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RIBOSWITCHES CHIRAGKUMAR D . DHOBI
SEM- 1 (408)
SHRI A.N.PATEL P.G.INSTITUTE
ANAND |
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CONTENTS Different functions of Rna
History of Riboswitches
RIBOSWITCHES :- definition & explanation
STRUCTURE OF RIBOSWITCHES
CHARACTERISTICS OF RIBOSWITCHES
SIMPLE MECHANISM OF REGULATION
AN EXAMPLE OF REGULATION BY RIBOSWITCHES IN E.COLI
OCCURANCE OF RIBOSWITCHES
GALLERY OF RIBOSWITCHES
RECENT DEVELOPMENT IN THE FIELD OF RIBOSWITCHES |
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RIBOSWITCHES More specifically:
“Riboswitches are regulatory RNA element that act as direct sensor of small molecule metabolites/Ions to control gene transcription or translation”
RIBOSE SWITCH RNA ELEMENT
Act as a direct sensor of small molecule metabolite A program (device) which active or
de-active function + |
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RNAs have many functions |
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The name Riboswitch was given by Dr. Ronald Breaker in 2002
Dr. Tina Hankins
First one who observed this special gene control system.
She found that there was a conserved sequence in the 5’ leader region of S-box gene family which involved in the biosynthesis of methionine and cysteine. This conserved sequence can form a secondary structure or possibly tertiary structure SCIENCE TIMES FROM : http://www.nature.com/scitable/topicpage/riboswitches - Since 2002 Dr. Ronald Breaker “Ancient RNA Relics and Modern Drug Discovery” DR. Tina M. Henkin discuss
"Sensing of Metabolic Signals by Nascent RNA Transcripts Until 2002,
Dr. Ronald Breaker
first demonstrated
that mRNAs can bind
metabolites directly in the absence of proteins &
he also developed a useful method, to detect the conformational change of mRNA. History of riboswitches |
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Riboswitches are divided into two parts (1) AN APTAMER
It is sensing region of riboswitch
Directly binds the small molecule,
(2) AN EXPRESSION PLATFORM
It undergoes structural changes in response to the changes
in the aptamer.
The expression platform is what regulates gene expression.
Expression platforms typically turn off gene expression in response to the small molecule, but some turn it on.
STRUCTURE OF RIBOSWITCHES |
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RIBOSWITCHES ARE THE NON-CODING PORTIONS OF MRNAS FOUND WITHIN 5’UTRs
THAT CAN FOLD COMPLEX STRUCTURE AND SERVE AS RECEPTORS OF SPECIFIC METABOLITES/IONS.
WHEN THEY BIND TO THEIR SPECIFIC METABOLITE, THEIR THREE-DIMENSIONAL STRUCTURES WILL CHANGE ALLOSTERICALLY AND THEREFORE REGULATE THE PROCESS OF TRANSCRIPTION AND OR TRANSLATION.
CHARACTERISTICS PURPOSE:-
Transcriptional
termination
Translation repression/initiation
mRNA stability
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Regulation of TRANScription |
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Regulation of TRANSLATION |
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REGULATION BY RIBOSWITCHES EXAMPLE Riboswitch controlled gene expression.
In E. coli TPP (thiamine pyrophosphate) Riboswitches suppress the translation of TPP biosynthetic and transport genes in response to TPP binding. |
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RIBOSWITCHES ARE FOUND IN BACTERIA, FUNGI, ALGAE, PLANTS |
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Gallery of Riboswitches |
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Recent development in riboswitches research Challenges of ligand identification for riboswitch candidates RNA Biology 8, 1: [Article link} http://www.landesbioscience.com/journals/rnabiology/article/13865/
A eubacterial riboswitch class that senses the coenzyme tetrahydrofolate. Chem Biol. 17(7): 681-5 [Article link] http://www.ncbi.nlm.nih.gov/pubmed/20659680
Evidence for Widespread Gene Control Function by the ydaO Riboswitch Candidate J. Bacteriol. [Article link] http://breaker.sites.yale.edu/Publications?date_filter[min][year]=2008&date_filter[max][year]=2011.
RNA switches out in the cold Mol Cell. 37(1): 1-2 [Article link] http://jb.asm.org/cgi/content/abstract/JB.00450-10v1
Engineering ligand-responsive gene-control elements: lessons learned from natural riboswitches. Gene Ther 16(10): 1189-201 [Article link] http://www.ncbi.nlm.nih.gov/pubmed/19587710
Design and Antimicrobial Action of Purine Analogs that Bind Guanine Riboswitches. ACS Chem Biol. 4(11): 915-27 [Article link]
http://www.ncbi.nlm.nih.gov/pubmed/19739679
Roseoflavin is a natural antibacterial compound that binds to FMN riboswitches and regulates gene expression. RNA Biol. 6(2): 187-94 [Article link]
http://www.ncbi.nlm.nih.gov/pubmed/19246992
Unique glycine-activated riboswitch linked to glycine-serine auxotrophy in SAR11. Environ Microbiol. 11(1): 230-8 [Article link]
http://www.ncbi.nlm.nih.gov/pubmed/19125817
Boese BJ, Corbino K, Breaker RR. (2008 Aug) In vitro selection and characterization of cellulose-binding RNA aptamers using isothermal amplification. Nucleosides Nucleotides Nucleic Acids. 27(8): 949-66 [Article link]
http://www.ncbi.nlm.nih.gov/pubmed/18696364
Weinberg Z, Regulski EE, Hammond MC, Barrick JE, Yao Z, Ruzzo WL, Breaker RR. (2008 May) The aptamer core of SAM-IV riboswitches mimics the ligand-binding site of SAM-I riboswitches. RNA 14(5): 822-8 [Article link] http://www.ncbi.nlm.nih.gov/pubmed/18369181?ordinalpos=2&itool=Entrez
Purine sensing by riboswitches. Biol Cell. 100(1): 1-11 [Article link} http://www.ncbi.nlm.nih.gov/pubmed/18072940
In-line probing analysis of riboswitches. Methods Mol Biol. 419: 53-67 [Article link] http://www.ncbi.nlm.nih.gov/pubmed/18369975 |
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REFERENCES
MOLECULAR BIOLOGY OF THE GENE (5TH Ed. 509-511)
[ james D. watson, Tania A.Baker, Stephen P. Bell, Alexander Gann ]
http://www.nature.com/scitable/topicpage/riboswitches-a-common-rna
http://en.wikipedia.org/wiki/Riboswitch
http://www.ias.ac.in/currsci/nov102004/1168.pdf
http://www.jbpub.com/genetics/essentials4e/flashcards.cfm
http://pubs.acs.org/doi/abs/10.1021/cb9003139 |
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