The primosomal protein DnaD inhibits cooperative DNA binding by the replication initiator DnaA in Bacillus subtilis.

Abstract:

:DnaA is an AAA+ ATPase and the conserved replication initiator in bacteria. Bacteria control the timing of replication initiation by regulating the activity of DnaA. DnaA binds to multiple sites in the origin of replication (oriC) and is required for recruitment of proteins needed to load the replicative helicase. DnaA also binds to other chromosomal regions and functions as a transcription factor at some of these sites. Bacillus subtilis DnaD is needed during replication initiation for assembly of the replicative helicase at oriC and during replication restart at stalled replication forks. DnaD associates with DnaA at oriC and at other chromosomal regions bound by DnaA. Using purified proteins, we found that DnaD inhibited the ability of DnaA to bind cooperatively to DNA and caused a decrease in the apparent dissociation constant. These effects of DnaD were independent of the ability of DnaA to bind or hydrolyze ATP. Other proteins known to regulate B. subtilis DnaA also affect DNA binding, whereas much of the regulation of Escherichia coli DnaA affects nucleotide hydrolysis or exchange. We found that the rate of nucleotide exchange for B. subtilis DnaA was high and not affected by DnaD. The rapid exchange is similar to that of Staphylococcus aureus DnaA and in contrast to the low exchange rate of Escherichia coli DnaA. We suggest that organisms in which DnaA has a high rate of nucleotide exchange predominantly regulate the DNA binding activity of DnaA and that those with low rates of exchange regulate hydrolysis and exchange.

journal_name

J Bacteriol

journal_title

Journal of bacteriology

authors

Bonilla CY,Grossman AD

doi

10.1128/JB.00958-12

subject

Has Abstract

pub_date

2012-09-01 00:00:00

pages

5110-7

issue

18

eissn

0021-9193

issn

1098-5530

pii

JB.00958-12

journal_volume

194

pub_type

杂志文章
  • Simultaneous inactivation of sigma factors B and D interferes with light acclimation of the cyanobacterium Synechocystis sp. strain PCC 6803.

    abstract::In cyanobacteria, gene expression is regulated mainly at the level of transcription initiation, which is mediated by the RNA polymerase holoenzyme. The RNA polymerase core is catalytically active, while the sigma factor recognizes promoter sequences. Group 2 sigma factors are similar to the principal sigma factor but ...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/JB.00132-09

    authors: Pollari M,Ruotsalainen V,Rantamäki S,Tyystjärvi E,Tyystjärvi T

    更新日期:2009-06-01 00:00:00

  • Identification and characterization of a new porin gene of Klebsiella pneumoniae: its role in beta-lactam antibiotic resistance.

    abstract::Klebsiella pneumoniae porin genes were analyzed to detect mutations accounting for the porin deficiency observed in many beta-lactam-resistant strains. PCR and Southern blot analysis revealed the existence of a third porin gene in addition to the OmpK36 and OmpK35 porin genes previously described. This new porin gene ...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/JB.181.9.2726-2732.1999

    authors: Doménech-Sánchez A,Hernández-Allés S,Martínez-Martínez L,Benedí VJ,Albertí S

    更新日期:1999-05-01 00:00:00

  • Transcriptional regulation of a promoter in the men gene cluster of Bacillus subtilis.

    abstract::The control of men gene expression during growth and sporulation of Bacillus subtilis was examined at the transcriptional level. Two different approaches were used. (i) Steady-state levels of men-specific mRNA were measured directly. (ii) A men'-lacZ gene fusion was constructed. In both cases, it was observed that men...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/jb.170.6.2742-2748.1988

    authors: Miller P,Mueller J,Hill K,Taber H

    更新日期:1988-06-01 00:00:00

  • Metabolism of D-arabinose by Aerobacter aerogenes: purification of the isomerase.

    abstract::In Aerobacter aerogenes, the mutational event permitting the utilization of d-arabinose as a source of carbon and energy is a regulatory mutation resulting in the constitutive synthesis of certain enzymes of the l-fucose catabolic pathway. l-Fucose isomerase catalyzes the isomerization of d-arabinose to d-ribulose. Th...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/JB.108.1.293-299.1971

    authors: Oliver EJ,Mortlock RP

    更新日期:1971-10-01 00:00:00

  • FlhD/FlhC is a regulator of anaerobic respiration and the Entner-Doudoroff pathway through induction of the methyl-accepting chemotaxis protein Aer.

    abstract::The regulation by two transcriptional activators of flagellar expression (FlhD and FlhC) and the chemotaxis methyl-accepting protein Aer was studied with glass slide DNA microarrays. An flhD::Kan insertion and an aer deletion were independently introduced into two Escherichia coli K-12 strains, and the effects upon ge...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/jb.185.2.534-543.2003

    authors: Prüss BM,Campbell JW,Van Dyk TK,Zhu C,Kogan Y,Matsumura P

    更新日期:2003-01-01 00:00:00

  • Proteus mirabilis mutants defective in swarmer cell differentiation and multicellular behavior.

    abstract::Proteus mirabilis is a dimorphic bacterium which exists in liquid cultures as a 1.5- to 2.0-microns motile swimmer cell possessing 6 to 10 peritrichous flagella. When swimmer cells are placed on a surface, they differentiate by a combination of events that ultimately produce a swarmer cell. Unlike the swimmer cell, th...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/jb.173.19.6279-6288.1991

    authors: Belas R,Erskine D,Flaherty D

    更新日期:1991-10-01 00:00:00

  • Molecular cloning and expression of an isomalto-dextranase gene from Arthrobacter globiformis T6.

    abstract::The gene encoding an extracellular isomalto-dextranase, designated imd, was isolated from the chromosomal DNA of Arthrobacter globiformis T6 and cloned and expressed in Escherichia coli. A single open reading frame consisting of 1,926 base pairs that encoded a polypeptide composed of a signal peptide of 39 amino acids...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/jb.176.24.7730-7734.1994

    authors: Iwai A,Ito H,Mizuno T,Mori H,Matsui H,Honma M,Okada G,Chiba S

    更新日期:1994-12-01 00:00:00

  • Comprehensive transcriptome analysis of the periodontopathogenic bacterium Porphyromonas gingivalis W83.

    abstract::High-density tiling microarray and RNA sequencing technologies were used to analyze the transcriptome of the periodontopathogenic bacterium Porphyromonas gingivalis. The compiled P. gingivalis transcriptome profiles were based on total RNA samples isolated from three different laboratory culturing conditions, and the ...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/JB.06385-11

    authors: Høvik H,Yu WH,Olsen I,Chen T

    更新日期:2012-01-01 00:00:00

  • Expression of Adhesive Pili and the Collagen-Binding Adhesin Ace Is Activated by ArgR Family Transcription Factors in Enterococcus faecalis.

    abstract::It was shown previously that the disruption of the ahrC gene encoding a predicted ArgR family transcription factor results in a severe defect in biofilm formation in vitro, as well as a significant attenuation of virulence of Enterococcus faecalis strain OG1RF in multiple experimental infection models. Using transcrip...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/JB.00269-18

    authors: Manias DA,Dunny GM

    更新日期:2018-08-24 00:00:00

  • Draft genome sequence of Clostridium sporogenes PA 3679, the common nontoxigenic surrogate for proteolytic Clostridium botulinum.

    abstract::Clostridium sporogenes PA 3679 is widely used as a nontoxigenic surrogate for proteolytic strains of Clostridium botulinum in the derivation and validation of thermal processes in food. Here we report the draft assembly and annotation of the C. sporogenes PA 3679 genome. Preliminary analysis demonstrates a high degree...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/JB.06765-11

    authors: Bradbury M,Greenfield P,Midgley D,Li D,Tran-Dinh N,Vriesekoop F,Brown JL

    更新日期:2012-03-01 00:00:00

  • Promoters of the CATG-specific methyltransferase gene hpyIM differ between iceA1 and iceA2 Helicobacter pylori strains.

    abstract::Helicobacter pylori strains can be divided into two groups, based on the presence of two unrelated genes, iceA1 and iceA2, that occupy the same genomic locus. hpyIM, located immediately downstream of either gene, encodes a functional CATG-specific methyltransferase. Despite the strong conservation of the hpyIM open re...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/JB.183.13.3875-3884.2001

    authors: Xu Q,Blaser MJ

    更新日期:2001-07-01 00:00:00

  • Partial characterization of the factor responsible for tryptophanless death in Bacillus subtilis.

    abstract::The decline in colony-forming ability observed during tryptophan starvation of Bacillus subtilis auxotrophs is a concentration-dependent phenomenon. It does not manifest itself when the initial cell concentration is 10(6) cells/ml or lower. This property has been used to test the killing activity of different fraction...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/JB.101.2.355-360.1970

    authors: Barlati S,Majerfeld I

    更新日期:1970-02-01 00:00:00

  • ArcB1, a homolog of Escherichia coli ArcB, regulates dimethyl sulfoxide reduction in Shewanella oneidensis MR-1.

    abstract::Shewanella oneidensis is a metal reducer that uses the cyclic AMP receptor protein, CRP, to regulate anaerobic respiration. In addition, ArcA(So) is required for anaerobic growth with dimethyl sulfoxide (DMSO) and plays a role in aerobic respiration. The sensor kinase that activates ArcA(So) in S. oneidensis is not kn...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/JB.01695-09

    authors: Shroff NP,Charania MA,Saffarini DA

    更新日期:2010-06-01 00:00:00

  • Metronidazole activation and isolation of Clostridium acetobutylicum electron transport genes.

    abstract::An Escherichia coli F19 recA, nitrate reductase-deficient mutant was constructed by transposon mutagenesis and shown to be resistant to metronidazole. This mutant was a most suitable host for the isolation of Clostridium acetobutylicum genes on recombinant plasmids, which activated metronidazole and rendered the E. co...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/jb.173.3.1088-1095.1991

    authors: Santangelo JD,Jones DT,Woods DR

    更新日期:1991-02-01 00:00:00

  • Transformation of Saccharomyces cerevisiae with linear DNA killer plasmids from Kluyveromyces lactis.

    abstract::Protoplasts of Saccharomyces cerevisiae were mixed with linear DNA plasmids, pGKl1 and pGKl2, isolated from a Kluyveromyces lactis killer strain and treated with polyethylene glycol. Out of 2,000 colonies regenerated on a nonselective medium, two killer transformants were obtained. The pGKl plasmids and the killer cha...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/JB.151.1.462-464.1982

    authors: Gunge N,Murata K,Sakaguchi K

    更新日期:1982-07-01 00:00:00

  • Characterization of the genetic locus encoding Haemophilus influenzae type b surface fibrils.

    abstract::Haemophilus influenzae is a common gram-negative pathogen that initiates infection by colonizing the upper respiratory tract epithelium. In previous work, we reported the isolation of a locus involved in expression of short, thin surface fibrils by H. influenzae type b and presented evidence that surface fibrils promo...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/jb.178.21.6281-6287.1996

    authors: St Geme JW 3rd,Cutter D,Barenkamp SJ

    更新日期:1996-11-01 00:00:00

  • Microarray-based analysis of the Staphylococcus aureus sigmaB regulon.

    abstract::Microarray-based analysis of the transcriptional profiles of the genetically distinct Staphylococcus aureus strains COL, GP268, and Newman indicate that a total of 251 open reading frames (ORFs) are influenced by sigmaB activity. While sigmaB was found to positively control 198 genes by a factor of > or =2 in at least...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/JB.186.13.4085-4099.2004

    authors: Bischoff M,Dunman P,Kormanec J,Macapagal D,Murphy E,Mounts W,Berger-Bächi B,Projan S

    更新日期:2004-07-01 00:00:00

  • Localization and regulation of bacteriophage Mu promoters.

    abstract::Mu promoters active during the lytic cycle were located by isolating RNA at various times after induction of Mu prophages, radiolabeling it by capping in vitro, and hybridizing it to Mu DNA fragments on Southern blots. Signals were detected from four new promoters in addition to the previously characterized Pe (early)...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/jb.171.6.3440-3448.1989

    authors: Stoddard SF,Howe MM

    更新日期:1989-06-01 00:00:00

  • Identification and complementation of frameshift mutations associated with loss of cytadherence in Mycoplasma pneumoniae.

    abstract::Mycoplasma pneumoniae cytadherence is mediated by a specialized, polar attachment organelle. Certain spontaneously arising cytadherence mutants (designated class I) lack HMW2, fail to localize the adhesin protein P1 to the attachment organelle, and exhibit accelerated turnover of proteins HMW1, HMW3, and P65. Insertio...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/JB.181.14.4404-4410.1999

    authors: Fisseha M,Göhlmann HW,Herrmann R,Krause DC

    更新日期:1999-07-01 00:00:00

  • Salmonella typhimurium LT2 mutation affecting the deletion of resistance determinants on R plasmids.

    abstract::Plasmid Rms312, specifying resistance to tetracycline (Tc), chloramphenicol (Cm), streptomycin (Sm), sulfonamide (Su), and mercury chloride (Mer), deletes both Tc and Cm Sm Su Mer determinants at a high frequency in Salmonella typhimurium LT2. S. typhimurium mutants that were stable carriers of Rms312 were isolated by...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/JB.142.1.145-152.1980

    authors: Watanabe H,Hashimoto H,Mitsuhashi S

    更新日期:1980-04-01 00:00:00

  • Inhibition of Mengo virus by interferon.

    abstract::Gauntt, Charles J. (The University of Texas, Austin), and Royce Z. Lockart, Jr. Inhibition of Mengo virus by interferon. J. Bacteriol. 91:176-182. 1966.-The inhibition of Mengo virus replication in L cells resulting from interferon was studied quantitatively. Interferon was titrated on L cells with Western equine ence...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/JB.91.1.176-182.1966

    authors: Gauntt CJ,Lockart RZ Jr

    更新日期:1966-01-01 00:00:00

  • Evidence for multiple terminal oxidases, including cytochrome d, in facultatively alkaliphilic Bacillus firmus OF4.

    abstract::The terminal oxidase content of Bacillus firmus OF4, a facultative alkaliphile that grows well over the pH range of 7.5 to 10.5, was studied by difference spectroscopy. Evidence was found for three terminal oxidases under different growth conditions. The growth pH and the stage of growth profoundly affected the expres...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/jb.173.16.5010-5016.1991

    authors: Hicks DB,Plass RJ,Quirk PG

    更新日期:1991-08-01 00:00:00

  • The Yersinia Yop virulon: LcrV is required for extrusion of the translocators YopB and YopD.

    abstract::LcrV, an essential piece of the Yop virulon, is encoded by the large lcrGVsycDyopBD operon. In spite of repeated efforts, the role of LcrV in the Yop virulon remains elusive. In an attempt to clarify this, we engineered a complete deletion of lcrV in the pYV plasmid of Yersinia enterocolitica E40 and characterized the...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/JB.180.5.1207-1214.1998

    authors: Sarker MR,Neyt C,Stainier I,Cornelis GR

    更新日期:1998-03-01 00:00:00

  • Location of sites that inhibit progression of replication forks in the terminus region of Escherichia coli.

    abstract::We used a Southern hybridization assay to locate precisely the sites at which DNA replication is arrested in the terminus region of the Escherichia coli chromosome. The assay was based on the properties of restriction fragments that contain stalled replication forks. Replication forks that entered the terminus from th...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/jb.170.9.4293-4298.1988

    authors: Pelletier AJ,Hill TM,Kuempel PL

    更新日期:1988-09-01 00:00:00

  • Mutants of Salmonella typhimurium that are insensitive to catabolite repression of proline degradation.

    abstract::In Salmonella typhimurium the two enzymes of proline catabolism, proline oxidase and Delta(1)-pyrroline-5-carboxylic acid dehydrogenase, are subject to catabolite repression when the cells are grown in the presence of glucose. Mutants partially relieved of catabolite repression (PutR) for the proline catabolic enzymes...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/JB.111.2.375-382.1972

    authors: Newell SL,Brill WJ

    更新日期:1972-08-01 00:00:00

  • DNA supercoiling and suppression of the leu-500 promoter mutation.

    abstract::top mutations (formerly supX) eliminate DNA topoisomerase I activity and suppress the leu-500 promoter mutation in Salmonella typhimurium (K. M. Overbye, S. K. Basu, and P. Margolin, Cold Spring Harbor Symp. Quant. Biol. 47:785-791, 1983). Sublethal doses of coumermycin which reduce intracellular levels of supercoilin...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/JB.164.2.947-949.1985

    authors: Pruss GJ,Drlica K

    更新日期:1985-11-01 00:00:00

  • Streptococcus faecium ATCC 9790 penicillin-binding proteins and penicillin sensitivity are heavily influenced by growth conditions: proposal for an indirect mechanism of growth inhibition by beta-lactams.

    abstract::The effects of variations in growth conditions on the penicillin response of Streptococcus faecium ATCC 9790 were studied. Changes in the growth temperature and medium composition were found to cause striking changes in the bacterial generation time, cellular penicillin sensitivity (minimum inhibitory concentration), ...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/JB.154.2.916-923.1983

    authors: Fontana R,Canepari P,Satta G,Coyette J

    更新日期:1983-05-01 00:00:00

  • Distinct Contributions of Enzymic Functional Groups to the 2',3'-Cyclic Phosphodiesterase, 3'-Phosphate Guanylylation, and 3'-ppG/5'-OH Ligation Steps of the Escherichia coli RtcB Nucleic Acid Splicing Pathway.

    abstract:UNLABELLED:Escherichia coli RtcB is a founding member of a family of manganese-dependent RNA repair enzymes that join RNA 2′,3′-cyclic phosphate (RNA>p) or RNA 3′-phosphate (RNAp) ends to 5′-OH RNA (HORNA) ends in a multistep pathway whereby RtcB (i) hydrolyzes RNA>p to RNAp, (ii) transfers GMP from GTP to RNAp to form...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/JB.00913-15

    authors: Maughan WP,Shuman S

    更新日期:2016-03-31 00:00:00

  • Diversity of genome structure in Salmonella enterica serovar Typhi populations.

    abstract::The genomes of most strains of Salmonella and Escherichia coli are highly conserved. In contrast, all 136 wild-type strains of Salmonella enterica serovar Typhi analyzed by partial digestion with I-CeuI (an endonuclease which cuts within the rrn operons) and pulsed-field gel electrophoresis and by PCR have rearrangeme...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/JB.187.8.2638-2650.2005

    authors: Kothapalli S,Nair S,Alokam S,Pang T,Khakhria R,Woodward D,Johnson W,Stocker BA,Sanderson KE,Liu SL

    更新日期:2005-04-01 00:00:00

  • Chloramphenicol-sensitive and-insensitive phases of the lethal action of streptomycin.

    abstract::Hurwitz, Charles (Veterans Administration Hospital, Albany, N.Y.) and Carmen L. Rosano. Chloramphenicol-sensitive and -insensitive phases of the lethal action of streptomycin. J. Bacteriol. 83:1202-1209. 1962.-If chloramphenicol is added to sensitive Escherichia coli cells at the same time as streptomycin, the lethal ...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/JB.83.6.1202-1209.1962

    authors: HURWITZ C,ROSANO CL

    更新日期:1962-06-01 00:00:00