葡萄球菌CRISPR-Cas系统的基因结构及其与耐药基因的关系
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摘要
目的对分析葡萄球菌基因组中CRISPR-Cas系统基因结构,探讨其与细菌耐药性之间的关系。方法 CRISPRdb数据库中公布的154株及NCBI中下载的171株葡萄球菌基因组共包含20个种,利用生物信息学方法分析CRISPR分布情况、重复序列、间隔序列、cas基因及CRISPR存在与细菌mecA基因之间的关系。结果 325株葡萄球菌基因组中共发现196个确定的CRISPR结构和1757个可疑的CRISPR结构;有25株含有cas基因簇,可分为Ⅲ-A(占48.1%)和Ⅱ-C(占51.9%)两型;确定CRISPR阵列中重复序列数大多数为2,有14种重复序列可以形成茎环结构,遗传进化分析显示其大致可以分为3类。确定CRISPR阵列中437种间隔序列有53种匹配质粒或噬菌体,部分序列同时匹配多个质粒或噬菌体。cas基因簇存在和不存在时的mecA携带率分别为28.00%和54.15%,差异有统计学意义(χ~2=6.37,P<0.05),两者呈负相关。结论葡萄球菌基因组中CRISPR-Cas系统携带率低,且基因座、cas基因的结构和功能均不完善,仅较少的菌株中含有完整的CRISPR-Cas系统,基因座中可疑结构较多,且DRs和spacer数量低于其他细菌。完整的葡萄球菌CRISPR-Cas系统可能限制mecA基因的水平转移。
Objectives To analyze the structure of the CRISPR-Cas system in the Staphylococcus genome and to investigate its relationship to bacterial resistance. Methods Materials used were 154 strains published in the CRISPRs database and 171 Staphylococcus genomes downloaded from NCBI, including 20 species. The distribution of confirmed and questionable CRISPR, repeat sequences, and spacers were determined bioinformatically. The relationship between the presence of the cas gene and CRISPR and drug resistance was analyzed. Results A total of 196 confirmed CRISPR structures and 1,757 questionable CRISPR structures were found in 325 Staphylococcus genomes. Only 25 strains contained the cas gene cluster and could be divided into two types, III-A(48.1%) and II-C(51.9%). Mostly there were 2 repeat sequences in the confirmed CRISPR array, and 14 repeat sequences formed a stem-loop structure. The results of genetic evolution analysis indicated that they could be roughly classified into three categories. There were 53 matching plasmids or bacteriophages in 437 spacers from confirmed CRISPR arrays, and some matched both multiple plasmids or phages. The presence of mecA differed significantly when the cas gene cluster was present or not. The presence of mecA was inversely correlated with the presence of the cas gene cluster. Conclusion Only a few strains in the genome of Staphylococcus contained a complete CRISPR-Cas system, which was type Ⅲ-A or type Ⅱ-C. However, few strains contained the cas gene cluster while many contained a questionable CRISPR structure. The number of DRs and spacers in the loci was much lower than that in other reported bacteria. A complete CRISPR-Cas system may limit the horizontal transfer of the mecA gene.
Objectives To analyze the structure of the CRISPR-Cas system in the Staphylococcus genome and to investigate its relationship to bacterial resistance. Methods Materials used were 154 strains published in the CRISPRs database and 171 Staphylococcus genomes downloaded from NCBI, including 20 species. The distribution of confirmed and questionable CRISPR, repeat sequences, and spacers were determined bioinformatically. The relationship between the presence of the cas gene and CRISPR and drug resistance was analyzed. Results A total of 196 confirmed CRISPR structures and 1,757 questionable CRISPR structures were found in 325 Staphylococcus genomes. Only 25 strains contained the cas gene cluster and could be divided into two types, III-A(48.1%) and II-C(51.9%). Mostly there were 2 repeat sequences in the confirmed CRISPR array, and 14 repeat sequences formed a stem-loop structure. The results of genetic evolution analysis indicated that they could be roughly classified into three categories. There were 53 matching plasmids or bacteriophages in 437 spacers from confirmed CRISPR arrays, and some matched both multiple plasmids or phages. The presence of mecA differed significantly when the cas gene cluster was present or not. The presence of mecA was inversely correlated with the presence of the cas gene cluster. Conclusion Only a few strains in the genome of Staphylococcus contained a complete CRISPR-Cas system, which was type Ⅲ-A or type Ⅱ-C. However, few strains contained the cas gene cluster while many contained a questionable CRISPR structure. The number of DRs and spacers in the loci was much lower than that in other reported bacteria. A complete CRISPR-Cas system may limit the horizontal transfer of the mecA gene.
引文
[1] 俞娟,戴璐.耐甲氧西林金黄色葡萄球菌SCCmec基因分型及耐药性分析[J].中国病原生物学杂志,2017,12(11):1066-9.
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[8] Tu Z,Yang W,Yan S,et al.CRISPR/Cas9:a powerful genetic engineering tool for establishing large animal models of neurodegenerative diseases[J].Mol Neurodegener,2015(10):35.
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[10] Lange SJ,Alkhnbashi OS,Rose D,et al.CRISPRmap:an automated classification of repeat conservation in prokaryotic adaptive immunesystems[J].Nucleic Acids Res,2013,41(17):8034-44.
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[13] Zhang F,Zhao S,Ren C,et al.CRISPRminer is a knowledge base for exploring CRISPR-Cas systems in microbe and phage interactions[J].Commun Biol,2018(1):180.
[14] van Belkum A,Soriaga LB,LaFave MC,et al.Phylogenetic distribution of CRISPR-Cas systems in antibiotic-resistant Pseudomonas aeruginosa[J].MBio,2015,6(6):e01796-15.
[15] 刘兴雨,毕春霞,辛晓妮,等.寡氧单胞菌中CRISPR位点的分析[J].微生物学杂志,2017,37(4):10-5.
[16] 付恒霞,毕春霞,张蒙蒙,等.不动杆菌CRISPR系统基因结构的分析及其与耐药性关系的研究[J].中国病原生物学杂志,2018,13(10):1073-7,1083.
[17] Gill SR,Fouts DE,Archer GL,et al.Insights on evolution of virulence and resistance from the complete genome analysis of an early methicillin-resistant Staphylococcus aureus strain and a biofilm-producing methicillin-resistant Staphylococcus epidermidis strain[J].J Bacteriol.2005,187(7):2426-38.
[18] Marraffini LA,Sontheimer EJ.CRISPR interference:RNA-directed adaptive immunity in bacteria and archaea[J].Nat Rev Genet,2010,11(3):181-90.
[19] Li Z,Hiasa H,Kumar U,et al.The traE gene of plasmid RP4 encodes a homologue of Escherichia coli DNA topoisomerase III[J].J Biol Chem,1997,272(31):19582-7.
[20] Touchon M,Charpentier S,Pognard D,et al.Antibiotic resistance plasmids spread among natural isolates of Escherichia coli in spite of CRISPR elements [J].Microbiology,2012,158(12):2997-3004.
[21] Palmer KL,Gilmore MS.Multidrug-resistant enterococci lack CRISPR-cas[J].MBio,2010,1(4):e00227-10.
[2] 左祥,查艳景,王征.金黄色葡萄球菌的临床分布及耐药基因研究[J].中国病原生物学杂志,2017,12(6):566-9.
[3] 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.
[4] Sorek R,Kunin V,Hugenholtz P,et al.CRISPR-a widespread system that provides acquired resistance against phages in bacteria and archaea[J].Nat Rev Microbiol,2008,6(3):181-6.
[5] Makarova KS,Wolf YI,Alkhnbashi OS,et al.An updated evolutionary classification of CRISPR-Cas systems[J].Nat Rev Microbiol,2015,13(11):722-36.
[6] Koonin EV,Makarova KS,Zhang F.Diversity,classification and evolution of CRISPR-Cas systems[J].Curr Opin Microbiol,2017(37):67-78.
[7] Shariat N,Dudley EG.CRISPRs:molecular signatures used for pathogen subtyping [J].Appl Environ Microbiol,2014,80(2):430-9.
[8] Tu Z,Yang W,Yan S,et al.CRISPR/Cas9:a powerful genetic engineering tool for establishing large animal models of neurodegenerative diseases[J].Mol Neurodegener,2015(10):35.
[9] Marraffini LA,Sontheimer EJ.CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA[J].Science,2008,322(5909):1843-5.
[10] Lange SJ,Alkhnbashi OS,Rose D,et al.CRISPRmap:an automated classification of repeat conservation in prokaryotic adaptive immunesystems[J].Nucleic Acids Res,2013,41(17):8034-44.
[11] Hofacker IL.Vienna RNA secondary structure server[J].Nucleic Acids Res,2003,31(13):3429-31.
[12] Grissa I,Bouchon P,Pourcel C,et al.On-line resources for bacterial micro-evolution studies using MLVA or CRISPR typing[J].Biochimie,2008,90(4):660-8.
[13] Zhang F,Zhao S,Ren C,et al.CRISPRminer is a knowledge base for exploring CRISPR-Cas systems in microbe and phage interactions[J].Commun Biol,2018(1):180.
[14] van Belkum A,Soriaga LB,LaFave MC,et al.Phylogenetic distribution of CRISPR-Cas systems in antibiotic-resistant Pseudomonas aeruginosa[J].MBio,2015,6(6):e01796-15.
[15] 刘兴雨,毕春霞,辛晓妮,等.寡氧单胞菌中CRISPR位点的分析[J].微生物学杂志,2017,37(4):10-5.
[16] 付恒霞,毕春霞,张蒙蒙,等.不动杆菌CRISPR系统基因结构的分析及其与耐药性关系的研究[J].中国病原生物学杂志,2018,13(10):1073-7,1083.
[17] Gill SR,Fouts DE,Archer GL,et al.Insights on evolution of virulence and resistance from the complete genome analysis of an early methicillin-resistant Staphylococcus aureus strain and a biofilm-producing methicillin-resistant Staphylococcus epidermidis strain[J].J Bacteriol.2005,187(7):2426-38.
[18] Marraffini LA,Sontheimer EJ.CRISPR interference:RNA-directed adaptive immunity in bacteria and archaea[J].Nat Rev Genet,2010,11(3):181-90.
[19] Li Z,Hiasa H,Kumar U,et al.The traE gene of plasmid RP4 encodes a homologue of Escherichia coli DNA topoisomerase III[J].J Biol Chem,1997,272(31):19582-7.
[20] Touchon M,Charpentier S,Pognard D,et al.Antibiotic resistance plasmids spread among natural isolates of Escherichia coli in spite of CRISPR elements [J].Microbiology,2012,158(12):2997-3004.
[21] Palmer KL,Gilmore MS.Multidrug-resistant enterococci lack CRISPR-cas[J].MBio,2010,1(4):e00227-10.