Leaderless genes in bacteria: clue to the evolution of translation initiation mechanisms in prokaryotes.
Leaderless genes in bacteria: clue to the evolution of translation initiation mechanisms in prokaryotes.
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细菌中的无领导基因：原核生物翻译起始机制进化的线索
DOI：
10.1186/1471-2164-12-361
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发表时间：
2011-07-12
期刊：
影响因子：
4.4
通讯作者：
Zhu H
中科院分区：
文献类型：
--
作者：
Zheng X;Hu GQ;She ZS;Zhu H
SD（Shine - Dalgarno）信号长期以来被视为原核生物中主要的翻译起始信号。最近，无先导序列基因（其mRNA上缺乏5' - 非翻译区（5' - UTR））在古菌中被发现大量存在。然而，目前对细菌起始机制的大规模计算机模拟分析主要基于SD引导的起始方式，而非无先导序列的方式。细菌中无先导序列基因的研究仍未完成，这导致对原核生物翻译起始机制的理解存在不确定性。
在此，我们研究了953个细菌基因组和72个古菌基因组中所有基因的翻译起始区域的信号，然后尝试根据细菌中的无先导序列基因构建一个进化场景。通过一种旨在识别基因组中基因上游区域多信号的算法，我们根据其上游序列中最可能的信号类别将所有基因分为SD引导、TA引导和非典型基因。特别是，在细菌中翻译起始位点（TIS）上游约10bp处出现类似TA的信号很可能意味着是无先导序列基因。
我们的分析表明，无先导序列基因在多种细菌中虽然不占主导地位，但完全是广泛存在的。特别是对于放线菌门和异常球菌 - 栖热菌门，超过20%的基因是无先导序列的。在密切相关的细菌基因组中分析，我们的结果表明，源自共同祖先的基因之间发生的翻译起始机制的变化与系统发育关系呈线性相关。对无先导序列基因宏观进化的分析进一步表明，细菌中无先导序列基因的比例在进化过程中有下降的趋势。
BackgroundShine-Dalgarno (SD) signal has long been viewed as the dominant translation initiation signal in prokaryotes. Recently, leaderless genes, which lack 5'-untranslated regions (5'-UTR) on their mRNAs, have been shown abundant in archaea. However, current large-scalein silicoanalyses on initiation mechanisms in bacteria are mainly based on the SD-led initiation way, other than the leaderless one. The study of leaderless genes in bacteria remains open, which causes uncertain understanding of translation initiation mechanisms for prokaryotes.ResultsHere, we study signals in translation initiation regions of all genes over 953 bacterial and 72 archaeal genomes, then make an effort to construct an evolutionary scenario in view of leaderless genes in bacteria. With an algorithm designed to identify multi-signal in upstream regions of genes for a genome, we classify all genes into SD-led, TA-led and atypical genes according to the category of the most probable signal in their upstream sequences. Particularly, occurrence of TA-like signals about 10 bp upstream to translation initiation site (TIS) in bacteria most probably means leaderless genes.ConclusionsOur analysis reveals that leaderless genes are totally widespread, although not dominant, in a variety of bacteria. Especially forActinobacteriaandDeinococcus-Thermus, more than twenty percent of genes are leaderless. Analyzed in closely related bacterial genomes, our results imply that the change of translation initiation mechanisms, which happens between the genes deriving from a common ancestor, is linearly dependent on the phylogenetic relationship. Analysis on the macroevolution of leaderless genes further shows that the proportion of leaderless genes in bacteria has a decreasing trend in evolution.
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影响因子：
3.2
作者：
Hahn, JS;Oh, SY;Roe, JH
通讯作者：
Roe, JH
原核生物基因组 TIS 注释的计算评估
影响因子：
3
作者：
Hu, Gang-Qing;Zheng, Xiaobin;Ju, Li-Ning;Zhu, Huaiqiu;She, Zhen-Su
通讯作者：
She, Zhen-Su
影响因子：
14.9
作者：
Besemer, J;Lomsadze, A;Borodovsky, M
通讯作者：
Borodovsky, M
影响因子：
3.6
作者：
Hong, HJ;Hutchings, MI;Buttner, MJ
通讯作者：
Buttner, MJ
影响因子：
5.8
作者：
Larkin, M. A.;Blackshields, G.;Higgins, D. G.
通讯作者：
Higgins, D. G.