Genetic analysis of riboswitch-mediated transcriptional regulation responding to Mn2+ in Salmonella [Signal Transduction]

March 4th, 2014 by Shi, Y., Zhao, G., Kong, W.

Riboswitches are a class of cis-acting regulatory RNAs normally characterized from the 5′ untranslated region (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 characterize a 5′UTR (UTR1) from mntH locus encoding a Mn2+ transporter, which can form 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 regulatory function of UTR1. RNA probing analyses outline a specific UTR1 conformation that favors the terminator structure in Mn2+-replete condition. A switch sequence GCUAUG can alternatively base-pair duplicated hexa-nucleotide 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 which 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 should have broader implications in bacterial gene expression. Additionally, high level of cytoplasmic Mn2+ can down-regulate transcription of 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 structure levels. Taken together, characterization of Mn2+-responsive riboswitches should expand the scope of RNA regulatory elements in response to inorganic ions.