猪链球菌中II型毒素-抗毒素系统的生物信息学分析与HigBA和SS-ATA的调控功能评估

doi:10.1016/j.jia.2024.03.001

Journal of Integrative Agriculture ›› 2025, Vol. 24 ›› Issue (5): 1958-1971.DOI: 10.1016/j.jia.2024.03.001

猪链球菌中II型毒素-抗毒素系统的生物信息学分析与HigBA和SS-ATA的调控功能评估

收稿日期:2023-07-04 修回日期:2024-03-02 接受日期:2024-01-07 出版日期:2025-05-20 发布日期:2025-04-18

Bioinformatics analysis of type II toxin–antitoxin systems and regulatory functional assessment of HigBA and SS-ATA in Streptococcus suis

Qibing Gu^{1, 3, 4*}, Xiayu Zhu^1*, Qiankun Bai^{1, 3, 4}, Chengyuan Ji^{1, 3, 4}, Yue Zhang^{1, 2, 4}, Jiale Ma^{1, 3, 4}, Huochun Yao^{1, 3, 4#}, Zihao Pan^{1, 3, 4#}

¹Ministry of Education (MOE) Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
²College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
³Key Lab of Animal Bacteriology, Ministry of Agriculture and Rural Affairs, Nanjing 210095, China
⁴WOAH Reference Lab for Swine Streptococcosis, Nanjing 210095, China

Received:2023-07-04 Revised:2024-03-02 Accepted:2024-01-07 Online:2025-05-20 Published:2025-04-18
About author:Qibing Gu, E-mail: 2020207030@stu.njau.edu.cn; #Correspondence Huochun Yao, E-mail: yaohch@njau.edu.cn; Zihao Pan, Tel: +86-25-84395328, E-mail: panzihao@njau.edu.cn * These authors contributed equally to this study.
Supported by:
This research was supported by the National Key Research and Development Program of China (2022YFD1800904), the National Natural Science Foundation of China (31972650 and 32102673), and the Postgraduate Research&Practice Innovation Program of Jiangsu Province, China (KYCX22_0780), and the China Postdoctoral Science Foundation (2020M682297).

摘要/Abstract

摘要： 【目的】毒素-抗毒素（Toxin-antitoxin, TA）系统在细菌和古细菌中广泛分布，其在细菌生理中发挥着多种作用，因此被认为在环境压力适应中发挥重要作用。尽管许多TA系统已经在不同的细菌中被表征，但对猪链球菌（Streptococcus suis, S. suis）中TA系统的研究仍然十分有限。对猪链球菌中Ⅱ型TA系统的系统分析与功能研究将有助于了解Ⅱ型TA系统的生物学功能，并为猪链球菌的致病与压力应激机制提供新的见解。【方法】利用在线工具TAfinder预测猪链球菌基因组上编码的Ⅱ型TA系统；通过氨基酸序列比对和系统发育分析对Ⅱ型TA系统进行生物信息学分析；进一步建立大肠杆菌诱导表达系统鉴定TA系统的活性；此外通过β-半乳糖苷酶活性分析与转录水平分析探究HigBA与SS-ATA的调控功能。【结果】通过对95株具有完整基因组的菌株预测，我们共检索了612个假定的Ⅱ型TA系统。值得注意的是，这些Ⅱ型TA系统在血清型2，4，5，9，14型和新的血清型Chz，NCL1和NCL3型菌株中编码率较高。通过建立的两种大肠杆菌诱导表达系统可以成功鉴定Ⅱ型TA系统的活性。进一步通过测定β-半乳糖苷酶活性与转录水平分析发现猪链球菌中HigBA系统对Ⅶ型分泌系统（T7SS）存在负调控作用。通过生物信息学分析发现猪链球菌中广泛编码一类新的Ⅱ型TA系统SS-ATA（抗毒素-毒素-抗毒素），这类Ⅱ型TA系统与下游的二元信号转导系统（TCSS）组成一个操纵子，并且SS-ATA对下游的TCSS存在负调控作用。【结论】本研究首次对猪链球菌中编码的Ⅱ型TA系统进行了系统分析，并且证实了HigBA和SS-ATA作为一种重要的调控元件在猪链球菌中广泛分布。【创新性】对猪链球菌中编码的Ⅱ型TA系统进行了系统的分析；鉴定了猪链球菌中编码的HigBA对T7SS具有负调控作用；在猪链球菌基因组中发现了一类广泛分布的新的Ⅱ型TA系统SS-ATA，其对下游的TCSS具有负调控作用。

Abstract:

Toxin–antitoxin (TA) systems, which are prevalent in bacteria and archaea, play diverse roles in bacterial physiology and have been proposed to be significant in stress adaptation. Despite the extensive characterization of numerous TA systems in various bacteria, the investigation of these systems within Streptococcus suis is still limited. Here, we systematically analyzed the type II TA systems of 95 S. suis genomes available in the GenBank database using TAfinder. A total of 612 putative type II TA systems were retrieved and classified into 10 categories by phylogenetic analysis. Notably, an elevated occurrence of these TA systems was observed among the important prevalent serotypes 2, 4, 5, 9, 14, Chz, NCL1, and NCL3 strains. The following study identified the activities of TA systems using 2 strategies and confirmed the regulatory effect of HigBA on the type VII secretion system in S. suis by measuring β-galactosidase activity and transcriptional changes. Moreover, we unveiled a hitherto uncharacterized, highly prevalent novel TA system, with the composition of antitoxin–toxin–antitoxin (SS-ATA), which regulates the downstream two-component signaling system. Altogether, this study systematically analyzed the type II TA systems within S. suis, highlighting the widespread distribution of HigBA and SS-ATA as important regulatory elements in S. suis.

Key words: type II toxin-antitoxin system , Streptococcus suis , HigBA , type VII secretion system , two-component signaling system , regulatory element

Qibing Gu, Xiayu Zhu, Qiankun Bai, Chengyuan Ji, Yue Zhang, Jiale Ma, Huochun Yao, Zihao Pan. 猪链球菌中II型毒素-抗毒素系统的生物信息学分析与HigBA和SS-ATA的调控功能评估[J]. Journal of Integrative Agriculture, 2025, 24(5): 1958-1971.

Qibing Gu, Xiayu Zhu, Qiankun Bai, Chengyuan Ji, Yue Zhang, Jiale Ma, Huochun Yao, Zihao Pan. Bioinformatics analysis of type II toxin–antitoxin systems and regulatory functional assessment of HigBA and SS-ATA in Streptococcus suis[J]. Journal of Integrative Agriculture, 2025, 24(5): 1958-1971.

参考文献

Ainelo A, Porosk R, Kilk K, Rosendahl S, Remme J, Hõrak R. 2019. Pseudomonas putida responds to the toxin GraT by inducing ribosome biogenesis factors and repressing TCA cycle enzymes. Toxins (Basel), 11, 103.

Akarsu H, Bordes P, Mansour M, Bigot D J, Genevaux P, Falquet L. 2019. TASmania: A bacterial toxin-antitoxin systems database. PLoS Computational Biology, 15, e1006946.

Christensen-Dalsgaard M, Gerdes K. 2008. Translation affects yoeB and mazF messenger RNA interferase activities by different mechanisms. Nucleic Acids Research, 36, 6472–6481.

Deep A, Tiwari P, Agarwal S, Kaundal S, Kidwai S, Singh R, Thakur K G. 2018. Structural, functional and biological insights into the role of Mycobacterium tuberculosis vapBC11 toxin–antitoxin system: Targeting a tRNase to tackle mycobacterial adaptation. Nucleic Acids Research, 46, 11639–11655.

Feng Y, Zhang H, Ma Y, Gao G F. 2010. Uncovering newly emerging variants of Streptococcus suis, an important zoonotic agent. Trends in Microbiology, 18, 124–131.

Feng Y, Zhang H, Wu Z, Wang S, Cao M, Hu D, Wang C. 2014. Streptococcus suis infection: An emerging/reemerging challenge of bacterial infectious diseases? Virulence, 5, 477–497.

Fernández-García L, Blasco L, Lopez M, Bou G, García-Contreras R, Wood T, Tomas M. 2016. Toxin–antitoxin systems in clinical pathogens. Toxins (Basel), 8, 227.

Gerdes K, Rasmussen P B, Molin S. 1986. Unique type of plasmid maintenance function: Postsegregational killing of plasmid-free cells. Proceedings of the National Academy of Sciences of the United States of America, 83, 3116–3120.

Goyette-Desjardins G, Auger J P, Xu J, Segura M, Gottschalk M. 2014. Streptococcus suis, an important pig pathogen and emerging zoonotic agent - an update on the worldwide distribution based on serotyping and sequence typing. Emerging Microbes & Infections, 3, e45.

Gu Q, He P, Wang D, Ma J, Zhong X, Zhu Y, Zhang Y, Bai Q, Pan Z, Yao H. 2021. An auto-regulating type II toxin–antitoxin system modulates drug resistance and virulence in Streptococcus suis. Frontiers in Microbiology, 12, 671706.

Guo Y, Sun C, Li Y, Tang K, Ni S, Wang X. 2019. Antitoxin higA inhibits virulence gene mvfR expression in Pseudomonas aeruginosa. Environmental Microbiology, 21, 2707–2723.

Harms A, Brodersen D E, Mitarai N, Gerdes K. 2018. Toxins, targets, and triggers: An overview of toxin-antitoxin biology. Molecular Cell, 70, 768–784.

Hill J E, Gottschalk M, Brousseau R, Harel J, Hemmingsen S M, Goh S H. 2005. Biochemical analysis, cpn60 and 16S rDNA sequence data indicate that Streptococcus suis serotypes 32 and 34, isolated from pigs, are Streptococcus orisratti. Veterinary Microbiology, 107, 63–69.

Huang J, Liu X, Chen H, Chen L, Gao X, Pan Z, Wang J, Lu C, Yao H, Wang L, Wu Z. 2019. Identification of six novel capsular polysaccharide loci (NCL) from Streptococcus suis multidrug resistant non-typeable strains and the pathogenic characteristic of strains carrying new NCLs. Transboundary and Emerging Diseases, 66, 995–1003.

Jurėnas D, Fraikin N, Goormaghtigh F, Van Melderen L. 2022. Biology and evolution of bacterial toxin–antitoxin systems. Nature Reviews Microbiology, 20, 335–350.

Lai L, Dai J, Tang H, Zhang S, Wu C, Qiu W, Lu C, Yao H, Fan H, Wu Z. 2017. Streptococcus suis serotype 9 strain GZ0565 contains a type VII secretion system putative substrate EsxA that contributes to bacterial virulence and a vanZ-like gene that confers resistance to teicoplanin and dalbavancin in Streptococcus agalactiae. Veterinary Microbiology, 205, 26–33.

Li M, Long Y, Liu Y, Chen R, Shi J, Zhang L, Jin Y, Yang L, Bai F, Jin S, Cheng Z, Wu W. 2016. HigB of Pseudomonas aeruginosa enhances killing of phagocytes by up-regulating the type III secretion system in ciprofloxacin induced persister cells. Frontiers in Cellular and Infection Microbiology, 6, 125.

Li M, Wang C, Feng Y, Pan X, Cheng G, Wang J, Ge J, Zheng F, Cao M, Dong Y, Liu D, Lin Y, Du H, Gao G F, Wang X, Hu F, Tang J. 2008. SalK/SalR, a two-component signal transduction system, is essential for full virulence of highly invasive Streptococcus suis serotype 2. PLoS ONE, 3, e2080.

Liu G, Gao T, Zhong X, Ma J, Zhang Y, Zhang S, Wu Z, Pan Z, Zhu Y, Yao H, Liu Y, Lu C. 2020. The novel streptococcal transcriptional regulator XtgS negatively regulates bacterial virulence and directly represses PseP transcription. Infection and Immunity, 88, e00035–20.

Livak K J, Schmittgen T D. 2001. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-delta delta C(T)) method. Methods, 25, 402–408.

Ma L, Zhang Y, Yan X, Guo L, Wang L, Qiu J, Yang R, Zhou D. 2012. Expression of the type VI secretion system 1 component Hcp1 is indirectly repressed by OpaR in Vibrio parahaemolyticus. The Scientific World Journal, 2012, 982140.

Van Melderen L, De Bast M S. 2009. Bacterial toxin-antitoxin systems: More than selfish entities? PLoS Genetics, 5, e1000437.

Mutschler H, Gebhardt M, Shoeman R L, Meinhart A. 2011. A novel mechanism of programmed cell death in bacteria by toxin-antitoxin systems corrupts peptidoglycan synthesis. PLoS Biology, 9, e1001033.

Ogura T, Hiraga S. 1983. Mini-F plasmid genes that couple host cell division to plasmid proliferation. Proceedings of the National Academy of Sciences of the United States of America, 80, 4784–4788.

Ovchinnikov S V, Bikmetov D, Livenskyi A, Serebryakova M, Wilcox B, Mangano K, Shiriaev D I, Osterman I A, Sergiev P V, Borukhov S, Vazquez-Laslop N, Mankin A S, Severinov K, Dubiley S. 2020. Mechanism of translation inhibition by type II GNAT toxin AtaT2. Nucleic Acids Research, 48, 8617–8625.

Pan Z, Ma J, Dong W, Song W, Wang K, Lu C, Yao H. 2015. Novel variant serotype of Streptococcus suis isolated from piglets with meningitis. Applied and Environmental Microbiology, 81, 976–985.

Sala A, Bordes P, Genevaux P. 2014. Multiple toxin–antitoxin systems in Mycobacterium tuberculosis. Toxins (Basel), 6, 1002–1020.

Sberro H, Leavitt A, Kiro R, Koh E, Peleg Y, Qimron U, Sorek R. 2013. Discovery of functional toxin/antitoxin systems in bacteria by shotgun cloning. Molecular Cell, 50, 136–148.

Song Y, Luo G, Zhu Y, Li T, Li C, He L, Zhao N, Zhao C, Yang J, Huang Q, Mu X, Tang X, Kang M, Wu S, He Y, Bao R. 2021a. Pseudomonas aeruginosa antitoxin HigA functions as a diverse regulatory factor by recognizing specific pseudopalindromic DNA motifs. Environmental Microbiology, 23, 1541–1558.

Song Y, Zhang S, Luo G, Shen Y, Li C, Zhu Y, Huang Q, Mou X, Tang X, Liu T, Wu S, Tong A, He Y, Bao R. 2021b. Type II antitoxin HigA is a key virulence regulator in Pseudomonas aeruginosa. ACS Infectious Diseases, 7, 2930–2940.

Song Y, Zhang S, Ye Z, Chen L, Tong A, He Y, Bao R. 2022. The novel type II toxin-antitoxin PacTA modulates Pseudomonas aeruginosa iron homeostasis by obstructing the DNA-binding activity of Fur. Nucleic Acids Research, 50, 10586–10600.

Tang J, Wang C, Feng Y, Yang W, Song H, Chen Z, Yu H, Pan X, Zhou X, Wang H, Wu B, Wang H, Zhao H, Lin Y, Yue J, Wu Z, He X, Gao F, Khan A H, Wang J, et al. 2006. Streptococcal toxic shock syndrome caused by Streptococcus suis serotype 2. PLoS Medicine, 3, e151.

Tiwari P, Arora G, Singh M, Kidwai S, Narayan O P, Singh R. 2015. MazF ribonucleases promote Mycobacterium tuberculosis drug tolerance and virulence in guinea pigs. Nature Communications, 6, 6059.

Wen W, Liu B, Xue L, Zhu Z, Niu L, Sun B. 2018. Autoregulation and virulence control by the toxin–antitoxin system SavRS in Staphylococcus aureus. Infection and Immunity, 86, e00032–18.

Wen Y, Behiels E, Devreese B. 2014. Toxin–antitoxin systems: Their role in persistence, biofilm formation, and pathogenicity. Pathogens Disease, 70, 240–249.

Wertheim H F, Nguyen H N, Taylor W, Lien T T, Ngo H T, Nguyen T Q, Nguyen B N, Nguyen H H, Nguyen H M, Nguyen C T, Dao T T, Nguyen T V, Fox A, Farrar J, Schultsz C, Nguyen H D, Nguyen K V, Horby P. 2009. Streptococcus suis, an important cause of adult bacterial meningitis in northern Vietnam. PLoS ONE, 4, e5973.

Wu Z, Wu C, Shao J, Zhu Z, Wang W, Zhang W, Tang M, Pei N, Fan H, Li J, Yao H, Gu H, Xu X, Lu C. 2014. The Streptococcus suis transcriptional landscape reveals adaptation mechanisms in pig blood and cerebrospinal fluid. RNA, 20, 882–898.

Xu J, Zhang N, Cao M, Ren S, Zeng T, Qin M, Zhao X, Yuan F, Chen H, Bei W. 2018. Identification of three type II toxin–antitoxin systems in Streptococcus suis serotype 2. Toxins (Basel), 10, 467.

Yang Q E, Walsh T R. 2017. Toxin–antitoxin systems and their role in disseminating and maintaining antimicrobial resistance. FEMS Microbiology Reviews, 41, 343–353.

Zaccaria E, van Baarlen P, de Greeff A, Morrison D A, Smith H, Wells J M. 2014. Control of competence for DNA transformation in Streptococcus suis by genetically transferable pherotypes. PLoS ONE, 9, e99394.

Zheng C, Xu J, Ren S, Li J, Xia M, Chen H, Bei W. 2015. Identification and characterization of the chromosomal yefM-yoeB toxin–antitoxin system of Streptococcus suis. Scientific Reports, 5, 13125.

Zhong X, Zhang Y, Zhu Y, Dong W, Ma J, Pan Z, Roy S, Lu C, Yao H. 2018. The two-component signaling system VraSR(ss) is critical for multidrug resistance and full virulence in Streptococcus suis serotype 2. Infection and Immunity, 86, e00096–18.

猪链球菌中II型毒素-抗毒素系统的生物信息学分析与HigBA和SS-ATA的调控功能评估

Bioinformatics analysis of type II toxin–antitoxin systems and regulatory functional assessment of HigBA and SS-ATA in Streptococcus suis

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