Compositional dynamics of guanine and cytosine content in prokaryotic genomes
Compositional dynamics of guanine and cytosine content in prokaryotic genomes
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DOI：
10.1016/j.resmic.2007.02.007
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发表时间：
2007-05-01
影响因子：
2.6
通讯作者：
Yu, Jun
中科院分区：
文献类型：
--
作者：
Hu, Jianfei;Zhao, Xiaoqian;Yu, Jun
基因组鸟嘌呤和胞嘧啶（gGC）含量的差异的核苷酸组成分析直接涉及到氨基酸组成，通过遗传密码的工会。在这里，我们分析了229个原核基因组，以解决gGC，氨基酸和它们的密码子在基因背景下的错综复杂的关系。首先，我们不仅证实了密码子位置1（GC 1）的平均GC含量总是高于密码子位置2（GC 2）的普遍规则，而且还扩展了该规则，以表明即使在每个基因的基础上计算密码子位置相关的GC含量时，该规则也成立。“GC 1> GC 2规则”基本上归因于在这两个密码子位置之一处具有GC或中间GC组氨基酸的少数优势氨基酸。其次，我们发现，gGC波动在很大程度上补偿了密码子水平，当密码子属于高GC和低GC氨基酸组相应地变化。最后，我们发现，原核基因也有一个GC含量梯度（Gd）分布沿着其转录本。Gd1、Gd2和Gd3三个密码子位置的梯度均与gGC在两个不同的方向上相关：Gd3为正相关，而其他两个为负相关。(c)2007年，Elsevier Masson SAS。All rights reserved.
Nucleotide compositional analyses of disparities in genomic guanine and cytosine (gGC) content directly relate to the amino acid composition, through the union of the genetic code. Here we analyzed 229 prokaryotic genomes to address the intricate relationships between gGC, amino acids and their codons in the context of genes. First, we not only confirmed the universal rule that the average GC content at codon position 1 (GC1) is always higher than that at codon position 2 (GC2), but also extended the rule to show that it holds true even when codon-position-related GC contents are calculated on a per gene basis. The "GC1 > GC2 rule" is attributable essentially to a few dominant amino acids that have GC at one of these two codon positions or the intermediate-GC group of amino acids. Second, we found that gGC fluctuations were largely compensated for at the codon level, when codons belonging to high-GC and low-GC amino acid groups varied accordingly. Finally, we found that prokaryotic genes also have a GC content gradient (Gd) distributed along their transcripts. The gradients at three codon positions (Gd1, Gd2 and Gd3) all correlated with gGC in two different directions: Gd3 was positive, whereas the other two were negative. (c) 2007 Elsevier Masson SAS. All rights reserved.