多杀性巴氏杆菌CRISPR-Cas系统生物信息学分析

doi:10.16431/j.cnki.1671-7236.2023.05.002

Abstract

Abstract: 【Objective】 This study was aimed to understand the structural characteristics of CRISPR-Cas system and the distribution of cas gene in Pasteurella multocida,and provide a basis for the application of different CRISPR subtypes and the antiviral evolution of Pasteurella multocida.【Method】 The CRISPR cluster and cas gene were screened in the genome of Pasteurella multocida via CRISPRCasfinder online website.The conservation of repeat and spacer sequence,the secondary structure of repeat,the conservation of nucleotide sequence of cas gene,and the similarity of CRISPR cluster in various subtype system were investigated using bioinformatics analysis.【Result】 There were three subtypes(Ⅰ-F,Ⅱ-C and Ⅲ-A) of CRISPR-Cas system identified in 19 selected Pasteurella multocida strains.The repeat sequences in the same CRISPR subtypes had a relatively conservative palindrome repeat sequence,whereas the palindromic repeats varied in the different CRISPR subtypes.The tracrRNA could bind with crRNA in subtype Ⅱ-C system and form conservative structures.In CRISPR system of each subtype,the newly acquired spacer was integrated both at the 5'-end,3'-end or internal locations of CRISPR cluster.Through the analysis of the spacer sequence of each strain,it was found that the same spacer sequence existed in the CRISPR sequence within or between strains,which might relate to the sequence recombination of repeat-spacer in bacteria or convergent evolution of gene level shifts during genetic evolution.【Conclusion】 The 19 strains of Pasteurella multocida contained 3 CRISPR-Cas systems of Ⅰ-F,Ⅱ-C and Ⅲ-A.The repeat sequence of different CRISPR subtypes was significantly different.The distribution of spacer characteristic repeats might be related to the sequence recombination of repeat spacer in Pasteurella multocida during genetic evolution.

Key words: Pasteurella multocida; CRISPR-Cas system; repeat sequence; spacer sequence; bioinformatic

CLC Number:

S852.61

LI Jiafu, MO Xiaobing. Bioinformatic Analysis of CRISPR-Cas System in Pasteurella multocida[J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(5): 1742-1753.

References

[1] MAKAROVA K S,WOLF Y I,KOONIN E V.The basic building blocks and evolution of CRISPR-CAS systems[J].Biochemical Society Transactions,2013,41(6):1392-1400.
[2] HILLE F,RICHTER H,WONG S P,et al.The biology of CRISPR-Cas:Backward and forward[J].Cell,2018,172(6):1239-1259.
[3] JANSEN R,EMBDEN J D,GAASTRA W,et al.Identification of genes that are associated with DNA repeats in prokaryotes[J].Molecular Microbiology,2002,43(6):1565-1575.
[4] MAKAROVA K S,WOLF Y I,ALKHNBASHI O S,et al.An updated evolutionary classification of CRISPR-Cas systems[J].Nature Reviews Microbiology,2015,13(11):722-736.
[5] MAKAROVA K S,WOLF Y I,IRANZO J,et al.Evolutionary classification of CRISPR-Cas systems:A burst of class 2 and derived variants[J].Nature Reviews Microbiology,2020,18(2):67-83.
[6] 胡丽,陈实.细菌CRISPR-Cas系统的研究进展[J].微生物学报,2017,52(6):675-683. HU L,CHEN S.Research progress of CRISPR-Cas system in bacteria[J].Acta Microbiologica Sinica,2017,52(6):675-683.(in Chinese)
[7] PENG Z,WANG X,ZHOU R,et al.Pasteurella multocida:Genotypes and genomics[J].Microbiology and Molecular Biology Reviews,2019,83(4):14-19.
[8] 周望舒.鸭源多杀性巴氏杆菌的分离鉴定及其CRISPR位点的分布和结构特征[D].雅安:四川农业大学,2016. ZHOU W S.Isolation and identification of duck-derived Pasteurella multocidalis and its distribution and structural characteristics of CRISPR sites[D].Ya'an:Sichuan Agricultural University,2016.(in Chinese)
[9] COUVIN D,BERNHEIM A,TOFFANO-NIOCHE C,et al.CRISPRCasfinder,an update of CRISRFinder,includes a portable version,enhanced performance and integrates search for Cas proteins[J].Nucleic Acids Research,2018,46(W1):W246-W251.
[10] GRISSA I,VERGNAUD G,POURCEL C.CRISPRFinder:A web tool to identify clustered regularly interspaced short palindromic repeats[J].Nucleic Acids Research,2007,35(Web Server issue):W52-W57.
[11] CROOKS G E,HON G,CHANDONIA J M,et al.WebLogo:A sequence logo generator[J].Genome Research,2004,14(6):1188-1190.
[12] DENMAN R B.Using RNAFOLD to predict the activity of small catalytic RNAs[J].Biotechniques,1993,15(6):1090-1095.
[13] BRINER A E,HENRIKSEN E D,BARRANGOU R.Prediction and validation of native and engineered Cas9 guide sequences[J].Cold Spring Harbor Protocols,2016,2016(7):628-634.
[14] BRINER A E,DONOHOUE P D,GOMAA A A,et al.Guide RNA functional modules direct Cas9 activity and orthogonality[J].Molecular Cell,2014,56(2):333-339.
[15] TAMURA K,STECHER G,KUMAR S.MEGA 11:Molecular evolutionary genetics analysis version 11[J].Molecular Biology and Evolution,2021,38(7):3022-3027.
[16] LEVY A,GOREN M G,YOSEF I,et al.CRISPR adaptation biases explain preference for acquisition of foreign DNA[J].Nature,2015,520(7548):505-510.
[17] YOGANAND K N,MURALIDHARAN M,NIMKAR S,et al.Fidelity of prespacer capture and processing is governed by the PAM-mediated interactions of Cas1-2 adaptation complex in CRISPR-Cas type Ⅰ-E system[J].Journal of Biological Chemistry,2019,294(52):20039-20053.
[18] MOSTERD C,MOINEAU S.Characterization of a type Ⅱ-A CRISPR-Cas system in Streptococcus mutans[J].mSphere,2020,5(3):e00235-20.
[19] TAMULAITIS G,VENCLOVAS C,SIKSNYS V.Type Ⅲ CRISPR-Cas immunity:Major differences brushed aside[J].Trends in Microbiology,2017,25(1):49-61.
[20] LIN J,FENG M,ZHANG H,et al.Characterization of a novel type Ⅲ CRISPR-Cas effector provides new insights into the allosteric activation and suppression of the Cas10 DNase[J].Cell Discovery,2020,6:29-45.
[21] YANG T,ALI M,LIN L,et al.Recoloring tomato fruit by CRISPR/Cas9-mediated multiplex gene editing.[J].Horticulture Research.2022,10(1):214-223.
[22] HAMADA T,YOKOYAMA S,AKAHANE T,et al.Genome editing using Cas9 ribonucleoprotein is effective for introducing PDGFRA variant in cultured human glioblastoma cell lines[J].International Journal of Molecular Sciences,2022,24(1),500-512.
[23] XU Z,LI Y,YAN A.Repurposing the native type Ⅰ-F CRISPR-Cas system in Pseudomonas aeruginosa for genome editing[J].STAR Protocols,2020,1(1):100039-100055.
[24] BUYUKYORUK M,WIEDENHEFT B.Type Ⅰ-F CRISPR-Cas provides protection from DNA,but not RNA phages[J].Cell Discovery,2019,5:54-56.
[25] PAUSCH P,MULLER-ESPARZA H,GLEDITZSCH D,et al.Structural variation of type Ⅰ-F CRISPR RNA guided DNA surveillance[J].Molecular Cell,2017,67(4):622-632.
[26] DEECKER S R,ENSMINGER A W.Type Ⅰ-F CRISPR-Cas distribution and array dynamics in Legionella pneumophila[J].G3-Genes Genom Genet,2020,10(3):1039-1050.
[27] TULADHAR R,YEU Y,TYLER PIAZZA J,et al.CRISPR-Cas9-based mutagenesis frequently provokes on-target mRNA misregulation[J].Nature Communication,2019,10(1):4056-4066.
[28] SMITS A H,ZIEBELL F,JOBERTY G,et al.Biological plasticity rescues target activity in CRISPR knock outs[J].Nature Methods,2019,16(11):1087-1093.
[29] MINKENBERG B,WHEATLEY M,YANG Y.CRISPR/Cas9-enabled multiplex genome editing and its application[J].Progress in Molecular Biology and Translational Science,2017,149:111-132.
[30] 邱桂如,王政,何婷婷,等.CRISPR/Cas9系统及其在鸡基因组编辑中应用的研究进展。[J].中国畜牧兽医,2018,45(6):1590-1598. QIU G R,WANG Z,HE T T,et al.Research advances on CRISPR/Cas9 system and its application in genome editing in chickens[J].China Aniaml Husbandry&Veterinary Medicine,2018,45(6):1590-1598.(in Chinese)

Bioinformatic Analysis of CRISPR-Cas System in Pasteurella multocida

PDF (PC)

Knowledge

Abstract

Cite this article

share this article

References

Related Articles 15

Recommended Articles

Metrics

Comments

[1]	WANG Saiqiao, ZHAO Lu, ZHAI Zhenhan, ZHANG Binglei, JIA Wanhang, WANG Yuqin. Tissue Expression and Bioinformatics Analysis of miR-449a/b Precursor Sequences in Sheep [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(6): 2175-2184.
[2]	WEI Mingbang, BIANBA Qiongda, XIAO Qingqing, DUAN Mengqi, CHAMBA Yangzom, SHANG Peng. Cloning,Bioinformatics and Expression Analysis of CDKN1B Gene in Tibetan Pigs [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(6): 2196-2206.
[3]	LI Yongbin, YANG Huilin, SONG Zihao, ZHANG Yu, YANG Jin, MENG Jia, CUI Xiaozhen, LYU Xiaoling, ZHENG Mingxue, BAI Rui. Cloning and Bioinformatics Analysis of MIF Gene in Eimeria tenella [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(6): 2450-2459.
[4]	ZHANG Dianqi, MA Xinhao, YANG Zhimei, MEI Chugang, ZAN Linsen. Bioinformatics Analysis of PAI1 Gene and Its Effect on the Proliferation and Differentiation of Intramuscular Adipocytes in Qinchuan Beef Cattle [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(5): 1729-1741.
[5]	WANG Haorui, YU Baojun, YANG Jiayi, WEI Rong, FU Xi, WANG Chuanchuan, ZHANG Di, LI Desheng, CAI Zhengyun, GU Yaling, ZHANG Juan. Bioinformatics Analysis and Tissue Expression of DERA Gene in Jingyuan Chickens [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(5): 1764-1773.
[6]	CHEN Meiting, ZHENG Congsen, LIANG Zexian, LIN Qiaoer, CHANG Chuanzhe, ZHOU Jun, FENG Jun, LI Linlin, QIN Limei. Cloning and Bioinformatics Analysis of env Gene of Avian Leukosis Virus Subgroup J Strain [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(5): 1785-1795.
[7]	PAN Pengcheng, LEI Zongquan, LI Xian, HU Xiangyun, QIN Qiantao, QIN Zhaoxian, GUAN Zhihui, CHEN Baojian, XIE Bingkun. Bioinformatics Analysis,Eukaryotic Expression Vector Construction and Tissue Expression of MYL2 Gene in Luchuan Pigs [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(5): 1796-1806.
[8]	LIU Jialong, ZHANG Yiwen, ZHANG Yueran, SUN Qijuan, CHEN Jian, HE Lei, JIA Yanyan, DING Ke, YU Zuhua. Cloning,Prokaryotic Expression and Bioinformatics Analysis of ELAVL1 Gene in Chicken [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(5): 1807-1817.
[9]	ZHUO Na, ZHU Zhongwu, LI Jing, HU Shixiang, WANG Jianchang, LIN Hua, CHEN Chaolin, HAN Diangang, AI Jun, CHEN Peifu. Bioinformatics Analysis and Eukaryotic Expression of ORF2 Protein of Swine Hepatitis E Virus [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(5): 1959-1970.
[10]	TAO Qinghua, HUANG Caiyun, CHEN Chao, LIU Wei, SUN Ningning, LI Ang. Cloning and Tissue Expression Difference Analysis of LIF Gene in White Muscovy Duck [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(4): 1296-1306.
[11]	FAN Bingfeng, LI Wen, LIU Lixiang, ZHAO Xiangyuan, SHAO Jing, LIN Lefeng, SUN Huimin, ZHANG Xulin, XU Baozeng. Cloning and Bioinformatics Analysis of AANAT Gene in Mink [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(4): 1307-1318.
[12]	ZHANG Zhewei, DAI Xiaotong, WEI Zudan, CHEN Yunpeng, GAN Jing, BEI Weicheng. Study on Prokaryotic Expression and Immunogenicity of OmpW and TbpA Proteins in Swine Pasteurella multocida [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(4): 1489-1498.
[13]	JIA Xinyue, MA Jing, ZHANG Yanyan, MA Xun, WANG Zhengrong, BO Xinwen. Bioinformatics Analysis and Prokaryotic Expression of EGR-07243 and EGR-07243 Genes of Echinococcus granulosus [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(3): 847-858.
[14]	LI Dan, ZHANG Haisen, WANG Yiqun, GAO Dengke, ZHAO Hongcong, LI Chao, JIN Yaping, CHEN Huatao. Eukaryotic Expression Vector Construction,Bioinformatics and Tissue Expression Profiles Analysis of CRY1 Gene in Dairy Cows [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(3): 870-881.
[15]	SONG Xingchao, MENG Jinzhu, ZHAO Yuanyuan, WU Zhenyang, AN Qingming. Cloning and Bioinformatics Analysis of MyoG Gene Promoter Region Sequence in Guizhou White Goat [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(3): 893-903.