Biopolym. Cell. 2005; 21(6):548-558.
http://dx.doi.org/10.7124/bc.000713
Bioinformatics
Comparative analysis of structural organization of cytoplasmic tyrosyl-tRNA synthetase genes of eukaryotes
1Odynets K. A., 1Kornelyuk A. I.
  1. Institute of Molecular Biology and Genetics, NAS of Ukraine
    150, Akademika Zabolotnoho Str., Kyiv, Ukraine, 03680

Abstract

A comparative bioinformational analysis has been performed for the structure of cytoplasmic tyrosyl-tRNA synthetase (TyrRS) genes from 54 eukaryotic organisms from different taxones. In some cases, the identification of the genes and their exons was verified by comparison with the experimental cDNA and EST sequences. The comparison of exon-intron structures shows that TyrRS genes of Chordata (16 species) have much more exons (13–14) than genes of Insecta (2–7 exons), yeasts and Protozoa (1–8 exons). The intron lengths increase intensively during the evolution due to integration of genomic repeats. The positions of some introns are conservative that marks their earlier integration into the gene of common ancestor of Chordata and Insecta. The TyrRS gene of human is analyzed in detail for alternative splicing mRNAs and genomic repeats.
Keywords: tyrosyl-tRNA synthetase, gene, exon-intron structure, evolution, databases
Full text: (PDF, in Ukrainian)

References

[1] Berthonneau E, Mirande M. A gene fusion event in the evolution of aminoacyl-tRNA synthetases. FEBS Lett. 2000;470(3):300-4.
[2] Brenner S, Corrochano LM. Translocation events in the evolution of aminoacyl-tRNA synthetases. Proc Natl Acad Sci U S A. 1996;93(16):8485-9.
[3] Diaz-Lazcoz Y, Aude JC, Nitschk? P, Chiapello H, Land?s-Devauchelle C, Risler JL. Evolution of genes, evolution of species: the case of aminoacyl-tRNA synthetases. Mol Biol Evol. 1998;15(11):1548-61.
[4] Wolf YI, Aravind L, Grishin NV, Koonin EV. Evolution of aminoacyl-tRNA synthetases--analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events. Genome Res. 1999;9(8):689-710.
[5] Doolittle RF, Handy J. Evolutionary anomalies among the aminoacyl-tRNA synthetases. Curr Opin Genet Dev. 1998;8(6):630-6.
[6] Weiner AM. Molecular evolution: aminoacyl-tRNA synthetases on the loose. Curr Biol. 1999;9(22):R842-4.
[7] Shiba K. Intron positions delineate the evolutionary path of a pervasively appended peptide in five human aminoacyl-tRNA synthetases. J Mol Evol. 2002;55(6):727-33.
[8] Brown JR, Robb FT, Weiss R, Doolittle WF. Evidence for the early divergence of tryptophanyl- and tyrosyl-tRNA synthetases. J Mol Evol. 1997;45(1):9-16.
[9] Kleeman TA, Wei D, Simpson KL, First EA. Human tyrosyl-tRNA synthetase shares amino acid sequence homology with a putative cytokine. J Biol Chem. 1997;272(22):14420-5.
[10] Chow CM, RajBhandary UL. Saccharomyces cerevisiae cytoplasmic tyrosyl-tRNA synthetase gene. Isolation by complementation of a mutant Escherichia coli suppressor tRNA defective in aminoacylation and sequence analysis. J Biol Chem. 1993;268(17):12855-63.
[11] Azad AK, Stanford DR, Sarkar S, Hopper AK. Role of nuclear pools of aminoacyl-tRNA synthetases in tRNA nuclear export. Mol Biol Cell. 2001;12(5):1381-92.
[12] Huang J, Xu Y, Gogarten JP. The presence of a haloarchaeal type tyrosyl-tRNA synthetase marks the opisthokonts as monophyletic. Mol Biol Evol. 2005;22(11):2142-6.
[13] Moreira D, L?pez-Garc?a P. Comment on "The 1.2-megabase genome sequence of Mimivirus". Science. 2005;308(5725):1114-5
[14] Kao J, Ryan J, Brett G, Chen J, Shen H, Fan YG, Godman G, Familletti PC, Wang F, Pan YC, et al. Endothelial monocyte-activating polypeptide II. A novel tumor-derived polypeptide that activates host-response mechanisms. J Biol Chem. 1992;267(28):20239-47.
[15] Kornelyuk AI, Tas MPR, Dubrovsky AL, Murray JC. Cytokine activity of the non-catalytic EMAP-2-like domain of mammalian tyrosyl-tRNA synthetase. Biopolym Cell. 1999; 15(2):168-72.
[16] Wakasugi K, Schimmel P. Two distinct cytokines released from a human aminoacyl-tRNA synthetase. Science. 1999;284(5411):147-51.
[17] Bernal A, Ear U, Kyrpides N. Genomes OnLine Database (GOLD): a monitor of genome projects world-wide. Nucleic Acids Res. 2001;29(1):126-7.
[18] Maglott D, Ostell J, Pruitt KD, Tatusova T. Entrez Gene: gene-centered information at NCBI. Nucleic Acids Res. 2005;33(Database issue):D54-8.
[19] Pruitt KD, Tatusova T, Maglott DR. NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 2005;33(Database issue):D501-4.
[20] Altschul SF, Madden TL, Sch?ffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25(17):3389-402.
[21] Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, Stange-Thomann N, Stojanovic N, Subramanian A, Wyman D, Rogers J, Sulston J, Ainscough R, Beck S, Bentley D, Burton J, Clee C, Carter N, Coulson A, Deadman R, Deloukas P, Dunham A, Dunham I, Durbin R, French L, Grafham D, Gregory S, Hubbard T, Humphray S, Hunt A, Jones M, Lloyd C, McMurray A, Matthews L, Mercer S, Milne S, Mullikin JC, Mungall A, Plumb R, Ross M, Shownkeen R, Sims S, Waterston RH, Wilson RK, Hillier LW, McPherson JD, Marra MA, Mardis ER, Fulton LA, Chinwalla AT, Pepin KH, Gish WR, Chissoe SL, Wendl MC, Delehaunty KD, Miner TL, Delehaunty A, Kramer JB, Cook LL, Fulton RS, Johnson DL, Minx PJ, Clifton SW, Hawkins T, Branscomb E, Predki P, Richardson P, Wenning S, Slezak T, Doggett N, Cheng JF, Olsen A, Lucas S, Elkin C, Uberbacher E, Frazier M, Gibbs RA, Muzny DM, Scherer SE, Bouck JB, Sodergren EJ, Worley KC, Rives CM, Gorrell JH, Metzker ML, Naylor SL, Kucherlapati RS, Nelson DL, Weinstock GM, Sakaki Y, Fujiyama A, Hattori M, Yada T, Toyoda A, Itoh T, Kawagoe C, Watanabe H, Totoki Y, Taylor T, Weissenbach J, Heilig R, Saurin W, Artiguenave F, Brottier P, Bruls T, Pelletier E, Robert C, Wincker P, Smith DR, Doucette-Stamm L, Rubenfield M, Weinstock K, Lee HM, Dubois J, Rosenthal A, Platzer M, Nyakatura G, Taudien S, Rump A, Yang H, Yu J, Wang J, Huang G, Gu J, Hood L, Rowen L, Madan A, Qin S, Davis RW, Federspiel NA, Abola AP, Proctor MJ, Myers RM, Schmutz J, Dickson M, Grimwood J, Cox DR, Olson MV, Kaul R, Raymond C, Shimizu N, Kawasaki K, Minoshima S, Evans GA, Athanasiou M, Schultz R, Roe BA, Chen F, Pan H, Ramser J, Lehrach H, Reinhardt R, McCombie WR, de la Bastide M, Dedhia N, Bl?cker H, Hornischer K, Nordsiek G, Agarwala R, Aravind L, Bailey JA, Bateman A, Batzoglou S, Birney E, Bork P, Brown DG, Burge CB, Cerutti L, Chen HC, Church D, Clamp M, Copley RR, Doerks T, Eddy SR, Eichler EE, Furey TS, Galagan J, Gilbert JG, Harmon C, Hayashizaki Y, Haussler D, Hermjakob H, Hokamp K, Jang W, Johnson LS, Jones TA, Kasif S, Kaspryzk A, Kennedy S, Kent WJ, Kitts P, Koonin EV, Korf I, Kulp D, Lancet D, Lowe TM, McLysaght A, Mikkelsen T, Moran JV, Mulder N, Pollara VJ, Ponting CP, Schuler G, Schultz J, Slater G, Smit AF, Stupka E, Szustakowski J, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Wallis J, Wheeler R, Williams A, Wolf YI, Wolfe KH, Yang SP, Yeh RF, Collins F, Guyer MS, Peterson J, Felsenfeld A, Wetterstrand KA, Patrinos A, Morgan MJ, de Jong P, Catanese JJ, Osoegawa K, Shizuya H, Choi S, Chen YJ; International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature. 2001;409(6822):860-921.
[22] Bedell JA, Korf I, Gish W. MaskerAid: a performance enhancement to RepeatMasker. Bioinformatics. 2000;16(11):1040-1.
[23] Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J. Repbase Update, a database of eukaryotic repetitive elements. Cytogenet Genome Res. 2005;110(1-4):462-7.
[24] Lynch M. Intron evolution as a population-genetic process. Proc Natl Acad Sci U S A. 2002;99(9):6118-23.