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Genome analysis of DNA repair genes in the alpha proteobacterium Caulobacter crescentus
BACKGROUND: The integrity of DNA molecules is fundamental for maintaining life. The DNA repair proteins protect organisms against genetic damage, by removal of DNA lesions or helping to tolerate them. DNA repair genes are best known from the gamma-proteobacterium Escherichia coli, which is the most...
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Formato: | Texto |
Lenguaje: | English |
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BioMed Central
2007
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1839093/ https://www.ncbi.nlm.nih.gov/pubmed/17352799 http://dx.doi.org/10.1186/1471-2180-7-17 |
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author | Martins-Pinheiro, Marinalva Marques, Regina CP Menck, Carlos FM |
author_facet | Martins-Pinheiro, Marinalva Marques, Regina CP Menck, Carlos FM |
author_sort | Martins-Pinheiro, Marinalva |
collection | PubMed |
description | BACKGROUND: The integrity of DNA molecules is fundamental for maintaining life. The DNA repair proteins protect organisms against genetic damage, by removal of DNA lesions or helping to tolerate them. DNA repair genes are best known from the gamma-proteobacterium Escherichia coli, which is the most understood bacterial model. However, genome sequencing raises questions regarding uniformity and ubiquity of these DNA repair genes and pathways, reinforcing the need for identifying genes and proteins, which may respond to DNA damage in other bacteria. RESULTS: In this study, we employed a bioinformatic approach, to analyse and describe the open reading frames potentially related to DNA repair from the genome of the alpha-proteobacterium Caulobacter crescentus. This was performed by comparison with known DNA repair related genes found in public databases. As expected, although C. crescentus and E. coli bacteria belong to separate phylogenetic groups, many of their DNA repair genes are very similar. However, some important DNA repair genes are absent in the C. crescentus genome and other interesting functionally related gene duplications are present, which do not occur in E. coli. These include DNA ligases, exonuclease III (xthA), endonuclease III (nth), O(6)-methylguanine-DNA methyltransferase (ada gene), photolyase-like genes, and uracil-DNA-glycosylases. On the other hand, the genes imuA and imuB, which are involved in DNA damage induced mutagenesis, have recently been described in C. crescentus, but are absent in E. coli. Particularly interesting are the potential atypical phylogeny of one of the photolyase genes in alpha-proteobacteria, indicating an origin by horizontal transfer, and the duplication of the Ada orthologs, which have diverse structural configurations, including one that is still unique for C. crescentus. CONCLUSION: The absence and the presence of certain genes are discussed and predictions are made considering the particular aspects of the C. crescentus among other known DNA repair pathways. The observed differences enlarge what is known for DNA repair in the Bacterial world, and provide a useful framework for further experimental studies in this organism. |
format | Text |
id | pubmed-1839093 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2007 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-18390932007-03-30 Genome analysis of DNA repair genes in the alpha proteobacterium Caulobacter crescentus Martins-Pinheiro, Marinalva Marques, Regina CP Menck, Carlos FM BMC Microbiol Research Article BACKGROUND: The integrity of DNA molecules is fundamental for maintaining life. The DNA repair proteins protect organisms against genetic damage, by removal of DNA lesions or helping to tolerate them. DNA repair genes are best known from the gamma-proteobacterium Escherichia coli, which is the most understood bacterial model. However, genome sequencing raises questions regarding uniformity and ubiquity of these DNA repair genes and pathways, reinforcing the need for identifying genes and proteins, which may respond to DNA damage in other bacteria. RESULTS: In this study, we employed a bioinformatic approach, to analyse and describe the open reading frames potentially related to DNA repair from the genome of the alpha-proteobacterium Caulobacter crescentus. This was performed by comparison with known DNA repair related genes found in public databases. As expected, although C. crescentus and E. coli bacteria belong to separate phylogenetic groups, many of their DNA repair genes are very similar. However, some important DNA repair genes are absent in the C. crescentus genome and other interesting functionally related gene duplications are present, which do not occur in E. coli. These include DNA ligases, exonuclease III (xthA), endonuclease III (nth), O(6)-methylguanine-DNA methyltransferase (ada gene), photolyase-like genes, and uracil-DNA-glycosylases. On the other hand, the genes imuA and imuB, which are involved in DNA damage induced mutagenesis, have recently been described in C. crescentus, but are absent in E. coli. Particularly interesting are the potential atypical phylogeny of one of the photolyase genes in alpha-proteobacteria, indicating an origin by horizontal transfer, and the duplication of the Ada orthologs, which have diverse structural configurations, including one that is still unique for C. crescentus. CONCLUSION: The absence and the presence of certain genes are discussed and predictions are made considering the particular aspects of the C. crescentus among other known DNA repair pathways. The observed differences enlarge what is known for DNA repair in the Bacterial world, and provide a useful framework for further experimental studies in this organism. BioMed Central 2007-03-12 /pmc/articles/PMC1839093/ /pubmed/17352799 http://dx.doi.org/10.1186/1471-2180-7-17 Text en Copyright © 2007 Martins-Pinheiro et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Martins-Pinheiro, Marinalva Marques, Regina CP Menck, Carlos FM Genome analysis of DNA repair genes in the alpha proteobacterium Caulobacter crescentus |
title | Genome analysis of DNA repair genes in the alpha proteobacterium Caulobacter crescentus |
title_full | Genome analysis of DNA repair genes in the alpha proteobacterium Caulobacter crescentus |
title_fullStr | Genome analysis of DNA repair genes in the alpha proteobacterium Caulobacter crescentus |
title_full_unstemmed | Genome analysis of DNA repair genes in the alpha proteobacterium Caulobacter crescentus |
title_short | Genome analysis of DNA repair genes in the alpha proteobacterium Caulobacter crescentus |
title_sort | genome analysis of dna repair genes in the alpha proteobacterium caulobacter crescentus |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1839093/ https://www.ncbi.nlm.nih.gov/pubmed/17352799 http://dx.doi.org/10.1186/1471-2180-7-17 |
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