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
Ben-Gurion
University
Why RNAs?
 Classical Picture:
DNA
RNA
PROTEINS
Transcription
 New Picture:
Translation
RNA*
DNA
PROTEINS
RNA* : RiboNucleic Acid
Research focus on riboswitches
Bioinformatics
Ben-Gurion
University
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).
Research focus on riboswitches
Bioinformatics
Ben-Gurion
University
Prokaryotic Transcription
Termination by Riboswitches
Nudler and coworkers (Mironov et al., Cell, 2002)
TPP-mediated
Attenuation
Control
(TPP=thiamin
Pyrophosphate):
TPP
Terminator
Anti-terminator
Research focus on riboswitches
Bioinformatics
Ben-Gurion
University
What are Riboswitches?
Terminator
Vitamin B1 biosynthesis in
bacteria:
TPP-mediated
attentuation control:
Aptamer
E. Nudler and coworkers:
(Mironov et al., Cell, 2002)
Thiamine pyrophosphate
are the metabolites that
alter conformation.
Research focus on riboswitches
With TPP
Bioinformatics
Ben-Gurion
University
What are Riboswitches?
Anti-terminator
Vitamin B1 biosynthesis in
bacteria:
TPP-mediated
attentuation control:
Aptamer
E. Nudler and coworkers:
(Mironov et al., Cell, 2002)
Thiamine pyrophosphate
are the metabolites that
alter conformation.
Research focus on riboswitches
Without
TPP
Bioinformatics
Ben-Gurion
University
Prokaryotic Translation
Initiation by Riboswitches
Breaker and coworkers (Winkler et al., Nature, 2002)
TPP-mediated
Attenuation
Control
(TPP=thiamin
Pyrophosphate):
TPP
Sequestor
Anti-sequestor
Research focus on riboswitches
Bioinformatics
Ben-Gurion
University
GCAGAACAAT
TCAATATGTA
TTCGTTTAA…
Deleterious mutation prediction in
TPP riboswitch using RNAMute
Predict conformational
switching mutations
RNAMute
Single point mutation
A158U
(Barash., Nucleic Acids Res., 2003)
Research focus on riboswitches
Bioinformatics
Ben-Gurion
University
Successful Computer Predictions
of Deleterious Mutations
(Barash and Gabdank, RNA Biology, 2010): special focus review
TPP-mediated
Attenuation
Control
(TPP=thiamin
Pyrophosphate):
TPP
Terminator
Anti-terminator
Research focus on riboswitches
Bioinformatics
Ben-Gurion
University
Searching for riboswitches in
eukaryotes by their aptamer
Sequence is not enough, need structure considerations!
Research focus on riboswitches
Bioinformatics
Ben-Gurion
University
Searching for riboswitches in
eukaryotes by their aptamer
(Cohen et al., In Silico Biology, 2008) – a riboswitch in plants?
Known consensus
in bacteria
Research focus on riboswitches
Our 3-stem junction
candidate in plants
Bioinformatics
Ben-Gurion
University
Riboswitches in Evolution Canyon
III. “Evolution Canyon”: Analyzing Bacillus
Subtilis Strains to Examine How Riboswitches
Adapt to Extreme Environments.
Research focus on riboswitches
Bioinformatics