Pathways Knowlegdes
Biological pathway database
| Pathway | DOIs | Note |
|---|---|---|
| archaetidylserine and archaetidylethanolamine biosynthesis Accession ID: BioCyc:META_PWY-6141 |
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Lombard J, López-García P, Moreira D. Phylogenomic investigation of phospholipid synthesis in archaea. Archaea. 2012;2012():630910. PMID: 23304072; PMCID: PMC3533463.; Daiyasu H, Kuma K, Yokoi T, Morii H, Koga Y, Toh H. A study of archaeal enzymes involved in polar lipid synthesis linking amino acid sequence information, genomic contexts and lipid composition. Archaea. 2005 Dec;1(6):399–410. PMID: 16243780; PMCID: PMC2685579.; Morii H, Koga Y. CDP-2,3-Di -O- Geranylgeranyl- sn -Glycerol: |
| indole-3-acetate biosynthesis I Accession ID: BioCyc:META_PWYDQC-4 |
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Zhao Y. Auxin Biosynthesis: A Simple Two-Step Pathway Converts Tryptophan to Indole-3-Acetic Acid in Plants. Molecular Plant. 2012 Mar;5(2):334–8. doi: 10.1093/mp/ssr104.; Won C, Shen X, Mashiguchi K, Zheng Z, Dai X, Cheng Y, Kasahara H, Kamiya Y, Chory J, Zhao Y. Conversion of tryptophan to indole-3-acetic acid by TRYPTOPHAN AMINOTRANSFERASES OF ARABIDOPSIS and YUCCAs in Arabidopsis. Proc. Natl. Acad. Sci. U.S.A. 2011 Oct 24;108(45):18518–23. doi: 10.1073/pnas.1108436108.; Mashiguchi K, Tanaka K, Sakai T, Sugawara S, Kawaide H, Natsume M, Hanada A, Yaeno T, Shirasu K, Yao H, McSteen P, Zhao Y, Hayashi K, Kamiya Y, Kasahara H. The main auxin biosynthesis pathway in Arabidopsis. Proc. Natl. Acad. Sci. U.S.A. 2011 Oct 24;108(45):18512–7. doi: 10.1073/pnas.1108434108.; Tao Y, Ferrer J, Ljung K, Pojer F, Hong F, Long JA, Li L, Moreno JE, Bowman ME, Ivans LJ, Cheng Y, Lim J, Zhao Y, Ballaré CL, Sandberg G, Noel JP, Chory J. Rapid Synthesis of Auxin via a New Tryptophan-Dependent Pathway Is Required for Shade Avoidance in Plants. Cell. 2008 Apr;133(1):164–76. doi: 10.1016/j.cell.2008.01.049. |
| fatty acids biosynthesis (yeast) Accession ID: BioCyc:META_PWY-5970 |
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Lomakin IB, Xiong Y, Steitz TA. The crystal structure of yeast fatty acid synthase, a cellular machine with eight active sites working together. Cell. 2007 Apr 20;129(2):319–32. doi: 10.1016/j.cell.2007.03.013. PMID: 17448991. |
| indole-3-acetate biosynthesis II Accession ID: BioCyc:META_PWY-581 |
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Won C, Shen X, Mashiguchi K, Zheng Z, Dai X, Cheng Y, Kasahara H, Kamiya Y, Chory J, Zhao Y. Conversion of tryptophan to indole-3-acetic acid by TRYPTOPHAN AMINOTRANSFERASES OF ARABIDOPSIS and YUCCAs in Arabidopsis. Proc. Natl. Acad. Sci. U.S.A. 2011 Oct 24;108(45):18518–23. doi: 10.1073/pnas.1108436108.; Mashiguchi K, Tanaka K, Sakai T, Sugawara S, Kawaide H, Natsume M, Hanada A, Yaeno T, Shirasu K, Yao H, McSteen P, Zhao Y, Hayashi K, Kamiya Y, Kasahara H. The main auxin biosynthesis pathway in Arabidopsis. Proc. Natl. Acad. Sci. U.S.A. 2011 Oct 24;108(45):18512–7. doi: 10.1073/pnas.1108434108.; Tao Y, Ferrer J, Ljung K, Pojer F, Hong F, Long JA, Li L, Moreno JE, Bowman ME, Ivans LJ, Cheng Y, Lim J, Zhao Y, Ballaré CL, Sandberg G, Noel JP, Chory J. Rapid Synthesis of Auxin via a New Tryptophan-Dependent Pathway Is Required for Shade Avoidance in Plants. Cell. 2008 Apr;133(1):164–76. doi: 10.1016/j.cell.2008.01.049.; Stepanova AN, Robertson-Hoyt J, Yun J, Benavente LM, Xie DY, Dolezal K, Schlereth A, Jürgens G, Alonso JM. TAA1-mediated auxin biosynthesis is essential for hormone crosstalk and plant development. Cell. 2008 Apr 04;133(1):177–91. doi: 10.1016/j.cell.2008.01.047. PMID: 18394997.; Naur P, Hansen CH, Bak S, Hansen BG, Jensen NB, Nielsen HL, Halkier BA. CYP79B1 from Sinapis alba converts tryptophan to indole-3-acetaldoxime. Archives of Biochemistry and Biophysics. 2003 Jan;409(1):235–41. doi: 10.1016/s0003-9861(02)00567-2.; Zhao Y, Hull AK, Gupta NR, Goss KA, Alonso J, Ecker JR, Normanly J, Chory J, Celenza JL. Trp-dependent auxin biosynthesis in Arabidopsis: involvement of cytochrome P450s CYP79B2 and CYP79B3. Genes Dev. 2002 Dec 01;16(23):3100–12. PMID: 12464638; PMCID: PMC187496.; Zhao Y, Christensen SK, Fankhauser C, Cashman JR, Cohen JD, Weigel D, Chory J. A role for flavin monooxygenase-like enzymes in auxin biosynthesis. Science. 2001 Jan 12;291(5502):306–9. doi: 10.1126/science.291.5502.306. PMID: 11209081.; Ouyang J, Shao X, Li J. Indole-3-glycerol phosphate, a branchpoint of indole-3-acetic acid biosynthesis from the tryptophan biosynthetic pathway in Arabidopsis thaliana. The Plant Journal. 2000 Nov;24(3):327–34. doi: 10.1046/j.1365-313x.2000.00883.x.; Mikkelsen MD, Hansen CH, Wittstock U, Halkier BA. Cytochrome P450 CYP79B2 from Arabidopsis Catalyzes the Conversion of Tryptophan to Indole-3-acetaldoxime, a Precursor of Indole Glucosinolates and Indole-3-acetic Acid. Journal of Biological Chemistry. 2000 Oct;275(43):33712–7. doi: 10.1074/jbc.m001667200.; Hull AK, Vij R, Celenza JL. Arabidopsis cytochrome P450s that catalyze the first step of tryptophan-dependent indole-3-acetic acid biosynthesis. Proc. Natl. Acad. Sci. U.S.A. 2000 Feb 18;97(5):2379–84. doi: 10.1073/pnas.040569997.; Kobayashi M, Suzuki T, Fujita T, Masuda M, Shimizu S. Occurrence of enzymes involved in biosynthesis of indole-3-acetic acid from indole-3-acetonitrile in plant-associated bacteria, Agrobacterium and Rhizobium. Proc Natl Acad Sci U S A. 1995 Jan 31;92(3):714–8. PMID: 11607511; PMCID: PMC42690. |
| scopoletin biosynthesis Accession ID: BioCyc:META_PWY-6792 |
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Kai K, Mizutani M, Kawamura N, Yamamoto R, Tamai M, Yamaguchi H, Sakata K, Shimizu B. Scopoletin is biosynthesized viaortho-hydroxylation of feruloyl CoA by a 2-oxoglutarate-dependent dioxygenase inArabidopsis thaliana. The Plant Journal. 2008 Sep;55(6):989–99. doi: 10.1111/j.1365-313x.2008.03568.x. |
| seleno-amino acid detoxification and volatilization II Accession ID: BioCyc:META_PWY-6935 |
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Lyi SM, Heller LI, Rutzke M, Welch RM, Kochian LV, Li L. Molecular and biochemical characterization of the selenocysteine Se-methyltransferase gene and Se-methylselenocysteine synthesis in broccoli. Plant Physiol. 2005 May;138(1):409–20. PMID: 15863700; PMCID: PMC1104194.; Tagmount A, Berken A, Terry N. An Essential Role ofS-Adenosyl- |
| arachidonate biosynthesis III (6-desaturase, mammals) Accession ID: BioCyc:META_PWY-7592 |
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Cho HP, Nakamura M, Clarke SD. Cloning, expression, and fatty acid regulation of the human delta-5 desaturase. J Biol Chem. 1999 Dec 24;274(52):37335–9. doi: 10.1074/jbc.274.52.37335. PMID: 10601301. |
| L-tryptophan degradation V (side chain pathway) Accession ID: BioCyc:META_PWY-3162 |
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Narumiya S, Takai K, Tokuyama T, Noda Y, Ushiro H, Hayaishi O. A new metabolic pathway of tryptophan initiated by tryptophan side chain oxidase. Journal of Biological Chemistry. 1979 Aug;254(15):7007–15. doi: 10.1016/s0021-9258(18)50276-3.; Roberts J, Rosenfeld HJ. Isolation, crystallization, and properties of indolyl-3-alkane alpha-hydroxylase. A novel tryptophan-metabolizing enzyme. Journal of Biological Chemistry. 1977 Apr;252(8):2640–7. doi: 10.1016/s0021-9258(17)40506-0.; Takai K, Ushiro H, Noda Y, Narumiya S, Tokuyama T. Crystalline hemoprotein from Pseudomonas that catalyzes oxidation of side chain of tryptophan and other indole derivatives. Journal of Biological Chemistry. 1977 Apr;252(8):2648–56. doi: 10.1016/s0021-9258(17)40507-2. |
| esculetin biosynthesis Accession ID: BioCyc:META_PWY-5349 |
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Yang S, Shim GY, Kim B, Ahn J. Biological synthesis of coumarins in Escherichia coli. Microbial Cell Factories. 2015 May 01;14(1):65. doi: 10.1186/s12934-015-0248-y.; Kai K, Mizutani M, Kawamura N, Yamamoto R, Tamai M, Yamaguchi H, Sakata K, Shimizu B. Scopoletin is biosynthesized viaortho-hydroxylation of feruloyl CoA by a 2-oxoglutarate-dependent dioxygenase inArabidopsis thaliana. The Plant Journal. 2008 Sep;55(6):989–99. doi: 10.1111/j.1365-313x.2008.03568.x. |
| demethylmenaquinol-4 biosynthesis Accession ID: BioCyc:META_PWY-7997 |
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Tonhosolo R, Gabriel HB, Matsumura MY, Cabral FJ, Yamamoto MM, D'Alexandri FL, Sussmann RAC, Belmonte R, Peres VJ, Crick DC, Wunderlich G, Kimura EA, Katzin AM. Intraerythrocytic stages of Plasmodium falciparum biosynthesize menaquinone. FEBS Letters. 2010 Oct 29;584(23):4761–8. doi: 10.1016/j.febslet.2010.10.055. |
| TCA cycle VII (acetate-producers) Accession ID: BioCyc:META_PWY-7254 |
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Mullins EA, Francois JA, Kappock TJ. A Specialized Citric Acid Cycle Requiring Succinyl-Coenzyme A (CoA):Acetate CoA-Transferase (AarC) Confers Acetic Acid Resistance on the Acidophile Acetobacter aceti. J Bacteriol. 2008 Jul 15;190(14):4933–40. doi: 10.1128/jb.00405-08. |
| L-tryptophan degradation X (mammalian, via tryptamine) Accession ID: BioCyc:META_PWY-6307 |
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Yu A, Granvil CP, Haining RL, Krausz KW, Corchero J, Küpfer A, Idle JR, Gonzalez FJ. The Relative Contribution of Monoamine Oxidase and Cytochrome P450 Isozymes to the Metabolic Deamination of the Trace Amine Tryptamine. The Journal of Pharmacology and Experimental Therapeutics. 2003 Feb;304(2):539–46. doi: 10.1124/jpet.102.043786.; Mousseau DD. Tryptamine: a metabolite of tryptophan implicated in various neuropsychiatric disorders. Metab Brain Dis. 1993 Mar;8(1):1–44. doi: 10.1007/bf01000528. PMID: 8098507.; Susilo R, Höfle G, Rommelspacher H. Degradation of tryptamine in pig brain: Identification of a new condensation product. Biochemical and Biophysical Research Communications. 1987 Nov;148(3):1045–52. doi: 10.1016/s0006-291x(87)80237-1.; Yamada J, Sugimoto Y, Horisaka K. Determination of endogeneous indoleacetic acid and tryptophol in mouse brain by high performance liquid chromatography with fluorometric detection. Life Sci. 1983 Nov 14;33(20):2043–7. doi: 10.1016/0024-3205(83)90744-0. PMID: 6645790.; Jaeger CB, Teitelman G, Joh TH, Albert VR, Park DH, Reis DJ. Some neurons of the rat central nervous system contain aromatic-L-amino-acid decarboxylase but not monoamines. Science. 1983 Mar 11;219(4589):1233–5. doi: 10.1126/science.6131537. PMID: 6131537.; Young SN, Davis BA, Gauthier S. Precursors and metabolites of phenylethylamine, m and p-tyramine and tryptamine in human lumbar and cisternal cerebrospinal fluid. Journal of Neurology, Neurosurgery & Psychiatry. 1982 Jul 01;45(7):633–9. doi: 10.1136/jnnp.45.7.633.; Young SN, Gauthier S, Anderson GM, Purdy WC. Tryptophan, 5-hydroxyindoleacetic acid and indoleacetic acid in human cerebrospinal fluid: interrelationships and the influence of age, sex, epilepsy and anticonvulsant drugs. Journal of Neurology, Neurosurgery & Psychiatry. 1980 May 01;43(5):438–45. doi: 10.1136/jnnp.43.5.438. |
| TCA cycle II (plants and fungi) Accession ID: BioCyc:META_PWY-5690 |
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Krebs HA, Eggleston LV. Metabolism of acetoacetate in animal tissues. 1. Biochem J. 1945;39(5):408–19. PMID: 16747930; PMCID: PMC1258257.; Krebs HA, Salvin E, Johnson WA. The formation of citric and alpha-ketoglutaric acids in the mammalian body. Biochem J. 1938 Jan;32(1):113–7. PMID: 16746585; PMCID: PMC1264001.; Krebs HA, Johnson WA. Acetopyruvic acid (alphagamma-diketovaleric acid) as an intermediate metabolite in animal tissues. Biochem J. 1937 May;31(5):772–9. PMID: 16746397; PMCID: PMC1267003. |
| β-D-mannosyl phosphomycoketide biosynthesis Accession ID: BioCyc:META_PWY-7740 |
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Matsunaga I, Bhatt A, Young DC, Cheng TY, Eyles SJ, Besra GS, Briken V, Porcelli SA, Costello CE, Jacobs WR, Moody DB. Mycobacterium tuberculosis pks12 produces a novel polyketide presented by CD1c to T cells. J Exp Med. 2004 Dec 20;200(12):1559–69. PMID: 15611286; PMCID: PMC2211992. |
| reductive acetyl coenzyme A pathway I (homoacetogenic bacteria) Accession ID: BioCyc:META_CODH-PWY |
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Diekert G, Wohlfarth G. Metabolism of homocetogens. Antonie Van Leeuwenhoek. 1994;66(1-3):209–21. doi: 10.1007/bf00871640. PMID: 7747932. |
| vitamin B6 degradation Accession ID: BioCyc:META_PWY-5499 |
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Yokochi N, Nishimura S, Yoshikane Y, Ohnishi K, Yagi T. Identification of a new tetrameric pyridoxal 4-dehydrogenase as the second enzyme in the degradation pathway for pyridoxine in a nitrogen-fixing symbiotic bacterium, Mesorhizobium loti. Archives of Biochemistry and Biophysics. 2006 Aug;452(1):1–8. doi: 10.1016/j.abb.2006.06.002.; Burg RW, Rodwell VW, Snell EE. Bacterial Oxidation of Vitamin B6. Journal of Biological Chemistry. 1960 Apr;235(4):1164–9. doi: 10.1016/s0021-9258(18)69498-0. |
| CO2 fixation into oxaloacetate (anaplerotic) Accession ID: BioCyc:META_PWYQT-4429 |
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Sánchez R, Flores A, Cejudo FJ. Arabidopsis phosphoenolpyruvate carboxylase genes encode immunologically unrelated polypeptides and are differentially expressed in response to drought and salt stress. Planta. 2006 Apr;223(5):901–9. doi: 10.1007/s00425-005-0144-5. PMID: 16283377.; Murakami H, Sly WS. Purification and characterization of human salivary carbonic anhydrase. Journal of Biological Chemistry. 1987 Jan;262(3):1382–8. doi: 10.1016/s0021-9258(19)75797-4. |
| phthiocerol biosynthesis Accession ID: BioCyc:META_PWY-7741 |
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Siméone R, Léger M, Constant P, Malaga W, Marrakchi H, Daffé M, Guilhot C, Chalut C. Delineation of the roles of FadD22, FadD26 and FadD29 in the biosynthesis of phthiocerol dimycocerosates and related compounds in Mycobacterium tuberculosis. The FEBS Journal. 2010 Jun;277(12):2715–25. doi: 10.1111/j.1742-4658.2010.07688.x.; Azad AK, Sirakova TD, Fernandes ND, Kolattukudy PE. Gene Knockout Reveals a Novel Gene Cluster for the Synthesis of a Class of Cell Wall Lipids Unique to Pathogenic Mycobacteria. Journal of Biological Chemistry. 1997 Jul;272(27):16741–5. doi: 10.1074/jbc.272.27.16741. |
| superpathway of L-phenylalanine biosynthesis Accession ID: BioCyc:META_PWY-6628 |
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Weigent DA, Nester EW. Purification and properties of two aromatic aminotransferases in Bacillus subtilis. Journal of Biological Chemistry. 1976 Nov;251(22):6974–80. doi: 10.1016/s0021-9258(17)32929-0. |
| pinosylvin metabolism Accession ID: BioCyc:META_PWY-5045 |
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Seppänen SK, Syrjälä L, von Weissenberg K, Teeri TH, Paajanen L, Pappinen A. Antifungal activity of stilbenes in in vitro bioassays and in transgenic Populus expressing a gene encoding pinosylvin synthase. Plant Cell Rep. 2004 Mar;22(8):584–93. doi: 10.1007/s00299-003-0728-0. PMID: 14714142.; Kodan A, Kuroda H, Sakai F. A stilbene synthase from Japanese red pine ( Pinus densiflora ): Implications for phytoalexin accumulation and down-regulation of flavonoid biosynthesis. Proc. Natl. Acad. Sci. U.S.A. 2002 Mar 05;99(5):3335–9. doi: 10.1073/pnas.042698899.; Yamazaki Y, Suh DY, Sitthithaworn W, Ishiguro K, Kobayashi Y, Shibuya M, Ebizuka Y, Sankawa U. Diverse chalcone synthase superfamily enzymes from the most primitive vascular plant, Psilotum nudum. Planta. 2001 Nov;214(1):75–84. doi: 10.1007/s004250100586. PMID: 11762173.; Chiron H, Drouet A, Claudot AC, Eckerskorn C, Trost M, Heller W, Ernst D, Sandermann H. Molecular cloning and functional expression of a stress-induced multifunctional O-methyltransferase with pinosylvin methyltransferase activity from Scots pine (Pinus sylvestris L.). Plant Mol Biol. 2000 Dec;44(6):733–45. doi: 10.1023/a:1026507707186. PMID: 11202436.; Chiron H, Drouet A, Lieutier F, Payer HD, Ernst D, Sandermann H. Gene induction of stilbene biosynthesis in Scots pine in response to ozone treatment, wounding, and fungal infection. Plant Physiol. 2000 Oct;124(2):865–72. PMID: 11027734; PMCID: PMC59190.; Preisig-Müller R, Schwekendiek A, Brehm I, Reif HJ, Kindl H. Characterization of a pine multigene family containing elicitor-responsive stilbene synthase genes. Plant Mol Biol. 1999 Jan;39(2):221–9. doi: 10.1023/a:1006163030646. PMID: 10080690.; Tropf S, Kärcher B, Schröder G, Schröder J. Reaction mechanisms of homodimeric plant polyketide synthase (stilbenes and chalcone synthase). A single active site for the condensing reaction is sufficient for synthesis of stilbenes, chalcones, and 6'-deoxychalcones. J Biol Chem. 1995 Apr 07;270(14):7922–8. doi: 10.1074/jbc.270.14.7922. PMID: 7713888.; Raiber S, Schröder G, Schröder J. Molecular and enzymatic characterization of two stilbene synthases from Eastern white pine (Pinus strobus). A single Arg/His difference determines the activity and the pH dependence of the enzymes. FEBS Lett. 1995 Mar 20;361(2-3):299–302. doi: 10.1016/0014-5793(95)00199-j. PMID: 7698342.; Tropf S, Lanz T, Rensing SA, Schröder J, Schröder G. Evidence that stilbene synthases have developed from chalcone synthases several times in the course of evolution. Journal of Molecular Evolution. 1994 Jun;38(6):610–8. doi: 10.1007/bf00175881.; Schanz S, Schröder G, Schröder J. Stilbene synthase from Scots pine (Pinus sylvestris). FEBS Lett. 1992 Nov 16;313(1):71–4. doi: 10.1016/0014-5793(92)81187-q. PMID: 1426272.; Schwekendiek A, Pfeffer G, Kindl H. Pine stilbene synthase cDNA, a tool for probing environmental stress. FEBS Lett. 1992 Apr 13;301(1):41–4. doi: 10.1016/0014-5793(92)80206-v. PMID: 1451785.; Fliegmann J, Schröder G, Schanz S, Britsch L, Schröder J. Molecular analysis of chalcone and dihydropinosylvin synthase from Scots pine (Pinus sylvestris), and differential regulation of these and related enzyme activities in stressed plants. Plant Mol Biol. 1992 Feb;18(3):489–503. doi: 10.1007/bf00040665. PMID: 1536925.; Lanz T, Tropf S, Marner FJ, Schröder J, Schröder G. The role of cysteines in polyketide synthases. Site-directed mutagenesis of resveratrol and chalcone synthases, two key enzymes in different plant-specific pathways. Journal of Biological Chemistry. 1991 May;266(15):9971–6. doi: 10.1016/s0021-9258(18)92914-5. |