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FRAGMENT-BASED STUDIES ON RIBOSWITCHES

Riboswitches are conserved regions of mRNA that adopt well defined secondary and tertiary structures. They directly bind certain small molecules with high affinity and selectivity. Their cellular function is to repress or activate essential genes (for example those involved in biosynthesis and transport of metabolites) in response to the intracellular level of their ligand. Ligand binding stabilises either an "on" or "off" conformation which alters mRNA transcription, protein translation or mRNA splicing.

Riboswitches are widespread in bacteria, whereas they appear to be less common in eukaryotes. So far, no riboswitches have been identified in animals, and due to their role in regulating vital cellular processes, they are potential targets for antimicrobial drugs. Alternatively, they could have chemical genetics applications as gene control elements.

We are interested in studying thiamine pyrophosphate (TPP, coenzyme B1) and adenosyl cobalamine (coenzyme B12) binding riboswitches (in collaboration with Professor Alison Smith, Dr. Finian Leeper and Professor Martin Warren (Kent)). We have developed methods, using biophysical techniques (equilibrium dialysis, ITC and NMR) to test small molecules (including fragments and ligand analogues) for binding to riboswitches [Chem. Sci, 2011]. We have identified fragments with high ligand efficiencies and thiamine analogues with high binding affinity for the E. coli TPP thiM riboswitch, and have carried out structural studies on these systems in collaboration with Professor Adrian Ferre-D'Amare (NIH) [Chem Biol., 2014, A.C.S. Chem. Biol. 2010].

Riboswitch Fig 1

Riboswitch controlled gene expression. In E. coli TPP riboswitches suppress the translation of TPP biosynthetic and transport genes in response to TPP binding.

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