1. 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 †
Research focus on riboswitches
Bioinformatics

2. 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

3. 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

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
Research focus on riboswitches
Bioinformatics

5. 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

6. 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

7. 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

8. 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

9. 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

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

11. 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

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