Synonymous codon usage in Cryptosporidium parvum:: identification of two distinct trends among genes
Synonymous codon usage in Cryptosporidium parvum:: identification of two distinct trends among genes
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DOI：
10.1016/s0020-7519(01)00129-1
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发表时间：
2001-04-01
影响因子：
4
通讯作者：
Sharp, PM
中科院分区：
文献类型：
--
作者：
Grocock, RJ;Sharp, PM
研究了顶复门隐孢子虫隐孢子虫中交替同义密码子的使用。分析了54个基因的数据集。总的来说。以A和U结尾的密码子占优势。正如在富含A + T的基因组中所预期的那样。对应分析发现基因间密码子使用变异有两种趋势。主要的趋势是在一个子集的使用程度，大概是预防性最佳密码子。在预期高水平表达的基因中以显著更高的频率使用。18个密码子中的15个被鉴定为最佳的密码子比其他常见密码子更富含G + C。因此，与翻译相关的密码子选择与一般突变偏好相反。在这些最佳密码子频率较低的40个基因中，鉴定出G + C含量的次要趋势。在这些基因中，在密码子的同义可变的第三位置处的G + C含量与5'和3'侧翼序列中的G + C含量相关，指示G + C含量的区域变化，这可能反映了突变偏好的区域变化。(C)2001年澳大利亚寄生虫学会由Elsevier Science Ltd.出版，版权所有。
The usage of alternative synonymous codons in the apicomplexan Cryptosporidium parvum has been investigated. A data set of 54 genes was analysed. Overall. A- and U-ending codons predominate. as expected in an A + T-rich genome. Two trends of codon usage variation among genes were identified using correspondence analysis. The primary trend is in the extent of usage of a subset of presumably translationally optimal codons. that are used at significantly higher frequencies in genes expected to be expressed at high levels. Fifteen of the 18 codons identified as optimal are more G + C-rich than the otherwise common codons. so that codon selection associated with translation opposes the general mutation bias, Among 40 genes with lower frequencies of these optimal codons, a secondary trend in G + C content was identified. In these genes, G + C content at synonymously variable third positions of codons is correlated with that in 5' and 3' flanking sequences, indicative of regional variation in G + C content, perhaps reflecting regional variation in mutational biases. (C) 2001 Australian Society for Parasitology Inc. Published by Elsevier Science Ltd. All rights reserved.