On the molecular mechanism of GC content variation among eubacterial genomes.
On the molecular mechanism of GC content variation among eubacterial genomes.
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DOI：
10.1186/1745-6150-7-2
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发表时间：
2012-01-10
期刊：
影响因子：
5.5
通讯作者：
Yu J
中科院分区：
文献类型：
--
作者：
Wu H;Zhang Z;Hu S;Yu J
细菌基因组GC含量作为基因组序列变异的关键参数，已经被研究了半个多世纪，并提出了许多假说来解释这种GC含量变异及其与其他基本过程的关系。以前，我们根据一种假设将真细菌分类为基于dna E的组(DNA聚合酶IIIα亚基的二聚体组合)，其中GC含量的变化基本上由基因组复制和DNA修复机制控制。进一步的研究发现，两个主要的突变子基因Polc和dna E2可能对基因组GC含量的变化负责。因此，我们进行了深入的分析，以评估与真细菌基因组中GC含量变化相关的各种潜在的内在和外在因素。突变基因，特别是那些在突变谱上具有显性效应的基因，偏向于GC或AT丰度，它们在两个相反的方向上改变基因组GC含量。细菌基因组大小(或基因数量)的增加似乎依赖于基因组GC含量的增加；然而，尚不清楚这种变化是否与某些环境压力直接相关。某些环境和细菌学特征与GC含量变化有关，但在基于dna E的分组方案下分析时，它们的趋势更为明显。大多数陆地细菌、植物相关细菌和固氮菌都属于dna E1|dna E2组，而昆虫中的大多数致病细菌或共生细菌以及生活在水生环境中的细菌主要是dna E1|polV组的成员。我们的研究提供了几条证据表明，α聚合酶IIIDNA亚基及其异构体参与复制(如PolC)或SOS突变/跨损伤合成(如dNAE2)，在决定GC变异性方面发挥主导作用。其他环境或细菌因素，如基因组大小、温度、需氧量和栖息地，要么起辅助作用，要么间接依赖不同的突变体基因来微调GC含量。这些结果提供了一个全面的洞察GC含量变化的机制，以及优生菌基因组在数十亿年来适应不断变化的环境的稳健性。本文由尼古拉斯·加尔蒂埃、亚当·艾尔-沃克和尤金·库宁撰写。
As a key parameter of genome sequence variation, the GC content of bacterial genomes has been investigated for over half a century, and many hypotheses have been put forward to explain this GC content variation and its relationship to other fundamental processes. Previously, we classified eubacteria into dnaE-based groups (the dimeric combination of DNA polymerase III alpha subunits), according to a hypothesis where GC content variation is essentially governed by genome replication and DNA repair mechanisms. Further investigation led to the discovery that two major mutator genes, polC and dnaE2, may be responsible for genomic GC content variation. Consequently, an in-depth analysis was conducted to evaluate various potential intrinsic and extrinsic factors in association with GC content variation among eubacterial genomes. Mutator genes, especially those with dominant effects on the mutation spectra, are biased towards either GC or AT richness, and they alter genomic GC content in the two opposite directions. Increased bacterial genome size (or gene number) appears to rely on increased genomic GC content; however, it is unclear whether the changes are directly related to certain environmental pressures. Certain environmental and bacteriological features are related to GC content variation, but their trends are more obvious when analyzed under the dnaE-based grouping scheme. Most terrestrial, plant-associated, and nitrogen-fixing bacteria are members of the dnaE1|dnaE2 group, whereas most pathogenic or symbiotic bacteria in insects, and those dwelling in aquatic environments, are largely members of the dnaE1|polV group. Our studies provide several lines of evidence indicating that DNA polymerase III α subunit and its isoforms participating in either replication (such as polC) or SOS mutagenesis/translesion synthesis (such as dnaE2), play dominant roles in determining GC variability. Other environmental or bacteriological factors, such as genome size, temperature, oxygen requirement, and habitat, either play subsidiary roles or rely indirectly on different mutator genes to fine-tune the GC content. These results provide a comprehensive insight into mechanisms of GC content variation and the robustness of eubacterial genomes in adapting their ever-changing environments over billions of years. This paper was reviewed by Nicolas Galtier, Adam Eyre-Walker, and Eugene Koonin.
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