Molecular and functional evolution of human DHRS2 and DHRS4 duplicated genes

Gene

Volumn 511, Issue 2, 2012, Pages 461-469

  Gabrielli, Franco ^a   Tofanelli, Sergio ^a  

^a UNIVERSITY OF PISA   (Italy)

Author keywords

DHRS2; DHRS4; Duplicated genes; Molecular and functional evolution; Positive selection; SDR enzymes

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; CELL FUNCTION; CELLULAR DISTRIBUTION; CONTROLLED STUDY; DHRS2 GENE; DHRS4 GENE; DUPLICATE GENE; ENZYME ACTIVE SITE; ENZYME SPECIFICITY; EVOLUTION; GENE; GENE DUPLICATION; GENETIC SELECTION; HUMAN; MOLECULAR EVOLUTION; PRIORITY JOURNAL; PROTEIN SYNTHESIS REGULATION;

ALCOHOL OXIDOREDUCTASES; AMINO ACID SEQUENCE; ANIMALS; CATALYSIS; EVOLUTION, MOLECULAR; GENE DUPLICATION; HUMANS; MOLECULAR SEQUENCE DATA; NUCLEAR PROTEINS; OXIDOREDUCTASES; PHYLOGENY; SEQUENCE HOMOLOGY, AMINO ACID; SUBSTRATE SPECIFICITY;

MAMMALIA;

EID: 84868202886     PISSN: 03781119     EISSN: 18790038     Source Type: Journal    
DOI: 10.1016/j.gene.2012.09.013     Document Type: Article

References (47)

1. Bhati R., et al. Molecular characterization of human breast tumor vascular cells. Am. J. Pathol. 2008, 172:1381-1390.
2. Bhattacharyya C., et al. Simultaneous classification and relevant feature identification in high-dimensional spaces: application to molecular profiling data. Signal Process. 2003, 83:729-743.
3. Bray J.E., Marsden B.D., Oppermann U. The human short-chain dehydrogenase/reductase (SDR) superfamily: a bioinformatics summary. Chem. Biol. Interact. 2009, 178:99-109.
4. Brock A., Brandt W., Dräger B. The functional divergence of short-chain dehydrogenases involved in tropinone reduction. Plant J. 2008, 54:388-401.
5. Byun-McKay S.A., Geeta R. Protein subcellular relocalization: a new perspective on the origin of novel genes. Trends Ecol. Evol. 2007, 22:338-344.
6. Deisenroth C., Thorner A.R., Enomoto T., Perou C.M., Zhang Y. Mitochondrial HEP27 is a c-Myb target gene that inhibits Mdm2 and stabilizes p53. Mol. Cell. Biol. 2010, 30:3981-3993.
7. Donadel G., Garzelli C., Frank R., Gabrielli F. Identification of a novel nuclear protein synthesized in growth-arrested human hepatoblastoma HepG2 cells. Eur. J. Biochem. 1991, 195:723-729.
8. El-Kabbani O., Carbone V., Darmanin C., Ishikura S., Hara A. Structure of the tetrameric form of human L-xylulose reductase: probing the inhibitor-binding site with molecular modeling and site-directed mutagenesis. Proteins 2005, 60:424-432.
9. Endo S., et al. Characterization of an oligomeric carbonyl reductase of dog liver: its identity with peroxisomal tetrameric carbonyl reductase. Biol. Pharm. Bull. 2007, 30:787-1791.
10. Endo S., et al. Molecular determinants for the stereospecific reduction of 3-ketosteroids and reactivity towards all-trans-retinal of a short-chain dehydrogenase/reductase (DHRS4). Arch. Biochem. Biophys. 2009, 481:183-190.
11. Felsenstein J. PHYLIP (Phylogeny Inference Package) version 3.6 2005, Distributed by the author, Department of Genome Science, University of Washington, Seattle.
12. Gabrielli F., Donadel G., Bensi G., Heguy A., Melli M. A nuclear protein, synthesized in growth-arrested human hepatoblastoma cells, is a novel member of the short-chain alcohol dehydrogenase family. Eur. J. Biochem. 1995, 232:473-477.
13. Han M.V., Demuth J.P., McGrath C.L., Casola C., Hahn M.W. Adaptive evolution of young gene duplicates in mammals. Genome Res. 2009, 19:859-867.
14. Heinz S., Krause S.W., Gabrielli F., Wagner H.M., Andreesen R., Rehli M. Genomic organization of the human Hep27 gene: alternative promoter usage in HepG2 cells and monocyte-derived dendritic cells. Genomics 2002, 79:608-615.
15. Huang X., Miller W. A time-efficient, linear-space local similarity algorithm. Adv. Appl. Math. 1991, 12:337-357.
16. Irimia M.I., Roy S.W. Spliceosomal introns as tools for genomic and evolutionary analysis. Nucleic Acids Res. 2008, 36:1703-1712.
17. Jornvall H., et al. Short-chain dehydrogenases/reductases (SDR). Biochemistry 1995, 34:6003-6013.
18. Lametschwandtner G., Brocard C., Fransen M., Van Veldhoven P., Berger J., Hartig A. The difference in recognition of terminal tripeptides as peroxisomal targeting signal 1 between yeast and human is due to different affinities of their receptor Pex5p to the cognate signal and to residues adjacent. J. Biol. Chem. 1998, 273:33635-33643.
19. Larkin M.A., et al. Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 2000, 155:431-449.
20. Larkin M.A., et al. Clustal W and Clustal X version 2.0. Bioinformatics 2007, 24:2947-2948.
21. Lei Z., Chen W., Zhang M., Napoli J.L. Reduction of all-trans-retinal in the mouse liver peroxisome fraction by the short-chain dehydrogenase/reductase RRD, induction by the PPARR ligand clofibrate. Biochemistry 2003, 42:4190-4196.
22. Marques A.C., Vinckenbosch N., Brawand D., Kaessmann H. Functional diversification of duplicate genes through subcellular adaptation of encoded proteins. Genome Biol. 2008, 9:R54.
23. Matsunaga T., et al. Characterization of human DHRS4, an inducible short-chain dehydrogenase/reductase enzyme with 3b-hydroxysteroid-dehydrogenase activity. Arch. Biochem. Biophys. 2008, 477:339-347.
24. Monge M., et al. Proteomic approach to ETV5 during endometrial carcinoma invasion reveals a link to oxidative stress. Carcinogenesis 2009, 30:1288-1297.
25. Nielsen R., Yang Z. Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics 1998, 148:929-936.
26. Oppermann U. Carbonyl reductases: the complex relationships of mammalian carbonyl- and quinone-reducing enzymes and their role in physiology. Annu. Rev. Pharmacol. Toxicol. 2007, 47:293-322.
27. Oppermann U., Filling C., Jornvall H. Forms and functions of human SDR enzymes. Chem. Biol. Interact. 2001, 130-132:699-705.
28. Pellegrini S., et al. A human short-chain dehydrogenase/reductase gene: structure., chromosomal localization, tissue expression and subcellular localization of its product. Biochim. Biophys. Acta 2002, 1574(3):215-222.
29. Peltoketo H., Luu-The V., Simard J., Adamski J. 17b-hydroxysteroid dehydrogenase (HSD)/17-ketosteroid reductase (KSR) family; nomenclature and main characteristics of the 17HSD/KSR enzymes. J. Mol. Endocrinol. 1999, 23:1-11.
30. Peterson L.E., et al. Artificial neural network analysis of DNA microarray-based prostate cancer recurrence. Proceedings of the IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology 2005, 1-8. 10.1109/CIBCB.2005.1594929.
31. Pichersky E., Noel J.P., Dudareva N. Biosynthesis of plant volatiles: nature's diversity and ingenuity. Science 2006, 311:808-811.
32. Rushton J.J., Davis L.M., Lei W., Mo X., Leutz A., Ness S.A. Distinct changes in gene expression induced by A-Myb., B-Myb and c-Myb proteins. Oncogene 2003, 22:308-313.
33. Saitou N., Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 1987, 4:406-425.
34. Shafqat N., et al. Hep27, a member of the short-chain dehydrogenase/reductase family, is an NADPH-dependent dicarbonyl reductase expressed in vascular endothelial tissue. Cell. Mol. Life Sci. 2006, 63:1205-1213.
35. Shedden K.A., et al. Accurate molecular classification of human cancers based on gene expression using a simple classifier with a pathological tree-based framework. Am. J. Pathol. 2003, 163:1985-1995.
36. Tanaka N., Nonaka T., Nakamura K.T., Hara A. SDR: structure., mechanism of action, and substrate recognition. Curr. Org. Chem. 2001, 5:89-111.
37. Tanaka N., et al. Molecular basis for peroxisomal localization of tetrameric carbonyl reductase. Structure 2008, 16:388-397.
38. Taylor J.S., Raes J. Duplication and divergence: the evolution of new genes and old ideas. Annu. Rev. Genet. 2004, 38:615-643.
39. Thanaraj T.A., Clark F. Human GC-AG alternative intron isoforms with weak donor sites show enhanced consensus at acceptor exon positions. Nucleic Acids Res. 2001, 29:2581-2593.
40. Thorner A.R., Parker J.S., Hoadley K.A., Perou C.M. Potential tumor suppressor role for the c-Myb oncogene in luminal breast cancer. PLoS One 2010, 5:e13073.
41. Tress M.L., et al. Determination and validation of principal gene products. Bioinformatics 2008, 24:11-17.
42. Usami N., et al. Cloning, expression and tissue distribution of a tetrameric form of pig carbonyl reductase. Chem. Biol. Interact. 2003, 143-144:353-361.
43. Wu X., Lukacik P., Kavanagh K.L., Oppermann U. SDR-type human hydroxysteroid dehydrogenases involved in steroid hormone activation. Mol. Cell. Endocrinol. 2007, 265-266:71-76.
44. Yang Z. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 1997, 13:555-556.
45. Yang Z., Nielsen R. Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol. Biol. Evol. 2002, 19:908-917.
46. Yang Z., Wong W.S., Nielsen R. Bayes empirical bayes inference of amino acid sites under positive selection. Mol. Biol. Evol. 2005, 22:1107-1118.
47. Zhang J. Evolution by gene duplication: an update. Trends Ecol. Evol. 2003, 18:292-298.