Pathways Knowlegdes
Biological pathway database
| Pathway | DOIs | Note |
|---|---|---|
| base-degraded thiamine salvage Accession ID: BioCyc:META_PWY-6899 |
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French JB, Begley TP, Ealick SE. Structure of trifunctional THI20 from yeast. Acta Crystallogr D Biol Crystallogr. 2011 Aug 09;67(9):784–91. doi: 10.1107/s0907444911024814.; Onozuka M, Konno H, Kawasaki Y, Akaji K, Nosaka K. Involvement of thiaminase II encoded by the THI20 gene in thiamin salvage of Saccharomyces cerevisiae. FEMS Yeast Res. 2008 Mar;8(2):266–75. doi: 10.1111/j.1567-1364.2007.00333.x. PMID: 18028398.; Jenkins AL, Zhang Y, Ealick SE, Begley TP. Mutagenesis studies on TenA: A thiamin salvage enzyme from Bacillus subtilis. Bioorganic Chemistry. 2008 Feb;36(1):29–32. doi: 10.1016/j.bioorg.2007.10.005.; Jenkins AH, Schyns G, Potot S, Sun G, Begley TP. A new thiamin salvage pathway. Nat Chem Biol. 2007 Aug;3(8):492–7. doi: 10.1038/nchembio.2007.13. PMID: 17618314.; Haas AL, Laun NP, Begley TP. Thi20, a remarkable enzyme from Saccharomyces cerevisiae with dual thiamin biosynthetic and degradation activities. Bioorg Chem. 2005 Aug;33(4):338–44. doi: 10.1016/j.bioorg.2005.04.001. PMID: 15967475. |
| 3-phosphoinositide biosynthesis Accession ID: BioCyc:META_PWY-6352 |
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Kapeller R, Cantley LC. Phosphatidylinositol 3-kinase. Bioessays. 1994 Aug;16(8):565–76. doi: 10.1002/bies.950160810. PMID: 8086005. |
| 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 IV (bacteria) Accession ID: BioCyc:META_PWY-5025 |
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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. |
| 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. |
| 1,4-dichlorobenzene degradation Accession ID: BioCyc:META_14DICHLORBENZDEG-PWY |
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Spiess E, Sommer C, Görisch H. Degradation of 1,4-dichlorobenzene by Xanthobacter flavus 14p1. Appl Environ Microbiol. 1995 Nov;61(11):3884–8. doi: 10.1128/aem.61.11.3884-3888.1995. |
| 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. |
| methanol oxidation to formaldehyde IV Accession ID: BioCyc:META_PWY-5506 |
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Sakai Y, Tani Y. Cloning and sequencing of the alcohol oxidase-encoding gene (AOD1) from the formaldehyde-producing asporogeneous methylotrophic yeast, Candida boidinii S2. Gene. 1992 May 01;114(1):67–73. doi: 10.1016/0378-1119(92)90708-w. PMID: 1587486. |
| methanol oxidation to formaldehyde III Accession ID: BioCyc:META_PWY-6509 |
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Vonck J, Arfman N, De Vries GE, Van Beeumen J, Van Bruggen EF, Dijkhuizen L. Electron microscopic analysis and biochemical characterization of a novel methanol dehydrogenase from the thermotolerant Bacillus sp. C1. Journal of Biological Chemistry. 1991 Feb;266(6):3949–54. doi: 10.1016/s0021-9258(19)67885-3. |
| 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. |
| methanol oxidation to formaldehyde II Accession ID: BioCyc:META_PWY-6510 |
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Arfman N, Hektor HJ, Bystrykh LV, Govorukhina NI, Dijkhuizen L, Frank J. Properties of an NAD(H)-Containing Methanol Dehydrogenase and its Activator Protein from Bacillus methanolicus. European Journal of Biochemistry. 1997 Mar;244(2):426–33. doi: 10.1111/j.1432-1033.1997.00426.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. |
| suberin monomers biosynthesis Accession ID: BioCyc:META_PWY-1121 |
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Compagnon V, Diehl P, Benveniste I, Meyer D, Schaller H, Schreiber L, Franke R, Pinot F. CYP86B1 is required for very long chain omega-hydroxyacid and alpha, omega -dicarboxylic acid synthesis in root and seed suberin polyester. Plant Physiol. 2009 Aug;150(4):1831–43. PMID: 19525321; PMCID: PMC2719127. |
| 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. |
| selenate reduction Accession ID: BioCyc:META_PWY-6932 |
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Sors TG, Ellis DR, Salt DE. Selenium uptake, translocation, assimilation and metabolic fate in plants. Photosynth Res. 2005 Dec;86(3):373–89. doi: 10.1007/s11120-005-5222-9. PMID: 16307305.; Sors TG, Ellis DR, Na GN, Lahner B, Lee S, Leustek T, Pickering IJ, Salt DE. Analysis of sulfur and selenium assimilation in Astragalus plants with varying capacities to accumulate selenium. The Plant Journal. 2005 May 05;42(6):785–97. doi: 10.1111/j.1365-313x.2005.02413.x.; Pilon-Smits EAH, Hwang S, Mel Lytle C, Zhu Y, Tai JC, Bravo RC, Chen Y, Leustek T, Terry N. Overexpression of ATP Sulfurylase in Indian Mustard Leads to Increased Selenate Uptake, Reduction, and Tolerance1. 1999 Jan 01;119(1):123–32. doi: 10.1104/pp.119.1.123.; Turner RJ, Weiner JH, Taylor DE. Selenium metabolism in Escherichia coli. Biometals. 1998 Sep;11(3):223–7. doi: 10.1023/a:1009290213301. PMID: 9850565.; Bick J, Åslund F, Chen Y, Leustek T. Glutaredoxin function for the carboxyl-terminal domain of the plant-type 5'-adenylylsulfate reductase. Proc. Natl. Acad. Sci. U.S.A. 1998 Jul 07;95(14):8404–9. doi: 10.1073/pnas.95.14.8404.; Burnell JN. Selenium Metabolism in Neptunia amplexicaulis. Plant Physiol. 1981 Feb 01;67(2):316–24. doi: 10.1104/pp.67.2.316.; Dilworth GL, Bandurski RS. Activation of selenate by adenosine 5'-triphosphate sulphurylase from Saccharomyces cerevisiae. Biochem J. 1977 Jun 01;163(3):521–9. PMID: 328009; PMCID: PMC1164733.; Hsieh HS, Ganther HE. Acid-volatile selenium formation catalyzed by glutathione reductase. Biochemistry. 1975 Apr 22;14(8):1632–6. doi: 10.1021/bi00679a014. PMID: 235962.; Shaw WH, Anderson JW. Purification, properties and substrate specificity of adenosine triphosphate sulphurylase from spinach leaf tissue. Biochem J. 1972 Mar;127(1):237–47. PMID: 5073745; PMCID: PMC1178578. |
| esculetin modification Accession ID: BioCyc:META_PWY-7058 |
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Blagbrough IS, Bayoumi SA, Rowan MG, Beeching JR. Cassava: an appraisal of its phytochemistry and its biotechnological prospects. Phytochemistry. 2010 Dec;71(17-18):1940–51. doi: 10.1016/j.phytochem.2010.09.001. PMID: 20943239.; Bayoumi SA, Rowan MG, Beeching JR, Blagbrough IS. Investigation of biosynthetic pathways to hydroxycoumarins during post-harvest physiological deterioration in Cassava roots by using stable isotope labelling. Chembiochem. 2008 Dec 15;9(18):3013–22. doi: 10.1002/cbic.200800515. PMID: 19035613.; Griesser M, Vitzthum F, Fink B, Bellido ML, Raasch C, Munoz-Blanco J, Schwab W. Multi-substrate flavonol O-glucosyltransferases from strawberry (Fragaria x ananassa) achene and receptacle. J Exp Bot. 2008;59(10):2611–25. PMID: 18487633; PMCID: PMC2486459.; Weis M, Lim EK, Bruce NC, Bowles DJ. Engineering and kinetic characterisation of two glucosyltransferases from Arabidopsis thaliana. Biochimie. 2008 May;90(5):830–4. doi: 10.1016/j.biochi.2008.01.013. PMID: 18295607.; KIM BG, LEE Y, HUR H, LIM Y, AHN J. Production of ThreeO-Methhylated Esculetins withEscherichia coliExpressingO-Methyltransferase from Poplar. Bioscience, Biotechnology, and Biochemistry. 2006 May 23;70(5):1269–72. doi: 10.1271/bbb.70.1269.; Fraissinet-Tachet L, Baltz R, Chong J, Kauffmann S, Fritig B, Saindrenan P. Two tobacco genes induced by infection, elicitor and salicylic acid encode glucosyltransferases acting on phenylpropanoids and benzoic acid derivatives, including salicylic acid. FEBS Lett. 1998 Oct 23;437(3):319–23. doi: 10.1016/s0014-5793(98)01257-5. PMID: 9824316.; Werner C, Matile P. Accumulation of coumarylglucosides in vacuoles of barley mesophyll protoplasts. J Plant Physiol. 1985 Mar;118(3):237–49. doi: 10.1016/s0176-1617(85)80225-x. PMID: 23196008. |
| L-tryptophan degradation IV (via indole-3-lactate) Accession ID: BioCyc:META_TRPKYNCAT-PWY |
- | Williams RA, Mamotte CD, Burnett JR. Phenylketonuria: an inborn error of phenylalanine metabolism. Clin Biochem Rev. 2008 Feb;29(1):31–41. PMID: 18566668; PMCID: PMC2423317. |