Definition of the Mycobacterial SOS Box and Use To Identify LexA-Regulated Genes in Mycobacterium tuberculosis

ABSTRACT The bases of the mycobacterial SOS box important for LexA binding were determined by replacing each base with every other and examining the effect on the induction of a reporter gene following DNA damage. This analysis revealed that the SOS box was longer than originally thought by 2 bp in each half of the palindromic site. A search of the Mycobacterium tuberculosis genome sequence with the new consensus, TCGAAC(N)4GTTCGA, identified 4 sites which were perfect matches and 12 sites with a single mismatch which were predicted to bind LexA. Genes which could potentially be regulated by these SOS boxes were ascertained from their positions relative to the sites. Examination of expression data for these genes following DNA damage identified 12 new genes which are most likely regulated by LexA as well as the known M. tuberculosis DNA damage-inducible genes recA, lexA, and ruvC. Of these 12 genes, only 2 have a predicted function: dnaE2, a component of DNA polymerase III, and linB, which is similar to 1,3,4,6-tetrachloro-1,4-cylcohexadiene hydrolase. Curiously, of the remaining 10 genes predicted to be LexA regulated, 7 are members of the M. tuberculosis 13E12 repeat family, which has some of the characteristics of mobile elements.

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Identification of Some DNA Damage-Inducible Genes of Mycobacterium tuberculosis: Apparent Lack of Correlation with LexA Binding

Journal of Bacteriology ◽

10.1128/jb.183.15.4459-4467.2001 ◽

2001 ◽

Vol 183 (15) ◽

pp. 4459-4467 ◽

Cited By ~ 49

Author(s):

Patricia C. Brooks ◽

Farahnaz Movahedzadeh ◽

Elaine O. Davis

Keyword(s):

Escherichia Coli ◽

Dna Damage ◽

Mycobacterium Tuberculosis ◽

Binding Sites ◽

Alternative Mechanism ◽

Intracellular Pathogens ◽

Apparent Lack ◽

E Coli ◽

Lexa Binding ◽

Inducible Genes

ABSTRACT The repair of DNA damage is expected to be particularly important to intracellular pathogens such as Mycobacterium tuberculosis, and so it is of interest to examine the response ofM. tuberculosis to DNA damage. The expression ofrecA, a key component in DNA repair and recombination, is induced by DNA damage in M. tuberculosis. In this study, we have analyzed the expression following DNA damage in M. tuberculosis of a number of other genes which are DNA damage inducible in Escherichia coli. While many of these genes were also induced by DNA damage in M. tuberculosis, some were not. In addition, one gene (ruvC) which is not induced by DNA damage in E. coli was induced in M. tuberculosis, a result likely linked to its different transcriptional arrangement in M. tuberculosis. We also searched the sequences upstream of the genes being studied for the mycobacterial SOS box (the binding site for LexA) and assessed LexA binding to potential sites identified. LexA is the repressor protein responsible for regulating expression of these SOS genes in E. coli. However, two of the genes which were DNA damage inducible in M. tuberculosis did not have identifiable sites to which LexA bound. The absence of binding sites for LexA upstream of these genes was confirmed by analysis of LexA binding to overlapping DNA fragments covering a region from 500 bp upstream of the coding sequence to 100 bp within it. Therefore, it appears most likely that an alternative mechanism of gene regulation in response to DNA damage exists in M. tuberculosis.

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A Tale of Ice and Fire: The Dual Role for 17β-Estradiol in Balancing DNA Damage and Genome Integrity

Cancers ◽

10.3390/cancers13071583 ◽

2021 ◽

Vol 13 (7) ◽

pp. 1583

Author(s):

Sara Pescatori ◽

Francesco Berardinelli ◽

Jacopo Albanesi ◽

Paolo Ascenzi ◽

Maria Marino ◽

...

Keyword(s):

Dna Damage ◽

Cellular Transformation ◽

Genome Integrity ◽

Physiological Effects ◽

Dna Damages ◽

Cellular Effects ◽

Damage Response ◽

17Β Estradiol ◽

Cellular Pathways ◽

Definition Of

17β-estradiol (E2) regulates human physiology both in females and in males. At the same time, E2 acts as a genotoxic substance as it could induce DNA damages, causing the initiation of cellular transformation. Indeed, increased E2 plasma levels are a risk factor for the development of several types of cancers including breast cancer. This paradoxical identity of E2 undermines the foundations of the physiological definition of “hormone” as E2 works both as a homeostatic regulator of body functions and as a genotoxic compound. Here, (i) the molecular circuitries underlying this double face of E2 are reviewed, and (ii) a possible framework to reconcile the intrinsic discrepancies of the E2 function is reported. Indeed, E2 is a regulator of the DNA damage response, which this hormone exploits to calibrate its genotoxicity with its physiological effects. Accordingly, the genes required to maintain genome integrity belong to the E2-controlled cellular signaling network and are essential for the appearance of the E2-induced cellular effects. This concept requires an “upgrade” to the vision of E2 as a “genotoxic hormone”, which balances physiological and detrimental pathways to guarantee human body homeostasis. Deregulation of this equilibrium between cellular pathways would determine the E2 pathological effects.

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Interactions and Localization of Escherichia coli Error-Prone DNA Polymerase IV after DNA Damage

Journal of Bacteriology ◽

10.1128/jb.00101-15 ◽

2015 ◽

Vol 197 (17) ◽

pp. 2792-2809 ◽

Cited By ~ 20

Author(s):

Sarita Mallik ◽

Ellen M. Popodi ◽

Andrew J. Hanson ◽

Patricia L. Foster

Keyword(s):

Dna Damage ◽

Dna Polymerase ◽

Dna Helicase ◽

Dna Lesions ◽

Replication Forks ◽

Content Type ◽

Pol Iv ◽

Dna Polymerase Iv ◽

Stalled Replication Forks

ABSTRACTEscherichia coli's DNA polymerase IV (Pol IV/DinB), a member of the Y family of error-prone polymerases, is induced during the SOS response to DNA damage and is responsible for translesion bypass and adaptive (stress-induced) mutation. In this study, the localization of Pol IV after DNA damage was followed using fluorescent fusions. After exposure ofE. colito DNA-damaging agents, fluorescently tagged Pol IV localized to the nucleoid as foci. Stepwise photobleaching indicated ∼60% of the foci consisted of three Pol IV molecules, while ∼40% consisted of six Pol IV molecules. Fluorescently tagged Rep, a replication accessory DNA helicase, was recruited to the Pol IV foci after DNA damage, suggesting that thein vitrointeraction between Rep and Pol IV reported previously also occursin vivo. Fluorescently tagged RecA also formed foci after DNA damage, and Pol IV localized to them. To investigate if Pol IV localizes to double-strand breaks (DSBs), an I-SceI endonuclease-mediated DSB was introduced close to a fluorescently labeled LacO array on the chromosome. After DSB induction, Pol IV localized to the DSB site in ∼70% of SOS-induced cells. RecA also formed foci at the DSB sites, and Pol IV localized to the RecA foci. These results suggest that Pol IV interacts with RecAin vivoand is recruited to sites of DSBs to aid in the restoration of DNA replication.IMPORTANCEDNA polymerase IV (Pol IV/DinB) is an error-prone DNA polymerase capable of bypassing DNA lesions and aiding in the restart of stalled replication forks. In this work, we demonstratein vivolocalization of fluorescently tagged Pol IV to the nucleoid after DNA damage and to DNA double-strand breaks. We show colocalization of Pol IV with two proteins: Rep DNA helicase, which participates in replication, and RecA, which catalyzes recombinational repair of stalled replication forks. Time course experiments suggest that Pol IV recruits Rep and that RecA recruits Pol IV. These findings providein vivoevidence that Pol IV aids in maintaining genomic stability not only by bypassing DNA lesions but also by participating in the restoration of stalled replication forks.

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Depletion of the DarG antitoxin in Mycobacterium tuberculosis triggers the DNA‐damage response and leads to cell death

Molecular Microbiology ◽

10.1111/mmi.14571 ◽

2020 ◽

Vol 114 (4) ◽

pp. 641-652 ◽

Cited By ~ 1

Author(s):

Anisha Zaveri ◽

Ruojun Wang ◽

Laure Botella ◽

Ritu Sharma ◽

Linnan Zhu ◽

...

Keyword(s):

Dna Damage ◽

Cell Death ◽

Mycobacterium Tuberculosis ◽

Dna Damage Response ◽

Damage Response

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NSC666715 and Its Analogs Inhibit Strand-Displacement Activity of DNA Polymerase β and Potentiate Temozolomide-Induced DNA Damage, Senescence and Apoptosis in Colorectal Cancer Cells

PLoS ONE ◽

10.1371/journal.pone.0123808 ◽

2015 ◽

Vol 10 (5) ◽

pp. e0123808 ◽

Cited By ~ 12

Author(s):

Aruna S. Jaiswal ◽

Harekrushna Panda ◽

Brian K. Law ◽

Jay Sharma ◽

Jitesh Jani ◽

...

Keyword(s):

Colorectal Cancer ◽

Dna Damage ◽

Cancer Cells ◽

Dna Polymerase ◽

Strand Displacement ◽

Dna Polymerase Β ◽

Displacement Activity ◽

Colorectal Cancer Cells

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KGF facilitates repair of radiation-induced DNA damage in alveolar epithelial cells

AJP Lung Cellular and Molecular Physiology ◽

10.1152/ajplung.1997.272.6.l1174 ◽

1997 ◽

Vol 272 (6) ◽

pp. L1174-L1180 ◽

Cited By ~ 25

Author(s):

M. Takeoka ◽

W. F. Ward ◽

H. Pollack ◽

D. W. Kamp ◽

R. J. Panos

Keyword(s):

Dna Damage ◽

Dna Repair ◽

Epithelial Cells ◽

Dna Polymerase ◽

Dna Polymerases ◽

Dna Strand Breaks ◽

Strand Breaks ◽

Alveolar Epithelial ◽

Radiation Induced ◽

Dna Strand

Administration of exogenous keratinocyte growth factor (KGF) prevents or attenuates several forms of oxidant-mediated lung injury. Because DNA damage in epithelial cells is a component of radiation pneumotoxicity, we determined whether KGF ameliorated DNA strand breaks in irradiated A549 cells. Cells were exposed to 137Cs gamma rays, and DNA damage was measured by alkaline unwinding and ethidium bromide fluorescence after a 30-min recovery period. Radiation induced a dose-dependent increase in DNA strand breaks. The percentage of double-stranded DNA after exposure to 30 Gy increased from 44.6 +/- 3.5% in untreated control cells to 61.6 +/- 5.0% in cells cultured with 100 ng/ml KGF for 24 h (P < 0.05). No reduction in DNA damage occurred when the cells were cultured with KGF but maintained at 0 degree C during and after irradiation. The sparing effect of KGF on radiation-induced DNA damage was blocked by aphidicolin, an inhibitor of DNA polymerases-alpha, -delta, and -epsilon and by butylphenyl dGTP, which blocks DNA polymerase-alpha strongly and polymerases-delta and -epsilon less effectively. However, dideoxythymidine triphosphate, a specific inhibitor of DNA polymerase-beta, did not abrogate the KGF effect. Thus KGF increases DNA repair capacity in irradiated pulmonary epithelial cells, an effect mediated at least in part by DNA polymerases-alpha, -delta, and -epsilon. Enhancement of DNA repair capability after cell damage may be one mechanism by which KGF is able to ameliorate oxidant-mediated alveolar epithelial injury.

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Characterization of the Two Mycobacterium tuberculosis recA Promoters

Journal of Bacteriology ◽

10.1128/jb.185.20.6005-6015.2003 ◽

2003 ◽

Vol 185 (20) ◽

pp. 6005-6015 ◽

Cited By ~ 21

Author(s):

Krishna K. Gopaul ◽

Patricia C. Brooks ◽

Jean-François Prost ◽

Elaine O. Davis

Keyword(s):

Escherichia Coli ◽

Dna Damage ◽

Mycobacterium Tuberculosis ◽

Promoter Activity ◽

The Other ◽

Expression Level ◽

Promoter Elements ◽

Kinetics Of

ABSTRACT The recA gene of Mycobacterium tuberculosis is unusual in that it is expressed from two promoters, one of which, P1, is DNA damage inducible independently of LexA and RecA, while the other, P2, is regulated by LexA in the classical way (E. O. Davis, B. Springer, K. K. Gopaul, K. G. Papavinasasundaram, P. Sander, and E. C. Böttger, Mol. Microbiol. 46:791-800, 2002). In this study we characterized these two promoters in more detail. Firstly, we localized the promoter elements for each of the promoters, and in so doing we identified a mutation in each promoter which eliminates promoter activity. Interestingly, a motif with similarity to Escherichia coli σ70 −35 elements but located much closer to the −10 element is important for optimal expression of P1, whereas the sequence at the −35 location is not. Secondly, we found that the sequences flanking the promoters can have a profound effect on the expression level directed by each of the promoters. Finally, we examined the contribution of each of the promoters to recA expression and compared their kinetics of induction following DNA damage.

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