scholarly journals Competition of Escherichia coli DNA Polymerases I, II and III with DNA Pol IV in Stressed Cells

PLoS ONE ◽  
2010 ◽  
Vol 5 (5) ◽  
pp. e10862 ◽  
Author(s):  
P. J. Hastings ◽  
Megan N. Hersh ◽  
P. C. Thornton ◽  
Natalie C. Fonville ◽  
Andrew Slack ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Dna Polymerases ◽  
Pol Iv ◽  
Stressed Cells ◽  
Dna Pol Iv

scholarly journals Effect of SOS-induced Pol II, Pol IV, and Pol V DNA polymerases on UV-induced mutagenesis and MFD repair in Escherichia coli cells.

2005 ◽  
Vol 52 (1) ◽  
pp. 139-147
Author(s):  
Michał Wrzesiński ◽  
Anetta Nowosielska ◽  
Jadwiga Nieminuszczy ◽  
Elzbieta Grzesiuk
Keyword(s):  
Escherichia Coli ◽  
Uv Light ◽  
Dna Polymerases ◽  
Dna Lesions ◽  
Uv Mutagenesis ◽  
Pol Ii ◽  
Pol Iv ◽  
Pol V ◽  
Induced Mutagenesis ◽  
Pol Iii

Irradiation of organisms with UV light produces genotoxic and mutagenic lesions in DNA. Replication through these lesions (translesion DNA synthesis, TSL) in Escherichia coli requires polymerase V (Pol V) and polymerase III (Pol III) holoenzyme. However, some evidence indicates that in the absence of Pol V, and with Pol III inactivated in its proofreading activity by the mutD5 mutation, efficient TSL takes place. The aim of this work was to estimate the involvement of SOS-inducible DNA polymerases, Pol II, Pol IV and Pol V, in UV mutagenesis and in mutation frequency decline (MFD), a mechanism of repair of UV-induced damage to DNA under conditions of arrested protein synthesis. Using the argE3-->Arg(+) reversion to prototrophy system in E. coli AB1157, we found that the umuDC-encoded Pol V is the only SOS-inducible polymerase required for UV mutagenesis, since in its absence the level of Arg(+) revertants is extremely low and independent of Pol II and/or Pol IV. The low level of UV-induced Arg(+) revertants observed in the AB1157mutD5DumuDC strain indicates that under conditions of disturbed proofreading activity of Pol III and lack of Pol V, UV-induced lesions are bypassed without inducing mutations. The presented results also indicate that Pol V may provide substrates for MFD repair; moreover, we suggest that only those DNA lesions which result from umuDC-directed UV mutagenesis are subject to MFD repair.

scholarly journals Escherichia coli DNA Polymerase IV Mutator Activity: Genetic Requirements and Mutational Specificity

2000 ◽  
Vol 182 (16) ◽  
pp. 4587-4595 ◽  
Author(s):  
Jérôme Wagner ◽  
Takehiko Nohmi
Keyword(s):  
Escherichia Coli ◽  
Dna Polymerase ◽  
Amino Acid Level ◽  
Nucleotide Substitutions ◽  
Pol Iv ◽  
Mutator Activity ◽  
Sequence Homologies ◽  
In The Wild ◽  
Dna Polymerase Iv ◽  
Dna Pol Iv

ABSTRACT The dinB gene of Escherichia coli is known to be involved in the untargeted mutagenesis of λ phage. Recently, we have demonstrated that this damage-inducible and SOS-controlled gene encodes a novel DNA polymerase, DNA Pol IV, which is able to dramatically increase the untargeted mutagenesis of F′ plasmid. At the amino acid level, DNA Pol IV shares sequence homologies with E. coli UmuC (DNA Pol V), Rev1p, and Rad30p (DNA polymerase η) ofSaccharomyces cerevisiae and human Rad30A (XPV) proteins, all of which are involved in translesion DNA synthesis. To better characterize the Pol IV-dependent untargeted mutagenesis, i.e., the DNA Pol IV mutator activity, we analyzed the genetic requirements of this activity and determined the forward mutation spectrum generated by this protein within the cII gene of λ phage. The results indicated that the DNA Pol IV mutator activity is independent ofpolA, polB, recA,umuDC, uvrA, and mutS functions. The analysis of more than 300 independent mutations obtained in the wild-type or mutS background revealed that the mutator activity clearly promotes single-nucleotide substitutions as well as one-base deletions in the ratio of about 1:2. The base changes were strikingly biased for substitutions toward G:C base pairs, and about 70% of them occurred in 5′-GX-3′ sequences, where X represents the base (T, A, or C) that is mutated to G. These results are discussed with respect to the recently described biochemical characteristics of DNA Pol IV.

Roles of chromosomal and episomal dinB genes encoding DNA pol IV in targeted and untargeted mutagenesis in Escherichia coli

2001 ◽  
Vol 266 (2) ◽  
pp. 207-215 ◽  
Author(s):  
S.-R. Kim ◽  
K. Matsui ◽  
M. Yamada ◽  
P. Gruz ◽  
T. Nohmi
Keyword(s):  
Escherichia Coli ◽  
Pol Iv ◽  
Genes Encoding ◽  
Dna Pol Iv

scholarly journals Role of Accessory DNA Polymerases in DNA Replication in Escherichia coli: Analysis of the dnaX36 Mutator Mutant

2007 ◽  
Vol 190 (5) ◽  
pp. 1730-1742 ◽  
Author(s):  
Damian Gawel ◽  
Phuong T. Pham ◽  
Iwona J. Fijalkowska ◽  
Piotr Jonczyk ◽  
Roel M. Schaaper
Keyword(s):  
Escherichia Coli ◽  
Gene Dosage ◽  
Dna Polymerases ◽  
Dependent Manner ◽  
Mutator Phenotype ◽  
Pol Ii ◽  
Pol Iv ◽  
High Fraction ◽  
Pol Iii

ABSTRACT The dnaX36(TS) mutant of Escherichia coli confers a distinct mutator phenotype characterized by enhancement of transversion base substitutions and certain (−1) frameshift mutations. Here, we have further investigated the possible mechanism(s) underlying this mutator effect, focusing in particular on the role of the various E. coli DNA polymerases. The dnaX gene encodes the τ subunit of DNA polymerase III (Pol III) holoenzyme, the enzyme responsible for replication of the bacterial chromosome. The dnaX36 defect resides in the C-terminal domain V of τ, essential for interaction of τ with the α (polymerase) subunit, suggesting that the mutator phenotype is caused by an impaired or altered α-τ interaction. We previously proposed that the mutator activity results from aberrant processing of terminal mismatches created by Pol III insertion errors. The present results, including lack of interaction of dnaX36 with mutM, mutY, and recA defects, support our assumption that dnaX36-mediated mutations originate as errors of replication rather than DNA damage-related events. Second, an important role is described for DNA Pol II and Pol IV in preventing and producing, respectively, the mutations. In the system used, a high fraction of the mutations is dependent on the action of Pol IV in a (dinB) gene dosage-dependent manner. However, an even larger but opposing role is deduced for Pol II, revealing Pol II to be a major editor of Pol III mediated replication errors. Overall, the results provide insight into the interplay of the various DNA polymerases, and of τ subunit, in securing a high fidelity of replication.

scholarly journals An Active Site Aromatic Triad in Escherichia coli DNA Pol IV Coordinates Cell Survival and Mutagenesis in Different DNA Damaging Agents

PLoS ONE ◽  
2011 ◽  
Vol 6 (5) ◽  
pp. e19944 ◽  
Author(s):  
Ryan W. Benson ◽  
Matthew D. Norton ◽  
Ida Lin ◽  
William S. Du Comb ◽  
Veronica G. Godoy
Keyword(s):  
Escherichia Coli ◽  
Cell Survival ◽  
Active Site ◽  
Pol Iv ◽  
Dna Damaging Agents ◽  
Dna Pol Iv

scholarly journals Antimutator mutations in the alpha subunit of Escherichia coli DNA polymerase III: identification of the responsible mutations and alignment with other DNA polymerases.

Genetics ◽  
1993 ◽  
Vol 134 (4) ◽  
pp. 1039-1044 ◽  
Author(s):  
I J Fijalkowska ◽  
R M Schaaper
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Dna Polymerase ◽  
Dna Polymerases ◽  
Alpha Subunit ◽  
Sequence Motifs ◽  
Dna Polymerase Iii ◽  
Conserved Sequence ◽  
Polymerase Iii ◽  
Dna Replication Errors

Abstract The dnaE gene of Escherichia coli encodes the DNA polymerase (alpha subunit) of the main replicative enzyme, DNA polymerase III holoenzyme. We have previously identified this gene as the site of a series of seven antimutator mutations that specifically decrease the level of DNA replication errors. Here we report the nucleotide sequence changes in each of the different antimutator dnaE alleles. For each a single, but different, amino acid substitution was found among the 1,160 amino acids of the protein. The observed substitutions are generally nonconservative. All affected residues are located in the central one-third of the protein. Some insight into the function of the regions of polymerase III containing the affected residues was obtained by amino acid alignment with other DNA polymerases. We followed the principles developed in 1990 by M. Delarue et al. who have identified in DNA polymerases from a large number of prokaryotic and eukaryotic sources three highly conserved sequence motifs, which are suggested to contain components of the polymerase active site. We succeeded in finding these three conserved motifs in polymerase III as well. However, none of the amino acid substitutions responsible for the antimutator phenotype occurred at these sites. This and other observations suggest that the effect of these mutations may be exerted indirectly through effects on polymerase conformation and/or DNA/polymerase interactions.

scholarly journals Polymerases Leave Fingerprints: Analysis of the Mutational Spectrum in Escherichia coli rpoB To Assess the Role of Polymerase IV in Spontaneous Mutation

2004 ◽  
Vol 186 (9) ◽  
pp. 2900-2905 ◽  
Author(s):  
Erika Wolff ◽  
Mandy Kim ◽  
Kaibin Hu ◽  
Hanjing Yang ◽  
Jeffrey H. Miller
Keyword(s):  
Escherichia Coli ◽  
Exponential Growth ◽  
Hot Spots ◽  
Liquid Culture ◽  
Spontaneous Mutation ◽  
Mutational Spectrum ◽  
Pol Iv ◽  
Rifampin Resistance ◽  
Plasmid Amplification

ABSTRACT We compared the distribution of mutations in rpoB that lead to rifampin resistance in strains with differing levels of polymerase IV (Pol IV), including strains with deletions of the Pol IV-encoding dinB gene, strains with a chromosomal copy of dinB, strains with the F′128 plasmid, and strains with plasmid amplification of either the dinB operon (dinB-yafNOP) or the dinB gene alone. This analysis identifies several hot spots specific to Pol IV which are virtually absent from the normal spontaneous spectrum, indicating that Pol IV does not contribute significantly to mutations occurring during exponential growth in liquid culture.

Escherichia coli DNA polymerase II is homologous to α-like DNA polymerases

1991 ◽  
Vol 226-226 (1-2) ◽  
pp. 24-33 ◽  
Author(s):  
Hiroshi Iwasaki ◽  
Yoshizumi Ishino ◽  
Hiroyuki Toh ◽  
Atsuo Nakata ◽  
Hideo Shinagawa
Keyword(s):  
Escherichia Coli ◽  
Dna Polymerase ◽  
Dna Polymerases ◽  
Dna Polymerase Ii

scholarly journals A Novel DNA Polymerase Family Found inArchaea

1998 ◽  
Vol 180 (8) ◽  
pp. 2232-2236 ◽  
Author(s):  
Yoshizumi Ishino ◽  
Kayoko Komori ◽  
Isaac K. O. Cann ◽  
Yosuke Koga
Keyword(s):  
Escherichia Coli ◽  
Dna Polymerase ◽  
Pyrococcus Furiosus ◽  
Dna Polymerases ◽  
Open Reading Frames ◽  
Gene Products ◽  
Polymerase Gene ◽  
Hyperthermophilic Archaeon ◽  
Dna Polymerase Ii ◽  
Reading Frames

ABSTRACT One of the most puzzling results from the complete genome sequence of the methanogenic archaeon Methanococcus jannaschii was that the organism may have only one DNA polymerase gene. This is because no other DNA polymerase-like open reading frames (ORFs) were found besides one ORF having the typical α-like DNA polymerase (family B). Recently, we identified the genes of DNA polymerase II (the second DNA polymerase) from the hyperthermophilic archaeonPyrococcus furiosus, which has also at least one α-like DNA polymerase (T. Uemori, Y. Sato, I. Kato, H. Doi, and Y. Ishino, Genes Cells 2:499–512, 1997). The genes in M. jannaschiiencoding the proteins that are homologous to the DNA polymerase II ofP. furiosus have been located and cloned. The gene products of M. jannaschii expressed in Escherichia colihad both DNA polymerizing and 3′→5′ exonuclease activities. We propose here a novel DNA polymerase family which is entirely different from other hitherto-described DNA polymerases.

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