Research Focus: Searching for Novel Riboswitches in Newly Sequenced Genomes

1. Biological Application: RNAs Research Focus: Searching for Novel Riboswitches in Newly Sequenced Genomes Danny Barash† Department of Computer Science Ben-Gurion University †email: dbarash@cs.bgu.ac.il Bioinformatics

2. Why RNAs? • Classical Picture: DNARNAPROTEINS Transcription Translation • New Picture: RNA* DNA PROTEINS RNA* : RiboNucleic Acid Bioinformatics

3. What are Riboswitches? • “Riboswitches”: RNA genetic control elements that influence transcription termination or translation initiation by conformation rearrangement of the RNA in response to direct metabolite binding. • Since the mid-90’s, Breaker has been trying to artificially design RNA switches that respond to metabolite binding (Soukup and Breaker, Trends. Biotechnol., 1999). • In 2002, both R. Breaker’s lab (Yale) and E. Nudler’s lab (NYU medical school) discovered these RNA genetic control elements in bacteria (Winkler et al., Nature, 2002); (Mironov et al., Cell, 2002). These RNA regulatory systems are widespread in bacteria and are speculated to date back to early times in evolution (perhaps belonging to the RNA World). Bioinformatics

4. Prokaryotic Transcription Termination by Riboswitches Nudler and coworkers (Mironov et al., Cell, 2002) TPP-mediated Attenuation Control (TPP=thiamin Pyrophosphate): Terminator TPP Anti-terminator Bioinformatics

5. With TPP What are Riboswitches? Terminator Vitamin B1 biosynthesis in bacteria: TPP-mediated attentuation control: E. Nudler and coworkers: (Mironov et al., Cell, 2002) Thiamine pyrophosphate are the metabolites that alter conformation. Aptamer Bioinformatics

6. Without TPP What are Riboswitches? Anti-terminator Vitamin B1 biosynthesis in bacteria: TPP-mediated attentuation control: E. Nudler and coworkers: (Mironov et al., Cell, 2002) Thiamine pyrophosphate are the metabolites that alter conformation. Aptamer Bioinformatics

7. Prokaryotic TranslationInitiation by Riboswitches Breaker and coworkers (Winkler et al., Nature, 2002) TPP-mediated Attenuation Control (TPP=thiamin Pyrophosphate): Sequestor TPP Anti-sequestor Bioinformatics

8. Deleterious mutation prediction inTPP riboswitch using RNAMute Predict conformational switching mutations GCAGAACAAT TCAATATGTA TTCGTTTAA… RNAMute Single point mutation A158U (Barash., Nucleic Acids Res., 2003) Bioinformatics

9. Successful Computer Predictionsof Deleterious Mutations (Barash and Gabdank, RNA Biology, 2010): special focus review TPP-mediated Attenuation Control (TPP=thiamin Pyrophosphate): Terminator TPP Anti-terminator Bioinformatics

10. Searching for riboswitches ineukaryotes by their aptamer Sequence is not enough, need structure considerations! Bioinformatics

11. Searching for riboswitches ineukaryotes by their aptamer (Cohen et al., In Silico Biology, 2008) – a riboswitch in plants? Our 3-stem junction candidate in plants Known consensus in bacteria Bioinformatics

12. Riboswitches in Evolution Canyon III. “Evolution Canyon”: Analyzing Bacillus Subtilis Strains to Examine How Riboswitches Adapt to Extreme Environments. Bioinformatics