Bioinformatics Analysis of Clustered Regularly Interspaced Short Palindromic Repeats in the Genomes of <i>Shigella</i>_Journal of Biomedical Engineering

Authors：

WANGPengfei ¹ , WANGYingfang ^1,2 ,  DUANGuangcai ^1,3 , XUEZerun ¹ , WANGLinlin ¹ , GUOXiangjiao ¹ , YANGHaiyan ¹ , XIYuanlin ¹

1. Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou 450001, China;
2. Department of Public Health, College of Medical Science, Henan University of Science and Technology, Luoyang 471003, China;
3. Xinxiang Medical University, Xinxiang 453003, China;

Corresponding author：

DUANGuangcai, Email: gcduan@zzu.edu.cn

Keywords：

Shigella; clustered regularly interspaced short palindromic repeats; flanking sequence; repeats sequence; spacer sequence

DOI：

10.7507/1001-5515.20150063

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Abstract Full text Figures/Tables Video References Cited by

This study was aimed to explore the features of clustered regularly interspaced short palindromic repeats (CRISPR) structures in Shigella by using bioinformatics. We used bioinformatics methods, including BLAST, alignment and RNA structure prediction, to analyze the CRISPR structures of Shigella genomes. The results showed that the CRISPRs existed in the four groups of Shigella, and the flanking sequences of upstream CRISPRs could be classified into the same group with those of the downstream. We also found some relatively conserved palindromic motifs in the leader sequences. Repeat sequences had the same group with corresponding flanking sequences, and could be classified into two different types by their RNA secondary structures, which contain "stem" and "ring". Some spacers were found to homologize with part sequences of plasmids or phages. The study indicated that there were correlations between repeat sequences and flanking sequences, and the repeats might act as a kind of recognition mechanism to mediate the interaction between foreign genetic elements and Cas proteins.

Citation： WANGPengfei, WANGYingfang, DUANGuangcai, XUEZerun, WANGLinlin, GUOXiangjiao, YANGHaiyan, XIYuanlin. Bioinformatics Analysis of Clustered Regularly Interspaced Short Palindromic Repeats in the Genomes of Shigella. Journal of Biomedical Engineering, 2015, 32(2): 343-349. doi: 10.7507/1001-5515.20150063 Copy

1.	WANG Y, SONG C, DUAN G, et al. Transposition of ISEcp1 modulates blaC TX-M-55-mediated Shigella flexneri resistance to cefalothin[J]. Int J Antimicrob Agents, 2013, 42(6):507-512.
2.	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.
3.	MARRAFFINI L A, SONTHEIMER E J. CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA[J]. Science, 2008, 322(5909):1843-1845.
4.	HORVATH P, BARRANGOU R. CRISPR/CAS, the immune system of bacteria and archaea[J]. Science, 2010, 327(5962):167-170.
5.	RANDOW F, MACMICKING J D, JAMES L C. Cellular self-defense:how cell-autonomous immunity protects against pathogens[J]. Science, 2013, 340(6133):701-706.
6.	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.
7.	YANG H, DUAN G, ZHU J, et al. Prevalence and characterisation of plasmid-mediated quinolone resistance and mutations in the gyrase and topoisomeraseⅣgenes among Shigella isolates from Henan, China, between 2001 and 2008[J]. Int J Antimicrob Agents, 2013, 42(2):173-177.
8.	MALI P, YANG L, ESVELT K M, et al. RNA-guided human genome engineering via Cas9[J]. Science, 2013, 339(6121):823-826.
9.	REEKS J, NAISMITH J H, WHITE M F. CRISPR interference:a structural perspective[J]. Biochem J, 2013, 453(2):155-166.
10.	张帆, 张兵, 向华, 等.极端嗜盐古菌中CRISPR结构的生物信息学分析[J].微生物学报, 2009, 49(11):1445-1453.
11.	王琰, 喻婵, 王阶平, 等.蜡状芽孢杆菌群中规律成簇间隔短回文重复序列的生物信息学分析[J].中国生物工程杂志, 2011, 31(7):72-78.
12.	王建, 邱少富, 宋宏彬, 等.CRISPR在细菌分型和进化中的研究进展[J].生物技术通讯, 2013, (03):414-417.
13.	DEVEAU H, GARNEAU J E, MOINEAU S. CRISPR/Cas system and its role in phage-bacteria interactions[J]. Annu Rev Microbiol, 2010, 64:475-493.
14.	KUNIN V, SOREK R, HUGENHOLTZ P. Evolutionary conservation of sequence and secondary structures in CRISPR repeats[J]. Genome Biol, 2007, 8(4):R61.
15.	CONG L, RAN F A, COX D, et al. Multiplex genome engineering using CRISPR/Cas systems[J]. Science, 2013, 339(6121):819-823.
16.	JINEK M, CHYLINSKI K, FONFARA I, et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity[J]. Science, 2012, 337(6096):816-821.

1. WANG Y, SONG C, DUAN G, et al. Transposition of ISEcp1 modulates blaC TX-M-55-mediated Shigella flexneri resistance to cefalothin[J]. Int J Antimicrob Agents, 2013, 42(6):507-512.
2. 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.
3. MARRAFFINI L A, SONTHEIMER E J. CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA[J]. Science, 2008, 322(5909):1843-1845.
4. HORVATH P, BARRANGOU R. CRISPR/CAS, the immune system of bacteria and archaea[J]. Science, 2010, 327(5962):167-170.
5. RANDOW F, MACMICKING J D, JAMES L C. Cellular self-defense:how cell-autonomous immunity protects against pathogens[J]. Science, 2013, 340(6133):701-706.
6. 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.
7. YANG H, DUAN G, ZHU J, et al. Prevalence and characterisation of plasmid-mediated quinolone resistance and mutations in the gyrase and topoisomeraseⅣgenes among Shigella isolates from Henan, China, between 2001 and 2008[J]. Int J Antimicrob Agents, 2013, 42(2):173-177.
8. MALI P, YANG L, ESVELT K M, et al. RNA-guided human genome engineering via Cas9[J]. Science, 2013, 339(6121):823-826.
9. REEKS J, NAISMITH J H, WHITE M F. CRISPR interference:a structural perspective[J]. Biochem J, 2013, 453(2):155-166.
10. 张帆, 张兵, 向华, 等.极端嗜盐古菌中CRISPR结构的生物信息学分析[J].微生物学报, 2009, 49(11):1445-1453.
11. 王琰, 喻婵, 王阶平, 等.蜡状芽孢杆菌群中规律成簇间隔短回文重复序列的生物信息学分析[J].中国生物工程杂志, 2011, 31(7):72-78.
12. 王建, 邱少富, 宋宏彬, 等.CRISPR在细菌分型和进化中的研究进展[J].生物技术通讯, 2013, (03):414-417.
13. DEVEAU H, GARNEAU J E, MOINEAU S. CRISPR/Cas system and its role in phage-bacteria interactions[J]. Annu Rev Microbiol, 2010, 64:475-493.
14. KUNIN V, SOREK R, HUGENHOLTZ P. Evolutionary conservation of sequence and secondary structures in CRISPR repeats[J]. Genome Biol, 2007, 8(4):R61.
15. CONG L, RAN F A, COX D, et al. Multiplex genome engineering using CRISPR/Cas systems[J]. Science, 2013, 339(6121):819-823.
16. JINEK M, CHYLINSKI K, FONFARA I, et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity[J]. Science, 2012, 337(6096):816-821.

Journal of Biomedical Engineering

Bioinformatics Analysis of Clustered Regularly Interspaced Short Palindromic Repeats in the Genomes of Shigella

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