754
Views
10
CrossRef citations to date
0
Altmetric
Award Review

Mechanisms of the tRNA wobble cytidine modification essential for AUA codon decoding in prokaryotes

Pages 347-353 | Received 20 Aug 2014, Accepted 01 Oct 2014, Published online: 28 Oct 2014

References

  • Björk GR. Biosynthesis and function of modified nucleosides. In: Söll D, RajBhandary UL, editors. tRNA: structure, biosynthesis, and function. Washington, DC: American Society for Microbiology; 1995. p. 165–205.
  • Yokoyama S, Nishimura S. Modified nucleosides and codon recognition. In: Söll D, RajBhandary UL, editors. tRNA: structure, biosynthesis, and function. Washington DC: American Society for Microbiology; 1995. p. 207–224.
  • Suzuki T. Biosynthesis and function of tRNA wobble modifications. In: Grosjean H, editor. Topics in current genetics: fine-tuning of RNA functions by modification and editing. New York, NY: Springer-Verlag; 2005. p. 23–69.
  • Muramatsu T, Yokoyama S, Horie N, Matsuda A, Ueda T, Yamaizumi Z, Kuchino Y, Nishimura S, Miyazawa T. A novel lysine-substituted nucleoside in the first position of the anticodon of minor isoleucine tRNA from Escherichia coli. J. Biol. Chem. 1988;263:9261–9267.
  • Ikeuchi Y, Kimura S, Numata T, Nakamura D, Yokogawa T, Ogata T, Wada T, Suzuki T, Suzuki T. Agmatine-conjugated cytidine in a tRNA anticodon is essential for AUA decoding in archaea. Nat. Chem. Biol. 2010;6:277–282.10.1038/nchembio.323
  • Mandal D, Kohrer C, Su D, Russell SP, Krivos K, Castleberry CM, Blum P, Limbach PA, Soll D, RajBhandary UL. Agmatidine, a modified cytidine in the anticodon of archaeal tRNAIle, base pairs with adenosine but not with guanosine. Proc. Nat. Acad. Sci. USA. 2010;107:2872–2877.10.1073/pnas.0914869107
  • Muramatsu T, Nishikawa K, Nemoto F, Kuchino Y, Nishimura S, Miyazawa T, Yokoyama S. Codon and amino-acid specificities of a transfer RNA are both converted by a single post-transcriptional modification. Nature. 1988;336:179–181.10.1038/336179a0
  • Köhrer C, Srinivasan G, Mandal D, Mallick B, Ghosh Z, Chakrabarti J, Rajbhandary UL. Identification and characterization of a tRNA decoding the rare AUA codon in Haloarcula marismortui. RNA. 2008;14:117–126.
  • Soma A, Ikeuchi Y, Kanemasa S, Kobayashi K, Ogasawara N, Ote T, Kato J, Watanabe K, Sekine Y, Suzuki T. An RNA-modifying enzyme that governs both the codon and amino acid specificities of isoleucine tRNA. Mol. Cell. 2003;12:689–698.10.1016/S1097-2765(03)00346-0
  • Ikeuchi Y, Soma A, Ote T, Kato J, Sekine Y, Suzuki T. Molecular mechanism of lysidine synthesis that determines tRNA identity and codon recognition. Mol. Cell. 2005;19:235–246.10.1016/j.molcel.2005.06.007
  • Blaby IK, Phillips G, Blaby-Haas CE, Gulig KS, El Yacoubi B, de Crécy-Lagard V. Towards a systems approach in the genetic analysis of archaea: accelerating mutant construction and phenotypic analysis in Haloferax volcanii. Archaea. 2010;2010:426239.
  • Nakanishi K, Fukai S, Ikeuchi Y, Soma A, Sekine Y, Suzuki T, Nureki O. Structural basis for lysidine formation by ATP pyrophosphatase accompanied by a lysine-specific loop and a tRNA-recognition domain. Proc. Nat. Acad. Sci. USA. 2005;102:7487–7492.10.1073/pnas.0501003102
  • Kuratani M, Yoshikawa Y, Bessho Y, Higashijima K, Ishii T, Shibata R, Takahashi S, Yutani K, Yokoyama S. Structural basis of the initial binding of tRNAIle lysidine synthetase TilS with ATP and l-lysine. Structure. 2007;15:1642–1653.10.1016/j.str.2007.09.020
  • Nakanishi K, Bonnefond L, Kimura S, Suzuki T, Ishitani R, Nureki O. Structural basis for translational fidelity ensured by transfer RNA lysidine synthetase. Nature. 2009;461:1144–1148.10.1038/nature08474
  • Osawa T, Kimura S, Terasaka N, Inanaga H, Suzuki T, Numata T. Structural basis of tRNA agmatinylation essential for AUA codon decoding. Nat. Struct. Mol. Biol. 2011;18:1275–1280.10.1038/nsmb.2144
  • Numata T, Ikeuchi Y, Fukai S, Suzuki T, Nureki O. Snapshots of tRNA sulphuration via an adenylated intermediate. Nature. 2006;442:419–424.10.1038/nature04896
  • Losey HC, Ruthenburg AJ, Verdine GL. Crystal structure of Staphylococcus aureus tRNA adenosine deaminase TadA in complex with RNA. Nat. Struct. Mol. Biol. 2006;13:153–159.10.1038/nsmb1047
  • Xie W, Liu X, Huang RH. Chemical trapping and crystal structure of a catalytic tRNA guanine transglycosylase covalent intermediate. Nat. Struct. Biol. 2003;10:781–788.10.1038/nsb976
  • Cusack S, Yaremchuk A, Krikliviy I, Tukalo M. tRNAPro anticodon recognition by Thermus thermophilus prolyl-tRNA synthetase. Structure. 1998;6:101–108.10.1016/S0969-2126(98)00011-2
  • Fukai S, Nureki O, Sekine S, Shimada A, Vassylyev DG, Yokoyama S. Mechanism of molecular interactions for tRNAVal recognition by valyl-tRNA synthetase. RNA. 2003;9:100–111.10.1261/rna.2760703
  • Bork P, Koonin EV. A P-loop-like motif in a widespread ATP pyrophosphatase domain: implications for the evolution of sequence motifs and enzyme activity. Proteins. 1994;20:347–355.10.1002/(ISSN)1097-0134
  • Terasaka N, Kimura S, Osawa T, Numata T, Suzuki T. Biogenesis of 2-agmatinylcytidine catalyzed by the dual protein and RNA kinase TiaS. Nat. Struct. Mol. Biol. 2011;18:1268–1274.10.1038/nsmb.2121

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.