Comparative genomic analysis of six new-found integrative conjugative elements (ICEs) in Vibrio alginolyticus
Luo, Peng; He, Xiangyan; Wang, Yanhong; Liu, Qiuting; Hu, Chaoqun; Hu, CQ (reprint author), Chinese Acad Sci, South China Sea Inst Oceanol, Key Lab Trop Marine Bioresources & Ecol, Guangzhou 510301, Guangdong, Peoples R China.; Hu, CQ (reprint author), Chinese Acad Sci, Guangdong Key Lab Appl Marine Biol, Guangzhou 510301, Guangdong, Peoples R China.; Hu, CQ (reprint author), South China Sea Bioresource Exploitat & Utilizat, Guangzhou 510275, Guangdong, Peoples R China.
2016
发表期刊BMC MICROBIOLOGY
卷号16页码:79
摘要Background: Vibrio alginolyticus is ubiquitous in marine and estuarine environments. In 2012-2013, SXT/R391-like integrative conjugative elements (ICEs) in environmental V. alginolyticus strains were discovered and found to occur in 8.9 % of 192 V. alginolyticus strains, which suggests that V. alginolyticus may be a natural pool possessing resourceful ICEs. However, complete ICE sequences originating from this bacterium have not been reported, which represents a significant barrier to characterizing the ICEs of this bacterium and exploring their relationships with other ICEs. In the present study, we acquired six ICE sequences from five V. alginolyticus strains and performed a comparative analysis of these ICE genomes. Results: A sequence analysis showed that there were only 14 variable bases dispersed between ICEVa/E0601 and ICEVa/HN492. ICEVa/E0601 and ICEVa/HN492 were treated as the same ICE. ICEVa/A056-1, ICEVa/E0601 and ICEVa/HN492 integrate into the 5' end of the host's prfC gene, and their Int and Xis share at least 97 % identity with their counterparts from SXT. ICEVa/E0601 or ICEVa/HN492 contain 50 of 52 conserved core genes in the SXT/R391 ICEs (not s025 or s026). ICEVa/A056-2, ICEVa/HN396 and ICEVa/HN437 have a different tRNA-ser integration site and a distinct int/xis module; however, the remaining backbone genes are highly similar to their counterparts in SXT/R391 ICEs. DNA sequences inserted into hotspot and variable regions of the ICEs are of various sizes. The variable genes of six ICEs encode a large array of functions to bestow various adaptive abilities upon their hosts, and only ICEVa/A056-1 contains drug-resistant genes. Many variable genes have orthologous and functionally related genes to those found in SXT/R391 ICEs, such as genes coding for a toxin-antitoxin system, a restriction-modification system, helicases and endonucleases. Six ICEs also contain a large number of unique genes or gene clusters that were not found in other ICEs. Six ICEs harbor more abundant transposase genes compared with other parts of their host genomes. A phylogenetic analysis indicated that transposase genes in these ICEs are highly diverse. Conclusions: ICEVa/A056-1, ICEVa/E0601 and ICEVa/HN492 are typical members of the SXT/R391 family. ICEVa/A056-2, ICEVa/HN396 and ICEVa/HN437 form a new atypical group belonging to the SXT/R391 family. In addition to the many genes found to be present in other ICEs, six ICEs contain a large number of unique genes or gene clusters that were not found in other ICEs. ICEs may serve as a carrier for transposable genetic elements (TEs) and largely facilitate the dissemination of TEs.
部门归属[Luo, Peng; He, Xiangyan; Wang, Yanhong; Liu, Qiuting; Hu, Chaoqun] Chinese Acad Sci, South China Sea Inst Oceanol, Key Lab Trop Marine Bioresources & Ecol, Guangzhou 510301, Guangdong, Peoples R China; [Luo, Peng; Wang, Yanhong; Hu, Chaoqun] Chinese Acad Sci, Guangdong Key Lab Appl Marine Biol, Guangzhou 510301, Guangdong, Peoples R China; [Luo, Peng; Hu, Chaoqun] South China Sea Bioresource Exploitat & Utilizat, Guangzhou 510275, Guangdong, Peoples R China; [He, Xiangyan; Liu, Qiuting] Univ Chinese Acad Sci, Beijing 100049, Peoples R China ; LMB
关键词Vibrio Alginolyticus Integrative Conjugative Elements (Ices) Comparative Genomics Transposable Genetic Elements (Tes)
学科领域Microbiology
文献类型期刊论文
条目标识符http://ir.scsio.ac.cn/handle/344004/15419
专题中科院海洋生物资源可持续利用重点实验室
通讯作者Hu, CQ (reprint author), Chinese Acad Sci, South China Sea Inst Oceanol, Key Lab Trop Marine Bioresources & Ecol, Guangzhou 510301, Guangdong, Peoples R China.; Hu, CQ (reprint author), Chinese Acad Sci, Guangdong Key Lab Appl Marine Biol, Guangzhou 510301, Guangdong, Peoples R China.; Hu, CQ (reprint author), South China Sea Bioresource Exploitat & Utilizat, Guangzhou 510275, Guangdong, Peoples R China.
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Luo, Peng,He, Xiangyan,Wang, Yanhong,et al. Comparative genomic analysis of six new-found integrative conjugative elements (ICEs) in Vibrio alginolyticus[J]. BMC MICROBIOLOGY,2016,16:79.
APA Luo, Peng.,He, Xiangyan.,Wang, Yanhong.,Liu, Qiuting.,Hu, Chaoqun.,...&Hu, CQ .(2016).Comparative genomic analysis of six new-found integrative conjugative elements (ICEs) in Vibrio alginolyticus.BMC MICROBIOLOGY,16,79.
MLA Luo, Peng,et al."Comparative genomic analysis of six new-found integrative conjugative elements (ICEs) in Vibrio alginolyticus".BMC MICROBIOLOGY 16(2016):79.
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