Comparative genomic analysis of human and chimpanzee proteases

Genomics

Volumn 86, Issue 6, 2005, Pages 638-647

  Puente, Xose S ^a   Gutiérrez Fernández, Ana ^a   Ordóñez, Gonzalo R ^a   Hillier, LaDeana W ^b   López Otín, Carlos ^a  

^a DEPARTAMENTO DE BIOQUÍMICA Y BIOLOGÍA MOLECULAR   (Spain)

^b WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Chimpanzee; Degradome; Human; Immune system; Proteases

Indexed keywords

MATRIX METALLOPROTEINASE; METALLOPROTEINASE; PROTEINASE; SERINE PROTEINASE;

ANIMAL CELL; ARTICLE; CHIMPANZEE; CHROMOSOME MAP; CONTROLLED STUDY; ENZYME ANALYSIS; GENE DUPLICATION; GENE FUNCTION; GENE INACTIVATION; GENE LOCATION; GENE SEQUENCE; GENETIC CODE; GENETIC CONSERVATION; GENETIC SUSCEPTIBILITY; GENOME ANALYSIS; HUMAN; HUMAN CELL; IMMUNE SYSTEM; MACROPHAGE; MALE; MOUSE; NONHUMAN; PRIORITY JOURNAL; PSEUDOGENE; SINGLE NUCLEOTIDE POLYMORPHISM; SPECIES DIFFERENCE; TRYPANOSOMA; TRYPANOSOMA BRUCEI;

ANIMALIA; MAMMALIA; PAN; PAN TROGLODYTES; TRYPANOSOMA; TRYPANOSOMA BRUCEI;

EID: 28644432882     PISSN: 08887543     EISSN: 10898646     Source Type: Journal    
DOI: 10.1016/j.ygeno.2005.07.009     Document Type: Article

References (59)

1. E.S. Lander, L.M. Linton, B. Birren, C. Nusbaum, M.C. Zody, J. Baldwin, K. Devon, K. Dewar, M. Doyle, and W. FitzHugh Initial sequencing and analysis of the human genome Nature 409 2001 860 921
2. J.C. Venter, M.D. Adams, E.W. Myers, P.W. Li, R.J. Mural, G.G. Sutton, H.O. Smith, M. Yandell, C.A. Evans, and R.A. Holt The sequence of the human genome Science 291 2001 1304 1351
3. The Chimpanzee Sequencing and Analysis Consortium Initial sequence of the chimpanzee genome and comparison with the human genome Nature 437 2005 69 87
4. M.V. Olson, and A. Varki Sequencing the chimpanzee genome: insights into human evolution and disease Nat. Rev. Genet. 4 2003 20 28
5. S. Caenepeel, G. Charydczak, S. Sudarsanam, T. Hunter, and G. Manning The mouse kinome: discovery and comparative genomics of all mouse protein kinases Proc. Natl. Acad. Sci. USA 101 2004 11707 11712
6. X.S. Puente, L.M. Sánchez, C.M. Overall, and C. López-Otín Human and mouse proteases: a comparative genomic approach Nat. Rev. Genet. 4 2003 544 558
7. T. Angata, E.H. Margulies, E.D. Green, and A. Varki Large-scale sequencing of the CD33-related Siglec gene cluster in five mammalian species reveals rapid evolution by multiple mechanisms Proc. Natl. Acad. Sci. USA 2004
8. Z. Zhang, P.E. Burch, A.J. Cooney, R.B. Lanz, F.A. Pereira, J. Wu, R.A. Gibbs, G. Weinstock, and D.A. Wheeler Genomic analysis of the nuclear receptor family: new insights into structure, regulation, and evolution from the rat genome Genome Res. 14 2004 580 590
9. R.D. Emes, S.A. Beatson, C.P. Ponting, and L. Goodstadt Evolution and comparative genomics of odorant- and pheromone-associated genes in rodents Genome Res. 14 2004 591 602
10. A. Fischer, Y. Gilad, O. Man, and S. Paabo Evolution of bitter taste receptors in humans and apes Mol. Biol. Evol. 22 2005 432 436
11. G. Suske, E. Bruford, and S. Philipsen Mammalian SP/KLF transcription factors: bring in the family Genomics 85 2005 551 556
12. C. López-Otín, and C.M. Overall Protease degradomics: a new challenge for proteomics Nat. Rev. Mol. Cell. Biol. 3 2002 509 519
13. C.M. Overall, and C. López-Otín Strategies for MMP inhibition in cancer: innovations for the post-trial era Nat. Rev. Cancer 2 2002 657 672
14. R. Vassar Beta-secretase (BACE) as a drug target for Alzheimer's disease Adv. Drug Delivery Rev. 54 2002 1589 1602
15. W.P. Esler, and M.S. Wolfe A portrait of Alzheimer secretases - New features and familiar faces Science 293 2001 1449 1454
16. Y. Liu, L. Fallon, H.A. Lashuel, Z. Liu, and P.T. Lansbury Jr. The UCH-L1 gene encodes two opposing enzymatic activities that affect alpha-synuclein degradation and Parkinson's disease susceptibility Cell 111 2002 209 218
17. E. Petek, C. Windpassinger, J.B. Vincent, J. Cheung, A.P. Boright, S.W. Scherer, P.M. Kroisel, and K. Wagner Disruption of a novel gene (IMMP2L) by a breakpoint in 7q31 associated with Tourette syndrome Am. J. Hum. Genet. 68 2001 848 858
18. W. Enard, P. Khaitovich, J. Klose, S. Zollner, F. Heissig, P. Giavalisco, K. Nieselt-Struwe, E. Muchmore, A. Varki, and R. Ravid Intra- and interspecific variation in primate gene expression patterns Science 296 2002 340 343
19. P. Khaitovich, B. Muetzel, X. She, M. Lachmann, I. Hellmann, J. Dietzsch, S. Steigele, H.H. Do, G. Weiss, and W. Enard Regional patterns of gene expression in human and chimpanzee brains Genome Res. 14 2004 1462 1473
20. X.S. Puente, and C. López-Otín A genomic analysis of rat proteases and protease inhibitors Genome Res. 14 2004 609 622
21. A. Fortna, Y. Kim, E. MacLaren, K. Marshall, G. Hahn, L. Meltesen, M. Brenton, R. Hink, S. Burgers, and T. Hernandez-Boussard Lineage-specific gene duplication and loss in human and great ape evolution PLoS Biol. 2 2004 E207
22. G. Velasco, A.M. Pendás, A. Fueyo, V. Knäuper, G. Murphy, and C. López-Otín Cloning and characterization of human MMP-23, a new matrix metalloproteinase predominantly expressed in reproductive tissues and lacking conserved domains in other family members J. Biol. Chem. 274 1999 4570 4576
23. R. Gururajan, J.M. Lahti, J. Grenet, J. Easton, I. Gruber, P.F. Ambros, and V.J. Kidd Duplication of a genomic region containing the Cdc2L1-2 and MMP21-22 genes on human chromosome 1p36.3 and their linkage to D1Z2 Genome Res. 8 1998 929 939
24. C. Chen, A.L. Darrow, J.S. Qi, M.R. D'Andrea, and P. Andrade-Gordon A novel serine protease predominately expressed in macrophages Biochem. J. 374 2003 97 107
25. N.C. Cheng, N. Van Roy, A. Chan, M. Beitsma, A. Westerveld, F. Speleman, and R. Versteeg Deletion mapping in neuroblastoma cell lines suggests two distinct tumor suppressor genes in the 1p35-36 region, only one of which is associated with N-myc amplification Oncogene 10 1995 291 297
26. B.J. Dave, D.L. Pickering, M.M. Hess, D.D. Weisenburger, J.O. Armitage, and W.G. Sanger Deletion of cell division cycle 2-like 1 gene locus on 1p36 in non-Hodgkin lymphoma Cancer Genet. Cytogenet. 108 1999 120 126
27. I. Dunham, N. Shimizu, B.A. Roe, S. Chissoe, A.R. Hunt, J.E. Collins, R. Bruskiewich, D.M. Beare, M. Clamp, and L.J. Smink The DNA sequence of human chromosome 22 Nature 402 1999 489 495
28. P.G. Buckley, K.K. Mantripragada, M. Benetkiewicz, I. Tapia-Paez, T. Diaz De Stahl, M. Rosenquist, H. Ali, C. Jarbo, C. De Bustos, and C. Hirvela A full-coverage, high-resolution human chromosome 22 genomic microarray for clinical and research applications Hum. Mol. Genet. 11 2002 3221 3229
29. R.A. Gibbs, G.M. Weinstock, M.L. Metzker, D.M. Muzny, E.J. Sodergren, S. Scherer, G. Scott, D. Steffen, K.C. Worley, and P.E. Burch Genome sequence of the Brown Norway rat yields insights into mammalian evolution Nature 428 2004 493 521
30. P.J. Tatnell, D.J. Powell, J. Hill, T.S. Smith, D.G. Tew, and J. Kay Napsins: new human aspartic proteinases: distinction between two closely related genes FEBS Lett. 441 1998 43 48
31. M. Cook, F. Buhling, S. Ansorge, P.J. Tatnell, and J. Kay Pronapsin A and B gene expression in normal and malignant human lung and mononuclear blood cells Biochim. Biophys. Acta 1577 2002 10 16
32. B.P. Shum, L.R. Flodin, D.G. Muir, R. Rajalingam, S.I. Khakoo, S. Cleland, L.A. Guethlein, M. Uhrberg, and P. Parham Conservation and variation in human and common chimpanzee CD94 and NKG2 genes J. Immunol. 168 2002 240 252
33. D. Meyer-Olson, K.W. Brady, J.T. Blackard, T.M. Allen, S. Islam, N.H. Shoukry, K. Hartman, C.M. Walker, and S.A. Kalams Analysis of the TCR beta variable gene repertoire in chimpanzees: identification of functional homologs to human pseudogenes J. Immunol. 170 2003 4161 4169
34. E.J. Adams, S. Cooper, and P. Parham A novel, nonclassical MHC class I molecule specific to the common chimpanzee J. Immunol. 167 2001 3858 3869
35. T. Anzai, T. Shiina, N. Kimura, K. Yanagiya, S. Kohara, A. Shigenari, T. Yamagata, J.K. Kulski, T.K. Naruse, and Y. Fujimori Comparative sequencing of human and chimpanzee MHC class I regions unveils insertions/deletions as the major path to genomic divergence Proc. Natl. Acad. Sci. USA 100 2003 7708 7713
36. H. Fischer, U. Koenig, L. Eckhart, and E. Tschachler Human caspase 12 has acquired deleterious mutations Biochem. Biophys. Res. Commun. 293 2002 722 726
37. M. Saleh, J.P. Vaillancourt, R.K. Graham, M. Huyck, S.M. Srinivasula, E.S. Alnemri, M.H. Steinberg, V. Nolan, C.T. Baldwin, and R.S. Hotchkiss Differential modulation of endotoxin responsiveness by human caspase-12 polymorphisms Nature 429 2004 75 79
38. S.M. McEvoy, and N. Maeda Complex events in the evolution of the haptoglobin gene cluster in primates J. Biol. Chem. 263 1988 15740 15747
39. L.M. Erickson, H.S. Kim, and N. Maeda Junctions between genes in the haptoglobin gene cluster of primates Genomics 14 1992 948 958
40. A.B. Smith, J.D. Esko, and S.L. Hajduk Killing of trypanosomes by the human haptoglobin-related protein Science 268 1995 284 286
41. L. Vanhamme, F. Paturiaux-Hanocq, P. Poelvoorde, D.P. Nolan, L. Lins, J. Van Den Abbeele, A. Pays, P. Tebabi, H. Van Xong, and A. Jacquet Apolipoprotein L-I is the trypanosome lytic factor of human serum Nature 422 2003 83 87
42. H.L. Paulson, N.M. Bonini, and K.A. Roth Polyglutamine disease and neuronal cell death Proc. Natl. Acad. Sci. USA 97 2000 12957 12958
43. M. Llamazares, S. Cal, V. Quesada, and C. López-Otín Identification and characterization of ADAMTS-20 defines a novel subfamily of metalloproteinases-disintegrins with multiple thrombospondin-1 repeats and a unique GON domain J. Biol. Chem. 278 2003 13382 13389
44. R. Pfutzer, E. Myers, S. Applebaum-Shapiro, R. Finch, I. Ellis, J. Neoptolemos, J.A. Kant, and D.C. Whitcomb Novel cationic trypsinogen (PRSS1) N29T and R122C mutations cause autosomal dominant hereditary pancreatitis Gut 50 2002 271 272
45. M. Balbín, A. Fueyo, A.M. Tester, A.M. Pendás, A.S. Pitiot, A. Astudillo, C.M. Overall, S.D. Shapiro, and C. López-Otín Loss of collagenase-2 confers increased skin tumor susceptibility to male mice Nat. Genet. 35 2003 252 257
46. L.M. Coussens, C.L. Tinkle, D. Hanahan, and Z. Werb MMP-9 supplied by bone marrow-derived cells contributes to skin carcinogenesis Cell 103 2000 481 490
47. L.M. Coussens, and Z. Werb Inflammation and cancer Nature 420 2002 860 867
48. D.S. Beniashvili An overview of the world literature on spontaneous tumors in nonhuman primates J. Med. Primatol. 18 1989 423 437
49. A. Varki A chimpanzee genome project is a biomedical imperative Genome Res. 10 2000 1065 1070
50. M.I. Jensen-Seaman, and W.H. Li Evolution of the hominoid semenogelin genes, the major proteins of ejaculated semen J. Mol. Evol. 57 2003 261 270
51. T. Nakagawa, H. Zhu, N. Morishima, E. Li, J. Xu, B.A. Yankner, and J. Yuan Caspase-12 mediates endoplasmic-reticulum-specific apoptosis and cytotoxicity by amyloid-beta Nature 403 2000 98 103
52. C. Rao, D. Foernzler, S.K. Loftus, S. Liu, J.D. McPherson, K.A. Jungers, S.S. Apte, W.J. Pavan, and D.R. Beier A defect in a novel ADAMTS family member is the cause of the belted white-spotting mutation Development 130 2003 4665 4672
53. R. Blelloch, S.S. Anna-Arriola, D. Gao, Y. Li, J. Hodgkin, and J. Kimble The gon-1 gene is required for gonadal morphogenesis in Caenorhabditis elegans Dev. Biol. 216 1999 382 393
54. W.C. Parks, C.L. Wilson, and Y.S. Lopez-Boado Matrix metalloproteinases as modulators of inflammation and innate immunity Nat. Rev. Immunol. 4 2004 617 629
55. H. Tsukada, and T. Pourmotabbed Unexpected crucial role of residue 272 in substrate specificity of fibroblast collagenase J. Biol. Chem. 277 2002 27378 27384
56. B.P. Lawrence, Y. Will, D.J. Reed, and N.I. Kerkvliet Gamma-glutamyltranspeptidase knockout mice as a model for understanding the consequences of diminished glutathione on T cell-dependent immune responses Eur. J. Immunol. 30 2000 1902 1910
57. W.J. Kent BLAT - The BLAST-like alignment tool Genome Res. 12 2002 656 664
58. S.F. Altschul, T.L. Madden, A.A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D.J. Lipman Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Nucleic Acids Res. 25 1997 3389 3402
59. J.M. Comeron K-Estimator: calculation of the number of nucleotide substitutions per site and the confidence intervals Bioinformatics 15 1999 763 764