Conserved intergenic sequences revealed by CTAG-profiling in Salmonella: thermodynamic modeling for function prediction.
Conserved intergenic sequences revealed by CTAG-profiling in Salmonella: thermodynamic modeling for function prediction.
复制标题
沙门氏菌 CTAG 分析揭示的保守基因间序列：功能预测的热力学模型
DOI：
10.1038/srep43565
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发表时间：
2017-03-06
影响因子：
4.6
通讯作者：
Liu SL
中科院分区：
文献类型：
--
作者：
Tang L;Zhu S;Mastriani E;Fang X;Zhou YJ;Li YG;Johnston RN;Guo Z;Liu GR;Liu SL
高度保守的短序列有助于识别功能基因组区域并促进基因组注释。我们使用沙门氏菌作为模型，以搜索基因组的进化保守区域，并专注于四核苷酸序列CTAG的潜在重要功能。在沙门氏菌中，CTAG在整个谱系中高度保守，并且大量含有CTAG的短序列落在基因间区域，强烈表明它们的生物学重要性。计算机模拟表明，在一些含有CTAG的基因间区域中存在稳定的茎环结构，CTAG序列的核苷酸取代将从根本上重新排列自由能并破坏结构。假定的变性CTAG在沙门氏菌谱系中采取不同的模式，并提供了有关这些细菌病原体的基因组分歧和进化的新信息。垂直和水平传输的基因组片段的比较显示出不同的CTAG分布景观，与基因组改善过程，以消除CTAG发生向内从两个终端的水平收购的部分。
Highly conserved short sequences help identify functional genomic regions and facilitate genomic annotation. We used Salmonella as the model to search the genome for evolutionarily conserved regions and focused on the tetranucleotide sequence CTAG for its potentially important functions. In Salmonella, CTAG is highly conserved across the lineages and large numbers of CTAG-containing short sequences fall in intergenic regions, strongly indicating their biological importance. Computer modeling demonstrated stable stem-loop structures in some of the CTAG-containing intergenic regions, and substitution of a nucleotide of the CTAG sequence would radically rearrange the free energy and disrupt the structure. The postulated degeneration of CTAG takes distinct patterns among Salmonella lineages and provides novel information about genomic divergence and evolution of these bacterial pathogens. Comparison of the vertically and horizontally transmitted genomic segments showed different CTAG distribution landscapes, with the genome amelioration process to remove CTAG taking place inward from both terminals of the horizontally acquired segment.