Pathways Knowlegdes
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| Pathway | DOIs | Note |
|---|---|---|
| secologanin and strictosidine biosynthesis Accession ID: BioCyc:META_PWY-5290 |
|
Miettinen K, Dong L, Navrot N, Schneider T, Burlat V, Pollier J, Woittiez L, van der Krol S, Lugan R, Ilc T, Verpoorte R, Oksman-Caldentey K, Martinoia E, Bouwmeester H, Goossens A, Memelink J, Werck-Reichhart D. Erratum: Corrigendum: The seco-iridoid pathway from Catharanthus roseus. Nature Communications. 2014 Jun 24;5(1):4175. doi: 10.1038/ncomms5175.; Geu-Flores F, Sherden NH, Courdavault V, Burlat V, Glenn WS, Wu C, Nims E, Cui Y, O’Connor SE. An alternative route to cyclic terpenes by reductive cyclization in iridoid biosynthesis. Nature. 2012 Nov 21;492(7427):138–42. doi: 10.1038/nature11692. |
| polymethylated quercetin glucoside biosynthesis I - quercetin series (Chrysosplenium) Accession ID: BioCyc:META_PWY-7150 |
|
Anzellotti D, Ibrahim RK. Molecular characterization and functional expression of flavonol 6-hydroxylase. BMC Plant Biol. 2004 Dec 13;4():20. PMID: 15596008; PMCID: PMC544895.; Seguin J, Muzac I, Ibrahim RK. Purification and immunological characterization of a recombinant trimethylflavonol 3'-O-methyltransferase. Phytochemistry. 1998 Sep;49(2):319–25. doi: 10.1016/s0031-9422(98)00138-1. PMID: 9747535.; Gauthier A, Gulick PJ, Ibrahim RK. cDNA cloning and characterization of a 3'/5'-O-methyltransferase for partially methylated flavonols from Chrysosplenium americanum. Plant Mol Biol. 1996 Dec;32(6):1163–9. doi: 10.1007/bf00041401. PMID: 9002616.; Latchinian-Sadek L, Ibrahim RK. Flavonol ring B-specific O-glucosyltransferases: Purification, production of polyclonal antibodies, and immunolocalization. Archives of Biochemistry and Biophysics. 1991 Aug;289(1):230–6. doi: 10.1016/0003-9861(91)90466-v.; Khouri HE, De Luca V, Ibrahim RK. Enzymatic synthesis of polymethylated flavonols in Chrysosplenium americanum. III. Purification and kinetic analysis of S-adenosyl-L-methionine:3-methylquercetin 7-O-methyltransferase. Arch Biochem Biophys. 1988 Aug 15;265(1):1–7. doi: 10.1016/0003-9861(88)90364-5. PMID: 3415239.; De Luca V, Ibrahim RK. Enzymatic synthesis of polymethylated flavonols in Chrysosplenium americanum. I. Partial purification and some properties of S-adenosyl-l-methionine: Flavonol 3-, 6-, 7-, and 4'-O-methyltransferases. Archives of Biochemistry and Biophysics. 1985 May;238(2):596–605. doi: 10.1016/0003-9861(85)90205-x.; De Luca V, Ibrahim RK. Enzymatic synthesis of polymethylated flavonols in Chrysosplenium americanum. II. Substrate interaction and product inhibition studies of flavonol 3-, 6-, and 4'-O-methyltransferases. Archives of Biochemistry and Biophysics. 1985 May;238(2):606–18. doi: 10.1016/0003-9861(85)90206-1.; KHOURI H, IBRAHIM RK. Kinetic mechanism of a flavonol-ring-B O-glucosyltransferase from Chrysosplenium americanum. European Journal of Biochemistry. 1984 Aug;142(3):559–64. doi: 10.1111/j.1432-1033.1984.tb08322.x.; Bajaj KL, de Luca V, Khouri H, Ibrahim RK. Purification and Properties of Flavonol-Ring B Glucosyltransferase from Chrysosplenium americanum. Plant Physiol. 1983 Jul 01;72(3):891–6. doi: 10.1104/pp.72.3.891. |
| 1,4-dihydroxy-6-naphthoate biosynthesis II Accession ID: BioCyc:META_PWY-7371 |
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Mahanta N, Fedoseyenko D, Dairi T, Begley TP. Menaquinone biosynthesis: formation of aminofutalosine requires a unique radical SAM enzyme. J Am Chem Soc. 2013 Oct 16;135(41):15318–21. PMID: 24083939; PMCID: PMC3855536.; Li X, Apel D, Gaynor EC, Tanner ME. 5'-Methylthioadenosine Nucleosidase Is Implicated in Playing a Key Role in a Modified Futalosine Pathway for Menaquinone Biosynthesis in Campylobacter jejuni. Journal of Biological Chemistry. 2011 Jun;286(22):19392–8. doi: 10.1074/jbc.m111.229781.; HIRATSUKA T, ITOH N, SETO H, DAIRI T. Enzymatic Properties of Futalosine Hydrolase, an Enzyme Essential to a Newly Identified Menaquinone Biosynthetic Pathway. Bioscience, Biotechnology, and Biochemistry. 2009 May 23;73(5):1137–41. doi: 10.1271/bbb.80906.; Hiratsuka T, Furihata K, Ishikawa J, Yamashita H, Itoh N, Seto H, Dairi T. An alternative menaquinone biosynthetic pathway operating in microorganisms. Science. 2008 Sep 19;321(5896):1670–3. doi: 10.1126/science.1160446. PMID: 18801996. |
| 1,4-dihydroxy-6-naphthoate biosynthesis I Accession ID: BioCyc:META_PWY-7374 |
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Goble AM, Toro R, Li X, Ornelas A, Fan H, Eswaramoorthy S, Patskovsky Y, Hillerich B, Seidel R, Sali A, Shoichet BK, Almo SC, Swaminathan S, Tanner ME, Raushel FM. Deamination of 6-aminodeoxyfutalosine in menaquinone biosynthesis by distantly related enzymes. Biochemistry. 2013 Sep 17;52(37):6525–36. PMID: 23972005; PMCID: PMC3813303.; Li X, Apel D, Gaynor EC, Tanner ME. 5'-Methylthioadenosine Nucleosidase Is Implicated in Playing a Key Role in a Modified Futalosine Pathway for Menaquinone Biosynthesis in Campylobacter jejuni. Journal of Biological Chemistry. 2011 Jun;286(22):19392–8. doi: 10.1074/jbc.m111.229781.; HIRATSUKA T, ITOH N, SETO H, DAIRI T. Enzymatic Properties of Futalosine Hydrolase, an Enzyme Essential to a Newly Identified Menaquinone Biosynthetic Pathway. Bioscience, Biotechnology, and Biochemistry. 2009 May 23;73(5):1137–41. doi: 10.1271/bbb.80906.; Hiratsuka T, Furihata K, Ishikawa J, Yamashita H, Itoh N, Seto H, Dairi T. An alternative menaquinone biosynthetic pathway operating in microorganisms. Science. 2008 Sep 19;321(5896):1670–3. doi: 10.1126/science.1160446. PMID: 18801996. |
| sulfoacetaldehyde degradation III Accession ID: BioCyc:META_PWY-6718 |
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Krejcík Z, Hollemeyer K, Smits THM, Cook AM. Isethionate formation from taurine in Chromohalobacter salexigens: purification of sulfoacetaldehyde reductase. Microbiology (Reading). 2010 May;156(Pt 5):1547–55. doi: 10.1099/mic.0.036699-0. PMID: 20133363.; Styp von Rekowski K, Denger K, Cook AM. Isethionate as a product from taurine during nitrogen-limited growth of Klebsiella oxytoca TauN1. Arch Microbiol. 2005 Aug;183(5):325–30. doi: 10.1007/s00203-005-0776-7. PMID: 15883781. |
| nicotine biosynthesis Accession ID: BioCyc:META_PWY-5316 |
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Siminszky B, Gavilano L, Bowen SW, Dewey RE. Conversion of nicotine to nornicotine in Nicotiana tabacum is mediated by CYP82E4, a cytochrome P450 monooxygenase. Proc. Natl. Acad. Sci. U.S.A. 2005 Sep 28;102(41):14919–24. doi: 10.1073/pnas.0506581102.; Heim WG, Jelesko JG. Association of diamine oxidase and S-adenosylhomocysteine hydrolase in Nicotiana tabacum extracts. Plant Mol Biol. 2004 Sep;56(2):299–308. doi: 10.1007/s11103-004-3352-7. PMID: 15604745. |
| ABH and Lewis epitopes biosynthesis from type 2 precursor disaccharide Accession ID: BioCyc:META_PWY-7831 |
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Marsolais F, Boyd J, Paredes Y, Schinas AM, Garcia M, Elzein S, Varin L. Molecular and biochemical characterization of two brassinosteroid sulfotransferases from Arabidopsis, AtST4a (At2g14920) and AtST1 (At2g03760). Planta. 2007 Apr;225(5):1233–44. doi: 10.1007/s00425-006-0413-y. PMID: 17039368. |
| 8-methylmenaquinone biosynthesis Accession ID: BioCyc:META_PWY-7864 |
|
Hein S, Klimmek O, Polly M, Kern M, Simon J. A class C radical S-adenosylmethionine methyltransferase synthesizes 8-methylmenaquinone. Molecular Microbiology. 2017 Feb 28;104(3):449–62. doi: 10.1111/mmi.13638. |
| hexaprenyl diphosphate biosynthesis Accession ID: BioCyc:META_HEXPPSYN-PWY |
|
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. |
| sulfoacetaldehyde degradation I Accession ID: BioCyc:META_PWY-1281 |
|
Ruff J, Denger K, Cook AM. Sulphoacetaldehyde acetyltransferase yields acetyl phosphate: purification from Alcaligenes defragrans and gene clusters in taurine degradation. Biochem J. 2003 Jan 15;369(Pt 2):275–85. PMID: 12358600; PMCID: PMC1223080. |
| heptaprenyl diphosphate biosynthesis Accession ID: BioCyc:META_PWY-5807 |
|
Collins MD, Jones D. Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication. Microbiol Rev. 1981 Jun;45(2):316–54. doi: 10.1128/mr.45.2.316-354.1981. |
| chrysin biosynthesis Accession ID: BioCyc:META_PWY-5363 |
|
Leonard E, Yan Y, Lim KH, Koffas MAG. Investigation of Two Distinct Flavone Synthases for Plant-Specific Flavone Biosynthesis inSaccharomyces cerevisiae. Appl Environ Microbiol. 2005 Dec;71(12):8241–8. doi: 10.1128/aem.71.12.8241-8248.2005.; Miyahisa I, Funa N, Ohnishi Y, Martens S, Moriguchi T, Horinouchi S. Combinatorial biosynthesis of flavones and flavonols in Escherichia coli. Applied Microbiology and Biotechnology. 2005 Aug 18;71(1):53–8. doi: 10.1007/s00253-005-0116-5. |
| polymethylated quercetin glucoside biosynthesis II - quercetagetin series (Chrysosplenium) Accession ID: BioCyc:META_PWY-7151 |
|
Anzellotti D, Ibrahim RK. Molecular characterization and functional expression of flavonol 6-hydroxylase. BMC Plant Biol. 2004 Dec 13;4():20. PMID: 15596008; PMCID: PMC544895.; Gauthier A, Gulick PJ, Ibrahim RK. cDNA cloning and characterization of a 3'/5'-O-methyltransferase for partially methylated flavonols from Chrysosplenium americanum. Plant Mol Biol. 1996 Dec;32(6):1163–9. doi: 10.1007/bf00041401. PMID: 9002616.; Latchinian-Sadek L, Ibrahim RK. Flavonol ring B-specific O-glucosyltransferases: Purification, production of polyclonal antibodies, and immunolocalization. Archives of Biochemistry and Biophysics. 1991 Aug;289(1):230–6. doi: 10.1016/0003-9861(91)90466-v.; De Luca V, Ibrahim RK. Enzymatic synthesis of polymethylated flavonols in Chrysosplenium americanum. I. Partial purification and some properties of S-adenosyl-l-methionine: Flavonol 3-, 6-, 7-, and 4'-O-methyltransferases. Archives of Biochemistry and Biophysics. 1985 May;238(2):596–605. doi: 10.1016/0003-9861(85)90205-x.; De Luca V, Ibrahim RK. Enzymatic synthesis of polymethylated flavonols in Chrysosplenium americanum. II. Substrate interaction and product inhibition studies of flavonol 3-, 6-, and 4'-O-methyltransferases. Archives of Biochemistry and Biophysics. 1985 May;238(2):606–18. doi: 10.1016/0003-9861(85)90206-1.; KHOURI H, IBRAHIM RK. Kinetic mechanism of a flavonol-ring-B O-glucosyltransferase from Chrysosplenium americanum. European Journal of Biochemistry. 1984 Aug;142(3):559–64. doi: 10.1111/j.1432-1033.1984.tb08322.x.; Bajaj KL, de Luca V, Khouri H, Ibrahim RK. Purification and Properties of Flavonol-Ring B Glucosyltransferase from Chrysosplenium americanum. Plant Physiol. 1983 Jul 01;72(3):891–6. doi: 10.1104/pp.72.3.891.; Schnitsky S. Own your own telephone system? Dent Manage. 1976 Jun;16(6):15–6, 19, 21. PMID: 1068865. |
| NAD/NADH phosphorylation and dephosphorylation Accession ID: BioCyc:META_PWY-5083 |
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Turner WL, Waller JC, Snedden WA. Identification, molecular cloning and functional characterization of a novel NADH kinase from Arabidopsis thaliana (thale cress). Biochem J. 2005 Jan 01;385(Pt 1):217–23. PMID: 15347288; PMCID: PMC1134690.; Turner WL, Waller JC, Vanderbeld B, Snedden WA. Cloning and characterization of two NAD kinases from Arabidopsis. identification of a calmodulin binding isoform. Plant Physiol. 2004 Jul;135(3):1243–55. PMID: 15247403; PMCID: PMC519044.; Heazlewood JL, Howell KA, Millar AH. Mitochondrial complex I from Arabidopsis and rice: orthologs of mammalian and fungal components coupled with plant-specific subunits. Biochimica et Biophysica Acta (BBA) - Bioenergetics. 2003 Jul;1604(3):159–69. doi: 10.1016/s0005-2728(03)00045-8.; Kemmer G, Reilly TJ, Schmidt-Brauns J, Zlotnik GW, Green BA, Fiske MJ, Herbert M, Kraiß A, Schlo¨r S, Smith A, Reidl J. NadN and e (P4) Are Essential for Utilization of NAD and Nicotinamide Mononucleotide but Not Nicotinamide Riboside in Haemophilus influenzae. J Bacteriol. 2001 Jul;183(13):3974–81. doi: 10.1128/jb.183.13.3974-3981.2001.; Møller IM. P |
| α-dystroglycan glycosylation Accession ID: BioCyc:META_PWY-7981 |
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| NAD phosphorylation and transhydrogenation Accession ID: BioCyc:META_NADPHOS-DEPHOS-PWY-1 |
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| nonaprenyl diphosphate biosynthesis II Accession ID: BioCyc:META_PWY-6520 |
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Hirooka K, Bamba T, Fukusaki E, Kobayashi A. Cloning and kinetic characterization of Arabidopsis thaliana solanesyl diphosphate synthase. Biochem J. 2003 Mar 01;370(Pt 2):679–86. PMID: 12437513; PMCID: PMC1223189. |
| NAD phosphorylation and dephosphorylation Accession ID: BioCyc:META_NADPHOS-DEPHOS-PWY |
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Kemmer G, Reilly TJ, Schmidt-Brauns J, Zlotnik GW, Green BA, Fiske MJ, Herbert M, Kraiß A, Schlo¨r S, Smith A, Reidl J. NadN and e (P4) Are Essential for Utilization of NAD and Nicotinamide Mononucleotide but Not Nicotinamide Riboside in Haemophilus influenzae. J Bacteriol. 2001 Jul;183(13):3974–81. doi: 10.1128/jb.183.13.3974-3981.2001.; Reidl J, Schlör S, Kraiss A, Schmidt-Brauns J, Kemmer G, Soleva E. NADP and NAD utilization in Haemophilus influenzae. Mol Microbiol. 2000 Mar;35(6):1573–81. doi: 10.1046/j.1365-2958.2000.01829.x. PMID: 10760156. |
| mucin core 1 and core 2 O-glycosylation Accession ID: BioCyc:META_PWY-7433 |
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Jensen PH, Kolarich D, Packer NH. Mucin-type O-glycosylation--putting the pieces together. FEBS J. 2010 Jan;277(1):81–94. doi: 10.1111/j.1742-4658.2009.07429.x. PMID: 19919547. |
| decaprenoxanthin diglucoside biosynthesis Accession ID: BioCyc:META_PWY18HP-2 |
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Heider SAE, Peters-Wendisch P, Netzer R, Stafnes M, Brautaset T, Wendisch VF. Production and glucosylation of C50 and C40 carotenoids by metabolically engineered Corynebacterium glutamicum. Applied Microbiology and Biotechnology. 2013 Nov 24;98(3):1223–35. doi: 10.1007/s00253-013-5359-y.; Heider SAE, Peters-Wendisch P, Wendisch VF. Carotenoid biosynthesis and overproduction in Corynebacterium glutamicum. BMC Microbiology. 2012 Sep 10;12(1):198. doi: 10.1186/1471-2180-12-198.; Netzer R, Stafsnes MH, Andreassen T, Goksøyr A, Bruheim P, Brautaset T. Biosynthetic Pathway for ?-Cyclic Sarcinaxanthin in Micrococcus luteus : Heterologous Expression and Evidence for Diverse and Multiple Catalytic Functions of C 50 Carotenoid Cyclases. J Bacteriol. 2010 Nov;192(21):5688–99. doi: 10.1128/jb.00724-10.; Krubasik P, Takaichi S, Maoka T, Kobayashi M, Masamoto K, Sandmann G. Detailed biosynthetic pathway to decaprenoxanthin diglucoside in Corynebacterium glutamicum and identification of novel intermediates. Arch Microbiol. 2001 Sep;176(3):217–23. doi: 10.1007/s002030100315. PMID: 11511870.; Krubasik P, Kobayashi M, Sandmann G. Expression and functional analysis of a gene cluster involved in the synthesis of decaprenoxanthin reveals the mechanisms for C50 carotenoid formation. European Journal of Biochemistry. 2001 Jul;268(13):3702–8. doi: 10.1046/j.1432-1327.2001.02275.x. |