Bioinformatics analyses of Shigella CRISPR structure and spacer classification

详细信息    查看全文

• 作者：Pengfei Wang ; Bing Zhang ; Guangcai Duan…
• 关键词：Shigella ; CRISPR ; Repeat ; Cas ; Spacer
• 刊名：World Journal of Microbiology & Biotechnology
• 出版年：2016
• 出版时间：March 2016
• 年：2016
• 卷：32
• 期：3
• 全文大小：1,298 KB
• 参考文献：Biswas A, Gagnon JN, Brouns SJ, Fineran PC, Brown CM (2013) CRISPRTarget: bioinformatic prediction and analysis of crRNA targets. RNA Biol 10:817–827CrossRef
  Bland C, Ramsey TL, Sabree F, Lowe M, Brown K, Kyrpides NC, Hugenholtz P (2007) CRISPR recognition tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats. BMC Bioinform 8:209. doi:10.​1186/​1471-2105-8-209 CrossRef
  Cong L et al (2013) Multiplex genome engineering using CRISPR/Cas systems. Science (New York, NY) 339:819–823CrossRef
  Diez-Villasenor C, Almendros C, Garcia-Martinez J, Mojica FJ (2010) Diversity of CRISPR loci in Escherichia coli. Microbiology 156:1351–1361CrossRef
  Grissa I, Vergnaud G, Pourcel C (2007) The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats. BMC Bioinform 8:172. doi:10.​1186/​1471-2105-8-172 CrossRef
  Guo X et al (2014) Detection and analysis of CRISPRs of shigella. Curr Microbiol 70:85–90CrossRef
  He L, Fan X, Xie J (2012) Comparative genomic structures of mycobacterium CRISPR-Cas. J Cell Biochem 113:2464–2473CrossRef
  Horvath P, Barrangou R (2010) CRISPR/Cas, the immune system of bacteria and archaea. Science (New York, NY) 327:167–170CrossRef
  Horvath P et al (2008) Diversity, activity, and evolution of CRISPR loci in streptococcus thermophilus. J Bacteriol 190:1401–1412CrossRef
  Kiro R, Goren MG, Yosef I, Qimron U (2013) CRISPR adaptation in Escherichia coli subtypeI-E system. Biochem Soc Trans 41:1412–1415CrossRef
  Kunin V, Sorek R, Hugenholtz P (2007) Evolutionary conservation of sequence and secondary structures in CRISPR repeats. Genome Biol 8:R61. doi:10.​1186/​gb-2007-8-4-r61 CrossRef
  Kuscu C, Arslan S, Singh R, Thorpe J, Adli M (2014) Genome-wide analysis reveals characteristics of off-target sites bound by the Cas9 endonuclease. Nat Biotechnol 32:677–683CrossRef
  Lorenz R, Bernhart SH, Honer Zu Siederdissen C, Tafer H, Flamm C, Stadler PF, Hofacker IL (2011) ViennaRNA package 2.0 algorithms for molecular. Biol AMB 6:26. doi:10.​1186/​1748-7188-6-26
  Mali P et al (2013) RNA-guided human genome engineering via Cas9. Science (New York, NY) 339:823–826CrossRef
  Marraffini LA, Sontheimer EJ (2008) CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA. Science (New York, NY) 322:1843–1845CrossRef
  Palmer KL, Gilmore MS (2010) Multidrug-resistant enterococci lack CRISPR-cas. mBio 1:e0022710. doi:10.​1128/​mBio.​00227-10
  Pattanayak V, Lin S, Guilinger JP, Ma E, Doudna JA, Liu DR (2013) High-throughput profiling of off-target DNA cleavage reveals RNA-programmed Cas9 nuclease specificity. Nat Biotechnol 31:839–843CrossRef
  Randow F, MacMicking JD, James LC (2013) Cellular self-defense: how cell-autonomous immunity protects against pathogens. Science (New York, NY) 340:701–706CrossRef
  Reeks J, Naismith JH, White MF (2013) CRISPR interference: a structural perspective. Biochem J 453:155–166CrossRef
  Toro M et al (2014) Association of clustered regularly interspaced short palindromic repeat (CRISPR) elements with specific serotypes and virulence potential of shiga toxin-producing Escherichia coli. Appl Environ Microbiol 80:1411–1420CrossRef
  Touchon M, Rocha EP (2010) The small, slow and specialized CRISPR and anti-CRISPR of Escherichia and Salmonella. PLoS ONE 5:e11126. doi:10.​1371/​journal.​pone.​0011126 CrossRef
  Touchon M, Charpentier S, Clermont O, Rocha EPC, Denamur E, Branger C (2011) CRISPR distribution within the Escherichia coli species is not suggestive of immunity-associated diversifying selection. J Bacteriol 193:2460–2467CrossRef
  Wang Y, Song C, Duan G, Zhu J, Yang H, Xi Y, Fan Q (2013) Transposition of ISEcp1 modulates blaCTX-M-55-mediated Shigella flexneri resistance to cefalothin. Int J Antimicrob Agents 42:507–512CrossRef
  Yang H, Sun W, Duan G, Zhu J, Zhang W, Xi Y, Fan Q (2013) Serotype distribution and characteristics of antimicrobial resistance in Shigella isolated from Henan province, China, 2001–2008. Epidemiol Infect 141:1946–1952CrossRef
  Yin S, Jensen MA, Bai J, Debroy C, Barrangou R, Dudley EG (2013) The evolutionary divergence of Shiga toxin-producing Escherichia coli is reflected in clustered regularly interspaced short palindromic repeat (CRISPR) spacer composition. Appl Environ Microbiol 79:5710–5720CrossRef
  
• 作者单位：Pengfei Wang (1)
  Bing Zhang (1)
  Guangcai Duan (1) (2)
  Yingfang Wang (1) (3)
  Lijuan Hong (1)
  Linlin Wang (1)
  Xiangjiao Guo (1)
  Yuanlin Xi (1)
  Haiyan Yang (1)
  
  1. Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, 450001, Henan, People’s Republic of China
  2. Henan Innovation Center of Molecular Diagnosis and Laboratory Medicine, Xinxiang Medical University, Xinxiang, 453003, Henan, People’s Republic of China
  3. Department of Public Health, College of Medical Sciences, Henan University of Science and Technology, Luoyang, 471023, Henan, People’s Republic of China
  
• 刊物类别：Chemistry and Materials Science
• 刊物主题：Chemistry
  Applied Microbiology
  Biotechnology
  Biochemistry
  Environmental Biotechnology
  Microbiology
  
• 出版者：Springer Netherlands
• ISSN：1573-0972

文摘

Clustered regularly interspaced short palindromic repeats (CRISPR) are inheritable genetic elements of a variety of archaea and bacteria and indicative of the bacterial ecological adaptation, conferring acquired immunity against invading foreign nucleic acids. Shigella is an important pathogen for anthroponosis. This study aimed to analyze the features of Shigella CRISPR structure and classify the spacers through bioinformatics approach. Among 107 Shigella, 434 CRISPR structure loci were identified with two to seven loci in different strains. CRISPR-Q1, CRISPR-Q4 and CRISPR-Q5 were widely distributed in Shigella strains. Comparison of the first and last repeats of CRISPR1, CRISPR2 and CRISPR3 revealed several base variants and different stem-loop structures. A total of 259 cas genes were found among these 107 Shigella strains. The cas gene deletions were discovered in 88 strains. However, there is one strain that does not contain cas gene. Intact clusters of cas genes were found in 19 strains. From comprehensive analysis of sequence signature and BLAST and CRISPRTarget score, the 708 spacers were classified into three subtypes: Type I, Type II and Type III. Of them, Type I spacer referred to those linked with one gene segment, Type II spacer linked with two or more different gene segments, and Type III spacer undefined. This study examined the diversity of CRISPR/cas system in Shigella strains, demonstrated the main features of CRISPR structure and spacer classification, which provided critical information for elucidation of the mechanisms of spacer formation and exploration of the role the spacers play in the function of the CRISPR/cas system. Keywords Shigella CRISPR Repeat Cas Spacer