Differential degeneration of the ACTAGT sequence among Salmonella: a reflection of distinct nucleotide amelioration patterns during bacterial divergence.
Differential degeneration of the ACTAGT sequence among Salmonella: a reflection of distinct nucleotide amelioration patterns during bacterial divergence.
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沙门氏菌 ACTAGT 序列的差异变性：细菌分化过程中不同核苷酸改善模式的反映
DOI：
10.1038/s41598-017-11226-9
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发表时间：
2017-09-08
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;Mastriani E;Zhou YJ;Zhu S;Fang X;Liu YP;Liu WQ;Li YG;Johnston RN;Guo Z;Liu GR;Liu SL
当细菌分化时，它们需要通过积累有益的基因组变异来适应新的环境，例如新的宿主或同一宿主的不同组织，但由于缺乏适当的方法，一般情况尚不清楚。在这里，我们分析了ACTAGT序列及其简并形式（即，具有不同于ACTAGT的六个核苷酸之一的六个核苷酸序列），以估计细菌基因组的核苷酸改善过程。ACTAGT主要位于编码序列中，但也存在于几个基因间区域，其简并形式广泛分散在细菌基因组中。我们推测，ACTAGT及其退化形式的分布可能是谱系特异性的结果，不同的选择压力施加在不同的基因组位置（在基因或基因间区域）之间的不同沙门氏菌谱系ACTAGT。为了验证这一推测，我们模拟了沙门氏菌和许多其他肠道细菌中保守的含ACTAGT序列的二级结构。与保守区域的ACTAGT相比，退化形式分布在整个细菌基因组中，同一系统发育谱系的细菌之间的退化模式高度相似，但在不同谱系之间存在根本差异。这一发现表明，在不同的选择压力下，细菌之间的偏见改善，并提供了深入了解细菌分化过程中的基因组进化。
When bacteria diverge, they need to adapt to the new environments, such as new hosts or different tissues of the same host, by accumulating beneficial genomic variations, but a general scenario is unknown due to the lack of appropriate methods. Here we profiled the ACTAGT sequence and its degenerated forms (i.e., hexa-nucleotide sequences with one of the six nucleotides different from ACTAGT) in Salmonella to estimate the nucleotide amelioration processes of bacterial genomes. ACTAGT was mostly located in coding sequences but was also found in several intergenic regions, with its degenerated forms widely scattered throughout the bacterial genomes. We speculated that the distribution of ACTAGT and its degenerated forms might be lineage-specific as a consequence of different selection pressures imposed on ACTAGT at different genomic locations (in genes or intergenic regions) among different Salmonella lineages. To validate this speculation, we modelled the secondary structures of the ACTAGT-containing sequences conserved across Salmonella and many other enteric bacteria. Compared to ACTAGT at conserved regions, the degenerated forms were distributed throughout the bacterial genomes, with the degeneration patterns being highly similar among bacteria of the same phylogenetic lineage but radically different across different lineages. This finding demonstrates biased amelioration under distinct selection pressures among the bacteria and provides insights into genomic evolution during bacterial divergence.
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DOI：
10.1073/pnas.93.19.10303
发表时间：
1996-09-17
影响因子：
11.1
作者：
Liu, SL;Sanderson, KE
通讯作者：
Sanderson, KE
影响因子：
14.9
作者：
PHILLIPS, GJ;ARNOLD, J;IVARIE, R
通讯作者：
IVARIE, R
DOI：
10.1007/s10482-011-9680-0
发表时间：
2012-01-01
影响因子：
2.6
作者：
Tang, Le;Liu, Shu-Lin
通讯作者：
Liu, Shu-Lin
影响因子：
14.9
作者：
BHAGWAT, AS;MCCLELLAND, M
通讯作者：
MCCLELLAND, M
影响因子：
4
作者：
Ochman, H
通讯作者：
Ochman, H