Archaeal DNA polymerase D but not DNA polymerase B is required for genome replication in Thermococcus kodakarensis.

Abstract:

:Three evolutionarily distinct families of replicative DNA polymerases, designated polymerase B (Pol B), Pol C, and Pol D, have been identified. Members of the Pol B family are present in all three domains of life, whereas Pol C exists only in Bacteria and Pol D exists only in Archaea. Pol B enzymes replicate eukaryotic chromosomal DNA, and as members of the Pol B family are present in all Archaea, it has been assumed that Pol B enzymes also replicate archaeal genomes. Here we report the construction of Thermococcus kodakarensis strains with mutations that delete or inactivate key functions of Pol B. T. kodakarensis strains lacking Pol B had no detectable loss in viability and no growth defects or changes in spontaneous mutation frequency but had increased sensitivity to UV irradiation. In contrast, we were unable to introduce mutations that inactivated either of the genes encoding the two subunits of Pol D. The results reported establish that Pol D is sufficient for viability and genome replication in T. kodakarensis and argue that Pol D rather than Pol B is likely the replicative DNA polymerase in this archaeon. The majority of Archaea contain Pol D, and, as discussed, if Pol D is the predominant replicative polymerase in Archaea, this profoundly impacts hypotheses for the origin(s), evolution, and distribution of the different DNA replication enzymes and systems now employed in the three domains of life.

journal_name

J Bacteriol

journal_title

Journal of bacteriology

authors

Cubonová L,Richardson T,Burkhart BW,Kelman Z,Connolly BA,Reeve JN,Santangelo TJ

doi

10.1128/JB.02037-12

subject

Has Abstract

pub_date

2013-05-01 00:00:00

pages

2322-8

issue

10

eissn

0021-9193

issn

1098-5530

pii

JB.02037-12

journal_volume

195

pub_type

杂志文章
  • Clustering of mutations affecting central pathway enzymes of carbohydrate catabolism in Pseudomonas aeruginosa.

    abstract::Mutations in carbohydrate-negative mutants of Pseudomonas aeruginosa PAO1 individually deficient in glucose 6-phosphate dehydrogenase (zwf), 6-phosphogluconate dehydratase (edd), or pyruvate carboxylase (pyc) were mapped on the chromosome by plasmid R68.45-mediated conjugation and by bacteriophage F116L-mediated trans...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/JB.156.3.1123-1129.1983

    authors: Roehl RA,Feary TW,Phibbs PV Jr

    更新日期:1983-12-01 00:00:00

  • Purification and characterization of a molybdenum-pterin-binding protein (Mop) in Clostridium pasteurianum W5.

    abstract::A large-scale fractionation scheme purified the major molybdenum(Mo)-binding protein (Mop) from crude extracts of Clostridium pasteurianum, with a 10 and 0.2% yield of Mo and protein, respectively. The apparent molecular weight of the purified molybdoprotein is 5,700, as determined by sodium dodecyl sulfate-polyacryla...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/jb.168.2.688-693.1986

    authors: Hinton SM,Merritt B

    更新日期:1986-11-01 00:00:00

  • Characterization of iucA and iucC genes of the aerobactin system of plasmid ColV-K30 in Escherichia coli.

    abstract::A cloned 8.3-kilobase-pair DNA fragment carrying all the genes (iucABCD iutA) of the aerobactin iron transport system of plasmid pColV-K30 was subjected to in vitro mutagenesis to afford mutant genes iucA, iucC, and iucA iucC. Complementation analyses and identification of aerobactin precursors accumulated by Escheric...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/jb.167.1.350-355.1986

    authors: de Lorenzo V,Neilands JB

    更新日期:1986-07-01 00:00:00

  • Characterization of the functional sites in the oriT region involved in DNA transfer promoted by sex factor plasmid R100.

    abstract::We have previously identified three sites, named sbi, ihfA, and sbyA, specifically recognized or bound by the TraI, IHF, and TraY proteins, respectively; these sites are involved in nicking at the origin of transfer, oriT, of plasmid R100. In the region next to these sites, there exists the sbm region, which consists ...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/jb.177.15.4350-4355.1995

    authors: Abo T,Ohtsubo E

    更新日期:1995-08-01 00:00:00

  • Anaerobic regulation of the hydrogenase 1 (hya) operon of Escherichia coli.

    abstract::Using a transcriptional fusion to the lacZ gene, we have analyzed the anaerobic regulation of the hydrogenase 1 (hya) operon in response to different anaerobic growth conditions and to mutations in regulatory genes. We found that the transcription of the hya operon was induced when the growth condition was changed fro...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/jb.176.17.5423-5428.1994

    authors: Brøndsted L,Atlung T

    更新日期:1994-09-01 00:00:00

  • Amphilphilic nature of spiralin, the major protein of the Spiroplasma citri cell membrane.

    abstract::Spiralin could not be solubilized in the absence of detergents, and it was shown by charge-shift crossed immunoelectrophoresis that this protein was capable of binding detergents under nondenaturing conditions. These properties indicate the amphiphilic nature of spiralin, which therefore should be regarded as an intri...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/JB.140.2.738-741.1979

    authors: Wróblewski H

    更新日期:1979-11-01 00:00:00

  • The mRNA for an inducible chloramphenicol acetyltransferase gene is cleaved into discrete fragments in Bacillus subtilis.

    abstract::cat-86 is a promoter-deficient plasmid gene that encodes chloramphenicol acetyltransferase (CAT). Insertion of a promoter at a site 144 base pairs 5' to the cat-86 coding sequence activates transcription of the gene and allows cat-86 to specify chloramphenicol-inducible CAT activity in Bacillus subtilis. Induction of ...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/jb.169.3.967-972.1987

    authors: Ambulos NP Jr,Duvall EJ,Lovett PS

    更新日期:1987-03-01 00:00:00

  • Use of the beta-lactamase inhibitor clavulanic acid in the isolation of auxotrophic mutants of Bacillus licheniformis.

    abstract::The isolation of auxotrophic mutants of Bacillus licheniformis, a microbe containing constitutive beta-lactamase activity, was found to be facilitated by the addition of clavulanic acid and cefotaxime during enrichment. ...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/JB.159.2.803-804.1984

    authors: Fields PI,Schreier HJ,Saha AL,Bernlohr RW

    更新日期:1984-08-01 00:00:00

  • A long T. A tract in the upp initially transcribed region is required for regulation of upp expression by UTP-dependent reiterative transcription in Escherichia coli.

    abstract::In Escherichia coli, pyrimidine-mediated regulation of upp expression occurs by UTP-sensitive selection of alternative transcriptional start sites, which produces transcripts that differ in the ability to be elongated. The upp initially transcribed region contains the sequence GATTTTTTTTG (nontemplate strand). Initiat...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/JB.183.1.221-228.2001

    authors: Cheng Y,Dylla SM,Turnbough CL Jr

    更新日期:2001-01-01 00:00:00

  • INHIBITORY ACTION OF PHAGE K ON STAPHYLOCOCCAL DEHYDROGENASES. II. ITS POSSIBLE RELATIONSHIP TO SENSITIZATION AND CELL LYSIS.

    abstract::Ralston, D. J. (University of California, Berkeley) and M. D. Perry. Inhibitory action of phage K on staphylococcal dehydrogenases. II. Its possible relationship to sensitization and cell lysis. J. Bacteriol. 86:740-748. 1963.-By measuring the reduction of the dye triphenyl tetrazolium chloride to the insoluble red fo...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/JB.86.4.740-748.1963

    authors: RALSTON DJ,PERRY MD

    更新日期:1963-10-01 00:00:00

  • Repair of extensive ionizing-radiation DNA damage at 95 degrees C in the hyperthermophilic archaeon Pyrococcus furiosus.

    abstract::We investigated the capacity of the hyperthermophile Pyrococcus furiosus for DNA repair by measuring survival at high levels of 60Co gamma-irradiation. The P. furiosus 2-Mb chromosome was fragmented into pieces ranging from 500 kb to shorter than 30 kb at a dose of 2,500 Gy and was fully restored upon incubation at 95...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/jb.179.14.4643-4645.1997

    authors: DiRuggiero J,Santangelo N,Nackerdien Z,Ravel J,Robb FT

    更新日期:1997-07-01 00:00:00

  • Regulation of the Streptomyces coelicolor calcium-dependent antibiotic by absA, encoding a cluster-linked two-component system.

    abstract::The Streptomyces coelicolor absA two-component system was initially identified through analysis of mutations in the sensor kinase absA1 that caused inhibition of all four antibiotics synthesized by this strain. Previous genetic analysis had suggested that the phosphorylated form of AbsA2 acted as a negative regulator ...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/jb.184.3.794-805.2002

    authors: Ryding NJ,Anderson TB,Champness WC

    更新日期:2002-02-01 00:00:00

  • Lowering S-adenosylmethionine levels in Escherichia coli modulates C-to-T transition mutations.

    abstract::Deoxycytosine methylase (Dcm) enzyme activity causes mutagenesis in vitro either directly by enzyme-induced deamination of cytosine to uracil in the absence of the methyl donor, S-adenosylmethionine (SAM), or indirectly through spontaneous deamination of [5-methyl]cytosine to thymine. Using a Lac reversion assay, we i...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/JB.183.3.921-927.2001

    authors: Macintyre G,Atwood CV,Cupples CG

    更新日期:2001-02-01 00:00:00

  • Identification of elements involved in transcriptional regulation of the Escherichia coli cad operon by external pH.

    abstract::Expression of the lysine decarboxylase gene (cadA) of Escherichia coli is induced upon external acidification. To dissect the molecular mechanisms responsible for this regulation, we analyzed a 4.2-kbp region upstream from cadA. DNA sequencing revealed two long open reading frames upstream of and on the same strand as...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/jb.174.2.530-540.1992

    authors: Watson N,Dunyak DS,Rosey EL,Slonczewski JL,Olson ER

    更新日期:1992-01-01 00:00:00

  • Comparison of dnaA nucleotide sequences of Escherichia coli, Salmonella typhimurium, and Serratia marcescens.

    abstract::The dnaA genes of Salmonella typhimurium and Serratia marcescens, which complemented the temperature-sensitive dnaA46 mutation of Escherichia coli, were cloned and sequenced. They were very homologous to the dnaA gene of E. coli. The 63 N-terminal amino acids and the 333 C-terminal amino acids of the corresponding Dna...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/jb.169.9.3976-3981.1987

    authors: Skovgaard O,Hansen FG

    更新日期:1987-09-01 00:00:00

  • Secretion of nuclease across the outer membrane of Serratia marcescens and its energy requirements.

    abstract::Extracellular secretion of Serratia marcescens nuclease occurs as a two-step process via a periplasmic intermediate. Unlike other extracellular proteins secreted by gram-negative bacteria by the general secretory pathway, nuclease accumulates in the periplasm in its active form for an unusually long time before its ex...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/jb.179.3.677-683.1997

    authors: Suh Y,Benedik MJ

    更新日期:1997-02-01 00:00:00

  • Specificity in deoxyribonucleic acid uptake by transformable Haemophilus influenzae.

    abstract::Cells of Haemophilus influenzae strain Rd competent for genetic transformation irreversibly bound approximately five molecular fragments of H. influenzae deoxyribonucleic acid (DNA) per cell; under identical conditions, DNA derived from Escherichia coli B was not taken up (<1 molecule per 50 cells). Similarly, DNA fro...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/JB.118.2.369-373.1974

    authors: Scocca JJ,Poland RL,Zoon KC

    更新日期:1974-05-01 00:00:00

  • CATALASE ACTIVITY IN ANAPLASMA MARGINALE.

    abstract::Wallace, W. R. (Louisiana State University, Baton Rouge), and G. T. Dimopoullos. Catalase activity in Anaplasma marginale. J. Bacteriol. 91:309-311. 1965.-Extracts of erythrocytes infected with Anaplasma marginale were found to contain more catalase activity than normal erythrocytic preparations. The increase in catal...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/JB.90.2.309-311.1965

    authors: WALLACE WR,DIMOPOULLOS GT

    更新日期:1965-08-01 00:00:00

  • Glucose- and glucokinase-controlled mal gene expression in Escherichia coli.

    abstract::MalT is the central transcriptional activator of all mal genes in Escherichia coli. Its activity is controlled by the inducer maltotriose. It can be inhibited by the interaction with certain proteins, and its expression can be controlled. We report here a novel aspect of mal gene regulation: the effect of cytoplasmic ...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/JB.00767-08

    authors: Lengsfeld C,Schönert S,Dippel R,Boos W

    更新日期:2009-02-01 00:00:00

  • Specialized transduction with lambda plac5: dependence on recB.

    abstract::Genetically disabled lambda plac5 transducing phage derivatives were used to study the recB dependence of recombination during specialized transduction. The frequency of transduction was normalized to colony-forming units, and the end product of recombination was monitored by scoring for addition and substitution tran...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/JB.150.3.1485-1488.1982

    authors: Porter RD,Welliver RA,Witkowski TA

    更新日期:1982-06-01 00:00:00

  • Identification of repressor binding sites controlling expression of tetracycline resistance encoded by Tn10.

    abstract::The regulatory region controlling the expression of tetracycline resistance and repressor genes contains two nearly identical regions of dyad symmetry. Deletions of this control region were isolated by digestion with S1 nuclease. The ability of these deletions to bind the tet repressor was determined by an in vivo rep...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/JB.156.3.1188-1191.1983

    authors: Wray LV Jr,Reznikoff WS

    更新日期:1983-12-01 00:00:00

  • Nucleotide sequence of a Pseudomonas denitrificans 5.4-kilobase DNA fragment containing five cob genes and identification of structural genes encoding S-adenosyl-L-methionine: uroporphyrinogen III methyltransferase and cobyrinic acid a,c-diamide synthase.

    abstract::A 5.4-kilobase DNA fragment carrying Pseudomonas denitrificans cob genes has been sequenced. The nucleotide sequence and genetic analysis revealed that this fragment carries five different cob genes (cobA to cobE). Four of these genes present the characteristics of translationally coupled genes. cobA has been identifi...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/jb.172.10.5968-5979.1990

    authors: Crouzet J,Cauchois L,Blanche F,Debussche L,Thibaut D,Rouyez MC,Rigault S,Mayaux JF,Cameron B

    更新日期:1990-10-01 00:00:00

  • Role for the A domain of unprocessed accumulation-associated protein (Aap) in the attachment phase of the Staphylococcus epidermidis biofilm phenotype.

    abstract::The polysaccharide intercellular adhesin or the cell wall-anchored accumulation-associated protein (Aap) mediates cellular accumulation during Staphylococcus epidermidis biofilm maturation. Mutation of sortase, which anchors up to 11 proteins (including Aap) to the cell wall, blocked biofilm development by the cerebro...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/JB.01946-14

    authors: Conlon BP,Geoghegan JA,Waters EM,McCarthy H,Rowe SE,Davies JR,Schaeffer CR,Foster TJ,Fey PD,O'Gara JP

    更新日期:2014-12-01 00:00:00

  • Tricistronic operon expression of the genes gcaD (tms), which encodes N-acetylglucosamine 1-phosphate uridyltransferase, prs, which encodes phosphoribosyl diphosphate synthetase, and ctc in vegetative cells of Bacillus subtilis.

    abstract::The gcaD, prs, and ctc genes were shown to be organized as a tricistronic operon. The transcription of the prs gene, measured as phosphoribosyl diphosphate synthetase activity, and of the ctc gene, measured as beta-galactosidase activity specified by a ctc-lacZ protein fusion, were dependent on the promoter in front o...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/jb.177.24.7280-7284.1995

    authors: Hilden I,Krath BN,Hove-Jensen B

    更新日期:1995-12-01 00:00:00

  • Mutations that affect control of the methylesterase activity of CheB, a component of the chemotaxis adaptation system in Escherichia coli.

    abstract::Sensory adaptation by the chemotaxis system of Escherichia coli requires adjustments of the extent of methyl esterification of the chemotaxis receptor proteins. One mechanism utilized by E. coli to make such adjustments is to control the activity of CheB, the enzyme responsible for removing receptor methyl ester group...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/jb.172.6.3388-3399.1990

    authors: Stewart RC,Roth AF,Dahlquist FW

    更新日期:1990-06-01 00:00:00

  • Murein structure and lack of DD- and LD-carboxypeptidase activities in Caulobacter crescentus.

    abstract::High-pressure liquid chromatography of a muramidase digest of murein sacculi from Caulobacter crescentus showed that the absence of D-alanine carboxypeptidase activity in the cells was reflected by a very high content of pentapeptide in the murein. Approximately half of the pentapeptide side chains were shown to conta...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/JB.156.2.649-655.1983

    authors: Markiewicz Z,Glauner B,Schwarz U

    更新日期:1983-11-01 00:00:00

  • Distance between alleles as a determinant of linkage in natural transformation of Acinetobacter calcoaceticus.

    abstract::Cotransformation frequencies of 16, 39, 51, and 60% were observed when donor alleles were separated by distances of 9.2, 7.4, 6.3, and 5.1 kb, respectively, in donor Acinetobacter calcoaceticus DNA. A different and unexpected pattern was observed when the distance between recipient alleles was reduced from 9.2 to 5.1 ...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/jb.177.20.6015-6017.1995

    authors: Kloos DU,DiMarco AA,Elsemore DA,Timmis KN,Ornston LN

    更新日期:1995-10-01 00:00:00

  • Substrate recognition properties of oligopeptidase B from Salmonella enterica serovar Typhimurium.

    abstract::Oligopeptidase B (OpdB) is a serine peptidase broadly distributed among unicellular eukaryotes, gram-negative bacteria, and spirochetes which has emerged as an important virulence factor and potential therapeutic target in infectious diseases. We report here the cloning and expression of the opdB homologue from Salmon...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/jb.184.12.3329-3337.2002

    authors: Morty RE,Fülöp V,Andrews NW

    更新日期:2002-06-01 00:00:00

  • Isolation and characterization of multiflagellate mutants of Pseudomonas aeruginosa.

    abstract::Multitrichously polar flagellated mutants were isolated from a monotrichously flagellated strain of Pseudomonas aeruginosa. The ability of the mutant cells to swarm in semisolid media at given gel strengths was increased by the multiflagellation. Observations of the mutant cells by electron microscopy revealed that th...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/JB.143.3.1471-1479.1980

    authors: Suzuki T,Iino T

    更新日期:1980-09-01 00:00:00

  • PHAGE ISOLATED FROM LYSOGENIC BACILLUS ANTHRACIS.

    abstract::Buck, C. A. (Kansas State University, Manhattan), R. L. Anacker, F. S. Newman, and A. Eisenstark. Phage isolated from lysogenic Bacillus anthracis. J. Bacteriol. 85:1423-1430. 1963.-Bacillus anthracis cultures (a total of 311) were obtained from several laboratories throughout the world; 139 of these were screened for...

    journal_title:Journal of bacteriology

    pub_type: 杂志文章

    doi:10.1128/JB.85.6.1423-1430.1963

    authors: BUCK CA,ANACKER RL,NEWMAN FS,EISENSTARK A

    更新日期:1963-06-01 00:00:00