Integrated Transcriptomic and Proteomic Analyses Reveal CsrA-Mediated Regulation of Virulence and Metabolism in Vibrio alginolyticus

<i>Vibrio alginolyticus</i>, a common Gram-negative opportunistic pathogen of marine animals and humans, is known for its rapid growth in organic-matter-rich environments. However, it remains unclear how it incorporates metabolic pathways in response to diverse carbon and nitrogen sources and rapidly alters gene expression. Increasing evidence suggests that post-transcriptional regulation by RNA-binding proteins and small RNAs (sRNAs) plays a crucial role in bacterial adaptation and metabolism. CsrA (carbon storage regulator A), a conserved post-transcriptional regulator in <i>Gammaproteobacteria</i>, is poorly characterized in <i>Vibrio</i> species. Using integrated transcriptomic and proteomic analyses, we found that CsrA alters the expression of 661 transcripts and 765 protein transcripts in <i>V. alginolyticus</i>, influencing key pathways including central carbon metabolism, amino acid metabolism and transport, quorum sensing, and bacterial secretion systems. Through directed CsrA-RNA EMSAs, we identified several direct mRNA targets of CsrA, including <i>gltB</i>, <i>gcvP</i>, <i>aceE</i>, and <i>tdh</i>, as well as secretion system components (<i>tagH</i>, <i>tssL</i>, <i>yopD</i>, and <i>sctC</i>). Notably, CsrA also directly regulates <i>rraA</i>, a key modulator of ribonuclease activity, suggesting a broader role in RNA metabolism. Our findings establish CsrA as a global regulator in <i>V. alginolyticus</i>, expanding the known targets of CsrA and providing new insights into its regulatory roles.