Genome-wide survey and evolutionary analysis of trypsin proteases in apicomplexan parasites

Genomics, Proteomics and Bioinformatics

Volumn 8, Issue 2, 2010, Pages 103-112

  Arenas, Aylan Farid ^a   Osorio Méndez, Juan Felipe ^a   Gutierrez, Andres Julian ^a   Gomez Marin, Jorge E ^a  

^a UNIVERSIDAD DEL QUINDÍO   (Colombia)

Author keywords

Apicomplexa; Endosymbiotic gene transfer; Trypsin

Indexed keywords

PROTEINASE; TRYPSIN; PROTOZOAL DNA;

APICOMPLEXA; ARTICLE; EVOLUTION; GENE SEQUENCE; GENE TRANSFER; GENOME; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; AMINO ACID SEQUENCE; ENZYMOLOGY; GENE; GENETICS; HORIZONTAL GENE TRANSFER; MOLECULAR EVOLUTION; MOLECULAR GENETICS; SEQUENCE ALIGNMENT;

AMINO ACID SEQUENCE; APICOMPLEXA; DNA, PROTOZOAN; EVOLUTION, MOLECULAR; GENE TRANSFER, HORIZONTAL; GENES, PROTOZOAN; GENOME, PROTOZOAN; MOLECULAR SEQUENCE DATA; PHYLOGENY; SEQUENCE ALIGNMENT; TRYPSIN;

EID: 77955332414     PISSN: 16720229     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1672-0229(10)60011-3     Document Type: Article

References (48)

1. Hyde J.E. Drug-resistant malaria. Trends Parasitol. 2005, 21:494-498.
2. Plowe C.V. Antimalarial drug resistance in Africa: strategies for monitoring and deterrence. Curr. Top Microbiol. Immunol. 2005, 295:55-79.
3. Carruthers V., Boothroyd J.C. Pulling together: an integrated model of Toxoplasma cell invasion. Curr. Opin. Microbiol. 2007, 10:83-89.
4. Kim K. Role of proteases in host cell invasion by Toxoplasma gondii and other Apicomplexa. Acta Trop. 2004, 91:69-81.
5. Rawlings N.D., et al. MEROPS: the peptidase database. Nucleic Acids Res. 2008, 36:D320-D325.
6. Hartley B.S. Amino-acid sequence of bovine chymotrypsinogen-A. Nature 1964, 201:1284-1287.
7. Dixon G.H., et al. Peptides combined with 14C-diisopropyl phosphoryl following degradation of 14C-DIP-trypsin with alpha-chymotrypsin. Biochim. Biophys. Acta 1956, 19:193-195.
8. Shaw E., et al. Evidence for an active-center histidine in trypsin through use of a specific reagent, 1-chloro-3-tosylamido-7-amino-2-heptanone, the chloromethyl ketone derived from Na-tosyl-L-lysine. Biochemistry 1965, 4:2219-2224.
9. Baptista A.M., et al. The origin of trypsin: evidence for multiple gene duplications in trypsins. J. Mol. Evol. 1998, 47:353-362.
10. Blackman M.J. Proteases involved in erythrocyte invasion by the malaria parasite: function and potential as chemotherapeutic targets. Curr. Drug Targets 2000, 1:59-83.
11. Huang J., et al. A first glimpse into the pattern and scale of gene transfer in Apicomplexa. Int. J. Parasitol. 2004, 34:265-274.
12. Wang S., et al. Concerted evolution within a trypsin gene cluster in Drosophila. Mol. Biol. Evol. 1999, 16:1117-1124.
13. Tripathi L.P., Sowdhamini R. Cross genome comparisons of serine proteases in Arabidopsis and rice. BMC Genomics 2006, 7:200.
14. Neurath H. Evolution of proteolytic enzymes. Science 1984, 224:350-357.
15. Neurath H. The diversity of proteolytic enzymes. Proteolytic Enzymes: A Practical Approach 1989, 1-13. IRL Press, Oxford, UK. R.J. Beynon, J.S. Bond (Eds.).
16. Davis C.A., et al. A gene family in Drosophila melanogaster coding for trypsin-like enzymes. Nucleic Acids Res. 1985, 13:6605-6619.
17. Muller H.M., et al. Members of a trypsin gene family in Anopheles gambiae are induced in the gut by blood meal. EMBO J. 1993, 12:2891-2900.
18. Casu R.E., et al. Isolation of a trypsin-like serine protease gene family from the sheep blowfly Lucilia cuprina. Insect Mol. Biol. 1994, 3:159-170.
19. Emi M., et al. Cloning, characterization and nucleotide sequence of two cDNAs encoding human pancreatic trypsinogens. Gene 1986, 41:305-310.
20. Stevenson B.J., et al. Sequence organization and transcriptional regulation of the mouse elastase II and trypsin genes. Nucleic Acids Res. 1986, 14:8307-8330.
21. Shi Y.B., Brown D.D. Developmental and thyroid hormone-dependent regulation of pancreatic genes in Xenopus laevis. Genes Dev. 1990, 4:1107-1113.
22. Wang K., et al. Isolation and characterization of the chicken trypsinogen gene family. Biochem. J. 1995, 307:471-479.
23. Roach J.C., et al. The molecular evolution of vertebrate trypsinogens. J. Mol. Evol. 1997, 45:640-652.
24. Rowen L., et al. The complete 685-kilobase DNA sequence of the human beta T cell receptor locus. Science 1996, 272:1755-1762.
25. Ponting C.P., Russell R.R. The natural history of protein domains. Annu. Rev. Biophys. Biomol. Struct. 2002, 31:45-71.
26. Vogel C., et al. Structure, function and evolution of multidomain proteins. Curr. Opin. Struct. Biol. 2004, 14:208-216.
27. Pallen M.J., et al. The HtrA family of serine proteases. Mol. Microbiol. 1997, 26:209-221.
28. Ponting C.P. Evidence for PDZ domains in bacteria, yeast, and plants. Protein Sci. 1997, 6:464-468.
29. Spiers A., et al. PDZ domains facilitate binding of high temperature requirement protease A (HtrA) and tail-specific protease (Tsp) to heterologous substrates through recognition of the small stable RNA A (ssrA)-encoded peptide. J. Biol. Chem. 2002, 277:39443-39449.
30. Murwantoko M.Y., et al. Binding of proteins to the PDZ domain regulates proteolytic activity of HtrA1 serine protease. Biochem. J. 2004, 381:895-904.
31. Wilken C., et al. Crystal structure of the DegS stress sensor: how a PDZ domain recognizes misfolded protein and activates a protease. Cell 2004, 117:483-494.
32. McFadden G.I., et al. Plastid in human parasites. Nature 1996, 381:482.
33. Fast N.M., et al. Nuclear-encoded, plastid-targeted genes suggest a single common origin for apicomplexan and dinoflagellate plastids. Mol. Biol. Evol. 2001, 18:418-426.
34. Köhler S., et al. A plastid of probable green algal origin in Apicomplexan parasites. Science 1997, 275:1485-1489.
35. Delwiche C.F. Tracing the thread of plastid diversity through the tapestry of life. Am. Nat. 1999, 154:S164-S177.
36. Keeling P.J., Palmer J.D. Lateral transfer at the gene and subgenic levels in the evolution of eukaryotic enolase. Proc. Natl. Acad. Sci. USA 2001, 98:10745-10750.
37. Salzberg S.L., et al. Microbial genes in the human genome: lateral transfer or gene loss?. Science 2001, 292:1903-1906.
38. Stanhope M.J. Phylogenetic analyses do not support horizontal gene transfers from bacteria to vertebrates. Nature 2001, 411:940-944.
39. Schultz J., et al. SMART, a simple modular architecture research tool: identification of signaling domains. Proc. Natl. Acad. Sci. USA 1998, 95:5857-5864.
40. Hofmann K., et al. The PROSITE database, its status in 1999. Nucleic Acids Res. 1999, 27:215-219.
41. Altschul S.F., et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997, 25:3389-3402.
42. Eddy S.R. Profile hidden Markov models. Bioinformatics 1998, 14:755-763.
43. Thompson J., et al. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994, 22:4673-4680.
44. Tamura K., et al. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol. Biol. Evol. 2007, 24:1596-1599.
45. Emanuelsson O., et al. Predicting subcellular localization of proteins based on their N-terminal amino acid sequence. J. Mol. Biol. 2000, 300:1005-1016.
46. Bendtsen J.D., et al. Improved prediction of signal peptides: SignalP 3.0. J. Mol. Biol. 2004, 340:783-795.
47. Bendtsen J.D. Non-classical protein secretion in bacteria. BMC Microbiol. 2005, 5:58.
48. Gissot M. Epigenomic modifications predict active promoters and gene structure in Toxoplasma gondii. PLoS Pathog. 2007, 3:e77.