Pathways Knowlegdes
Biological pathway database
| Pathway | DOIs | Note |
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| S-adenosylmethionine cycle Accession ID: BioCyc:CALBI_PWY-5041 |
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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.; Suliman HS, Sawyer GM, Appling DR, Robertus JD. Purification and properties of cobalamin-independent methionine synthase from Candida albicans and Saccharomyces cerevisiae. Archives of Biochemistry and Biophysics. 2005 Sep;441(1):56–63. doi: 10.1016/j.abb.2005.06.016.; Eschrich D, Buchhaupt M, Kötter P, Entian KD. Nep1p (Emg1p), a novel protein conserved in eukaryotes and archaea, is involved in ribosome biogenesis. Curr Genet. 2002 Feb;40(5):326–38. doi: 10.1007/s00294-001-0269-4. PMID: 11935223.; 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.; Mountain HA, Byström AS, Larsen JT, Korch C. Four major transcriptional responses in the methionine/threonine biosynthetic pathway of Saccharomyces cerevisiae. Yeast. 1991 Nov;7(8):781–803. doi: 10.1002/yea.320070804. PMID: 1789001.; Shapiro SK, Schlenk F. Conversion of 5'-Methylthioadenosine into S-adenosylmethionine by yeast cells. Biochimica et Biophysica Acta (BBA) - General Subjects. 1980 Dec 01;633(2):176–80. doi: 10.1016/0304-4165(80)90403-1.; Schlenk F, Hannum CH, Ferro AJ. Biosynthesis of adenosyl-d-methionine and adenosyl-2-methylmethionine by Candida utilis. Archives of Biochemistry and Biophysics. 1978 Apr;187(1):191–6. doi: 10.1016/0003-9861(78)90022-x.; Holcomb ER, Shapiro SK. Assay and regulation of S-adenosylmethionine synthetase in Saccharomyces cerevisiae and Candida utilis. J Bacteriol. 1975 Jan;121(1):267–71. doi: 10.1128/jb.121.1.267-271.1975.; Nakamura KD, Schlenk F. Examination of Isolated Yeast Cell Vacuoles for Active Transport. J Bacteriol. 1974 Apr;118(1):314–6. doi: 10.1128/jb.118.1.314-316.1974.; Balish E. S-adenosylmethionine metabolism by members of the genus Candida. Can J Microbiol. 1973 Oct;19(10):1297–303. doi: 10.1139/m73-208. PMID: 4587092.; Schlenk F, Zydek-Cwick CR, Dainko JL. 5'-methylthioadenosine and related compounds as precursors of S-adenosylmethionine in yeast. Biochimica et Biophysica Acta (BBA) - General Subjects. 1973 Sep;320(2):357–62. doi: 10.1016/0304-4165(73)90316-4.; Balish E. Methionine biosynthesis and S-adenosylmethionine degradation during an induced morphogenesis of Candida albicans. Can J Microbiol. 1973 Jul;19(7):847–53. doi: 10.1139/m73-135. PMID: 4580452.; 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.; Salem AR, Foster MA. The microbial biosynthesis of methionine. Biochem J. 1972 May;127(5):845–53. PMID: 4627687; PMCID: PMC1178794.; Mardon DN, Balish E. Methionine biosynthesis in Candida albicans. I. S-Adenosyl- |
| biotin biosynthesis Accession ID: BioCyc:CALBI_BIOTIN-SYNTHESIS-PWY |
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Wu H, Ito K, Shimoi H. Identification and Characterization of a Novel Biotin Biosynthesis Gene inSaccharomyces cerevisiae. Appl Environ Microbiol. 2005 Nov;71(11):6845–55. doi: 10.1128/aem.71.11.6845-6855.2005.; Streit WR, Entcheva P. Biotin in microbes, the genes involved in its biosynthesis, its biochemical role and perspectives for biotechnological production. Applied Microbiology and Biotechnology. 2002 Dec 24;61(1):21–31. doi: 10.1007/s00253-002-1186-2.; OHSUGI M, MIYAUCHI K, TACHIBANA K, NAKAO S. Formation of a biotin precursor, pimelic acid, in yeasts from C18 fatty acids. Journal of Nutritional Science and Vitaminology, J Nutr Sci Vitaminol. 1988;34(4):343–52. doi: 10.3177/jnsv.34.343.; Vidotto V, Pugliese A, Gioannini P. Growth of Candida albicans in a minimal synthetic medium without biotin. Mycopathologia. 1987 Oct;100(1):7–15. doi: 10.1007/bf00769562. PMID: 3317062.; Yamaguchi H. Mycelial development and chemical alteration of Candida albicans from biotin insufficiency. Sabouraudia. 1974 Nov;12(3):320–8. PMID: 4610824.; Keränen AJ. On the synthesis of biotin in yeast. Antonie Van Leeuwenhoek. 1969 Jun;35():Suppl:H7–8. PMID: 5312028.; Firestone BY, Koser SA. GROWTH PROMOTING EFFECT OF SOME BIOTIN ANALOGUES FOR CANDIDA ALBICANS. J Bacteriol. 1960 May;79(5):674–6. doi: 10.1128/jb.79.5.674-676.1960. |
| superpathway of ergosterol biosynthesis Accession ID: BioCyc:CALBI_ERGOSTEROL-SYN-PWY |
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Sun LM, Lv BB, Cheng AX, Wu XZ, Lou HX. The Effect of Plagiochin E Alone and in Combination with Fluconazole on the Ergosterol Biosynthesis of Candida albicans. Biological & Pharmaceutical Bulletin. 2009;32(1):36–40. doi: 10.1248/bpb.32.36. |
| polyamine biosynthesis Accession ID: BioCyc:CALBI_POLYAMSYN-YEAST-PWY |
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Ueno Y, Fukumatsu M, Ogasawara A, Watanabe T, Mikami T, Matsumoto T. Hyphae Formation of Candida albicans Is Regulated by Polyamines. Biological & Pharmaceutical Bulletin. 2004;27(6):890–2. doi: 10.1248/bpb.27.890.; White WH, Gunyuzlu PL, Toyn JH. Saccharomyces cerevisiae is capable of de Novo pantothenic acid biosynthesis involving a novel pathway of beta-alanine production from spermine. J Biol Chem. 2001 Apr 06;276(14):10794–800. doi: 10.1074/jbc.m009804200. PMID: 11154694.; Herrero AB, Lo´pez MC, Garci´a S, Schmidt A, Spaltmann F, Ruiz-Herrera J, Dominguez A. Control of Filament Formation in Candida albicans by Polyamine Levels. Infect Immun. 1999 Sep;67(9):4870–8. doi: 10.1128/iai.67.9.4870-4878.1999.; Hamasaki-Katagiri N, Katagiri Y, Tabor CW, Tabor H. Spermine is not essential for growth of Saccharomyces cerevisiae: identification of the SPE4 gene (spermine synthase) and characterization of a spe4 deletion mutant. Gene. 1998 Apr 14;210(2):195–201. doi: 10.1016/s0378-1119(98)00027-4. PMID: 9573363.; McNemar MD, Gorman JA, Buckley HR. Isolation and sequence of the gene encoding ornithine decarboxylase, SPE1, from Candida albicans by complementation of a spe1 delta strain of Saccharomyces cerevisiae. Yeast. 1997 Nov;13(14):1383–9. doi: 10.1002/(sici)1097-0061(199711)13:14<1383::aid-yea189>3.0.co;2-m. PMID: 9392083.; López MC, García S, Ruiz-Herrera J, Domínguez A. The ornithine decarboxylase gene from Candida albicans. Sequence analysis and expression during dimorphism. Curr Genet. 1997 Aug;32(2):108–14. doi: 10.1007/s002940050254. PMID: 9294258.; Martinez JP, Lopez-Ribot JL, Gil ML, Sentandreu R, Ruiz-Herrera J. Inhibition of the dimorphic transition of Candida albicans by the ornithine decarboxylase inhibitor 1,4-diaminobutanone: alterations in the glycoprotein composition of the cell wall. Journal of General Microbiology. 1990 Oct 01;136(10):1937–43. doi: 10.1099/00221287-136-10-1937.; Bezjak V, al-Nakib T, Chandy R, Verghese R. Cell-constituent polyamines in Candida species and new biotyping of Candida albicans, Candida tropicalis and Candida parapsilosis strains. J Med Vet Mycol. 1990;28(4):267–73. PMID: 2269908.; Hamana K, Matsuzaki S, Hosaka K, Yamashita S. Interconversion of polyamines in wild-type strains and mutants of yeasts and the effects of polyamines on their growth. FEMS Microbiol Lett. 1989 Oct 01;52(1-2):231–6. doi: 10.1016/0378-1097(89)90202-4. PMID: 2689281.; Pfaller MA, Riley J, Gerarden T. Polyamine depletion and growth inhibition in Candida albicans and Candida tropicalis by alpha-difluoromethylornithine and cyclohexylamine. J Med Vet Mycol. 1988 Apr;26(2):119–26. PMID: 3138402. |
| ubiquinone (coenzyme Q) biosynthesis Accession ID: BioCyc:CALBI_PWY3B3-10 |
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| phospholipid biosynthesis Accession ID: BioCyc:CALBI_PHOSLIPSYN2-PWY |
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Klig LS, Friedli L, Schmid E. Phospholipid biosynthesis in Candida albicans: regulation by the precursors inositol and choline. J Bacteriol. 1990 Aug;172(8):4407–14. doi: 10.1128/jb.172.8.4407-4414.1990.; Mago N, Khuller GK. Subcellular localization of enzymes of phospholipid metabolism in Candida albicans. J Med Vet Mycol. 1990;28(5):355–62. PMID: 2283583.; Trivedi A, Dudani AK, Prasad R. Why choline supplementation did not enhance phosphatidylcholine level in Candida albicans. Biochem Int. 1983 Jan;6(1):119–28. PMID: 6089802.; Rattray JB, Schibeci A, Kidby DK. Lipids of yeasts. Bacteriol Rev. 1975 Sep;39(3):197–231. doi: 10.1128/br.39.3.197-231.1975. |
| siroheme biosynthesis Accession ID: BioCyc:CALBI_PWY-5194 |
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| ergosterol biosynthesis Accession ID: BioCyc:CALBI_PWY-6075 |
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| Sterol biosynthesis Accession ID: Plant Reactome:R-HVU-1119370 |
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| Metabolism and regulation Accession ID: Plant Reactome:R-OAU-2744345 |
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| Amino acid metabolism Accession ID: Plant Reactome:R-OAU-2744343 |
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| SMM cycle Accession ID: Plant Reactome:R-OAU-1119349 |
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| Ethene biosynthesis from methionine Accession ID: Plant Reactome:R-OAU-1119334 |
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Voesenek LACJ, Bailey-Serres J. Flood adaptive traits and processes: an overview. New Phytol. 2015 Apr;206(1):57–73. doi: 10.1111/nph.13209. PMID: 25580769. |
| Tricin biosynthesis Accession ID: Plant Reactome:R-OAU-9609573 |
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Lam PY, Liu H, Lo C. Completion of Tricin Biosynthesis Pathway in Rice: Cytochrome P450 75B4 Is a Unique Chrysoeriol 5'-Hydroxylase. Plant Physiol. 2015 Aug;168(4):1527–36. PMID: 26082402; PMCID: PMC4528758.; Lan W, Lu F, Regner M, Zhu Y, Rencoret J, Ralph SA, Zakai UI, Morreel K, Boerjan W, Ralph J. Tricin, a flavonoid monomer in monocot lignification. Plant Physiol. 2015 Apr;167(4):1284–95. PMID: 25667313; PMCID: PMC4378158.; Lam PY, Zhu FY, Chan WL, Liu H, Lo C. Cytochrome P450 93G1 Is a Flavone Synthase II That Channels Flavanones to the Biosynthesis of Tricin O-Linked Conjugates in Rice. Plant Physiol. 2014 Jul;165(3):1315–27. PMID: 24843076; PMCID: PMC4081339.; Moheb A, Grondin M, Ibrahim RK, Roy R, Sarhan F. Winter wheat hull (husk) is a valuable source for tricin, a potential selective cytotoxic agent. Food Chem. 2013 Jun 01;138(2-3):931–7. doi: 10.1016/j.foodchem.2012.09.129. PMID: 23411198.; Shalini V, Bhaskar S, Kumar KS, Mohanlal S, Jayalekshmy A, Helen A. Molecular mechanisms of anti-inflammatory action of the flavonoid, tricin from Njavara rice (Oryza sativa L.) in human peripheral blood mononuclear cells: possible role in the inflammatory signaling. Int Immunopharmacol. 2012 Sep;14(1):32–8. doi: 10.1016/j.intimp.2012.06.005. PMID: 22705359.; Chang CL, Wang GJ, Zhang LJ, Tsai WJ, Chen RY, Wu YC, Kuo YH. Cardiovascular protective flavonolignans and flavonoids from Calamus quiquesetinervius. Phytochemistry. 2010 Feb;71(2-3):271–9. doi: 10.1016/j.phytochem.2009.09.025. PMID: 20006366.; Shih CH, Chu H, Tang LK, Sakamoto W, Maekawa M, Chu IK, Wang M, Lo C. Functional characterization of key structural genes in rice flavonoid biosynthesis. Planta. 2008 Nov;228(6):1043–54. doi: 10.1007/s00425-008-0806-1. PMID: 18726614.; Kong CH, Zhao H, Xu XH, Wang P, Gu Y. Activity and allelopathy of soil of flavone o-glycosides from rice. J Agric Food Chem. 2007 Jul 25;55(15):6007–12. doi: 10.1021/jf0703912. PMID: 17602647.; Duarte-Almeida JM, Negri G, Salatino A, de Carvalho JE, Lajolo FM. Antiproliferative and antioxidant activities of a tricin acylated glycoside from sugarcane (Saccharum officinarum) juice. Phytochemistry. 2007 Apr;68(8):1165–71. doi: 10.1016/j.phytochem.2007.01.015. PMID: 17350657.; Cai H, Boocock DJ, Steward WP, Gescher AJ. Tissue distribution in mice and metabolism in murine and human liver of apigenin and tricin, flavones with putative cancer chemopreventive properties. Cancer Chemother Pharmacol. 2007 Jul;60(2):257–66. doi: 10.1007/s00280-006-0368-5. PMID: 17089164.; Kim BG, Lee Y, Hur HG, Lim Y, Ahn JH. Flavonoid 3'-O-methyltransferase from rice: cDNA cloning, characterization and functional expression. Phytochemistry. 2006 Feb;67(4):387–94. doi: 10.1016/j.phytochem.2005.11.022. PMID: 16412485.; Kong C, Xu X, Zhou B, Hu F, Zhang C, Zhang M. Two compounds from allelopathic rice accession and their inhibitory activity on weeds and fungal pathogens. Phytochemistry. 2004 Apr;65(8):1123–8. doi: 10.1016/j.phytochem.2004.02.017. PMID: 15110693. |
| Response to iron deficiency Accession ID: Plant Reactome:R-OAU-9025714 |
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| Yang cycle Accession ID: Plant Reactome:R-CME-1119624 |
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| Amine and polyamine biosynthesis Accession ID: Plant Reactome:R-CME-5096066 |
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Fuell C, Elliott KA, Hanfrey CC, Franceschetti M, Michael AJ. Polyamine biosynthetic diversity in plants and algae. Plant Physiol Biochem. 2010 Jul;48(7):513–20. doi: 10.1016/j.plaphy.2010.02.008. PMID: 20227886. |
| Biotin biosynthesis II Accession ID: Plant Reactome:R-CME-1119610 |
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| Hormone signaling, transport, and metabolism Accession ID: Plant Reactome:R-CME-2744341 |
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| Inorganic nutrients metabolism Accession ID: Plant Reactome:R-CME-5368291 |
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