Identification of a promoter motif regulating the major DNA damage response mechanism of

Gamulin, Vera; Ćetković, Helena; Ahel, Ivan

doi:10.1016/j.femsle.2004.07.017

Cited by 19 publications

(27 citation statements)

References 16 publications

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“…However, the molecular mechanisms of RecA-independent regulation of DNA repair genes had not yet been clearly defined in M. tuberculosis and related species. Using a bioinformatic approach, Gamulin et al (12) mapped out a highly conserved RecA-NDp motif within the promoter regions of 47 RecA-independent genes in M. tuberculosis. However, a regulator that recognizes and binds to the conserved RecA-NDp motif within these promoter regions had not been characterized.…”

Section: Discussionmentioning

confidence: 99%

“…However, a recent study found that expression of the DNA repair genes recA and recG were induced, and two other DNA repair genes, uvrB and uvrD2, were repressed when Rv2745c was overexpressed in M. tuberculosis CDC1551 (31). Curiously, all four DNA repair genes contain the conserved RecA-NDp motif in their promoter sequences (12). Using the MycoRegNet web tool, which is based on the the C. glutamicum transcriptional network CoryneRegNet (35) for analyzing mycobacterial transcriptional regulatory networks, Krawczyk et al (36) suggested that Rv2745c is involved in the SOS stress response and controls the expression of recR in M. tuberculosis.…”

Section: Discussionmentioning

confidence: 99%

“…Recently, a highly conserved motif was characterized by bioinformatics within the promoter regions of 47 RecA-independent genes in M. tuberculosis (12). The identified motif had high conservation in two blocks of consensus sequences, tTGTC(G/A)gtg and TAnnnT, which are similar to 70 recognition elements except that the two motifs in the RecA-independent gene promoters are positioned only eight nucleotides Tables S1-S3 and Fig.…”

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confidence: 99%

“…1 Both authors contributed equally to this work. 2 apart (12). This RecA-independent promoter (RecA-NDp) has been associated with DNA repair genes in M. tuberculosis and in many other Actinomycetales (12).…”

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confidence: 99%

“…2 apart (12). This RecA-independent promoter (RecA-NDp) has been associated with DNA repair genes in M. tuberculosis and in many other Actinomycetales (12). However, the transcription factor that recognizes the motif remains to be characterized in M. tuberculosis and related species.…”

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confidence: 99%

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ClpR Protein-like Regulator Specifically Recognizes RecA Protein-independent Promoter Motif and Broadly Regulates Expression of DNA Damage-inducible Genes in Mycobacteria

Wang¹,

Huang²,

Xue

et al. 2011

Journal of Biological Chemistry

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The RecA-dependent DNA damage response pathway (SOS response) appears to be the major DNA repair mechanism in most bacteria, but it has been suggested that a RecA-independent mechanism is responsible for controlling expression of most damage-inducible DNA repair genes in Mycobacterium tuberculosis. The specific reparative responses and molecular mediators involved in the DNA repair mechanism remain largely unclear in this pathogen and its related species. In this study, a mycobacterial ClpR-like regulator, corresponding to Rv2745c in M. tuberculosis and to Ms2694 in M. smegmatis mc 2 155, was found to interact with the promoter regions of multiple damage-inducible DNA repair genes. Specific binding of the ClpR-like factor to the conserved RecA-independent promoter RecA-NDp motif was then confirmed using in vitro electrophoretic mobility shift assays as well as in vivo chromatin immunoprecipitation experiments. The ClpR knock-out experiments, in combination with quantitative real time PCR assays, demonstrated that the expression of these RecA-independent genes were significantly down-regulated in the mutant strain of M. smegmatis in response to a DNA-damaging agent compared with the wild type strain. Furthermore, the ClpR-like factor was shown to contribute to mycobacterial genomic stability. These results enhance our understanding of the function of the ClpR regulator and the regulatory mechanism of RecA-independent DNA repair in mycobacteria.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

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confidence: 99%

mentioning

confidence: 99%

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ClpR Protein-like Regulator Specifically Recognizes RecA Protein-independent Promoter Motif and Broadly Regulates Expression of DNA Damage-inducible Genes in Mycobacteria

Wang¹,

Huang²,

Xue

et al. 2011

Journal of Biological Chemistry

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Streptomyces coelicolor macrodomain hydrolase SCO6735 cleaves thymidine-linked ADP-ribosylation of DNA

Hloušek-Kasun

Mikolčević²,

Rack³

et al. 2022

Computational and Structural Biotechnology Journal

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Characterisation of the Mycobacterium tuberculosis alternative sigma factor SigG: Its operon and regulon

Gaudion¹,

Dawson²,

Davis³

et al. 2013

Tuberculosis

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SummaryA major step in the pathogenesis of Mycobacterium tuberculosis is the ability to survive inside macrophages, where it is exposed to a number of DNA damaging agents. The alternative sigma factor SigG has been shown to be upregulated by DNA damaging agents and by macrophage infection, but not to regulate genes of the DNA repair pathway. Here we show that SigG is expressed from at least two promoters, the most dominant of these being the DNA damage inducible RecA_Ndp promoter. This promoter is located within the annotated coding region of SigG and so the correct translational start site was determined experimentally and found to be 114 bp downstream of the annotated start site. Examining the gene expression profile of a SigG over-expression strain found a small number of genes to up-regulated, two of these encoded proteins containing glyoxylase-like domains.

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Identification of a promoter motif regulating the major DNA damage response mechanism of

Cited by 19 publications

References 16 publications

ClpR Protein-like Regulator Specifically Recognizes RecA Protein-independent Promoter Motif and Broadly Regulates Expression of DNA Damage-inducible Genes in Mycobacteria

ClpR Protein-like Regulator Specifically Recognizes RecA Protein-independent Promoter Motif and Broadly Regulates Expression of DNA Damage-inducible Genes in Mycobacteria

Streptomyces coelicolor macrodomain hydrolase SCO6735 cleaves thymidine-linked ADP-ribosylation of DNA

Characterisation of the Mycobacterium tuberculosis alternative sigma factor SigG: Its operon and regulon

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