Secondary structures and functional requirements for thiM riboswitches from Desulfovibrio vulgaris, Erwinia carotovora and Rhodobacter spheroides

Andrea Rentmeister, G. Mayer, Nicole Kuhn, Michael Famulok

Research output: Contribution to journalArticle

13 Citations (Scopus)

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.
Original languageEnglish
Pages (from-to)127-134
Number of pages7
JournalJournal of Biological Chemistry
Volume389
Issue number2
DOIs
Publication statusPublished - Feb 2008

Keywords

  • chemical probing
  • Desulfovibrio vulgaris
  • Erwinia carotovora
  • hairpin
  • Rhodobacter spheroides
  • riboswitch
  • thiamine pyrophosphate
  • thiM

Fingerprint Dive into the research topics of 'Secondary structures and functional requirements for thiM riboswitches from Desulfovibrio vulgaris, Erwinia carotovora and Rhodobacter spheroides'. Together they form a unique fingerprint.

  • Cite this