Predicted secondary structure and sequence conservation of TPP
Identifiers
Symbol
TPP
Alt. Symbols
THI
Rfam
RF00059
Other data
RNA type
Cis-reg; riboswitch
Domain(s)
Eukaryota; Bacteria; Archaea
GO
GO:0030976
SO
SO:0000035
PDB structures
PDBe 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]
^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.
^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.
^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.
^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.
^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.
^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.
^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.
^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.
functional riboswitches of one type (the TPPriboswitch) have been discovered in archaea, plants and certain fungi. TPP riboswitches have also been predicted...
The TPPriboswitch, also known as the THI element and Thi-box riboswitch, is a highly conserved RNA secondary structure. It serves as a riboswitch that...
the biosynthesis are produced. The specific riboswitch, the TPPriboswitch, is the only known riboswitch found in both eukaryotic and prokaryotic organisms...
question in elucidating the cofactor thiamine pyrophosphate (TPP) riboswitch. The TPPriboswitch structure showed the assistance of two hydrated Mg2+ ions...
deprotonated at C2 to become an ylid. A full view of TPP. The arrow indicates the acidic proton. TPPriboswitch Pietrzak I (1995). "[Vitamin disturbances in chronic...
Cobalamin riboswitch is a cis-regulatory element which is widely distributed in 5' untranslated regions of vitamin B12 (Cobalamin) related genes in bacteria...
riboswitches and TPP riboswitches where they allow the cell to turn genes off or on within a smaller change of concentration of the riboswitch ligand. In other...