1. Ben-Gurion University Research focus on riboswitches Bioinformatics 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 Biological Application: RNAs

2. Ben-Gurion University Research focus on riboswitches Bioinformatics Why RNAs?  Classical Picture: DNA RNA PROTEINS Transcription Translation  New Picture: RNA* DNA PROTEINS RNA* : RiboNucleic Acid

3. Ben-Gurion University Research focus on 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). What are Riboswitches?

4. Ben-Gurion University 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 Anti-terminator TPP

5. Ben-Gurion University Research focus on riboswitches Bioinformatics With TPP Vitamin B 1 biosynthesis in bacteria: TPP-mediated attentuation control: E. Nudler and coworkers: (Mironov et al., Cell, 2002) Thiamine pyrophosphate are the metabolites that alter conformation. What are Riboswitches? Terminator Aptamer

6. Ben-Gurion University Research focus on riboswitches Bioinformatics Without TPP What are Riboswitches? Anti-terminator Aptamer Vitamin B 1 biosynthesis in bacteria: TPP-mediated attentuation control: E. Nudler and coworkers: (Mironov et al., Cell, 2002) Thiamine pyrophosphate are the metabolites that alter conformation.

7. Ben-Gurion University 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 Anti-sequestor TPP

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

9. Ben-Gurion University 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 Anti-terminator TPP

10. Ben-Gurion University Research focus on riboswitches Bioinformatics Searching for riboswitches in eukaryotes by their aptamer Sequence is not enough, need structure considerations!

11. Ben-Gurion University Research focus on riboswitches Bioinformatics Searching for riboswitches in eukaryotes 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

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