Evolutionary fate of duplicate genes encoding aspartic proteinases. Nothepsin case study

Gene

Volumn 368, Issue 1-2, 2006, Pages 101-109

  Borrelli, Lucia ^a   De Stasio, Roberta ^a   Filosa, Silvana ^a   Parisi, Elio ^b   Riggio, Marilisa ^a   Scudiero, Rosaria ^a   Trinchella, Francesca ^a  

^a UNIVERSITY OF NAPLES FEDERICO II   (Italy)

^b INSTITUTE OF PROTEIN BIOCHEMISTRY   (Italy)

Author keywords

Cathepsin D; Functional divergence; Gene preservation; Positive selection

Indexed keywords

AMINO ACID; ASPARTIC PROTEINASE; CATHEPSIN D; ENZYME; ESTROGEN;

AMINO ACID SUBSTITUTION; ANIMAL EXPERIMENT; ANIMAL TISSUE; ARTICLE; CELL LINEAGE; CLADISTICS; ENZYME METABOLISM; FEMALE; FISH; FOWL; GENE; GENE CONTROL; GENE DUPLICATION; GENE EXPRESSION; GENE LOSS; GENE MUTATION; GENETIC CODE; GENETIC VARIABILITY; GENOME; HORMONE ACTION; HUMAN; LIVER; LIZARD; MALE; METABOLISM; MOLECULAR EVOLUTION; MULTIGENE FAMILY; NATURAL SELECTION; NONHUMAN; NOTHEPSIN GENE; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; PROMOTER REGION; REPTILE; TISSUE SPECIFICITY;

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ANIMALS; ASPARTIC ENDOPEPTIDASES; BASE SEQUENCE; CATHEPSIN D; EVOLUTION, MOLECULAR; FISHES; GENE DUPLICATION; LIZARDS; MOLECULAR SEQUENCE DATA; PHYLOGENY;

ANIMALIA; AVES; MURINAE; PISCES; REPTILIA; SQUAMATA;

EID: 33344471384     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.gene.2005.10.024     Document Type: Article

References (29)

1. J. Adachi, and M. Hasegawa MOLPHY: programs for molecular phylogenetics, I: PROTML: maximum-likelihood inference of protein phylogeny Computer Sciences Monographs vol. 27 1992 Institute of Statistical Mathematics Tokyo
2. J.P. Bielawski, and Z. Yang Maximum likelihood methods for detecting adaptive evolution after gene duplication J. Struct. Funct. Genomics 3 2003 201 212
3. C. Capasso Molecular cloning and sequence determination of a novel aspartic proteinase from Antarctic fish Biochim. Biophys. Acta 1387 1998 457 461
4. V. Carginale, F. Trinchella, C. Capasso, R. Scudiero, M. Riggio, and E. Parisi Adaptive evolution and functional divergence of pepsin gene family Gene 333 2004 81 90
5. P. Chomczynski, and N. Sacchi Single step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction Anal. Biochem. 162 1987 156 159
6. C. Creevey, and J.O. McInerney An algorithm for detecting directional and non-directional positive selection, neutrality and negative selection in protein coding DNA sequences Gene 300 2002 43 51
7. R. De Stasio, L. Borrelli, P. Kille, E. Parisi, and S. Filosa Isolation, characterization and molecular cloning of cathepsin D from lizard ovary: changes in enzyme activity and mRNA expression throughout ovarian cycle Mol. Reprod. Dev. 52 1999 126 134
8. A. Force, M. Lynch, F. Pickett, A. Amores, Y. Yan, and J. Postlethwait Preservation of duplicate genes by complementary, degenerative mutations Genetics 151 1999 1531 1545
9. X. Gu Statistical methods for testing functional divergence after gene duplication Mol. Biol. Evol. 16 1999 1664 1674
10. M. Hetman, A. Perschl, P. Saftig, K. Von Figura, and C. Peters Mouse cathepsin D gene: molecular organization, characterization of the promoter, and chromosomal localization DNA Cell Biol. 13 1994 419 427
11. I.N. Hsu, L.T.J. Delabaere, and M.N.G. James Penicillopepsin from Penicillinum janhtinellum crystal structure at 2.8 A and sequence homology with porcine pepsin Nature 266 1977 140 145
12. J.P.H. Huelsenbeck, and F. Ronquist MRBAYES: Bayesian inference of phylogeny Bioinformatics 17 2001 754 755
13. T. Kageyama Pepsinogen, progastricsin, and prochymosin: structure, function, evolution, and development CMLS, Cell. Mol. Life Sci. 59 2002 288 306
14. S. Kumar, K. Tamura, I.B. Jakobsen, and M. Nei MEGA2: molecular evolutionary genetics analysis software Bioinformatics 17 2001 1244 1245
15. M. Lynch, and A. Force The probability of duplicate genes preservation by subfunctionalization Genetics 154 2000 459 473
16. T.P. Mommsen Salmon spawning migration and muscle protein metabolism: the August Krogh principle at work Comp. Biochem. Physiol., Part B Biochem. Mol. Biol. 139 2004 383 400
17. J.H. Nadeau, and D. Sankoff Comparable rates of gene loss and functional divergence after genome duplications early in vertebrate evolution Genetics 147 1997 1259 1266
18. M. Nei, and T. Gojobori Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions Mol. Biol. Evol. 3 1986 418 426
19. S. Ohno Evolution by Gene Duplication 1970 Springer-Verlag Heidelberg, Germany
20. W.R. Pearson Using the FASTA program to search protein and DNA sequence databases Methods Mol. Biol. 25 1994 365 389
21. M. Riggio, R. Scudiero, S. Filosa, and E. Parisi Sex- and tissue-specific expression of aspartic proteinases in Danio rerio (zebrafish) Gene 260 2000 67 75
22. M. Riggio, R. Scudiero, S. Filosa, and E. Parisi Oestrogen-induced expression of a novel liver-specific aspartic proteinase in Danio rerio (zebrafish) Gene 295 2002 241 246
23. J. Sambrook, and D.W. Russel Molecular Cloning. A Laboratory Manual 2001 Harbor Laboratory Press New York
24. F. Sanger, S. Nicklen, and A.R. Coulson DNA sequencing with chain-terminating inhibitors Proc. Natl. Acad. Sci. U. S. A. 74 1977 5463 5467
25. P. Sepulveda, J. Marciniszyn, D. Liu, and J. Tang Primary structure of porcine pepsin. III. Amino acid sequence of a cyanogen bromide fragment, CB2A, and the complete structure of porcine pepsin J. Biol. Chem. 250 1975 5082 5088
26. K. Strimmer, and A. von Haeseler Quartet puzzling: a quartet maximum likelihood method for reconstructing tree topologies Mol. Biol. Evol. 13 1996 964 969
27. J. Tang, M.N.G. James, I.N. Hsu, J.A. Jenkins, and T.L. Blundell Structural evidence for gene duplication in the evolution of the acid proteases Nature 271 1978 618 621
28. Y. Wang, and X. Gu Functional divergence in the caspase gene family and altered functional constraints: statistical analysis and prediction Genetics 158 2001 1311 1320
29. J. Zhang Evolution by gene duplication: an update Trends Ecol. Evol. 18 2003 292 298