The emergence and fate of horizontally acquired genes in Escherichia coli.
The emergence and fate of horizontally acquired genes in Escherichia coli.
复制标题
DOI：
10.1371/journal.pcbi.1000059
复制
发表时间：
2008-04-11
影响因子：
4.3
通讯作者：
Ochman, Howard
中科院分区：
文献类型：
--
作者：
van Passel, Mark W. J.;Marri, Pradeep Reddy;Ochman, Howard
细菌物种，甚至是物种内的菌株，在基因含量和代谢能力上都有很大差异。我们研究这种多样性的演变，通过评估每个基因的分布和祖先在13个测序分离的大肠杆菌和志贺氏菌。我们专注于两个特定类别的基因，ORFans（在目前的数据库中没有同源物的基因）和HOPs（基因与遥远的同源物）的出现和消亡，因为这些基因，在最保守的祖先序列相比，被称为是一个主要来源的新功能，在每个菌株。我们发现，这些基因的获得和丢失率在菌株之间以及随着时间的推移变化很大，并且ORFans和HOPs在它们的出现和死亡方面表现出非常不同的行为。虽然HOPs主要代表从其他细菌获得的基因，起源更频繁，但ORFan更有可能持续存在。这种差异表明，许多适应性特征是由不起源于其他细菌基因组的全新基因赋予的。关于这些获得的基因的消亡，我们发现志贺氏菌菌株丢失基因，无论是通过破坏事件还是通过完全去除，都在加速。遗传库的变化可以改变生物体的适应策略，尤其是在细菌中，其中基因不断获得和丢失。在大肠杆菌和志贺氏菌的密集测序分支中绘制基因的获得和丢失表明，这些基因组包含两种类型的获得性基因：HOPs，这是那些在远亲细菌中具有同源物的获得性基因;和ORFans，这是没有任何已知同源物的基因。令人惊讶的是，这两类获得性基因显示出非常不同的获得和丧失模式。HOPs更频繁地获得，尽管它们很少在受体基因组中持续存在。相比之下，ORFans更有可能在进化的时间尺度上保持不变，这表明尽管它们的起源未知，但它们更经常地赋予受体基因组新的和有益的特征。
Bacterial species, and even strains within species, can vary greatly in their gene contents and metabolic capabilities. We examine the evolution of this diversity by assessing the distribution and ancestry of each gene in 13 sequenced isolates of Escherichia coli and Shigella. We focus on the emergence and demise of two specific classes of genes, ORFans (genes with no homologs in present databases) and HOPs (genes with distant homologs), since these genes, in contrast to most conserved ancestral sequences, are known to be a major source of the novel features in each strain. We find that the rates of gain and loss of these genes vary greatly among strains as well as through time, and that ORFans and HOPs show very different behavior with respect to their emergence and demise. Although HOPs, which mostly represent gene acquisitions from other bacteria, originate more frequently, ORFans are much more likely to persist. This difference suggests that many adaptive traits are conferred by completely novel genes that do not originate in other bacterial genomes. With respect to the demise of these acquired genes, we find that strains of Shigella lose genes, both by disruption events and by complete removal, at accelerated rates. Changes in genetic repertoires can alter the adaptive strategy of an organism, especially in bacteria, in which genes are continually gained and lost. Mapping the gains and losses of genes in the densely sequenced clade of Escherichia coli and Shigella shows that these genomes harbour two types of acquired genes: HOPs, which are those acquired genes with homologs in distantly related bacteria; and ORFans, which are genes without any known homologs. Surprisingly, the two classes of acquired genes display very different patterns of gain and loss. HOPs are acquired more frequently, though they rarely persist in the recipient genomes. In contrast, ORFans are much more likely to be maintained over evolutionary timescales, suggesting that despite their unknown origins, they will more often confer novel and beneficial traits to the recipient genome.
登录
查看更多内容
影响因子：
10.7
作者：
Castresana, J
通讯作者：
Castresana, J
影响因子：
14.9
作者：
Lerat, E;Ochman, H
通讯作者：
Ochman, H
影响因子：
7
作者：
Normand, Philippe;Lapierre, Pascal;Benson, David R.
通讯作者：
Benson, David R.
影响因子：
4.4
作者：
Konstantinidis, Konstantinos T.;Ramette, Alban;Tiedje, James M.
通讯作者：
Tiedje, James M.
影响因子：
3.9
作者：
Lawrence, JG;Ochman, H
通讯作者：
Ochman, H