Origin and evolution of glutamyl-prolyl tRNA synthetase WHEP domains reveal evolutionary relationships within holozoa

PLoS ONE

Volumn 9, Issue 6, 2014, Pages

  Ray, Partho Sarothi ^a,b   Fox, Paul L ^a  

^a LERNER RESEARCH INSTITUTE   (United States)

^b INDIAN INSTITUTE OF SCIENCE EDUCATION AND RESEARCH KOLKATA   (India)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID TRANSFER RNA LIGASE; GLUTAMYLPROLYL TRNA SYNTHETASE; UNCLASSIFIED DRUG; GLUTAMYL-PROLYL-TRNA SYNTHETASE;

AMINO ACID COMPOSITION; AMINO ACID SEQUENCE; AMINOACYLATION; ANIMAL; ARTICLE; BIOGENESIS; CHOANOFLAGELLATE; CHOANOZOAN; CLADISTICS; CONTROLLED STUDY; ENZYME ACTIVE SITE; FILOZOA; GENE CLUSTER; GENETIC REASSORTMENT; HOLOZOA; ICHTHYOSPOREA; MOLECULAR EVOLUTION; NONHUMAN; PHYLOGENY; PROTEIN DOMAIN; VERTEBRATE; CHEMISTRY; GENETICS; HUMAN; PROTEIN TERTIARY STRUCTURE;

AMINO ACYL-TRNA SYNTHETASES; ANIMALS; EVOLUTION, MOLECULAR; HUMANS; PHYLOGENY; PROTEIN STRUCTURE, TERTIARY;

EID: 84903397374     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0098493     Document Type: Article

References (38)

1. Rokas A, King N, Finnerty J, Carroll SB (2003) Conflicting phylogenetic signals at the base of the metazoan tree. Evol Dev 5: 346-359. (Pubitemid 36893144)
2. Baldauf SL, Roger AJ, Wenk-Siefert I, Doolittle WF (2000) A kingdom-level phylogeny of eukaryotes based on combined protein data. Science 290: 972-977.
3. Wolf YI, Rogozin IB, Koonin EV (2004) Coelomata and not Ecdysozoa: evidence from genome-wide phylogenetic analysis. Genome Res 14: 29-36. (Pubitemid 38088522)
4. Salichos L, Rokas A (2013) Inferring ancient divergences requires genes with strong phylogenetic signals. Nature 497: 327-331.
5. Rokas A, Holland PW (2000) Rare genomic changes as a tool for phylogenetics. Trends Ecol Evol 15: 454-459.
6. Rogozin IB, Wolf YI, Carmel L, Koonin EV (2007) Ecdysozoan clade rejected by genome-wide analysis of rare amino acid replacements. Mol Biol Evol 24: 1080-1090. (Pubitemid 46536720)
7. Rho SB, Lee KH, Kim JW, Shiba K, Jo YJ, et al. (1996) Interaction between human tRNA synthetases involves repeated sequence elements. Proc Natl Acad Sci U S A 93: 10128-10133. (Pubitemid 26314586)
8. Cerini C, Semeriva M, Gratecos D (1997) Evolution of the aminoacyl-tRNA synthetase family and the organization of the Drosophila glutamyl-prolyl-tRNA synthetase gene. Intron/exon structure of the gene, control of expression of the two mRNAs, selective advantage of the multienzyme complex. Eur J Biochem 244: 176-185. (Pubitemid 27079712)
9. Cahuzac B, Berthonneau E, Birlirakis N, Guittet E, Mirande M (2000) A recurrent RNA-binding domain is appended to eukaryotic aminoacyl-tRNA synthetases. EMBO J 19: 445-452. (Pubitemid 30072614)
10. Ibba M, Söll D (2000) Aminoacyl-tRNA synthesis. Annu Rev Biochem 69: 617-650.
11. Guo M, Yang XL, Schimmel P (2010) New functions of aminoacyl-tRNA synthetases beyond translation. Nat Rev Mol Cell Biol 11: 668-674.
12. Ray PS, Fox PL (2007) A post-transcriptional pathway represses monocyte VEGF-A expression and angiogenic activity. EMBO J 26: 3360-3372. (Pubitemid 47123539)
13. Sampath P, Mazumder B, Seshadri V, Gerber CA, Chavatte L, et al. (2004) Noncanonical function of glutamyl-prolyl-tRNA synthetase: gene-specific silencing of translation. Cell 119: 195-208. (Pubitemid 39360902)
14. Jia J, Arif A, Ray PS, Fox PL (2008) WHEP domains direct noncanonical function of glutamyl-prolyl tRNA synthetase in translational control of gene expression. Mol Cell 29: 679-690. (Pubitemid 351400920)
15. Shiba K (2002) Intron positions delineate the evolutionary path of a pervasively appended peptide in five human aminoacyl-tRNA synthetases. J Mol Evol 55: 727-733.
16. Ray PS, Sullivan JC, Jia J, Francis J, Finnerty JR, et al. (2011) Evolution of function of a fused metazoan tRNA synthetase. Mol Biol Evol 28: 437-447.
17. Pustell J, Kafatos FC (1982) A high speed, high capacity homology matrix: zooming through SV40 and polyoma. Nucleic Acids Res 10: 4765-4782.
18. Consortium ICGS (2004) Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432: 695-716.
19. Warren WC, Hillier LW, Marshall Graves JA, Birney E, Ponting CP, et al. (2008) Genome analysis of the platypus reveals unique signatures of evolution. Nature 453: 175-183.
20. Delsuc F, Brinkmann H, Chourrout D, Philippe H (2006) Tunicates and not cephalochordates are the closest living relatives of vertebrates. Nature 439: 965-968. (Pubitemid 43292413)
21. Bourlat SJ, Juliusdottir T, Lowe CJ, Freeman R, Aronowicz J, et al. (2006) Deuterostome phylogeny reveals monophyletic chordates and the new phylum Xenoturbellida. Nature 444: 85-88. (Pubitemid 44684760)
22. Aguinaldo AM, Turbeville JM, Linford LS, Rivera MC, Garey JR, et al. (1997) Evidence for a clade of nematodes, arthropods and other moulting animals. Nature 387: 489-493. (Pubitemid 27235464)
23. Dunn CW, Hejnol A, Matus DQ, Pang K, Browne WE, et al. (2008) Broad phylogenomic sampling improves resolution of the animal tree of life. Nature 452: 745-749. (Pubitemid 351522763)
24. Blair JE, Ikeo K, Gojobori T, Hedges SB (2002) The evolutionary position of nematodes. BMC Evol Biol 2: 7.
25. Berthonneau E, Mirande M (2000) A gene fusion event in the evolution of aminoacyl-tRNA synthetases. FEBS Lett 470: 300-304. (Pubitemid 30169281)
26. Brady SG, Schultz TR, Fisher BL, Ward PS (2006) Evaluating alternative hypotheses for the early evolution and diversification of ants. Proc Natl Acad Sci U S A 103: 18172-18177. (Pubitemid 44871631)
27. Gerardo NM, Altincicek B, Anselme C, Atamian H, Barribeau SM, et al. (2010) Immunity and other defenses in pea aphids, Acyrthosiphon pisum. Genome Biol 11: R21.
28. King N, Westbrook MJ, Young SL, Kuo A, Abedin M, et al. (2008) The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans. Nature 451: 783-788. (Pubitemid 351253174)
29. Shalchian-Tabrizi K, Minge MA, Espelund M, Orr R, Ruden T, et al. (2008) Multigene phylogeny of choanozoa and the origin of animals. PLoS One 3: e2098.
30. Douzery EJ, Snell EA, Bapteste E, Delsuc F, Philippe H (2004) The timing of eukaryotic evolution: does a relaxed molecular clock reconcile proteins and fossils? Proc Natl Acad Sci U S A 101: 15386-15391. (Pubitemid 39441551)
31. Boore JL (2006) The use of genome-level characters for phylogenetic reconstruction. Trends Ecol Evol 21: 439-446.
32. Nikaido M, Rooney AP, Okada N (1999) Phylogenetic relationships among cetartiodactyls based on insertions of short and long interpersed elements: hippopotamuses are the closest extant relatives of whales. Proc Natl Acad Sci U S A 96: 10261-10266. (Pubitemid 29422546)
33. Iwabe N, Kuma K, Hasegawa M, Osawa S, Miyata T (1989) Evolutionary relationship of archaebacteria, eubacteria, and eukaryotes inferred from phylogenetic trees of duplicated genes. Proc Natl Acad Sci U S A 86: 9355-9359. (Pubitemid 20010424)
34. Ribas de Pouplana L, Brown JR, Schimmel P (2001) Structure-based phylogeny of class IIa tRNA synthetases in relation to an unusual biochemistry. J Mol Evol 53: 261-268. (Pubitemid 32889534)
35. Jermiin LS, Poladian L, Charleston MA (2005) Is the "Big Bang" in animal evolution real? Science 310: 1910-1911. (Pubitemid 43005974)
36. Rokas A, Kruger D, Carroll SB (2005) Animal evolution and the molecular signature of radiations compressed in time. Science 310: 1933-1938. (Pubitemid 43005982)
37. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, et al. (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28: 2731-2739.
38. Whelan S, Goldman N (2001) A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol Biol Evol 18: 691-699. (Pubitemid 32372940)