Functionality of essential genes drives gene strand-bias in bacterial genomes
Functionality of essential genes drives gene strand-bias in bacterial genomes
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必需基因的功能驱动细菌基因组中的基因链偏向
DOI：
10.1016/j.bbrc.2010.04.119
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发表时间：
2010-05-28
影响因子：
3.1
通讯作者：
Zhang, Chun-Ting
中科院分区：
文献类型：
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作者：
Lin, Yan;Gao, Feng;Zhang, Chun-Ting
必需基因，有机体生存不可或缺的基因，编码被认为是生命基础的功能。基于 10 种细菌的实验确定，我们发现对于所有研究的 10 个基因组来说，必需基因更优先位于前导链而不是滞后链，这证实了之前基于较小数据集或通过同源搜索推定指定数据集的发现。此外，我们发现，不是所有必需基因，只有那些具有信息存储和处理的COG功能类别（J、K和L）以及子类别D（细胞周期控制）、M（细胞壁生物发生）、O（翻译后修饰）、C（能量产生和转换）、G（碳水化合物运输和代谢）、E（氨基酸运输和代谢）和F（核苷酸运输和代谢）的基因优先位于前导链。相比之下，其他 COG 功能子类别中必需基因的链偏向在统计上并不显着。这些结果表明，必需基因分布的显着链偏倚主要与上述功能相关，因此，这可能在塑造细菌基因组中的基因链偏倚中发挥关键作用。 (C) 2010 Elsevier Inc. 保留所有权利。
Essential genes, indispensable genes for an organism's survival, encode functions that are considered a foundation of life. Based on those experimentally determined for 10 bacteria, we find that essential genes are more preferentially situated at the leading strand than at the lagging strand, for all the 10 genomes studied, confirming previous findings based on either smaller datasets or putatively assigned ones by homology search. Furthermore, we find that rather than all essential genes, only those with the COG functional category of information storage and process (J, K and L), and subcategories D (cell cycle control), M (cell wall biogenesis), O (posttranslational modification), C (energy production and conversion), G (carbohydrate transport and metabolism), E (amino acid transport and metabolism) and F (nucleotide transport and metabolism) are preferentially situated at the leading strand. In contrast, the strand-bias for essential genes in other COG functional subcategories is not statistically significant. These results suggest that the remarkable strand-bias of the distribution of essential genes is mainly relevant to the aforementioned functionalities, which, therefore, likely play a key role in shaping the gene strand-bias in bacterial genomes. (C) 2010 Elsevier Inc. All rights reserved.