A dual‐function RNA balances carbon uptake and central metabolism in Vibrio cholerae

Abstract

Bacterial small RNAs (sRNAs) are well known to modulate gene expression by base pairing with trans‐encoded transcripts and are typically non‐coding. However, several sRNAs have been reported to also contain an open reading frame and thus are considered dual‐function RNAs. In this study, we discovered a dual‐function RNA from Vibrio cholerae, called VcdRP, harboring a 29 amino acid small protein (VcdP), as well as a base‐pairing sequence. Using a forward genetic screen, we identified VcdRP as a repressor of cholera toxin production and link this phenotype to the inhibition of carbon transport by the base‐pairing segment of the regulator. By contrast, we demonstrate that the VcdP small protein acts downstream of carbon transport by binding to citrate synthase (GltA), the first enzyme of the citric acid cycle. Interaction of VcdP with GltA results in increased enzyme activity and together VcdR and VcdP reroute carbon metabolism. We further show that transcription of vcdRP is repressed by CRP allowing us to provide a model in which VcdRP employs two different molecular mechanisms to synchronize central metabolism in V. cholerae.

Glutamine synthetase mRNA releases sRNA from its 3’UTR to regulate carbon/nitrogen metabolic balance

“…A Gram-positive bacterium, Corynebacterium glutamicum , also tunes the bottleneck in the TCA cycle to produce high levels of Glu by inhibiting the OGDH activity with a 15-kDa protein OdhI depending on its phosphorylation state (Niebisch et al , 2006). Surprisingly, in V. cholerae , the VcdRP dual-functional sRNA represses the PTS-coding mRNAs while the 29-aa small protein VcdP activates citrate synthase GltA to accumulate 2-OG and Glu (Venkat et al , 2021). Altogether, bacteria and archaea employ various RNAs and proteins to regulate the crucial metabolic pathways.…”

Glutamine synthetase mRNA releases sRNA from its 3′UTR to regulate carbon/nitrogen metabolic balance in Enterobacteriaceae

“…Corynebacterium glutamicum produces high levels of Glu by inhibiting the OGDH activity with a 15 kDa protein OdhI depending on its phosphorylation state ( Niebisch et al, 2006 ). In V. cholerae , the VcdRP dual-functional sRNA represses the PTS-coding mRNAs while the 29-aa small protein VcdP activates citrate synthase GltA to accumulate 2-OG and Glu ( Venkat et al, 2021 ).…”

Targeting Virulence Genes Expression in Vibrio vulnificus by Alternative Carbon Sources

“…The close link between environmental conditions and virulence is well-established, and it is reasonable to hypothesize that the involvement of the cAMP Receptor Protein (CRP) in the transcriptional regulation of several virulence factors might be a relevant bridge between carbon source availability and virulence [ 21 ]. Moreover, a small dual-function RNA, named VcdRP and regulated by CRP, has been recently identified in V. cholerae as involved in toxin production, carbon uptake and regulation of global metabolism [ 22 ]. A nearly identical locus , mapping on chromosome 1 of V. vulnificus , has been reported [ 22 ], though it has not been investigated, so far.…”

“…Moreover, a small dual-function RNA, named VcdRP and regulated by CRP, has been recently identified in V. cholerae as involved in toxin production, carbon uptake and regulation of global metabolism [ 22 ]. A nearly identical locus , mapping on chromosome 1 of V. vulnificus , has been reported [ 22 ], though it has not been investigated, so far. Based on such knowledge, as well as on previous data about human pathogenic bacteria closely related to V. vulnificus (namely, V. parahaemolitycus and V. alginolyticus ) [ 23 ], we aimed to investigate whether selected chemicals (suitable for, or already in clinical use, also in the setting of sepsis) could down-regulate the most relevant virulence genes.…”