Pathways Knowlegdes
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| Pathway | DOIs | Note |
|---|---|---|
| superpathway of phenylalanine, tyrosine and tryptophan biosynthesis Accession ID: BioCyc:CALBI_COMPLETE-ARO-PWY |
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| tetrahydrofolate biosynthesis Accession ID: BioCyc:CALBI_PWY-3742 |
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Cossins EA, Chen L. Folates and one-carbon metabolism in plants and fungi. Phytochemistry. 1997 Jun;45(3):437–52. doi: 10.1016/s0031-9422(96)00833-3. PMID: 9190084.; Daly S, Mastromei G, Yacoub A, Lorenzetti R. Sequence of a dihydrofolate reductase-encoding gene from Candida albicans. Gene. 1994 Sep 15;147(1):115–8. doi: 10.1016/0378-1119(94)90049-3. PMID: 7916311. |
| TCA cycle, aerobic respiration Accession ID: BioCyc:CALBI_PWY3B3-100 |
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Yasutake Y, Watanabe S, Yao M, Takada Y, Fukunaga N, Tanaka I. Crystal Structure of the Monomeric Isocitrate Dehydrogenase in the Presence of NADP+. Journal of Biological Chemistry. 2003 Sep;278(38):36897–904. doi: 10.1074/jbc.m304091200.; Oyedotun KS, Lemire BD. The Carboxyl Terminus of the Saccharomyces cerevisiaeSuccinate Dehydrogenase Membrane Subunit, SDH4p, Is Necessary for Ubiquinone Reduction and Enzyme Stability. Journal of Biological Chemistry. 1997 Dec;272(50):31382–8. doi: 10.1074/jbc.272.50.31382.; Haselbeck RJ, McAlister-Henn L. Function and expression of yeast mitochondrial NAD- and NADP-specific isocitrate dehydrogenases. Journal of Biological Chemistry. 1993 Jun;268(16):12116–22. doi: 10.1016/s0021-9258(19)50315-5.; RAO GR, SIRSI M, RAMAKRISHNAN T. Enzymes in Candida albicans. II. Tricarboxylic acid cycle and related enzymes. J Bacteriol. 1962 Oct;84():778–83. PMID: 13973046; PMCID: PMC277958. |
| tryptophan biosynthesis Accession ID: BioCyc:CALBI_TRPSYN-PWY |
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Kingsbury JM, Goldstein AL, McCusker JH. Role of Nitrogen and Carbon Transport, Regulation, and Metabolism Genes for Saccharomyces cerevisiae Survival In Vivo. Eukaryot Cell. 2006 May;5(5):816–24. doi: 10.1128/ec.5.5.816-824.2006.; Toyn JH, Gunyuzlu PL, White WH, Thompson LA, Hollis GF. A counterselection for the tryptophan pathway in yeast: 5-fluoroanthranilic acid resistance. Yeast. 2000 Apr;16(6):553–60. doi: 10.1002/(sici)1097-0061(200004)16:6<553::aid-yea554>3.0.co;2-7. PMID: 10790693.; Graf R, Mehmann B, Braus GH. Analysis of feedback-resistant anthranilate synthases from Saccharomyces cerevisiae. J Bacteriol. 1993 Feb;175(4):1061–8. doi: 10.1128/jb.175.4.1061-1068.1993.; Braus GH. Aromatic amino acid biosynthesis in the yeast Saccharomyces cerevisiae: a model system for the regulation of a eukaryotic biosynthetic pathway. Microbiol Rev. 1991 Sep;55(3):349–70. doi: 10.1128/mr.55.3.349-370.1991.; Zalkin H, Paluh JL, van Cleemput M, Moye WS, Yanofsky C. Nucleotide sequence of Saccharomyces cerevisiae genes TRP2 and TRP3 encoding bifunctional anthranilate synthase: indole-3-glycerol phosphate synthase. Journal of Biological Chemistry. 1984 Mar;259(6):3985–92. doi: 10.1016/s0021-9258(17)43193-0. |
| pyruvate dehydrogenase complex Accession ID: BioCyc:CALBI_PYRUVDEHYD-PWY |
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| tyrosine biosynthesis Accession ID: BioCyc:CALBI_PWY3O-4120 |
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Kingsbury JM, Goldstein AL, McCusker JH. Role of Nitrogen and Carbon Transport, Regulation, and Metabolism Genes for Saccharomyces cerevisiae Survival In Vivo. Eukaryot Cell. 2006 May;5(5):816–24. doi: 10.1128/ec.5.5.816-824.2006.; Urrestarazu A, Vissers S, Iraqui I, Grenson M. Phenylalanine- and tyrosine-auxotrophic mutants of Saccharomyces cerevisiae impaired in transamination. Molecular Genetics and Genomics. 1998 Jan;257(2):230–7. doi: 10.1007/s004380050643.; Braus GH. Aromatic amino acid biosynthesis in the yeast Saccharomyces cerevisiae: a model system for the regulation of a eukaryotic biosynthetic pathway. Microbiol Rev. 1991 Sep;55(3):349–70. doi: 10.1128/mr.55.3.349-370.1991.; BODE R, MELO C, BIRNBAUM D. Absolute Dependence of Phenylalanine and Tyrosine Biosynthetic Enzyme on Tryptophan inCandida maltosa. Hoppe-Seyler´s Zeitschrift für physiologische Chemie. 1984 Jan;365(2):799–804. doi: 10.1515/bchm2.1984.365.2.799.; Kradolfer P, Niederberger P, Hütter R. Tryptophan degradation in Saccharomyces cerevisiae: characterization of two aromatic aminotransferases. Arch Microbiol. 1982 Dec 11;133(3):242–8. doi: 10.1007/bf00415010. PMID: 6763508. |
| alanine degradation Accession ID: BioCyc:CALBI_ALANINE-DEG3-PWY |
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Biallasiewicz D, Kwasniewska J. [The capability of deamination of aminoacids by selected strains of fungi]. Wiad Parazytol. 2001;47(3):339–44. PMID: 16894744.; Umemura I, Yanagiya K, Komatsubara S, Sato T, Tosa T. Purification and Some Properties of Alanine Aminotransferase fromCandida maltosa. Bioscience, Biotechnology, and Biochemistry. 1994 Jan;58(2):283–7. doi: 10.1271/bbb.58.283. |
| tyrosol biosynthesis Accession ID: BioCyc:CALBI_PWY3O-4108 |
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Blankenship JR, Mitchell AP. How to build a biofilm: a fungal perspective. Curr Opin Microbiol. 2006 Dec;9(6):588–94. doi: 10.1016/j.mib.2006.10.003. PMID: 17055772.; Nickerson KW, Atkin AL, Hornby JM. Quorum sensing in dimorphic fungi: farnesol and beyond. Appl Environ Microbiol. 2006 Jun;72(6):3805–13. PMID: 16751484; PMCID: PMC1489610.; Hogan DA. Talking to themselves: autoregulation and quorum sensing in fungi. Eukaryot Cell. 2006 Apr;5(4):613–9. PMID: 16607008; PMCID: PMC1459667.; Urrestarazu A, Vissers S, Iraqui I, Grenson M. Phenylalanine- and tyrosine-auxotrophic mutants of Saccharomyces cerevisiae impaired in transamination. Molecular Genetics and Genomics. 1998 Jan;257(2):230–7. doi: 10.1007/s004380050643.; Iraqui I, Vissers S, Cartiaux M, Urrestarazu A. Characterisation of Saccharomyces cerevisiae ARO8 and ARO9 genes encoding aromatic aminotransferases I and II reveals a new aminotransferase subfamily. Molecular Genetics and Genomics. 1998 Jan;257(2):238–48. doi: 10.1007/s004380050644.; Kradolfer P, Niederberger P, Hütter R. Tryptophan degradation in Saccharomyces cerevisiae: characterization of two aromatic aminotransferases. Arch Microbiol. 1982 Dec 11;133(3):242–8. doi: 10.1007/bf00415010. PMID: 6763508.; SENTHESHANMUGANATHAN S. The purification and properties of the tyrosine-2-oxoglutarate transaminase of Saccharomyces cerevisiae. Biochem J. 1960 Dec;77():619–25. PMID: 13750129; PMCID: PMC1205084.; SENTHESHANMUGANATHAN S, ELSDEN SR. The mechanism of the formation of tyrosol by Saccharomyces cerevisiae. Biochem J. 1958 Jun;69(2):210–8. PMID: 13546168; PMCID: PMC1196540. |
| gluconeogenesis Accession ID: BioCyc:CALBI_GLUCONEO-PWY |
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Klein CJL, Olsson L, Nielsen J. Glucose control in Saccharomyces cerevisiae: the role of Mig1 in metabolic functions. Microbiology (Reading). 1998 Jan;144 ( Pt 1)():13–24. doi: 10.1099/00221287-144-1-13. PMID: 9467897. |
| ubiquinone (coenzyme Q) biosynthesis Accession ID: BioCyc:CALBI_PWY3B3-10 |
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| serine degradation Accession ID: BioCyc:CALBI_SERDEG-PWY |
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Bornaes C, Petersen JG, Holmberg S. Serine and threonine catabolism in Saccharomyces cerevisiae: the CHA1 polypeptide is homologous with other serine and threonine dehydratases. Genetics. 1992 Jul;131(3):531–9. PMID: 1628804; PMCID: PMC1205027. |
| aspartate biosynthesis Accession ID: BioCyc:CALBI_ASPBIO-PWY |
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| phenylalanine degradation Accession ID: BioCyc:CALBI_PWY-5079 |
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Derrick S, Large PJ. Activities of the enzymes of the Ehrlich pathway and formation of branched-chain alcohols in Saccharomyces cerevisiae and Candida utilis grown in continuous culture on valine or ammonium as sole nitrogen source. Journal of General Microbiology. 1993 Nov 01;139(11):2783–92. doi: 10.1099/00221287-139-11-2783. |
| glycine biosynthesis from alanine Accession ID: BioCyc:CALBI_GLYSYN-ALA-PWY |
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Schlösser T, Gätgens C, Weber U, Stahmann KP. Alanine : glyoxylate aminotransferase of Saccharomyces cerevisiae-encoding gene AGX1 and metabolic significance. Yeast. 2004 Jan 15;21(1):63–73. doi: 10.1002/yea.1058. PMID: 14745783.; Remm M, Storm CEV, Sonnhammer ELL. Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. Journal of Molecular Biology. 2001 Dec;314(5):1041–52. doi: 10.1006/jmbi.2000.5197. |
| isoleucine biosynthesis Accession ID: BioCyc:CALBI_ILEUSYN-PWY |
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Kingsbury JM, Goldstein AL, McCusker JH. Role of Nitrogen and Carbon Transport, Regulation, and Metabolism Genes for Saccharomyces cerevisiae Survival In Vivo. Eukaryot Cell. 2006 May;5(5):816–24. doi: 10.1128/ec.5.5.816-824.2006.; Holmberg S, Petersen JG. Regulation of isoleucine-valine biosynthesis in Saccharomyces cerevisiae. Curr Genet. 1988 Mar;13(3):207–17. doi: 10.1007/bf00387766. PMID: 3289762.; Kakar SN, Magee PT. Genetic analysis of Candida albicans: identification of different isoleucine-valine, methionine, and arginine alleles by complementation. J Bacteriol. 1982 Sep;151(3):1247–52. doi: 10.1128/jb.151.3.1247-1252.1982.; Szentirmai A, Horváth I. Regulation of branched-chain amino acid biosynthesis. Acta Microbiol Acad Sci Hung. 1976;23(2):137–49. PMID: 788468. |
| methylglyoxal pathway Accession ID: BioCyc:CALBI_PWY3B3-2134 |
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| tetrapyrrole biosynthesis Accession ID: BioCyc:CALBI_PWY3B3-2 |
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C. Hunter T, K. Mehra R. A role for HEM2 in cadmium tolerance1DNA sequence reported here has been submitted to GenBank (Accession number BankIt160246 AF038566).1. Journal of Inorganic Biochemistry. 1998 Mar;69(4):293–303. doi: 10.1016/s0162-0134(98)00005-1.; Urban-Grimal D, Labbe-Bois R. Genetic and biochemical characterization of mutants of Saccharomyces cerevisiae blocked in six different steps of heme biosynthesis. Molecular Genetics and Genomics. 1981 Sep;183(1):85–92. doi: 10.1007/bf00270144.; Gollub EG, Liu KP, Dayan J, Adlersberg M, Sprinson DB. Yeast mutants deficient in heme biosynthesis and a heme mutant additionally blocked in cyclization of 2,3-oxidosqualene. Journal of Biological Chemistry. 1977 May;252(9):2846–54. doi: 10.1016/s0021-9258(17)40440-6. |
| superpathway of glycine biosynthesis Accession ID: BioCyc:CALBI_PWY3O-645 |
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Remm M, Storm CEV, Sonnhammer ELL. Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. Journal of Molecular Biology. 2001 Dec;314(5):1041–52. doi: 10.1006/jmbi.2000.5197.; McNeil JB, Flynn J, Tsao N, Monschau N, Stahmann K, Haynes RH, McIntosh EM, Pearlman RE. Glycine metabolism in Candida albicans: characterization of the serine hydroxymethyltransferase (SHM1, SHM2) and threonine aldolase (GLY1) genes. Yeast. 2000 Jan 30;16(2):167–75. doi: 10.1002/(sici)1097-0061(20000130)16:2<167::aid-yea519>3.0.co;2-1. PMID: 10641038. |
| cysteine and homocysteine interconversion Accession ID: BioCyc:CALBI_PWY-801 |
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Nobile CJ, Mitchell AP. Genetics and genomics of Candida albicans biofilm formation. Cell Microbiol. 2006 Sep;8(9):1382–91. doi: 10.1111/j.1462-5822.2006.00761.x. PMID: 16848788.; Murillo LA, Newport G, Lan C, Habelitz S, Dungan J, Agabian NM. Genome-Wide Transcription Profiling of the Early Phase of Biofilm Formation by Candida albicans. Eukaryot Cell. 2005 Sep;4(9):1562–73. doi: 10.1128/ec.4.9.1562-1573.2005.; Mulet JM, Alemany B, Ros R, Calvete JJ, Serrano R. Expression of a plant serine O-acetyltransferase in Saccharomyces cerevisiae confers osmotic tolerance and creates an alternative pathway for cysteine biosynthesis. Yeast. 2004 Mar;21(4):303–12. doi: 10.1002/yea.1076. PMID: 15042590.; Ono BI, Hazu T, Yoshida S, Kawato T, Shinoda S, Brzvwczy J, Paszewski A. Cysteine biosynthesis in Saccharomyces cerevisiae: a new outlook on pathway and regulation. Yeast. 1999 Sep 30;15(13):1365–75. doi: 10.1002/(sici)1097-0061(19990930)15:13<1365::aid-yea468>3.0.co;2-u. PMID: 10509018.; Thomas D, Surdin-Kerjan Y. Metabolism of sulfur amino acids in Saccharomyces cerevisiae. Microbiol Mol Biol Rev. 1997 Dec;61(4):503–32. doi: 10.1128/mmbr.61.4.503-532.1997.; Morzycka E, Paszewski A. Cysteine and homocysteine synthesis in Saccharomycopsis lipolytica; identification and characterization of two cysteine synthases. Acta Biochim Pol. 1982;29(1-2):81–93. PMID: 7180327.; Paszewski A, Grabski J. On sulfhydrylation of O-acetylserine and O-acetylhomoserine in homocysteine synthesis in yeast. Acta Biochim Pol. 1976;23(4):321–4. PMID: 1015154.; Wain WH, Price MF, Cawson RA. A re-evaluation of the effect of cysteine or Candida albicans. Sabouraudia. 1975 Mar;13 Pt 1():74–82. PMID: 1092000.; Mardon DN. In vivo synthesis of sulfur containing amino acids in Candida albicans. Can J Microbiol. 1973 Feb;19(2):155–61. doi: 10.1139/m73-024. PMID: 4572423.; Schlenk F, Zydek CR. Observations on the metabolism of sulfur amino acid derivatives in yeast. Archives of Biochemistry and Biophysics. 1968 Mar;123(3):438–46. doi: 10.1016/0003-9861(68)90164-1. |
| fermentation Accession ID: BioCyc:CALBI_PWY3B3-8 |
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Mukherjee PK, Mohamed S, Chandra J, Kuhn D, Liu S, Antar OS, Munyon R, Mitchell AP, Andes D, Chance MR, Rouabhia M, Ghannoum MA. Alcohol dehydrogenase restricts the ability of the pathogen Candida albicans to form a biofilm on catheter surfaces through an ethanol-based mechanism. Infect Immun. 2006 Jul;74(7):3804–16. PMID: 16790752; PMCID: PMC1489753.; Ogasawara A, Odahara K, Toume M, Watanabe T, Mikami T, Matsumoto T. Change in the Respiration System of Candida albicans in the Lag and Log Growth Phase. Biological & Pharmaceutical Bulletin. 2006;29(3):448–50. doi: 10.1248/bpb.29.448.; Samaranayake LP, Geddes DA, Weetman DA, MacFarlane TW. Growth and acid production of Candida albicans in carbohydrate supplemented media. Microbios. 1983;37(148):105–15. PMID: 6353167. |