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

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

Animal Science · Veterinary Medicine

Advanced Online Publication | Current Issue | Archive | Adv Search

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

Highlights
● A comprehensive analysis and identification of the type II toxin-antitoxin system encoded within Streptococcus suis was conducted.
● The HigBA TA system was identified as a negative regulator of the type VII secretion system (T7SS) in Streptococcus suis.
● A novel, widely distributed type II TA system (designated SS-ATA) was identified in the Streptococcus suis genome, which exerts negative regulation on the downstream two-component signaling system (TCSS).

Abstract
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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.

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

Received: 04 July 2023 Online: 02 March 2024 Accepted: 07 January 2024

Fund: 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).

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.

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

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