Department of Computer Science Ben-Gurion University 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 Research focus on riboswitches Bioinformatics

RNA* : RiboNucleic Acid Why RNAs? Classical Picture: DNA RNA PROTEINS Transcription Translation New Picture: RNA* DNA PROTEINS RNA* : RiboNucleic Acid Research focus on riboswitches Bioinformatics

What are Riboswitches? Bioinformatics “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). Research focus on riboswitches Bioinformatics

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

What are Riboswitches? Vitamin B1 biosynthesis in bacteria: With TPP 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 Research focus on riboswitches Bioinformatics

What are Riboswitches? Vitamin B1 biosynthesis in bacteria: Without TPP 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. Anti-terminator Aptamer Research focus on riboswitches Bioinformatics

Prokaryotic Translation Initiation by Riboswitches Breaker and coworkers (Winkler et al., Nature, 2002) TPP-mediated Attenuation Control (TPP=thiamin Pyrophosphate): Sequestor TPP Anti-sequestor Research focus on riboswitches Bioinformatics

Deleterious mutation prediction in TPP riboswitch using RNAMute Predict conformational switching mutations GCAGAACAAT TCAATATGTA TTCGTTTAA… RNAMute Single point mutation A158U (Barash., Nucleic Acids Res., 2003) Research focus on riboswitches Bioinformatics

Successful Computer Predictions of Deleterious Mutations (Barash and Gabdank, RNA Biology, 2010): special focus review TPP-mediated Attenuation Control (TPP=thiamin Pyrophosphate): Terminator TPP Anti-terminator Research focus on riboswitches Bioinformatics

Searching for riboswitches in eukaryotes by their aptamer Sequence is not enough, need structure considerations! Research focus on riboswitches Bioinformatics

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

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