RCPdb: An evolutionary classification and codon usage database for repeat-containing proteins
RCPdb: An evolutionary classification and codon usage database for repeat-containing proteins
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RCPdb： 含重复蛋白质的进化分类和密码子使用数据库
DOI：
10.1101/gr.6255407
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发表时间：
2007-07-01
期刊：
影响因子：
7
通讯作者：
Whisstock, James C.
中科院分区：
文献类型：
--
作者：
Faux, Noel G.;Huttley, Gavin A.;Whisstock, James C.
超过3%的人类蛋白质包含单一氨基酸重复序列（含重复序列的蛋白质，RCPs）。许多重复序列（同型肽）定位于参与转录的重要蛋白质中，并且某些重复序列的扩增，特别是多聚谷氨酰胺（poly - Q）和多聚丙氨酸（poly - A）序列，也可能导致神经系统疾病的发生。先前的研究表明，同型肽的组成是编码基因中富含G + C序列存在的结果，并且扩增是通过复制滑动发生的。在此，我们对13个物种中编码RCPs的基因变异进行了大规模的基因组分析，并将这些数据呈现在一个在线数据库（http://repeats.med.monash.edu.au/genetic_analysis/）中。这一资源允许对所考虑的真核生物物种中的RCPs、同型肽及其潜在的基因序列进行快速比较和分析。我们报告了三个主要发现。首先，在同型肽内重复的密码子只有一小部分存在偏向性，并且相对于生物体的转录组不存在G + C或A + T偏向性。其次，同型密码子的单碱基对颠换异常常见，这可能代表一种降低同型肽突变率的机制。第三，在不同物种间保守的同型肽位于受到更强纯化选择的区域，这与非保守的同型肽形成对比。
Over 3% of human proteins contain single amino acid repeats (repeat-containing proteins, RCPs). Many repeats (homopeptides) localize to important proteins involved in transcription, and the expansion of certain repeats, in particular poly-Q and poly-A tracts, can also lead to the development of neurological diseases. Previous studies have suggested that the homopeptide makeup is a result of the presence of G+C-rich tracts in the encoding genes and that expansion occurs via replication slippage. Here, we have performed a large-scale genomic analysis of the variation of the genes encoding RCPs in 13 species and present these data in an online database (http://repeats. med. monash. edu.au/genetic_analysis/). This resource allows rapid comparison and analysis of RCPs, homopeptides, and their underlying genetic tracts across the eukaryotic species considered. We report three major findings. First, there is a bias for a small subset of codons being reiterated within homopeptides, and there is no G+C or A+T bias relative to the organism's transcriptome. Second, single base pair transversions from the homocodon are unusually common and may represent a mechanism of reducing the rate of homopeptide mutations. Third, homopeptides that are conserved across different species lie within regions that are under stronger purifying selection in contrast to nonconserved homopeptides.