Selection on the codon bias of chloroplast and cyanelle genes in different plant and algal lineages
Selection on the codon bias of chloroplast and cyanelle genes in different plant and algal lineages
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DOI：
10.1007/pl00006325
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发表时间：
1998-04-01
影响因子：
3.9
通讯作者：
Morton, BR
中科院分区：
文献类型：
--
作者：
Morton, BR
在植物叶绿体基因组中，高表达的psbA基因的密码子使用是独特的，并且适应于tRNA群体，可能是由于翻译效率的选择。在本研究中，通过测量对密码子使用模式的适应，除了莱茵衣藻外，还研究了选择在每个完全测序的叶绿体基因组中对密码子使用的作用。本文提出了一种方法，通过构建与该基因具有相同氨基酸组成的序列，并根据该基因组非编码区域的核苷酸组成随机分配密码子，来单独测试每个基因的选择。然后将实际基因的密码子偏差与随机序列的分布进行比较。结果表明，藻内的选择作用在蓝藻中较强，对大部分基因有影响，在中华斑藻中中等强度，在紫菜和绿藻中较弱。在植物中，松（Pinus thunbergii）和被子植物的选择作用较弱，而地茅（Marchantia polymorpha）存在中等水平的选择作用。然后在两个比较研究中进一步调查了选择的作用。结果表明，平均相对密码子偏倚与表达水平相关，尽管替代水平饱和，但藻类基因组之间同源基因的密码子偏倚程度存在很强的相关性。这些数据表明，翻译效率选择在决定叶绿体基因密码子偏向性中起着重要作用，但在不同的谱系中作用的强度不同。一般来说，藻类比高等植物更强，但在藻类中发现了几种不同寻常的特征，值得注意。讨论了可能导致不同基因组之间这种强度变化的因素。
In the plant chloroplast genome the codon usage of the highly expressed psbA gene is unique and is adapted to the tRNA population, probably due to selection for translation efficiency. In this study the role of selection on codon usage in each of the fully sequenced chloroplast genomes, in addition to Chlamydomonas reinhardtii, is investigated by measuring adaptation to this pattern of codon usage. A method is developed which tests selection on each gene individually by constructing sequences with the same amino acid composition as the gene and randomly assigning codons based on the nucleotide composition of noncoding regions of that genome. The codon bias of the actual gene is then compared to a distribution of random sequences. The data indicate that within the algae selection is strong in Cyanophora paradoxa, affecting a majority of genes, of intermediate intensity in Odontella sinensis, and weaker in Porphyra purpurea and Euglena gracilis. In the plants, selection is found to be quite weak in Pinus thunbergii and the angiosperms but there is evidence that an intermediate level of selection exists in the liverwort Marchantia polymorpha. The role of selection is then further investigated in two comparative studies. It is shown that average relative codon bias is correlated with expression level and that, despite saturation levels of substitution, there is a strong correlation among the algae genomes in the degree of codon bias of homologous genes. All of these data indicate that selection for translation efficiency plays a significant role in determining the codon bias of chloroplast genes but that it acts with different intensities in different lineages. In general it is stronger in the algae than the higher plants, but within the algae Euglena is found to have several unusual features which are noted. The factors that might be responsible for this variation in intensity among the various genomes are discussed.