EuPathDomains: The divergent domain database for eukaryotic pathogens

Infection, Genetics and Evolution

Volumn 11, Issue 4, 2011, Pages 698-707

  Ghouila, Amel ^a,b,c   Terrapon, Nicolas ^a   Gascuel, Olivier ^a   Guerfali, Fatma Z ^a   Laouini, Dhafer ^a   Maréchal, Eric ^d   Bréhélin, Laurent ^a  

^a CNRS   (France)

^b PASTEUR INSTITUTE OF TUNIS   (Tunisia)

^c FACULTÉ DES SCIENCES DE TUNIS   (Tunisia)

^d CEA GRENOBLE   (France)

Author keywords

Database; Functional annotations; HMMs; Pathogens; Pfam; Protein domains

Indexed keywords

ARTICLE; BACTERIAL GENOME; CERTIFICATION; COMPUTER INTERFACE; CRYPTOSPORIDIUM PARVUM; EUKARYOTIC PATHOGENS DOMAINS DATABASE; GIARDIA LAMBLIA; LEISHMANIA; NONHUMAN; PLASMODIUM FALCIPARUM; PRIORITY JOURNAL; PROTEIN DATABASE; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTOZOAL GENETICS; TOXOPLASMA GONDII; TRYPANOSOMA BRUCEI;

COMPUTATIONAL BIOLOGY; CRYPTOSPORIDIUM PARVUM; DATABASES, PROTEIN; EUKARYOTA; GIARDIA LAMBLIA; HUMANS; LEISHMANIA; MOLECULAR SEQUENCE ANNOTATION; PLASMODIUM; PROTEIN BINDING; PROTEIN INTERACTION DOMAINS AND MOTIFS; PROTOZOAN PROTEINS; TOXOPLASMA; TRYPANOSOMA BRUCEI BRUCEI;

EUKARYOTA; PLASMODIUM (APICOMPLEXA); PLASMODIUM FALCIPARUM; TOXOPLASMA GONDII;

EID: 79956322055     PISSN: 15671348     EISSN: 15677257     Source Type: Journal    
DOI: 10.1016/j.meegid.2010.09.008     Document Type: Article

References (48)

1. Abrahamsen M.S., Templeton T.J., et al. Complete genome sequence of the apicomplexan, Cryptosporidium parvum. Science 2004, 304(5669):441-445.
2. Albrecht M., Lengauer T. Survey on the PABC recognition motif PAM2. Biochem. Biophys. Res. Commun. 2004, 316(1):129-138.
3. Apic G. Domain combinations in archeal, eubacterial and eukayotic proteomes. J. Mol. Biol. 2001, 310:311-325.
4. Aurrecoechea C., et al. EuPathDB: a portal to eukaryotic pathogen databases. Nucleic Acids Res. 2010, 38. Database issue D415-D419.
5. Beaussart F., Weiner J., Bornberg-Bauer E. Automated improvement of domain annotations using context analysis of domain arrangements (AIDAN). Bioinformatics 2007, 23(14):1834-1836.
6. Beißbarth T., Speed T.P. GOstat: Find Statistically Overrepresented Gene Ontologies within a Group of Gene 2004, vol. 20. pp. 1464-1465.
7. Bernstein K.A., et al. The small-subunit processome is a ribosome assembly intermediate. Eukaryot. Cell 2004, 3(December 6):1619-1626.
8. Bischoff E., Vaquero C. In silico and biological survey of transcription-associated proteins implicated in the transcriptional machinery during the erythrocytic development of Plasmodium falciparum. BMC Genomics 2010, 11(1). art no. 34.
9. Blader J., Saeij J.P. Communication between Toxoplasma gondii and its host: impact on parasite growth, development, immune evasion, and virulence. APMIS 2009, 117:458-476.
10. Clayton C., Shapira M. Post-transcriptional regulation of gene expression in trypanosomes and leishmanias. Mol. Biochem. Parasitol. 2007, 156(2):93-101.
11. Coronin P.J. Diversity of WD-repeat proteins. Subcell Biochem. 2008, 48:116-123.
12. Smith T.F. Subcell Biochem. 2008, 48:20-30.
13. Cummings B.S., McHowat J., Schnellmann R.G. Phospholipase A2s in cell injury and death. J. Pharmacol. Exp. Ther. 2000, 294:793-799.
14. Dragon F., et al. A large nucleolar U3 ribonucleoprotein required for 18S ribosomal RNA biogenesis. Nature 2002, 417:967-970.
15. Du Z., Zhao Y., Li N. Genome-wide analysis reveals regulatory role of G4 DNA in gene transcription. Genome Res. 2008, 18:233-241.
16. Durbin R. Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids 1998, Cambridge University Press, Cambridge, UK.
17. Eddy S.R. Profile hidden Markov models. Bioinformatics 1998, 14:755-763.
18. Essien K., Stoeckert C.J. Conservation and divergence of known apicomplexan transcriptional regulons. BMC Genomics 2010, 11(1). art no. 147.
19. Finn R. The Pfam protein families database. Nucleic Acids Res. 2008, 36:D281-D288.
20. Forslund K., Sonnhammer E.L. Predicting protein function from domain content. Bioinformatics 2008, 24:1681-1687.
21. Gatei W., Wamae C.N., Mbae C., et al. Cryptosporidiosis: prevalence, genotype analysis, and symptoms associated with infections in children in Kenya. Am. J. Trop. Med. Hyg. 2006, 75(1):78-82.
22. Haile S., Papadopoulou B. Developmental regulation of gene expression in trypanosomatid parasitic protozoa. Curr. Opin. Microbiol. 2007, 10(6):569-577.
23. Haldar K., Kamoun S., Hiller N.L., Bhattacharje S., Ooij C. Common infection strategies of pathogenic eukaryotes. Nat. Rev. Microbiol. 2006, 4:922-931.
24. Hanakahi L.A., Sun H.N.J. High affinity interactions of nucleolin with G-G-paired rDNA. J. Biol. Chem. 1999, 274:15908-15912.
25. Hegyi H., Gerstein M. Annotation transfer for genomics: measuring functional divergence in multi-domain proteins. Genome Res. 2001, 11:1632-1640.
26. Hunter S., Apweiler R., Attwood T.K., Bairoch A., Bateman A., Binns D., Bork P., Das U., Daugherty L., Duquenne L., Finn R.D., Gough J., Haft D., Hulo N., Kahn D., Kelly E., Laugraud A., Letunic I., Lonsdale D., Lopez R., Madera M., Maslen J., McAnulla C., McDowall J., Mitchell A., Mulder N., Natale D., Orengo C., Quinn A.F., Selengut J.D., Sigrist C.J., Thimma M., Thomas P.D., Valentin F., Wilson D., Wu C.H., Yeats C. InterPro: the integrative protein signature database. Nucleic Acids Res. 2009, 3.
27. Hybiske K., Stephens R.S. Exit strategies of intracellular pathogens. Nat. Rev. Microbiol. 2008, 6:99-110.
28. Julius P.K. Infection, Resistance and Immunity 2002, second ed.
29. Kooij T.W.A., Carlton J.M., Bidwell S.L., Hall N., Ramesar J., et al. A Plasmodium whole-genome synteny map: indels and synteny breakpoints as foci for species-specific genes. PLoS Pathog. 2005, 1(4):349-361.
30. Krauss G. Biochemistry of signal transduction and regulation. Other Receptor Classes 2001, Wiley-VCH, 377-384 (Chapter 12). second ed.
31. Lamers M.H., Winterwerp H.H., Sixma T.K. The alternating ATPase domains of MutS control DNA mismatch repair. EMBO J. 2003, 22(3):746-756.
32. Maizels N. Dynamic roles for G4 DNA in the biology of eukaryotic cells. Nat. Struct. Mol. Biol. 2006, 13:1055-1059.
33. Mansfield J.M., Oliver M. Immune evasion by parasites. Immunology of Infectious Diseases 2002, P.S.H.E. Kaufmann, A. Sher, R. Ahmed (Eds.).
34. Mathee K., Narasimhan G. Detection of DNA-Binding helix-turn-helix motifs in proteins using the pattern dictionary method. Methods Enzymol. 2003, 370:250-264.
35. Morrison H.G., McArthur A.G., Gillin F.D., et al. Genomic minimalism in the early diverging intestinal parasite Giardia lamblia. Science 2007, 317(September (5846)):1921-1926.
36. Nonhoff, et al. Ataxin-2 interacts with the DEAD/H-Box RNA helicase DDX6 and interferes with P-bodies and stress granules. Mol. Cell Biol. 2007, 18:1385-1396.
37. Ochman H., Moran N.A. Genes lost and genes found: evolution of bacterial pathogenesis and symbiosis. Science 2001, 292(5519):1096-1099.
38. Pao G.M., Saier M.H. Response regulators of bacterial signal transduction systems: selective domain shuffling during evolution. J. Mol. Evol. 1995, 40(2):136-154.
39. Parkinson G.N., Lee M.P., Neidle S. Crystal structure of parallel quadruplexes from human telomeric DNA. Nature 2002, 417:876-880.
40. Peacock C.S., et al. Comparative genomic analysis of three Leishmania species that cause diverse human disease. Nat. Genetics 2007, 39:839-847.
41. Richardson J. The anatomy and taxonomy of protein structure. Adv. Protein Chem. 1981, 34:167-339.
42. Skerker J.M., Prasol M.S., Perchuk B.S., Biondi Ee.G., Laub M.T. Two-component signal transduction pathways regulating growth and cell cycle progression in a bacterium: a system-level analysis. PLoS Biol. 2005, 3(10):e334.
43. Struhl K. Helix-turn-helix, zinc-finger, and leucine-zipper motifs for eukaryotic transcriptional regulatory proteins. Trends Biochem. Sci. 1989, 14(4):137-140.
44. Svärd S.G., Meng T.C., Hetsko M.L., McCaffery J.M., Gillin F.D. Differentiation-associated surface antigen variation in the ancient eukaryote Giardia lamblia. Mol. Microbiol. 1998, 30(December (5)):979-989.
45. Terrapon N., Gascuel O., Maréchal É., Bréhélin L. Detection of new protein domains using co-occurrence: application to Plasmodium falciparum. Bioinformatics 2009, 25(23):3077-3083.
46. Tovar J., León-Avila G., Sánchez L.B., et al. Mitochondrial remnant organelles of Giardia function in iron-sulphur protein maturation. Nature 2003, 426(6963):172-176.
47. Wardl P., Equinet L., Packer J., Doerig C. Protein kinases of the human malaria parasite Plasmodium falciparum: the kinome of a divergent eukaryote. BMC Genomics 2004, 5:79.
48. Whitworth D.E., Cock P.J. Evolution of prokaryotic two-component systems: insights from comparative genomics. Amino Acids 2009, 37(3):459-466.