A Presentation by

N.Yaseswini
07311A2323
CONTENTS:
Introduction
Structure and Function
Mechanism of action
Prokaryotes
Eukaryotes

Applications
Conclusion
 Introduction

A riboswitch is a part of an mRNA molecule

that can directly bind a small target
molecule, and whose binding of the target
affects the gene's activity. 
 Introduction…..
• The structure of riboswitches were
elucidated in the 1990's.

• Experimental evidence : Published in

2002 by
Ronald Breaker (Yale University and
given credit for coining the term) and
Evgeny Nudler (New York University).
• Most known riboswitches
occur in  bacteria.

• Functional riboswitches
of one type (the TPP
riboswitch) have been
discovered in plants and
certain fungi. 

• In 2009, the first human

riboswitch was
discovered. 3-D STRUCTURE OF
LYSINE RIBOSWITCH
Riboswitches…..

• Represent one of the oldest regulatory

systems.

• Non-coding regions of mRNA.

• Directly bind to ligands.

• Fold into compact structure.

• Regulate metabolic pathways.

• Sequence conservation - not

confined to paired regions but also
found in single strands.

• First studied riboswitch in vitamins.

 STRUCTURE
• Present in 5’ leader region of mRNA
• Two structural components:

1. Aptamer

Binds the small molecules-ligands

2. Expression platform

Undergoes structural change in response to

the changes in aptamer.
 Functions
• The function of riboswitches is to
regulate the gene activity.

• Regulation occurs at different levels:

1. Transcription
2. Processing
3. Translation
Regulation is caused due
to the formation of
alternative RNA
structures…
 Mechanism

• Prokaryotes :

Regulation of gene activity at different stages…

1. Premature termination of transcription

2. Translational initiation inhibition.
3. Auto-cleavage
Three known
mechanisms of
riboswitch action
upon binding of
metabolite (M): a)
Transcription
termination.
b) Inhibition of
translation
initiation.
c)Auto-cleavage.
 Example 1:
Thiamine pyrophosphate sensing riboswitches(TPP)

• Thiamine –precursor for TPP.

• Regulation studied in E.coli, R.etli, B.subtilis.
• In most cases, negatively controlled by
thiamine and TPP.
• Thi operon posses untranslated leader sequence
–thi box
• Repression by thiamine was observed to be a
post translational event.
• No repression factor was identified.
• Hence it was assumed that thiamine
directly binds to the mRNA

• It inhibits the translational initiation

Figure :
Translational
regulation by
riboswitch
Eg: TPP riboswitch
 Example 2:
Riboswitch acting as a Ribozyme
• Studied in B.subtilis.
• glms gene
• Codes for the enzyme glutaminefructose-6-
phosphate amidotransferase.
• Enzyme-induces conformational change in the
leader sequence and activates ribozyme
• Cleavage of the leader region occurs 245
nucleotides upstream of the AUG codon.
• Leads to reduced expression.
• Cleavage enhanced by 1000 fold in the presence of
GlcN6P.
The B. subtilis glmS riboswitch is conserved upstream of the glmS gene [11!!]. During
conditions of excess GlcN6P, the glmS 50-UTR is stimulated to self-cleave at a
specific site at its 50-end (indicated by the black arrow). Cleavage leads toglmS
repression through an unknown mechanism.
• Eukaryotes :

Regulation of gene activity at different stages….

1. RNA processing
2. RNA transport
3. Expression pathway
 Example
Regulation in N.crassa
• nmt-1 pre-mRNA regulation.
• In the absence of thiamine, nmt-1 pre-mRNA
is spliced into a small mature mRNA
• In the presence of thiamine, nmt-1 pre-mRNA
is spliced into a large transcript.
• Large transcript-shift in 5’ splice site.
• Stops the translation of the mRNA.
 Human
riboswitch…!!!
 Applications…

• Used in development of antimicrobials.

Eg: Pyrithiamine

• Synthetic aptamers – as molecular sensors

• Glycine riboswitch from B.subtilis was used for

glycine inducible production of beta galactosidase.
•Application in taxonomy

• Can be used in bioremediation

- chemotaxsis signaling protein (cheZ) under the control of
a theophylline sensitive riboswitch.
- cells localize to regions of high theophylline concentration
which is not observed naturally.
 Conclusion
Just as natural riboswitches can regulate gene expression
in response to small-molecule ligands during transcription
or translation, synthetic riboswitches can be engineered to
repress or activate gene expression in a ligand-dependent
fashion.

This feature should enable RNA switches to play an

increasingly important role as chemical biologists seek to
modulate many types of cellular behavior in response to a
broad range of chemical signals.

In the years to come, riboswitches will become a standard

tool for the chemical biologist.
REFERENCES…….
www.castu.tsinghua.edu.cn
www.microbemagazine.org
www.courses.biology.utah.edu
(Bacterial gene regulation: from transcription attenuation to riboswitch and ribozymes,
Sabine Brantl AG Bakteriengenetik, Friedrich-Schiller-Universita¨Jena, Hans-Kno¨ ll-Str. 2, D-
07745 Jena, Germany)

www.microbio.edu
www.nature.com
www.fungalgenome.org
www.wikipedia.org
www.pubs.acs.org
www.ctbp.ucsd.edu
www.scq.ubc.ca
www.scienceblogs.com
Riboswitches and the role of noncoding RNAs in bacterial metabolic control
(Wade C Winkler)
The riboswitch control of bacterial metabolism
(Evgeny Nudler1 and Alexander S)