Genetic Analysis of Riboswitch-mediated Transcriptional Regulation Responding to Mn2+ in Salmonella

Background: Divalent cation binding to riboswitch RNAs regulates expression of their transporter genes in bacteria. Results: Mn2+ interacts with Salmonella riboswitches characterized from Mn2+ transporter mntH and Mg2+ transporter mgtA to modulate transcription of the downstream coding region. Conclusion: Specific riboswitches control gene expression in response to Mn2+ in bacteria. Significance: This is the discovery of a Mn2+ riboswitch. Riboswitches are a class of cis-acting regulatory RNAs normally characterized from the 5-UTR of bacterial transcripts that bind a specific ligand to regulate expression of associated genes by forming alternative conformations. Here, we present a riboswitch that contributes to transcriptional regulation through sensing Mn2+ in Salmonella typhimurium. We characterized a 5-UTR (UTR1) from the mntH locus encoding a Mn2+ transporter, which forms a Rho-independent terminator to implement transcription termination with a high Mn2+ selectivity both in vivo and in vitro. Nucleotide substitutions that cause disruption of the terminator interfere with the regulatory function of UTR1. RNA probing analyses outlined a specific UTR1 conformation that favors the terminator structure in Mn2+-replete condition. Switch sequence GCUAUG can alternatively base pair duplicated hexanucleotide CAUAGC to form either a pseudoknot or terminator stem. Mn2+, but not Mg2+, and Ca2+, can enhance cleavage at specific nucleotides in UTR1. We conclude that UTR1 is a riboswitch that senses cytoplasmic Mn2+ and therefore participates in Mn2+-responsive mntH regulation in Salmonella. This riboswitch domain is also conserved in several Gram-negative enteric bacteria, indicating that this Mn2+-responsive mechanism could have broader implications in bacterial gene expression. Additionally, a high level of cytoplasmic Mn2+ can down-regulate transcription of the Salmonella Mg2+ transporter mgtA locus in a Mg2+ riboswitch-dependent manner. On the other hand, these two types of cation riboswitches do not share similarity at the primary or secondary structural levels. Taken together, characterization of Mn2+-responsive riboswitches should expand the scope of RNA regulatory elements in response to inorganic ions.