TPP riboswitch

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TPP riboswitch (THI element)
Predicted secondary structure and sequence conservation of TPP
Identifiers
SymbolTPP
Alt. SymbolsTHI
RfamRF00059
Other data
RNA typeCis-reg; riboswitch
Domain(s)Eukaryota; Bacteria; Archaea
GOGO:0030976
SOSO:0000035
PDB structuresPDBe 4nyc

The TPP riboswitch, also known as the THI element and Thi-box riboswitch, is a highly conserved RNA secondary structure. It serves as a riboswitch[1][2] that binds thiamine pyrophosphate (TPP) directly and modulates gene expression through a variety of mechanisms in archaea, bacteria and eukaryotes.[3][4][5] TPP is the active form of thiamine (vitamin B1), an essential coenzyme synthesised by coupling of pyrimidine and thiazole moieties in bacteria. The THI element is an extension of a previously detected thiamin-regulatory element, the thi box, there is considerable variability in the predicted length and structures of the additional and facultative stem-loops represented in dark blue in the secondary structure diagram [6] Analysis of operon structures has identified a large number of new candidate thiamin-regulated genes, mostly transporters, in various prokaryotic organisms.[7] The x-ray crystal structure of the TPP riboswitch aptamer has been solved.[8]

  • Experimental 3D structure of the TPP riboswitch (PDB: 2HOJ​).[9]
    Experimental 3D structure of the TPP riboswitch (PDB: 2HOJ​).[9]

References

  1. ^ Winkler W, Nahvi A, Breaker RR (October 2002). "Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression". Nature. 419 (6910): 952–956. doi:10.1038/nature01145. PMID 12410317. S2CID 4408592.
  2. ^ Mironov AS, Gusarov I, Rafikov R, Lopez LE, Shatalin K, Kreneva RA, Perumov DA, Nudler E (November 2002). "Sensing small molecules by nascent RNA: a mechanism to control transcription in bacteria". Cell. 111 (5): 747–756. doi:10.1016/S0092-8674(02)01134-0. PMID 12464185.
  3. ^ Sudarsan N, Barrick JE, Breaker RR (June 2003). "Metabolite-binding RNA domains are present in the genes of eukaryotes". RNA. 9 (6): 644–647. doi:10.1261/rna.5090103. PMC 1370431. PMID 12756322.
  4. ^ Bocobza S, Adato A, Mandel T, Shapira M, Nudler E, Aharoni A (November 2007). "Riboswitch-dependent gene regulation and its evolution in the plant kingdom". Genes & Development. 21 (22): 2874–2879. doi:10.1101/gad.443907. PMC 2049190. PMID 18006684.
  5. ^ Kubodera T, Watanabe M, Yoshiuchi K, Yamashita N, Nishimura A, Nakai S, Gomi K, Hanamoto H (December 2003). "Thiamine-regulated gene expression of Aspergillus oryzae thiA requires splicing of the intron containing a riboswitch-like domain in the 5'-UTR". FEBS Letters. 555 (3): 516–520. doi:10.1016/S0014-5793(03)01335-8. PMID 14675766.
  6. ^ Rodionov DA, Vitreschak AG, Mironov AA, Gelfand MS (December 2002). "Comparative genomics of thiamin biosynthesis in procaryotes. New genes and regulatory mechanisms". The Journal of Biological Chemistry. 277 (50): 48949–48959. doi:10.1074/jbc.M208965200. PMID 12376536.
  7. ^ Miranda-Ríos J, Navarro M, Soberón M (August 2001). "A conserved RNA structure (thi box) is involved in regulation of thiamin biosynthetic gene expression in bacteria". Proceedings of the National Academy of Sciences of the United States of America. 98 (17): 9736–9741. doi:10.1073/pnas.161168098. PMC 55522. PMID 11470904.
  8. ^ Serganov A, Polonskaia A, Phan AT, Breaker RR, Patel DJ (June 2006). "Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch". Nature. 441 (7097): 1167–1171. doi:10.1038/nature04740. PMC 4689313. PMID 16728979.
  9. ^ Edwards TE, Ferré-D'Amaré AR (September 2006). "Crystal structures of the thi-box riboswitch bound to thiamine pyrophosphate analogs reveal adaptive RNA-small molecule recognition". Structure. 14 (9): 1459–1468. doi:10.1016/j.str.2006.07.008. PMID 16962976.

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