Abstract
Vibrio alginolyticus is an important foodborne pathogen that can infect both humans and marine animals and cause massive economic losses in aquaculture. Small noncoding RNAs (sRNAs) are emerging posttranscriptional regulators that affect bacterial physiology and pathological processes. In the present work, a new cell density-dependent sRNA, Qrr4, was characterized in V. alginolyticus based on a previously reported RNA-seq analysis and bioinformatics approach. The effects of Qrr4 actions on the physiology, virulence, and metabolism of V. alginolyticus were comprehensively investigated based on molecular biology and metabolomics approaches. The results showed that qrr4 deletion markedly inhibited growth, motility and extracellular protease activities. Additionally, nontargeted metabolism and lipidomics analyses revealed that qrr4 deletion induced significant disturbance of multiple metabolic pathways. The key metabolic remodelling that occurred in response to qrr4 deletion was found to involve phospholipid, nucleotide, carbohydrate and amino acid metabolic pathways, providing novel clues about a potential mechanism via which mutation of qrr4 could interfere with cellular energy homeostasis, modulate membrane phospholipid composition and inhibit nucleic acid and protein syntheses to regulate the motility, growth and virulence characteristics of V. alginolyticus. Overall, this study provides a comprehensive understanding of the regulatory roles of the new cell density-dependent sRNA Qrr4 in V. alginolyticus.
Key points
• A novel cell density-dependent sRNA, Qrr4, was cloned in V. alginolyticus.
•Qrr4 regulated growth and virulence factors of V. alginolyticus.
• Phospholipid, nucleotide and energy metabolisms were modulated obviously by Qrr4.
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Data availability
All data generated or analysed during this study are included in this published article (and its supplementary information files).
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Acknowledgements
We thank Qinfeng Xu for technical assistance.
Funding
This research was supported by the foundations (Nos. 31800328, and 32070129) from the National Natural Science Foundation of China, Key Research Project of Shaanxi Provincial Science and Technology Department (No.2021NY-164, and 2023-YBNY-171), Young Talent Fund of University Association for Science and Technology of Shaanxi (No.20210213), Xi’an Science and Technology Project (22NYYF036), Hebei Province Natural Science Foundation (B2019415024), Hebei Province Scientific Research Key Projects of Education Department (ZD2021038) and Key Research and Development Program of Hebei Province under Grant (20373902D).
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YNZ and HL conceived and designed the study. NNZ, JMR and WL performed the experiments and analysed the data. CZ, JYZ, JJC, JFY and JH provided expertise and analysis support. HL guided the whole manuscript writing. YNZ and NNZ wrote the manuscript. XFC corrected the manuscript. All authors read and approved the manuscript.
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Zhao, Y., Zhou, N., Ren, J. et al. Comprehensive insights into the metabolism characteristics of small RNA Qrr4 in Vibrio alginolyticus. Appl Microbiol Biotechnol 107, 1887–1902 (2023). https://doi.org/10.1007/s00253-023-12435-1
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DOI: https://doi.org/10.1007/s00253-023-12435-1