TPP riboswitch

{{Short description|RNA secondary structure}}

{{Infobox rfam

| Name = TPP riboswitch (THI element)

| image = RF00059-rscape.svg

| width =

| caption = Predicted secondary structure and sequence conservation of TPP

| Symbol = TPP

| AltSymbols = THI

| Rfam = RF00059

| miRBase =

| miRBase_family =

| RNA_type = Cis-reg; riboswitch

| Tax_domain = Eukaryota; Bacteria; Archaea

| GO = {{GO|0030976}}

| SO = {{SO|0000035}}

| CAS_number =

| EntrezGene =

| HGNCid =

| OMIM =

| PDB = 4nyc

| RefSeq =

| Chromosome =

| Arm =

| Band =

| LocusSupplementaryData =

}}

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{{cite journal | vauthors = Winkler W, Nahvi A, Breaker RR | title = Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression | journal = Nature | volume = 419 | issue = 6910 | pages = 952–956 | date = October 2002 | pmid = 12410317 | doi = 10.1038/nature01145 | bibcode = 2002Natur.419..952W | s2cid = 4408592 }}{{cite journal | vauthors = Mironov AS, Gusarov I, Rafikov R, Lopez LE, Shatalin K, Kreneva RA, Perumov DA, Nudler E | title = Sensing small molecules by nascent RNA: a mechanism to control transcription in bacteria | journal = Cell | volume = 111 | issue = 5 | pages = 747–756 | date = November 2002 | pmid = 12464185 | doi = 10.1016/S0092-8674(02)01134-0 | doi-access = free }} that binds thiamine pyrophosphate (TPP) directly and modulates gene expression through a variety of mechanisms in archaea, bacteria and eukaryotes.{{cite journal | vauthors = Sudarsan N, Barrick JE, Breaker RR | title = Metabolite-binding RNA domains are present in the genes of eukaryotes | journal = RNA | volume = 9 | issue = 6 | pages = 644–647 | date = June 2003 | pmid = 12756322 | pmc = 1370431 | doi = 10.1261/rna.5090103 }}{{cite journal | vauthors = Bocobza S, Adato A, Mandel T, Shapira M, Nudler E, Aharoni A | title = Riboswitch-dependent gene regulation and its evolution in the plant kingdom | journal = Genes & Development | volume = 21 | issue = 22 | pages = 2874–2879 | date = November 2007 | pmid = 18006684 | pmc = 2049190 | doi = 10.1101/gad.443907 }}{{cite journal | vauthors = Kubodera T, Watanabe M, Yoshiuchi K, Yamashita N, Nishimura A, Nakai S, Gomi K, Hanamoto H | title = Thiamine-regulated gene expression of Aspergillus oryzae thiA requires splicing of the intron containing a riboswitch-like domain in the 5'-UTR | journal = FEBS Letters | volume = 555 | issue = 3 | pages = 516–520 | date = December 2003 | pmid = 14675766 | doi = 10.1016/S0014-5793(03)01335-8 | doi-access = free | bibcode = 2003FEBSL.555..516K }} 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 {{cite journal | vauthors = Rodionov DA, Vitreschak AG, Mironov AA, Gelfand MS | title = Comparative genomics of thiamin biosynthesis in procaryotes. New genes and regulatory mechanisms | journal = The Journal of Biological Chemistry | volume = 277 | issue = 50 | pages = 48949–48959 | date = December 2002 | pmid = 12376536 | doi = 10.1074/jbc.M208965200 | doi-access = free }} Analysis of operon structures has identified a large number of new candidate thiamin-regulated genes, mostly transporters, in various prokaryotic organisms.{{cite journal | vauthors = Miranda-Ríos J, Navarro M, Soberón M | title = A conserved RNA structure (thi box) is involved in regulation of thiamin biosynthetic gene expression in bacteria | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 98 | issue = 17 | pages = 9736–9741 | date = August 2001 | pmid = 11470904 | pmc = 55522 | doi = 10.1073/pnas.161168098 | doi-access = free }} The x-ray crystal structure of the TPP riboswitch aptamer has been solved.{{cite journal | vauthors = Serganov A, Polonskaia A, Phan AT, Breaker RR, Patel DJ | title = Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch | journal = Nature | volume = 441 | issue = 7097 | pages = 1167–1171 | date = June 2006 | pmid = 16728979 | pmc = 4689313 | doi = 10.1038/nature04740 | bibcode = 2006Natur.441.1167S }}

File:TPP_riboswitch_pdb-2hoj.png | Experimental 3D structure of the TPP riboswitch ({{PDB|2HOJ}}).{{cite journal | vauthors = Edwards TE, Ferré-D'Amaré AR | title = Crystal structures of the thi-box riboswitch bound to thiamine pyrophosphate analogs reveal adaptive RNA-small molecule recognition | journal = Structure | volume = 14 | issue = 9 | pages = 1459–1468 | date = September 2006 | pmid = 16962976 | doi = 10.1016/j.str.2006.07.008 }}