Transcriptomic profile of Vibrio parahaemolyticus in the intermediate state of biofilm formation

Abstract:

[Objective] To investigate the differentially expressed genes (DEGs) of Vibrio parahaemolyticus in the intermediate state of biofilm formation, and thus provide gene information for the future studies about the regulatory mechanisms of biofilm formation. [Methods] Illumina HiSeq and RNA sequencing (RNA-seq) assay were employed to analyze the gene expression of V. parahaemolyticus in the intermediate state of biofilm formation, and the results were then validated by quantitative real-time PCR (qPCR). [Results] A total of 979 DEGs were identified, including 379 down-regulated genes and 600 up-regulated genes. According to the results of gene ontology (GO) annotation, 363 DEGs were annotated to three functional categories (biological process, molecular function, and cellular component) and 30 sub-categories. The results of Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment showed that 706 DEGs were enriched in 37 pathways (Q value<0.05) and mainly involved in cellular metabolism and transport pathways. The results of clusters of orthologous groups (COG) classification showed that 888 DEGs were assigned to 20 categories, and the DEGs were mainly involved in amino acid transport and metabolism, general function prediction only, energy production and conversion, and function unknown. The expression trends of the DEGs validated by qPCR were consistent with the results of RNA-seq. In addition, the biofilm-associated genes and major virulence genes were identified from the RNA-seq data, including 10 c-di-GMP metabolism-associated genes, 1 lateral flagellar gene (lafA), 13 polar flagellar genes, 6 capsular polysaccharide synthesis genes, 6 exopolysaccharide synthesis genes, 5 type IV pilus synthesis genes, 6 membrane fusion protein (mfp) genes (cpsQ-mfpABC), 14 type III secretion system 1 (T3SS1) genes, 14 Vp-PAI genes (tdh2 and 13 T3SS2 genes), 3 type VI secretion system 1 (T6SS1) genes, 6 T6SS2 genes, 45 putative regulator genes, and 15 putative outer membrane protein genes. [Conclusion] A large number of genes demonstrate changed expression levels during the biofilm formation of V. parahaemolyticus, including the biofilm-associated genes, key virulence factor genes, and putative regulator genes. The data presented here provided important gene information for the future studies about the regulation of biofilm formation.