The repertoire of ICE in prokaryotes underscores the unity, diversity, and ubiquity of conjugation.
The repertoire of ICE in prokaryotes underscores the unity, diversity, and ubiquity of conjugation.
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DOI：
10.1371/journal.pgen.1002222
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发表时间：
2011-08
期刊：
影响因子：
4.5
通讯作者：
Rocha EP
中科院分区：
文献类型：
--
作者：
Guglielmini J;Quintais L;Garcillán-Barcia MP;de la Cruz F;Rocha EP
水平基因转移通过允许快速获得新的适应性功能来塑造原核生物的基因组。缀合允许每个转移事件的最宽范围和最高基因转移输入。虽然接合质粒已经研究了几十年，但原核生物中整合接合元件（ICE）的数量和多样性仍然未知。我们定义了一个大的蛋白质图谱的接合机制，扫描超过1,000个原核生物的基因组。我们发现了682个假定的接合系统中所有主要的系统发育分支，并表明ICE是最丰富的接合元件在原核生物。近一半的基因组含有IV型分泌系统（T4 SS），较大的基因组编码更多的接合系统。令人惊讶的是，几乎一半的染色体T4 SS缺乏共定位的松弛酶，因此，可能致力于蛋白质运输，而不是共轭。这类元件在小基因组中占优势，与整合酶的相关性较低，在质粒中更少见。变形菌中的ICE和接合质粒对每种类型的T4 SS有不同的偏好，但所有类型都存在于染色体和质粒中。可移动的元素超过自我共轭元素在ICE和质粒，这表明广泛使用的T4 SS的反式。我们的进化分析表明，开关的质粒和ICE是频繁的，现存的元素开始分化只是相对最近。根据目前的研究结果，ICE是最丰富的接合元件在几乎所有的原核细胞分支，并可能更频繁地驯化成非接合蛋白质运输系统比以前认为的。虽然接合质粒和ICE具有不同的基因组稳定化手段，但它们通过接合的移动性机制显示出惊人的保守模式，主张通过水平基因转移形成原核生物基因组的接合的统一观点。一些移动的遗传元件通过接合在原核生物之间水平传播遗传信息，接合是DNA直接从一个细胞转移到另一个细胞的机制。在允许细胞之间遗传转移的过程中，接合是允许大量DNA和最不相关的细胞之间同时转移的过程。因此，接合系统是水平转移的关键参与者，包括对许多人类病原体的抗生素抗性的转移以及许多人类病原体之间的抗生素抗性的转移。接合系统在质粒和染色体中都有编码。后者被称为整合共轭元素（ICE）;它们的数量，身份和共轭机制知之甚少。我们已经开发了一种方法来识别和表征这些元素，并发现更多的ICE比接合质粒的基因组。虽然ICE和质粒都使用类似的接合系统，但某些元件对某些系统有显着的偏好。我们的进化分析表明，质粒接合系统往往引起ICE，反之亦然。因此，ICE和接合质粒应被视为同一种质粒，它们在细胞中存在方式的差异可能是对它们所含遗传信息的稳定性和/或传递性的不同要求的结果。
Horizontal gene transfer shapes the genomes of prokaryotes by allowing rapid acquisition of novel adaptive functions. Conjugation allows the broadest range and the highest gene transfer input per transfer event. While conjugative plasmids have been studied for decades, the number and diversity of integrative conjugative elements (ICE) in prokaryotes remained unknown. We defined a large set of protein profiles of the conjugation machinery to scan over 1,000 genomes of prokaryotes. We found 682 putative conjugative systems among all major phylogenetic clades and showed that ICEs are the most abundant conjugative elements in prokaryotes. Nearly half of the genomes contain a type IV secretion system (T4SS), with larger genomes encoding more conjugative systems. Surprisingly, almost half of the chromosomal T4SS lack co-localized relaxases and, consequently, might be devoted to protein transport instead of conjugation. This class of elements is preponderant among small genomes, is less commonly associated with integrases, and is rarer in plasmids. ICEs and conjugative plasmids in proteobacteria have different preferences for each type of T4SS, but all types exist in both chromosomes and plasmids. Mobilizable elements outnumber self-conjugative elements in both ICEs and plasmids, which suggests an extensive use of T4SS in trans. Our evolutionary analysis indicates that switch of plasmids to and from ICEs were frequent and that extant elements began to differentiate only relatively recently. According to the present results, ICEs are the most abundant conjugative elements in practically all prokaryotic clades and might be far more frequently domesticated into non-conjugative protein transport systems than previously thought. While conjugative plasmids and ICEs have different means of genomic stabilization, their mechanisms of mobility by conjugation show strikingly conserved patterns, arguing for a unitary view of conjugation in shaping the genomes of prokaryotes by horizontal gene transfer. Some mobile genetic elements spread genetic information horizontally between prokaryotes by conjugation, a mechanism by which DNA is transferred directly from one cell to the other. Among the processes allowing genetic transfer between cells, conjugation is the one allowing the simultaneous transfer of larger amounts of DNA and between the least related cells. As such, conjugative systems are key players in horizontal transfer, including the transfer of antibiotic resistance to and between many human pathogens. Conjugative systems are encoded both in plasmids and in chromosomes. The latter are called Integrative Conjugative Elements (ICE); and their number, identity, and mechanism of conjugation were poorly known. We have developed an approach to identify and characterize these elements and found more ICEs than conjugative plasmids in genomes. While both ICEs and plasmids use similar conjugative systems, there are remarkable preferences for some systems in some elements. Our evolutionary analysis shows that plasmid conjugative systems have often given rise to ICEs and vice versa. Therefore, ICEs and conjugative plasmids should be regarded as one and the same, the differences in their means of existence in cells probably the result of different requirements for stabilization and/or transmissibility of the genetic information they contain.
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影响因子：
3.6
作者：
Daccord, Aurelie;Ceccarelli, Daniela;Burrus, Vincent
通讯作者：
Burrus, Vincent
影响因子：
3.7
作者：
Douard G;Praud K;Cloeckaert A;Doublet B
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Doublet B
影响因子：
6.5
作者：
Anisimova, Maria;Gascuel, Olivier
通讯作者：
Gascuel, Olivier
DOI：
10.1073/pnas.0611553104
发表时间：
2007-05-08
影响因子：
11.1
作者：
Cho, Nam-Hyuk;Kim, Hang-Rae;Kim, Ik-Sang
通讯作者：
Kim, Ik-Sang
影响因子：
7
作者：
Blanc, Guillaume;Ogata, Hiroyuki;Raoult, Didier
通讯作者：
Raoult, Didier