Pathways Knowlegdes
Biological pathway database
| Pathway | DOIs | Note |
|---|---|---|
| ubiquinol-9 biosynthesis (eukaryotic) Accession ID: BioCyc:META_PWY-5871 |
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Sadre R, Pfaff C, Buchkremer S. Plastoquinone-9 biosynthesis in cyanobacteria differs from that in plants and involves a novel 4-hydroxybenzoate solanesyltransferase. Biochem J. 2012 Mar 15;442(3):621–9. doi: 10.1042/bj20111796. PMID: 22166075.; Trumpower BL, Houser RM, Olson RE. Studies on ubiquinone. Demonstration of the total biosynthesis of ubiquinone-9 in rat liver mitochondria. J Biol Chem. 1974 May 25;249(10):3041–8. PMID: 4378394.; Momose K, Rudney H. 3-Polyprenyl-4-hydroxybenzoate synthesis in the inner membrane of mitochondria from p-hydroxybenzoate and isopentenylpyrophosphate. A demonstration of isoprenoid synthesis in rat liver mitochondria. J Biol Chem. 1972 Jun 25;247(12):3930–40. PMID: 4338233. |
| ubiquinol-9 biosynthesis (prokaryotic) Accession ID: BioCyc:META_PWY-5856 |
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Sadre R, Pfaff C, Buchkremer S. Plastoquinone-9 biosynthesis in cyanobacteria differs from that in plants and involves a novel 4-hydroxybenzoate solanesyltransferase. Biochem J. 2012 Mar 15;442(3):621–9. doi: 10.1042/bj20111796. PMID: 22166075.; Uchida K, Aida K. Incorporation of molecular oxygen during the biosynthesis of ubiquinone in an aerobic bacterium, Pseudomonas desmolytica. Biochemical and Biophysical Research Communications. 1972 Jan;46(1):130–5. doi: 10.1016/0006-291x(72)90640-7. |
| heterolactic fermentation Accession ID: BioCyc:META_P122-PWY |
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Helanto M, Aarnikunnas J, Palva A, Leisola M, Nyyssölä A. Characterization of genes involved in fructose utilization by Lactobacillus fermentum. Arch Microbiol. 2006 Jul;186(1):51–9. doi: 10.1007/s00203-006-0120-x. PMID: 16741753.; Levy HR, Vought VE, Yin X, Adams MJ. Identification of an arginine residue in the dual coenzyme-specific glucose-6-phosphate dehydrogenase from Leuconostoc mesenteroides that plays a key role in binding NADP+ but not NAD+. Arch Biochem Biophys. 1996 Feb 01;326(1):145–51. doi: 10.1006/abbi.1996.0058. PMID: 8579362.; Stournaras C, Maurer P, Kurz G. 6-phospho-D-gluconate dehydrogenase from Pseudomonas fluorescens. Properties and subunit structure. Eur J Biochem. 1983 Feb 01;130(2):391–6. doi: 10.1111/j.1432-1033.1983.tb07165.x. PMID: 6402366.; Ben-Bassat A, Goldberg I. Purification and properties of glucose-6-phosphate dehydrogenase (NADP+/NAD+) and 6-phosphogluconate dehydrogenase (NADP+/NAD+) from methanol-grown Pseudomonas C. Biochimica et Biophysica Acta (BBA) - Enzymology. 1980 Jan;611(1):1–10. doi: 10.1016/0005-2744(80)90036-4. |
| aspartate superpathway Accession ID: BioCyc:META_PWY0-781 |
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Devenish SR, Blunt JW, Gerrard JA. NMR studies uncover alternate substrates for dihydrodipicolinate synthase and suggest that dihydrodipicolinate reductase is also a dehydratase. J Med Chem. 2010 Jun 24;53(12):4808–12. doi: 10.1021/jm100349s. PMID: 20503968.; Chassagnole C, Raïs B, Quentin E, Fell DA, Mazat JP. An integrated study of threonine-pathway enzyme kinetics in Escherichia coli. Biochem J. 2001 Jun 01;356(Pt 2):415–23. PMID: 11368768; PMCID: PMC1221852.; Begley TP, Kinsland C, Mehl RA, Osterman A, Dorrestein P. The biosynthesis of nicotinamide adenine dinucleotides in bacteria. Vitam Horm. 2001;61():103–19. doi: 10.1016/s0083-6729(01)61003-3. PMID: 11153263.; Soda K. Microbial sulfur amino acids: an overview. Methods Enzymol. 1987;143():453–9. doi: 10.1016/0076-6879(87)43080-2. PMID: 3309561.; POWELL JT, MORRISON JF. The Purification and Properties of the Aspartate Aminotransferase and Aromatic-Amino-Acid Aminotransferase from Escherichia coli. European Journal of Biochemistry. 1978 Jun;87(2):391–400. doi: 10.1111/j.1432-1033.1978.tb12388.x.; Farkas W, Gilvarg C. The Reduction Step in Diaminopimelic Acid Biosynthesis. Journal of Biological Chemistry. 1965 Dec;240(12):4717–22. doi: 10.1016/s0021-9258(18)97014-6.; Kindler SH, Gilvarg C. N-Succinyl-l-a, e-diaminopimelic Acid Deacylase. Journal of Biological Chemistry. 1960 Dec;235(12):3532–5. doi: 10.1016/s0021-9258(18)64502-8.; Cohen GN, Hirsch M. THREONINE SYNTHASE, A SYSTEM SYNTHESIZING |
| superpathway of atrazine degradation Accession ID: BioCyc:META_PWY-5724 |
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Shapir N, Mongodin EF, Sadowsky MJ, Daugherty SC, Nelson KE, Wackett LP. Evolution of catabolic pathways: Genomic insights into microbial s-triazine metabolism. J Bacteriol. 2007 Feb;189(3):674–82. PMID: 17114259; PMCID: PMC1797303. |
| thiamine diphosphate biosynthesis II (Bacillus) Accession ID: BioCyc:META_PWY-6893 |
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Hazra A, Chatterjee A, Begley TP. Biosynthesis of the Thiamin Thiazole in Bacillus subtilis: Identification of the Product of the Thiazole Synthase-Catalyzed Reaction. J. Am. Chem. Soc. 2009 Feb 13;131(9):3225–9. doi: 10.1021/ja806752h. |
| pentose phosphate pathway (oxidative branch) I Accession ID: BioCyc:META_OXIDATIVEPENT-PWY |
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| betaxanthin biosynthesis Accession ID: BioCyc:META_PWY-5426 |
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Cai Y, Sun M, Corke H. HPLC Characterization of Betalains from Plants in the Amaranthaceae. Journal of Chromatographic Science. 2005 Oct 01;43(9):454–60. doi: 10.1093/chromsci/43.9.454.; Böhm H, Mäck G. Betaxanthin formation and free amino acids in hairy roots of Beta vulgaris var. lutea depending on nutrient medium and glutamate or glutamine feeding. Phytochemistry. 2004 May;65(10):1361–8. doi: 10.1016/j.phytochem.2004.03.008. PMID: 15231409.; Strack D, Vogt T, Schliemann W. Recent advances in betalain research. Phytochemistry. 2003 Feb;62(3):247–69. doi: 10.1016/s0031-9422(02)00564-2. PMID: 12620337.; Schliemann, Kobayashi, Strack. The decisive step in betaxanthin biosynthesis is a spontaneous reaction1 . Plant Physiol. 1999 Apr;119(4):1217–32. PMID: 10198080; PMCID: PMC32006.; Facchini PJ, De Luca V. Phloem-Specific Expression of Tyrosine/Dopa Decarboxylase Genes and the Biosynthesis of Isoquinoline Alkaloids in Opium Poppy. Plant Cell. 1995 Nov;7(11):1811–21. PMID: 12242361; PMCID: PMC161040.; Facchini PJ, De Luca V. Differential and tissue-specific expression of a gene family for tyrosine/dopa decarboxylase in opium poppy. Journal of Biological Chemistry. 1994 Oct;269(43):26684–90. doi: 10.1016/s0021-9258(18)47073-1. |
| hydrogen production V Accession ID: BioCyc:META_PWY-6772 |
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Yoshida A, Nishimura T, Kawaguchi H, Inui M, Yukawa H. Enhanced Hydrogen Production from Formic Acid by Formate Hydrogen Lyase-Overexpressing Escherichia coli Strains. Appl Environ Microbiol. 2005 Nov;71(11):6762–8. doi: 10.1128/aem.71.11.6762-6768.2005. |
| superpathway of demethylmenaquinol-9 biosynthesis Accession ID: BioCyc:META_PWY-5862 |
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Huycke MM, Moore D, Joyce W, Wise P, Shepard L, Kotake Y, Gilmore MS. Extracellular superoxide production by Enterococcus faecalis requires demethylmenaquinone and is attenuated by functional terminal quinol oxidases. Molecular Microbiology. 2001 Nov;42(3):729–40. doi: 10.1046/j.1365-2958.2001.02638.x. |
| superpathway of ubiquinol-8 biosynthesis (prokaryotic) Accession ID: BioCyc:META_UBISYN-PWY |
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Meganathan R. Ubiquinone biosynthesis in microorganisms. FEMS Microbiol Lett. 2001 Sep 25;203(2):131–9. doi: 10.1111/j.1574-6968.2001.tb10831.x. PMID: 11583838. |
| L-carnitine biosynthesis Accession ID: BioCyc:META_PWY-6100 |
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van Vlies N, Wanders RJ, Vaz FM. Measurement of carnitine biosynthesis enzyme activities by tandem mass spectrometry: differences between the mouse and the rat. Anal Biochem. 2006 Jul 01;354(1):132–9. doi: 10.1016/j.ab.2006.04.007. PMID: 16707092.; Steiber A, Kerner J, Hoppel CL. Carnitine: a nutritional, biosynthetic, and functional perspective. Mol Aspects Med. 2004 Oct;25(5-6):455–73. doi: 10.1016/j.mam.2004.06.006. PMID: 15363636.; Vaz FM, Wanders RJ. Carnitine biosynthesis in mammals. Biochem J. 2002 Feb 01;361(Pt 3):417–29. PMID: 11802770; PMCID: PMC1222323.; Hulse JD, Ellis SR, Henderson LM. Carnitine biosynthesis. beta-Hydroxylation of trimethyllysine by an alpha-ketoglutarate-dependent mitochondrial dioxygenase. Journal of Biological Chemistry. 1978 Mar;253(5):1654–9. doi: 10.1016/s0021-9258(17)34915-3.; Kaufman RA, Broquist HP. Biosynthesis of carnitine in Neurospora crassa. Journal of Biological Chemistry. 1977 Nov;252(21):7437–9. doi: 10.1016/s0021-9258(17)40983-5. |
| superpathway of fumitremorgin biosynthesis Accession ID: BioCyc:META_PWY-7537 |
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KATO N, SUZUKI H, OKUMURA H, TAKAHASHI S, OSADA H. A Point Mutation inftmDBlocks the Fumitremorgin Biosynthetic Pathway inAspergillus fumigatusStrain Af293. Bioscience, Biotechnology, and Biochemistry. 2013 May 23;77(5):1061–7. doi: 10.1271/bbb.130026.; Ishikura M, Abe T, Choshi T, Hibino S. Simple indole alkaloids and those with a non-rearranged monoterpenoid unit. Nat Prod Rep. 2013 May;30(5):694–752. doi: 10.1039/c3np20118j. PMID: 23467716.; Wollinsky B, Ludwig L, Xie X, Li SM. Breaking the regioselectivity of indole prenyltransferases: identification of regular C3-prenylated hexahydropyrrolo[2,3-b]indoles as side products of the regular C2-prenyltransferase FtmPT1. Org Biomol Chem. 2012 Dec 14;10(46):9262–70. doi: 10.1039/c2ob26149a. PMID: 23090579.; Mundt K, Wollinsky B, Ruan HL, Zhu T, Li SM. Identification of the verruculogen prenyltransferase FtmPT3 by a combination of chemical, bioinformatic and biochemical approaches. Chembiochem. 2012 Nov 26;13(17):2583–92. doi: 10.1002/cbic.201200523. PMID: 23109474.; Borthwick AD. 2,5-Diketopiperazines: synthesis, reactions, medicinal chemistry, and bioactive natural products. Chem Rev. 2012 Jul 11;112(7):3641–716. doi: 10.1021/cr200398y. PMID: 22575049.; Kato N, Suzuki H, Takagi H, Uramoto M, Takahashi S, Osada H. Gene disruption and biochemical characterization of verruculogen synthase of Aspergillus fumigatus. Chembiochem. 2011 Mar 21;12(5):711–4. doi: 10.1002/cbic.201000562. PMID: 21404415.; Jost M, Zocher G, Tarcz S, Matuschek M, Xie X, Li SM, Stehle T. Structure-function analysis of an enzymatic prenyl transfer reaction identifies a reaction chamber with modifiable specificity. J Am Chem Soc. 2010 Dec 22;132(50):17849–58. doi: 10.1021/ja106817c. PMID: 21105662.; Li SM. Genome mining and biosynthesis of fumitremorgin-type alkaloids in ascomycetes. J Antibiot (Tokyo). 2011 Jan;64(1):45–9. doi: 10.1038/ja.2010.128. PMID: 21063425.; Morace G, Borghi E. Fungal infections in ICU patients: epidemiology and the role of diagnostics. Minerva Anestesiol. 2010 Nov;76(11):950–6. PMID: 21102391.; Ding Y, Wet JRD, Cavalcoli J, Li S, Greshock TJ, Miller KA, Finefield JM, Sunderhaus JD, McAfoos TJ, Tsukamoto S, Williams RM, Sherman DH. Genome-Based Characterization of Two Prenylation Steps in the Assembly of the Stephacidin and Notoamide Anticancer Agents in a Marine-Derived Aspergillus sp. J. Am. Chem. Soc. 2010 Aug 19;132(36):12733–40. doi: 10.1021/ja1049302.; Ben-Ami R, Lewis RE, Kontoyiannis DP. Enemy of the (immunosuppressed) state: an update on the pathogenesis of Aspergillus fumigatus infection. Br J Haematol. 2010 Aug;150(4):406–17. doi: 10.1111/j.1365-2141.2010.08283.x. PMID: 20618330.; Li SM. Prenylated indole derivatives from fungi: structure diversity, biological activities, biosynthesis and chemoenzymatic synthesis. Nat Prod Rep. 2010 Jan;27(1):57–78. doi: 10.1039/b909987p. PMID: 20024094.; Steffan N, Grundmann A, Afiyatullov S, Ruan H, Li SM. FtmOx1, a non-heme Fe(II) and alpha-ketoglutarate-dependent dioxygenase, catalyses the endoperoxide formation of verruculogen in Aspergillus fumigatus. Org Biomol Chem. 2009 Oct 07;7(19):4082–7. doi: 10.1039/b908392h. PMID: 19763315.; Kato N, Suzuki H, Takagi H, Asami Y, Kakeya H, Uramoto M, Usui T, Takahashi S, Sugimoto Y, Osada H. Identification of cytochrome P450s required for fumitremorgin biosynthesis in Aspergillus fumigatus. Chembiochem. 2009 Mar 23;10(5):920–8. doi: 10.1002/cbic.200800787. PMID: 19226505.; Frisvad JC, Rank C, Nielsen KF, Larsen TO. Metabolomics of Aspergillus fumigatus. Med Mycol. 2009;47 Suppl 1():S53–71. doi: 10.1080/13693780802307720. PMID: 18763205.; Grundmann A, Kuznetsova T, Afiyatullov SSh, Li SM. FtmPT2, an N-prenyltransferase from Aspergillus fumigatus, catalyses the last step in the biosynthesis of fumitremorgin B. Chembiochem. 2008 Sep 01;9(13):2059–63. doi: 10.1002/cbic.200800240. PMID: 18683158.; Maiya S, Grundmann A, Li SM, Turner G. The fumitremorgin gene cluster of Aspergillus fumigatus: identification of a gene encoding brevianamide F synthetase. Chembiochem. 2006 Jul;7(7):1062–9. doi: 10.1002/cbic.200600003. PMID: 16755625.; Krishnamurthy P, Schuetz JD. Role of ABCG2/BCRP in biology and medicine. Annu Rev Pharmacol Toxicol. 2006;46():381–410. doi: 10.1146/annurev.pharmtox.46.120604.141238. PMID: 16402910.; Nierman WC, Pain A, Anderson MJ, Wortman JR, Kim HS, Arroyo J, Berriman M, Abe K, Archer DB, Bermejo C, Bennett J, Bowyer P, Chen D, Collins M, Coulsen R, Davies R, Dyer PS, Farman M, Fedorova N, Fedorova N, Feldblyum TV, Fischer R, Fosker N, Fraser A, García JL, García MJ, Goble A, Goldman GH, Gomi K, Griffith-Jones S, Gwilliam R, Haas B, Haas H, Harris D, Horiuchi H, Huang J, Humphray S, Jiménez J, Keller N, Khouri H, Kitamoto K, Kobayashi T, Konzack S, Kulkarni R, Kumagai T, Lafton A, Latgé J, Li W, Lord A, Lu C, Majoros WH, May GS, Miller BL, Mohamoud Y, Molina M, Monod M, Mouyna I, Mulligan S, Murphy L, O'Neil S, Paulsen I, Peñalva MA, Pertea M, Price C, Pritchard BL, Quail MA, Rabbinowitsch E, Rawlins N, Rajandream M, Reichard U, Renauld H, Robson GD, de Córdoba SR, Rodríguez-Peña JM, Ronning CM, Rutter S, Salzberg SL, Sanchez M, Sánchez-Ferrero JC, Saunders D, Seeger K, Squares R, Squares S, Takeuchi M, Tekaia F, Turner G, de Aldana CRV, Weidman J, White O, Woodward J, Yu J, Fraser C, Galagan JE, Asai K, Machida M, Hall N, Barrell B, Denning DW. Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus. Nature. 2005 Dec 22;438(7071):1151–6. doi: 10.1038/nature04332.; Goffeau A. Genomics: multiple moulds. Nature. 2005 Dec 22;438(7071):1092–3. doi: 10.1038/4381092b. PMID: 16371993.; Keller NP, Turner G, Bennett JW. Fungal secondary metabolism - from biochemistry to genomics. Nat Rev Microbiol. 2005 Dec;3(12):937–47. doi: 10.1038/nrmicro1286. PMID: 16322742.; Grundmann A, Li SM. Overproduction, purification and characterization of FtmPT1, a brevianamide F prenyltransferase from Aspergillus fumigatus. Microbiology (Reading). 2005 Jul;151(Pt 7):2199–207. doi: 10.1099/mic.0.27962-0. PMID: 16000710.; Sabater-Vilar M, Nijmeijer S, Fink-Gremmels J. Genotoxicity assessment of five tremorgenic mycotoxins (fumitremorgen B, paxilline, penitrem A, verruculogen, and verrucosidin) produced by molds isolated from fermented meats. J Food Prot. 2003 Nov;66(11):2123–9. doi: 10.4315/0362-028x-66.11.2123. PMID: 14627292.; Zhao S, Smith KS, Deveau AM, Dieckhaus CM, Johnson MA, Macdonald TL, Cook JM. Biological activity of the tryprostatins and their diastereomers on human carcinoma cell lines. J Med Chem. 2002 Apr 11;45(8):1559–62. doi: 10.1021/jm0155953. PMID: 11931609.; Hibino S, Choshi T. Simple indole alkaloids and those with a nonrearranged monoterpenoid unit. Nat Prod Rep. 2001 Feb;18(1):66–87. doi: 10.1039/b004055j. PMID: 11245401.; Sanz-Cervera JF, Stocking EM, Usui T, Osada H, Williams RM. Synthesis and evaluation of microtubule assembly inhibition and cytotoxicity of prenylated derivatives of cyclo-l-Trp-l-Pro. Bioorganic & Medicinal Chemistry. 2000 Oct;8(10):2407–15. doi: 10.1016/s0968-0896(00)00171-1.; Rabindran SK, Ross DD, Doyle LA, Yang W, Greenberger LM. Fumitremorgin C reverses multidrug resistance in cells transfected with the breast cancer resistance protein. Cancer Res. 2000 Jan 01;60(1):47–50. PMID: 10646850.; Usui T, Kondoh M, Cui CB, Mayumi T, Osada H. Tryprostatin A, a specific and novel inhibitor of microtubule assembly. Biochem J. 1998 Aug 01;333 ( Pt 3)():543–8. PMID: 9677311; PMCID: PMC1219615.; Cui CB, Kakeya H, Okada G, Onose R, Osada H. Novel mammalian cell cycle inhibitors, tryprostatins A, B and other diketopiperazines produced by Aspergillus fumigatus. I. Taxonomy, fermentation, isolation and biological properties. J Antibiot (Tokyo). 1996 Jun;49(6):527–33. doi: 10.7164/antibiotics.49.527. PMID: 8698634.; Nielsen PV, Beuchat LR, Frisvad JC. Growth of and fumitremorgin production by Neosartorya fischeri as affected by temperature, light, and water activity. Appl Environ Microbiol. 1988 Jun;54(6):1504–10. doi: 10.1128/aem.54.6.1504-1510.1988.; Yamazaki M, Fujimoto H, Kawasaki T. Chemistry of tremorogenic metabolites. I. Fumitremorgin A from Aspergillus fumigatus. Chem Pharm Bull (Tokyo). 1980 Jan;28(1):245–54. doi: 10.1248/cpb.28.245. PMID: 6988091.; Yamazaki M, Suzuki S, Miyaki K. Tremorgenic toxins from Aspergillus fumigatus Fres. Chem Pharm Bull (Tokyo). 1971 Aug;19(8):1739–40. doi: 10.1248/cpb.19.1739. PMID: 5122678.; WILSON BJ, WILSON CH. TOXIN FROM ASPERGILLUS FLAVUS: PRODUCTION ON FOOD MATERIALS OF A SUBSTANCE CAUSING TREMORS IN MICE. Science. 1964 Apr 10;144(3615):177–8. doi: 10.1126/science.144.3615.177. PMID: 14107473. |
| flavonoid biosynthesis Accession ID: BioCyc:META_PWY1F-FLAVSYN |
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Xu F, Li L, Zhang W, Cheng H, Sun N, Cheng S, Wang Y. Isolation, characterization, and function analysis of a flavonol synthase gene from Ginkgo biloba. Molecular Biology Reports. 2011 Jun 05;39(3):2285–96. doi: 10.1007/s11033-011-0978-9.; Lukacin R, Wellmann F, Britsch L, Martens S, Matern U. Flavonol synthase from Citrus unshiu is a bifunctional dioxygenase. Phytochemistry. 2003 Feb;62(3):287–92. doi: 10.1016/s0031-9422(02)00567-8. PMID: 12620339.; Wellmann F, Lukacin R, Moriguchi T, Britsch L, Schiltz E, Matern U. Functional expression and mutational analysis of flavonol synthase from Citrus unshiu. European Journal of Biochemistry. 2002 Aug;269(16):4134–42. doi: 10.1046/j.1432-1033.2002.03108.x.; Winkel-Shirley B. Flavonoid biosynthesis. A colorful model for genetics, biochemistry, cell biology, and biotechnology. Plant Physiol. 2001 Jun;126(2):485–93. PMID: 11402179; PMCID: PMC1540115.; Burbulis IE, Winkel-Shirley B. Interactions among enzymes of the Arabidopsis flavonoid biosynthetic pathway. Proc. Natl. Acad. Sci. U.S.A. 1999 Oct 26;96(22):12929–34. doi: 10.1073/pnas.96.22.12929.; Veit M, Pauli GF. Major flavonoids from Arabidopsis thaliana leaves. J Nat Prod. 1999 Sep;62(9):1301–3. doi: 10.1021/np990080o. PMID: 10514319. |
| flavonoid di-C-glucosylation Accession ID: BioCyc:META_PWY-7897 |
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Ito T, Fujimoto S, Suito F, Shimosaka M, Taguchi G. C-Glycosyltransferases catalyzing the formation of di-C-glucosyl flavonoids in citrus plants. The Plant Journal. 2017 Jun 05;91(2):187–98. doi: 10.1111/tpj.13555.; Du Y, Chu H, Chu IK, Lo C. CYP93G2 is a flavanone 2-hydroxylase required for C-glycosylflavone biosynthesis in rice. Plant Physiol. 2010 Sep;154(1):324–33. PMID: 20647377; PMCID: PMC2938165.; Gosch C, Halbwirth H, Stich K. Phloridzin: biosynthesis, distribution and physiological relevance in plants. Phytochemistry. 2010 Jun;71(8-9):838–43. doi: 10.1016/j.phytochem.2010.03.003. PMID: 20356611.; Brazier-Hicks M, Evans KM, Gershater MC, Puschmann H, Steel PG, Edwards R. The C-Glycosylation of Flavonoids in Cereals. Journal of Biological Chemistry. 2009 Jul;284(27):17926–34. doi: 10.1074/jbc.m109.009258. |
| naringenin biosynthesis (engineered) Accession ID: BioCyc:META_PWY-7397 |
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Santos CN, Koffas M, Stephanopoulos G. Optimization of a heterologous pathway for the production of flavonoids from glucose. Metab Eng. 2011 Jul;13(4):392–400. doi: 10.1016/j.ymben.2011.02.002. PMID: 21320631.; Watts KT, Mijts BN, Lee PC, Manning AJ, Schmidt-Dannert C. Discovery of a substrate selectivity switch in tyrosine ammonia-lyase, a member of the aromatic amino acid lyase family. Chem Biol. 2006 Dec;13(12):1317–26. doi: 10.1016/j.chembiol.2006.10.008. PMID: 17185227.; Rösler J, Krekel F, Amrhein N, Schmid J. Maize phenylalanine ammonia-lyase has tyrosine ammonia-lyase activity. Plant Physiol. 1997 Jan;113(1):175–9. PMID: 9008393; PMCID: PMC158128. |
| superpathway of aerobic toluene degradation Accession ID: BioCyc:META_PWY-5183 |
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Marín M, Plumeier I, Pieper DH. Degradation of 2,3-dihydroxybenzoate by a novel meta-cleavage pathway. J Bacteriol. 2012 Aug;194(15):3851–60. PMID: 22609919; PMCID: PMC3416551.; Johnson DR, Park J, Kukor JJ, Abriola LM. Effect of carbon starvation on toluene degradation activity by toluene monooxygenase-expressing bacteria. Biodegradation. 2006 Oct;17(5):437–45. doi: 10.1007/s10532-005-9014-x. PMID: 16477358.; Fishman A, Tao Y, Wood TK. Toluene 3-Monooxygenase of Ralstonia pickettii PKO1 Is a para -Hydroxylating Enzyme. J Bacteriol. 2004 May 15;186(10):3117–23. doi: 10.1128/jb.186.10.3117-3123.2004.; Newman LM, Wackett LP. Purification and characterization of toluene 2-monooxygenase from Burkholderia cepacia G4. Biochemistry. 1995 Oct 31;34(43):14066–76. doi: 10.1021/bi00043a012. PMID: 7578004.; Inoue J, Shaw JP, Rekik M, Harayama S. Overlapping substrate specificities of benzaldehyde dehydrogenase (the xylC gene product) and 2-hydroxymuconic semialdehyde dehydrogenase (the xylG gene product) encoded by TOL plasmid pWW0 of Pseudomonas putida. J Bacteriol. 1995 Mar;177(5):1196–201. doi: 10.1128/jb.177.5.1196-1201.1995.; Olsen RH, Kukor JJ, Kaphammer B. A novel toluene-3-monooxygenase pathway cloned from Pseudomonas pickettii PKO1. J Bacteriol. 1994 Jun;176(12):3749–56. doi: 10.1128/jb.176.12.3749-3756.1994.; Shaw JP, Rekik M, Schwager F, Harayama S. Kinetic studies on benzyl alcohol dehydrogenase encoded by TOL plasmid pWWO. A member of the zinc-containing long chain alcohol dehydrogenase family. Journal of Biological Chemistry. 1993 May;268(15):10842–50. doi: 10.1016/s0021-9258(18)82062-2.; Yen KM, Karl MR, Blatt LM, Simon MJ, Winter RB, Fausset PR, Lu HS, Harcourt AA, Chen KK. Cloning and characterization of a Pseudomonas mendocina KR1 gene cluster encoding toluene-4-monooxygenase. J Bacteriol. 1991 Sep;173(17):5315–27. doi: 10.1128/jb.173.17.5315-5327.1991.; Kukor JJ, Olsen RH. Genetic organization and regulation of a meta cleavage pathway for catechols produced from catabolism of toluene, benzene, phenol, and cresols by Pseudomonas pickettii PKO1. J Bacteriol. 1991 Aug;173(15):4587–94. doi: 10.1128/jb.173.15.4587-4594.1991.; Menn FM, Zylstra GJ, Gibson DT. Location and sequence of the todF gene encoding 2-hydroxy-6-oxohepta-2,4-dienoate hydrolase in Pseudomonas putida F1. Gene. 1991 Jul 31;104(1):91–4. doi: 10.1016/0378-1119(91)90470-v. PMID: 1916282. |
| 3-chlorocatechol degradation III (meta pathway) Accession ID: BioCyc:META_PWY-6214 |
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Kaschabek SR, Kasberg T, Mu¨ller D, Mars AE, Janssen DB, Reineke W. Degradation of Chloroaromatics: Purification and Characterization of a Novel Type of Chlorocatechol 2,3-Dioxygenase of Pseudomonas putida GJ31. J Bacteriol. 1998 Jan 15;180(2):296–302. doi: 10.1128/jb.180.2.296-302.1998. |
| superpathway of glyoxylate bypass and TCA Accession ID: BioCyc:META_TCA-GLYOX-BYPASS |
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Baldwin JE, Krebs H. The evolution of metabolic cycles. Nature. 1981 Jun 04;291(5814):381–2. doi: 10.1038/291381a0. PMID: 7242661.; KORNBERG HL, KREBS HA. Synthesis of cell constituents from C2-units by a modified tricarboxylic acid cycle. Nature. 1957 May 18;179(4568):988–91. doi: 10.1038/179988a0. PMID: 13430766. |
| (S)-reticuline biosynthesis I Accession ID: BioCyc:META_PWY-3581 |
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Samanani N, Liscombe DK, Facchini PJ. Molecular cloning and characterization of norcoclaurine synthase, an enzyme catalyzing the first committed step in benzylisoquinoline alkaloid biosynthesis. Plant J. 2004 Oct;40(2):302–13. doi: 10.1111/j.1365-313x.2004.02210.x. PMID: 15447655.; Facchini PJ. A |