title: Genetic analysis of riboswitch-mediated transcriptional regulation responding to Mn2+ in Salmonella.
abstract: 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 Mn(2+) in Salmonella typhimurium. We characterized a 5'-UTR (UTR1) from the mntH locus encoding a Mn(2+) transporter, which forms a Rho-independent terminator to implement transcription termination with a high Mn(2+) 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 Mn(2+)-replete condition. Switch sequence GCUAUG can alternatively base pair duplicated hexanucleotide CAUAGC to form either a pseudoknot or terminator stem. Mn(2+), but not Mg(2+), and Ca(2+), can enhance cleavage at specific nucleotides in UTR1. We conclude that UTR1 is a riboswitch that senses cytoplasmic Mn(2+) and therefore participates in Mn(2+)-responsive mntH regulation in Salmonella. This riboswitch domain is also conserved in several Gram-negative enteric bacteria, indicating that this Mn(2+)-responsive mechanism could have broader implications in bacterial gene expression. Additionally, a high level of cytoplasmic Mn(2+) can down-regulate transcription of the Salmonella Mg(2+) transporter mgtA locus in a Mg(2+) 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 Mn(2+)-responsive riboswitches should expand the scope of RNA regulatory elements in response to inorganic ions.
authors.affiliation: Center for Infectious Diseases and Vaccinology, Biodesign Institute, and Arizona State University, Tempe, Arizona 85287-4501; School of Life Sciences, Arizona State University, Tempe, Arizona 85287-4501. Electronic address: yixin.shi@asu.edu.
authors.forename: Yixin
authors.initials: Y
authors.lastname: Shi
authors.affiliation: Center for Infectious Diseases and Vaccinology, Biodesign Institute, and Arizona State University, Tempe, Arizona 85287-4501.
authors.forename: Guang
authors.initials: G
authors.lastname: Zhao
authors.affiliation: Center for Infectious Diseases and Vaccinology, Biodesign Institute, and Arizona State University, Tempe, Arizona 85287-4501.
authors.forename: Wei
authors.initials: W
authors.lastname: Kong
mesh_terms: D020121:5' Untranslated Regions / Q000502:physiology; D000251:Adenosine Triphosphatases / Q000096:biosynthesis / Q000235:genetics; D001426:Bacterial Proteins / Q000096:biosynthesis* / Q000235:genetics; D002118:Calcium / Q000378:metabolism; D027682:Cation Transport Proteins / Q000096:biosynthesis* / Q000235:genetics; D015964:Gene Expression Regulation, Bacterial / Q000502:physiology*; D056426:Genetic Loci / Q000502:physiology*; D017136:Ion Transport / Q000502:physiology; D008274:Magnesium / Q000378:metabolism; D008345:Manganese / Q000378:metabolism*; D026901:Membrane Transport Proteins / Q000096:biosynthesis / Q000235:genetics; D058928:Riboswitch / Q000502:physiology*; D012486:Salmonella typhimurium / Q000235:genetics / Q000378:metabolism*
chemical_list: D020121:5' Untranslated Regions; D001426:Bacterial Proteins; D027682:Cation Transport Proteins; D026901:Membrane Transport Proteins; C433793:MntH protein, bacteria; D058928:Riboswitch; D008345:Manganese; D000251:Adenosine Triphosphatases; C093585:MgtA protein, bacteria; D008274:Magnesium; D002118:Calcium
keywords: 5′-Untranslated Region; Magnesium; Manganese; Riboswitch; Transcription Regulation; Transcription Termination