弧菌基因组中抗噬菌体防御系统的构成与分布特征分析

doi:10.16288/j.yczz.24-290

遗传 ›› 2025, Vol. 47 ›› Issue (9): 1057-1068.doi: 10.16288/j.yczz.24-290

• 研究报告 • 上一篇

弧菌基因组中抗噬菌体防御系统的构成与分布特征分析

徐雪峰¹^,²(), 金兴坤¹^,², 史燕¹^,², 赵哲¹^,²()

1.河海大学江苏省海洋生物资源可持续利用工程研究中心, 南京 210024
2.河海大学海洋学院海洋生物系, 南京 210024

收稿日期:2024-12-02 修回日期:2025-03-07 出版日期:2025-03-08 发布日期:2025-03-07
通讯作者: 赵哲，博士，教授，研究方向：海洋微生物与水产病害。E-mail: zhezhao@hhu.edu.cn
作者简介:徐雪峰，硕士研究生，专业方向：微生物免疫。E-mail: jiayueshisan@gmail.com
基金资助:
国家自然科学基金项目(31872597);国家自然科学基金项目(42376119);江苏省农业科技自主创新资金(CX[23]1007)

Comprehensive analysis of the composition and distribution of anti-phage defense systems in Vibrio genomes

Xuefeng Xu¹^,²(), Xingkun Jin¹^,², Yan Shi¹^,², Zhe Zhao¹^,²()

1. Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization, Hohai University, Nanjing 210024, China
2. Department of Marine Biology, College of Oceanography, Hohai University, Nanjing 210024, China

Received:2024-12-02 Revised:2025-03-07 Published:2025-03-08 Online:2025-03-07
Supported by:
National Natural Science Foundation of China(31872597);National Natural Science Foundation of China(42376119);Jiangsu Agricultural Science and Technology Independent Innovation Fund(CX[23]1007)

摘要/Abstract

摘要：

细菌与其病毒(噬菌体)的长期共同演化推动了抗噬菌体防御系统的多样化发展。弧菌属细菌作为海洋生态系统的重要成员，具有庞大且复杂的基因组。为揭示弧菌属成员基因组中抗噬菌体防御系统的构成及分布特征，本研究从GTDB、NCBI数据库中收集了242个弧菌属代表性基因组，利用Defense Finder等生物信息学工具对其编码的抗噬菌体防御系统进行分析，共鉴定出108种不同的抗噬菌体防御系统，包括GAPS系统、dGTPase系统、RM系统等。不同弧菌菌株的防御能力存在显著差异：5个菌株编码超过20种防御系统，显示出较高的防御潜力；超过30个菌株仅编码5种或更少的防御系统；特别是在‘Vibrio katoptron’中未发现任何已知的防御系统。不同弧菌分支的防御系统多样性也存在差异，其中Cholerae分支的防御系统多样性(防御熵)最高。此外，对这些防御系统的组成、结构及功能机制进行了深入分析。弧菌属细菌拥有复杂多样的抗噬菌体防御系统，但许多系统的具体功能尚未明确。由于弧菌基因组的复杂性，未来仍有许多潜在的防御系统有待发现。本研究系统揭示了弧菌属防御系统的基因组结构特征，为深入探索弧菌与噬菌体的相互作用及其演化动态提供了重要的理论依据。

关键词: 弧菌, 噬菌体, 抗噬菌体防御系统, 微生物相互作用, 生物信息学分析

Abstract:

The long-term co-evolution between bacteria and their viruses (bacteriophages) drives the diversification of anti-phage defense systems. As key members of marine ecosystems, Vibrio species are known for their large and complex genomes. To investigate the composition and distribution of anti-phage defense systems in Vibrio genomes, we collect 242 representative genomes from the GTDB and NCBI databases. Using bioinformatics tools (including Defense Finder), we analyze the anti-phage defense systems encoded by these genomes and identify a total of 108 distinct systems, including GAPS, dGTPase, RM systems, etc. We observe significant variation in defense capabilities among different Vibrio strains: five strains encode more than 20 defense systems, highlighting their high defense potential, while over 30 strains encode five or fewer defense systems. Notably, we find no known defense systems in ‘Vibrio katoptron’. Furthermore, we note that the diversity of defense systems varies among Vibrio clades, with the Cholerae clade exhibiting the highest entropy in its defense systems. We conduct a detailed analysis of the composition, structure, and functional mechanisms of these defense systems. Although Vibrio species exhibit a complex and diverse array of anti-phage defense systems, the specific functions of many remain unknown. Given the complexity of Vibrio genomes, we suggest that numerous potential defense systems are yet to be discovered. This study provides a comprehensive overview of the genomic characteristics of Vibrio defense systems, laying a foundation for future research into the interactions and evolutionary dynamics between Vibrio and bacteriophages.

Key words: Vibrio, phage, anti-phage defense system, microbial interactions, bioinformatics analysis

徐雪峰, 金兴坤, 史燕, 赵哲. 弧菌基因组中抗噬菌体防御系统的构成与分布特征分析[J]. 遗传, 2025, 47(9): 1057-1068.

Xuefeng Xu, Xingkun Jin, Yan Shi, Zhe Zhao. Comprehensive analysis of the composition and distribution of anti-phage defense systems in Vibrio genomes[J]. Hereditas(Beijing), 2025, 47(9): 1057-1068.

图/表 6

图1

图2

附图1

图3

图4

图5

参考文献 40

[1]	Yan MC, Chen SB, Shan LZ, Xie QL. A critical review: pathogenic Vibrio in maricultural animals. Fish Sci, 2009, 28(8): 475-481.
	闫茂仓, 陈少波, 单乐州, 谢起浪. 海水养殖动物致病弧菌的研究进展. 水产科学, 2009, 28(8): 475-481.
[2]	Zheng HY, Yan L, Yang C, Wu YR, Qin JL, Hao TY, Yang DJ, Guo YC, Pei XY, Zhao TY, Cui YJ. Population genomics study of Vibrio alginolyticus. Hereditas(Beijing), 2021, 43(4): 350-361.
	郑宏源, 闫琳, 杨超, 武雅蓉, 秦婧靓, 郝彤宇, 杨大进, 郭云昌, 裴晓燕, 赵彤言, 崔玉军. 溶藻弧菌群体基因组学研究. 遗传, 2021, 43(4): 350-361.
[3]	Baker-Austin C, Oliver JD, Alam M, Ali A, Waldor MK, Qadri F, Martinez-Urtaza J. Vibrio spp. infections. Nat Rev Dis Primers, 2018, 4(1): 8. pmid: 30002421
[4]	Erken M, Lutz C, McDougald D. The rise of pathogens: predation as a factor driving the evolution of human pathogens in the environment. Microb Ecol, 2013, 65(4): 860-868. pmid: 23354181
[5]	Molina-Quiroz RC, Silva-Valenzuela CA. Interactions of Vibrio phages and their hosts in aquatic environments. Curr Opin Microbiol, 2023, 74: 102308. pmid: 37062175
[6]	Faruque SM, Mekalanos JJ. Phage-bacterial interactions in the evolution of toxigenic Vibrio cholerae. Virulence, 2012, 3(7): 556-565. pmid: 23076327
[7]	Li M, Cheng FY, Gong LY, Xiang H. Systematic discovery of novel prokaryotic defense systems: progress and prospects. Hereditas(Beijing), 2018, 40(4): 259-265.
	李明, 程飞跃, 龚路遥, 向华. 微生物新型防御系统的系统性发现与展望. 遗传, 2018, 40(4): 259-265.
[8]	Rostøl JT, Marraffini L. (Ph)ighting phages: how bacteria resist their parasites. Cell Host Microbe, 2019, 25(2): 184-194. pmid: 30763533
[9]	Georjon H, Bernheim A. The highly diverse antiphage defence systems of bacteria. Nat Rev Microbiol, 2023, 21(10): 686-700. pmid: 37460672
[10]	Tesson F, Hervé A, Mordret E, Touchon M, d’Humières C, Cury J, Bernheim A. Systematic and quantitative view of the antiviral arsenal of prokaryotes. Nat Commun, 2022, 13(1): 2561. pmid: 35538097
[11]	Payne LJ, Meaden S, Mestre MR, Palmer C, Toro N, Fineran PC, Jackson SA. PADLOC: a web server for the identification of antiviral defence systems in microbial genomes. Nucleic Acids Res, 2022, 50(W1): W541-W550. pmid: 35639517
[12]	Hendry TA, Dunlap PV. The uncultured luminous symbiont of Anomalops katoptron (Beryciformes: Anomalopidae) represents a new bacterial genus. Mol Phylogenet Evol, 2011, 61(3): 834-843. pmid: 21864694
[13]	Costa AR, van den Berg DF, Esser JQ, Muralidharan A, van den Bossche H, Bonilla BE, van der Steen BA, Haagsma AC, Fluit AC, Nobrega FL, Haas PJ, Brouns SJJ. Accumulation of defense systems in phage-resistant strains of Pseudomonas aeruginosa. Sci Adv, 2024, 10(8): eadj0341. pmid: 38394193
[14]	Johnson MC, Laderman E, Huiting E, Zhang C, Davidson A, Bondy-Denomy J. Core defense hotspots within Pseudomonas aeruginosa are a consistent and rich source of anti-phage defense systems. Nucleic Acids Res, 2023, 51(10): 4995-5005. pmid: 37140042
[15]	Kushwaha SK, Wu Y, Avila HL, Anand A, Sicheritz- Pontén T, Millard A, Marathe SA, Nobrega FL. Comprehensive blueprint of Salmonella genomic plasticity identifies hotspots for pathogenicity genes. PLoS Biol, 2024, 22(8): e3002746. pmid: 39110680
[16]	Tal N, Millman A, Stokar-Avihail A, Fedorenko T, Leavitt A, Melamed S, Yirmiya E, Avraham C, Brandis A, Mehlman T, Amitai G, Sorek R. Bacteria deplete deoxynucleotides to defend against bacteriophage infection. Nat Microbiol, 2022, 7(8): 1200-1209. pmid: 35817891
[17]	Wein T, Sorek R. Bacterial origins of human cell- autonomous innate immune mechanisms. Nat Rev Immunol, 2022, 22(10): 629-638. pmid: 35396464
[18]	Mega R, Kondo N, Nakagawa N, Kuramitsu S, Masui R. Two dNTP triphosphohydrolases from Pseudomonas aeruginosa possess diverse substrate specificities. FEBS J, 2009, 276(12): 3211-3221. pmid: 19438719
[19]	Bernheim A, Millman A, Ofir G, Meitav G, Avraham C, Shomar H, Rosenberg MM, Tal N, Melamed S, Amitai G, Sorek R. Prokaryotic viperins produce diverse antiviral molecules. Nature, 2021, 589(7840): 120-124. pmid: 32937646
[20]	Makarova KS, Wolf YI, Koonin EV. Comparative genomics of defense systems in archaea and bacteria. Nucleic Acids Res, 2013, 41(8): 4360-4377. pmid: 23470997
[21]	Oliveira PH, Touchon M, Rocha EPC. The interplay of restriction-modification systems with mobile genetic elements and their prokaryotic hosts. Nucleic Acids Res, 2014, 42(16): 10618-10631. pmid: 25120263
[22]	Matsuzaki S, Inoue T, Tanaka S. Evidence for the existence of a restriction-modification system common to several species of the family Vibrionaceae. FEMS Microbiol Lett, 1992, 94(1-2): 191-194. pmid: 1521769
[23]	Barrangou R, Fremaux C, Deveau H, Richards M, Boyaval P, Moineau S, Romero DA, Horvath P. CRISPR provides acquired resistance against viruses in prokaryotes. Science, 2007, 315(5819): 1709-1712. pmid: 17379808
[24]	Box AM, McGuffie MJ, O’Hara BJ, Seed KD. Functional analysis of bacteriophage immunity through a type I-E CRISPR-Cas system in Vibrio cholerae and its application in bacteriophage genome engineering. J Bacteriol, 2016, 198(3): 578-590. pmid: 26598368
[25]	Jiang CQ, Tanaka M, Nishikawa S, Mino S, Romalde JL, Thompson FL, Gomez-Gil B, Sawabe T. Vibrio Clade 3.0: new Vibrionaceae evolutionary units using genome-based approach. Curr Microbiol, 2021, 79(1): 10. pmid: 34905112
[26]	Fan CL, Liu S, Dai WF, He L, Xu HQ, Zhang HY, Xue QG. Characterization of Vibrio mediterranei isolates as causative agents of vibriosis in marine bivalves. Microbiol Spectr, 2023, 11(2): e0492322. pmid: 36728415
[27]	Wang WJ, Liu HX, Yue HY, Zhao TR, Zhang MM. Genome-wide characterization of 7 strains of Vibrio cholerae isolated from aquatic products. J Food Saf Qual, 2024, 15(19): 314-320.
	王伟杰, 刘海霞, 岳航羽, 赵韬然, 张眉眉. 7株水产品来源的霍乱弧菌的全基因组特征分析. 食品安全质量检测学报, 2024, 15(19): 314-320.
[28]	Lutz C, Erken M, Noorian P, Sun SY, McDougald D. Environmental reservoirs and mechanisms of persistence of Vibrio cholerae. Front Microbiol, 2013, 4: 375. pmid: 24379807
[29]	Tan DM, Svenningsen SL, Middelboe M. Quorum sensing determines the choice of antiphage defense strategy in Vibrio anguillarum. mBio, 2015, 6(3): e00627. pmid: 26081633
[30]	Sun SY, Wu SB, Zhang XQ, Liang CC, Qiao JJ. Advances in quorum-sensing bidirectional interactions between phages and bacteria. Chin Biotechnol, 2024, 44(1): 107-117.
	孙舒扬, 吴胜波, 张欣乔, 梁畅畅, 乔建军. 噬菌体与细菌基于群体感应的双向互作. 中国生物工程杂志, 2024, 44(1): 107-117.
[31]	Reyes-Robles T, Dillard RS, Cairns LS, Silva-Valenzuela CA, Housman M, Ali A, Wright ER, Camilli A. Vibrio cholerae outer membrane vesicles inhibit bacteriophage infection. J Bacteriol, 2018, 200(15): e00792-17. pmid: 29661863
[32]	Depardieu F, Didier JP, Bernheim A, Sherlock A, Molina H, Duclos B, Bikard D. A eukaryotic-like serine/threonine kinase protects staphylococci against phages. Cell Host Microbe, 2016, 20(4): 471-481. pmid: 27667697
[33]	Doron S, Melamed S, Ofir G, Leavitt A, Lopatina A, Keren M, Amitai G, Sorek R. Systematic discovery of antiphage defense systems in the microbial pangenome. Science, 2018, 359(6379): eaar4120. pmid: 29371424
[34]	Hochhauser D, Millman A, Sorek R. The defense island repertoire of the Escherichia coli pan-genome. PLoS Genet, 2023, 19(4): e1010694. pmid: 37023146
[35]	Tang DM, Chen YJ, Chen H, Jia TT, Chen Q, Yu YM. Multiple enzymatic activities of a Sir2-HerA system cooperate for anti-phage defense. Mol Cell, 2023, 83(24): 4600-4613.e6. pmid: 38096825
[36]	Macdonald E, Wright R, Connolly JPR, Strahl H, Brockhurst M, van Houte S, Blower TR, Palmer T, Mariano G. The novel anti-phage system Shield co-opts an RmuC domain to mediate phage defense across Pseudomonas species. PLoS Genet, 2023, 19(6): e1010784. pmid: 37276233
[37]	Barcia-Cruz R, Goudenège D, de Sousa JAM, Piel D, Marbouty M, Rocha EPC, Le Roux F. Phage-inducible chromosomal minimalist islands (PICMIs), a novel family of small marine satellites of virulent phages. Nat Commun, 2024, 15(1): 664. pmid: 38253718
[38]	Tesson F, Planel R, Egorov AA, Georjon H, Vaysset H, Brancotte B, Néron B, Mordret E, Atkinson GC, Bernheim A, Cury J. A comprehensive resource for exploring antiphage defense: defensefinder webservice, wiki and databases. Peer Community J, 2024, 4: e91.
[39]	Vassallo CN, Doering CR, Littlehale ML, Teodoro GIC, Laub MT. A functional selection reveals previously undetected anti-phage defence systems in the E. coli pangenome. Nat Microbiol, 2022, 7(10): 1568-1579. pmid: 36123438
[40]	Bernheim A, Sorek R. The pan-immune system of bacteria: antiviral defence as a community resource. Nat Rev Microbiol, 2020, 18(2): 113-119. pmid: 31695182

编辑推荐

Metrics

www.chinagene.cn
备案号：京ICP备09063187号-4
总访问:,今日访问:,当前在线:

弧菌基因组中抗噬菌体防御系统的构成与分布特征分析

Comprehensive analysis of the composition and distribution of anti-phage defense systems in Vibrio genomes

RichHTML

PDF (PC)

可视化

摘要/Abstract

引用本文

使用本文

图/表 6

参考文献 40

相关文章 15

编辑推荐

Metrics

[1]	马佳雯, 梁新乐. 基于宏病毒组测序技术解析异常发酵醋醪噬菌体群落结构与功能[J]. 遗传, 2025, 47(4): 489-498.
[2]	陈荟玉, 赵素文. 噬菌体Z基因组生物合成通路的研究进展[J]. 遗传, 2023, 45(10): 887-903.
[3]	王姗姗, 赵琬怡, 吴慧潇, 舒梦, 袁嘉欣, 方丽, 徐潮. 特发性低促性腺激素性性腺功能减退症FGFR1与CEP290基因变异研究[J]. 遗传, 2022, 44(10): 937-949.
[4]	郑宏源, 闫琳, 杨超, 武雅蓉, 秦婧靓, 郝彤宇, 杨大进, 郭云昌, 裴晓燕, 赵彤言, 崔玉军. 溶藻弧菌群体基因组学研究[J]. 遗传, 2021, 43(4): 350-361.
[5]	陈学梅, 魏云林, 季秀玲. 前噬菌体研究进展[J]. 遗传, 2021, 43(3): 240-248.
[6]	徐志伟, 魏云林, 季秀玲. 假单胞菌噬菌体基因组学研究进展[J]. 遗传, 2020, 42(8): 752-759.
[7]	卢涣滋,王迪侃,王智. HPV阳性口咽癌患者预后与T细胞浸润和新抗原负荷相关性分析[J]. 遗传, 2019, 41(8): 725-735.
[8]	梁彩娇, 孟繁梅, 艾云灿. 基于CRISPR/Cas系统的噬菌体基因组编辑[J]. 遗传, 2018, 40(5): 378-389.
[9]	李明,程飞跃,龚路遥,向华. 微生物新型防御系统的系统性发现与展望[J]. 遗传, 2018, 40(4): 259-265.
[10]	李晓旭, 刘成, 李伟, 张增林, 高晓明, 周慧, 郭永峰. 番茄WOX转录因子家族的鉴定及其进化、表达分析[J]. 遗传, 2016, 38(5): 444-460.
[11]	樊祥宇, 何颖, 谢建平. 以分枝杆菌噬菌体为例探索生命科学研究型教学[J]. 遗传, 2014, 36(8): 842-846.
[12]	杨姗姗，孙晓丽，于洋，才华，纪巍，柏锡，朱延明. 酵母双杂交筛选与GsCBRLK相互作用的蛋白质[J]. 遗传, 2013, 35(3): 388-394.
[13]	李铁民，杜波. CRISPR-Cas系统与细菌和噬菌体的共进化[J]. 遗传, 2011, 33(3): 213-218.
[14]	孟繁梅，张朝辉，艾云灿. 噬菌体展示技术系统发展进展[J]. 遗传, 2011, 33(10): 1113-1120.
[15]	傅天韵，娄维义，石铁流. 不同宿主H1N1病毒血凝素蛋白(HA)受体结合位点的变异特征[J]. 遗传, 2010, 32(7): 701-711.