Genome-wide analysis of acid tolerance genes of Enterococcus faecalis with RNA-seq and Tn-seq

• Published in: BMC genomics Vol. 25; no. 1; p. 261
• Main Authors: Chen, Zhanyi, Niu, Chenguang, Wei, Lifan, Huang, Zhengwei, Ran, Shujun
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 08.03.2024; BioMed Central; BMC
• Subjects: Acid stress; Acid tolerance; Acids; Amino acids; Bacteria; Bacteria, Pathogenic; Bacterial genetics; Bacterial infections; Biosynthesis; Communicable diseases; Endocarditis; Enterococcus; Enterococcus faecalis; Enterococcus faecalis - genetics; Extreme environments; Gene Expression Profiling; Gene sequencing; Genes; Genetic aspects; Genetic research; Genome; Genomes; Genomics; Identification and classification; Infections; Infectious diseases; Microbial metabolism; Mismatch repair; Nosocomial infection; Nutrient deficiency; Opportunist infection; Organic acids; Pathogens; Physiological aspects; Ribonucleic acid; RNA; RNA-Seq; Stress (Physiology); Survival; TIS; Transcriptomes; Transposons; China; United States > US; Enterococcus faecalis; RNA-seq; Acid stress; Acid tolerance; TIS
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/s12864-024-10162-z

Enterococcus faecalis, a formidable nosocomial and community-acquired opportunistic pathogen, can persist a wide range of extreme environments, including low pH and nutrient deficiency. Clarifying the survival mechanism of E. faecalis in low-pH conditions is the key to combating the infectious diseases caused by E. faecalis. In this study, we combined transcriptome profiling (RNA-seq) and transposon insertion sequencing (TIS) to comprehensively understand the genes that confer these features on E. faecalis. The metadata showed that genes whose products are involved in cation transportation and amino acid biosynthesis were predominantly differentially expressed under acid conditions. The products of genes such as opp1C and copY reduced the hydrion concentration in the cell, whereas those of gldA2, gnd2, ubiD, and ubiD2 mainly participated in amino metabolism, increasing matters to neutralize excess acid. These, together with the folE and hexB genes, which are involved in mismatch repair, form a network of E. faecalis genes necessary for its survival under acid conditions.