沙门氏菌CRISPR位点的结构特征比较

Genomics comparison between CRISPR loci and plasmid in Salmonella enteric

摘要:

成簇规律间隔的短回文重复序列（Clustered regularly interspaced short palindromic repeats，CRISPR），是存在于多数细菌和古菌中的遗传结构，能够有效防御外源DNA的入侵（质粒、噬菌体等），进而防御外源基因的水平转移。[目的]本研究以沙门氏菌属中常见的鸡伤寒沙门氏菌（Salmonella gallinarum）、鼠伤寒沙门氏菌（Salmonella typhimurium）、猪霍乱沙门氏菌（Salmonella choleraesuis）以及肠炎沙门氏菌（salmonella enteritidis）等30个菌株为研究对象。探索CRISPR位点在不同沙门氏菌种中的结构差异。[方法]通过生物信息学的方法比较间隔序列与插入序列的同源性以及CRISPR位点与质粒数量关系。[结果]30株沙门氏菌中均存在CRISPR结构，包括CRISPR位点61个以及可疑位点12个。重复序列和cas1基因均不能作为这4类细菌的分类依据。[结论]虽然我们发现CRISPR位点数量与间隔区数量和质粒数量之间均不存在统计学关系，但间隔序列整合子、耐药基因等移动遗传原件具有一定的同源性，说明沙门氏菌在进化过程中不断受外源基因的侵袭。

Abstract:

Clustered regularly interspaced short palindromic repeats (CRISPR) is the genetic structure found in most of bacteria and archaea. The function of CRISPR is defending against the invasion of exogenous DNA (plasmid, phage, etc.), preventing heterologous gene transfer. [Objective] This study is to study the structural differences of CRISPR loci in several Salmonella sp.[Methods] The molecular structure of CRISPR and the relationship between CRISPR and plasmid was analyzed in 30 strains, including Salmonella gallinarum, S. typhimurium, S. choleraesuis and S. enteritidis by bioinformatics.[Results] CRISPR structure existed in the 30 strains of Salmonella, totally 61 conformed CRISPR loci and 12 possible ones. Neither repeat sequence nor cas1 gene could be used for the classification of these strains.[Conclusion] Although the number of CRISPR loci and spacer sequence have no statistical relationship with the number of plasmid, the spacer sequence has genetic homology with plasmid, transposons, integron and resistant genes. This suggests that Salmonella sp. are attacked by exogenous genes constantly during evolution, and CRISPR loci of Salmonella sp. play a role in resisting exogenous genes.