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The 109-nucleotide Spot 42 RNA whose transcription is repressed by the cyclic adenosine monophosphate receptor protein (CRP) is one of the best-characterized base-pairing small RNAs (sRNAs) in Escherichia coli. Consistent with high levels of Spot 42 in glucosegrown cells, the RNA blocks the expression of transporters and enzymes involved in the utilization of nonpreferred carbon, such as galactose. We now document that Spot 42 also encodes a 15–amino acid protein denoted SpfP. Previous studies showed that overexpression of Spot 42 reduces growth in galactose and other nonpreferred carbon sources. Overexpression of just the small protein from a Spot 42 derivative deficient in base-pairing activity also prevented growth on galactose, revealing that the sRNA and protein impact the same pathway. Copurification experiments showed that SpfP binds CRP. This binding blocks the ability of CRP to activate specific genes, such as the galETKM operon, impacting the kinetics of induction when cells are shifted from glucose to galactose medium. Thus, the small protein reinforces the feedforward loop regulated by the base-pairing activity of the Spot 42 RNA. [ABSTRACT FROM AUTHOR]

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. SYNOPSIS: Traditionally considered to be non‐coding, several bacterial small regulatory RNAs (sRNAs) have been found to also encode small proteins and thus are referred to as dual‐function RNAs. Here, a forward genetic screen identifies VcdRP as the first dual‐function RNA in Vibrio cholerae, where it balances carbon uptake and metabolism. Over‐expression of VcdRP inhibits cholera toxin production.Transcription of vcdRP is controlled by cAMP‐CRP.The base‐pairing element VcdR blocks the synthesis of PTS sugar transporters.A 29 amino‐acid VcdP‐encoded protein enhances enzymatic activity of citrate synthase. [ABSTRACT FROM AUTHOR]