Modulation of Hachiman defence by a type II toxin-antitoxin system via balancing trade-off between the fitness cost and antiphage activity

Abstract

Hachiman systems provide innate antiphage immunity across prokaryotic domains. The system encodes a HamA nuclease and a HamB helicase both of which exhibit great diversity in sequence. Phylogenetic analyses of HamA and HamB proteins revealed similar phylogenetic trees for both proteins, falling into three major types. Close examination of one of the subclades identified a distinct subfamily in which most of these Hachiman systems stands alone, however, Hachiman in the Streptococcus genus is combined with PezAT, a distinct pneumococcal epsilon zeta toxin-antitoxin system, yielding the Pez-Ham system. Investigation of a S. thermophilus Pez-Ham system revealed that only the Hachiman system is required for mediating antiphage defence. Biochemical characterization of encoded proteins, i.e., HamA or HamB individually or in protein complex revealed that the HamA nuclease is inactive alone, but upon the formation of heterologous dimer with HamB, the resulting protein complex effectively cleaves DNAs of various forms with a broad specificity (5′-CNNNG-3′), and the nuclease activity is greatly facilitated by ATP-binding in HamB and to a less degree by ATP hydrolysis. Genetic investigations further showed, while the Pez system did not function in antiphage immunity in Escherichia coli, the system repressed the expression of Hachiman, and thereby balancing the trade-off between the fitness cost and the effectiveness of antiphage defence.

Keywords

Antiphage defence / Toxin-antitoxin systems / Expression regulation / Defence tradeoffs / Hachiman helicase-nuclease effectors

Data availability statement

All data generated or analyzed during this study are included in this published article and its supplementary information files or are available upon request.

CRediT authorship contribution statement

Xuhui Tian: Writing - original draft, Data curation, Conceptualization. Ruyi Zheng: Data curation. Xin Li: Data curation. Suping Jiang: Data curation. Fang Wang: Writing - review & editing, Supervision. Yulong Shen: Writing - review & editing. Qunxin She: Writing - review & editing, Supervision, Project administration.

Declaration of competing interest

The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Given his role as Executive Editor, Dr. Qunxin She, had no involvement in the peer-review of this article and has no access to information regarding its peer-review. Full responsibility for the editorial process for this article was delegated to Dr. Xiaoxue Wang.

Acknowledgements

This study was supported by grants from the National Key R & D Program of China (2021YFA0717000 to QS), the National Natural Science Foundation of China (31771380 and 32393972), the Frontiers and Challenges Projects (SKLMTFCP-2023-01) from the State Key Laboratory of Microbial Technology at Shandong University, and the Natural Science Foundation of Shandong Province, China (ZR2024QC307).

We would like to thank all members in the CRISPR and Archaea Biology Research Centre for helpful discussions. We also thank Jing Zhu, Zhifeng Li, Guannan Lin, and Jingyao Qu of the Core Facilities for Life and Environmental Sciences, State Key Laboratory of Microbial Technology of Shandong University for their helps in protein analysis, flow cytometry and microscopy.

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