DNA topology of highly transcribed operons in Salmonella enterica serovar Typhimurium.

Abstract:

:Bacteria differ from eukaryotes by having the enzyme DNA gyrase, which catalyses the ATP-dependent negative supercoiling of DNA. Negative supercoils are essential for condensing chromosomes into an interwound (plectonemic) and branched structure known as the nucleoid. Topo-1 removes excess supercoiling in an ATP-independent reaction and works with gyrase to establish a topological equilibrium where supercoils move within 10 kb domains bounded by stochastic barriers along the sequence. However, transcription changes the stochastic pattern by generating supercoil diffusion barriers near the sites of gene expression. Using supercoil-dependent Tn3 and γδ resolution assays, we studied DNA topology upstream, downstream and across highly transcribed operons. Whenever two Res sites flanked efficiently transcribed genes, resolution was inhibited and the loss in recombination efficiency was proportional to transcription level. Ribosomal RNA operons have the highest transcription rates, and resolution assays at the rrnG and rrnH operons showed inhibitory levels 40-100 times those measured in low-transcription zones. Yet, immediately upstream and downstream of RNA polymerase (RNAP) initiation and termination sites, supercoiling characteristics were similar to poorly transcribed zones. We present a model that explains why RNAP blocks plectonemic supercoil movement in the transcribed track and suggests how gyrase and TopA control upstream and downstream transcription-driven supercoiling.

journal_name

Mol Microbiol

journal_title

Molecular microbiology

authors

Booker BM,Deng S,Higgins NP

doi

10.1111/j.1365-2958.2010.07394.x

subject

Has Abstract

pub_date

2010-12-01 00:00:00

pages

1348-64

issue

6

eissn

0950-382X

issn

1365-2958

journal_volume

78

pub_type

杂志文章
  • The Rcs phosphorelay system is specific to enteric pathogens/commensals and activates ydeI, a gene important for persistent Salmonella infection of mice.

    abstract::Bacteria utilize phosphorelay systems to respond to environmental or intracellular stimuli. Salmonella enterica encodes a four-step phosphorelay system that involves two sensor kinase proteins, RcsC and RcsD, and a response regulator, RcsB. The physiological stimulus for Rcs phosphorelay activation is unknown; however...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1111/j.1365-2958.2006.05420.x

    authors: Erickson KD,Detweiler CS

    更新日期:2006-11-01 00:00:00

  • Regulation of the KstR2 regulon of Mycobacterium tuberculosis by a cholesterol catabolite.

    abstract::Cholesterol catabolism is widespread in actinobacteria and is critical for Mycobacterium tuberculosis (Mtb) virulence. Catabolism of steroid nucleus rings C and D is poorly understood: it is initiated by the CoA thioesterification of 3aα-H-4α(3'-propanoate)-7aβ-methylhexahydro-1,5-indanedione (HIP) by FadD3, whose gen...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1111/mmi.12340

    authors: Casabon I,Zhu SH,Otani H,Liu J,Mohn WW,Eltis LD

    更新日期:2013-09-01 00:00:00

  • Salmonella acquires ferrous iron from haemophagocytic macrophages.

    abstract::Bacteria harbour both ferrous and ferric iron transporters. We now report that infection of macrophages and mice with a Salmonella enterica Typhimurium strain containing an inactivated feoB-encoded ferrous iron transporter results in increased bacterial replication, compared to infection with wild type. Inactivation o...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1111/mmi.12739

    authors: Nagy TA,Moreland SM,Detweiler CS

    更新日期:2014-09-01 00:00:00

  • Distinct roles for Caf1, Ccr4, Edc3 and CutA in the co-ordination of transcript deadenylation, decapping and P-body formation in Aspergillus nidulans.

    abstract::Transcript degradation is a key step in gene regulation. In eukaryotes, mRNA decay is generally initiated by removal of the poly(A) tail mediated by the Ccr4-Caf1-Not complex. Deadenylated transcripts are then rapidly degraded, primarily via the decapping-dependent pathway. Components of this pathway can be localized ...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1111/j.1365-2958.2010.07118.x

    authors: Morozov IY,Jones MG,Spiller DG,Rigden DJ,Dattenböck C,Novotny R,Strauss J,Caddick MX

    更新日期:2010-04-01 00:00:00

  • An unorthodox sensor protein (TorS) mediates the induction of the tor structural genes in response to trimethylamine N-oxide in Escherichia coli.

    abstract::We isolated and characterized three spontaneous mutations leading to trimethylamine N-oxide (TMAO)-independent expression of the tor operon encoding the TMAO-reductase anaerobic respiratory system in Escherichia coli. The mutations lie in a new for regulatory gene, the torS gene, which probably encodes a sensor protei...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1111/j.1365-2958.1996.tb02648.x

    authors: Jourlin C,Bengrine A,Chippaux M,Méjean V

    更新日期:1996-06-01 00:00:00

  • Determinants of the streptococcal surface glycoprotein GspB that facilitate export by the accessory Sec system.

    abstract::GspB is a large cell-surface glycoprotein expressed by Streptococcus gordonii M99 that mediates binding of this organism to human platelets. This adhesin is glycosylated in the cytoplasm, and is then transported to the cell surface via an accessory Sec system. To assess the structural features of GspB that are needed ...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1111/j.1365-2958.2005.04919.x

    authors: Bensing BA,Takamatsu D,Sullam PM

    更新日期:2005-12-01 00:00:00

  • Legionella pneumophila CsrA is a pivotal repressor of transmission traits and activator of replication.

    abstract::Legionella pneumophila can replicate inside amoebae and also alveolar macrophages to cause Legionnaires' Disease in susceptible hosts. When nutrients become limiting, a stringent-like response coordinates the differentiation of L. pneumophila to a transmissive form, a process mediated by the two-component system LetA/...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1046/j.1365-2958.2003.03706.x

    authors: Molofsky AB,Swanson MS

    更新日期:2003-10-01 00:00:00

  • Activation of both acfA and acfD transcription by Vibrio cholerae ToxT requires binding to two centrally located DNA sites in an inverted repeat conformation.

    abstract::The Gram-negative bacterium Vibrio cholerae is the infectious agent responsible for the disease Asiatic cholera. The genes required for V. cholerae virulence, such as those encoding the cholera toxin (CT) and toxin-coregulated pilus (TCP), are controlled by a cascade of transcriptional activators. Ultimately, the dire...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1111/j.1365-2958.2005.04589.x

    authors: Withey JH,DiRita VJ

    更新日期:2005-05-01 00:00:00

  • The hmuUV genes of Sinorhizobium meliloti 2011 encode the permease and ATPase components of an ABC transport system for the utilization of both haem and the hydroxamate siderophores, ferrichrome and ferrioxamine B.

    abstract::Sinorhizobium meliloti, the endosymbiont of Medicago sativa, can use haem compounds, including haemoglobin and leghaemoglobin, when growing in the free-living state. The components of the system involved in haem acquisition were confirmed to be ShmR, an outer membrane receptor, and HmuTUV, predicted to be an ABC trans...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1111/j.1365-2958.2008.06479.x

    authors: Cuív PO,Keogh D,Clarke P,O'Connell M

    更新日期:2008-12-01 00:00:00

  • Genetically distinct pathways guide effector export through the type VI secretion system.

    abstract::Bacterial secretion systems often employ molecular chaperones to recognize and facilitate export of their substrates. Recent work demonstrated that a secreted component of the type VI secretion system (T6SS), haemolysin co-regulated protein (Hcp), binds directly to effectors, enhancing their stability in the bacterial...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1111/mmi.12571

    authors: Whitney JC,Beck CM,Goo YA,Russell AB,Harding BN,De Leon JA,Cunningham DA,Tran BQ,Low DA,Goodlett DR,Hayes CS,Mougous JD

    更新日期:2014-05-01 00:00:00

  • Isolation and molecular characterization of the gene encoding allophycocyanin B, a terminal energy acceptor in cyanobacterial phycobilisomes.

    abstract::Phycobilisomes are the major constituents of the light-harvesting apparatus in both cyanobacteria and red algae and consist of a central core with radiating rods. From a genomic library of the cyanobacterium Calothrix 7601, a DNA fragment encoding allophycocyanin B, one of the two terminal energy acceptors of the core...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:

    authors: Houmard J,Capuano V,Coursin T,Tandean de Marsac N

    更新日期:1988-01-01 00:00:00

  • Septal membrane fusion--a pivotal event in bacterial spore formation?

    abstract::Formation of the asymmetrically located septum divides sporulating bacilli into two distinct cells: the mother cell and the prespore. The rigidifying wall material in the septum is subsequently removed by autolysis. Examination of published electron micrographs indicates that the two septal membranes then fuse to form...

    journal_title:Molecular microbiology

    pub_type: 杂志文章,评审

    doi:10.1111/j.1365-2958.1992.tb01433.x

    authors: Higgins ML,Piggot PJ

    更新日期:1992-09-01 00:00:00

  • Transcriptional coupling of DNA repair in sporulating Bacillus subtilis cells.

    abstract::In conditions of halted or limited genome replication, like those experienced in sporulating cells of Bacillus subtilis, a more immediate detriment caused by DNA damage is altering the transcriptional programme that drives this developmental process. Here, we report that mfd, which encodes a conserved bacterial protei...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1111/mmi.12417

    authors: Ramírez-Guadiana FH,Del Carmen Barajas-Ornelas R,Ayala-García VM,Yasbin RE,Robleto E,Pedraza-Reyes M

    更新日期:2013-12-01 00:00:00

  • Disruption of msl3 abolishes the synthesis of mycolipanoic and mycolipenic acids required for polyacyltrehalose synthesis in Mycobacterium tuberculosis H37Rv and causes cell aggregation.

    abstract::Cell wall lipids of Mycobacterium tuberculosis containing multiple methylbranched fatty acids play critical roles in pathogenesis and thus offer targets for new antimycobacterial drugs. Mycocerosicacid synthase gene (mas) encodes the enzyme that produces one class of such acids. Seven mas-like genes (msls) were identi...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1046/j.1365-2958.2002.03119.x

    authors: Dubey VS,Sirakova TD,Kolattukudy PE

    更新日期:2002-09-01 00:00:00

  • Tag-mediated fractionation of yeast ribosome populations proves the monomeric organization of the eukaryotic ribosomal stalk structure.

    abstract::The analysis of the not well understood composition of the stalk, a key ribosomal structure, in eukaryotes having multiple 12 kDa P1/P2 acidic protein components has been approached using these proteins tagged with a histidine tail at the C-terminus. Tagged Saccharomyces cerevisiae ribosomes, which contain two P1 prot...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1046/j.1365-2958.2003.03733.x

    authors: Guarinos E,Santos C,Sánchez A,Qiu DY,Remacha M,Ballesta JP

    更新日期:2003-10-01 00:00:00

  • The essential cell division protein FtsN contains a critical disulfide bond in a non-essential domain.

    abstract::Disulfide bonds are found in many proteins associated with the cell wall of Escherichia coli, and for some of these proteins the disulfide bond is critical to their stability and function. One protein found to contain a disulfide bond is the essential cell division protein FtsN, but the importance of this bond to the ...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1111/mmi.13565

    authors: Meehan BM,Landeta C,Boyd D,Beckwith J

    更新日期:2017-02-01 00:00:00

  • Determinants of segregational stability of the linear plasmid-prophage N15 of Escherichia coli.

    abstract::N15 is a bacteriophage of Escherichia coli that resembles lambda, but, unlike lambda, it lysogenizes as a linear plasmid. We show that stable maintenance of this unusual plasmid-prophage depends on the parA and parB genes, relatives of the partition genes of F and P1 plasmids. ParB of N15, like its F- and P1-encoded h...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1046/j.1365-2958.2001.02632.x

    authors: Grigoriev PS,Lobocka MB

    更新日期:2001-10-01 00:00:00

  • The complete nucleotide sequence of the Pasteurella multocida toxin gene and evidence for a transcriptional repressor, TxaR.

    abstract::The osteolytic toxin of Pasteurella multocida induces bone resorption in vivo and in vitro (Foged et al., 1988; Kimman et al., 1987). In this report the toxin-encoding toxA gene is sequenced, and the deduced primary structure of the toxin shows a protein of 1285 amino acids, containing a striking homology to a metal-b...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1111/j.1365-2958.1990.tb00652.x

    authors: Petersen SK

    更新日期:1990-05-01 00:00:00

  • The frequency of expression of pyelonephritis-associated pili is under regulatory control.

    abstract::The Escherichia coli urinary tract isolate C1212 contains two pyelonephritis-associated pili (pap) DNA sequences designated here as pap-17 and pap-21. Each of these pap sequences encodes antigenically-distinct pilin monomers, pilin-17 and pilin-21, respectively. Most individual strain C1212 cells isolated from a singl...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1111/j.1365-2958.1987.tb01940.x

    authors: Low D,Robinson EN Jr,McGee ZA,Falkow S

    更新日期:1987-11-01 00:00:00

  • New insights into the role of CcmC, CcmD and CcmE in the haem delivery pathway during cytochrome c maturation by a complete mutational analysis of the conserved tryptophan-rich motif of CcmC.

    abstract::Maturation of c-type cytochromes in Escherichia coli is a complex process requiring eight membrane proteins encoded by the ccmABCDEFGH operon. CcmE is a mediator of haem delivery. It binds haem transiently at a conserved histidine residue and releases it for directed transfer to apocytochrome c. CcmC, an integral memb...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1046/j.1365-2958.2000.02083.x

    authors: Schulz H,Pellicioli EC,Thöny-Meyer L

    更新日期:2000-09-01 00:00:00

  • Closing in on the toxic domain through analysis of a variant Clostridium difficile cytotoxin B.

    abstract::Strain 1470 is the standard typing strain for serogroup F of Clostridium difficile containing both toxin genes, toxA-1470 and toxB-1470. A polymerase chain reaction (PCR)-based approach to the sequencing of the total toxB-1470 gene identified an open reading frame (ORF) of 7104 nucleotides. In comparison with the prev...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1111/j.1365-2958.1995.mmi_17020313.x

    authors: von Eichel-Streiber C,Meyer zu Heringdorf D,Habermann E,Sartingen S

    更新日期:1995-07-01 00:00:00

  • Thermostabilization of cellulosomal endoglucanase EngB from Clostridium cellulovorans by in vitro DNA recombination with non-cellulosomal endoglucanase EngD.

    abstract::Enhancement of enzyme thermostability by protein engineering gives us information about the thermostabilization mechanism as well as advantages for industrial use of enzymes. In this study, we enhanced the thermostability of endoglucanase EngB, one component of the cellulase complex (cellulosome) from Clostridium cell...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1046/j.1365-2958.2002.03049.x

    authors: Murashima K,Kosugi A,Doi RH

    更新日期:2002-08-01 00:00:00

  • Crystal structure of enterotoxigenic Escherichia coli colonization factor CS6 reveals a novel type of functional assembly.

    abstract::Coli surface antigen 6 (CS6) is a widely expressed enterotoxigenic Escherichia coli (ETEC) colonization factor that mediates bacterial attachment to the small intestinal epithelium. CS6 is a polymer of two protein subunits CssA and CssB, which are secreted and assembled on the cell surface via the CssC/CssD chaperone ...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1111/mmi.12044

    authors: Roy SP,Rahman MM,Yu XD,Tuittila M,Knight SD,Zavialov AV

    更新日期:2012-12-01 00:00:00

  • Phenotypic repertoire of the FNR regulatory network in Escherichia coli.

    abstract::The FNR protein in Escherichia coli is an O(2) sensor that modifies global gene expression to adapt the cell to anaerobic growth. Regulation of FNR involves continuous cycling of the protein between its active and inactive states under aerobic conditions without apparent function. This raises the question of what bene...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1111/j.1365-2958.2010.07437.x

    authors: Tolla DA,Savageau MA

    更新日期:2011-01-01 00:00:00

  • Carbohydrate-binding agents act as potent trypanocidals that elicit modifications in VSG glycosylation and reduced virulence in Trypanosoma brucei.

    abstract::The surface of Trypanosoma brucei is covered by a dense coat of glycosylphosphatidylinositol-anchored glycoproteins. The major component is the variant surface glycoprotein (VSG) which is glycosylated by both paucimannose and oligomannose N-glycans. Surface glycans are poorly accessible and killing mediated by peptide...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1111/mmi.12359

    authors: Castillo-Acosta VM,Vidal AE,Ruiz-Pérez LM,Van Damme EJ,Igarashi Y,Balzarini J,González-Pacanowska D

    更新日期:2013-11-01 00:00:00

  • Socializing, networking and development: a report from the second 'Young Microbiologists Symposium on Microbe Signalling, Organization and Pathogenesis'.

    abstract::In mid-June, the second Young Microbiologists Symposium took place under the broad title of 'Microbe signalling, organization and pathogenesis' on the picturesque campus of University College Cork, Ireland. The symposium attracted 150 microbiologists from 15 different countries. The key feature of this meeting was tha...

    journal_title:Molecular microbiology

    pub_type:

    doi:10.1111/mmi.12016

    authors: Caly DL,Coulthurst SJ,Geoghegan JA,Malone JG,Ryan RP

    更新日期:2012-11-01 00:00:00

  • Regulation of Salmonella enterica pathogenicity island 1 (SPI-1) by the LysR-type regulator LeuO.

    abstract::LeuO is a quiescent LysR-type regulator belonging to the H-NS regulon. Activation of leuO transcription represses expression of pathogenicity island 1 (SPI-1) in Salmonella enterica serovar Typhimurium and inhibits invasion of epithelial cells. Loss of HilE suppresses LeuO-mediated downregulation of SPI-1. Activation ...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1111/mmi.12500

    authors: Espinosa E,Casadesús J

    更新日期:2014-03-01 00:00:00

  • Plasmodium pyruvate dehydrogenase activity is only essential for the parasite's progression from liver infection to blood infection.

    abstract::Plasmodium parasites possess a single pyruvate dehydrogenase (PDH) enzyme complex that is localized to the plastid-like organelle known as the apicoplast. Unlike most eukaryotes, Plasmodium parasites lack a mitochondrial PDH. The PDH complex catalyses the conversion of pyruvate to acetyl-CoA, an important precursor fo...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1111/j.1365-2958.2009.07034.x

    authors: Pei Y,Tarun AS,Vaughan AM,Herman RW,Soliman JM,Erickson-Wayman A,Kappe SH

    更新日期:2010-02-01 00:00:00

  • Carbon catabolite repression in Aspergillus nidulans involves deubiquitination.

    abstract::The best studied role of ubiquitination is to mark proteins for destruction by the proteasome but, in addition, it has recently been shown to promote macromolecular assembly and function, and alter protein function, thus playing a regulatory role distinct from protein degradation. Deubiquinating enzymes, the ubiquitin...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1046/j.1365-2958.2001.02474.x

    authors: Lockington RA,Kelly JM

    更新日期:2001-06-01 00:00:00

  • The solution structure of the periplasmic domain of the TonB system ExbD protein reveals an unexpected structural homology with siderophore-binding proteins.

    abstract::The transport of iron complexes through outer membrane transporters from Gram-negative bacteria is highly dependent on the TonB system. Together, the three components of the system, TonB, ExbB and ExbD, energize the transport of iron complexes through the outer membrane by utilizing the proton motive force across the ...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1111/j.1365-2958.2007.05957.x

    authors: Garcia-Herrero A,Peacock RS,Howard SP,Vogel HJ

    更新日期:2007-11-01 00:00:00