Pathways Knowlegdes

Biological pathway database

Pathway DOIs Note
3-carene biosynthesis

Accession ID: BioCyc:META_PWY-6451
  • 10.1016/s0031-9422(02)00674-x
 Hoelscher DJ, Williams DC, Wildung MR, Croteau R. A cDNA clone for 3-carene synthase from Salvia stenophylla??The nucleotide sequence reported in this article has been deposited with the GenBank/EMBL Database under accession number AF527416. Phytochemistry. 2003 Apr;62(7):1081–6. doi: 10.1016/s0031-9422(02)00674-x.
L-phenylalanine biosynthesis I

Accession ID: BioCyc:META_PHESYN
  • 10.1016/s0021-9258(17)32929-0
 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.
medicarpin conjugates interconversion

Accession ID: BioCyc:META_PWY-2561
  • 10.1093/jexbot/52.357.681
 Tebayashi S, Ishihara A, Iwamura H. Elicitor-induced changes in isoflavonoid metabolism in red clover roots. J Exp Bot. 2001 Apr;52(357):681–9. doi: 10.1093/jexbot/52.357.681. PMID: 11413204.
Ac/N-end rule pathway

Accession ID: BioCyc:META_PWY-7800
  • 10.14348/molcells.2016.2329
 Lee K, Heo J, Kim J, Hwang C. N-Terminal Acetylation-Targeted N-End Rule Proteolytic System: The Ac/N-End Rule Pathway. Molecules and Cells. 2016 Mar;39(3):169–78. doi: 10.14348/molcells.2016.2329.
(-)-medicarpin biosynthesis

Accession ID: BioCyc:META_PWY-2463
  • 10.1016/0003-9861(95)90019-5
  • 10.1016/0014-5793(94)01267-9
  • 10.1016/s0021-9258(17)31799-4
  • 10.1105/tpc.6.12.1789
 Guo L, Paiva NL. Molecular cloning and expression of alfalfa (Medicago sativa L.) vestitone reductase, the penultimate enzyme in medicarpin biosynthesis. Archives of Biochemistry and Biophysics. 1995 Jul;320(2):353–60. doi: 10.1016/0003-9861(95)90019-5.; Guo L, Dixon RA, Paiva NL. The 'pterocarpan synthase' of alfalfa: association and co-induction of vestitone reductase and 7,2'-dihydroxy-4'-methoxy-isoflavanol (DMI) dehydratase, the two final enzymes in medicarpin biosynthesis. FEBS Lett. 1994 Dec 19;356(2-3):221–5. doi: 10.1016/0014-5793(94)01267-9. PMID: 7805842.; Oommen A, Dixon RA, Paiva NL. The elicitor-inducible alfalfa isoflavone reductase promoter confers different patterns of developmental expression in homologous and heterologous transgenic plants. Plant Cell. 1994 Dec;6(12):1789–803. PMID: 7866024; PMCID: PMC160562.; Guo L, Dixon RA, Paiva NL. Conversion of vestitone to medicarpin in alfalfa (Medicago sativa L.) is catalyzed by two independent enzymes. Identification, purification, and characterization of vestitone reductase and 7,2‘-dihydroxy-4‘-methoxyisoflavanol dehydratase. Journal of Biological Chemistry. 1994 Sep;269(35):22372–8. doi: 10.1016/s0021-9258(17)31799-4.
stipitatate biosynthesis

Accession ID: BioCyc:META_PWY-7687
  • 10.1073/pnas.1201469109
 Davison J, al Fahad A, Cai M, Song Z, Yehia SY, Lazarus CM, Bailey AM, Simpson TJ, Cox RJ. Genetic, molecular, and biochemical basis of fungal tropolone biosynthesis. Proc Natl Acad Sci U S A. 2012 May 15;109(20):7642–7. PMID: 22508998; PMCID: PMC3356636.
fenchol biosynthesis I

Accession ID: BioCyc:META_PWY-6437
  • 10.1104/pp.104.051318
 Iijima Y, Davidovich-Rikanati R, Fridman E, Gang DR, Bar E, Lewinsohn E, Pichersky E. The biochemical and molecular basis for the divergent patterns in the biosynthesis of terpenes and phenylpropenes in the peltate glands of three cultivars of basil. Plant Physiol. 2004 Nov;136(3):3724–36. PMID: 15516500; PMCID: PMC527170.
sophoraflavanone G biosynthesis

Accession ID: BioCyc:META_PWY-6914
  • 10.1104/pp.107.110544
 Sasaki K, Mito K, Ohara K, Yamamoto H, Yazaki K. Cloning and characterization of naringenin 8-prenyltransferase, a flavonoid-specific prenyltransferase of Sophora flavescens. Plant Physiol. 2008 Mar;146(3):1075–84. PMID: 18218974; PMCID: PMC2259047.
pyrimidine deoxyribonucleotides de novo biosynthesis III

Accession ID: BioCyc:META_PWY-6545
  • 10.1042/bst0320231
  • 10.1126/science.1072113
 Leduc D, Graziani S, Meslet-Cladiere L, Sodolescu A, Liebl U, Myllykallio H. Two distinct pathways for thymidylate (dTMP) synthesis in (hyper)thermophilic Bacteria and Archaea. Biochem Soc Trans. 2004 Apr;32(Pt 2):231–5. doi: 10.1042/bst0320231. PMID: 15046578.; Myllykallio H, Lipowski G, Leduc D, Filee J, Forterre P, Liebl U. An alternative flavin-dependent mechanism for thymidylate synthesis. Science. 2002 Jul 05;297(5578):105–7. doi: 10.1126/science.1072113. PMID: 12029065.
2-methylcitrate cycle II

Accession ID: BioCyc:META_PWY-5747
  • 10.1110/ps.072801907
 Garvey GS, Rocco CJ, Escalante-Semerena JC, Rayment I. The three-dimensional crystal structure of the PrpF protein of Shewanella oneidensis complexed with trans-aconitate: Insights into its biological function. Protein Science. 2007 Jul;16(7):1274–84. doi: 10.1110/ps.072801907.
chlorogenic acid biosynthesis II

Accession ID: BioCyc:META_PWY-6040
  • 10.1016/0003-9861(87)90339-0
 Kühnl T, Koch U, Heller W, Wellmann E. Chlorogenic acid biosynthesis: Characterization of a light-induced microsomal 5-O-(4-coumaroyl)-d-quinate/shikimate 3'-hydroxylase from carrot (Daucus carota L.) cell suspension cultures. Archives of Biochemistry and Biophysics. 1987 Oct;258(1):226–32. doi: 10.1016/0003-9861(87)90339-0.
methylthiolincosamide biosynthesis

Accession ID: BioCyc:META_PWY-7548
  • 10.1021/ja308221z
  • 10.1021/ja412194w
 Lin C, Sasaki E, Zhong A, Liu H. In Vitro Characterization of LmbK and LmbO: Identification of GDP-d-erythro-a-d-gluco-octose as a Key Intermediate in Lincomycin A Biosynthesis. J. Am. Chem. Soc. 2014 Jan 10;136(3):906–9. doi: 10.1021/ja412194w.; Sasaki E, Lin CI, Lin KY, Liu HW. Construction of the octose 8-phosphate intermediate in lincomycin A biosynthesis: characterization of the reactions catalyzed by LmbR and LmbN. J Am Chem Soc. 2012 Oct 24;134(42):17432–5. PMID: 22989310; PMCID: PMC3486926.
bornyl diphosphate biosynthesis

Accession ID: BioCyc:META_PWY-5813
  • 10.1006/abbi.2001.2442
 Schwab W, Williams DC, Davis EM, Croteau R. Mechanism of Monoterpene Cyclization: Stereochemical Aspects of the Transformation of Noncyclizable Substrate Analogs by Recombinant (-)-Limonene Synthase, (+)-Bornyl Diphosphate Synthase, and (-)-Pinene Synthase. Archives of Biochemistry and Biophysics. 2001 Aug;392(1):123–36. doi: 10.1006/abbi.2001.2442.
propanoyl-CoA degradation II

Accession ID: BioCyc:META_PWY-7574
  • 10.1074/jbc.m113.517672
 Otzen C, Bardl B, Jacobsen ID, Nett M, Brock M. Candida albicans Utilizes a Modified ß-Oxidation Pathway for the Degradation of Toxic Propionyl-CoA. Journal of Biological Chemistry. 2014 Mar;289(12):8151–69. doi: 10.1074/jbc.m113.517672.
indican biosynthesis

Accession ID: BioCyc:META_PWY-6068
  • 10.1016/s0031-9422(99)00430-6
  • 10.1093/pcp/41.2.218
 Minami Y, Nishimura O, Hara-Nishimura I, Nishimura M, Matsubara H. Tissue and intracellular localization of indican and the purification and characterization of indican synthase from indigo plants. Plant Cell Physiol. 2000 Feb;41(2):218–25. doi: 10.1093/pcp/41.2.218. PMID: 10795317.; Marcinek H, Weyler W, Deus-Neumann B, Zenk MH. Indoxyl-UDPG-glucosyltransferase from Baphicacanthus cusia. Phytochemistry. 2000 Jan;53(2):201–7. doi: 10.1016/s0031-9422(99)00430-6. PMID: 10680172.
paerucumarin biosynthesis

Accession ID: BioCyc:META_PWY-7955
  • 10.1016/j.jmb.2008.09.027
  • 10.1186/1475-2859-11-42
 Lin Y, Yan Y. Biosynthesis of caffeic acid in Escherichia coli using its endogenous hydroxylase complex. Microbial Cell Factories. 2012 Apr 04;11(1):42. doi: 10.1186/1475-2859-11-42.; Drake EJ, Gulick AM. Three-dimensional Structures of Pseudomonas aeruginosa PvcA and PvcB, Two Proteins Involved in the Synthesis of 2-Isocyano-6,7-dihydroxycoumarin. Journal of Molecular Biology. 2008 Dec;384(1):193–205. doi: 10.1016/j.jmb.2008.09.027.
gliotoxin inactivation

Accession ID: BioCyc:META_PWY-7534
  • 10.1007/s00253-010-2657-5
  • 10.1016/0006-2952(80)90029-5
  • 10.1016/0006-2952(95)00039-3
  • 10.1016/j.chembiol.2014.07.006
  • 10.1016/j.femsle.2005.05.046
  • 10.1016/j.mycres.2007.08.017
  • 10.1016/j.pbi.2009.06.004
  • 10.1016/s0021-9258(19)81385-6
  • 10.1016/s0306-3623(96)00083-3
  • 10.1021/cr200398y
  • 10.1021/ja103262m
  • 10.1021/ja5033106
  • 10.1038/2041333b0
  • 10.1038/icb.1994.73
  • 10.1038/ja.2006.35
  • 10.1039/c3np70097f
  • 10.1080/13693780802056012
  • 10.1086/525044
  • 10.1099/mic.0.27847-0
  • 10.1128/aac.2.4.261
  • 10.1128/iai.00780-06
  • 10.1128/iai.62.4.1192-1198.1994
  • 10.1371/journal.ppat.1000952
 Dolan SK, Owens RA, O'Keeffe G, Hammel S, Fitzpatrick DA, Jones GW, Doyle S. Regulation of nonribosomal peptide synthesis: bis-thiomethylation attenuates gliotoxin biosynthesis in Aspergillus fumigatus. Chem Biol. 2014 Aug 14;21(8):999–1012. doi: 10.1016/j.chembiol.2014.07.006. PMID: 25126990.; Scharf DH, Habel A, Heinekamp T, Brakhage AA, Hertweck C. Opposed Effects of Enzymatic Gliotoxin N- and S-Methylations. J. Am. Chem. Soc. 2014 Aug 07;136(33):11674–9. doi: 10.1021/ja5033106.; Welch TR, Williams RM. Epidithiodioxopiperazines. occurrence, synthesis and biogenesis. Nat Prod Rep. 2014 Oct;31(10):1376–404. PMID: 24816491; PMCID: PMC4162872.; 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.; Scharf DH, Remme N, Heinekamp T, Hortschansky P, Brakhage AA, Hertweck C. Transannular disulfide formation in gliotoxin biosynthesis and its role in self-resistance of the human pathogen Aspergillus fumigatus. J Am Chem Soc. 2010 Jul 28;132(29):10136–41. doi: 10.1021/ja103262m. PMID: 20593880.; Schrettl M, Carberry S, Kavanagh K, Haas H, Jones GW, O'Brien J, Nolan A, Stephens J, Fenelon O, Doyle S. Self-protection against gliotoxin--a component of the gliotoxin biosynthetic cluster, GliT, completely protects Aspergillus fumigatus against exogenous gliotoxin. PLoS Pathog. 2010 Jun 10;6(6):e1000952. PMID: 20548963; PMCID: PMC2883607.; Reverberi M, Ricelli A, Zjalic S, Fabbri AA, Fanelli C. Natural functions of mycotoxins and control of their biosynthesis in fungi. Applied Microbiology and Biotechnology. 2010 May 22;87(3):899–911. doi: 10.1007/s00253-010-2657-5.; Möbius N, Hertweck C. Fungal phytotoxins as mediators of virulence. Curr Opin Plant Biol. 2009 Aug;12(4):390–8. doi: 10.1016/j.pbi.2009.06.004. PMID: 19608453.; Kwon-Chung KJ, Sugui JA. What do we know about the role of gliotoxin in the pathobiology ofAspergillus fumigatus?. Med Mycol. 2009 Jan;47(s1):S97–S103. doi: 10.1080/13693780802056012.; Spikes S, Xu R, Nguyen CK, Chamilos G, Kontoyiannis DP, Jacobson RH, Ejzykowicz DE, Chiang LY, Filler SG, May GS. Gliotoxin production in Aspergillus fumigatus contributes to host-specific differences in virulence. J Infect Dis. 2008 Feb 01;197(3):479–86. doi: 10.1086/525044. PMID: 18199036.; Fox EM, Howlett BJ. Biosynthetic gene clusters for epipolythiodioxopiperazines in filamentous fungi. Mycol Res. 2008 Feb;112(Pt 2):162–9. doi: 10.1016/j.mycres.2007.08.017. PMID: 18272357.; Bok JW, Chung D, Balajee SA, Marr KA, Andes D, Nielsen KF, Frisvad JC, Kirby KA, Keller NP. GliZ, a transcriptional regulator of gliotoxin biosynthesis, contributes to Aspergillus fumigatus virulence. Infect Immun. 2006 Dec;74(12):6761–8. PMID: 17030582; PMCID: PMC1698057.; Li X, Kim SK, Nam KW, Kang JS, Choi HD, Son BW. A new antibacterial dioxopiperazine alkaloid related to gliotoxin from a marine isolate of the fungus Pseudallescheria. J Antibiot (Tokyo). 2006 Apr;59(4):248–50. doi: 10.1038/ja.2006.35. PMID: 16830893.; Gardiner DM, Howlett BJ. Bioinformatic and expression analysis of the putative gliotoxin biosynthetic gene cluster of Aspergillus fumigatus. FEMS Microbiol Lett. 2005 Jul 15;248(2):241–8. doi: 10.1016/j.femsle.2005.05.046. PMID: 15979823.; Gardiner DM, Waring P, Howlett BJ. The epipolythiodioxopiperazine (ETP) class of fungal toxins: distribution, mode of action, functions and biosynthesis. Microbiology (Reading). 2005 Apr;151(Pt 4):1021–32. doi: 10.1099/mic.0.27847-0. PMID: 15817772.; Waring P, Beaver J. Gliotoxin and related epipolythiodioxopiperazines. General Pharmacology: The Vascular System. 1996 Dec;27(8):1311–6. doi: 10.1016/s0306-3623(96)00083-3.; Waring P, Sjaarda A, Lin QH. Gliotoxin inactivates alcohol dehydrogenase by either covalent modification or free radical damage mediated by redox cycling. Biochem Pharmacol. 1995 May 11;49(9):1195–201. doi: 10.1016/0006-2952(95)00039-3. PMID: 7539267.; Beaver JP, Waring P. Lack of correlation between early intracellular calcium ion rises and the onset of apoptosis in thymocytes. Immunol Cell Biol. 1994 Dec;72(6):489–99. doi: 10.1038/icb.1994.73. PMID: 7535293.; Sutton P, Newcombe NR, Waring P, Müllbacher A. In vivo immunosuppressive activity of gliotoxin, a metabolite produced by human pathogenic fungi. Infect Immun. 1994 Apr;62(4):1192–8. doi: 10.1128/iai.62.4.1192-1198.1994.; Waring P, Eichner RD, Müllbacher A, Sjaarda A. Gliotoxin induces apoptosis in macrophages unrelated to its antiphagocytic properties. Journal of Biological Chemistry. 1988 Dec;263(34):18493–9. doi: 10.1016/s0021-9258(19)81385-6.; Weisiger RA, Pinkus LM, Jakoby WB. Thiol S-methyltransferase: suggested role in detoxication of intestinal hydrogen sulfide. Biochem Pharmacol. 1980 Oct 15;29(20):2885–7. doi: 10.1016/0006-2952(80)90029-5. PMID: 7437088.; Trown PW, Bilello JA. Mechanism of action of gliotoxin: elimination of activity by sulfhydryl compounds. Antimicrob Agents Chemother. 1972 Oct;2(4):261–6. PMID: 4670497; PMCID: PMC444303.; RIGHTSEL WA, SCHNEIDER HG, SLOAN BJ, GRAF PR, MILLER FA, BARTZ OR, EHRLICH J, DIXON GJ. ANTIVIRAL ACTIVITY OF GLIOTOXIN AND GLIOTOXIN ACETATE. Nature. 1964 Dec 26;204():1333–4. doi: 10.1038/2041333b0. PMID: 14254440.
paxilline and diprenylpaxilline biosynthesis

Accession ID: BioCyc:META_PWY-7493
  • 10.1007/s00253-013-4834-9
  • 10.1021/ja3116636
  • 10.1021/ol049115o
  • 10.1074/jbc.m701626200
  • 10.3390/toxins5081422
 Scott B, Young CA, Saikia S, McMillan LK, Monahan BJ, Koulman A, Astin J, Eaton CJ, Bryant A, Wrenn RE, Finch SC, Tapper BA, Parker EJ, Jameson GB. Deletion and gene expression analyses define the paxilline biosynthetic gene cluster in Penicillium paxilli. Toxins (Basel). 2013 Aug 14;5(8):1422–46. PMID: 23949005; PMCID: PMC3760044.; Liu C, Noike M, Minami A, Oikawa H, Dairi T. Functional analysis of a prenyltransferase gene (paxD) in the paxilline biosynthetic gene cluster. Applied Microbiology and Biotechnology. 2013 Mar 24;98(1):199–206. doi: 10.1007/s00253-013-4834-9.; Tagami K, Liu C, Minami A, Noike M, Isaka T, Fueki S, Shichijo Y, Toshima H, Gomi K, Dairi T, Oikawa H. Reconstitution of biosynthetic machinery for indole-diterpene paxilline in Aspergillus oryzae. J Am Chem Soc. 2013 Jan 30;135(4):1260–3. doi: 10.1021/ja3116636. PMID: 23311903.; Saikia S, Parker EJ, Koulman A, Scott B. Defining paxilline biosynthesis in Penicillium paxilli: functional characterization of two cytochrome P450 monooxygenases. J Biol Chem. 2007 Jun 08;282(23):16829–37. doi: 10.1074/jbc.m701626200. PMID: 17428785.; Fueki S, Tokiwano T, Toshima H, Oikawa H. Biosynthesis of indole diterpenes, emindole, and paxilline: involvement of a common intermediate. Org Lett. 2004 Aug 05;6(16):2697–700. doi: 10.1021/ol049115o. PMID: 15281747.
ethanol degradation II

Accession ID: BioCyc:META_PWY66-21		 -
ethanol degradation I

Accession ID: BioCyc:META_ETOH-ACETYLCOA-ANA-PWY
  • 10.1074/jbc.m005464200
 Membrillo-Hernandez J, Echave P, Cabiscol E, Tamarit J, Ros J, Lin EC. Evolution of the adhE gene product of Escherichia coli from a functional reductase to a dehydrogenase. Genetic and biochemical studies of the mutant proteins. J Biol Chem. 2000 Oct 27;275(43):33869–75. doi: 10.1074/jbc.m005464200. PMID: 10922373.