[1]张 博,姚学萍*,曹随忠,等. 空肠弯曲菌CRISPR-Cas系统生物信息学分析[J].中国预防兽医学报,2018,(10):960-964.[doi:10.3969/j.issn.1008-0589.201712005]
 ZHANG Bo,YAO Xue-ping*,CAO Sui-zhong,et al. Bioinformatic analysis of CRISPR-Cas system in Campylobacter jejuni[J].Chinese journal of preventive veterinary medicine,2018,(10):960-964.[doi:10.3969/j.issn.1008-0589.201712005]
点击复制

 

空肠弯曲菌CRISPR-Cas系统生物信息学分析

()
分享到:

《中国预防兽医学报》[ISSN:1008-0589/CN:23-1417/S]

卷:
期数:
2018年10
页码:
960-964
栏目:
研究简报
出版日期:
2018-11-15

文章信息/Info

Title:
 

Bioinformatic analysis of CRISPR-Cas system in Campylobacter jejuni

文章编号:
1008-0589(2018)10-0960-05
作者:
 

张 博1姚学萍12*曹随忠12王 印12杨泽晓12

 

(1. 四川农业大学 动物医学院,四川 成都 611130;2. 动物疫病与人类健康四川省重点实验室,四川 成都 611130)

Author(s):
 

ZHANG Bo1 YAO Xue-ping12* CAO Sui-zhong12 WANG Yin12 YANG Ze-xiao12

 

(1. College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China

2. Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu 611130, China)

关键词:
空肠弯曲菌CRISPR-Cas系统重复序列间隔序列生物信息学
Keywords:
 

 Campylobacter jejuni CRISPR-Cas system repeat sequence spacer sequence bioinformatics

分类号:
S852.61
DOI:
10.3969/j.issn.1008-0589.201712005
文献标志码:
A
摘要:
 

为分析GenBank中登录的国内外空肠弯曲菌及其亚种中所含CRISPR-Cas系统的结构特征及同源关系,本研究利用生物信息学方法预测GenBank中已登录的空肠弯曲菌所含的CRISPR-Cas系统的基因序列,对其进行比对、保守性分析、RNA二级结构预测、重复序列的GC含量分析及其遗传进化分析。结果显示,空肠弯曲菌及其亚种中所含CRISPR-Cas系统的重复序列高度保守、GC含量较低(28.57 %以下),差异性主要呈现于两端游离部分;CRISPR中的间隔序列差异性较大致使CRISPR具有多态性;Cas蛋白序列同源性较高(96.8 %以上),遗传动态变化较低,与基因水平转移产生的趋同进化有潜在相关性。空肠弯曲菌CRISPR-Cas系统中的间隔序列具有多态性与该菌的遗传进化差异有关,重复序列及cas基因保守性较强,与其共同进化有潜在相关性。通过对不同空肠弯曲菌CRISPR-Cas系统生物信息学分析,为进一步研究该菌CRISPR-Cas系统结构特征、基因进化关系奠定了基础。

 

Abstract:
 

To analyze the structural features and homology relations of the CRISPR-Cas system in Campylobacter jejuni available in GenBank, the gene sequence of CRISPR-Cas system in C.jejuni from GenBank was predicted by the bioinformatics methods. The comparison, conservative analysis, RNA secondary structure prediction and GC content analysis of the repeat sequences of CRISPR-Cas system in C.jejuni were performed, and the genetic evolution trees of repeat sequences were constructed. The results showed that the conservation of repeat sequences of CRISPR-Cas system in C.jejuni was high and GC content was below 28.57%. The difference appeared in both end of repeat sequence and the main difference of spacer sequence resulted in the polymorphism of CRISPR. The homology of Cas protein sequence was over 96.8%, and the genetic dynamic change was weak, which potentially related to the convergent evolution of gene level shifts. The polymorphism of spacer sequence of CRISPR-Cas system in C.jejuni was related to the genetic evolutionary difference, and the conservation of repeat sequence and cas genes was high, and there was a potential correlation with the coevolution of repeat sequence and cas genes. Analyzing the biological information of CRISPR-Cassystem in different C.jejuni could lay the foundation for further study on the structural characteristics and evolution relationship of CRISPR-Cas system.

参考文献/References:

 

[1]Marchfelder A. Special focusCRISPR-Cas [J]. RNA Biol, 2013, 10(5): 655-658.

[2]张博,姚学萍,王印,等. CRISPR-Cas系统调控细菌生理功能的机制研究进展[J]. 微生物学通报,2017,44(12):3045-3052.

[3]Koonin E V, Makarova K S. CRISPR-Cas: evolution of an RNA-based adaptive immunity system in prokaryotes [J]. RNA Biol, 2013, 10(5): 679-686.

[4]Haft D H, Selengut J, Mongodin E F, et al. A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/ Cas subtypes exist in prokaryotic genomes [J]. PLoS Comput Biol, 2005, 1(6): e60.

[5]冯红,董阁,雍彬,等. 原核CRISPR-Cas系统的结构功能及应用[J]. 四川师范大学学报(自然科学版),2014,37(2):268-281.

[6]Grissa I, Vergnaud G, Pourcel C. The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats [J]. BMC Bioinformatics, 2007, 8(1): 172.

[7]杨泽民,谢数涛,章群,等. RNA二级结构预测及其在分子分类研究中的应用[J]. 安徽农业科学,2012,(7):3919-3922.

[8]Schouls L M, Reulen S, Duim B, et al. Comparative genotyping of Campylobacter jejuni by amplified fragment length polymorphism, multilocus sequence typing, and short repeat sequencing: strain diversity, host range, and recombination [J]. J Clin Microbiol, 2003, 41(1): 15-26.

[9]刘杨,崔晓龙,李文均,等. RNA二级结构在微生物系统发育分析上的应用[J]. 微生物学通报,2006,33(2):147-150.

[10]Makarova K S, Haft D H, Barrangou R, et al. Evolution and classification of the CRISPR-Cas systems [J]. Nat Rev Microbiol, 2011, 9(6): 467-477.

[11]Shalem O, Sanjana N E, Hartenian E, et al. Genome-scale CRISPR-Cas9 knockout screening in human cells [J]. Science, 2014, 343(6166): 84-87.

[12]Louwen R, Staals R H J, Endtz H P, et al. The role of CRISPR- Cas systems in virulence of pathogenic bacteria [J]. Microbiol Mol Biol Rev, 2014, 78(1): 74.

[13]Ge Bei-lei, Wang Fei, Sj?觟lund-Karlsson M, et al. Antimicrobial resistance incampylobacter:susceptibility testing methods and resistance trends [J]. J Microbiol Methods, 2013, 95(1): 57-67.

(本文编辑:李 爽)

相似文献/References:

[1]徐君怡*,曹际娟,郑秋月,等.多重PCR-变性高效液相色谱检测食品中空肠弯曲菌和结肠弯曲菌[J].中国预防兽医学报,2009,(03):207.
 XU Jun-yi*,CAO Ji-juan,ZHENG Qiu-yue,et al.A multiplex PCR and denaturing high-performance liquid chromatography method for identifying Campylobacter jejuni and Campylobacter coli [J].Chinese journal of preventive veterinary medicine,2009,(10):207.
[2]黄金林,许海燕,郑国军,等.部分省市鸡群空肠弯曲菌和结肠弯曲菌的流行状况分析[J].中国预防兽医学报,2008,(01):72.
 HUANG Jin-lin,XU Hai-yan,ZHENG Guo-jun,et al.Epidemiological survey of Campylobacter spp. in chickens in parts of China[J].Chinese journal of preventive veterinary medicine,2008,(10):72.
[3]徐义刚,李丹丹,刘忠梅,等.基于DPO引物的空肠弯曲菌PCR检测方法的建立与初步应用[J].中国预防兽医学报,2014,(04):293.[doi:10.3969/j.issn.1008-0589.2014.04.10]
 XU Yi-gang,LI Dan-dan,LIU Zhong-mei,et al. Development and preliminary application of DPO-based PCR method for detection of Campylobacter jejuni[J].Chinese journal of preventive veterinary medicine,2014,(10):293.[doi:10.3969/j.issn.1008-0589.2014.04.10]
[4]张 博,姚学萍*,王 印,等.15株禽源空肠弯曲菌的分离鉴定及CheW基因序列分析[J].中国预防兽医学报,2018,(01):78.[doi:0.3969/j.issn.1008-0589.201704036]
 ZHANG Bo,YAO Xue-ping*,WANG Yin,et al. Isolation and identification of 15 Campylobacter jejuni strains from poultry and sequence analysis of CheW gene[J].Chinese journal of preventive veterinary medicine,2018,(10):78.[doi:0.3969/j.issn.1008-0589.201704036]
[5]王 莉,沙 洲,李诗语,等.空肠弯曲菌荧光偏振抗体检测方法的建立[J].中国预防兽医学报,2018,(03):220.[doi:0.3969/j.issn.1008-0589.201704026]
 WANG Li,SHA Zhou,LI Shi-yu,et al.Establishment of fluorescent polarization assay for detection of antibody to Campylobacter jejuni[J].Chinese journal of preventive veterinary medicine,2018,(10):220.[doi:0.3969/j.issn.1008-0589.201704026]

更新日期/Last Update: 2018-11-28