Proteolytic systems: Constructing degradomes

Methods in Molecular Biology

Volumn 539, Issue , 2009, Pages 33-47

  Ordóñez, Gonzalo R ^a   Puente, Xose S ^a   Quesada, Víctor ^a   López Otín, Carlos ^a  

^a DEPARTAMENTO DE BIOQUÍMICA Y BIOLOGÍA MOLECULAR   (Spain)

Author keywords

Bioinformatics; Degradome; Disease; Evolution; Genome; Protease

Indexed keywords

MAMMALIA; PAN; RATTUS;

PEPTIDE HYDROLASE;

ANIMAL; BIOLOGY; GENETICS; GENOMICS; HUMAN; HUMAN GENOME; METHODOLOGY; MOLECULAR EVOLUTION; REVIEW;

ANIMALS; COMPUTATIONAL BIOLOGY; EVOLUTION, MOLECULAR; GENOME, HUMAN; GENOMICS; HUMANS; PEPTIDE HYDROLASES;

EID: 78649646060     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-60327-003-8_2     Document Type: Article

References (52)

1. Fujinaga, M., et al (2004) The molecular structure and catalytic mechanism of a novel carboxyl peptidase from Scytalidium ligni-colum. Proc Natl Acad Sci USA 101 (10), 3364-9. (Pubitemid 38338200)
2. Gomis-Ruth, F.X. (2003) Structural aspects of the metzincin clan of metalloendopeptidases. Mol Biotechnol 24 (2), 157-202. (Pubitemid 36623584)
3. Polgar, L. (2005) The catalytic triad of serine peptidases. Cell Mol Life Sci 62 (19-20), 2161-72. (Pubitemid 41500536)
4. Rawlings, N.D., D.P. Tolle, and A.J. Barrett (2004) MEROPS: the peptidase database. Nucleic Acids Res 32 (Database issue), D160-4. (Pubitemid 38081629)
5. Barrett, A.J., N.D. Rawlings, and J.F. Woess-ner (2004) Handbook of proteolytic enzymes, 2nd ed. Amsterdam: Elsevier.
6. Hooper, N.M. (2002) Proteases in biology and medicine. London: Portland Press.
7. López-Otín, C. and L.M. Matrisian (2007) Emerging roles of proteases in tumour suppression. Nat Rev Cancer 7 (10), 800-8. (Pubitemid 47463671)
8. Overall, C.M. and C. López-Otín (2002) Strategies for MMP inhibition in cancer: innovations for the post-trial era. Nat Rev Cancer 2 (9), 657-72. (Pubitemid 37328917)
9. Puente, X.S., et al. (2003) Human and mouse proteases: a comparative genomic approach. Nat Rev Genet 4 (7), 544-58. (Pubitemid 36781345)
10. Bowen, D.J. (2002) Haemophilia A and haemophilia B: molecular insights. Mol Pathol 55 (2), 127-44.
11. Sherrington, R., et al. (1995) Cloning of a gene bearing missense mutations in early-onset familial Alzheimer's disease. Nature 375 (6534), 754-60.
12. Whitcomb, D.C., et al. (1996), A gene for hereditary pancreatitis maps to chromosome 7q35. Gastroenterology 110 (6), 1975-80. (Pubitemid 26169237)
13. Varela, I., et al. (2005) Accelerated ageing in mice deficient in Zmpste24 protease is linked to p53 signalling activation. Nature 437 (7058), 564-8. (Pubitemid 41613555)
14. López-Otín, C. and C.M. Overall (2002) Protease degradomics: a new challenge for pro-teomics. Nat Rev Mol Cell Biol 3 (7), 509-19. (Pubitemid 34733432)
15. TCSAC. (2005) Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437 (7055), 69-87.
16. Gibbs, R.A., et al. (2004) Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 428 (6982), 493-521.
17. Lander, E.S., et al. (2001), Initial sequencing and analysis of the human genome. Nature 409 (6822), 860-921. (Pubitemid 32165345)
18. Venter, J.C., et al. (2001) The sequence of the human genome. Science 291 (5507), 1304-51.
19. Waterston, R.H., et al. (2002) Initial sequencing and comparative analysis of the mouse genome. Nature 420 (6915), 520-62. (Pubitemid 35477048)
20. Lewis, S., M. Ashburner, and M.G. Reese (2000) Annotating eukaryote genomes. Curr Opin Struct Biol 10 (3), 349-54. (Pubitemid 30333106)
21. Stein, L. (2001) Genome annotation: from sequence to biology. Nat Rev Genet 2 (7), 493-503. (Pubitemid 33674023)
22. Reed, J.L., et al. (2006) Towards multidimensional genome annotation. Nat Rev Genet 7 (2), 130-41. (Pubitemid 43128898)
23. Brent, M.R. (2005) Genome annotation past, present, and future: how to define an ORF at each locus. Genome Res 15 (12), 1777-86. (Pubitemid 41780408)
24. Shmatkov, A.M., et al. (1999) Finding prokaryotic genes by the 'frame-by-frame' algorithm: targeting gene starts and overlapping genes. Bioinformatics 15 (11), 874-86. (Pubitemid 30103158)
25. Claverie, J.M. (1997) Computational methods for the identification of genes in vertebrate genomic sequences. Hum Mol Genet 6 (10), 1735-44.
26. Burge, C.B. and S. Karlin (1998) Finding the genes in genomic DNA. Curr Opin Struct Biol 8 (3), 346-54. (Pubitemid 28321363)
27. Zhang, M.Q. (2002) Computational prediction of eukaryotic protein-coding genes. Nat Rev Genet 3 (9), 698-709. (Pubitemid 34984258)
28. Fitch, W.M. (2000) Homology a personal view on some of the problems. Trends Genet 16 (5), 227-31. (Pubitemid 30216555)
29. Lynch, M. and J.S. Conery (2000) The evolutionary fate and consequences of duplicate genes. Science 290 (5494), 1151-5.
30. Wagner, A. (2002) Selection and gene duplication: a view from the genome. Genome Biol 3 (5), 1012.
31. Altschul, S.F. (1991) Amino acid substitution matrices from an information theoretic perspective. J Mol Biol 219 (3), 555-65.
32. Henikoff, S. and J.G. Henikoff. (1992) Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci USA 89 (22) 10915-9.
33. Wheeler, D.L., et al. (2007) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 35 (Database issue), D5-12.
34. Hubbard, T.J., et al. (2007) Ensembl 2007. Nucleic Acids Res 35 (Database issue), D610-7. (Pubitemid 46056279)
35. Letunic, I., et al. (2006) SMART 5: domains in the context of genomes and networks. Nucleic Acids Res 34 (Database issue), D257-60.
36. Schultz, J., et al. (1998) SMART, a simple modular architecture research tool: identification of signaling domains. Proc Natl Acad Sci USA 95 (11), 5857-64. (Pubitemid 28248931)
37. Rawlings, N.D., F.R. Morton, and A.J. Barrett (2006) MEROPS: the peptidase database. Nucleic Acids Res 34 (Database issue), D270-2.
38. Puente, X.S., et al. (2005) Comparative genomic analysis of human and chimpanzee proteases. Genomics 86 (6), 638-47. (Pubitemid 41752944)
39. Puente, X.S. and C. López-Otín (2004) A genomic analysis of rat proteases and protease inhibitors. Genome Res 14 (4), 609-22. (Pubitemid 38500232)
40. Hulo, N., et al. (2006) The PROSITE database. Nucleic Acids Res 34 (Database issue), D227-30.
41. Mulder, N.J., et al. (2007) New developments in the InterPro database. Nucleic Acids Res 35 (Database issue), D224-8. (Pubitemid 46056203)
42. Altschul, S.F., et al. (1990) Basic local alignment search tool. J Mol Biol 215 (3), 403-10.
43. Kent, W.J. (2002) BLAT-the BLAST-like alignment tool. Genome Res 12 (4), 656-64.
44. Kent, W.J., et al. (2002) The human genome browser at UCSC. Genome Res 12 (6), 996-1006.
45. Eddy, S.R. (1998) Profile hidden Markov models. Bioinformatics 14 (9), 755-63. (Pubitemid 28552108)
46. Thompson, J.D., D.G. Higgins, and T.J. Gibson (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 (22), 4673-80. (Pubitemid 24354800)
47. Altschul, S.F., et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25 (17), 3389-402. (Pubitemid 27359211)
48. Puente, X.S., et al. (2005) A genomic view of the complexity of mammalian proteolytic systems. Biochem Soc Trans 33 (Pt 2), 331-4. (Pubitemid 40604365)
49. Esler, W. P. and M.S. Wolfe (2001) A portrait of Alzheimer secretases-new features and familiar faces. Science 293 (5534), 1449-54. (Pubitemid 32801541)
50. Vassar, R. (2002), Beta-secretase (BACE) as a drug target for Alzheimer's disease. Adv Drug Deliv Rev 54 (12), 1589-602. (Pubitemid 35346833)
51. Petek, E., et al. (2001) Disruption of a novel gene (IMMP2L) by a breakpoint in 7q31 associated with Tourette syndrome. Am J Hum Genet 68 (4), 848-58. (Pubitemid 32289730)
52. Puente, X.S., et al. (2006) Comparative analysis of cancer genes in the human and chimpanzee genomes. BMC Genomics 7 (1), 15.