Martins-Pinheiro Marinalva, Marques Regina C P, Menck Carlos F M
Department of Microbiology, Institute of Biomedical Sciences, São Paulo, SP, Brazil.
BMC Microbiol. 2007 Mar 12;7:17. doi: 10.1186/1471-2180-7-17.
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.
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), O6-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.
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.
DNA分子的完整性是维持生命的基础。DNA修复蛋白通过去除DNA损伤或帮助耐受损伤来保护生物体免受遗传损害。DNA修复基因在γ-变形菌大肠杆菌中最为人所知，它是研究最透彻的细菌模型。然而，基因组测序引发了关于这些DNA修复基因和途径的一致性和普遍性的问题，这进一步凸显了识别可能在其他细菌中对DNA损伤作出反应的基因和蛋白质的必要性。
在本研究中，我们采用生物信息学方法，分析并描述了来自α-变形菌新月柄杆菌基因组中可能与DNA修复相关的开放阅读框。这是通过与公共数据库中已知的DNA修复相关基因进行比较来完成的。正如预期的那样，尽管新月柄杆菌和大肠杆菌属于不同的系统发育类群，但它们的许多DNA修复基因非常相似。然而，新月柄杆菌基因组中缺少一些重要的DNA修复基因，并且存在其他有趣的功能相关基因重复，而这些在大肠杆菌中并不存在。这些基因包括DNA连接酶、核酸外切酶III（xthA）、核酸内切酶III（nth）、O6-甲基鸟嘌呤-DNA甲基转移酶（ada基因）、光解酶样基因和尿嘧啶-DNA-糖基化酶。另一方面，参与DNA损伤诱导诱变的imuA和imuB基因最近在新月柄杆菌中被发现，但在大肠杆菌中不存在。特别有趣的是α-变形菌中一个光解酶基因的潜在非典型系统发育，表明其起源于水平转移；以及Ada直系同源基因的重复，这些基因具有不同的结构构型，包括一种对新月柄杆菌来说仍然独特的构型。
讨论了某些基因的缺失和存在情况，并结合新月柄杆菌在其他已知DNA修复途径中的特殊情况进行了预测。观察到的差异扩展了我们对细菌世界中DNA修复的认识，并为该生物体的进一步实验研究提供了有用的框架。
