霍乱弧菌N16961超级整合子重复序列及基因盒分析

Vibrio cholerae Repeat and Gene Cassette Analysis in the Super Integron of O1 El Tor V.cholerae Strain N16961

目的:确定O1群El Tor型霍乱弧菌N16961超级整合子(SI)中霍乱弧菌重复序列(VCR)的序列特点,以及VCR和基因盒的数量及位置。方法:用局部序列比对软件BLAST将VCR参考序列与霍乱弧菌N16961的Ⅱ号染色体进行比对,用Artemis Comparison Tool查看比对结果获得比对区域的位置信息,并采用perl语言脚本获得霍乱弧菌N16961的Ⅱ号染色体VCR相应区域的序列;用全局比对软件Clustal W将上一步获得的所有VCR序列进行多序列比对,采用perl语言脚本处理比对结果获得一致性序列;用MEGA4.0软件查看多序列比对结果,并采用perl语言脚本计算各位置变异频率,据此分析霍乱弧菌N16961的Ⅱ号染色体上VCR和基因盒的特点。结果:在N16961的超级整合子中有158个VCR,其核苷酸长度为117～124 bp;其一致性序列有126个核苷酸,其中37个为保守核苷酸位点,89个为可变核苷酸位点;139个VCR与相邻的VCR之间至少有1个基因,19个VCR相互之间没有任何基因;N16961的SI中共存在146个基因盒,基因盒大小为390～5924 bp不等,每个基因盒中整合的基因数目为1～9个不等。结论:建立了SI中VCR和基因盒的分析流程,分析了SI中VCR的保守及变异位点,明确了霍乱弧菌N16961的SI中VCR和基因盒的信息,为霍乱弧菌和其他细菌中SI的研究提供了分析基础。

Objective： To determine the number and position of Vibiro cholerae repeat（VCR） and gene cassette in the super integron（SI） of V.cholerae N16961.Methods： Perform comparison between the VCR and chromosome Ⅱ of N16961 with BLAST,and then get the position information of the VCR in N16961 with Artemis Comparison Tool.Get the sequence of each VCR with a script written in PERL.Perform global multiple comparison of all of the VCR found in BLAST with Clustal W and get the consensus sequence of these VCR.View the multiple com-parison result in MEGA 4.0 and calculate the variation frequency of each nucleotide.Results： In total,158 VCR were determined in the SI of N16961.The VCR size ranged from 117 to 124 bp.The consensus sequence of VCR consisted of 126 nucleotides,37 and 89 of which are conservative and variable sites respectively.In 139 VCR,at least one ORF was inserted between two adjacent VCR.No VCR were inserted between any two or more ORF in 19 VCR.In total 146 gene cassettes were confirmed with the size ranged from 390 to 5924 bp.The ORF number in a gene cassette ranged from 1 to 9.Conclusion： A protocol to determine VCR and gene cassette was estab-lished.The conservative and variable nucleotide site of VCR in N16961 has been determined.The VCR and gene cassette information in the SI of N16961 were confirmed.This information can be used to study the dynamics of SI in V.choalere and is useful to the analysis of the SI in other species.