- Prokaryotic transcriptomics: a new view on regulation, physiology and pathogenicity
Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
Nat Rev Genet 11:9-16. 2010
..Deep RNA sequencing and tiling array studies are now revolutionizing our understanding of the complexity, plasticity and regulation of microbial transcriptomes...
- The primary transcriptome of the major human pathogen Helicobacter pylori
Cynthia M Sharma
Max Planck Institute for Infection Biology, RNA Biology Group, D 10117 Berlin, Germany
Nature 464:250-5. 2010
..Our approach establishes a paradigm for mapping and annotating the primary transcriptomes of many living species...
- A single-base resolution map of an archaeal transcriptome
Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
Genome Res 20:133-41. 2010
..of 625 million bases of sequenced cDNAs yielded a single-base-pair resolution map of transcription start sites and operon structures for more than 1000 transcriptional units...
- The complete genome sequence of Escherichia coli K-12
F R Blattner
Laboratory of Genetics, University of Wisconsin Madison, 445 Henry Mall, Madison, WI 53706, USA
Science 277:1453-62. 1997
..The genome also contains insertion sequence (IS) elements, phage remnants, and many other patches of unusual composition indicating genome plasticity through horizontal transfer...
- Tight regulation, modulation, and high-level expression by vectors containing the arabinose PBAD promoter
L M Guzman
Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
J Bacteriol 177:4121-30. 1995
..have constructed a series of plasmid vectors (pBAD vectors) containing the PBAD promoter of the araBAD (arabinose) operon and the gene encoding the positive and negative regulator of this promoter, araC...
- Transcriptome complexity in a genome-reduced bacterium
Centre for Genomic Regulation CRG, Universitat Pompeu Fabra, Barcelona, Spain
Science 326:1268-71. 2009
..Frequent antisense transcripts, alternative transcripts, and multiple regulators per gene imply a highly dynamic transcriptome, more similar to that of eukaryotes than previously thought...
- Prokaryotic toxin-antitoxin stress response loci
Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK 5230 Odense M, Denmark
Nat Rev Microbiol 3:371-82. 2005
..It has been proposed that toxin-antitoxin loci function in bacterial programmed cell death, but evidence now indicates that these loci provide a control mechanism that helps free-living prokaryotes cope with nutritional stress...
- An efficient recombination system for chromosome engineering in Escherichia coli
Gene Regulation and Chromosome Biology Laboratory and Mouse Cancer Genetics Program, National Cancer Institute, Division of Basic Science, National Cancer Institute Frederick Cancer Research and Development Center, Frederick, MD 21702, USA
Proc Natl Acad Sci U S A 97:5978-83. 2000
..This system will be especially useful for the engineering of large bacterial plasmids such as those from bacterial artificial chromosome libraries...
- STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene
European Molecular Biology Laboratory, Meyerhofstrasse 1, D 69117 Heidelberg, Germany
Nucleic Acids Res 28:3442-4. 2000
..The usefulness of STRING is illustrated with an example that suggests a functional context for an RNA methylase with unknown specificity...
- DOOR: a database for prokaryotic operons
Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
Nucleic Acids Res 37:D459-63. 2009
..All the operons in DOOR are predicted using our own prediction program, which was ranked to be the best among 14 operon prediction programs by a recent independent review...
- RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes
Pavel S Novichkov
Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA, State Scientific Center GosNIIGenetika, Moscow 117545, Russia
Nucleic Acids Res 38:D111-8. 2010
..Another section in the database represents the results of accurate regulon propagation to the closely related genomes...
- 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...
- AraC protein, regulation of the l-arabinose operon in Escherichia coli, and the light switch mechanism of AraC action
Biology Department, Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21218, USA
FEMS Microbiol Rev 34:779-96. 2010
This review covers the physiological aspects of regulation of the arabinose operon in Escherichia coli and the physical and regulatory properties of the operon's controlling gene, araC...
- The Listeria transcriptional landscape from saprophytism to virulence
Institut Pasteur, Unité des Interactions Bactéries Cellules, F 75015 Paris, France
Nature 459:950-6. 2009
..We provide the complete Listeria operon map and have uncovered far more diverse types of RNAs than expected: in addition to 50 small RNAs (<500 ..
- Comprehensive comparative-genomic analysis of type 2 toxin-antitoxin systems and related mobile stress response systems in prokaryotes
Kira S Makarova
National Center for Biotechnology Information, NLM, National Institutes of Health, Bethesda, Maryland 20894, USA
Biol Direct 4:19. 2009
- 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
..The two major operons involved in Fe-S cluster assembly showed different behavior; the isc operon appears to be a direct target of RyhB action, while the suf operon does not...
- Prokaryotic genome regulation: multifactor promoters, multitarget regulators and hierarchic networks
Department of Frontier Bioscience, Hosei University, Koganei, Tokyo 184 8584, Japan
FEMS Microbiol Rev 34:628-45. 2010
..The multifactor promoters and the multitarget transcription factors can be assembled into complex networks of transcription regulation, forming hierarchical networks...
- Functional analysis of genes for biosynthesis of pyocyanin and phenazine-1-carboxamide from Pseudomonas aeruginosa PAO1
D V Mavrodi
Department of Plant Pathology, Agricultural Research Service, Washington State University, Pullman, Washington 99164 6430, USA
J Bacteriol 183:6454-65. 2001
..aeruginosa consisting of two core loci responsible for synthesis of PCA and three additional genes encoding unique enzymes involved in the conversion of PCA to pyocyanin, 1-hydroxyphenazine, and phenazine-1-carboxamide...
- 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...
- Molecular mechanisms of HipA-mediated multidrug tolerance and its neutralization by HipB
Maria A Schumacher
Department of Biochemistry and Molecular Biology, University of Texas, M D Anderson Cancer Center, Unit 1000, Houston, TX 77030, USA
Science 323:396-401. 2009
..Dimeric HipB interacts with two HipA molecules to inhibit its kinase activity through sequestration and conformational inactivation. Combined, these studies suggest mechanisms for HipA-mediated persistence and its neutralization by HipB...
- 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
..regulated by several global regulatory circuits, which converge to modulate the overall expression of the master operon for flagellum biosynthesis, flhDC. We now show that the global regulator CsrA of E...
- A master regulator for biofilm formation by Bacillus subtilis
Daniel B Kearns
Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
Mol Microbiol 55:739-49. 2005
..Critical to biofilm formation is the eps operon, which is believed to be responsible for the biosynthesis of an exopolysaccharide that binds chains of cells ..
- CmeABC functions as a multidrug efflux system in Campylobacter jejuni
Food Animal Health Research Program, Department of Veterinary Preventive Medicine, The Ohio State University, Wooster, Ohio 44691, USA
Antimicrob Agents Chemother 46:2124-31. 2002
..Here we characterized an efflux pump encoded by a three-gene operon (designated cmeABC) that contributes to multidrug resistance in C. jejuni 81-176...
- The Brucella suis virB operon is induced intracellularly in macrophages
Maria Laura Boschiroli
Institut National de la Sante et de la Recherche Medicale, Unité 431, Faculte de Medecine, 30900 Nimes, France
Proc Natl Acad Sci U S A 99:1544-9. 2002
..Reverse transcriptase-PCR showed that the 12 genes encoding the Brucella suis VirB system form an operon. Semiquantitative measurements of virB mRNA levels by slot blotting showed that transcription of the virB operon, ..
- Bacterial toxin-antitoxin systems: more than selfish entities?
Laurence Van Melderen
Laboratoire de Génétique et Physiologie Bactérienne, IBMM, Faculte des Sciences, Universite Libre de Bruxelles, Gosselies, Belgium
PLoS Genet 5:e1000437. 2009
..This Review discusses current hypotheses regarding the biological roles of these evolutionarily successful small operons. We consider the various selective forces that could drive the maintenance of TA systems in bacterial genomes...
- Processing of a sporulation sigma factor in Bacillus subtilis: how morphological structure could control gene expression
Institut de Microbiologie, Universite Paris Sud, Orsay, France
Cell 52:697-704. 1988
..According to this model, a morphological structure would directly control the synthesis of a developmental sigma factor and would modify gene expression...
- Mechanisms causing rapid and parallel losses of ribose catabolism in evolving populations of Escherichia coli B
V S Cooper
Center for Microbial Ecology, Michigan State University, East Lansing, Michigan 48824, USA
J Bacteriol 183:2834-41. 2001
..At the molecular level, the loss of ribose catabolic function involved the deletion of part or all of the ribose operon (rbs genes)...
- Group A streptococcal growth phase-associated virulence factor regulation by a novel operon (Fas) with homologies to two-component-type regulators requires a small RNA molecule
Department of Medical Microbiology and Hygiene, University Hospital Ulm, Robert-Koch-Str. 8, D-89081 Ulm, Germany
Mol Microbiol 39:392-406. 2001
..The fas operon, present in all 12 tested M serotypes, was transcribed as polycystronic message (fasBCA) and contained genes ..
- Salmonella enterica serovar Typhi possesses a unique repertoire of fimbrial gene sequences
S M Townsend
Department of Medical Microbiology and Immunology, College of Medicine, Texas A and M University, College Station, Texas 77843, USA
Infect Immun 69:2894-901. 2001
..genome, which has been sequenced by the Typhi Sequencing Group at the Sanger Centre, contained a type IV fimbrial operon, an orthologue of the agf operon, and 12 putative fimbrial operons of the chaperone-usher assembly class...
- A major protein component of the Bacillus subtilis biofilm matrix
Steven S Branda
Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA 02115, USA
Mol Microbiol 59:1229-38. 2006
..Having defined the major components of the biofilm matrix and the control of their synthesis by the global regulator SinR, we present a working model for how B. subtilis switches between nomadic and sedentary lifestyles...
- The pio operon is essential for phototrophic Fe(II) oxidation in Rhodopseudomonas palustris TIE-1
Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125, USA
J Bacteriol 189:1765-73. 2007
..Here we report the discovery, with Rhodopseudomonas palustris TIE-1 as a model organism, of a three-gene operon, designated the pio operon (for phototrophic iron oxidation), that is necessary for phototrophic Fe(II) oxidation...
- Genetic organization and iron-responsive regulation of the Brucella abortus 2,3-dihydroxybenzoic acid biosynthesis operon, a cluster of genes required for wild-type virulence in pregnant cattle
Bryan H Bellaire
Department of Microbiology and Immunology, Louisiana State University Health Sciences Center, Shreveport, LA 71130 3932, USA
Infect Immun 71:1794-803. 2003
..of total RNA with dhb-specific primers demonstrated that dhbC, -B, and -A are transcribed as components of an operon, together with dhbE, a functional homolog of the Escherichia coli entE gene. Homologs of the E...
- Genome-wide polysome profiling reveals an inflammation-responsive posttranscriptional operon in gamma interferon-activated monocytes
Center for Gene Regulation in Health and Disease and Department of Biology, Cleveland State University, Cleveland, Ohio 44115, USA
Mol Cell Biol 29:458-70. 2009
..Our studies have identified a new inflammation-responsive posttranscriptional operon that can be regulated directly at the level of translation in IFN-gamma-activated monocytes...
- Functional characterization of the sigmaB-dependent yabJ-spoVG operon in Staphylococcus aureus: role in methicillin and glycopeptide resistance
Institute of Medical Microbiology, University of Zurich, Gloriastr 32, 8006 Zurich, Switzerland
Antimicrob Agents Chemother 53:1832-9. 2009
..aureus (GISA) strains. We show here that deletion of the sigma(B)-controlled yabJ-spoVG operon, which codes for potential downstream regulators of sigma(B), abolished capsule synthesis and reduced resistance ..
- 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...
- Identification of an aggregative adhesion fimbria (AAF) type III-encoding operon in enteroaggregative Escherichia coli as a sensitive probe for detecting the AAF-encoding operon family
Unité de Pathogénie Bactérienne des Muqueuses, Groupe d Etude des Infections Diarrhéiques GEID, Institut Pasteur, 75724 Paris Cedex 15, France
Infect Immun 70:4302-11. 2002
..We developed PCR assays specific for the agg-3 operon. In our collection, the frequency of AAF-III strains was similar (12%) to that of AAF-I strains (16%) but higher ..
- 50 million years of genomic stasis in endosymbiotic bacteria
Department of Molecular Evolution, Evolutionary Biology Center, University of Uppsala, Uppsala, Sweden
Science 296:2376-9. 2002
..The genomic stasis of B. aphidicola, likely attributable to the loss of phages, repeated sequences, and recA, indicates that B. aphidicola is no longer a source of ecological innovation for its hosts...
- Global gene expression profiling of Yersinia pestis replicating inside macrophages reveals the roles of a putative stress-induced operon in regulating type III secretion and intracellular cell division
Hana S Fukuto
Center for Infectious Diseases, Department of Molecular Genetics and Biology, Stony Brook University, Stony Brook, NY 11794 5120, USA
Infect Immun 78:3700-15. 2010
..A putative stress-induced operon consisting of y2313, y2315, and y2316 (y2313-y2316), and a previously unidentified open reading frame, orfX, was ..
- Description of staphylococcus serine protease (ssp) operon in Staphylococcus aureus and nonpolar inactivation of sspA-encoded serine protease
University of Toronto Department of Laboratory Medicine and Pathobiology, and Sunnybrook and Womens College Health Science Centre, Department of Microbiology, North York, Ontario, Canada M4N 3M5
Infect Immun 69:159-69. 2001
..In this study, we describe an operon structure within the ssp locus of S. aureus RN6390...
- The σB-dependent yabJ-spoVG operon is involved in the regulation of extracellular nuclease, lipase, and protease expression in Staphylococcus aureus
Institute of Medical Microbiology, University of Zurich, Gloriastrasse 32, 8006 Zurich, Switzerland
J Bacteriol 193:4954-62. 2011
..The σ(B)-controlled yabJ-spoVG operon encodes two such putative downstream elements. We report here transcriptome analysis in S...
- The dhb operon of Bacillus subtilis encodes the biosynthetic template for the catecholic siderophore 2,3-dihydroxybenzoate-glycine-threonine trimeric ester bacillibactin
J J May
Department of Chemistry, Philipps Universitat Marburg, D 35032 Marburg, Germany
J Biol Chem 276:7209-17. 2001
..Comparative mass spectrometric analysis of culture extracts from both the wild type and the dhbF mutant led to the identification of a mass peak at m/z 881 ([M-H](1-)) that corresponds to a cyclic trimeric ester of DHB-glycine-threonine...
- Identification of psl, a locus encoding a potential exopolysaccharide that is essential for Pseudomonas aeruginosa PAO1 biofilm formation
Kara D Jackson
Department of Microbiology and Immunology, Wake Forest University School of Medicine, Medical Center Blvd, Winston Salem, NC 27157 1064, USA
J Bacteriol 186:4466-75. 2004
..Understanding psl-encoded exopolysaccharide expression and protection in biofilms will provide insight into the pathogenesis of P. aeruginosa in cystic fibrosis and other infections involving biofilms...
- Combinatorial engineering of intergenic regions in operons tunes expression of multiple genes
Brian F Pfleger
Department of Chemical Engineering, University of California Berkeley, Berkeley, CA 94720 1462, USA
Nat Biotechnol 24:1027-32. 2006
..the relative expression of two reporter genes over a 100-fold range and balance expression of three genes in an operon that encodes a heterologous mevalonate biosynthetic pathway, resulting in a sevenfold increase in mevalonate ..
- Overexpression of the mexC-mexD-oprJ efflux operon in nfxB-type multidrug-resistant strains of Pseudomonas aeruginosa
Department of Microbiology and Immunology, Queen s University, Kingston, Ontario, Canada
Mol Microbiol 21:713-24. 1996
..sequencing of portions of these fragments revealed that oprJ was the terminal gene in a putative three-gene operon, mexC-mexD-oprJ...
- Functional and comparative genomic analyses of an operon involved in fructooligosaccharide utilization by Lactobacillus acidophilus
Genomic Sciences Program and Southeast Dairy Foods Research Center, North Carolina State University, Raleigh, NC 27695, USA
Proc Natl Acad Sci U S A 100:8957-62. 2003
..Transcriptional analysis of this operon demonstrated that gene expression was induced by sucrose and FOS but not by glucose or fructose, suggesting some ..
- Transcriptional regulation of the cellobiose operon of Streptococcus mutans
Department of Oral Biology, University of Florida, Gainesville, 32610, USA
J Bacteriol 191:2153-62. 2009
..the hydrolysis of cellulose, is shown to be regulated by a transcriptional regulator, CelR, which is encoded by an operon with a phospho-beta-glucosidase (CelA) and a cellobiose-specific sugar phosphotransferase system (PTS) permease (..
- The Staphylococcus aureus lrgAB operon modulates murein hydrolase activity and penicillin tolerance
K H Groicher
Department of Microbiology, Molecular Biology and Biochemistry, University of Idaho, Moscow, Idaho 83844 3052, USA
J Bacteriol 182:1794-801. 2000
..A LytSR-regulated dicistronic operon has also been identified and shown to encode two potential membrane-associated proteins, designated LrgA and LrgB, ..
- mexEF-oprN multidrug efflux operon of Pseudomonas aeruginosa: regulation by the MexT activator in response to nitrosative stress and chloramphenicol
Department of Microbiology and Immunology, Queen s University, Kingston, Ontario, Canada
Antimicrob Agents Chemother 55:508-14. 2011
A null mutation in the mexS gene of Pseudomonas aeruginosa yielded an increased level of expression of a 3-gene operon containing a gene, xenB, whose product is highly homologous to a xenobiotic reductase in Pseudomonas fluorescens shown ..
- The fox operon from Rhodobacter strain SW2 promotes phototrophic Fe(II) oxidation in Rhodobacter capsulatus SB1003
Laura R Croal
California Institute of Technology, Pasadena, CA 91125, USA
J Bacteriol 189:1774-82. 2007
..study, we circumvented this problem by taking a heterologous-complementation approach to identify a three-gene operon (the foxEYZ operon) from Rhodobacter sp...
- Multiple antibiotic resistance in Pseudomonas aeruginosa: evidence for involvement of an efflux operon
Department of Microbiology and Immunology, Queen s University, Kingston, Ontario, Canada
J Bacteriol 175:7363-72. 1993
..The gene encoding OprK (previously identified as ORFC) forms part of an operon composed of three genes (ORFABC) implicated in the secretion of the siderophore pyoverdine...
- HCF152, an Arabidopsis RNA binding pentatricopeptide repeat protein involved in the processing of chloroplast psbB-psbT-psbH-petB-petD RNAs
Heinrich Heine Universitat, Institut für Entwicklungs und Molekularbiologie der Pflanzen, 40225 Dusseldorf, Germany
Plant Cell 15:1480-95. 2003
The psbB-psbT-psbH-petB-petD operon of higher plant chloroplasts is a heterogeneously composed transcriptional unit that undergoes complex RNA processing events until the mature oligocistronic RNAs are formed...
- Identification of the maturation factor for dual oxidase. Evolution of an eukaryotic operon equivalent
Department of Medicine, University of Chicago, Illinois 60637, USA
J Biol Chem 281:18269-72. 2006
..The identification of DUOXA genes has important implications for studies of the molecular mechanisms controlling DUOX expression and the molecular genetics of congenital hypothyroidism...
- Short RNA half-lives in the slow-growing marine cyanobacterium Prochlorococcus
Massachusetts Institute of Technology, Department of Civil and Environmental Engineering, Cambridge, MA 02139, USA
Genome Biol 11:R54. 2010
..We investigated whole-genome RNA stability of Prochlorococcus, a relatively slow-growing marine cyanobacterium doubling approximately once a day, which is extremely abundant in the oceans...
- Characterization of the ebp(fm) pilus-encoding operon of Enterococcus faecium and its role in biofilm formation and virulence in a murine model of urinary tract infection
Department of Internal Medicine, and Center for the Study of Emerging and Re emerging Pathogens, Division of Infectious Diseases, University of Texas Medical School at Houston, Houston, TX, USA
Virulence 1:236-46. 2010
..predicted pilus-encoding gene clusters; we also demonstrated that one of these, ebpABC(fm), is transcribed as an operon, that its putative major pilus subunit, EbpC(fm) (also called pilB), is polymerized into high molecular weight ..
- Physiological studies of tryptophan transport and tryptophanase operon induction in Escherichia coli
Department of Biological Sciences, Stanford University, California 94305 5020
J Bacteriol 173:6009-17. 1991
..We have exploited the fact that the tryptophanase (tna) operon is induced by tryptophan to infer how tryptophan transport is influenced by the growth medium and by mutations ..
- OperonDB: a comprehensive database of predicted operons in microbial genomes
Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
Nucleic Acids Res 37:D479-82. 2009
..OperonDB, first released in 2001, is a database containing the results of a computational algorithm for locating operon structures in microbial genomes...
- Role of the Pseudomonas aeruginosa oxyR-recG operon in oxidative stress defense and DNA repair: OxyR-dependent regulation of katB-ankB, ahpB, and ahpC-ahpF
U A Ochsner
Department of Microbiology, University of Colorado Health Sciences Center, Denver, Colorado 80262, USA
J Bacteriol 182:4533-44. 2000
..and recG-lacZ reporter activities and oxyR-recG mRNA analysis showed that oxyR and recG are organized in an operon and expressed constitutively with regard to oxidative stress from a single promoter upstream of oxyR...
- The methanogen-specific transcription factor MsvR regulates the fpaA-rlp-rub oxidative stress operon adjacent to msvR in Methanothermobacter thermautotrophicus
Elizabeth A Karr
Department of Botany and Microbiology, University of Oklahoma, Norman, OK 73019, USA
J Bacteriol 192:5914-22. 2010
..assays were used to demonstrate that MsvR regulates transcription of the divergently transcribed fpaA-rlp-rub operon in Methanothermobacter thermautotrophicus in addition to transcription from its own promoter...
- Unusual regulation of a leaderless operon involved in the catabolism of dimethylsulfoniopropionate in Rhodobacter sphaeroides
Matthew J Sullivan
School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
PLoS ONE 6:e15972. 2011
..It does so by using a lyase encoded by dddL, the promoter-distal gene of a three-gene operon, acuR-acuI-dddL...
- Identification of a reactivating factor for adenosylcobalamin-dependent ethanolamine ammonia lyase
Department of Bioscience and Biotechnology, Faculty of Engineering, Okayama University, Tsushima Naka, Okayama 700 8530, Japan
J Bacteriol 186:6845-54. 2004
..The reactivation was observed in the permeabilized E. coli cells carrying a plasmid containing the E. coli eut operon as well...
- Transcriptional regulation of the Clostridium cellulolyticum cip-cel operon: a complex mechanism involving a catabolite-responsive element
Laboratoire de Bioenergetique et Ingenierie des Proteines, UPR 9036 CNRS, Universite d Aix Marseille, Marseille, France
J Bacteriol 190:1499-506. 2008
..414 nucleotides downstream from the transcriptional start site has been shown to be involved in regulating this operon by a carbon catabolite repression mechanism...
- An oxygen-sensing diguanylate cyclase and phosphodiesterase couple for c-di-GMP control
Jason R Tuckerman
Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390 9038, USA
Biochemistry 48:9764-74. 2009
..Here we describe an Escherichia coli two-gene operon, dosCP, for control of c-di-GMP by oxygen...
- Noncognate Mycobacterium tuberculosis toxin-antitoxins can physically and functionally interact
Department of Biochemistry, Robert Wood Johnson Medical School, Piscataway, New Jersey 08854 5635, USA
J Biol Chem 285:39732-8. 2010
..As is characteristic of all toxin-antitoxin systems, each of the mazF-mt toxin genes is organized in an operon downstream of putative antitoxin genes...
- Role of the multidrug resistance regulator MarA in global regulation of the hdeAB acid resistance operon in Escherichia coli
Center for Adaptation Genetics and Drug Resistance, Tufts University School of Medicine, 136 Harrison Ave, Boston, MA 02111, USA
J Bacteriol 190:1290-7. 2008
..5. These findings show that repression of hdeAB by MarA depends on pH, growth phase, and other regulators of hdeAB and is associated with reduced resistance to acid conditions...
- Binding of Pseudomonas aeruginosa AlgZ to sites upstream of the algZ promoter leads to repression of transcription
Deborah M Ramsey
Department of Microbiology and Immunology, Wake Forest University School of Medicine, Medical Center Blvd, Winston Salem, NC 27157, USA
J Bacteriol 187:4430-43. 2005
..The genes encoding the alginate biosynthetic enzymes are clustered in a single operon, which is under tight transcriptional control...
- Conserved residues Asp16 and Pro24 of TnaC-tRNAPro participate in tryptophan induction of Tna operon expression
Luis R Cruz-Vera
Department of Biological Sciences, Stanford University, Stanford, CA 94305, USA
J Bacteriol 190:4791-7. 2008
..inhibition delays ribosome release, thereby inhibiting Rho factor binding and action, resulting in increased tna operon transcription...
- Salt stress in Desulfovibrio vulgaris Hildenborough: an integrated genomics approach
Virtual Institute of Microbial Stress and Survival, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
J Bacteriol 188:4068-78. 2006
..vulgaris responded similarly to the two stresses. Integration of data from multiple methods allowed us to develop a conceptual model for the salt stress response in D. vulgaris that can be compared to those in other microorganisms...
- The relBE2Spn toxin-antitoxin system of Streptococcus pneumoniae: role in antibiotic tolerance and functional conservation in clinical isolates
Centro de Investigaciones Biologicas, Consejo Superior de Investigaciones Cientificas, Madrid, Spain
PLoS ONE 5:e11289. 2010
..We conclude that even though the relBE2Spn TAS is not essential for pneumococcus, it may provide additional advantages to the bacteria for colonization and/or infection...
- Operon structure of Staphylococcus aureus
Nicole J P ten Broeke-Smits
Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
Nucleic Acids Res 38:3263-74. 2010
..Operons play a key role in regulating expression of diverse genes involved in metabolism and virulence. However, operon structures in pathogenic bacteria have been determined only by in silico approaches that are dependent on factors ..
- Involvement of the mpo operon in resistance to class IIa bacteriocins in Listeria monocytogenes
MFA, Laboratoire de Chimie de l Ean et de l Environnement, UMR CNRA 6008, Universite de Poitiers, 40 Avenue du Recteur Pineau, 86022 Poitiers Cedex, France
FEMS Microbiol Lett 238:37-41. 2004
..to class IIa bacteriocins in Listeria monocytogenes has been clearly linked to lack of expression of the mptACD operon, encoding the EIIt Man mannose PTS permease...
- Regulation of Streptococcus pneumoniae clp genes and their role in competence development and stress survival
, Institut Pasteur, URA 2172 du Centre National de la Recherche Scientifique, 75724 Paris Cedex 15, France
J Bacteriol 183:7295-307. 2001
..Streptococcus pneumoniae chromosomal DNA was used to isolate regulatory mutants affecting expression of the comCDE operon, encoding the peptide quorum-sensing two-component signal transduction system controlling competence development...
- Multiple stress signal integration in the regulation of the complex sigma S-dependent csiD-ygaF-gabDTP operon in Escherichia coli
Institut fur Biologie, Mikrobiologie, Freie Universitat Berlin, 14195 Berlin, Germany
Mol Microbiol 51:799-811. 2004
..We find that this region constitutes a complex operon with expression being controlled by three differentially regulated promoters: (i) csiDp, which affects the ..
- Analysis of Pseudomonas aeruginosa conditional psl variants reveals roles for the psl polysaccharide in adhesion and maintaining biofilm structure postattachment
Wake Forest University School of Medicine, Winston Salem, NC 27157, USA
J Bacteriol 188:8213-21. 2006
..The 15-gene psl operon encodes a putative polysaccharide that plays an important role in biofilm initiation in nonmucoid P...
- The presence of the glycolysis operon in SAR11 genomes is positively correlated with ocean productivity
M S Schwalbach
Oregon State University, Department of Microbiology, 220 Nash Hall, Corvallis, OR 97331, USA
Environ Microbiol 12:490-500. 2010
..Subsequent microarray analysis of a coastal isolate suggested that an operon encoding a variant of the Entner-Doudoroff pathway is likely responsible for the observed differences in glucose ..
- Assessment of three Resistance-Nodulation-Cell Division drug efflux transporters of Burkholderia cenocepacia in intrinsic antibiotic resistance
Department of Genetics and Microbiology, University of Pavia, Pavia, Italy
BMC Microbiol 9:200. 2009
..cenocepacia J2315, but the contribution of these pumps to the intrinsic drug resistance of this bacterium remains unclear...
- A matter of life and death: cell wall homeostasis and the WalKR (YycGF) essential signal transduction pathway
Biology of Gram Positive Pathogens, CNRS URA 2172, Department of Microbiology, Institut Pasteur, 25, rue du Dr Roux, 75724 Paris Cedex 15, France
Mol Microbiol 70:1307-22. 2008
..in different bacterial species, focusing on the function of genes in its regulon, as well as variations in walRK operon structure and the composition of its regulon...
- Transcriptome analysis of the responses of Staphylococcus aureus to antimicrobial peptides and characterization of the roles of vraDE and vraSR in antimicrobial resistance
Antimicrobial Resistance Unit, Department of Infectious Disease Surveillance and Control, National Institute for Health and Welfare THL, PL 30, 00271 Helsinki, Finland
BMC Genomics 10:429. 2009
..Three antimicrobial peptides were used in the analysis, two are derived from frog, temporin L and dermaseptin K4-S4(1-16), and the ovispirin-1 is obtained from sheep...
- Role of mexA-mexB-oprM in antibiotic efflux in Pseudomonas aeruginosa
X Z Li
Department of Molecular and Cell Biology, University of California, Berkeley 94720, USA
Antimicrob Agents Chemother 39:1948-53. 1995
We have earlier described mexA-mexB-oprK, an operon involved in pyoverdine export in Pseudomonas aeruginosa, and suggested that the products of these genes also contribute to the active efflux of several antibiotics (K. Poole, K...
- Aerobic regulation of cytochrome d oxidase (cydAB) operon expression in Escherichia coli: roles of Fnr and ArcA in repression and activation
P A Cotter
Department of Microbiology and Molecular Genetics and the Molecular Biology Institute, University of California, Los Angeles 90095 1489, USA
Mol Microbiol 25:605-15. 1997
The cydAB operon of Escherichia coli encodes the cytochrome d oxidase complex, one of two aerobic terminal oxidases that catalyses the oxidation of ubiquinol-8 and the reduction of oxygen to water...
- Escherichia coli gene purR encoding a repressor protein for purine nucleotide synthesis. Cloning, nucleotide sequence, and interaction with the purF operator
R J Rolfes
Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907
J Biol Chem 263:19653-61. 1988
..These four repressors are likely homologous. Amino acid sequence similarity is greatest in an amino-terminal region presumed to contain a DNA-binding domain. A similarity is also noted in the operator sites for these repressors...
- Improved genome assembly and evidence-based global gene model set for the chordate Ciona intestinalis: new insight into intron and operon populations
Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto, Japan
Genome Biol 9:R152. 2008
- Pseudomonas aeruginosa uses a cyclic-di-GMP-regulated adhesin to reinforce the biofilm extracellular matrix
Bradley R Borlee
Department of Microbiology, University of Washington, Box 357242, Seattle, WA 98195 7242, USA
Mol Microbiol 75:827-42. 2010
..The cdrA gene is in a two gene operon that also encodes a putative outer membrane transporter, CdrB...
- The fbpABC operon is required for Ton-independent utilization of xenosiderophores by Neisseria gonorrhoeae strain FA19
Heather R Strange
Department of Microbiology and Immunology, Medical College of Virginia Campus, Virginia Commonwealth University, Richmond, Virginia 23298, USA
Infect Immun 79:267-78. 2011
..The fbpABC operon encodes a periplasmic-binding-protein-dependent ABC transport system that enables the gonococcus to transport iron ..
- Identification and characterization of a germination operon on the virulence plasmid pXO1 of Bacillus anthracis
Unité Toxines et Pathogénie Bactériennes, CNRS URA1858, Institut Pasteur, 25 rue du Dr Roux, 75015 Paris, France
Mol Microbiol 33:407-14. 1999
..blot analysis of total RNA from sporulating cells indicated that the gerX locus was organized as a tricistronic operon (gerXB, gerXA and gerXC)...
- Regulatory features of the trp operon and the crystal structure of the trp RNA-binding attenuation protein from Bacillus stearothermophilus
X P Chen
Department of Biological Sciences, State University of New York, Buffalo, NY, 14260, USA
J Mol Biol 289:1003-16. 1999
..of both the cis and trans -acting regulatory elements indicates that the Bacillus stearothermophilustrp operon is regulated by an attenuation mechanism similar to that which controls the trp operon in Bacillus subtilis...
- Expression and operon structure of the sel genes of Escherichia coli and identification of a third selenium-containing formate dehydrogenase isoenzyme
Lehrstuhl fur Mikrobiologie, Universitat Munchen, Germany
J Bacteriol 173:4983-93. 1991
..and selB genes formed one transcriptional unit (sel vector AB), while selD was shown to be the central gene in an operon including two other genes, the promoter distal of which (topB) encodes topoisomerase III...
- A 35.7 kb DNA fragment from the Bacillus subtilis chromosome containing a putative 12.3 kb operon involved in hexuronate catabolism and a perfectly symmetrical hypothetical catabolite-responsive element
Institut de Génétique et de Biologie Microbiennes, Universite de Lausanne, Switzerland
Microbiology 144:877-84. 1998
..The remaining three ORFs encode two dehydrogenases and a transcriptional regulator. The operon is preceded by a putative catabolite-responsive element (CRE), located between a hypothetical promoter and the RBS ..
- Features of ribosome-peptidyl-tRNA interactions essential for tryptophan induction of tna operon expression
Luis Rogelio Cruz-Vera
Department of Biological Sciences, Stanford University, Stanford, California 94305, USA
Mol Cell 19:333-43. 2005
..The 24 residue leader peptidyl-tRNA of the tna operon of E. coli, TnaC-tRNA(Pro), in the presence of excess tryptophan, resists cleavage at the tnaC stop codon...
- Mutational analyses of open reading frames within the vraSR operon and their roles in the cell wall stress response of Staphylococcus aureus
Institute of Medical Microbiology, University of Zurich, Gloriastr 32, 8006 Zurich, Switzerland
Antimicrob Agents Chemother 55:1391-402. 2011
..The vraSR genes form part of the four-cistron autoregulatory operon orf1-yvqF-vraS-vraR...
- Identification of the pH-inducible, proton-translocating F1F0-ATPase (atpBEFHAGDC) operon of Lactobacillus acidophilus by differential display: gene structure, cloning and characterization
M J Kullen
Department of Food Science, Southeast Dairy Foods Research Center, North Carolina State University, Raleigh, NC 27695 7624, USA
Mol Microbiol 33:1152-61. 1999
..5. One of these products, a 0.7 kb fragment, showed sequence similarity to bacterial atpBEF genes of the atp operon, whose genes encode the various subunits of the F1F0-ATPase. With the 0...
- The rate of TRAP binding to RNA is crucial for transcription attenuation control of the B. subtilis trp operon
Maria V Barbolina
Department of Biological Sciences, State University of New York, Buffalo, New York, USA
J Mol Biol 370:925-38. 2007
..Transcription of the trpEDCFBA operon is controlled by an attenuation mechanism involving two overlapping RNA secondary structures in the 5' leader ..
- Horizontal transfer of the photosynthesis gene cluster and operon rearrangement in purple bacteria
Department of Biology, Tokyo Metropolitan University, Minamiohsawa 1-1, Hachioji, Tokyo 192-0397, Japan
J Mol Evol 52:333-41. 2001
- Comparison of tryptophan biosynthetic operon regulation in different Gram-positive bacterial species
Departmento de Microbiologia Molecular, Instituto de Biotecnologia, Universidad Nacional Autonoma de Mexico, Cuernavaca, Morelos 62210, Mexico
Trends Genet 23:422-6. 2007
The tryptophan biosynthetic operon has been widely used as a model system for studying transcription regulation. In Bacillus subtilis, the trp operon is primarily regulated by a tryptophan-activated RNA-binding protein, TRAP...
- Characterization of relationships between transcriptional units and operon structures in Bacillus subtilis and Escherichia coli
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611 0011, Japan
BMC Genomics 8:48. 2007
b>Operon structures play an important role in transcriptional regulation in prokaryotes. However, there have been fewer studies on complicated operon structures in which the transcriptional units vary with changing environmental conditions...
- Phosphorylation of either crh or HPr mediates binding of CcpA to the bacillus subtilis xyn cre and catabolite repression of the xyn operon
, CNRS UPR 412, Lyon Cedex 07, F 69367, France
J Mol Biol 286:307-14. 1999
..Fructose 1,6-bisphosphate was found to strongly enhance binding of the P-Ser-HPr/CcpA and P-Ser-Crh/CcpA complexes to the xyn cre, but had no effect on binding of CcpA alone...
- The long-chain fatty acid sensor, PsrA, modulates the expression of rpoS and the type III secretion exsCEBA operon in Pseudomonas aeruginosa
Department of Microbiology, University of Hawaii at Manoa, Honolulu, Hawaii, USA
Mol Microbiol 73:120-36. 2009
The Pseudomonas aeruginosa PsrA autorepressor has dual roles as a repressor of the fadBA5beta-oxidation operon and an activator of the stationary-phase sigma factor rpoS and exsCEBA operon of the type III secretion system (TTSS)...
- nalD encodes a second repressor of the mexAB-oprM multidrug efflux operon of Pseudomonas aeruginosa
Department of Microbiology and Immunology, Queen s University, Kingston, ON, Canada K7L 3N6
J Bacteriol 188:8649-54. 2006
..Moreover, increased expression from this promoter was seen in a nalD mutant, consistent with NalD directly controlling mexAB-oprM expression from a second promoter...
- The SmtB/ArsR family of metalloregulatory transcriptional repressors: Structural insights into prokaryotic metal resistance
Laura S Busenlehner
Department of Biochemistry and Biophysics, Center for Advanced Biomolecular Research, 2128 TAMU, Texas A and M University, College Station, TX 77843 2128, USA
FEMS Microbiol Rev 27:131-43. 2003
..We hypothesize that distinct allosteric pathways for metal sensing have co-evolved with metal specificities of distinct alpha3N and alpha5 coordination complexes...
- Mammalian cell-entry proteins encoded by the mce3 operon of Mycobacterium tuberculosis are expressed during natural infection in humans
Department of Microbiology, Faculty of Medicine, Kuwait University, Safat, Kuwait
Scand J Immunol 60:382-91. 2004
The mammalian cell-entry (mce)3 operon is one of four homologous mce operons on Mycobacterium tuberculosis genome that encodes six putative invasin/ adhesin-like proteins (Mce3A-F) possibly involved in the entry and survival of this ..
- Involvement of SirABC in iron-siderophore import in Staphylococcus aureus
Suzanne E Dale
Department of Microbiology and Immunology, University of Western Ontario, London, Ontario, Canada N6A 5C1
J Bacteriol 186:8356-62. 2004
..Here, we show that the iron-regulated sirABC operon is divergently transcribed from the sbn operon that encodes enzymes involved in the synthesis of staphylobactin, a ..
- The molybdate-responsive Escherichia coli ModE transcriptional regulator coordinates periplasmic nitrate reductase (napFDAGHBC) operon expression with nitrate and molybdate availability
Paul M McNicholas
Department of Microbiology, University of California, Los Angeles, Los Angeles, California 90095 1489, USA
J Bacteriol 184:3253-9. 2002
Expression of the Escherichia coli napFDAGHBC operon (also known as aeg46...