志贺菌中成簇的规律间隔短回文重复序列的特点及其关联性分析

doi:10.13481/j.1671-587x.20180604

Abstract

Abstract: Objective: To analyze the characteristics of clustered regularly interspaced short palindromic repeats (CRISPR) in Shigella from the database and clinic, and to explore the characteristics of CRISPR-Q1 and the correlations among CRISPRs.Methods: According to the genome database of Shigella, the primer sequences and PCR amplication were used to obtain the CRISPR sequences of Shigella, and the multiple sequence alignment was used to analyze the CRISPR distribution, the number and features of spacer; BLAST was used to analyze the repeats and spacers in CRISPR-Q1;the distribution characteristics of the repeats and spacers in Shigella and the location and features of CRISPR-Q1 in the strain were detected; the relationships between the spacer number of CRISPR-Q1 and CRISPR1/CRISPR2 in the database and laboratory were analyzed.Results: Among 107 Shigella strains in the database, 106 Shigella strains contained CRISPR1 or CRISPR2, 8 Shigella strains contained severial spacers; 106 Shigella strains contained CRISPR-Q1, and 13 Shigella strains contained severial spacers.A total of 6 among 12 Shigella strains in the laboratory contained CRISPR1 or CRISPR2, all of the 12 strains contained CRISPR-Q1. A portion of the CRISPR-Q1 spacer (about 35 bp) widely distributed in the genome of the same strain of chromosome, as was the repeat sequence; CRISPR-Q1 contained the repetitive extragenic palindromic elements (REP). The spacer number of CRISPR-Q1 was related to the CRISPR1 or CRISPR2 of Shigella in the database(χ²=61.60,P<0.01) and in the laboratory (P=0.015).Conclusion: CRISPR-Q1 widely distributes in Shigella and the REP elements can be found in CRISPR-Q1.There are correlations between CRISPR1 or CRISPR2 and CRISPR-Q1 in Shigella.

Key words: Shigella, clustered regularly interspaced short palindromic repeats, spacer, repetitive extragenic palindromic

CLC Number:

WANG Yingfang, WANG Pengfei, DUAN Guangcai, XI Yuanlin, ZHANG Xiaomeng, ZHAN Yuhui. Characteristics of clustered regularly interspaced short palindromic repeats in Shigella and their correlation analysis[J].Journal of Jilin University(Medicine Edition), 2018, 44(06): 1131-1137.

References

[1] Shariat N, Timme RE, Pettengill JB, et al. Characterization and evolution of salmonella CRISPR-Cas Systems[J]. Microbiology, 2015, 161(Pt2):374-386.
[2] 杨海燕, 段广才, 张卫东, 等. 河南省睢县2001-2008年志贺菌群分布及其耐药分析[J]. 中华流行病学杂志, 2010, 31(3):351-353.
[3] Wang Y, Song C, Duan G, et al. Transposition of ISEcp1 modulates blaCTX-M-55-mediated Shigella flexneri resistance to cefalothin[J]. Int J Antimicrob Agents, 2013, 42(6):507-512.
[4] Yang H, Duan G, Zhu J, et al. Prevalence and characterisation of plasmid-mediated quinolone resistance and mutations in the gyrase and topoisomerase Ⅳ genes among Shigella isolates from Henan, China, between 2001 and 2008[J]. Int J Antimicrob Agents, 2013, 42(2):173-177.
[5] Yang H, Sun W, Duan G, et al. Serotype distribution and characteristics of antimicrobial resistance in Shigella isolated from Henan province, China, 2001-2008[J]. Epidemiol Infect, 2013, 141(9):1946-1952.
[6] Palmer KL, Gilmore MS. Multidrug-resistant enterococci lack CRISPR-cas[J]. mBio, 2010, 1(4):e0022710.
[7] Cooper LA, Stringer AM, Wade JT. Determining the specificity of cascade binding, interference, and primed adaptation in vivo in the Escherichia coli type I-E CRISPR-cas system[J]. mBio, 2018, 9(2):e02100-17.
[8] Savitskaya E, Lopatina A, Medvedeva S, et al. Dynamics of Escherichia coli type I-E CRISPR spacers over 42000 years[J]. Mol Ecol, 2017, 26(7):2019-2026.
[9] 张冰, 洪丽娟, 段广才, 等. 4株志贺菌无抗生素压力下连续传代90次的耐药表型及CRISPR/Cas系统变化[J]. 中华流行病学杂志, 2017, 38(2):235-239.
[10] 张冰, 王鹏飞, 段广才, 等. CRISPR/Cas系统间隔序列同源质粒耐药信息与志贺菌耐药的关系[J]. 中国病原生物学杂志, 2016(10):881-887.
[11] 洪丽娟, 张冰, 段广才, 等. CRISPR/Cas系统与志贺菌毒力和耐药的关系及插入序列IS600对cse2表达水平的影响[J]. 微生物学报, 2016(12):1912-1923.
[12] Krivoy A, Rutkauskas M, Kuznedelov K, et al. Primed CRISPR adaptation in Escherichia coli cells does not depend on conformational changes in the Cascade effector complex detected in vitro[J]. Nucleic Acids Res, 2018, 46(8):4087-4098.
[13] Champer J, Liu J, Oh SY, et al. Reducing resistance allele formation in CRISPR gene drive[J]. Proc Natl Acad Sci U S A, 2018, 115(21):5522-5527.
[14] 王鹏飞, 王颖芳, 段广才, 等. 志贺菌成簇的规律间隔的短回文重复序列系统结构特征的生物信息学分析[J]. 生物医学工程学杂志, 2015, 32(2):343-349.
[15] 王鹏飞, 王颖芳, 段广才, 等. 志贺菌成簇的规律间隔短回文重复序列的检测及同源性分析[J]. 吉林大学学报:医学版, 2015, 41(2):261-268.
[16] Guo X, Wang Y, Duan G, et al. Detection and analysis of CRISPRs of Shigella[J]. Curr Microbiol, 2015, 70(1):85-90.
[17] Wang P, Zhang B, Duan G, et al. Bioinformatics analyses of Shigella CRISPR structure and spacer classification[J]. World J Microbiol Biotechnol, 2016, 32(3):38.
[18] Yin S, Jensen MA, Bai J, et al. The evolutionary divergence of Shiga toxin-producing Escherichia coli is reflected in clustered regularly interspaced short palindromic repeat (CRISPR) spacer composition[J]. Appl Environ Microbiol, 2013, 79(18):5710-5720.
[19] Touchon M, Rocha EP. The small, slow and specialized CRISPR and anti-CRISPR of Escherichia and Salmonella[J]. PLoS One, 2010, 5(6):e11126.
[20] Horvath P, Romero DA, Coute-monvoisin AC, et al. Diversity, activity, and evolution of CRISPR loci in Streptococcus thermophilus[J]. J Bacteriol, 2008, 190(4):1401-1412.
[21] 薛泽润, 王颖芳, 段广才, 等, 志贺菌成簇规律间隔短回文重复序列相关蛋白基因cas1和cas2研究[J]. 中华流行病学杂志, 2014, 35(5):581-584.
[22] Strotskaya A, Savitskaya E, Metlitskaya A, et al. The action of Escherichia coli CRISPR-Cas system on lytic bacteriophages with different lifestyles and development strategies[J]. Nucleic Acids Res, 2017, 45(4):1946-1957.
[23] 赵燕梅, 张吉明, 许庆方. Rep-PCR技术及其应用现状[J]. 中国草食动物科学, 2014, 34(3):55-57.
[24] Cao Y, Wei D, Kamara IL, et al. Multi-locus sequence typing (MLST) and repetitive extragenic palindromic polymerase chain reaction (REP-PCR), characterization of Shigella spp. over two decades in Tianjin China[J]. Int J Mol Epidemiol Genet, 2012, 3(4):321-332.

Characteristics of clustered regularly interspaced short palindromic repeats in Shigella and their correlation analysis

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