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Burby PE, Simmons LA. A bacterial DNA repair pathway specific to a natural antibiotic. Mol Microbiol 2018; 111:338-353. [PMID: 30379365 DOI: 10.1111/mmi.14158] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/28/2018] [Indexed: 12/17/2022]
Abstract
All organisms possess DNA repair pathways that are used to maintain the integrity of their genetic material. Although many DNA repair pathways are well understood, new pathways continue to be discovered. Here, we report an antibiotic specific DNA repair pathway in Bacillus subtilis that is composed of a previously uncharacterized helicase (mrfA) and exonuclease (mrfB). Deletion of mrfA and mrfB results in sensitivity to the DNA damaging agent mitomycin C, but not to any other type of DNA damage tested. We show that MrfAB function independent of canonical nucleotide excision repair, forming a novel excision repair pathway. We demonstrate that MrfB is a metal-dependent exonuclease and that the N-terminus of MrfB is required for interaction with MrfA. We determined that MrfAB failed to unhook interstrand cross-links in vivo, suggesting that MrfAB are specific to the monoadduct or the intrastrand cross-link. A phylogenetic analysis uncovered MrfAB homologs in diverse bacterial phyla, and cross-complementation indicates that MrfAB function is conserved in closely related species. B. subtilis is a soil dwelling organism and mitomycin C is a natural antibiotic produced by the soil bacterium Streptomyces lavendulae. The specificity of MrfAB suggests that these proteins are an adaptation to environments with mitomycin producing bacteria.
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Affiliation(s)
- Peter E Burby
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Lyle A Simmons
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
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Jalili Z, Saleh M, Bouzari S, Pooya M. Characterization of killed but metabolically active uropathogenic Escherichia coli strain as possible vaccine candidate for urinary tract infection. Microb Pathog 2018; 122:184-190. [DOI: 10.1016/j.micpath.2018.06.027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Revised: 05/28/2018] [Accepted: 06/15/2018] [Indexed: 12/19/2022]
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Moghaddam TK, Zhang J, Du G. UvrA expression of Lactococcus lactis NZ9000 improve multiple stresses tolerance and fermentation of lactic acid against salt stress. Journal of Food Science and Technology 2017; 54:639-649. [PMID: 28298677 DOI: 10.1007/s13197-017-2493-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 12/30/2016] [Accepted: 01/11/2017] [Indexed: 11/25/2022]
Abstract
Lactococcus lactis is subjected to several stressful conditions during industrial fermentation including oxidation, heating and cooling, acid, high osmolarity/dehydration and starvation. DNA lesion is a major cause of genetic instability in L. lactis that usually occurs at a low frequency, but it is greatly enhanced by environmental stresses. DNA damages produced by these environmental stresses are thought to induce DNA double-strand breaks, leading to illegitimate recombination. Nucleotide excision repair (NER) protein UvrA suppresses multiple stresses-induced illegitimate recombination. UvrA protein can survive a coincident condition of environmental harsh conditions, multiple stress factors supposedly encountered in the host and inducing UvrA in L. lactis. In this study the expression of UvrA and growth performance and viability of control strain L. lactisVector and recombinant strain L. lactisUvrA under multiple stress conditions were determined. The recombinants strain had 30.70 and 52.67% higher growth performances when subjected to acidic and osmotic stresses conditions. In addition, the L. lactisUvrA strain showed 1.85-, 1.65-, and 2.40-fold higher biomass, lactate production, and lactate productivity, compared with the corresponding values for L. lactisVector strain during the osmotic stress. Results demonstrated NER system is involved in adaptation to various stress conditions and suggested that cells with a compromised UvrA as DNA repair system have an enhanced protection behavior in L. lactis NZ9000 against DNA damage.
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Affiliation(s)
- Taher Khakpour Moghaddam
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, Jiangsu 214122 People's Republic of China.,School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122 People's Republic of China
| | - Juan Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, Jiangsu 214122 People's Republic of China.,School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122 People's Republic of China
| | - Guocheng Du
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, Jiangsu 214122 People's Republic of China.,School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122 People's Republic of China
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Cho Endonuclease Functions during DNA Interstrand Cross-Link Repair in Escherichia coli. J Bacteriol 2016; 198:3099-3108. [PMID: 27573016 DOI: 10.1128/jb.00509-16] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 08/22/2016] [Indexed: 01/21/2023] Open
Abstract
DNA interstrand cross-links are complex lesions that covalently link both strands of the duplex DNA. Lesion removal is proposed to be initiated via the UvrABC nucleotide excision repair complex; however, less is known about the subsequent steps of this complex repair pathway. In this study, we characterized the contribution of nucleotide excision repair mutants to survival in the presence of psoralen-induced damage. Unexpectedly, we observed that the nucleotide excision repair mutants exhibit differential sensitivity to psoralen-induced damage, with uvrC mutants being less sensitive than either uvrA or uvrB We show that Cho, an alternative endonuclease, acts with UvrAB and is responsible for the reduced hypersensitivity of uvrC mutants. We find that Cho's contribution to survival correlates with the presence of DNA interstrand cross-links, rather than monoadducts, and operates at a step after, or independently from, the initial incision during the global repair of psoralen DNA adducts from the genome. IMPORTANCE DNA interstrand cross-links are complex lesions that covalently bind to both strands of the duplex DNA and whose mechanism of repair remains poorly understood. In this study, we show that Cho, an alternative endonuclease, acts with UvrAB and participates in the repair of DNA interstrand cross-links formed in the presence of photoactivated psoralens. Cho's contribution to survival correlates with the presence of DNA interstrand cross-links and operates at a step after, or independently from, the initial incision during the repair process.
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Acosta S, Carela M, Garcia-Gonzalez A, Gines M, Vicens L, Cruet R, Massey SE. DNA Repair Is Associated with Information Content in Bacteria, Archaea, and DNA Viruses. J Hered 2015; 106:644-59. [PMID: 26320243 DOI: 10.1093/jhered/esv055] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 07/07/2015] [Indexed: 11/13/2022] Open
Abstract
The concept of a "proteomic constraint" proposes that DNA repair capacity is positively correlated with the information content of a genome, which can be approximated to the size of the proteome (P). This in turn implies that DNA repair genes are more likely to be present in genomes with larger values of P. This stands in contrast to the common assumption that informational genes have a core function and so are evenly distributed across organisms. We examined the presence/absence of 18 DNA repair genes in bacterial genomes. A positive relationship between gene presence and P was observed for 17 genes in the total dataset, and 16 genes when only nonintracellular bacteria were examined. A marked reduction of DNA repair genes was observed in intracellular bacteria, consistent with their reduced value of P. We also examined archaeal and DNA virus genomes, and show that the presence of DNA repair genes is likewise related to a larger value of P. In addition, the products of the bacterial genes mutY, vsr, and ndk, involved in the correction of GC/AT mutations, are strongly associated with reduced genome GC content. We therefore propose that a reduction in information content leads to a loss of DNA repair genes and indirectly to a reduction in genome GC content in bacteria by exposure to the underlying AT mutation bias. The reduction in P may also indirectly lead to the increase in substitution rates observed in intracellular bacteria via loss of DNA repair genes.
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Affiliation(s)
- Sharlene Acosta
- From the Department of Biology, University of Puerto Rico-Rio Piedras, PO Box 23360, San Juan 00931, Puerto Rico (Acosta, Carela, Garcia-Gonzalez, Gines, Vicens, Cruet, and Massey)
| | - Miguelina Carela
- From the Department of Biology, University of Puerto Rico-Rio Piedras, PO Box 23360, San Juan 00931, Puerto Rico (Acosta, Carela, Garcia-Gonzalez, Gines, Vicens, Cruet, and Massey)
| | - Aurian Garcia-Gonzalez
- From the Department of Biology, University of Puerto Rico-Rio Piedras, PO Box 23360, San Juan 00931, Puerto Rico (Acosta, Carela, Garcia-Gonzalez, Gines, Vicens, Cruet, and Massey)
| | - Mariela Gines
- From the Department of Biology, University of Puerto Rico-Rio Piedras, PO Box 23360, San Juan 00931, Puerto Rico (Acosta, Carela, Garcia-Gonzalez, Gines, Vicens, Cruet, and Massey)
| | - Luis Vicens
- From the Department of Biology, University of Puerto Rico-Rio Piedras, PO Box 23360, San Juan 00931, Puerto Rico (Acosta, Carela, Garcia-Gonzalez, Gines, Vicens, Cruet, and Massey)
| | - Ricardo Cruet
- From the Department of Biology, University of Puerto Rico-Rio Piedras, PO Box 23360, San Juan 00931, Puerto Rico (Acosta, Carela, Garcia-Gonzalez, Gines, Vicens, Cruet, and Massey)
| | - Steven E Massey
- From the Department of Biology, University of Puerto Rico-Rio Piedras, PO Box 23360, San Juan 00931, Puerto Rico (Acosta, Carela, Garcia-Gonzalez, Gines, Vicens, Cruet, and Massey).
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Fernandes ADS, Alencar AS, Evangelista H, Mazzei JL, Felzenszwalb I. Photoprotective and toxicological activities of extracts from the Antarctic moss Sanionia uncinata. Pharmacogn Mag 2015; 11:38-43. [PMID: 25709208 PMCID: PMC4329630 DOI: 10.4103/0973-1296.149701] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Revised: 04/27/2014] [Accepted: 01/21/2015] [Indexed: 11/11/2022] Open
Abstract
Background: The Antarctic moss Sanionia uncinata (Hedw.) Loeske has shown high ultraviolet (UV)-absorbers content after exposition to high levels of UV-B radiation and can be an important source of antioxidants. Objective: The aim was to investigate photoprotection and mutagenicity by the aqueous extract (AE) and hydroethanolic extract (HE) from the Antarctic moss S. uncinata. Materials and Methods: Photoprotective activities were determined through survival curves of Escherichia coli strains, after UV irradiation in an aqueous solution of thymine and in vitro sun protection factor (SPF). The Salmonella/microsome assays were applied to assess the mutagenicity. Results: Both extracts induced photoprotection against UV-C radiation. The AE showed a higher protection than the hydroethanolic one against UV-induced thymine dimerization. The SPFs were low in both extracts. In association to benzophenone-3 a significant increase in the SPF was detected for the AE, and a significant decrease was induced by the HE. No mutagenicity was found in the both extracts. Furthermore, it was observed absence of cytotoxicity. Conclusion: Water-extractable compounds seem to contribute on photoprotection of this Antarctic moss.
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Affiliation(s)
- Andréia da Silva Fernandes
- Department of Biophysics and Biometry, Institute of Biology Roberto Alcantara Gomes, Rio de Janeiro State University, Rio de Janeiro, Brazil
| | - Alexandre Santos Alencar
- Department of Biophysics and Biometry, Institute of Biology Roberto Alcantara Gomes, Rio de Janeiro State University, Rio de Janeiro, Brazil
| | - Heitor Evangelista
- Department of Biophysics and Biometry, Institute of Biology Roberto Alcantara Gomes, Rio de Janeiro State University, Rio de Janeiro, Brazil
| | - José Luiz Mazzei
- Platform of Analytical Chemistry, Farmanguinhos, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Israel Felzenszwalb
- Department of Biophysics and Biometry, Institute of Biology Roberto Alcantara Gomes, Rio de Janeiro State University, Rio de Janeiro, Brazil
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Sidorenko J, Ukkivi K, Kivisaar M. NER enzymes maintain genome integrity and suppress homologous recombination in the absence of exogenously induced DNA damage in Pseudomonas putida. DNA Repair (Amst) 2015; 25:15-26. [DOI: 10.1016/j.dnarep.2014.11.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Revised: 10/29/2014] [Accepted: 11/05/2014] [Indexed: 02/04/2023]
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Felício DF, Vidal LDS, Irineu RS, Leitão AC, von Kruger WA, Britto CDP, Cardoso A, Cardoso JS, Lage C. Overexpression of Escherichia coli nucleotide excision repair genes after cisplatin-induced damage. DNA Repair (Amst) 2013; 12:63-72. [DOI: 10.1016/j.dnarep.2012.10.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Revised: 10/25/2012] [Accepted: 10/30/2012] [Indexed: 12/12/2022]
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Shanmughapriya V, Munavar MH. Evidence for involvement of UvrB in elicitation of 'SIR' phenotype by rpoB87-gyrA87 mutations in lexA3 mutant of Escherichia coli. DNA Repair (Amst) 2012; 11:915-25. [PMID: 23058633 DOI: 10.1016/j.dnarep.2012.09.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Revised: 07/16/2012] [Accepted: 09/11/2012] [Indexed: 11/17/2022]
Abstract
An unconventional DNA repair termed SIR (SOS Independent Repair), specific to mitomycin C (MMC) damage elicited by a combination of specific Rif(R) (rpoB87) and Nal(R) (gyrA87) mutations in SOS un-inducible strains of Escherichia coli was reported by Kumaresan and Jayaraman (1988). We report here that the rpoB87 mutation defines a C(1565)→T(1565) transition changing S(522)→F(522) and gyrA87 defines a G(244)→A(244) transition changing D(82)→N(82). The reconstructed lexA3 rpoB87 gyrA87 strain (DM49RN) exhibited resistance to MMC but not to UV as expected. When mutations in several genes implicated in SOS/NER were introduced into DM49RN strain, uvrB mutation alone decreased the MMC resistance and suppressed SIR phenotype. This was alleviated about two fold by a plasmid clone bearing the uvrB(+) allele. Neither SulA activity as measured based on filamentation and sulA::gfp fluorescence analyses nor the transcript levels of sulA as seen based on RT-PCR analyses indicate a change in sulA expression in DM49RN strain. However, uvrB transcript levels are increased with or without MMC treatment in the same strain. While the presence of lexA3 allele in a plasmid clone was found to markedly decrease the MMC resistance of the DM49RN strain, the additional presence of uvrB(+) allele in the same clone alleviated the suppression of MMC resistance by lexA3 allele to a considerable extent. These results indicate the increased expression of uvrB in the DM49RN strain is probably from the LexA dependent promoter of uvrB. The sequence analyses of various uvrB mutants including those isolated in this study using localized mutagenesis indicate the involvement of the nucleotide phosphate binding domain (ATPase domain) and the ATP binding domain and/or the DNA binding domain of the UvrB protein in the MMC repair in DM49RN. The possible involvement of UvrB protein in the MMC damage repair in DM49RN strain in relation to DNA repair is discussed.
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Affiliation(s)
- V Shanmughapriya
- Department of Molecular Biology, School of Biological Sciences, Centre for Excellence in Genomic Sciences, Madurai Kamaraj University (University with Potential for Excellence), Madurai 625021, Tamil Nadu, India
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