Secondary structures and functional requirements for thiM riboswitches from Desulfovibrio vulgaris, Erwinia carotovora and Rhodobacter spheroides.
Abstract Bacterial thiM riboswitches contain aptamer domains that bind the metabolite thiamine pyrophosphate (TPP). Binding of TPP to the aptamer domain induces structural rearrangements that are relayed to the expression domain, thereby interfering with gene expression. Here, we report identification of three putative thiM riboswitches from different bacteria and analysis of their secondary structures. Chemical probing revealed that the riboswitches share similar secondary structures in their aptamer domains that can communicate with the highly variant expression domains in a mechanism likely involving sequestration of the Shine-Dalgarno sequence. Remarkably, the aptamer domain of the thiM gene of Desulfovibrio vulgaris binds TPP with similar affinity and selectivity as that of Escherichia coli, although nucleotides previously shown to form direct contacts to the metabolite are mutated. We also designed small RNA hairpins for each riboswitch that bind the RNA only in the absence of the metabolite. Our study shows that aptamer domains in riboswitches with high similarity in their secondary structures can communicate with a broad variety of non-related expression domains by similar mechanisms.
Rentmeister
Andrea
A
LIMES-Institute, Program Unit Chemical Biology and Medicinal Chemistry, c/o Kekulé-Institute for Organic Chemistry and Biochemistry of the University of Bonn, Gerhard-Domagk-Strasse 1, D-53121 Bonn, Germany.
Mayer
Günter
G
Kuhn
Nicole
N
Famulok
Michael
M
D052158:Aptamers, Peptide; D016969:Desulfovibrio vulgaris; D006090:Gram-Negative Bacteria / Q000737:chemistry*; D016973:Pectobacterium carotovorum; D017853:Phosphotransferases (Alcohol Group Acceptor) / Q000737:chemistry* / Q000378:metabolism / Q000502:physiology*; D054730:Protein Interaction Domains and Motifs; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D012242:Rhodobacter sphaeroides; D013835:Thiamine Pyrophosphate / Q000378:metabolism
D052158:Aptamers, Peptide; D017853:Phosphotransferases (Alcohol Group Acceptor); C051254:hydroxyethylthiazole kinase; D013835:Thiamine Pyrophosphate