Aerobic prokaryotes do not have higher GC contents than anaerobic prokaryotes, but obligate aerobic prokaryotes have
Aerobic prokaryotes do not have higher GC contents than anaerobic prokaryotes, but obligate aerobic prokaryotes have
复制标题
需氧原核生物并不比厌氧原核生物具有更高的GC含量，但专性需氧原核生物具有更高的GC含量。
DOI：
10.1186/s12862-019-1365-8
复制
发表时间：
2019-01-28
影响因子：
3.4
通讯作者：
Niu, Deng-Ke
中科院分区：
文献类型：
--
作者：
Aslam, Sidra;Lan, Xin-Ran;Niu, Deng-Ke
背景在四种碱基中，鸟嘌呤是最容易受到氧化应激损伤的碱基。含有受损鸟嘌呤的DNA的复制导致G到T突变。因此，氧化性DNA损伤导致的突变通常预期主要由G至T（以及当受损鸟嘌呤不在参考链中时C至A）组成，并导致GC含量降低。然而，16年前在一项原核生物基因组的研究中报道了相反的模式。虽然这一结果已被广泛引用，并证实了9个后来的研究与类似的方法，遗漏的影响，共同的祖先需要重新检查的可靠性的结果。结果当好氧和专性好氧原核生物混合在一起，厌氧和专性厌氧原核生物混合在一起，系统发育控制分析没有发现好氧和厌氧原核生物之间的GC含量的显着差异。这一结果与两个通常被忽视的研究，占系统发育关系是一致的。然而，当专性好氧原核生物分别与好氧原核生物，厌氧原核生物和专性厌氧原核生物进行系统发育回归分析时，观察到无论是从全基因组序列还是从蛋白质编码基因的4倍简并位点计算的GC含量之间的显着正相关。专性需氧菌有显着较高的GC含量比需氧菌，厌氧菌，专性厌氧菌。ConclusionsThe positive association between aerobiosis and GC content may be attained to a mutational force resulting from incorporation of damaged deoxyguanosine during DNA replication rather than oxidation of guanine nucleotides within DNA sequences.我们的研究结果表明，一个等级的好氧相关的突变力，强的专性好氧菌，中等的好氧菌，弱的厌氧菌和专性厌氧菌。
BackgroundAmong the four bases, guanine is the most susceptible to damage from oxidative stress. Replication of DNA containing damaged guanines results in G to T mutations. Therefore, the mutations resulting from oxidative DNA damage are generally expected to predominantly consist of G to T (and C to A when the damaged guanine is not in the reference strand) and result in decreased GC content. However, the opposite pattern was reported 16years ago in a study of prokaryotic genomes. Although that result has been widely cited and confirmed by nine later studies with similar methods, the omission of the effect of shared ancestry requires a re-examination of the reliability of the results.ResultsWhen aerobic and obligate aerobic prokaryotes were mixed together and anaerobic and obligate anaerobic prokaryotes were mixed together, phylogenetic controlled analyses did not detect significant difference in GC content between aerobic and anaerobic prokaryotes. This result is consistent with two generally neglected studied that had accounted for the phylogenetic relationship. However, when obligate aerobic prokaryotes were compared with aerobic prokaryotes, anaerobic prokaryotes, and obligate anaerobic prokaryotes separately using phylogenetic regression analysis, a significant positive association was observed between aerobiosis and GC content, no matter it was calculated from whole genome sequences or the 4-fold degenerate sites of protein-coding genes. Obligate aerobes have significantly higher GC content than aerobes, anaerobes, and obligate anaerobes.ConclusionsThe positive association between aerobiosis and GC content could be attributed to a mutational force resulting from incorporation of damaged deoxyguanosine during DNA replication rather than oxidation of the guanine nucleotides within DNA sequences. Our results indicate a grade in the aerobiosis-associated mutational force, strong in obligate aerobes, moderate in aerobes, weak in anaerobes and obligate anaerobes.