Two novel genes identified by large-scale transcriptomic analysis are essential for biofilm and rugose colony development of Vibrio vulnificus

• DOI: 10.1371/journal.ppat.1011064
• Publication Date: 2023-01-19T18:44:14Z
• Authors: Hojun Lee; Hanhyeok Im; Seung-Ho Hwang; Duhyun Ko; Sang Ho Choi
• Keywords: 0301 basic medicine; QH301-705.5; Gene Expression Regulation, Bacterial; RC581-607; 03 medical and health sciences; Genes, Bacterial; Biofilms; Humans; Immunologic diseases. Allergy; Biology (General); Transcriptome; Vibrio vulnificus; Research Article; Vibrio

Many pathogenic bacteria form biofilms to survive under environmental stresses and host immune defenses. Differential expression (DE) analysis of the genes in biofilm and planktonic cells under a single condition, however, has limitations to identify the genes essential for biofilm formation. Independent component analysis (ICA), a machine learning algorithm, was adopted to comprehensively identify the biofilm genes ofVibrio vulnificus, a fulminating human pathogen, in this study. ICA analyzed the large-scale transcriptome data ofV.vulnificuscells under various biofilm and planktonic conditions and then identified a total of 72 sets of independently co-regulated genes, iModulons. Among the three iModulons specifically activated in biofilm cells, BrpT-iModulon mainly consisted of known genes of the regulon of BrpT, a transcriptional regulator controlling biofilm formation ofV.vulnificus. Interestingly, the BrpT-iModulon additionally contained two novel genes, VV1_3061 and VV2_1694, designated ascabHandbrpN, respectively.cabHandbrpNwere shared in otherVibriospecies and not yet identified by DE analyses. Genetic and biochemical analyses revealed thatcabHandbrpNare directly up-regulated by BrpT. The deletion ofcabHandbrpNimpaired the robust biofilm and rugose colony formation. CabH, structurally similar to the previously known calcium-binding matrix protein CabA, was essential for attachment to the surface. BrpN, carrying an acyltransferase-3 domain as observed in BrpL, played an important role in exopolysaccharide production. Altogether, ICA identified two novel genes,cabHandbrpN, which are regulated by BrpT and essential for the development of robust biofilms and rugose colonies ofV.vulnificus.