Pathways Knowlegdes
Biological pathway database
| Pathway | DOIs | Note |
|---|---|---|
| prodigiosin biosynthesis Accession ID: BioCyc:META_PWY-7547 |
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Kasparyan E, Richter M, Dresen C, Walter LS, Fuchs G, Leeper FJ, Wacker T, Andrade SLA, Kolter G, Pohl M, Müller M. Asymmetric Stetter reactions catalyzed by thiamine diphosphate-dependent enzymes. Applied Microbiology and Biotechnology. 2014 Jun 24;98(23):9681–90. doi: 10.1007/s00253-014-5850-0.; Williamson NR, Simonsen HT, Ahmed RAA, Goldet G, Slater H, Woodley L, Leeper FJ, Salmond GPC. Biosynthesis of the red antibiotic, prodigiosin, in Serratia: identification of a novel 2-methyl-3-n-amyl-pyrrole (MAP) assembly pathway, definition of the terminal condensing enzyme, and implications for undecylprodigiosin biosynthesis in Streptomyces. Molecular Microbiology. 2005 Apr 07;56(4):971–89. doi: 10.1111/j.1365-2958.2005.04602.x. |
| glycine cleavage Accession ID: BioCyc:META_GLYCLEAV-PWY |
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Douce R, Bourguignon J, Neuburger M, Rébeillé F. The glycine decarboxylase system: a fascinating complex. Trends Plant Sci. 2001 Apr;6(4):167–76. doi: 10.1016/s1360-1385(01)01892-1. PMID: 11286922.; Perham RN. Swinging arms and swinging domains in multifunctional enzymes: catalytic machines for multistep reactions. Annu Rev Biochem. 2000;69():961–1004. doi: 10.1146/annurev.biochem.69.1.961. PMID: 10966480.; Fujiwara K, Okamura-Ikeda K, Motokawa Y. Mechanism of the glycine cleavage reaction. Further characterization of the intermediate attached to H-protein and of the reaction catalyzed by T-protein. Journal of Biological Chemistry. 1984 Sep;259(17):10664–8. doi: 10.1016/s0021-9258(18)90562-4.; Hiraga K, Kochi H, Hayasaka K, Kikuchi G, Nyhan WL. Defective glycine cleavage system in nonketotic hyperglycinemia. Occurrence of a less active glycine decarboxylase and an abnormal aminomethyl carrier protein. J Clin Invest. 1981 Aug;68(2):525–34. PMID: 6790577; PMCID: PMC370827.; MASSEY V, GIBSON QH, VEEGER C. Intermediates in the catalytic action of lipoyl dehydrogenase (diaphorase). Biochem J. 1960 Nov;77():341–51. PMID: 13767908; PMCID: PMC1204990.; SAVAGE N. Preparation and properties of highly purified diaphorase. Biochem J. 1957 Sep;67(1):146–55. PMID: 13471525; PMCID: PMC1200122.; Straub FB. Isolation and properties of a flavoprotein from heart muscle tissue. Biochem J. 1939 May;33(5):787–92. PMID: 16746974; PMCID: PMC1264446. |
| 6-methylpretetramide biosynthesis Accession ID: BioCyc:META_PWY-7811 |
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Wang P, Gao X, Chooi YH, Deng Z, Tang Y. Genetic characterization of enzymes involved in the priming steps of oxytetracycline biosynthesis in Streptomyces rimosus. Microbiology (Reading). 2011 Aug;157(Pt 8):2401–9. doi: 10.1099/mic.0.048439-0. PMID: 21622525.; Zhang W, Watanabe K, Wang CCC, Tang Y. Investigation of Early Tailoring Reactions in the Oxytetracycline Biosynthetic Pathway. Journal of Biological Chemistry. 2007 Aug;282(35):25717–25. doi: 10.1074/jbc.m703437200.; Zhang W, Ames BD, Tsai S, Tang Y. Engineered Biosynthesis of a Novel Amidated Polyketide, Using the Malonamyl-Specific Initiation Module from the Oxytetracycline Polyketide Synthase. Appl Environ Microbiol. 2006 Apr;72(4):2573–80. doi: 10.1128/aem.72.4.2573-2580.2006. |
| holomycin biosynthesis Accession ID: BioCyc:META_PWY-7690 |
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Li B, Walsh CT. Streptomyces clavuligerus HlmI Is an Intramolecular Disulfide-Forming Dithiol Oxidase in Holomycin Biosynthesis. Biochemistry. 2011 May 06;50(21):4615–22. doi: 10.1021/bi200321c.; Li B, Walsh CT. Identification of the gene cluster for the dithiolopyrrolone antibiotic holomycin in Streptomyces clavuligerus. Proc. Natl. Acad. Sci. U.S.A. 2010 Nov;107(46):19731–5. doi: 10.1073/pnas.1014140107. |
| elloramycin biosynthesis Accession ID: BioCyc:META_PWY-7483 |
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Ramos A, Lombó F, Braña AF, Rohr J, Méndez C, Salas JA. Biosynthesis of elloramycin in Streptomyces olivaceus requires glycosylation by enzymes encoded outside the aglycon cluster. Microbiology (Reading). 2008 Mar;154(Pt 3):781–8. doi: 10.1099/mic.0.2007/014035-0. PMID: 18310024.; Patallo EP, Blanco G, Fischer C, Brana AF, Rohr J, Mendez C, Salas JA. Deoxysugar methylation during biosynthesis of the antitumor polyketide elloramycin by Streptomyces olivaceus. Characterization of three methyltransferase genes. J Biol Chem. 2001 Jun 01;276(22):18765–74. doi: 10.1074/jbc.m101225200. PMID: 11376004.; Blanco G, Patallo EP, Braña AF, Trefzer A, Bechthold A, Rohr J, Méndez C, Salas JA. Identification of a sugar flexible glycosyltransferase from Streptomyces olivaceus, the producer of the antitumor polyketide elloramycin. Chem Biol. 2001 Mar;8(3):253–63. doi: 10.1016/s1074-5521(01)00010-2. PMID: 11306350. |
| itaconate biosynthesis II Accession ID: BioCyc:META_PWY-8018 |
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Geiser E, Przybilla SK, Friedrich A, Buckel W, Wierckx N, Blank LM, Bölker M. Ustilago maydis produces itaconic acid via the unusual intermediate trans -aconitate. Microbial Biotechnology. 2015 Dec 07;9(1):116–26. doi: 10.1111/1751-7915.12329. |
| itaconate biosynthesis I Accession ID: BioCyc:META_PWY-5750 |
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Bonnarme P, Gillet B, Sepulchre AM, Role C, Beloeil JC, Ducrocq C. Itaconate biosynthesis in Aspergillus terreus. J Bacteriol. 1995 Jun;177(12):3573–8. doi: 10.1128/jb.177.12.3573-3578.1995. |
| staphyloferrin B biosynthesis Accession ID: BioCyc:META_PWY-8008 |
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Verstraete MM, Perez-Borrajero C, Brown KL, Heinrichs DE, Murphy MEP. SbnI is a free serine kinase that generates O -phospho-l-serine for staphyloferrin B biosynthesis in Staphylococcus aureus. J Biol Chem. 2018 Apr 20;293(16):6147–60. PMID: 29483190; PMCID: PMC5912478.; Beasley FC, Cheung J, Heinrichs DE. Mutation of L-2,3-diaminopropionic acid synthase genes blocks staphyloferrin B synthesis in Staphylococcus aureus. BMC Microbiology. 2011 Sep 09;11(1):199. doi: 10.1186/1471-2180-11-199.; Cheung J, Beasley FC, Liu S, Lajoie GA, Heinrichs DE. Molecular characterization of staphyloferrin B biosynthesis in Staphylococcus aureus. Molecular Microbiology. 2009 Oct 22;74(3):594–608. doi: 10.1111/j.1365-2958.2009.06880.x. |
| superpathway of polybrominated aromatic compound biosynthesis Accession ID: BioCyc:META_PWY-7933 |
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Agarwal V, El Gamal AA, Yamanaka K, Poth D, Kersten RD, Schorn M, Allen EE, Moore BS. Biosynthesis of polybrominated aromatic organic compounds by marine bacteria. Nature Chemical Biology. 2014 Jun 29;10(8):640–7. doi: 10.1038/nchembio.1564. |
| pyoluteorin biosynthesis Accession ID: BioCyc:META_PWY-7930 |
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Gross H, Loper JE. Genomics of secondary metabolite production by Pseudomonas spp. Nat Prod Rep. 2009 Nov;26(11):1408–46. doi: 10.1039/b817075b. PMID: 19844639.; Dorrestein PC, Yeh E, Garneau-Tsodikova S, Kelleher NL, Walsh CT. Dichlorination of a pyrrolyl-S-carrier protein by FADH 2 -dependent halogenase PltA during pyoluteorin biosynthesis. Proc. Natl. Acad. Sci. U.S.A. 2005 Sep 14;102(39):13843–8. doi: 10.1073/pnas.0506964102.; Thomas MG, Burkart MD, Walsh CT. Conversion of L-proline to pyrrolyl-2-carboxyl-S-PCP during undecylprodigiosin and pyoluteorin biosynthesis. Chem Biol. 2002 Feb;9(2):171–84. doi: 10.1016/s1074-5521(02)00100-x. PMID: 11880032. |
| validamycin biosynthesis Accession ID: BioCyc:META_PWY-5818 |
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Mahmud T, Flatt PM, Wu X. Biosynthesis of Unusual Aminocyclitol-Containing Natural Products. J. Nat. Prod. 2007 Jul 28;70(8):1384–91. doi: 10.1021/np070210q.; Minagawa K, Zhang Y, Ito T, Bai L, Deng Z, Mahmud T. ValC, a new type of C7-Cyclitol kinase involved in the biosynthesis of the antifungal agent validamycin A. Chembiochem. 2007 Apr 16;8(6):632–41. PMID: 17335096; PMCID: PMC3136165. |
| fatty acid α-oxidation I Accession ID: BioCyc:META_PWY-2501 |
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Hamberg M, Sanz A, Rodriguez MJ, Calvo AP, Castresana C. Activation of the fatty acid alpha-dioxygenase pathway during bacterial infection of tobacco leaves. Formation of oxylipins protecting against cell death. J Biol Chem. 2003 Dec 19;278(51):51796–805. doi: 10.1074/jbc.m310514200. PMID: 14522973.; Hamberg M, Ponce de León I, Sanz A, Castresana C. Fatty acid alpha-dioxygenases. Prostaglandins Other Lipid Mediat. 2002 Aug;68-69():363–74. doi: 10.1016/s0090-6980(02)00040-0. PMID: 12432929.; De León IP, Sanz A, Hamberg M, Castresana C. Involvement of the Arabidopsis alpha-DOX1 fatty acid dioxygenase in protection against oxidative stress and cell death. Plant J. 2002 Jan;29(1):61–2. doi: 10.1046/j.1365-313x.2002.01195.x. PMID: 12060227.; Saffert A, Hartmann-Schreier J, Schön A, Schreier P. A dual function alpha-dioxygenase-peroxidase and NAD(+) oxidoreductase active enzyme from germinating pea rationalizing alpha-oxidation of fatty acids in plants. Plant Physiol. 2000 Aug;123(4):1545–52. PMID: 10938370; PMCID: PMC59111.; Hamberg M, Sanz A, Castresana C. alpha-oxidation of fatty acids in higher plants. Identification of a pathogen-inducible oxygenase (piox) as an alpha-dioxygenase and biosynthesis of 2-hydroperoxylinolenic acid. J Biol Chem. 1999 Aug 27;274(35):24503–13. doi: 10.1074/jbc.274.35.24503. PMID: 10455113. |
| mevalonate pathway I Accession ID: BioCyc:META_PWY-922 |
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Zhong JJ, Yue CJ. Plant cells: secondary metabolite heterogeneity and its manipulation. Adv Biochem Eng Biotechnol. 2005;100():53–88. doi: 10.1007/b136412. PMID: 16270656.; KUZUYAMA T. Mevalonate and Nonmevalonate Pathways for the Biosynthesis of Isoprene Units. Bioscience, Biotechnology, and Biochemistry. 2002 Jan 01;66(8):1619–27. doi: 10.1271/bbb.66.1619.; Daum G, Lees ND, Bard M, Dickson R. Biochemistry, cell biology and molecular biology of lipids of Saccharomyces cerevisiae. Yeast. 1998 Dec;14(16):1471–510. doi: 10.1002/(sici)1097-0061(199812)14:16<1471::aid-yea353>3.0.co;2-y. PMID: 9885152. |
| myo-, chiro- and scyllo-inositol degradation Accession ID: BioCyc:META_PWY-7237 |
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Morinaga T, Ashida H, Yoshida KI. Identification of two scyllo-inositol dehydrogenases in Bacillus subtilis. Microbiology (Reading). 2010 May;156(Pt 5):1538–46. doi: 10.1099/mic.0.037499-0. PMID: 20133360.; Yoshida K, Yamaguchi M, Morinaga T, Kinehara M, Ikeuchi M, Ashida H, Fujita Y. myo-Inositol Catabolism in Bacillus subtilis. Journal of Biological Chemistry. 2008 Apr;283(16):10415–24. doi: 10.1074/jbc.m708043200.; Yoshida K, Yamaguchi M, Morinaga T, Ikeuchi M, Kinehara M, Ashida H. Genetic Modification of Bacillus subtilis for Production of |
| hydroxylated fatty acid biosynthesis (plants) Accession ID: BioCyc:META_PWY-6433 |
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Thelen JJ, Ohlrogge JB. Metabolic engineering of fatty acid biosynthesis in plants. Metab Eng. 2002 Jan;4(1):12–21. doi: 10.1006/mben.2001.0204. PMID: 11800570.; Moon H, Smith MA, Kunst L. A condensing enzyme from the seeds of Lesquerella fendleri that specifically elongates hydroxy fatty acids. Plant Physiol. 2001 Dec;127(4):1635–43. PMID: 11743108; PMCID: PMC133568.; Ghanevati M, Jaworski JG. Active-site residues of a plant membrane-bound fatty acid elongase ß-ketoacyl-CoA synthase, FAE1 KCS. Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids. 2001 Jan;1530(1):77–85. doi: 10.1016/s1388-1981(00)00168-2.; Smith M, Moon H, Kunst L. Production of hydroxy fatty acids in the seeds of Arabidopsis thaliana. Biochem. Soc. Trans. 2000 Dec 01;28(6):947. doi: 10.1042/0300-5127:0280947.; Broun P, Boddupalli S, Somerville C. A bifunctional oleate 12-hydroxylase: desaturase from Lesquerella fendleri. The Plant Journal. 1998 Jan;13(2):201–10. doi: 10.1046/j.1365-313x.1998.00023.x.; Reed DW, Taylor DC, Covello PS. Metabolism of Hydroxy Fatty Acids in Developing Seeds in the Genera Lesquerella (Brassicaceae) and Linum (Linaceae). Plant Physiol. 1997 May;114(1):63–8. PMID: 12223689; PMCID: PMC158279.; Broun P, Somerville C. Accumulation of ricinoleic, lesquerolic, and densipolic acids in seeds of transgenic Arabidopsis plants that express a fatty acyl hydroxylase cDNA from castor bean. Plant Physiol. 1997 Mar;113(3):933–42. PMID: 9085577; PMCID: PMC158213.; Lin JT, McKeon TA, Goodrich-Tanrikulu M, Stafford AE. Characterization of oleoyl-12-hydroxylase in castor microsomes using the putative substrate, 1-acyl-2-oleoyl-sn-glycero-3-phosphocholine. Lipids. 1996 Jun;31(6):571–7. doi: 10.1007/bf02523827. PMID: 8784737.; Bafor M, Smith MA, Jonsson L, Stobart K, Stymne S. Ricinoleic acid biosynthesis and triacylglycerol assembly in microsomal preparations from developing castor-bean (Ricinus communis) endosperm. Biochem J. 1991 Dec 01;280 ( Pt 2)():507–14. PMID: 1747126; PMCID: PMC1130577.; Fehling E, Mukherjee KD. Acyl-CoA elongase from a higher plant (Lunaria annua): metabolic intermediates of very-long-chain acyl-CoA products and substrate specificity. Biochimica et Biophysica Acta (BBA) - Lipids and Lipid Metabolism. 1991 Apr;1082(3):239–46. doi: 10.1016/0005-2760(91)90198-q.; Moreau RA, Stumpf PK. Recent studies of the enzymic synthesis of ricinoleic Acid by developing castor beans. Plant Physiol. 1981 Apr;67(4):672–6. PMID: 16661734; PMCID: PMC425752. |
| oxalate degradation V Accession ID: BioCyc:META_PWY-6698 |
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Tanner A, Bowater L, Fairhurst SA, Bornemann S. Oxalate decarboxylase requires manganese and dioxygen for activity. Overexpression and characterization of Bacillus subtilis YvrK and YoaN. J Biol Chem. 2001 Nov 23;276(47):43627–34. doi: 10.1074/jbc.m107202200. PMID: 11546787. |
| L-methionine salvage cycle III Accession ID: BioCyc:META_PWY-7527 |
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Sauter M, Moffatt B, Saechao MC, Hell R, Wirtz M. Methionine salvage and S-adenosylmethionine: essential links between sulfur, ethylene and polyamine biosynthesis. Biochem J. 2013 Apr 15;451(2):145–54. doi: 10.1042/bj20121744. PMID: 23535167.; Cobzaru C, Ganas P, Mihasan M, Schleberger P, Brandsch R. Homologous gene clusters of nicotine catabolism, including a new ?-amidase for a-ketoglutaramate, in species of three genera of Gram-positive bacteria. Res Microbiol. 2011 Apr;162(3):285–91. doi: 10.1016/j.resmic.2011.01.001. PMID: 21288482.; Albers E. Metabolic characteristics and importance of the universal methionine salvage pathway recycling methionine from 5'-methylthioadenosine. IUBMB Life. 2009 Dec;61(12):1132–42. doi: 10.1002/iub.278. PMID: 19946895.; Backlund PS, Chang CP, Smith RA. Identification of 2-keto-4-methylthiobutyrate as an intermediate compound in methionine synthesis from 5'-methylthioadenosine. Journal of Biological Chemistry. 1982 Apr;257(8):4196–202. doi: 10.1016/s0021-9258(18)34705-7. |
| phosphinothricin tripeptide biosynthesis Accession ID: BioCyc:META_PWY-6322 |
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Peck SC, Cooke HA, Cicchillo RM, Malova P, Hammerschmidt F, Nair SK, van der Donk WA. Mechanism and substrate recognition of 2-hydroxyethylphosphonate dioxygenase. Biochemistry. 2011 Aug 02;50(30):6598–605. PMID: 21711001; PMCID: PMC3143709.; Whitteck JT, Malova P, Peck SC, Cicchillo RM, Hammerschmidt F, van der Donk WA. On the Stereochemistry of 2-Hydroxyethylphosphonate Dioxygenase. J. Am. Chem. Soc. 2011 Mar 07;133(12):4236–9. doi: 10.1021/ja1113326.; Cicchillo RM, Zhang H, Blodgett JAV, Whitteck JT, Li G, Nair SK, van der Donk WA, Metcalf WW. An unusual carbon–carbon bond cleavage reaction during phosphinothricin biosynthesis. Nature. 2009 Jun;459(7248):871–4. doi: 10.1038/nature07972.; Blodgett JAV, Thomas PM, Li G, Velasquez JE, van der Donk WA, Kelleher NL, Metcalf WW. Unusual transformations in the biosynthesis of the antibiotic phosphinothricin tripeptide. Nature Chemical Biology. 2007 Jul 15;3(8):480–5. doi: 10.1038/nchembio.2007.9.; Schwartz D, Berger S, Heinzelmann E, Muschko K, Welzel K, Wohlleben W. Biosynthetic Gene Cluster of the Herbicide Phosphinothricin Tripeptide from Streptomyces viridochromogenes Tu¨494. Appl Environ Microbiol. 2004 Dec;70(12):7093–102. doi: 10.1128/aem.70.12.7093-7102.2004.; POLLACK SJ, FREEMAN S, POMPLIANO DL, KNOWLES JR. Cloning, overexpression and mechanistic studies of carboxyphosphonoenolpyruvate mutase from Streptomyces hygroscopicus. European Journal of Biochemistry. 1992 Oct;209(2):735–43. doi: 10.1111/j.1432-1033.1992.tb17342.x. |
| rifamycin B biosynthesis Accession ID: BioCyc:META_PWY-5984 |
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Floss HG, Yu TW. Rifamycin-mode of action, resistance, and biosynthesis. Chem Rev. 2005 Feb;105(2):621–32. doi: 10.1021/cr030112j. PMID: 15700959. |
| γ-resorcylate degradation II Accession ID: BioCyc:META_PWY-7772 |
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Kasai D, Araki N, Motoi K, Yoshikawa S, Iino T, Imai S, Masai E, Fukuda M. ?-Resorcylate catabolic-pathway genes in the soil actinomycete Rhodococcus jostii RHA1. Appl Environ Microbiol. 2015 Nov;81(21):7656–65. PMID: 26319878; PMCID: PMC4592853. |