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RNA processing

RNA processing. Proks vs. Euks In proks, transcription & translation coupled In euks, processes are temporally& spatially separated so more control. RNA processing. mRNA processing in eukaryotes: 5’-capping 3’-endonuclease cleavage and polyadenylation RNA splicing & editing.

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RNA processing

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  1. RNA processing Proks vs. Euks In proks, transcription & translation coupled In euks, processes are temporally& spatially separated so more control

  2. RNA processing mRNA processing in eukaryotes: 5’-capping 3’-endonuclease cleavage and polyadenylation RNA splicing & editing

  3. RNA processing mRNA processing: 5’-capping

  4. RNA processing mRNA processing: 3’-endonuclease cleavage & polyadenylation

  5. RNA processing mRNA processing: RNA splicing & editing

  6. RNA processing mRNA processing: RNA splicing & editing Mainly in eukaryotic organisms, highly conserved from yeast to human Spliceosome is an RNA-protein complex; RNA proposed to be catalytic

  7. RNA processing Alternative splicing

  8. RNA processing Alternative splicing

  9. RNA ProcessingNaturally occurring catalystsCatalytic RNA = Ribozyme • RNA cleavage glmS ribozyme - also a RIBOSWITCH!! (crystal structure)hammerhead ribozyme (crystal structure)hairpin ribozyme (crystal structure)Varkud satellite (VS) ribozyme (partial NMR structure)hepatitis delta virus (HDV) ribozyme (crystal structure)M1 RNA (RNase P) (partial crystal structure) • RNA splicing group I introns (crystal structure)group II introns (partial crystal structure)*** U2-U6 snRNA (spliceosome) (partial NMR structure) *** • Peptide bond formation ribosome (crystal structure)

  10. RNA processing RNA catalyzed splicing (ribozymes) Group I intron – found in fungi, algae, plants, bacteria Group I introns found in nuclear, mitochondrial and chloroplast genes of rRNAs, tRNAs and mRNAs

  11. Group I Intron crystal structure

  12. RNA processing RNA catalyzed self-cleavage (ribozymes) Hammerhead ribozyme (found in a virusoids, part of small RNA genome)

  13. RNA processing Riboswitches Tom Cech, Nature (2004) 428: 263-264.

  14. Riboswitches contain an aptamer (RNA binding) domain & expression platform

  15. Riboswitches J.K. Soukup and G.A. Soukup, Curr. Opin. Struct. Biol. (2004) 14: 344-349. Newly discovered riboswitches glycine, pre-Queuosine, 2’-deoxyguanosine, cyclic dimeric GMP

  16. Riboswitch mechanisms • Transcription termination and anti-termination • Translation initiation: RBS accessibility • RNA processing: Splicing or degradation Winkler & Breaker (2005) Annu Rev Microbiol59: 487-517

  17. TPP Riboswitch • Recognizes ligand phosphate through metal ion-mediated backbone and nucleobase contacts • Riboswitch regulation of gene expression is perturbed by the antibiotic PTPP • Riboswitch agonists or antagonists: novel antibiotics? Sudarsan et al. (2005) Chem Biol12:1325-1335; Serganov et al. (2006) Nature441:1167-1171; Thore et al. (2006) Science312:1208-1211

  18. Barrick & Breaker (2006) Scientific American296: 50-57

  19. Glucosamine 6-phosphate riboswitch Klein and Ferré-D'Amaré (2006) Science 313:1752-1756. Jansen, McCarthy, Soukup & Soukup (2006) Nat Struct Mol Biol 13:517-523.

  20. A conserved RNA structure precedes the glmS gene in Gram-positive organisms Kobayashi et al.,Proc. Natl. Acad. Sci. USA (2003) 10: 4678-4683.

  21. RNA Interference (RNAi) • RNAi is the process whereby double-stranded RNA (dsRNA) induces homology-dependent degradation of cognate RNA (i.e. gene silencing) • RNAi is highly conserved among eukaryotes (fungi, protozoans, plants, nematodes, invertebrates, mammals) Biological significance of RNAi Cellular immune response to viruses In certain organism (especially plants), RNAi serves as a first line of defense against viral infection, as viral replication typically includes dsRNA species Genetic stability RNAi repress the mobility of transposable genetic elements in C. elegans and S. pombe which requires the formation of dsRNA Organismal development and germline fate Developmental processes are affected by endogenous non-coding RNAs that function through the RNAi pathway (microRNAs)

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