- Regulatory RNAs in bacteria
Lauren S Waters
Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA
Cell 136:615-28. 2009
..Here, we review the known mechanisms and roles of regulatory RNAs, highlight emerging themes, and discuss remaining questions...
- Pathogenic Escherichia coli
James B Kaper
Center for Vaccine Development, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
Nat Rev Microbiol 2:123-40. 2004
..Several different E. coli strains cause diverse intestinal and extraintestinal diseases by means of virulence factors that affect a wide range of cellular processes...
- A common mechanism of cellular death induced by bactericidal antibiotics
Michael A Kohanski
Center for BioDynamics and Center for Advanced Biotechnology, Boston University, Boston, MA 02215, USA
Cell 130:797-810. 2007
- The Listeria transcriptional landscape from saprophytism to virulence
Institut Pasteur, Unité des Interactions Bactéries Cellules, F 75015 Paris, France
Nature 459:950-6. 2009
..Together, our data unravel successive and coordinated global transcriptional changes during infection and point to previously unknown regulatory mechanisms in bacteria...
- The small RNA chaperone Hfq and multiple small RNAs control quorum sensing in Vibrio harveyi and Vibrio cholerae
Derrick H Lenz
Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
Cell 118:69-82. 2004
..We propose that Hfq, together with these sRNAs, creates an ultrasensitive regulatory switch that controls the critical transition into the high cell density, quorum-sensing mode...
- Stochastic gene expression in a single cell
Michael B Elowitz
Laboratory of Cancer Biology, Center for Studies in Physics and Biology, Rockefeller University, New York, NY 10021, USA
Science 297:1183-6. 2002
..These results establish a quantitative foundation for modeling noise in genetic networks and reveal how low intracellular copy numbers of molecules can fundamentally limit the precision of gene regulation...
- Quorum sensing: cell-to-cell communication in bacteria
Christopher M Waters
Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544 1014, USA
Annu Rev Cell Dev Biol 21:319-46. 2005
- Bacterial iron homeostasis
Simon C Andrews
School of Animal and Microbial Sciences, University of Reading, Reading RG6 6AJ, UK
FEMS Microbiol Rev 27:215-37. 2003
- A small RNA regulates the expression of genes involved in iron metabolism in Escherichia coli
Laboratory of Molecular Biology, National Cancer Institute, Building 37, Room 5132, National Institutes of Health, Bethesda, MD 20892, USA
Proc Natl Acad Sci U S A 99:4620-5. 2002
- Evaluation of a nutrient starvation model of Mycobacterium tuberculosis persistence by gene and protein expression profiling
Joanna C Betts
Respiratory Pathogens, GlaxoSmithKline, Stevenage, Herts, UK
Mol Microbiol 43:717-31. 2002
..Thus, we have generated a model with which we can search for agents active against persistent M. tuberculosis and revealed a number of potential targets expressed under these conditions...
- Identification of a conserved bacterial protein secretion system in Vibrio cholerae using the Dictyostelium host model system
Department of Microbiology and Molecular Genetics, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
Proc Natl Acad Sci U S A 103:1528-33. 2006
..Thus, the genes encoding the VAS-related, type VI secretion system likely play an important conserved function in microbial pathogenesis and represent an additional class of targets for vaccine and antimicrobial drug-based therapies...
- Persister cells, dormancy and infectious disease
Antimicrobial Discovery Center, Department of Biology, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, USA
Nat Rev Microbiol 5:48-56. 2007
..The molecular mechanisms that underlie the formation of dormant persister cells are now being unravelled and are the focus of this Review...
- Carbon catabolite repression in bacteria: many ways to make the most out of nutrients
Department of General Microbiology, Institute of Microbiology and Genetics, Georg August University Gottingen, Grisebachstr 8, D 37077 Gottingen, Germany
Nat Rev Microbiol 6:613-24. 2008
..In this Review, we discuss the most recent findings on the different mechanisms that have evolved to allow bacteria to use carbon sources in a hierarchical manner...
- Identification, timing, and signal specificity of Pseudomonas aeruginosa quorum-controlled genes: a transcriptome analysis
Department of Microbiology and W M Keck Microbial Communities and Cell Signaling Program, University of Iowa, Iowa City, Iowa 52242, USA
J Bacteriol 185:2066-79. 2003
..Acyl-homoserine lactone quorum sensing appears to be a system that allows ordered expression of hundreds of genes during P. aeruginosa growth in culture...
- Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic pathogen
C K Stover
PathoGenesis Corporation, Seattle, Washington 98119, USA
Nature 406:959-64. 2000
..We propose that the size and complexity of the P. aeruginosa genome reflect an evolutionary adaptation permitting it to thrive in diverse environments and resist the effects of a variety of antimicrobial substances...
- Genome-wide analysis of the general stress response network in Escherichia coli: sigmaS-dependent genes, promoters, and sigma factor selectivity
Institut fur Biologie, Mikrobiologie, Freie Universitat Berlin, Königin Luise Str 12 16a, 14195 Berlin, Germany
J Bacteriol 187:1591-603. 2005
..Thus, not only the expression of genes within a regulatory network but also the architecture of the network itself can be subject to regulation...
- Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles
Jeremiah J Faith
Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
PLoS Biol 5:e8. 2007
..The compendium of expression data compiled in this study, coupled with RegulonDB, provides a valuable model system for further improvement of network inference algorithms using experimental data...
- DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information
Human Genome Center, The Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo, Japan
Nucleic Acids Res 36:D93-6. 2008
..DBTBS can be accessed at: http://dbtbs.hgc.jp...
- P. aeruginosa quorum-sensing systems and virulence
Roger S Smith
Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
Curr Opin Microbiol 6:56-60. 2003
..Therefore, via the regulation of multiple factors and the production of 3O-C(12)-HSL, quorum-sensing systems have a significant effect on the virulence of the bacteria and also on how the host responds to P. aeruginosa infections...
- Structure and function of the feed-forward loop network motif
Departments of Molecular Cell Biology and Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
Proc Natl Acad Sci U S A 100:11980-5. 2003
..Additional features, such as pulse generation and cooperativity, are discussed. This study defines the function of one of the most significant recurring circuit elements in transcription networks...
- Quorum-sensing regulators control virulence gene expression in Vibrio cholerae
Department of Microbiology and Molecular Genetics, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
Proc Natl Acad Sci U S A 99:3129-34. 2002
..Together these data suggest a role for quorum sensing in modulating expression of blocks of virulence genes in a reciprocal fashion in vivo...
- How phosphotransferase system-related protein phosphorylation regulates carbohydrate metabolism in bacteria
Microbiologie et Genetique Moleculaire, INRA CNRS INA PG UMR 2585, Thiverval Grignon, France
Microbiol Mol Biol Rev 70:939-1031. 2006
..As we shall see, the PTS regulation network not only controls carbohydrate uptake and metabolism but also interferes with the utilization of nitrogen and phosphorus and the virulence of certain pathogens...
- Bistability in bacteria
Public Health Research Institute, 225 Warren Street, Newark, NJ 07103, USA
Mol Microbiol 61:564-72. 2006
..A review describing additional examples of bistability in bacteria has been published recently...
- sigmaB modulates virulence determinant expression and stress resistance: characterization of a functional rsbU strain derived from Staphylococcus aureus 8325-4
Malcolm J Horsburgh
Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield, England S10 2TN
J Bacteriol 184:5457-67. 2002
..We suggest that SarA is not likely to be the effector in the overall sigmaB-mediated effect on agr expression...
- Phase and antigenic variation in bacteria
Marjan W van der Woude
Department of Microbiology, University of Pennsylvania, 202A Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, PA 19104 6076, USA
Clin Microbiol Rev 17:581-611, table of contents. 2004
..Finally, examples are presented to illustrate that phase-variable gene expression should be taken into account in the development of diagnostic assays and in the interpretation of experimental results and epidemiological studies...
- A genomic view of the human-Bacteroides thetaiotaomicron symbiosis
Department of Molecular Biology and Pharmacology, Washington University School of Medicine, St Louis, MO 63110, USA
Science 299:2074-6. 2003
..These and other expanded paralogous groups shed light on the molecular mechanisms underlying symbiotic host-bacterial relationships in our intestine...
- Analysis of Pseudomonas aeruginosa 4-hydroxy-2-alkylquinolines (HAQs) reveals a role for 4-hydroxy-2-heptylquinoline in cell-to-cell communication
Department of Surgery, Harvard Medical School and Shriners Burns Institute, Massachusetts General Hospital, Boston, MA 02114, USA
Proc Natl Acad Sci U S A 101:1339-44. 2004
..HAQ signaling represents a potential target for the pharmacological intervention of P. aeruginosa-mediated infections...
- Quantitative characteristics of gene regulation by small RNA
Center for Theoretical Biological Physics, University of California San Diego, La Jolla, California, United States of America
PLoS Biol 5:e229. 2007
..Our results may also help guide the design of synthetic genetic circuits that have properties difficult to attain with protein regulators alone...
- Bacterial interference caused by autoinducing peptide variants
Skirball Institute of Biomolecular Medicine, New York University Medical Center, New York, NY 10016, USA
Science 276:2027-30. 1997
..Cross-inhibition of gene expression represents a type of bacterial interference that could be correlated with the ability of one strain to exclude others from infection or colonization sites, or both...
- Genome sequence of Streptococcus mutans UA159, a cariogenic dental pathogen
Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
Proc Natl Acad Sci U S A 99:14434-9. 2002
- Microarray analysis of Pseudomonas aeruginosa quorum-sensing regulons: effects of growth phase and environment
Victoria E Wagner
Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, New York 14642, USA
J Bacteriol 185:2080-95. 2003
..Importantly, 222 genes were identified as being QS repressed. Environmental factors, such as medium composition and oxygen availability, eliminated detection of transcripts of many genes that were identified as being QS regulated...
- Phosphoenolpyruvate:carbohydrate phosphotransferase systems of bacteria
P W Postma
E C Slater Institute, University of Amsterdam, The Netherlands
Microbiol Rev 57:543-94. 1993
..In gram-positive bacteria, it has been demonstrated that HPr can be phosphorylated by ATP on a serine residue and this modification may perform a regulatory function...
- RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation
Program of Computational Genomics, Centro de Ciencias Genomicas, Universidad Nacional Autonoma de Mexico, A P 565 A, Cuernavaca, Morelos 62100, Mexico
Nucleic Acids Res 36:D120-4. 2008
..The data can be accessed through overviews of correlations about gene regulation. RegulonDB associated original literature, together with more than 4000 curation notes, can now be searched with the Textpresso text mining engine...
- Positive regulation of motility and flhDC expression by the RNA-binding protein CsrA of Escherichia coli
B L Wei
Department of Molecular Biology and Immunology, University of North Texas Health Science Center at Fort Worth, 3500 Camp Bowie Blvd, Fort Worth, TX 76107 2699, USA
Mol Microbiol 40:245-56. 2001
..Thus, CsrA stimulates flhDC gene expression by a post-transcriptional mechanism reminiscent of its function in the repression of glycogen biosynthesis...
- Translational control and target recognition by Escherichia coli small RNAs in vivo
Johannes H Urban
Max Planck Institute for Infection Biology, RNA Biology Group, Chariteplatz 1, 10117 Berlin, Germany
Nucleic Acids Res 35:1018-37. 2007
..We expect our GFP fusion approach to be applicable to sRNA targets of other bacteria, and also demonstrate that Vibrio RyhB sRNA represses a Vibrio sodB fusion when co-expressed in E.coli...
- Regulation of gene expression by cell-to-cell communication: acyl-homoserine lactone quorum sensing
Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
Annu Rev Genet 35:439-68. 2001
..Recent studies have begun to integrate acyl-HSL quorum sensing into global regulatory networks and establish its role in developing and maintaining the structure of bacterial communities...
- Engineering stability in gene networks by autoregulation
EMBL, Structures and Biocomputing, Heidelberg, Germany
Nature 405:590-3. 2000
..Here we have designed and constructed simple gene circuits consisting of a regulator and transcriptional repressor modules in Escherichia coli and we show the gain of stability produced by negative feedback...
- Biofilms: the matrix revisited
Steven S Branda
Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA 02115, USA
Trends Microbiol 13:20-6. 2005
..This review discusses recent advances in our understanding of the extracellular matrix and its role in biofilm biology...
- At the crossroads of bacterial metabolism and virulence factor synthesis in Staphylococci
Greg A Somerville
Department of Veterinary and Biomedical Sciences, University of Nebraska Lincoln, Lincoln, Nebraska 68583 0905, USA
Microbiol Mol Biol Rev 73:233-48. 2009
- Coupling of flagellar gene expression to flagellar assembly in Salmonella enterica serovar typhimurium and Escherichia coli
G S Chilcott
Department of Microbiology, University of Washington, Seattle, Washington 98195, USA
Microbiol Mol Biol Rev 64:694-708. 2000
..Cell cycle control and flagellar development are codependent. We discuss how all these levels of regulation ensure efficient assembly of the flagellum in response to environmental stimuli...
- SOS response promotes horizontal dissemination of antibiotic resistance genes
John W Beaber
Department of Microbiology, Tufts University School of Medicine and Howard Hughes Medical Institute, 136 Harrison Avenue, Boston, Massachusetts 02111, USA
Nature 427:72-4. 2004
..Thus, we present a mechanism by which therapeutic agents can promote the spread of antibiotic resistance genes...
- Transcriptional Adaptation of Mycobacterium tuberculosis within Macrophages: Insights into the Phagosomal Environment
Department of Microbiology and Immunology, Cornell University, 1300 York Avenue, New York, NY 10021, USA
J Exp Med 198:693-704. 2003
..The microbial transcriptome thus served as a bioprobe of the MTB phagosomal environment, showing it to be nitrosative, oxidative, functionally hypoxic, carbohydrate poor, and capable of perturbing the pathogen's cell envelope...
- Functions required for extracellular quinolone signaling by Pseudomonas aeruginosa
Larry A Gallagher
Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
J Bacteriol 184:6472-80. 2002
..Others of the pleiotropic phenazine-minus mutations appear to inactivate novel components of the quorum-sensing regulatory network, including one regulator (np20) previously shown to be required for virulence in neutropenic mice...
- Structures of the pleiotropic translational regulator Hfq and an Hfq-RNA complex: a bacterial Sm-like protein
Maria A Schumacher
Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, OR 97201 3098, USA
EMBO J 21:3546-56. 2002
..Such binding suggests a mechanism for Hfq function...
- Global gene expression in Staphylococcus aureus biofilms
Karen E Beenken
Department of Microbiology and Immunology, University of Arkansas for Medical Sciences, 4301 W Markham, Little Rock, AR 72205, USA
J Bacteriol 186:4665-84. 2004
..A primary theme that emerged from the analysis of these genes is that persistence within a biofilm requires an adaptive response that limits the deleterious effects of the reduced pH associated with anaerobic growth conditions...
- Optimality and evolutionary tuning of the expression level of a protein
Department of Molecular Cell Biology and Department of Physics of Complex Systems, The Weizmann Institute of Science, Rehovot 76100, Israel
Nature 436:588-92. 2005
..Thus, protein expression from the lac operon seems to be a solution of a cost-benefit optimization problem, and can be rapidly tuned by evolution to function optimally in new environments...
- Mistranslation of membrane proteins and two-component system activation trigger antibiotic-mediated cell death
Michael A Kohanski
Department of Biomedical Engineering, Center for BioDynamics, and Center for Advanced Biotechnology, Boston University, Boston, MA 02215, USA
Cell 135:679-90. 2008
- Transcription profiling of the stringent response in Escherichia coli
Department of Genetics, University of Wisconsin, Madison, Wisconsin 53706, USA
J Bacteriol 190:1084-96. 2008
..However, one-half of the up-regulated genes have unknown functions. How these results are correlated with the various effects of (p)ppGpp (in particular, RNA polymerase redistribution) is discussed...
- The transcriptional responses of Mycobacterium tuberculosis to inhibitors of metabolism: novel insights into drug mechanisms of action
Helena I M Boshoff
Tuberculosis Research Section, NIAID, National Institutes of Health, Rockville, Maryland 20852, USA
J Biol Chem 279:40174-84. 2004
- Multistability in the lactose utilization network of Escherichia coli
Ertugrul M Ozbudak
Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
Nature 427:737-40. 2004
..The phase diagram thus serves as a sensitive probe of molecular interactions and as a powerful tool for rational network design...
- Global analysis of the Mycobacterium tuberculosis Zur (FurB) regulon
Department of Genetics and Microbiology, University of Pavia, Pavia, Italy
J Bacteriol 189:730-40. 2007
- Optknock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization
Anthony P Burgard
Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
Biotechnol Bioeng 84:647-57. 2003
..Finally, the OptKnock procedure, by coupling biomass formation with chemical production, hints at a growth selection/adaptation system for indirectly evolving overproducing mutants...
- Yersinia pestis--etiologic agent of plague
R D Perry
Department of Microbiology and Immunology, University of Kentucky, Lexington 40536, USA
Clin Microbiol Rev 10:35-66. 1997
..These areas of research have provide new insights into the host-parasite relationship. This review will update our present understanding of the history, etiology, epidemiology, clinical aspects, and public health issues of plague...
- ppGpp: a global regulator in Escherichia coli
Lisa U Magnusson
Department of Cell and Molecular Biology Microbiology, Goteborg University, Box 462, 405 30 Goteborg, Sweden
Trends Microbiol 13:236-42. 2005
..In addition, new insights into the mechanism by which ppGpp affects gene expression have been achieved owing to in vitro studies of ppGpp function, complemented by structural studies of the ppGpp-RNA polymerase complex...
- Effect of RyhB small RNA on global iron use in Escherichia coli
Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
J Bacteriol 187:6962-71. 2005
..Our results demonstrate the broad effects of a single noncoding RNA on iron homeostasis...
- The Bacillus subtilis iron-sparing response is mediated by a Fur-regulated small RNA and three small, basic proteins
Department of Microbiology, Cornell University, Ithaca, NY 14853 8101, USA
Proc Natl Acad Sci U S A 105:11927-32. 2008
..Thus, iron deprivation in B. subtilis activates pathways to remodel the proteome to preserve iron for the most critical cellular functions...
- Small RNAs encoded within genetic islands of Salmonella typhimurium show host-induced expression and role in virulence
Department of Molecular Genetics and Biotechnology, The Hebrew University Hadassah Medical School, 91120, Jerusalem, Israel
Nucleic Acids Res 36:1913-27. 2008
..Our study suggests that the island encoded sRNA genes play an important role within the network that regulates bacterial adaptation to environmental changes and stress conditions and thus controls virulence...
- Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensis
John F Heidelberg
The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
Nat Biotechnol 20:1118-23. 2002
- DsrA RNA regulates translation of RpoS message by an anti-antisense mechanism, independent of its action as an antisilencer of transcription
Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
Proc Natl Acad Sci U S A 95:12462-7. 1998
..We propose that DsrA pairing stimulates RpoS translation by acting as an anti-antisense RNA, freeing the translation initiation region from the cis-acting antisense RNA and allowing increased translation...
- Persisters: a distinct physiological state of E. coli
Department of Biology, Northeastern University, 134 Mugar Hall, 360 Huntington Ave, Boston, MA 02115, USA
BMC Microbiol 6:53. 2006
..Recent progress in understanding persisters is encouraging, but the main obstacle in understanding their nature was our inability to isolate these elusive cells from a wild-type population since their discovery in 1944...
- A network of networks: quorum-sensing gene regulation in Pseudomonas aeruginosa
Department of Microbiology, University of Washington, 1959 NE Pacific Street, HSB I 420, Seattle, WA 98195, USA
Int J Med Microbiol 296:73-81. 2006
..Such epigenetic complexity may constitute the basis for the exceptional adaptability of P. aeruginosa to diverse environments...
- RNase E-based ribonucleoprotein complexes: mechanical basis of mRNA destabilization mediated by bacterial noncoding RNAs
Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya 464 8602, Japan
Genes Dev 19:2176-86. 2005
..The formation of ribonucleoprotein complexes containing RNases could be a general way by which small RNAs destabilize target mRNAs in both prokaryotes and eukaryotes...
- Transcriptional regulation in constraints-based metabolic models of Escherichia coli
Markus W Covert
Department of Bioengineering, University of California, San Diego, La Jolla, California 92093 0412, USA
J Biol Chem 277:28058-64. 2002
..This combined metabolic/regulatory model is thus an important step toward the goal of synthesizing genome-scale models that accurately represent E. coli behavior...
- Envelope stress responses and Gram-negative bacterial pathogenesis
Tracy L Raivio
Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
Mol Microbiol 56:1119-28. 2005
..This review highlights recent studies that indicate roles for the sigma(E), Cpx and Bae envelope stress responses in Gram-negative bacterial pathogenesis...
- A chemosensory system that regulates biofilm formation through modulation of cyclic diguanylate levels
Jason W Hickman
Department of Microbiology, Box 357242, University of Washington, 1959 Northeast Pacific Street, Seattle, WA 98195, USA
Proc Natl Acad Sci U S A 102:14422-7. 2005
..Together, the data suggest that the wsp signal transduction pathway regulates biofilm formation through modulation of cyclic diguanylate levels...
- Coding sequence targeting by MicC RNA reveals bacterial mRNA silencing downstream of translational initiation
Max Planck Institute for Infection Biology, RNA Biology Group, Berlin, Germany
Nat Struct Mol Biol 16:840-6. 2009
..The discovery of CDS targeting markedly expands the sequence space for sRNA target predictions in bacteria...
- Regulon and promoter analysis of the E. coli heat-shock factor, sigma32, reveals a multifaceted cellular response to heat stress
Department of Microbiology and Immunology, University of California at San Francisco, San Francisco, California 94143, USA
Genes Dev 20:1776-89. 2006
..The intimate connection of the response to the membrane rationalizes why a major regulator of the response resides in that cellular compartment...
- Iron and metal regulation in bacteria
Mikrobiologie Membranphysiologie, Universitat Tubingen, Auf der Morgenstelle 28, D 72076, Tubingen, Germany
Curr Opin Microbiol 4:172-7. 2001
..In organisms with Fur-dependent iron regulation, members of the DtxR family regulate manganese transport...
- The mechanisms of carbon catabolite repression in bacteria
Laboratorie de Microbiologie et Génétique Moléculaire, INRA AgroParisTech CNRS, F 78850 Thiverval Grignon, France
Curr Opin Microbiol 11:87-93. 2008
..PTS-independent CCR mechanisms are operative in several other bacteria...
- A small RNA regulates multiple ABC transporter mRNAs by targeting C/A-rich elements inside and upstream of ribosome-binding sites
Cynthia M Sharma
RNA Biology Group, Max Planck Institute for Infection Biology, 10117 Berlin, Germany
Genes Dev 21:2804-17. 2007
..Taken together, our study suggests highly conserved regions in sRNAs and mRNA regions distant from Shine-Dalgarno sequences as important elements for the identification of sRNA targets...
- The use of gene clusters to infer functional coupling
Mathematics and Computer Science Division, Argonne National Laboratory, 9700 S Cass Avenue, Argonne, IL 60439 4844, USA
Proc Natl Acad Sci U S A 96:2896-901. 1999
- Two GacA-dependent small RNAs modulate the quorum-sensing response in Pseudomonas aeruginosa
Département de Microbiologie Fondamentale, Universite de Lausanne, Building Biophore, CH 1015 Lausanne, Switzerland
J Bacteriol 188:6026-33. 2006
..Both mutants showed increased swarming ability, azurin release, and early biofilm development...
- Positive control of swarming, rhamnolipid synthesis, and lipase production by the posttranscriptional RsmA/RsmZ system in Pseudomonas aeruginosa PAO1
Institut de Microbiologie Fondamentale, Universite de Lausanne, CH 1015 Lausanne, Switzerland
J Bacteriol 186:2936-45. 2004
..Overexpression of rsmZ and a null mutation in rsmA resulted in quantitatively similar, negative or positive effects on target genes, in agreement with a model that postulates titration of RsmA protein by RsmZ RNA...
- Riboswitches in eubacteria sense the second messenger cyclic di-GMP
Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA
Science 321:411-3. 2008
..In addition, sequences matching the consensus for cyclic di-GMP riboswitches are present in the genome of a bacteriophage...
- Agr-mediated dispersal of Staphylococcus aureus biofilms
Blaise R Boles
Department of Microbiology, Roy J and Lucille A Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
PLoS Pathog 4:e1000052. 2008
..These findings indicate that induction of the agr system in established S. aureus biofilms detaches cells and demonstrate that the dispersal mechanism requires extracellular protease activity...
- The C-terminal domain of Escherichia coli Hfq is required for regulation
Max F Perutz Laboratories, University of Vienna, Dr Bohrgasse 9, 1030 Vienna, Austria
Nucleic Acids Res 36:133-43. 2008
..These studies indicate that the C-terminal extension of E. coli Hfq constitutes a hitherto unrecognized RNA interaction surface with specificity for mRNAs...
- Chitin induces natural competence in Vibrio cholerae
Karin L Meibom
Division of Infectious Diseases and Geographic Medicine, Department of Microbiology and Immunology, and Stanford Institute for the Environment, Stanford University, Stanford, CA 94305, USA
Science 310:1824-7. 2005
- A novel Staphylococcus aureus biofilm phenotype mediated by the fibronectin-binding proteins, FnBPA and FnBPB
School of Biomolecular and Biomedical Science, University College Dublin, Ardmore House, Belfield, Dublin 4, Ireland
J Bacteriol 190:3835-50. 2008
..These data identify a novel S. aureus biofilm phenotype promoted by FnBPA and FnBPB which is apparently independent of the known ligand-binding activities of these multifunctional surface proteins...
- Determination of the regulon and identification of novel mRNA targets of Pseudomonas aeruginosa RsmA
Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA 02115, USA
Mol Microbiol 72:612-32. 2009
..Our work supports a model in which RsmA acts as a negative translational regulator, and where its positive effects are achieved indirectly by RsmA-mediated interference with translation of specific regulatory factors...
- Targeting QseC signaling and virulence for antibiotic development
David A Rasko
Department of Microbiology, University of Texas UT Southwestern Medical Center, Dallas, TX 75390, USA
Science 321:1078-80. 2008
..Inhibition of signaling offers a strategy for the development of broad-spectrum antimicrobial drugs...
- Progression of primary pneumonic plague: a mouse model of infection, pathology, and bacterial transcriptional activity
Wyndham W Lathem
Department of Molecular Microbiology, Washington University School of Medicine, 660 South Euclid Avenue, St Louis, MO 63110, USA
Proc Natl Acad Sci U S A 102:17786-91. 2005
- A four-tiered transcriptional regulatory circuit controls flagellar biogenesis in Pseudomonas aeruginosa
Department of Medicine Infectious Diseases, University of Florida, Gainesville, FL 32610, USA
Mol Microbiol 50:809-24. 2003
..Two previously uncharacterized genes, which are coordinately regulated with known flagellar genes have been identified by genome-wide analysis and their role in flagellar biogenesis was analysed...
- The phosphate regulon and bacterial virulence: a regulatory network connecting phosphate homeostasis and pathogenesis
Martin G Lamarche
Groupe de Recherche sur les Maladies Infectieuses du Porc, Faculte de Medecine Veterinaire, Universite de Montreal, Saint Hyacinthe, Quebec, Canada
FEMS Microbiol Rev 32:461-73. 2008
..The Pho regulon is clearly not a simple regulatory circuit for controlling phosphate homeostasis; it is part of a complex network important for both bacterial virulence and stress response...
- The complete genome sequence of the gastric pathogen Helicobacter pylori
J F Tomb
Institute for Genomic Research, Rockville, Maryland 20850, USA
Nature 388:539-47. 1997
..pylori has a few regulatory networks, and a limited metabolic repertoire and biosynthetic capacity. Its survival in acid conditions depends, in part, on its ability to establish a positive inside-membrane potential in low pH...
- Autoinduction and signal transduction in the regulation of staphylococcal virulence
Richard P Novick
Program in Molecular Pathogenesis, Skirball Institute, Department of Microbiology, New York University School of Medicine, 10016, USA
Mol Microbiol 48:1429-49. 2003
..This review is an attempt to integrate a large body of data into the beginnings of a model that will hopefully help to guide research towards a full-scale test...
- H-NS: a modulator of environmentally regulated gene expression
Department of Chemistry and Life Sciences, Roskilde University, Denmark
Mol Microbiol 24:7-17. 1997
..Finally, we summarize the evolutionary and functional relationship between H-NS and the homologous StpA...
- Iron uptake regulation in Pseudomonas aeruginosa
Department of Molecular and Cellular Interactions, Laboratory of Microbial Interactions, Flanders Interuniversity Institute for Biotechnology, Vrije Universiteit Brussel, Brussels, Belgium
Biometals 22:15-22. 2009
..aeruginosa will be presented. An interesting feature revealed by this analysis of Fur-regulated genes is the overlap between the iron and the sulfur regulons as well with the quorum sensing system...
- Microarray-based analysis of the Staphylococcus aureus sigmaB regulon
Department of Medical Microbiology, University of Zurich, CH 8028 Zurich, Switzerland
J Bacteriol 186:4085-99. 2004
..We propose that this alternative transcription factor may be of importance for the invading pathogen to fine-tune its virulence factor production in response to changing host environments...
- Biological control of soil-borne pathogens by fluorescent pseudomonads
Department of Fundamental Microbiology, University of Lausanne, CH 1015 Lausanne, Switzerland
Nat Rev Microbiol 3:307-19. 2005
..Before engaging in these activities, biocontrol bacteria go through several regulatory processes at the transcriptional and post-transcriptional levels...
- Multiple small RNAs act additively to integrate sensory information and control quorum sensing in Vibrio harveyi
Kimberly C Tu
Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
Genes Dev 21:221-33. 2007
..Other regulators appear to be involved in control of V. harveyi qrr expression, allowing the integration of additional sensory information into the regulation of quorum-sensing gene expression...
- Nitrogen assimilation and global regulation in Escherichia coli
Department of Molecular and Cell Biology, The University of Texas at Dallas, Richardson, Texas 75080 0688, USA
Annu Rev Microbiol 57:155-76. 2003
..Guanosine tetraphosphate appears to control Lrp synthesis. In summary, a network of interacting global regulators that senses different aspects of metabolism integrates nitrogen assimilation with other metabolic processes...
- Regulation of RpoS by a novel small RNA: the characterization of RprA
Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bldg 37 Room 2E 18, Bethesda, MD 20892 4255, USA
Mol Microbiol 39:1382-94. 2001
..The existence of two very different small RNA regulators of RpoS translation suggests that such additional regulatory RNAs are likely to exist, both for regulation of RpoS and for regulation of other important cellular components...
- Structure and function of the LysR-type transcriptional regulator (LTTR) family proteins
Sarah E Maddocks
Department of Oral and Dental Science, University of Bristol, Lower Maudlin Street, Bristol BS1 2LY, UK
Microbiology 154:3609-23. 2008
- Sigma factors in Pseudomonas aeruginosa
Centre de Recherche sur la Fonction, Structure et Ingénierie des Protéines, Faculte de Medecine, Pavillon Charles Eugène Marchand, Universite Laval, Sainte Foy, Quebec, Canada
FEMS Microbiol Rev 32:38-55. 2008
..aeruginosasigma and ECF are expected to provide new means to prevent infection, new targets for antimicrobial therapy, as well as new insights into the infection process...
- The cellular concentration of the sigma S subunit of RNA polymerase in Escherichia coli is controlled at the levels of transcription, translation, and protein stability
Department of Biology, University of Konstanz, Germany
Genes Dev 8:1600-12. 1994
- Functional specialization within the Fur family of metalloregulators
Jin Won Lee
Department of Microbiology, Cornell University, Wing Hall, Ithaca, NY 14853 8101, USA
Biometals 20:485-99. 2007
..Despite numerous studies, the mechanism of metal ion sensing by Fur family proteins is still controversial. Other family members use metal catalyzed oxidation reactions to sense peroxide-stress (PerR) or the availability of heme (Irr)...
- A small, stable RNA induced by oxidative stress: role as a pleiotropic regulator and antimutator
Cell Biology and Metabolism Branch, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
Cell 90:43-53. 1997
..Our results suggest that the oxyS RNA acts as a regulator that integrates adaptation to hydrogen peroxide with other cellular stress responses and helps to protect cells against oxidative damage...
- DnaE2 polymerase contributes to in vivo survival and the emergence of drug resistance in Mycobacterium tuberculosis
Helena I M Boshoff
Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Twinbrook II, 12441 Parklawn Drive, Rockville, MD 20852, USA
Cell 113:183-93. 2003
..These results may indicate a potential new target for therapeutic intervention...
- A novel two-component system controls the expression of Pseudomonas aeruginosa fimbrial cup genes
Hemantha D Kulasekara
Department of Microbiology and Molecular Genetics, Harvard Medical School, 200 Longwood Ave, Boston, MA 02115, USA
Mol Microbiol 55:368-80. 2005
- A rough guide to the non-coding RNA world of Salmonella
RNA Biology Group, Max Planck Institute for Infection Biology, Chariteplatz 1, D 10117 Berlin, Germany
Mol Microbiol 71:1-11. 2009
- Escherichia coli acid resistance: tales of an amateur acidophile
John W Foster
Department of Microbiology and Immunology, University of South Alabama College of Medicine, Mobile, Alabama 36695, USA
Nat Rev Microbiol 2:898-907. 2004
..Surprisingly, certain microorganisms that grow at neutral pH have elegantly regulated systems that enable survival during excursions into acidic environments. The best-characterized acid-resistance system is found in E. coli...