Divergent structures of Caenorhabditis elegans cytochrome P450 genes suggest the frequent loss and gain of introns during the evolution of nematodes

Molecular Biology and Evolution

Volumn 15, Issue 11, 1998, Pages 1447-1459

  Gotoh, Osamu ^a  

^a SAITAMA CANCER CENTER   (Japan)

Author keywords

Caenorhabditis elegans; Cytochrome P450; Exon prediction; Exon theory; Gene organization; Sequence alignment

Indexed keywords

CYTOCHROME P450; DRUG METABOLIZING ENZYME;

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ARTICLE; CAENORHABDITIS ELEGANS; DNA SEQUENCE; EVOLUTION; EXON; GENE INSERTION; GENE LOSS; GENE STRUCTURE; GENETIC ORGANIZATION; INTRON; MULTIGENE FAMILY; NEMATODE; NONHUMAN; NUCLEOTIDE SEQUENCE; ANIMAL; CHROMOSOME MAP; COMPARATIVE STUDY; ENZYMOLOGY; GENE; GENE AMPLIFICATION; GENE DELETION; GENE EXPRESSION REGULATION; GENETIC DATABASE; GENETIC VARIABILITY; GENETICS; MOLECULAR EVOLUTION; MOLECULAR GENETICS; PHYLOGENY; PHYSIOLOGY; QUALITY CONTROL; SPLICEOSOME;

ARTHROPODA; CAENORHABDITIS ELEGANS; DEUTEROSTOMIA; MAMMALIA; NEMATODA;

AMINO ACID SEQUENCE; ANIMALS; CAENORHABDITIS ELEGANS; CHROMOSOME MAPPING; CYTOCHROME P-450 ENZYME SYSTEM; DATABASES, GENETIC; EVOLUTION, MOLECULAR; GENE AMPLIFICATION; GENE DELETION; GENES, HELMINTH; GENES, INSECT; INTRONS; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; MUTAGENESIS, INSERTIONAL; NEMATODA; PHYLOGENY; QUALITY CONTROL; SPLICEOSOMES; VARIATION (GENETICS);

EID: 0031760236     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/oxfordjournals.molbev.a025872     Document Type: Article

References (43)

1. ADACHI, J., and M. HASEGAWA. 1996. MOLPHY version 2.3: programs for molecular phylogenetics based on maximum likelihood. Comput. Sci. Monogr. 28:1-150.
2. ALTSCHUL, S. F., W. GISH, W. MILLER, E. W. MYERS, and D. J. LIPMAN. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403-410.
3. BURGE, C., and S. KARLIN. 1997. Prediction of complete gene structures in human genomic DNA. J. Mol. Biol. 268:78-94.
4. CARRILLO, H., and D. LIPMAN. 1988. The multiple sequence alignment problem in biology. SIAM J. Appl. Math. 48: 1073-1082.
5. CLAVERIE, J.-M., I. SAUVAGET, and L. BOUGUELERET. 1990. ktuple frequency analysis: from intron/exon discrimination to T-cell epitope mapping. Methods Enzymol. 183:237-252.
6. DAYHOFF, M., ed. 1978. Atlas of protein sequence and structure. Vol. 5, Suppl. 3. National Biomedical Research Foundation, Washington, D.C.
7. DE SOUZA, S. J., M. LONG, L. SCHOENBACH, S. W. ROY, and W. GILBERT. 1996. Intron positions correlate with module boundaries in ancient proteins. Proc. Natl. Acad. Sci. USA 93:14632-14636.
8. DIETMAIER, W., and S. FABRY. 1994. Analysis of the introns in genes encoding small G proteins. Curr. Genet. 26:497-505.
9. DOOLITTLE, R. F., D.-F. FENG, S. TSANG, G. CHO, and E. LITTLE. 1996. Determining divergence times of the major kingdoms of living organisms with a protein clock. Science 271: 470-477.
10. FEDOROV, A., G. SUBOCH, M. BUJAKOV, and L. FEDOROVA. 1992. Analysis of nonuniformity in intron phase distribution. Nucleic Acids Res. 20:2553-2557.
11. FELSENSTEIN, J. 1992. PHYLIP (phylogeny inference package). Version 3.5c. Distributed by the author, Department of Genetics, University of Washington, Seattle.
12. GELFAND, M. S., A. A. MIRONOV, and P. A. PEVZNER. 1996. Gene recognition via spliced sequence alignment. Proc. Natl. Acad. Sci. USA 93:9061-9066.
13. GILBERT, W. 1987. The exon theory of genes. Cold Spring Harb. Symp. Quant. Biol. 52:901-905.
14. GILBERT, W., and M. GLYNIAS. 1993. On the ancient nature of introns. Gene 135:137-144.
15. Go, M. 1981. Correlation of DNA exonic regions with protein structural units in haemoglobin. Nature 291:90-92.
16. GOTOH, O. 1987. Pattern matching of biological sequences with limited storage. Comput. Appl. Biosci. 3:17-20.
17. _. 1990. Optimal sequence alignment allowing for long gaps. Bull. Math. Biol. 52:359-373.
18. _. 1993a. Structure of P-450 genes. Pp. 207-223 in T. OMURA, Y. ISHIMURA, and Y. FUJII-KURIYAMA, eds. Cytochrome P-450. Kodansha, Tokyo.
19. _. 1993b. Evolution and differentiation of P-450 genes. Pp. 255-272 in T. OMURA, Y. ISHIMURA, and Y. FUJII-KURIYAMA, eds. Cytochrome P-450. Kodansha, Tokyo.
20. _. 1996. Significant improvement in accuracy of multiple protein sequence alignments by iterative refinement as assessed by reference to structural alignments. J. Mol. Biol. 264:823-838.
21. GRIBSKOV, M., A. D. MCLACHLAN, and D. EISENBERG. 1987. Profile analysis: detection of distantly related proteins. Proc. Natl. Acad. Sci. USA 84:4355-4358.
22. HASEMANN, C. A., R. G. KURUMBAIL, S. S. BODDUPALLI, J. A. PETERSON, and J. DEISENHOFER. 1995. Structure and function of cytochromes P450: a comparative analysis of three crystal structures. Structure 2:41-62.
23. HUANG, X., and J. ZHANG. 1996. Methods for comparing a K-DNA sequence with a protein sequence. Comput. Appl. Biosci. 12:497-506.
24. JONES, D. T., W. R. TAYLOR, and J. M. THORNTON. 1992. The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci. 8:275-282.
25. KERSANACH, R., H. BRINKMANN, M.-F. LIAUD, D.-X. ZHANG, W. MARTIN, and R. CERFF. 1994. Five identical intron positions in ancient duplicated genes of eubacterial origin. Nature 367:387-389.
26. KISHINO, H., T. MIYATA, and M. HASEGAWA. 1990. Maximum likelihood inference of protein phylogeny and the origin of chloroplasts. J. Mol. Evol. 31:151-160.
27. LOGSDON, J. M. JR., M. G. TYSHENKO, C. DIXON, J. D.-JAFARI, V. K. WALKER, and J. D. PALMER. 1995. Seven newly discovered intron positions in the triose-phosphate isomerase gene: evidence for the intron-late theory. Proc. Natl. Acad. Sci. USA 92:8507-8511.
28. LONG, M., S. J. DE SOUZA, C. ROSENBERG, and W. GILBERT. 1998. Relationship between "proto-splice sites" and intron phases: evidence from dicodon analysis. Proc. Natl. Acad. Sci. USA 95:219-223.
29. LONG, M., C. ROSENBERG, and W. GILBERT. 1995. Intron phase correlations and the evolution of the intron/exon structure of genes. Proc. Natl. Acad. Sci. USA 92:12495-12499.
30. NEEDLEMAN, S. B., and C. D. WUNSCH. 1970. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 48:443-453.
31. NELSON, D. R., T. KAMATAKI, D. J. WAXMAN et al. (12 coauthors). 1993. The P450 superfamily: update on new sequences, gene mapping, accession numbers, early trivial names of enzymes, and nomenclature. DNA Cell Biol. 12: 1-51.
32. NELSON, D. R., L. KOYMANS, T. KAMATAKI et al. (12 co-authors). 1996. P450 superfamily: update on new sequences, gene mapping, accession numbers, and nomenclature. Pharmacogenetics 6:1-42.
33. PALMER, J. D., and J. M. LOGSDON JR. 1991. The recent origins of introns. Curr. Opin. Genet. Dev. 1:470-477.
34. ROGERS, J. H. 1990. The role of introns in evolution. FEBS Lett. 268:339-343.
35. RZHETSKY, A., F. J. AYALA, L. C. HSU, C. CHANG, and A. YOSHIDA. 1997. Exon/intron structure of aldehyde dehydrogenase genes supports the "intron-late" theory. Proc. Natl. Acad. Sci. USA 94:6820-6825.
36. SAITOU, N., and M. NEI. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
37. SMITH, T. F., and M. S. WATERMAN. 1981. Identification of common molecular subsequences. J. Mol. Biol. 147:195-197.
38. SNYDER, E. E., and G. D. STORMO. 1995. Identification of protein coding regions in genomic DNA. J. Mol. Biol. 248:1-18.
39. STOLTZFUS, A., J. M. LOGSDON JR., J. D. PALMER, and W. F. DOOLITTLE. 1997. Intron "sliding" and the diversity of intron positions. Proc. Natl. Acad. Sci. USA 94:10739-10744.
40. STOLTZFUS, A., D. F. SPENCER, M. ZUKER, J. M. LOGSDON JR., and W. F. DOOLITTLE. 1994. Testing the exon theory of genes: the evidence from protein structure. Science 265: 202-207.
41. UBERBACHER, E. C., and R. J. MURAL. 1991. Locating protein-coding regions in human DNA sequences by a multiple sensor-neural network approach. Proc. Natl. Acad. Sci. USA 88:11261-11265.
42. YOSHIDA, Y., M. NOSHIRO, Y. AOYAMA, T. KAWAMOTO, T. HORIUCHI, and O. GOTOH. 1997. Structural and evolutionary studies on sterol 14-demethylase P450 (CYP51), the most conserved P450 monooxygenase II. Evolutionary analysis of protein and gene structures. J. Biochem. (Tokyo) 122:1122-1128.
43. ZHANG, M. Q. 1997. Identification of protein coding regions in the human genome by quadratic discriminant analysis. Proc. Natl. Acad. Sci. USA 94:565-568.