Differential RNA-seq of Vibrio cholerae identifies the VqmR small RNA as a regulator of biofilm formation

• Published in: Proceedings of the National Academy of Sciences - PNAS Vol. 112; no. 7; pp. E766 - E775
• Main Authors: Papenfort, Kai, Förstner, Konrad U, Cong, Jian-Ping, Sharma, Cynthia M, Bassler, Bonnie L
• Format: Journal Article
• Language: English
• Published: United States National Academy of Sciences 17-02-2015; National Acad Sciences
• Series: PNAS Plus
• Subjects: Base Sequence; Biofilms; Biological Sciences; Gene Expression Profiling; Genes, Bacterial; Molecular Sequence Data; Mutagenesis; Mutation; Oligonucleotide Array Sequence Analysis; PNAS Plus; Promoter Regions, Genetic; Proteins; Ribonucleic acid; RNA; RNA, Viral - genetics; Sequence Analysis, RNA; Sequence Homology, Nucleic Acid; Toxins; Transcription, Genetic; Vibrio cholerae; Vibrio cholerae - genetics; quorum sensing; RNA-seq; Vibrio cholerae; biofilm; sRNA
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.1500203112

Significance To our knowledge, this work describes the first genome-wide annotation of transcriptional start sites in Vibrio cholerae and the discovery and characterization of a regulatory RNA, named VqmR, which controls collective behaviors in this major human pathogen. We show that VqmR is activated by the VqmA transcriptional regulator. VqmR represses expression of multiple mRNA targets including those encoding the Rtx (repeats in toxin) toxin and VpsT, which is required for biofilm formation. Indeed, we show that VqmR controls biofilm formation through repression of vpsT .
Quorum sensing (QS) is a process of cell-to-cell communication that enables bacteria to transition between individual and collective lifestyles. QS controls virulence and biofilm formation in Vibrio cholerae , the causative agent of cholera disease. Differential RNA sequencing (RNA-seq) of wild-type V. cholerae and a locked low-cell-density QS-mutant strain identified 7,240 transcriptional start sites with ∼47% initiated in the antisense direction. A total of 107 of the transcripts do not appear to encode proteins, suggesting they specify regulatory RNAs. We focused on one such transcript that we name VqmR. vqmR is located upstream of the vqmA gene encoding a DNA-binding transcription factor. Mutagenesis and microarray analyses demonstrate that VqmA activates vqmR transcription, that vqmR encodes a regulatory RNA, and VqmR directly controls at least eight mRNA targets including the rtx (repeats in toxin) toxin genes and the vpsT transcriptional regulator of biofilm production. We show that VqmR inhibits biofilm formation through repression of vpsT . Together, these data provide to our knowledege the first global annotation of the transcriptional start sites in V. cholerae and highlight the importance of posttranscriptional regulation for collective behaviors in this human pathogen.