National Research Laboratory of Molecular Microbiology and Toxicology, Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea.
Center for Food and Bioconvergence, and Research Institute of Agriculture and Life Science, Seoul National University, Seoul, Republic of Korea.
PLoS Pathog. 2023 Jan 19;19(1):e1011064. doi: 10.1371/journal.ppat.1011064. eCollection 2023 Jan.
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 of Vibrio vulnificus, a fulminating human pathogen, in this study. ICA analyzed the large-scale transcriptome data of V. vulnificus cells 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 of V. vulnificus. Interestingly, the BrpT-iModulon additionally contained two novel genes, VV1_3061 and VV2_1694, designated as cabH and brpN, respectively. cabH and brpN were shared in other Vibrio species and not yet identified by DE analyses. Genetic and biochemical analyses revealed that cabH and brpN are directly up-regulated by BrpT. The deletion of cabH and brpN impaired 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, cabH and brpN, which are regulated by BrpT and essential for the development of robust biofilms and rugose colonies of V. vulnificus.
许多病原菌形成生物膜以在环境压力和宿主免疫防御下存活。然而，在单一条件下对生物膜和浮游细胞中的基因进行差异表达（DE）分析，在鉴定生物膜形成所必需的基因方面存在局限性。在这项研究中，采用独立成分分析（ICA），一种机器学习算法，全面鉴定了一种暴发性人类病原体创伤弧菌的生物膜基因。ICA 分析了创伤弧菌细胞在各种生物膜和浮游条件下的大规模转录组数据，然后总共鉴定了 72 组独立协同调控的基因，即 iModulons。在生物膜细胞中特异性激活的三个 iModulons 中，BrpT-iModulon 主要由转录调节剂 BrpT 的调控子的已知基因组成，该调控子控制创伤弧菌的生物膜形成。有趣的是，BrpT-iModulon 还包含两个新基因，VV1_3061 和 VV2_1694，分别命名为 cabH 和 brpN。cabH 和 brpN 在其他弧菌物种中共享，尚未通过 DE 分析鉴定。遗传和生化分析表明，cabH 和 brpN 直接受 BrpT 上调。cabH 和 brpN 的缺失会损害生物膜和粗糙菌落的形成。CabH 结构上与先前已知的钙结合基质蛋白 CabA 相似，对于附着在表面上是必需的。携带酰基转移酶-3 结构域的 BrpN 如 BrpL 中观察到的，在胞外多糖产生中发挥重要作用。总之，ICA 鉴定了两个新基因 cabH 和 brpN，它们受 BrpT 调控，对于创伤弧菌生物膜和粗糙菌落的形成至关重要。
