DNA Repair Is Associated with Information Content in Bacteria, Archaea, and DNA Viruses
DNA Repair Is Associated with Information Content in Bacteria, Archaea, and DNA Viruses
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DOI：
10.1093/jhered/esv055
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发表时间：
2015-09-01
影响因子：
3.1
通讯作者：
Massey, Steven E.
中科院分区：
文献类型：
--
作者：
Acosta, Sharlene;Carela, Miguelina;Massey, Steven E.
“蛋白质组学约束”的概念提出，DNA修复能力与基因组的信息含量正相关，基因组的信息含量可以近似为蛋白质组的大小（P）。这反过来又意味着DNA修复基因更有可能存在于具有较大P值的基因组中。这与信息基因具有核心功能并因此均匀分布于生物体中的常见假设形成对比。我们研究了细菌基因组中18个DNA修复基因的存在/不存在。基因存在和P之间的正相关关系，观察到17个基因的总数据集，和16个基因时，只有非细胞内的细菌进行了检查。我们还检查了古细菌和DNA病毒基因组，并表明DNA修复基因的存在同样与较大的P值有关。此外，细菌基因mutY，vsr和ndk的产物，参与GC/AT突变的校正，与降低的基因组GC含量密切相关。因此，我们提出，信息含量的减少导致DNA修复基因的丢失，并通过暴露于潜在的AT突变偏倚间接减少细菌基因组GC含量。P的减少也可能通过DNA修复基因的丢失间接导致在细胞内细菌中观察到的置换率的增加。
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.