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Bai T, Li J, Chi X, Li H, Tang Y, Liu Z, Ma X. Cooperative and Independent Functionality of tmRNA and SmpB in Aeromonas veronii: A Multifunctional Exploration Beyond Ribosome Rescue. Int J Mol Sci 2025; 26:409. [PMID: 39796263 PMCID: PMC11722516 DOI: 10.3390/ijms26010409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2024] [Revised: 12/30/2024] [Accepted: 12/31/2024] [Indexed: 01/13/2025] Open
Abstract
The trans-translation system, mediated by transfer-messenger RNA (tmRNA, encoded by the ssrA gene) and its partner protein SmpB, helps to release ribosomes stalled on defective mRNA and targets incomplete protein products for hydrolysis. Knocking out the ssrA and smpB genes in various pathogens leads to different phenotypic changes, indicating that they have both cooperative and independent functionalities. This study aimed to clarify the functional relationships between tmRNA and SmpB in Aeromonas veronii, a pathogen that poses threats in aquaculture and human health. We characterized the expression dynamics of the ssrA and smpB genes at different growth stages of the pathogen, assessed the responses of deletion strains ΔssrA and ΔsmpB to various environmental stressors and carbon source supplementations, and identified the gene-regulatory networks involving both genes by integrating transcriptomic and phenotypic analyses. Our results showed that the gene ssrA maintained stable expression throughout the bacterial growth period, while smpB exhibited upregulated expression in response to nutrient deficiencies. Compared to the wild type, both the ΔssrA and ΔsmpB strains exhibited attenuated resistance to most stress conditions. However, ΔssrA independently responded to starvation, while ΔsmpB specifically showed reduced resistance to lower concentrations of Fe3+ and higher concentrations of Na+ ions, as well as increased utilization of the carbon source β-Methyl-D-glucoside. The transcriptomic analysis supported these phenotypic results, demonstrating that tmRNA and SmpB cooperate under nutrient-deficient conditions but operate independently in nutrient-rich environments. Phenotypic experiments confirmed that SsrA and SmpB collaboratively regulate genes involved in siderophore synthesis and iron uptake systems in response to extracellular iron deficiency. The findings of the present study provide crucial insights into the functions of the trans-translation system and highlight new roles for tmRNA and SmpB beyond trans-translation.
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Affiliation(s)
- Taipeng Bai
- Pathogenesis and Control of Pathogenic Microorganisms Research Team, School of Life and Health Sciences, Hainan Province Key Laboratory of One Health, Collaborative Innovation Center of One Health, Hainan University, Haikou 570228, China; (T.B.); (J.L.); (X.C.); (H.L.); (Y.T.)
| | - Juanjuan Li
- Pathogenesis and Control of Pathogenic Microorganisms Research Team, School of Life and Health Sciences, Hainan Province Key Laboratory of One Health, Collaborative Innovation Center of One Health, Hainan University, Haikou 570228, China; (T.B.); (J.L.); (X.C.); (H.L.); (Y.T.)
| | - Xue Chi
- Pathogenesis and Control of Pathogenic Microorganisms Research Team, School of Life and Health Sciences, Hainan Province Key Laboratory of One Health, Collaborative Innovation Center of One Health, Hainan University, Haikou 570228, China; (T.B.); (J.L.); (X.C.); (H.L.); (Y.T.)
| | - Hong Li
- Pathogenesis and Control of Pathogenic Microorganisms Research Team, School of Life and Health Sciences, Hainan Province Key Laboratory of One Health, Collaborative Innovation Center of One Health, Hainan University, Haikou 570228, China; (T.B.); (J.L.); (X.C.); (H.L.); (Y.T.)
| | - Yanqiong Tang
- Pathogenesis and Control of Pathogenic Microorganisms Research Team, School of Life and Health Sciences, Hainan Province Key Laboratory of One Health, Collaborative Innovation Center of One Health, Hainan University, Haikou 570228, China; (T.B.); (J.L.); (X.C.); (H.L.); (Y.T.)
| | - Zhu Liu
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China;
| | - Xiang Ma
- Pathogenesis and Control of Pathogenic Microorganisms Research Team, School of Life and Health Sciences, Hainan Province Key Laboratory of One Health, Collaborative Innovation Center of One Health, Hainan University, Haikou 570228, China; (T.B.); (J.L.); (X.C.); (H.L.); (Y.T.)
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Liu T, Zhang M, Fan Y, Zhao L, Huang D, Zhao L, Tan M, Ye BC, Xu JY. Characterization of diverse lysine acylations in Bacillus thuringiensis: Substrate profiling and functional exploration. Proteomics 2024; 24:e2300350. [PMID: 38491406 DOI: 10.1002/pmic.202300350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 03/04/2024] [Accepted: 03/05/2024] [Indexed: 03/18/2024]
Abstract
Lysine acylation has been extensively investigated due to its regulatory role in a diverse range of biological functions across prokaryotic and eukaryotic species. In-depth acylomic profiles have the potential to enhance comprehension of the biological implications of organisms. However, the extent of research on global acylation profiles in microorganisms is limited. Here, four lysine acylomes were conducted in Bacillus thuringiensis by using the LC-MS/MS based proteomics combined with antibody-enrichment strategies, and a total of 3438 acetylated sites, 5797 propionylated sites, 1705 succinylated sites, and 925 malonylated sites were identified. The motif analysis of these modified proteins revealed a high conservation of glutamate in acetylation and propionylation, whereas such conservation was not observed in succinylation and malonylation modifications. Besides, conservation analysis showed that homologous acylated proteins in Bacillus subtilis and Escherichia coli were connected with ribosome and aminoacyl-tRNA biosynthesis. Further biological experiments showed that lysine acylation lowered the RNA binding ability of CodY and impaired the in vivo protein activity of MetK. In conclusion, our study expanded the current understanding of the global acylation in Bacillus, and the comparative analysis demonstrated that shared acylation proteins could play important roles in regulating both metabolism and RNA transcription progression.
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Affiliation(s)
- Tianxian Liu
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Mingya Zhang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Yameng Fan
- School of Pharmacy, Henan University, Kaifeng, China
| | - Lei Zhao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, China
| | - Dan Huang
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Liuchang Zhao
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Minjia Tan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- School of Pharmacy, Henan University, Kaifeng, China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, China
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, College of Pharmacy, Jiangsu Ocean University, Lianyungang, China
| | - Bang-Ce Ye
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Jun-Yu Xu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, China
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, College of Pharmacy, Jiangsu Ocean University, Lianyungang, China
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