TPP riboswitch explained

TPP riboswitch (THI element)
Symbol:	TPP
Altsymbols:	THI
Rfam:	RF00059
Rna Type:	Cis-reg riboswitch
Tax Domain:	Eukaryota Bacteria; Archaea
Pdb:	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]

See also

• Tetrahydrofolate riboswitch
• FMN riboswitch

External links

• • PDB entry for the TPP riboswitch tertiary structure

Notes and References

1. Winkler W, Nahvi A, Breaker RR . Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression . Nature . 419 . 6910 . 952–956 . October 2002 . 12410317 . 10.1038/nature01145 . 2002Natur.419..952W . 4408592 .
2. Mironov AS, Gusarov I, Rafikov R, Lopez LE, Shatalin K, Kreneva RA, Perumov DA, Nudler E . Sensing small molecules by nascent RNA: a mechanism to control transcription in bacteria . Cell . 111 . 5 . 747–756 . November 2002 . 12464185 . 10.1016/S0092-8674(02)01134-0 . free .
3. Sudarsan N, Barrick JE, Breaker RR . Metabolite-binding RNA domains are present in the genes of eukaryotes . RNA . 9 . 6 . 644–647 . June 2003 . 12756322 . 1370431 . 10.1261/rna.5090103 .
4. Bocobza S, Adato A, Mandel T, Shapira M, Nudler E, Aharoni A . Riboswitch-dependent gene regulation and its evolution in the plant kingdom . Genes & Development . 21 . 22 . 2874–2879 . November 2007 . 18006684 . 2049190 . 10.1101/gad.443907 .
5. Kubodera T, Watanabe M, Yoshiuchi K, Yamashita N, Nishimura A, Nakai S, Gomi K, Hanamoto H . 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 . December 2003 . 14675766 . 10.1016/S0014-5793(03)01335-8 . free . 2003FEBSL.555..516K .
6. Rodionov DA, Vitreschak AG, Mironov AA, Gelfand MS . Comparative genomics of thiamin biosynthesis in procaryotes. New genes and regulatory mechanisms . The Journal of Biological Chemistry . 277 . 50 . 48949–48959 . December 2002 . 12376536 . 10.1074/jbc.M208965200 . free .
7. Miranda-Ríos J, Navarro M, Soberón M . 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 . August 2001 . 11470904 . 55522 . 10.1073/pnas.161168098 . free .
8. Serganov A, Polonskaia A, Phan AT, Breaker RR, Patel DJ . Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch . Nature . 441 . 7097 . 1167–1171 . June 2006 . 16728979 . 4689313 . 10.1038/nature04740 . 2006Natur.441.1167S .