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Novel and diverse integron integrase genes and integron‐like gene cassettes are prevalent in deep‐sea hydrothermal vents
Author(s) -
Elsaied Hosam,
Stokes H. W.,
Nakamura Takamichi,
Kitamura Keiko,
Fuse Hiroyuki,
Maruyama Akihiko
Publication year - 2007
Publication title -
environmental microbiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.954
H-Index - 188
eISSN - 1462-2920
pISSN - 1462-2912
DOI - 10.1111/j.1462-2920.2007.01344.x
Subject(s) - biology , integron , integrase , orfs , hydrothermal vent , gene cassette , gene , genetics , open reading frame , plasmid , paleontology , hydrothermal circulation , peptide sequence
Summary 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.