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Riboswitches - a gene regulator by Chirag Dhobi

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Slide 1 : RIBOSWITCHES CHIRAGKUMAR D . DHOBI SEM- 1 (408) SHRI A.N.PATEL P.G.INSTITUTE ANAND
Slide 2 : 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
Slide 3 : 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 +
Slide 4 : RNAs have many functions
Slide 5 : 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
Slide 6 : 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
Slide 7 : 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
Slide 8 : Regulation of TRANScription
Slide 9 : Regulation of TRANSLATION
Slide 10 : 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.
Slide 11 : RIBOSWITCHES ARE FOUND IN BACTERIA, FUNGI, ALGAE, PLANTS
Slide 12 : Gallery of Riboswitches
Slide 13 : 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
Slide 14 : 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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