Novel and diverse integron integrase genes and integron-like gene cassettes are prevalent in deep-sea hydrothermal vents
Novel and diverse integron integrase genes and integron-like gene cassettes are prevalent in deep-sea hydrothermal vents
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DOI：
10.1111/j.1462-2920.2007.01344.x
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发表时间：
2007-09-01
影响因子：
5.1
通讯作者：
Maruyama, Akihiko
中科院分区：
文献类型：
--
作者：
Elsaied, Hosam;Stokes, H. W.;Maruyama, Akihiko
由于缺乏关于深海热液喷口中移动的DNA的信息，限制了我们对这些环境中细菌移动的基因组系统发育多样性的了解。我们使用文化独立的技术来探索的整合子/移动的基因盒系统在各种热液喷口社区的多样性。从日本伊豆-小笠原的水予海山和马里亚纳岛弧的皮卡地点采集了三个样品，其中包括两种不同的热液喷口流体和一种含有基本上单系硫氧化细菌内共生体的贻贝物种。首先，使用简并聚合酶链反应（PCR）引物，我们从每个样品的宏基因组DNA扩增整合子整合酶基因。从喷口流体中，我们发现了74个新的整合酶基因，被归类为11个以前未描述的整合子类。一个整合酶基因被记录在贻贝共生体，并与从喷口流体中回收的整合酶基因相距甚远。其次，使用PCR引物靶向基因盒重组位点（59-be），我们扩增并随后鉴定了60个不同的基因盒。在多盒扩增子中，共鉴定出13个59-be位点。大多数这些网站显示的功能是非典型的功能，以前很好地保存在这个家庭。Suiyo喷口流体的特征在于基因盒开放阅读框（ORF），与转移酶，DNA结合蛋白和金属转运蛋白具有显着的同源性，而大多数鼠兔喷口流体基因盒包含新的ORF，在数据库中没有可识别的同源物。发现共生体基因盒ORF与DNA修复蛋白、甲硫氨酸氨肽酶、氨肽酶N，O-唾液酸糖蛋白内肽酶和谷氨酸合酶匹配，这些蛋白预期在动物/共生体代谢中发挥作用。这项研究的成功表明，整合子/基因盒系统是常见的深海热液喷口，远离人为干扰的环境类型。
The lack of information about mobile DNA in deep-sea hydrothermal vents limits our understanding of the phylogenetic diversity of the mobile genome of bacteria in these environments. We used culture-independent techniques to explore the diversity of the integron/mobile gene cassette system in a variety of hydrothermal vent communities. Three samples, which included two different hydrothermal vent fluids and a mussel species that contained essentially monophyletic sulfur-oxidizing bacterial endosymbionts, were collected from Suiyo Seamount, Izu-Bonin, Japan, and Pika site, Mariana arc. First, using degenerate polymerase chain reaction (PCR) primers, we amplified integron integrase genes from metagenomic DNA from each sample. From vent fluids, we discovered 74 new integrase genes that were classified into 11 previously undescribed integron classes. One integrase gene was recorded in the mussel symbiont and was phylogenetically distant from those recovered from vent fluids. Second, using PCR primers targeting the gene cassette recombination site (59-be), we amplified and subsequently identified 60 diverse gene cassettes. In multicassette amplicons, a total of 13 59-be sites were identified. Most of these sites displayed features that were atypical of the features previously well conserved in this family. The Suiyo vent fluid was characterized by gene cassette open reading frames (ORFs) that had significant homologies with transferases, DNA-binding proteins and metal transporter proteins, while the majority of Pika vent fluid gene cassettes contained novel ORFs with no identifiable homologues in databases. The symbiont gene cassette ORFs were found to be matched with DNA repair proteins, methionine aminopeptidase, aminopeptidase N, O-sialoglycoprotein endopeptidase and glutamate synthase, which are proteins expected to play a role in animal/symbiont metabolism. The success of this study indicates that the integron/gene cassette system is common in deep-sea hydrothermal vents, an environment type well removed from anthropogenic disturbance.