Acosta Sharlene, Carela Miguelina, Garcia-Gonzalez Aurian, Gines Mariela, Vicens Luis, Cruet Ricardo, Massey Steven E
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).
J Hered. 2015 Sep-Oct;106(5):644-59. doi: 10.1093/jhered/esv055. Epub 2015 Aug 29.
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.
“蛋白质组限制”的概念提出，DNA修复能力与基因组的信息含量呈正相关，基因组信息含量可近似为蛋白质组（P）的大小。这进而意味着DNA修复基因更有可能存在于P值较大的基因组中。这与常见的假设形成对比，即信息基因具有核心功能，因此在生物体中均匀分布。我们研究了细菌基因组中18个DNA修复基因的有无情况。在整个数据集中，17个基因的基因存在情况与P呈正相关；仅研究非细胞内细菌时，16个基因呈现这种相关性。在细胞内细菌中观察到DNA修复基因显著减少，这与其较低的P值相符。我们还研究了古菌和DNA病毒基因组，结果表明DNA修复基因的存在同样与较大的P值相关。此外，参与GC/AT突变校正的细菌基因mutY、vsr和ndk的产物与基因组GC含量降低密切相关。因此，我们提出信息含量的减少会导致DNA修复基因的丢失，并通过暴露于潜在的AT突变偏好而间接导致细菌基因组GC含量降低。P值的降低还可能通过DNA修复基因的丢失间接导致细胞内细菌中观察到的替换率增加。
