Genomics and the evolution of aminoacyl-tRNA synthesis

• Autorzy: Ruan B. , Ahel I. , Ambrogelly A. , Becker H.D. , Bunjun S. , Feng L. , Tumbula-Hansen D. , Ibba M. , Korencic D. , Kobayashi H. , Jacquin-Becker C. , Mejlhede N. , Min B. , Raczniak G. , Rinehart J. , Stathopoulos C. , Li T. , Soll D.
• Języki publikacji: EN

Abstrakty

EN

Trans la tion is the pro cess by which ri bo somes di rect pro tein syn the sis us ing the ge­netic in for ma tion con tained in mes sen ger RNA (mRNA). Trans fer RNAs (tRNAs) are charged with an amino acid and brought to the ri bo some, where they are paired with the cor re spond ing trinucleotide codon in mRNA. The amino acid is at tached to the na­scent polypeptide and the ri bo some moves on to the next codon. Thus, the se quen tial pair ing of codons in mRNA with tRNA anticodons de ter mines the or der of amino ac­ids in a pro tein. It is there fore im per a tive for ac cu rate trans la tion that tRNAs are only cou pled to amino ac ids cor re spond ing to the RNA anticodon. This is mostly, but not exclusively, achieved by the di rectattachmentoftheappropriateaminoacidtothe 3 -end of the cor re spond ing tRNA by the aminoacyl-tRNA syn the tas es. To en sure the accurate translation of genetic information, the aminoacyl-tRNA synthetases must display an extremely high level of substrate specificity. Despite this highly conserved function, re cent stud ies aris ing from the anal y sis of whole genomes have shown a significant de gree of evo lu tion ary di ver sity in aminoacyl-tRNA syn the sis. For ex am ple, non-canonical routes have been iden ti fied for the syn the sis of Asn-tRNA, Cys-tRNA, Gln-tRNA and Lys-tRNA. Char ac ter iza tion of non-canonical aminoacyl-tRNA synthesis has re vealed an un ex pected level of evo lu tion ary di ver gence and has also pro vided new in sights into the pos si ble pre cur sors of con tem po rary aminoacyl-tRNA syn the tases.

Słowa kluczowe

EN

RNA; aminoacyl-tRNA synthesis; tRNA; aminoacyl-tRNA; translation; evolution; genome; protein synthesis

• Wydawca: -
• Czasopismo: Acta Biochimica Polonica
• Rocznik: 2001
• Tom: 48
• Numer: 2
• Opis fizyczny: p.313-321,fig.

Twórcy

autor

Ruan B.

• Yale University, New Haven, Connecticut, USA

autor

Ahel I.

autor

Ambrogelly A.

autor

Becker H.D.

autor

Bunjun S.

autor

Feng L.

autor

Tumbula-Hansen D.

autor

Ibba M.

autor

Korencic D.

autor

Kobayashi H.

autor

Jacquin-Becker C.

autor

Mejlhede N.

autor

Min B.

autor

Raczniak G.

autor

Rinehart J.

autor

Stathopoulos C.

autor

Li T.

autor

Soll D.

Bibliografia

• 1.Arnez, J.G. & Moras, D. (1997) Structural and functional considerations of the aminoacylation reaction. Trends Biochem. Sci. 22, 211-216.
• 2.Becker, H.D. & Kern, D. (1998) Thermus thermophilus: a link in evolution of the tRNA-dependent amino acid amidation pathways. Proc. Natl. Acad. Sci. U.S.A. 95, 12832-12837.
• 3.Brown, J.R. & Doolittle, W.F. (1999) Gene descent, duplication, and horizontal transfer in the evolution of glutamyl- and glutaminyl-tRNA synthetases. J. Mol. Evol. 49, 485-495.
• 4.Bult, C.J., White, O., Olsen, G.J., Zhou, L., Fleischmann, R.D., Sutton, G.G., Blake, J.A., FitzGerald, L.M., Clayton, R.A., Gocayne, J.D., Kerlavage, A.R., Dougherty, B.A., Tomb, J.F.,Adams, M.D., Reich, C.I., Overbeek, R., Kirkness, E.F., Weinstock, K.G., Merrick, J.M., Glodek, A., Scott, J.L., Geoghagen, N.S.M. & Venter, J.C. (1996) Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science273, 1058-1073.
• 5.Bunjun, S., Stathopoulos, C., Graham, D., Min, B., Kitabatake, M., Wang, A.L., Wang, C.C., Vivarcs, C.P., Weiss, L.M. & Soell, D. (2000) A dual-specificity aminoacyl-tRNA synthetase in the deep-rooted eukaryote Giardia lamblia. Proc. Natl. Acad. Sci. U.S.A. 97, 12997-13002.
• 6.Commans, S. & Boeck, A. (1999) Selenocysteine inserting tRNAs: An overview. FEMS Microbiol. Rev. 23, 335-351.
• 7.Crick, F.H.C. (1958) On protein synthesis. Symp. Soc. Exp. Biol. 12, 138-163.
• 8.Crick, F.H.C. (1970) Central dogma of molecular biology. Nature 227, 561-563.
• 9.Curnow, A. W., Ibba, M. & Soell, D. (1996) tRNA-dependent asparagine formation. Nature 382, 589-590.
• 10.Curnow, A.W., Hong, K.W., Yuan, R., Kim, S.I., Martins, O., Winkler, W., Henkin, T.M. & Soell, D. (1997) Glu-tRNAGln amidotransferase: A novel heterotrimeric enzyme required for correct decoding of glutamine codons during translation. Proc. Natl. Acad. Sci. U.S.A. 94, 11819-11826.
• 11.Curnow, A.W., Tumbula, D.L., Pelaschier, J.T., Min, B. & Soell, D. (1998) Glutamyl-tRNAGln amidotransferase in Deinococcus radiodurans may be confined to asparagine biosynthesis. Proc. Natl. Acad. Sci. U.S.A. 95, 12838- 12843.
• 12.Delarue, M. (1995) Partition of aminoacyl-tRNA synthetases in two different structural classes dating back to early metabolism: Implications for the origin of the genetic code and the nature of protein sequences. J. Mol. Evol. 41, 703-711.
• 13.Gesteland, R.F., Cech, T.R. & Atkins, J.F. (1999) TheRNA World. Cold Spring Harbor Laboratory Press.
• 14.Hutchison, C.A., Peterson, S.N., Gill, S.R., Cline, R.T., White, O., Fraser, C.M., Smith, H.O. & Venter, J.C. (1999) Global transposon mutagenesis and a minimal Mycoplasma genome. Science 286, 2165-2169.
• 15.Ibba, M., Bono, J.L., Rosa, P.A. & Soell, D. (1997a) Archaeal-type lysyl-tRNA synthetase in the Lyme disease spirochete Borrelia burgdorferi. Proc. Natl. Acad. Sci. U.S.A. 94, 14383-14388.
• 16.Ibba, M., Morgan, S., Curnow, A.W., Pridmore, D. R., Vothknecht, U. C., Gardner, W., Lin, W., Woese, C. R. & Soell, D. (1997b) A euryarchaeal lysyl-tRNA synthetase: Resemblance to class I synthetases. Science 278, 1119-1122.
• 17.Ibba, M., Losey, H.C., Kawarabayasi, Y., Kikuchi, H., Bunjun, S. & Soell, D. (1999) Substrate recognition by class I lysyl-tRNA synthetases: A molecular basis for gene displacement. Proc. Natl. Acad. Sci. U.S.A. 96, 418-423.
• 18.Ibba, M. & Soell, D. (1999) Quality control mechanisms during translation. Science 286, 1893-1897.
• 19.Ibba, M. & Soell, D. (2000) Aminoacyl-tRNA synthesis. Annu. Rev. Biochem. 69, 617-650.
• 20.Illangasekare, M., Sanchez, G., Nickles, T. & Yarus, M. (1995) Aminoacyl-RNA synthesis catalyzed by an RNA. Science 267, 643-647.
• 21.Lee, N., Bessho, Y., Wei, K., Szostak, J.W. & Suga, H. (2000) Ribozyme-catalyzed tRNA aminoacylation. Nat. Struct. Biol. 7, 28-33.
• 22.Maizels, N. & Weiner, A.M. (1994) Phylogeny from function: Evidence from the molecular fossil record that tRNA originated in replication, not translation. Proc. Natl. Acad. Sci. U.S.A. 91, 6729-6734.
• 23.Nabholz, C.E., Hauser, R. & Schneider, A. (1997) Leishmania tarentolae contains distinct cytosolic and mitochondrial glutaminyl-tRNA synthetase activities. Proc. Natl. Acad. Sci. U.S.A. 94, 7903-7908.
• 24.Nagel, G.M. & Doolittle, R.F. (1995) Phylogenetic analysis of the aminoacyl-tRNA synthetases. J. Mol. Evol. 40, 487-498.
• 25.RajBhandary, U.L. (1994) Initiator transfer RNAs. J. Bacteriol. 176, 547-552.
• 26.Ribas de Pouplana, L., Turner, R.J., Steer, B.A. & Schimmel, P. (1998) Genetic code origins: tRNAs older than their synthetases? Proc. Natl. Acad. Sci. U.S.A. 95, 11295-11300.
• 27.Schimmel, P. & Kelley, S.O. (2000) Exiting an RNA world. Nat. Struct. Biol. 7, 5-7.
• 28.Schoen, A., Kannangara, C.G., Gough, S. & Soell, D. (1988) Protein biosynthesis in organelles requires misaminoacylation of tRNA. Nature 331, 187-190.
• 29.Shiba, K. & Schimmel, P. (1992) Functional assembly of a randomly cleaved protein. Proc. Natl. Acad. Sci. U.S.A. 89, 1880-1884.
• 30.Smith, D.R., Doucette-Stamm, L.A., Deloughery, C., Lee, H., Dubois, J., Aldredge, T., Bashirzadeh, R., Blakely, D., Cook, R., Gilbert, K., Harrison, D., Hoang, L., Keagle, P., Lumm, W., Pothier, B., Qiu, D., Spadafora, R., Vicaire, R., Wang, Y., Wierzbowski, J., Gibson, R., Jiwani, N., Caruso, A., Bush, D. & Reeve, J.N. (1997) Complete genome sequence of Methanobacterium thermoautotrophicum H: Functional analysis and comparative genomics. J. Bacteriol. 179, 7135-7155.
• 31.Soell, D. & Schimmel, P.R. (1974) Aminoacyl-tRNA synthetases. The Enzymes 10, 489-538.
• 32.Stathopoulos, C., Li, T., Longman, R., Vothknecht, U.C., Becker, H.D., Ibba, M. & Soell, D. (2000) One polypeptide with two aminoacyl-tRNA synthetase activities. Science 287, 479-482.
• 33.Stathopoulos, C., Jacquin-Becker, C., Becker, H.D., Li, T., Ambrogelly, A. Longman, R. & Soell, D. (2001) Methanococcus jannaschii prolyl-cysteinyl-tRNA synthetase possesses overlapping amino acid binding sites. Biochemistry 40, 46-52.
• 34.Tumbula, D.L., Vothknecht, U.C., Kim, H.-S., Ibba, M., Min, B., Li, T., Pelaschier, J., Stathopoulos, C., Becker, H.D. & Soell, D. (1999) Archaeal aminoacyl-tRNA synthesis: Diversity replaces dogma. Genetics 152, 1269-1276.
• 35.Tumbula, D.L., Becker, H.D., Chang, W.-Z. & Soell, D. (2000) Domain-specific recruitment of amide amino acids for protein synthesis. Nature 407, 106-110.
• 36.White, B.N. & Bayley, S.T. (1972) Further codon assignments in an extremely halophilic bacterium using a cell-free protein-synthesizing system and a ribosomal binding assay. Can. J. Biochem. 50, 600-609.
• 37.Wilcox, M. & Nirenberg, M. (1968) Transfer RNA as a cofactor coupling amino acid synthesis with that of protein. Proc. Natl. Acad. Sci. U.S.A. 61, 229-236.
• 38.Woese, C.R., Olsen, G., Ibba, M. & Soell, D. (2000) Aminoacyl-tRNA synthetases, the genetic code, and the evolutionary process. Microbiol. Mol. Biol. Rev. 64, 202-236.