Riboswitch Regulation of

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Riboswitch Regulation of Gene Expression
Created by Dr. Gail Mitchell Emilsson
In the laboratory of Dr. Ronald R. Breaker at
Yale University 2004
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Riboswitches are present in untranslated regions
of mRNAs. Their purpose is to regulate gene
expression in response to binding small molecule
metabolites.
This movie demonstrates the molecular events
common to most bacterial riboswitches. Resources
are listed at the end of the movie.
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Part I Gene Regulation by a Typical Riboswitch
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Bacterial riboswitches are present in the 5
untranslated region of mRNAs. Transcription is
regulated by the gene promoter and transcription
initiation factors
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RNA polymerase initiates transcription.
A long untranslated leader is produced first.
DNA template
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Case 1
Cellular concentration of metabolite is too low
to occupy the riboswitch binding site.
Transcription and
RNA polymerase
RNA polymerase
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Case 1
Cellular concentration of metabolite is too low
to occupy the riboswitch binding site.
Transcription and intramolecular RNA folding
continue.
RNA polymerase
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Case 1
Cellular concentration of metabolite is too low
to occupy the riboswitch binding site.
Translation is initiated.
Transcription and intramolecular RNA folding
continue.
Typically the new mRNA codes for a biosynthetic
or transport protein that raises the
intracellular level of the metabolite.
Gene regulation (next case) is accomplished by
variations in the interactions of the regions
highlighted in orange.
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Case 2
Cellular concentration of metabolite (X) is high.
RNA polymerase produces the long untranslated
leader region.
Intramolecular folding can lead to an alternate
conformation.
X
X
X
X
Nascent RNA
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X
RNA polymerase
DNA template
The alternate riboswitch conformation is stable
when metabolite is bound.
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Case 2
Cellular concentration of metabolite (X) is high.
Transcription continues.
RNA polymerase produces the long untranslated
leader region.
Intramolecular folding can lead to an alternate
conformation.
X
X
X
X
X
X
RNA polymerase
The alternate riboswitch conformation is stable
when metabolite is bound.
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Case 2
Cellular concentration of metabolite (X) is high.
Transcription continues.
Now, RNA folding leads to formation of an
intrinsic terminator.
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X
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X
RNA polymerase
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Case 2
Cellular concentration of metabolite (X) is high.
Transcription continues.
Now, RNA folding leads to formation of an
intrinsic terminator.
X
X
X
X
X
RNA polymerase
The transcript is never completed and the
metabolite biosynthetic or transport protein is
not produced.
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Review
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X
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2
1
4
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X
Transcription is completed.
Transcription is terminated. Proteins are
downregulated.
Biosynthetic and/or transport proteins are
expressed.
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Part II The Expanding Universe of Riboswitches
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Riboswitch Functions
Riboswitches were defined earlier by two main
criteria

• Direct (protein-free) binding of metabolite to
  RNA
• Metabolite-dependent regulation of genes

These two activities are accomplished by two
functionally separate domains on the RNA
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4
2
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U
U
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Riboswitch Functions
Because of the modular nature of RNA structures,
different types of expression platform can be
linked to the conserved aptamer domain.
This leads to variations in riboswitch mechanism
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3
4
2
1
U
U
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U
U
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Riboswitch Mechanisms
This movie showed the most common case for
bacterial riboswitches
Ligand binding leads to transcription termination
and reduced gene expression.
X
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Riboswitch Mechanisms
Riboswitches also regulate translation and
anti-termination
Ligand binding leads to transcription termination
and reduced gene expression.
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X
U
U
U
U
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ORF
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Ligand binding sequesters the Shine-Dalgarno
sequence and reduces gene expression.
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AGGAGG
Ligand binding leads to antiterminator formation
and increased gene expression.
X
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Riboswitch Mechanisms
They also affect RNA integrity, and perhaps
splicing and stability.
Ligand binding leads to mRNA cleavage by a new
natural ribozyme.
X
Ligand binding could control splicing in
eukayotes.
Possibly, ligand binding to the 3 untranslated
region could affect mRNA stability.
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Riboswitch Ligands
There are 8 confirmed riboswitches with unique
metabolite ligands.
Many more conserved RNA motifs are currently
under investigation.
Figure shows the chemical structures of
riboswitch ligands and schematics of conserved
secondary structure in riboswitches.
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Riboswitch Gene Regulation
Riboswitches are an important mechanism of gene
regulation. For example, nearly 2 of the genes
of the model organism Bacillus subtilis appear to
be controlled by riboswitches.
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Metabolite Recognition
Riboswitches are an economical way to see small
molecules
Average metabolite
Coenzyme B12
tRNA
Riboswitch
Relative sizes of some molecules recognized for
gene regulation (metabolites and tRNAs) and some
agents that recognize them (riboswitches and
TRAP complex).
11-mer TRAP complex
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The End
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Special thanks to
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Riboswitch team
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For more information
http//www.yale.edu/breaker
For citations and additional information