Transcriptome analysis reveals the important roles of a two-component system, flagellar assembly, active efflux system and outer membrane proteins in the anti-quinolone ability of Vibrio harveyi from orange-spotted grouper (Epinephelus coioides)

The drug resistance of Vibrio harveyi in aquaculture became more severe because the control of Vibriosis depends majorly on the current antibiotics. Transcriptomes of a wild-type strain (VS) and its quinolone-resistant mutants (VR) of V. harveyi were respectively sequenced by RNA-seq technology. A total of 2,082 unigenes were obtained after de novo splicing and assembly. 129 genes were identified with significant differential expression in strain VR compared to strain VS, among which 65 were up-regulated and 64 down-regulated. Then, functional annotation and enrichment analysis of these differentially expressed genes (DEGs) were performed. GO enrichment results showed that DEGs focused mainly on cell structure, substance metabolism, and transporter. COG classification of the DEGs mainly focused on amino acid transport and metabolism, cell wall/membrane biosynthesis, carbohydrate transport and metabolism, ribosomal structure, and biosynthesis. KEGG pathways related to a two-component system, ABC transport system and flagellar assembly (ko02040) were enriched significantly, and 9 genes associated with quinolone-resistance ability, including genes for resistance-related transport proteins, outer membrane proteins, and DNA repair-related proteins were discovered through analysis of the drug-resistance related genes. Ten DEGs (including the above part genes of 9 drug resistance-related genes) in the transcriptome data were taken to analyze their expression with real-time qPCR. The results were the same as the changes of the above transcriptome analysis, further confirming the reliability of the transcriptome sequencing and data analysis. In a word, genes from a two-component system, flagellar assembly, active efflux system and outer membrane proteins take great roles in the quinolone-resistance of V. harveyi. These results provide enough information for further study on the molecular mechanism of quinolone-resistance and give a helpful transcriptomic resource to unravel the contact between quinolone-resistance and metabolic pathways in Vibrios.