An analysis of the Candida albicans genome database for soluble secreted proteins using computer-based prediction algorithms

Yeast

Volumn 20, Issue 7, 2003, Pages 595-610

  Lee, Samuel A ^a,b   Wormsley, Steven ^a   Kamoun, Sophien ^c   Lee, Austin F S ^d,e   Joiner, Keith ^a   Wong, Brian ^a,b  

^a YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b VA CONNECTICUT HEALTHCARE SYSTEM   (United States)

^c OHIO STATE UNIVERSITY   (United States)

^d BOSTON UNIVERSITY   (United States)

^e VETERANS AFFAIRS MEDICAL CENTER   (United States)

Author keywords

Fungi; Genomics; Secreted proteins; Yeast

Indexed keywords

FUNGAL PROTEIN; GLYPICAN; MEMBRANE PROTEIN; PROTEOME; SECRETORY PROTEIN;

ALGORITHM; AMINO TERMINAL SEQUENCE; CANDIDA ALBICANS; COMPUTER ANALYSIS; CONTROLLED STUDY; DATA BASE; FUNGAL GENE; GENETIC ANALYSIS; GENETIC CODE; GENETIC IDENTIFICATION; INTERNET; MITOCHONDRION; NONHUMAN; OPEN READING FRAME; PREDICTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN SECRETION; REVIEW; SIGNAL TRANSDUCTION; UNINDEXED SEQUENCE; VALIDATION PROCESS;

ALGORITHMS; CANDIDA ALBICANS; DATABASES, GENETIC; FUNGAL PROTEINS; GENOME, FUNGAL; OPEN READING FRAMES; PROTEIN SORTING SIGNALS; PROTEOME; SOFTWARE DESIGN; SOLUBILITY;

CANDIDA; CANDIDA ALBICANS; FUNGI;

EID: 0038290322     PISSN: 0749503X     EISSN: None     Source Type: Journal    
DOI: 10.1002/yea.988     Document Type: Review

References (54)

1. Alexandrov V, Gerstein M. 2001. Calculating populations of subcellular compartments using density matrix formalism. Int J Quant Chem 85: 693-696.
2. Beggah S, Lechenne B, Reichard U, Foundling S, Monod M. 2000. Intra- and intermolecular events direct the propeptide-mediated maturation of the Candida albicans secreted aspartic proteinase Sap1p. Microbiol 146: 2765-2773.
3. Caro LH, Tettelin H, Vossen JH, et al. 1997. In silicio identification of glycosyl-phosphatidylinositol-anchored plasma-membrane and cell wall proteins of Saccharomyces cerevisiae. Yeast 13: 1477-1489.
4. De Backer MD, Magee PT, Pla J. 2000. Recent developments in molecular genetics of Candida albicans. Ann Rev Microbiol 54: 463-498.
5. De Bernardis F, Muhlschlegel FA, Cassone A, Fonzi WA. 1998. The pH of the host niche controls gene expression in and virulence of Candida albicans. Infect Immun 66: 3317-3325.
6. Drawid A, Gerstein M. 2000. A Bayesian system integrating expression data with sequence patterns for localizing proteins: comprehensive application to the yeast genome. J Mol Biol 301: 1059-1075.
7. Drawid A, Jansen R, Gerstein M. 2000. Genome-wide analysis relating expression level with protein subcellular localization. Trends Genet 16: 426-430.
8. Cleves AE, Cooper DN, Barondes SH, Kelly RB. 1996. A new pathway for protein export in Saccharomyces cerevisiae. J Cell Biol 133: 1017-1026.
9. Eisenhaber B, Bork P, Eisenhaber F. 1999. Prediction of potential GPI-modification sites in proprotein sequences. J Mol Biol 292: 741-758.
10. Eisenhaber B, Bork P, Eisenhaber F. 2001. Post-translational GPI lipid anchor modification of proteins in kingdoms of life: analysis of protein sequence data from complete genomes. Protein Eng 14: 17-25.
11. Emanuelsson O, Nielsen H, Brunak S, von Heijne G. 2000. Predicting subcellular localization of proteins based on their N-terminal amino acid sequence. J Mol Biol 300: 1005-1016.
12. Emori TG, Gaynes RP. 1993. An overview of nosocomial infections, including the role of the microbiology laboratory. Clin Microbiol 6: 428-442.
13. Fonzi WA. 1999. PHR1 and PHR2 of Candida albicans encode putative glycosidases required for proper cross-linking of β-1,3-and β-1,6-glucans. J Bacteriol 181: 7070-7079.
14. Fu Y, Ibrahim AS, Fonzi W, et al. 1997. Cloning and characterization of a gene (LIP1) which encodes a lipase from the pathogenic yeast Candida albicans. Microbiology 143(2): 331-340.
15. Gale C, Finkel D, Tao N, et al. 1996. Cloning and expression of a gene encoding an integrin-like protein in Candida albicans. Proc Natl Acad Sci USA 93: 357-361.
16. Gale CA, Bendel CM, McClellan M, et al. 1998. Linkage of adhesion, filamentous growth, and virulence in Candida albicans to a single gene, INT1. Science 279: 1355-1358.
17. Ghannoum MA, Spellberg B, Saporito-Irwin SM, Fonzi WA. 1995. Reduced virulence of Candida albicans PHR1 mutants. Infect Immun 63: 4528-4530.
18. Ghannoum MA. 2000. Potential role of phospholipases in virulence and fungal pathogenesis. Clin Microbiol 13: 122-143.
19. Haynes K. 2001. Virulence in Candida species. Trends Microbiol 9: 591-596.
20. Hoegl L, Ollert M, Korting HC. 1996. The role of Candida albicans secreted aspartic proteinase in the development of candidoses. Mol Med 74: 135-142.
21. Hoyer LL. 2001. The ALS gene family of Candida albicans. Trends Microbiol 9: 176-180.
22. Hube B, Sanglard D, Odds FC, et al. 1997. Disruption of each of the secreted aspartyl proteinase genes SAP1, SAP2 and SAP3 of Candida albicans attenuates virulence. Infect Immun 65: 3529-3538.
23. Hube B, Stehr F, Bossenz M, et al. 2000. Secreted lipases of Candida albicans: cloning, characterisation and expression analysis of a new gene family with at least ten members. Arch Microbiol 174: 362-374.
24. Hull CM, Raisner RM, Johnson AD. 2000. Evidence for mating of the 'asexual' yeast Candida albicans in a mammalian host. Science 289: 307-310.
25. Jarvis WR. 1995. Epidemiology of nosocomial fungal infections, with emphasis on Candida species. Clin Infect Dis 20: 1526-1530.
26. Kamoun S, Dong S, Hamada W, et al. 2002. From sequence to phenotype: functional genomics of Phytophthora. Can J Plant Pathol 24: 6-9.
27. Kleinbaum DG, Kupper LL, Muller KE, Nizam A (eds). 1998. Applied Regression Analysis and other Multivariable Methods. Duxbury: Pacific Grove; 656-686.
28. Krogh A, Larsson B, von Heijne G, Sonnhammer EL. 2001. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 305: 567-580.
29. Kumar A, Agarwal S, Heyman JA, et al. 2002. Subcellular localization of the yeast proteome. Genes Dev 16: 707-719.
30. Lee SA, Mao Y, Zhang Z, Wong B. 2001. Overexpression of a dominant-negative allele of YPT1 inhibits growth and aspartyl proteinase secretion in Candida albicans. Microbiology 147: 1961-1970.
31. Leidich SD, Ibrahim AS, Fu Y, et al. 1998. Cloning and disruption of caPLB1, a phospholipase B gene involved in the pathogenicity of Candida albicans. J Biol Chem 273: 26 078-26 086.
32. Magee BB, Magee PT. 2000. Induction of mating in Candida albicans by construction of MTLa and MTLα strains. Science 289: 310-313.
33. Magee PT. 1998. Analysis of the Candida albicans genome. In Methods in Microbiology, vol 26. Academic Press: New York; 395-415.
34. Mao Y, Kalb VF, Wong B. 1999. Overexpression of a dominant-negative allele of SEC4 inhibits growth and protein secretion in Candida albicans. J Bacteriol 181: 7235-7242.
35. Martoglio B, Dobberstein B. 1998. Signal sequences: more than just greasy peptides. Trends Cell Biol 10: 410-415.
36. Matthews R, Wells C, Burnie JP. 1988. Characterisation and cellular localisation of the immunodominant 47 kDa antigen of Candida albicans. J Med Microbiol 27: 227-232.
37. Moller S, Croning MD, Apweiler R. 2001. Evaluation of methods for the prediction of membrane spanning regions. Bioinformatics 17: 646-653.
38. Monteoliva L, Matas ML, Gil C, Nombela C, Pla J. 2002. Large-scale identification of putative exported proteins in Candida albicans by genetic selection. Eukaryotic Cell 1: 514-525.
39. Mukherjee PK, Seshan KR, Leidich SD, et al. 2001. Reintroduction of the PLB1 gene into Candida albicans restores virulence in vivo. Microbiology 147(9): 2585-2597.
40. Nielsen H, Brunak S, von Heijne G. 1999. Machine learning approaches to the prediction of signal peptides and other protein sorting signals. Protein Eng 12: 3-9.
41. Nielsen H, Engelbrecht J, Brunak S, von Heijne G. 1997. Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Eng 10: 1-6.
42. Nielsen H, Krogh A. 1998. Prediction of signal peptides and signal anchors by a hidden Markov model. In Proceedings of the Sixth International Conference on Intelligent Systems for Molecular Biology (ISMB 6). AAAI Press: Menlo Park, CA; 122-130.
43. Niewerth M, Korting HC. 2001. Phospholipases of Candida albicans. Mycoses 44: 361-367.
44. Sanglard D, Hube B, Monod M, Odds F, Gow N. 1997. A triple deletion of the secreted aspartyl proteinase genes SAP4, SAP5 and SAP6 of Candida albicans causes attenuated virulence. Infect Immun 65: 3539-3546.
45. Saporito-Irwin SM, Birse CE, Sypherd PS, Fonzi WA. 1995. PHR1, a pH-regulated gene of Candida albicans is required for morphogenesis. Mol Cell Biol 15: 601-613.
46. Scherer S, Magee PT. 1990. Genetics of Candida albicans. Microbiology 54: 226-241.
47. Staab JF, Bradway SD, Fidel PL, Sundstrom P. 1999. Adhesive and mammalian transglutaminase substrate properties of Candida albicans Hwp1. Science 283: 1535-1538.
48. Sundstrom P. 2002. Adhesion in Candida spp. Cell Microbiol 4: 461-469.
49. Tait E, Simon MC, King S, et al. 1997. Candida albicans genome project: cosmid contigs, physical mapping, and gene isolation. Fungal Genet Biol 21: 308-314.
50. Tjalsma H, Bolhuis A, Jongbloed JD, Bron S, van Dijl JM. 2000. Signal peptide-dependent protein transport in Bacillus subtilis: a genome-based survey of the secretome. Microbiol Mol Biol 64: 515-547.
51. Tzung KW, Williams RM, Scherer S, et al. 2001. Genomic evidence for a complete sexual cycle in Candida albicans. Proc Natl Acad Sci USA 98: 3249-3253.
52. von Heijne G. 1990. Protein targeting signals. Curr Opin Cell Biol 4: 604-608.
53. White TC, Agabian N. 1995. Candida albicans secreted aspartyl proteinases: isoenzyme pattern is determined by cell type, and levels are determined by environmental factors. J Bacteriol 177: 5215-5221.
54. White TC, Marr KA, Bowden RA. 1998. Clinical, cellular, and molecular factors that contribute to antifungal drug resistance. Clin Microbiol 11: 382-402.