Uncovering the prevalence and diversity of integrating conjugative elements in actinobacteria.
Uncovering the prevalence and diversity of integrating conjugative elements in actinobacteria.
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揭示了整合静脉细菌中结合元素的普遍性和多样性。
DOI：
10.1371/journal.pone.0027846
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发表时间：
2011
期刊：
影响因子：
3.7
通讯作者：
Burrus V
中科院分区：
文献类型：
--
作者：
Ghinet MG;Bordeleau E;Beaudin J;Brzezinski R;Roy S;Burrus V
水平基因转移通过允许一步获得新功能，极大地促进了细菌对环境条件变化的快速遗传适应和新生态位的定植。接合是由接合质粒和整合接合元件（ICE）介导的水平基因转移的主要机制。虽然在大多数细菌接合系统中，DNA 易位需要组装复杂的 IV 型分泌系统 (T4SS)，但在放线菌中，需要单个 DNA FtsK/SpoIIIE 样易位蛋白。迄今为止，ICE 在放线菌中的作用和多样性很少受到关注。使用参与 ICE 维持和转移的蛋白质的 HMM 图谱在放线菌的 275 个基因组中搜索了假定的 ICE。这些详尽的分析揭示了 144 个假定的 FtsK/SpoIIIE 型 ICE 和 17 个假定的 T4SS 型 ICE。基于维护和转移蛋白的系统发育分析的 ICE 分组揭示了 ICE 不同亚家族之间的广泛交换。在 Frankia 属放线菌中发现了 17 种 ICE，Frankia 是全球重要的固氮微生物，可与放线菌植物建立根瘤共生关系。对 Frankia ICE 的结构分析揭示了它们意想不到的多样性和大量预测的适应功能。研究发现 Frankia ICE 在体外和植物中通过位点特异性重组从宿主染色体上切除，这表明无论 Frankiae 是作为土壤腐生菌还是植物内共生体，它们都是功能性移动元件。对参与 ICE 维持和转移的蛋白质的系统发育分析表明，ICE 货物携带基因和染色体基因之间的活跃交换发生在放线菌目内。 Frankia ICE 在体外和植物中的功能让我们预计，结合和 ICE 可以为这种具有挑战性的微生物和许多其他放线菌开发基因操作工具。
Horizontal gene transfer greatly facilitates rapid genetic adaptation of bacteria to shifts in environmental conditions and colonization of new niches by allowing one-step acquisition of novel functions. Conjugation is a major mechanism of horizontal gene transfer mediated by conjugative plasmids and integrating conjugative elements (ICEs). While in most bacterial conjugative systems DNA translocation requires the assembly of a complex type IV secretion system (T4SS), in Actinobacteria a single DNA FtsK/SpoIIIE-like translocation protein is required. To date, the role and diversity of ICEs in Actinobacteria have received little attention. Putative ICEs were searched for in 275 genomes of Actinobacteria using HMM-profiles of proteins involved in ICE maintenance and transfer. These exhaustive analyses revealed 144 putative FtsK/SpoIIIE-type ICEs and 17 putative T4SS-type ICEs. Grouping of the ICEs based on the phylogenetic analyses of maintenance and transfer proteins revealed extensive exchanges between different sub-families of ICEs. 17 ICEs were found in Actinobacteria from the genus Frankia, globally important nitrogen-fixing microorganisms that establish root nodule symbioses with actinorhizal plants. Structural analysis of ICEs from Frankia revealed their unexpected diversity and a vast array of predicted adaptive functions. Frankia ICEs were found to excise by site-specific recombination from their host's chromosome in vitro and in planta suggesting that they are functional mobile elements whether Frankiae live as soil saprophytes or plant endosymbionts. Phylogenetic analyses of proteins involved in ICEs maintenance and transfer suggests that active exchange between ICEs cargo-borne and chromosomal genes took place within the Actinomycetales order. Functionality of Frankia ICEs in vitro as well as in planta lets us anticipate that conjugation and ICEs could allow the development of genetic manipulation tools for this challenging microorganism and for many other Actinobacteria.
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影响因子：
3.6
作者：
Daccord, Aurelie;Ceccarelli, Daniela;Burrus, Vincent
通讯作者：
Burrus, Vincent
DOI：
10.1093/bioinformatics/btp348
发表时间：
2009-08-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Capella-Gutiérrez S;Silla-Martínez JM;Gabaldón T
通讯作者：
Gabaldón T
影响因子：
2.8
作者：
Askora, Ahmed;Kawasaki, Takeru;Yamada, Takashi
通讯作者：
Yamada, Takashi
影响因子：
14.9
作者：
Finn RD;Mistry J;Tate J;Coggill P;Heger A;Pollington JE;Gavin OL;Gunasekaran P;Ceric G;Forslund K;Holm L;Sonnhammer EL;Eddy SR;Bateman A
通讯作者：
Bateman A
影响因子：
3.2
作者：
BEGG, KJ;DEWAR, SJ;DONACHIE, WD
通讯作者：
DONACHIE, WD