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Регуляторные структуры РНК

Регуляторные структуры РНК. RNA genes: sRNAs : CsrB/RsmB , CsrC, DsrA, GadY, MicC, OxyS, RyhB, RydC, etc Antisense RNAs : CopA, DicF, MicF, RNAI, QaRNA etc Cys UTR regulatory RNAs : riboswitches, T-boxes, attenuators, IREs, etc. sRNAs. DsrA RNA . Regulation of rpoS :

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Регуляторные структуры РНК

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  1. Регуляторные структурыРНК

  2. RNA genes: • sRNAs: CsrB/RsmB, CsrC, DsrA, GadY, MicC, OxyS, RyhB, RydC, etc • Antisense RNAs: CopA, DicF, MicF, RNAI, QaRNA etc • Cys UTR regulatory RNAs: riboswitches, T-boxes, attenuators, IREs, etc.

  3. sRNAs DsrA RNA • Regulation of rpoS: • Overcoming transcriptional silencing • Promoting translation E. coli, salmonella spp., Shigella spp

  4. sRNAs CsrB/RsmB RNA family RNA binds to approximately 18 copies of the CsrA protein negative effect: glycogen biosynthesis, glyconeogenesis, glycogen catabolism positive effect: glycolysis conserved motif CAGGXX enterobacteria

  5. sRNAs PrrB/RsmZ RNA family Pseudomonas spp. 5'-AGGA-3' repeats in loops RNA possibly interacts with a CsrA-like protein Involvement in regulation of 2, 4-diacetylphloroglucinol (Phl) and hydrogen cyanide (HCN) production

  6. sRNAs RydC RNA GadY GadY interacts with the 3' UTR of mRNA gadX: increased stability to the transcript RydC is known to bind the protein Hfq The Hfq/RydC complexcauses degradation of the target nRNA E. coli, salmonella spp., Shigella spp. E. coli, salmonella spp.

  7. Antisense RNAs CopA-like RNA MicF RNA RNAs regulate plasmid copy number regulates ompF expression by inhibiting translation and inducing degradation four-way inhibition junction structurecopA-mRNA copT

  8. UTR RNA regulatory elements Mediators of regulation: Ribosomes (Transcription attenuation ) Repressor/Activator proteins (feedback inhibition of gene translation/splicing, antitermination (bgl), IREs (regulation of translation/mRNA stability), etc) Uncharged tRNA (T-boxes) Small molecules (various riboswitch regulatory elements)

  9. Alternative RNA structures in transcription termination Antitermination Termination (anti-antitermination)

  10. Attenuation of transcription (Yanovsky).

  11. Prediction of attenuators: Amino acid biosynthesis (branched amino acids (ILE, LEU, VAL), histidine, threonine, tryptophan, and phenylalanine) (gamma- and alpha-proteobacteria, in some cases low-GC Gram-positive bacteria, Thermotogales and Bacteroidetes/Chlorobi) • Three new histidine transporters were predicted: • ortholog of BS- yuiF and yvsH • from lysQ/lysP family • HI0325(Haemophylus influenzae)

  12. E. coli: three aspartate kinase isozymes, ThrA, MetL and LysC thrA: ILE-THR attenuator metL: MetJ lysC: LYS-element Pasteurellales (two aspartate kinase isozymes): thrA THR-MET-ILE attenuator LysC: LYS-element

  13. Detection of 5’ UTR RNA-elements • TheRNApattern program: • RNA pattern: • consensus motifs • RNA secondary structure: • number of helices • length of each helix • loop lengths • parameters of topology and distance between pairs of helices

  14. Partial alignment of predicted T-boxes Aminoacyl-tRNA synthetases Amino acid biosynthetic genes Amino acid transporters

  15. … continued Aminoacyl-tRNA synthetases Amino acid biosynthetic genes Amino acid transporters

  16. New predicted amino acid transporters

  17. Conserved RNA secondary structure of the regulatory RFN element Capitals: invariant (absolutely conserved) positions. Lower case letters: strongly conserved positions. Dashes and stars: obligatory and facultative base pairs Degenerate positions: R = A or G; Y = C or U; K = G or U; B= not A; V = not U. N: any nucleotide. X: any nucleotide or deletion

  18. 5’ UTR regionsof riboflavin genes from various bacteria

  19. Distribution of RFN-elements in bacterial genomes RFN regulates riboflavin biosynthetic genes and transporters Some predicted transporters are NEW

  20. Alternative RNA secondary structures upstream of riboflavin operons with RFN elementsAttenuation of transcription via antitermination mechanism Antiterminator Terminator +RBS sequestor The RFN element Antiterminator

  21. Alternative RNA secondary structures upstream of riboflavin genes with RFN elements Attenuation of translation by sequestering of the RBS Antisequestor RBS-sequestor The RFN element Direct RBS sequestering

  22. The predicted mechanism of the RFN-mediated regulation of riboflavin genes and operons • Transcription attenuation • Translation attenuation

  23. Phylogenetic tree of RFN-elements

  24. новыепотенциальные транспортеры флавинов: 1. ImpXнайден в Fusobacterium nucleatumиDesulfitobacterium halfniense: Имеет 9 предполагаемыхтрансмембранных сегментов; не имеет гомологии с какими-либо известными генами. 2. PnuXнайден в актинобактериях: Имеет6предполагаемыхтрансмембранных сегментов; гомологичен PnuC (транспортер N-рибозил никотинамида)

  25. Known Thi-box signal in diverse bacterial genomes (Miranda-Rios et.al., 1997)

  26. Predicted regulatory THI-elements in bacterial genomes

  27. Conserved RNA secondary structure of the regulatory THI element Capitals: strongly conserved positions. Dashes and points: obligatory and facultative base pairs Degenerate positions: R = A or G; Y = C or U; K = G or U; M= A or C; N = any nucleotide

  28. Distribution of THI elements in bacterial genomes THI-elementregulates thiamine biosynthetic genes and transporters. A number of NEW candidate thiamine-related transporters were identified.

  29. The predicted mechanism of the THI-mediated regulation of thiamin genes • Transcription attenuation • Bacillus/Clostridium group, • Thermotoga, • Fusobacterium, • Chloroflexus • Translation attenuation • Thermus/Deinococcus group, • CFB group • Proteobacteria, • Actinobacteria, • Cyanobacteria, • Archaea • Direct RBS sequestering

  30. New functional predictions Транспорт гидроксиэтил- тиазола (грамположительные бактерии) Транспорт гидроксиметилпиримидина (грамотрицательные бактерии)

  31. Predicted THI-regulated genes (more enzymes) • tenA: gene of unknown function somehow associated with thiD • Found in most firmicutes, some proteobacteria and archaea; • ThiD-TenA gene fusions in some eukaryotes; • Formsclusters with thiDand other THI-elements-regulated genes in most bacteria; • Single tenA gene is also regulated by THI-elements in some bacteria; • Not found in genomes without the thiamin pathway; • Always co-occurs with the thiDandthiEgenes • tenI: gene of unknown function, thiE paralog • Found in some unrelated bacteria; • Forms a separate branch in the phylogenetic tree for thiE; • In most bacteria, located in clusters of THI-elements-regulated genes. • ylmBfrom Bacillibelongs to ArgE/dapE/ACY1/CPG2/yscS family of metallopeptidases; • regulated by the THI-elements in B. subtilis and B. halodurans, not regulated in B. cereus. • thi-4 from Thermotoga maritimabelongs to a family of putative thiamine biosynthetic enzymes from archaea and eukaryotes. Located in the one operon with thiC and thiD. • oarX from Methylobacillus and Staphylococcusis a single THI-elements-regulated gene; belongs to short-chain dehydrogenase/reductase (SDR) superfamily

  32. Regulation of cobalamin-related genes: Experimentally known facts: Extensive region of the mRNA leader is essential for regulation of the btuB gene by vitamin B12. Involvement of highly conserved B12-box rAGYCMGgAgaCCkGCcd in regulation of the cobalamin biosynthetic genes (E. coli, S. typhimurium). Post-transcriptional regulation: RBS-sequestering hairpin is essential for regulation of the btuB and cbiA genes. Ado-CBL is an effector molecule involved in the regulation of the CBL genes. Identifying of other conserved sequenced regions and prediction of common RNA secondary structure of the B12-element.

  33. B12-элемент – регулятор кобаламинового пути

  34. Allignment of B12-elements alpha and beta proteobacteria

  35. Allignment of B12-elements (continued) Gamma-proteobacteria, the Bacillus/Clostridium group

  36. Allignment of B12-elements (continued) (Actinobacteria, Cyanobacteria, The CFB group, Thermotogales, The Thermus/Dienoccoccus group and some others) B2

  37. B12-regulon: identification of genes and regulatory elements

  38. B12-regulon: identification of genes and regulatory elements

  39. Distribution of B12-elements in bacterial genomes B12-elementregulates cobalamin biosynthetic genes and transporters, cobalt transporters and a number of other cobalamin related genes.

  40. Phylogenetic tree of B12-elements Without B2 domain (in gray squares)

  41. The predicted mechanism of the B12-mediated regulation of cobalamin genes

  42. Phylogenetic distribution of gene clusters regulated by B12-elements

  43. B12-dependent and B12-independent izozymes B12-independent izozymes of methionine synthase and ribonucleotide reductase are regulated by the B12-elements in the genomes possessing both izozymes (it was not known formerly)

  44. Conserved S-box structure

  45. Distriubtion of MET regulatory elements

  46. Phylogenetic tree of the NhaC Na+:H+ antiporter superfamily including predicted methionine-, lysine- and tyrosine-specific transporters

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