An evolutionary 'intermediate state' of mitochondrial translation systems found in Trichinella species of parasitic nematodes: Co-evolution of tRNA and EF-Tu

Nucleic Acids Research

Volumn 34, Issue 18, 2006, Pages 5291-5299

  Arita, Masashi ^a   Suematsu, Takuma ^a,b   Osanai, Arihiro ^c   Inaba, Takashi ^c,d   Kamiya, Haruo ^c   Kita, Kiyoshi ^b   Sisido, Masahiko ^a   Watanabe, Yoh Ichi ^b   Ohtsuki, Takashi ^a  

^a OKAYAMA UNIVERSITY   (Japan)

^b UNIVERSITY OF TOKYO   (Japan)

^c HIROSAKI UNIVERSITY   (Japan)

^d HIROSAKI UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ELONGATION FACTOR TU; TRANSFER RNA;

ARTICLE; CAENORHABDITIS ELEGANS; CONTROLLED STUDY; MITOCHONDRION; MOLECULAR EVOLUTION; MOUSE; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN RNA BINDING; SPECIES DIFFERENCE; TRICHINELLA BRITOVI;

AMINO ACID SEQUENCE; ANIMALS; BASE SEQUENCE; CAENORHABDITIS ELEGANS PROTEINS; EVOLUTION, MOLECULAR; HELMINTH PROTEINS; MITOCHONDRIA; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PEPTIDE ELONGATION FACTOR TU; PROTEIN BIOSYNTHESIS; RNA; RNA, HELMINTH; RNA, TRANSFER; RNA, TRANSFER, ALA; RNA, TRANSFER, SER; RNA, TRANSFER, TRP; SEQUENCE ALIGNMENT; TRICHINELLA;

ANIMALIA; CAENORHABDITIS ELEGANS; CHROMADOREA; ENOPLEA; NEMATODA; TRICHINELLA; TRICHINELLA BRITOVI;

EID: 33750974470     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkl526     Document Type: Article

References (43)

1. Boore,J.L. (1999) Animal mitochondrial genomes. Nucleic Acids Res., 27, 1767-1780.
2. Lynch,M., Koskella,B. and Schaack,S. (2006) Mutation pressure and the evolution of organelle genomic architecture. Science, 311, 1727-1730.
3. Sprinzl,M. and Vassilenko,K.S. (2005) Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res., 33, D139-D140.
4. Wolstenholme,D.R. (1992) Animal mitochondrial DNA: Structure and evolution. In Wolstenholme,D.R. and Jeon,K.W. (eds), Mitochondrial Genomes. Academic Press, NY, pp. 173-216.
5. Wolstenholme,D.R., Macfarlane,J.L., Okimoto,R., Clary,D.O. and Wahleithner,J.A. (1987) Bizarre tRNAs infered from DNA sequences of mitochondrial genomes of nematode worms. Proc. Natl Acad. Sci USA, 84, 1324-1328.
6. Okimoto,R. and Wolstenholme,D.R. (1990) A set of tRNAs that lack either the TyC arm or dihydrouridine arm: Towards a minimal tRNA adaptor. EMBO J., 9, 3405-3411.
7. Okimoto,R., Macfarlane,J.L., Clary,D.O. and Wolstenholme,D.R. (1992) The mitochondrial genomes of two nematodes, Caenorhabditis elegans and Ascaris suum. Genetics, 130, 471-498.
8. Watanabe,Y., Tsurui,H., Ueda,T., Furushima,R., Takamiya,S., Kita,K., Nishikawa,K. and Watanabe,K. (1994) Primary and higher order structures of Nematode (Ascaris suum) mitochondrial tRNAs lacking either the T or D stem. J. Biol. Chem., 269, 22902-22906.
9. Keddie,E.M., Higazi,T. and Unnasch,T.R. (1998) The mitochondrial genome of Onchocerca volvulus: Sequence, structure and phylogenetic analysis. Mol. Biochem. Parasitol., 95, 111-127.
10. Hu,M., Chilton,N.B. and Gasser,R.B. (2002) The mitochondrial genomes of the human hookworms, Ancylostoma duodenale and Necator americanus (Nematoda: Secernentea). Int. J. Parasitol., 32, 145-158.
11. Steinauer,M.L., Nickol,B.B., Broughton,R. and Orti,G. (2005) First sequenced mitochondrial genome from the phylum Acanthocephala (Leptorhynchoides thecatus) and its phylogenetic position within Metazoa. J. Mol. Evol., 60, 706-715.
12. Le,T.H., Blair,D. and McManus,D.P. (2002) Mitochondrial genomes of parasitic flatworms. Trends Parasitol., 18, 206-213.
13. Terrett,J.A., Miles,S. and Thomas,R.H. (1996) Complete DNA sequence of the mitochondrial genome of Cepaea nemoralis (Gastropoda: Pulmonata). J. Mol. Evol., 42, 160-168.
14. Yamazaki,N., Ueshima,R., Terrett,J.A., Yokobori,S., Kaifu,M., Segawa,R., Kobayashi,T., Numachi,K., Ueda,T., Nishikawa,K. et al. (1997) Evolution of pulmonate gastropod mitochondrial genomes: Comparisons of gene organizations of Euhadra, Cepaea and Albinaria and implications of unusual tRNA secondary structures. Genetics, 145, 749-758.
15. Noguchi,Y., Endo,K., Tajima,F. and Ueshima,R. (2000) The mitochondrial genome of the brachiopod Laqueus rubellus. Genetics, 155, 245-259.
16. Helfenbein,K.G., Brown,W.M. and Boore,J.L. (2001) The complete mitochondrial genome of the articulate brachiopod Terebratalia transversa. Mol. Biol. Evol., 18, 1734-1744.
17. Masta,S.E. and Boore,J.L. (2004) The complete mitochondrial genome sequence of the spider Habronattus oregonensis reveals rearranged and extremely truncated tRNAs. Mol. Biol. Evol., 21, 893-902.
18. Hu,M. and Gasser,R.B. (2006) Mitochondrial genomes of parasitic nematodes - progress and perspectives. Trends Parasitol., 22, 78-84.
19. Kim,K.H., Eom,K.S. and Park,J.K. (2006) The complete mitochondrial genome of Anisakis simplex (Ascaridida: Nematoda) and phylogenetic implications. Int. J. Parasitol., 36, 319-328.
20. Montiel,R., Lucena,M.A., Medeiros,J. and Simoes,N. (2006) The complete mitochondrial genome of the entomopathogenic Nematode Steinernema carpocapsae: Insights into Nematode mitochondrial DNA evolution and phylogeny. J. Mol. Evol., 62, 211-225.
21. Phe, EF-Tu, and a GTP analog. Science, 270, 1464-1472.
22. Cys-EF-Tu-GDPNP reveals general and specific features in the ternary complex and in tRNA. Structure, 7, 143-156.
23. Ohtsuki,T., Watanabe,Y., Takemoto,C., Kawai,G., Ueda,T., Kita,K., Kojima,S., Kaziro,Y., Nyborg,J. and Watanabe,K. (2001) An 'elongated' translation elongation factor Tu for truncated tRNAs in nematode mitochondria. J. Biol. Chem., 276, 21571-21577.
24. Ohtsuki,T., Sato,A., Watanabe,Y. and Watanabe,K. (2002) A unique serine-specific elongation factor Tu found in nematode mitochondria. Nature Struct. Biol., 9, 669-673.
25. Lavrov,D.V. and Brown,W.M. (2001) Trichinella spiralis mt DNA: A nematode mitochondrial genome that encodes a putative ATP8 and normally structured tRNAs and has a gene arrangement relatable to those of coelomate metazoans. Genetics, 157, 621-637.
26. Inaba,T., Sato,H. and Kamiya,H. (2003) Monoclonal IgA antibody-mediated expulsion of Trichinella from the intestine of mice. Parasitology, 591-598.
27. Thompson,J.D., Higgins,D.G. and Gibson,T.J. (1994) CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680.
28. Guindon,S. and Gascuel,O. (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol., 52, 696-704.
29. Whelan,S. and 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.
30. Ota,T. and Nei,M. (1994) Estimation of the number of amino-acid substitutions per site when the substitution rate varies among sites. J. Mol. Evol., 38, 642-643.
31. Sakurai,M., Ohtsuki,T. and Watanabe,K. (2005) Modification at position 9 with 1-methyladenosine is crucial for structure and function of nematode mitochondrial tRNAs lacking the entire T-arm. Nucleic Acids Res., 33, 1653-1661.
32. Fechter,P., Rudinger,J., Giege,R. and Theobald-Dietrich,A. (1998) Ribozyme processed tRNA transcripts with unfriendly internal promoter for T7 RNA polymerase: Production and activity. FEBS Lett., 436, 99-103.
33. Shimada,N., Suzuki,T. and Watanabe,K. (2001) Dual mode recognition of two isoacceptor tRNAs by mammalian mitochondrial seryl-tRNA synthetase. J. Biol. Chem., 276, 46770-46778.
34. Hohsaka,T., Ashizuka,Y., Murakami,H. and Sisido,M. (1996) Incorporation of nonnatural amino acids into streptavidin through in vitro frame-shift suppression. J. Am. Chem. Soc., 118, 9778-9779.
35. Phes. Biochemistry, 23, 1468-1473.
36. Pingoud,A., Urbanke,C., Krauss,G., Peters,F. and Maass,G. (1977) Ternary complex formation between elongation factor Tu, GTP and aminoacyl-tRNA: an equilibrium Study. Eur. J. Biochem., 78, 403-409.
37. Lavrov,D.V. and Brown,W.M. (2001) Trichinella spiralis mtDNA: A nematode mitochondrial genome that encodes a putative ATP8 and normally structured tRNAs and has a gene arrangement relatable to those of coelomate metazoans. Genetics, 157, 621-637.
38. LaRiviere,F.J., Wolfson,A.D. and Uhlenbeck,O.C. (2001) Uniform binding of aminoacyl-tRNAs to elongation factor Tu by thermodynamic compensation. Science, 294, 165-168.
39. Gebhardt-Singh,E. and Sprinzl,M. (1986) Ser-tRNAs from bovine mitochondrion form ternary complexes with bacterial elongation factor Tu and GTP. Nucleic Acids Res., 14, 7175-7188.
40. Phe lacking the 'conserved' GG and T psi CG sequences as inferred by enzymatic and chemical probing. Nucleic Acids Res., 22, 347-353.
41. Woriax,V.L., Burkhart,W. and Spremulli,L.L. (1995) Cloning, sequence analysis and expression of mammalian mitochondrial protein synthesis elongation factor Tu. Biochim. Biophys. Acta, 1264, 347-356.
42. Andersen,G.R., Thirup,S., Spremulli,L.L. and Nyborg,J. (2000) High resolution crystal structure of bovine mitochondrial EF-Tu in complex with GDP. J. Mol. Biol., 297, 421-436.
43. Lewis,D.L., Farr,C.L. and Kaguni,L.S. (1995) Drosophila melanogaster mitochondrial DNA: Completion of the nucleotide sequence and evolutionary comparisons. Insect. Mol. Biol., 4, 263-278.