title: Evidence for a second class of S-adenosylmethionine riboswitches and other regulatory RNA motifs in alpha-proteobacteria.
abstract: BACKGROUND
  Riboswitches are RNA elements in the 5' untranslated leaders of bacterial mRNAs that directly sense the levels of specific metabolites with a structurally conserved aptamer domain to regulate expression of downstream genes. Riboswitches are most common in the genomes of low GC Gram-positive bacteria (for example, Bacillus subtilis contains examples of all known riboswitches), and some riboswitch classes seem to be restricted to this group.
  
  
  RESULTS
  We used comparative sequence analysis and structural probing to identify five RNA elements (serC, speF, suhB, ybhL, and metA) that reside in the intergenic regions of Agrobacterium tumefaciens and many other alpha-proteobacteria. One of these, the metA motif, is found upstream of methionine biosynthesis genes and binds S-adenosylmethionine (SAM). This natural aptamer most likely functions as a SAM riboswitch (SAM-II) with a consensus sequence and structure that is distinct from the class of SAM riboswitches (SAM-I) predominantly found in Gram-positive bacteria. The minimal functional SAM-II aptamer consists of fewer than 70 nucleotides, which form a single stem and a pseudoknot. Despite its simple architecture and lower affinity for SAM, the SAM-II aptamer strongly discriminates against related compounds.
  
  
  CONCLUSIONS
  SAM-II is the only metabolite-binding riboswitch class identified so far that is not found in Gram-positive bacteria, and its existence demonstrates that biological systems can use multiple RNA structures to sense a single chemical compound. The two SAM riboswitches might be 'RNA World' relics that were selectively retained in certain bacterial lineages or new motifs that have emerged since the divergence of the major bacterial groups.
authors.affiliation: Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520-8103, USA. keith.corbino@yale.edu
authors.forename: Keith A
authors.initials: KA
authors.lastname: Corbino
authors.forename: Jeffrey E
authors.initials: JE
authors.lastname: Barrick
authors.forename: Jinsoo
authors.initials: J
authors.lastname: Lim
authors.forename: Rüdiger
authors.initials: R
authors.lastname: Welz
authors.forename: Brian J
authors.initials: BJ
authors.lastname: Tucker
authors.forename: Izabela
authors.initials: I
authors.lastname: Puskarz
authors.forename: Maumita
authors.initials: M
authors.lastname: Mandal
authors.forename: Noam D
authors.initials: ND
authors.lastname: Rudnick
authors.forename: Ronald R
authors.initials: RR
authors.lastname: Breaker
mesh_terms: D020561:Alphaproteobacteria / Q000235:genetics*; D052157:Aptamers, Nucleotide / Q000235:genetics; D001483:Base Sequence; D005812:Genes, Switch / Q000235:genetics*; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D012329:RNA, Bacterial / Q000737:chemistry / Q000235:genetics*; D038621:Regulatory Sequences, Ribonucleic Acid / Q000235:genetics*; D012436:S-Adenosylmethionine / Q000235:genetics* / Q000378:metabolism*
chemical_list: D052157:Aptamers, Nucleotide; D012329:RNA, Bacterial; D038621:Regulatory Sequences, Ribonucleic Acid; D012436:S-Adenosylmethionine