regulatory RNAs and Their Targets in Bacteria Dissertation zur Erlangung des akademischen Grades eines Doktors der Naturwissenschaften (Dr. rer. nat.) der Technischen Fakultat¨ der Universitat¨ Bielefeld vorgelegt von Cynthia Mira Sharma Bielefeld, im Mai 2009 Dissertation zur Erlangung des akademischen Grades eines Doktors der Naturwissenschaften (Dr. rer. nat.) der Technischen Fakultat¨ der Universitat¨ Bielefeld. Vorgelegt von: Dipl.-Biol. Cynthia Mira Sharma Angefertigt im: Max-Planck-Institut fur¨ Infektionsbiologie, Berlin Tag der Einreichung: 04. Mai 2009 Tag der Verteidigung: 22. Juli 2009 Gutachter: Prof. Dr. Robert Giegerich, Universitat¨ Bielefeld Dr. Jorg¨ Vogel, Max-Planck-Institut fur¨ Infektionsbiologie, Berlin Prof. Dr. Wolfgang Hess, Universitat¨ Freiburg Prufungsausschuss:¨ Prof. Dr. Jens Stoye, Universitat¨ Bielefeld Prof. Dr. Robert Giegerich, Universitat¨ Bielefeld Dr. Jorg¨ Vogel, Max-Planck-Institut fur¨ Infektionsbiologie, Berlin Prof. Dr. Wolfgang Hess, Universitat¨ Freiburg Dr. Marilia Braga, Universitat¨ Bielefeld Gedruckt auf alterungsbestandigem¨ Papier nach ISO 9706. Dedicated to my parents, Ingrid Sharma and Som Deo Sharma ACKNOWLEDGEMENTS At this point, I would like to thank everybody who contributed in whatever form to this thesis. In particular, I am grateful to the following persons: . my supervisor Dr. Jorg¨ Vogel for giving me the opportunity to work in a superb scientific environment and for his continuous support and guidance throughout the past several years, . Prof. Dr. Robert Giegerich for enabling me to submit this thesis to the University of Bielefeld and for valuable suggestions during several visits to his institute, . Prof. Dr. Wolfgang Hess for his willingness to evaluate this thesis, . Dr. Fabien Darfeuille (a. k. a. the “master of the gels”) for a great stay in his lab in Bordeaux and many fruitful discussions, . -
Identification and Characterization of Molecular Targets for Disease Management in Tree Fruit Pathogens
IDENTIFICATION AND CHARACTERIZATION OF MOLECULAR TARGETS FOR DISEASE MANAGEMENT IN TREE FRUIT PATHOGENS By Jingyu Peng A DISSERTATION Submitted to Michigan State University in partial fulfillment of the requirements for the degree of Plant Pathology – Doctor of Philosophy 2020 ABSTRACT IDENTIFICATION AND CHARACTERIZATION OF MOLECULAR TARGETS FOR DISEASE MANAGEMENT IN TREE FRUIT PATHOGENS By Jingyu Peng Fire blight, caused by Erwinia amylovora, is a devastating bacterial disease threatening the worldwide production of pome fruit trees, including apple and pear. Within host xylem vessels, E. amylovora cells restrict water flow and cause wilting symptoms through formation of biofilms, that are matrix-enmeshed surface-attached microcolonies of bacterial cells. Biofilm matrix of E. amylovora is primarily composed of several exopolysaccharides (EPSs), including amylovora, levan, and, cellulose. The final step of biofilm development is dispersal, which allows dissemination of a subpopulation of biofilm cells to resume the planktonic mode of growth and consequentially cause systemic infection. In this work, we demonstrate that identified the Hfq-dependent small RNA (sRNA) RprA positively regulates amylovoran production, T3SS, and flagellar-dependent motility, and negatively affects levansucrase activity and cellulose production. We also identified the in vitro and in vivo conditions that activate RprA, and demonstrated that RprA activation leads to decreased formation of biofilms and promotes the dispersal movement of biofilm cells. This work supports the involvement of RprA in the systemic infection of E. amylovora during its pathogenesis. Bacterial toxin-antitoxin (TA) systems are small genetic loci composed of a proteinaceous toxin and a counteracting antitoxin. In this work, we identified and characterized a chromosomally encoded hok/sok-like type I TA system in Erwinia amylovora Ea1189. -
Transcriptional Occlusion Caused by Overlapping Promoters
Transcriptional occlusion caused by overlapping promoters M. Ammar Zafara,1, Valerie J. Carabettab,1, Mark J. Mandelc, and Thomas J. Silhavya,2 aDepartment of Molecular Biology, Princeton University, Princeton, NJ 08544; bPublic Health Research Institute at New Jersey Medical School, Rutgers University, Newark, NJ 07103; and cDepartment of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 Contributed by Thomas J. Silhavy, December 17, 2013 (sent for review November 6, 2013) RpoS (σ38) is required for cell survival under stress conditions, but has as its basis two overlapping promoters and a long noncoding it can inhibit growth if produced inappropriately and, consequently, RNA (lncRNA). Expression of the shorter transcript blocks ex- its production and activity are elaborately regulated. Crl, a transcrip- pression of the longer, but the former cannot be translated be- tional activator that does not bind DNA, enhances RpoS activity by cause it lacks a ribosome-binding site (rbs). This simple, but stimulating the interaction between RpoS and the core polymerase. economical, mechanism allows a near instantaneous reduction crl The gene has two overlapping promoters, a housekeeping, RpoD- in Crl synthesis without the need to produce any transacting σ70 σ54 ( ) dependent promoter, and an RpoN ( )promoterthatis regulatory factor. strongly up-regulated under nitrogen limitation. However, transcrip- tion from the RpoN promoter prevents transcription from the RpoD Results promoter, and the RpoN-dependent transcript lacks a ribosome- The Role of Crl Under Nitrogen-Stress Conditions. In rapidly growing binding site. Thus, activation of the RpoN promoter produces cells, RpoS is made but it is directed by the adaptor protein SprE a long noncoding RNA that silences crl gene expression simply by being made. -
Dynamic Insights on Transcription Initiation and RNA Processing During Bacterial Adaptation
Downloaded from rnajournal.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press REPORT Dynamic insights on transcription initiation and RNA processing during bacterial adaptation CAROLINE LACOUX,1,7 AYMERIC FOUQUIER D’HÉROUËL,2 FRANÇOISE WESSNER-LE BOHEC,1 NICOLAS INNOCENTI,1,3,8 CHANTAL BOHN,4 SEAN P. KENNEDY,5 TATIANA ROCHAT,6 RÉMY A. BONNIN,4,9 PASCALE SERROR,1 ERIK AURELL,3 PHILIPPE BOULOC,4 and FRANCIS REPOILA1 1Université Paris-Saclay, INRAE, AgroParisTech, MIcalis Institute, 78350, Jouy-en-Josas, France 2Luxembourg Center for Systems Biomedicine, University of Luxembourg, 4367, Belvaux, Luxembourg 3Department of Computational Biology, Royal Institute of Technology, AlbaNova University Center, SE-10691 Stockholm, Sweden 4Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France 5Department of Computational Biology, USR3756 CNRS, Institut Pasteur, 75 015 Paris, France 6VIM, INRA, Université Paris-Saclay, 78350 Jouy-en-Josas, France ABSTRACT Transcription initiation and RNA processing govern gene expression and enable bacterial adaptation by reshaping the RNA landscape. The aim of this study was to simultaneously observe these two fundamental processes in a transcriptome responding to an environmental signal. A controlled σE system in E. coli was coupled to our previously described tagRNA- seq method to yield process kinetics information. Changes in transcription initiation frequencies (TIF) and RNA processing frequencies (PF) were followed using 5′′′′′ RNA tags. Changes in TIF showed a binary increased/decreased pattern that alter- nated between transcriptionally activated and repressed promoters, providing the bacterial population with transcription- al oscillation. PF variation fell into three categories of cleavage activity: (i) constant and independent of RNA levels, (ii) increased once RNA has accumulated, and (iii) positively correlated to changes in TIF. -
The Whole Set of the Constitutive Promoters Recognized by Four Minor Sigma Subunits of Escherichia Coli RNA Polymerase
RESEARCH ARTICLE The whole set of the constitutive promoters recognized by four minor sigma subunits of Escherichia coli RNA polymerase Tomohiro Shimada1,2¤, Kan Tanaka2, Akira Ishihama1* 1 Research Center for Micro-Nano Technology, Hosei University, Koganei, Tokyo, Japan, 2 Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Nagatsuda, Yokohama, Japan a1111111111 ¤ Current address: School of Agriculture, Meiji University, Kawasaki, Kanagawa, Japan a1111111111 * [email protected] a1111111111 a1111111111 a1111111111 Abstract The promoter selectivity of Escherichia coli RNA polymerase (RNAP) is determined by the sigma subunit. The model prokaryote Escherichia coli K-12 contains seven species of the OPEN ACCESS sigma subunit, each recognizing a specific set of promoters. For identification of the ªconsti- Citation: Shimada T, Tanaka K, Ishihama A (2017) tutive promotersº that are recognized by each RNAP holoenzyme alone in the absence of The whole set of the constitutive promoters other supporting factors, we have performed the genomic SELEX screening in vitro for their recognized by four minor sigma subunits of binding sites along the E. coli K-12 W3110 genome using each of the reconstituted RNAP Escherichia coli RNA polymerase. PLoS ONE 12(6): holoenzymes and a collection of genome DNA segments of E. coli K-12. The whole set of e0179181. https://doi.org/10.1371/journal. pone.0179181 constitutive promoters for each RNAP holoenzyme was then estimated based on the loca- tion of RNAP-binding sites. The first successful screening of the constitutive promoters was Editor: Dipankar Chatterji, Indian Institute of 70 Science, INDIA achieved for RpoD (σ ), the principal sigma for transcription of growth-related genes. -
Characterization of Novel Binding Sites and Regulatory
CHARACTERIZATION OF NOVEL BINDING SITES AND REGULATORY ACTIVITIES FOR THE TRANSCRIPTION SIGMA FACTOR, RpoN, IN SALMONELLA by ASHLEY CHRISTINE BONO (Under the Direction of ANNA KARLS) ABSTRACT During bacterial transcription, core RNA polymerase (ααββ’ω) transiently interacts with a σ factor to identify a promoter and then isomerizes into transcriptionally active open complex. Sigma54 (σ54 or RpoN) is the lone member of an alternative sigma factor family that is highly conserved across diverse bacterial species. Sigma54-RNA polymerase holoenzyme (Eσ54) is unique among bacterial holoenzymes, and similar to Pol II of eukaryotes, in its requirement for physical interaction with a protein activator and hydrolysis of ATP for isomerization into open complex. The focus of the original research presented in this dissertation is to define the global σ54 regulon in the model organism Salmonella enterica subspecies enterica serovar Typhimurium 14028s, and characterize the regulatory roles of σ54-dependent promoters and σ54 binding sites. Earlier work suggested that S. Typhimurium has a robust σ54-dependent regulon of diverse genes regulated by at least 13 bacterial enhancer binding proteins (bEBPs) that are each responsive to different environmental signals. To promote open complex formation by Eσ54 and stimulate expression of all σ54- dependent genes, a previously vetted, constitutively-active, promiscuous bEBP, DctD250 was expressed in wild-type and ΔrpoN strains. Transcriptome profiling and identification of σ54 DNA binding sites from immunoprecipitated σ54-chromosomal DNA (ChIP) were performed on tiling microarrays (chip). Three novel σ54-dependent transcripts, in addition to the previously predicted/known σ54-dependent transcripts, and 184 σ54 intergenic and intragenic DNA binding sites were defined. -
Escherichia Coli As a Host for Metabolic Engineering
Metabolic Engineering xxx (xxxx) xxx–xxx Contents lists available at ScienceDirect Metabolic Engineering journal homepage: www.elsevier.com/locate/meteng Escherichia coli as a host for metabolic engineering Sammy Pontrellia, Tsan-Yu Chiub, Ethan I. Lanc, Frederic Y.-H. Chena,b, Peiching Changd,e, ⁎ James C. Liaob, a Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, USA b Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan c Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan d Department of Chemical Engineering, National Tsing Hua University, Hsinchu, Taiwan e Material and Chemical Research Laboratories, Industrial Technology Research Institute, Hsinchu, Taiwan ABSTRACT Over the past century, Escherichia coli has become one of the best studied organisms on earth. Features such as genetic tractability, favorable growth conditions, well characterized biochemistry and physiology, and avail- ability of versatile genetic manipulation tools make E. coli an ideal platform host for development of industrially viable productions. In this review, we discuss the physiological attributes of E. coli that are most relevant for metabolic engineering, as well as emerging techniques that enable efficient phenotype construction. Further, we summarize the large number of native and non-native products that have been synthesized by E. coli, and address some of the future challenges in broadening substrate range and fighting phage infection. 1. Introduction acids which has traditionally been produced from the natural producer Corynebacterium glutamicum (Gusyatiner et al., 2017). E. coli production Escherichia coli is a Gram-negative, facultative anaerobic bacterium of n-butanol has also been demonstrated to the level similar to that originally discovered in the human colon in 1885 by German bacter- produced in Clostridia (Shen et al., 2011; Ohtake et al., 2017). -
Genome-Scale Analysis of Gene Function in the Hydrogenotrophic Methanogenic Archaeon Methanococcus Maripaludis
Genome-scale analysis of gene function in the hydrogenotrophic methanogenic archaeon Methanococcus maripaludis Felipe Sarmiento, Jan Mrázek, and William B. Whitman1 Department of Microbiology, University of Georgia, Athens, GA 30602 Edited by W. Ford Doolittle, Dalhousie University, Halifax, NS, Canada, and approved February 6, 2013 (received for review November 23, 2012) A comprehensive whole-genome analysis of gene function by redundancy may mask essential processes, polarity may cause transposon mutagenesis and deep sequencing methodology has genes downstream of an essential gene to falsely appear essen- been implemented successfully in a representative of the Archaea tial, truncated genes may retain some activity and falsely appear domain. Libraries of transposon mutants were generated for the nonessential, and small essential genes may escape detection. hydrogenotrophic, methanogenic archaeon Methanococcus mari- Moreover, it is difficult to distinguish genes that are truly es- paludis S2 using a derivative of the Tn5 transposon. About 89,000 sential, i.e., absolutely required for growth under the specified unique insertions were mapped to the genome, which allowed for conditions, from those that are advantageous for growth and the classification of 526 genes or about 30% of the genome as rapidly diluted out from the libraries by faster-growing mutants. possibly essential or strongly advantageous for growth in rich Although definitive assignments of essentiality still require de- medium. Many of these genes were homologous to eukaryotic tailed analyses of each gene, the methodology generates hy- genes that encode fundamental processes in replication, transcrip- potheses about the nature of specific genes and a great deal of tion, and translation, providing direct evidence for their impor- insight into specific questions regarding methanogens as well as tance in Archaea.