- 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...
- 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...
- 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 ..
- 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...
- 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...
- 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...
- 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...
- 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
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- ProOpDB: Prokaryotic Operon DataBase
Centro de Ciencias Aplicadas y Desarrollo Tecnologico, Universidad Nacional Autonoma de Mexico, Mexico, DF, Mexico
Nucleic Acids Res 40:D627-31. 2012
The Prokaryotic Operon DataBase (ProOpDB, http://operons.ibt.unam.mx/OperonPredictor) constitutes one of the most precise and complete repositories of operon predictions now available...
- Global analysis of small RNA and mRNA targets of Hfq
Cell Biology and Metabolism Branch, National Institute of Child Health and Development, Bethesda MD 20892, USA
Mol Microbiol 50:1111-24. 2003
..Within the argX-hisR-leuT-proM operon, Hfq appears to compete with RNase E and modulate RNA processing and degradation...
- 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...
- 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 ..
- Global RNA half-life analysis in Escherichia coli reveals positional patterns of transcript degradation
Douglas W Selinger
Harvard Medical School, Department of Genetics, Boston, Massachusetts 02115, USA
Genome Res 13:216-23. 2003
..Unexpectedly, transcription of a single operon (tdcABCDEFG) was relatively rifampicin-insensitive and showed significant increases 2...
- 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...
- A high resolution map of a cyanobacterial transcriptome
Graduate Program in Systems Biology, Harvard University, 52 Oxford Street, Northwest 445, 40, Cambridge, MA 02138, USA
Genome Biol 12:R47. 2011
- 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...
- 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...
- 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...
- Inactivation of the dlt operon in Staphylococcus aureus confers sensitivity to defensins, protegrins, and other antimicrobial peptides
Mikrobielle Genetik, Universitat Tubingen, Waldhäuser Strasse 70 8, 72076 Tubingen, Germany
J Biol Chem 274:8405-10. 1999
..Wild-type strains bearing additional copies of the dlt operon produced teichoic acids with higher amounts of D-alanine esters, bound cationic proteins less effectively and were ..
- Rv2686c-Rv2687c-Rv2688c, an ABC fluoroquinolone efflux pump in Mycobacterium tuberculosis
Maria Rosalia Pasca
Department of Genetics and Microbiology, University of Pavia, 27100 Pavia, Italy
Antimicrob Agents Chemother 48:3175-8. 2004
The Mycobacterium tuberculosis Rv2686c-Rv2687c-Rv2688c operon, encoding an ABC transporter, conferred resistance to ciprofloxacin and, to a lesser extent, norfloxacin, moxifloxacin, and sparfloxacin to Mycobacterium smegmatis...
- The recA gene of Streptococcus pneumoniae is part of a competence-induced operon and controls lysogenic induction
Microbiologie et Génétique Moléculaire CNRS UPR, Universite Paul Sabatier, Toulouse, France
Mol Microbiol 15:367-79. 1995
..7 kb long. This transcript indicated that recA is part of a competence-inducible (cin) operon. The major (about 4...
- Structural and operational complexity of the Geobacter sulfurreducens genome
Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, USA
Genome Res 20:1304-11. 2010
..The experimentally determined structural and operational annotations can be combined with functional annotation, yielding a new three-level annotation that greatly expands our understanding of prokaryotic genomes...
- The life-cycle of operons
Morgan N Price
Lawrence Berkeley National Laboratory, Berkeley, California, USA
PLoS Genet 2:e96. 2006
Operons are a major feature of all prokaryotic genomes, but how and why operon structures vary is not well understood...
- Evolution of the chaperone/usher assembly pathway: fimbrial classification goes Greek
Sean Paul Nuccio
Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, One Shields Ave, Davis, CA 95616 8645, USA
Microbiol Mol Biol Rev 71:551-75. 2007
..Members of each clade share related operon structures and encode fimbrial subunits with similar protein domains...
- A Bacillus subtilis sensor kinase involved in triggering biofilm formation on the roots of tomato plants
Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
Mol Microbiol 85:418-30. 2012
..We propose that small signalling molecules released by the roots of tomato plants are directly or indirectly recognized by KinD, triggering biofilm formation...
- Cell population heterogeneity during growth of Bacillus subtilis
Daniel B Kearns
Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
Genes Dev 19:3083-94. 2005
..SwrA stimulates the transcription of a large operon (the flagellum/chemotaxis operon), which includes the genes for sigma(D) and an activator of sigma(D)-directed ..
- Bistability and biofilm formation in Bacillus subtilis
Department of Molecular and Cellular Biology, The Biological Laboratories, Harvard University, Cambridge, MA 02138, USA
Mol Microbiol 67:254-63. 2008
..The exopolysaccharide is produced by enzymes encoded by the epsA-O operon and the gene encoding TasA is located in the yqxM-sipW-tasA operon...
- 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...
- 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...
- Targets of the master regulator of biofilm formation in Bacillus subtilis
Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
Mol Microbiol 59:1216-28. 2006
..The formation of these biofilms is mediated in part by the 15-gene exopolysaccharide operon, epsA-O, which is under the direct negative control of the SinR repressor...
- 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, ..
- Messenger RNA interferase RelE controls relBE transcription by conditional cooperativity
Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK 5230 Odense M, Denmark
Mol Microbiol 69:841-57. 2008
Prokaryotic toxin-antitoxin (TA) loci consist of two genes in an operon that encodes a metabolically stable toxin and an unstable antitoxin. The antitoxin neutralizes its cognate toxin by forming a tight complex with it...
- Molecular insights into the control of transcription initiation at the Staphylococcus aureus agr operon
Section of Microbiology, Faculty of Medicine and Centre for Molecular Microbiology and Infection, Imperial College London, London SW7 2AZ, UK
J Mol Biol 412:862-81. 2011
The accessory gene regulatory (agr) operon of the opportunistic human pathogen Staphylococcus aureus is a prime pathogenesis factor in this bacterium...
- The FleQ protein from Pseudomonas aeruginosa functions as both a repressor and an activator to control gene expression from the pel operon promoter in response to c-di-GMP
Department of Microbiology, University of Washington, Seattle, WA 98195 7735, USA
Nucleic Acids Res 40:7207-18. 2012
..The mechanism of action of FleQ is distinct from that of other bacterial transcription factors that both activate and repress gene expression from a single promoter...
- The emb operon, a gene cluster of Mycobacterium tuberculosis involved in resistance to ethambutol
Institute for Medical Microbiology, University of Bern, Switzerland
Nat Med 3:567-70. 1997
..Further characterization of these proteins might provide information on targets for new chemotherapeutic agents and might help development of diagnostic strategies for the detection of resistant M. tuberculosis...
- 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...
- Regulation of Pseudomonas quinolone signal synthesis in Pseudomonas aeruginosa
Dana S Wade
Department of Microbiology and Immunology, East Carolina University School of Medicine, BT 132, 600 Moye Blvd, Greenville, NC 27834, USA
J Bacteriol 187:4372-80. 2005
..Previous experiments showed that the transcription of this operon, and therefore PQS production, is negatively regulated by the rhl quorum-sensing system and positively regulated ..
- Ordering genes in a flagella pathway by analysis of expression kinetics from living bacteria
Department of Molecular Cell Biology, Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
Science 292:2080-3. 2001
..The observed temporal program of transcription was much more detailed than was previously thought and was associated with multiple steps of flagella assembly...
- 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 ..
- The specialized secretory apparatus ESX-1 is essential for DNA transfer in Mycobacterium smegmatis
The Microscopy and Imaging Center, Texas A and M University, 2257 TAMU, College Station, TX 77843, USA
Mol Microbiol 69:794-808. 2008
..smegmatis DNA transfer and M. tuberculosis virulence...
- 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...
- Multiple control of flagellum biosynthesis in Escherichia coli: role of H-NS protein and the cyclic AMP-catabolite activator protein complex in transcription of the flhDC master operon
Unité de Régulation de l Expression Génétique, Institut Pasteur, 75724 Paris Cedex 15, France
J Bacteriol 181:7500-8. 1999
..Overexpression of the flhDC master operon restored, at least in part, motility in crp and hns mutant strains, suggesting that this operon is the main target ..
- 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...
- 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 ..
- 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)...
- 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...
- Identification and characterization of a Streptococcus pyogenes operon involved in binding of hemoproteins and acquisition of iron
Christopher S Bates
Department of Biology, College of Arts and Sciences, Georgia State University, Atlanta, Georgia 30303, USA
Infect Immun 71:1042-55. 2003
..The sia transporter is part of a highly conserved, iron regulated, 10-gene operon. SiaA, which was localized to the cell membrane, could specifically bind hemoglobin...
- Curli fibers are highly conserved between Salmonella typhimurium and Escherichia coli with respect to operon structure and regulation
Department of Bacteriology, Microbiology and Tumorbiology Center, Karolinska Institutet, Stockholm, Sweden
J Bacteriol 180:722-31. 1998
..The high degree of conservation at the protein level and the identical regulation patterns in E. coli and S. typhimurium suggest similar roles of curli fibers in the same ecological niche in the two species...
- Glutamate decarboxylase-dependent acid resistance in orally acquired bacteria: function, distribution and biomedical implications of the gadBC operon
Daniela De Biase
Istituto Pasteur Fondazione Cenci Bolognetti, Dipartimento di Scienze e Biotecnologie Medico Chirurgiche, Sapienza Universita di Roma, 04100, Latina, Italy
Mol Microbiol 86:770-86. 2012
- A predicted operon map for Mycobacterium tuberculosis
Department of Mathematics, Statistics and Computer Science, St Olaf College, Northfield, MN 55057, USA
Nucleic Acids Res 35:5085-95. 2007
..From this model, we rank each potential operon pair by the strength of evidence for cotranscription, choose a classification threshold with a true positive rate ..
- Gene position in a long operon governs motility development in Bacillus subtilis
Loralyn M Cozy
Department of Biology, Indiana University, Bloomington, IN 47405, USA
Mol Microbiol 76:273-85. 2010
..The proportion of ON cells increased when sigD was artificially moved forward in the 27 kb fla/che operon. In addition, we identified a new sigma(D)-dependent promoter that increases sigD expression and may provide ..
- Glycogen in Bacillus subtilis: molecular characterization of an operon encoding enzymes involved in glycogen biosynthesis and degradation
J A Kiel
Department of Genetics, State University of Groningen, Haren, The Netherlands
Mol Microbiol 11:203-18. 1994
..subtilis containing a glycogen operon. The operon is located directly downstream from trnB, which maps at 275 degrees on the B. subtilis chromosome...
- 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...
- Regulation of Corynebacterium glutamicum heat shock response by the extracytoplasmic-function sigma factor SigH and transcriptional regulators HspR and HrcA
Research Institute of Innovative Technology for the Earth, 9 2 Kizugawadai, Kizugawa, Kyoto 619 0292, Japan
J Bacteriol 191:2964-72. 2009
..glutamicum heat shock response. Upregulation of 18 genes encoding transcriptional regulators by heat shock suggests a complex regulatory network of heat shock response in C. glutamicum...
- Activation of the Pseudomonas aeruginosa type III secretion system requires an intact pyruvate dehydrogenase aceAB operon
Departement de Biologie Moleculaire et Structurale, BBSI, UMR 5092 CNRS, CEA Grenoble, CHU Grenoble, Grenoble, France
Infect Immun 70:3973-7. 2002
..Among 25 mutants affected in TTSS function, 14 contained the insertion at different positions in the aceAB operon encoding the PDH-E1 and -E2 subunits of pyruvate dehydrogenase...
- Probing the ArcA-P modulon of Escherichia coli by whole genome transcriptional analysis and sequence recognition profiling
Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA 02115, USA
J Biol Chem 279:12588-97. 2004
..However, the discovery of 3 targets that are not implicated in respiratory metabolism (the tra operon for plasmid conjugation, psi site for Xer-based recombination, and oriC site for chromosome replication) suggests ..
- Ferric uptake regulation protein acts as a repressor, employing iron (II) as a cofactor to bind the operator of an iron transport operon in Escherichia coli
Department of Biochemistry, University of California, Berkeley 94720
Biochemistry 26:5471-7. 1987
The Fur (ferric uptake regulation) protein is a negative regulator of the aerobactin operon and of several other siderophore-mediated, high-affinity iron transport systems in Escherichia coli...
- Genomic arrangement of bacterial operons is constrained by biological pathways encoded in the genome
Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology and Institute of Bioinformatics, University of Georgia, Athens, GA 30605, USA
Proc Natl Acad Sci U S A 107:6310-5. 2010
..little is understood about what may determine the global arrangement of bacterial genes in a genome beyond the operon level...
- 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
- Formation of D-alanyl-lipoteichoic acid is required for adhesion and virulence of Listeria monocytogenes
Laboratoire de Microbiologie, INSERM U 411, Paris, France
Mol Microbiol 43:1-14. 2002
The dlt operon of Gram-positive bacteria comprises four genes (dltA, dltB, dltC and dltD) that catalyse the incorporation of D-alanine residues into the cell wall-associated lipoteichoic acids (LTAs)...
- 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...
- 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...
- 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...
- 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 ..
- 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...
- 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...
- 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 ..
- 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...
- 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 ..
- 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...
- 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 ..
- 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...
- 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 ..
- 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, ..
- 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 ..
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...