Induction of the Escherichia coli aidB gene under oxygen-limiting conditions requires a functional rpoS (katF) gene

Volkert, Michael R.; Hajec, Laurel I.; Matijašević, Zdenka; Fang, Ferric C.; Prince, Robert W.

doi:10.1128/jb.176.24.7638-7645.1994

Cited by 50 publications

(29 citation statements)

References 44 publications

(58 reference statements)

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“…In this state, rapid de novo protein synthesis may not be possible, and this may explain why certain activities that can be induced during exponential growth in response to external stresses are present at constitutively higher levels in stationary phase. The Ada protein, as reported in this paper, AidB, hydroperoxidase HPII, exonuclease III (apurinic endonuclease), and Dps (DNA binding protein) are notable examples of such activities (1,38,50,51) and together enhance the resistance of stationary-phase cells to sources of DNA-methylating agents and oxidative stress. The alternative sigma subunit of RNA polymerase, RpoS, is induced to a higher level in early-stationary-phase cells and has a central role in regulating expression of many genes under this condition (26), and, as shown here, this includes the ada gene.…”

Section: Discussionmentioning

confidence: 68%

Generation of an endogenous DNA-methylating agent by nitrosation in Escherichia coli

Taverna¹,

Sedgwick²

1996

J Bacteriol

144

113

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Escherichia coli ada ogt mutants, which are totally deficient in O 6 -methylguanine-DNA methyltransferases, have an increased spontaneous mutation rate. This phenotype is particularly evident in starving cells and suggests the generation of an endogenous DNA alkylating agent under this growth condition. We have found that in wild-type cells, the level of the inducible Ada protein is 20-fold higher in stationary-phase and starving cells than in rapidly growing cells, thus enhancing the defense of these cells against DNA damage. The increased level of Ada in stationary cells is dependent on RpoS, a stationary-phase-specific sigma subunit of RNA polymerase. We have also identified a potential source of the mutagenic agent. Nitrosation of amides and related compounds can generate directly acting methylating agents and can be catalyzed by bacterial enzymes. E. coli moa mutants, which are defective in the synthesis of a molybdopterin cofactor required by several reductases, are deficient in nitrosation activity. It is reported here that a moa mutant shows reduced generation of a mutagenic methylating agent from methylamine (or methylurea) and nitrite added to agar plates. Moreover, a moa mutation eliminates much of the spontaneous mutagenesis in ada ogt mutants. These observations indicate that the major endogenous mutagen is not S-adenosylmethionine but arises by bacterially catalyzed nitrosation.Only a few types of cancer have been attributed to environmental agents. Other carcinogens of primary concern may be transient but highly reactive metabolites that arise during normal metabolism (24, 36). Indeed, several metabolites of amino acids, sugars, oxygen, and lipids are known to be mutagenic. It is, therefore, important to identify metabolites that damage DNA in vivo and result in spontaneous mutagenesis in the absence of adequate DNA repair. For example, reactive oxygen species generated during aerobic metabolism damage DNA bases and sugar residues. Specific oxygen radical detoxification and DNA repair mechanisms prevent or remove this damage (13,14). The increase in the rate of spontaneous mutagenesis in bacteria and yeast mutants that are specifically deficient in the repair of aberrantly methylated DNA bases indicates that methylation of DNA also occurs endogenously (16,34,52,53). Rodent cells may be similarly affected (2).The major mutagenic adduct induced in DNA by methylating agents is O 6 -methylguanine (O 6 -meG). This modified base mispairs with thymine during DNA replication, resulting in GC-to-AT transition mutations. In wild-type cells, O 6 -meG is repaired by ubiquitous O 6 -meG-DNA methyltransferases that directly transfer the methyl group from the modified base to one of their own cysteine residues. As a result of this process, the methyltransferases are inactivated (25). Escherichia coli has two O 6 -meG-DNA methyltransferases, a constitutive Ogt protein and an inducible Ada protein. Each exponentially growing cell contains only two to four molecules of Ada protein and 10-fold more Ogt protein (32,3...

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Section: Discussionmentioning

confidence: 68%

Generation of an endogenous DNA-methylating agent by nitrosation in Escherichia coli

Taverna¹,

Sedgwick²

1996

J Bacteriol

144

113

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“…A similar role has been observed in the Dps protein, which protects DNA in starved E. coli against oxidative damage (11,12). Both AidB and Dps are up-regulated during stationary phase and are rpoSdependent (13,14). Interestingly, endogenous methylating agents such as nitrosamines are formed as by-products of stationary-phase metabolism (15).…”

Section: Discussionmentioning

confidence: 73%

Structure and DNA binding of alkylation response protein AidB

Bowles

Metz

O'Quin

et al. 2008

Proc. Natl. Acad. Sci. U.S.A.

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Exposure of Escherichia coli to alkylating agents activates expression of AidB in addition to DNA repair proteins Ada, AlkA, and AlkB. AidB was recently shown to possess a flavin adenine dinucleotide (FAD) cofactor and to bind to dsDNA, implicating it as a flavindependent DNA repair enzyme. However, the molecular mechanism by which AidB acts to reduce the mutagenic effects of specific DNA alkylators is unknown. We present a 1.7-Å crystal structure of AidB, which bears superficial resemblance to the acyl-CoA dehydrogenase superfamily of flavoproteins. The structure reveals a unique quaternary organization and a distinctive FAD active site that provides a rationale for AidB's limited dehydrogenase activity. A highly electropositive C-terminal domain not present in structural homologs was identified by mutational analysis as the DNA binding site. Structural analysis of the DNA and FAD binding sites provides evidence against AidB-catalyzed DNA repair and supports a model in which AidB acts to prevent alkylation damage by protecting DNA and destroying alkylating agents that have yet to reach their DNA target.acyl-CoA dehydrogenase ͉ adaptive response ͉ DNA repair ͉ flavin adenine dinucleotide

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“…Strains and Plasmids-The strains used in this study are the E. coli K12 strains MV1161 and its rpoS derivative MV2792 (34). These strains were transformed with derivatives of the reporter plasmid pRS1274 (36) carrying lacZ fusions under the control of either the wild type aidB promoter or its mutant derivatives.…”

Section: Methodsmentioning

confidence: 99%

“…The Ada protein, in its methylated form ( me Ada), can activate transcription at the aidB promoter (PaidB) by both the E 70 and E S forms of RNA polymerase (32,33). However, in the absence of activation by Ada, aidB expression is strictly S -dependent in vivo, and only the E S form of RNA polymerase can efficiently carry out transcription from PaidB in vitro (34,35). Although E 70 can bind PaidB in vitro in the absence of any activator, binding by E 70 results in an unusual complex that is partially resistant to heparin challenge but unable to carry out full promoter opening and transcription initiation (21).…”

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confidence: 99%

Nucleotides from –16 to –12 Determine Specific Promoter Recognition by Bacterial σS-RNA Polymerase

Lacour

Kolb

Landini

2003

Journal of Biological Chemistry

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The alternative sigma factor S , mainly active in stationary phase of growth, recognizes in vitro a ؊10 promoter sequence almost identical to the one for the main sigma factor, 70 , thus raising the problem of how specific promoter recognition by S -RNA polymerase (E S ) is achieved in vivo. We investigated the promoter features involved in selective recognition by E S at the strictly S -dependent aidB promoter. We show that the presence of a C nucleotide as first residue of the aidB ؊10 sequence (؊12C), instead of the T nucleotide canonical for 70 -dependent promoters, is the major determinant for selective recognition by E S . The presence of the ؊12C does not allow formation of an open complex fully proficient in transcription initiation by E 70 . The role of ؊12C as specific determinant for promoter recognition by E S was confirmed by sequence analysis of known E S -dependent promoters as well as site-directed mutagenesis at the promoters of the csgB and sprE genes. We propose that E S , unlike E 70 , can recognize both C and T as the first nucleotide in the ؊10 sequence. Additional promoter features such as the presence of a C nucleotide at position ؊13, contributing to open complex formation by E S , and a TG motif found at the unusual ؊16/؊15 location, possibly contributing to initial binding to the promoter, also represent important factors for S -dependent transcription. We propose a new sequence, TG(N) 0 -2 CCATA(c/a)T, as consensus ؊10 sequence for promoters exclusively recognized by E S .Bacterial cells adapt to changing environmental and physiological conditions by modulating gene expression. Sigma ( ) factors of RNA polymerase, as the subunits responsible for promoter recognition, play a major role in programming gene expression. At least seven different subunits have been identified in Escherichia coli; 70 is the main subunit and can carry out transcription from the majority of E. coli promoters. The alternative subunits can direct transcription toward specific sets of genes (i.e. heat-shock, extracellular proteins, etc.) whose transcription is directed by -specific promoter sequences. A partial exception to the typical role for alternative subunits is represented by S , the product of the rpoS gene, mainly expressed in the stationary phase of growth (1-3). Unlike the other subunits, S -RNA polymerase (E S ) 1 can initiate transcription from several promoters also recognized by E 70 , suggesting that they recognize similar promoter sequences (4). The recognition of similar promoter sequences by S and 70 is reflected by their strong similarity in the DNA binding domains (5). The alignment of E S -dependent promoters and the search for an optimal promoter for E S in vitro using the systematic evolution of ligands by exponential enrichment (SELEX) procedure have pointed to a Ϫ10 consensus sequence for E S , CTATA(c/a)T that is very similar to the canonical TATAAT sequence for 70 (6 -10). These results suggest that promoter selectivity between 70 and S might be determined by factors other than promote...

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Induction of the Escherichia coli aidB gene under oxygen-limiting conditions requires a functional rpoS (katF) gene

Cited by 50 publications

References 44 publications

Generation of an endogenous DNA-methylating agent by nitrosation in Escherichia coli

Generation of an endogenous DNA-methylating agent by nitrosation in Escherichia coli

Structure and DNA binding of alkylation response protein AidB

Nucleotides from –16 to –12 Determine Specific Promoter Recognition by Bacterial σS-RNA Polymerase

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