Pathways Knowlegdes

Biological pathway database

Pathway DOIs Note
L-phenylalanine biosynthesis III (cytosolic, plants)

Accession ID: BioCyc:META_PWY-7432
  • 10.1038/ncomms3833
  • 10.1074/jbc.m502107200
  • 10.1074/jbc.m702662200
  • 10.1093/jxb/erp390
  • 10.1093/mp/ssp106
  • 10.1104/pp.010675
  • 10.1104/pp.102.017319
  • 10.1104/pp.110.161430
  • 10.1105/tpc.109.073247
  • 10.1146/annurev-arplant-042110-103854
  • 10.1146/annurev-arplant-042811-105439
 Yoo H, Widhalm JR, Qian Y, Maeda H, Cooper BR, Jannasch AS, Gonda I, Lewinsohn E, Rhodes D, Dudareva N. An alternative pathway contributes to phenylalanine biosynthesis in plants via a cytosolic tyrosine:phenylpyruvate aminotransferase. Nature Communications. 2013 Nov 25;4(1):2833. doi: 10.1038/ncomms3833.; Maeda H, Dudareva N. The shikimate pathway and aromatic amino Acid biosynthesis in plants. Annu Rev Plant Biol. 2012;63():73–105. doi: 10.1146/annurev-arplant-042811-105439. PMID: 22554242.; Mithöfer A, Boland W. Plant defense against herbivores: chemical aspects. Annu Rev Plant Biol. 2012;63():431–50. doi: 10.1146/annurev-arplant-042110-103854. PMID: 22404468.; Dixon RA, Pasinetti GM. Flavonoids and isoflavonoids: from plant biology to agriculture and neuroscience. Plant Physiol. 2010 Oct;154(2):453–7. PMID: 20921162; PMCID: PMC2948995.; Maeda H, Shasany AK, Schnepp J, Orlova I, Taguchi G, Cooper BR, Rhodes D, Pichersky E, Dudareva N. RNAi suppression of Arogenate Dehydratase1 reveals that phenylalanine is synthesized predominantly via the arogenate pathway in petunia petals. Plant Cell. 2010 Mar;22(3):832–49. PMID: 20215586; PMCID: PMC2861463.; Gonda I, Bar E, Portnoy V, Lev S, Burger J, Schaffer AA, Tadmor Y, Gepstein S, Giovannoni JJ, Katzir N, Lewinsohn E. Branched-chain and aromatic amino acid catabolism into aroma volatiles in Cucumis melo L. fruit. J Exp Bot. 2010 Feb;61(4):1111–23. PMID: 20065117; PMCID: PMC2826658.; Vogt T. Phenylpropanoid biosynthesis. Mol Plant. 2010 Jan;3(1):2–20. doi: 10.1093/mp/ssp106. PMID: 20035037.; Cho MH, Corea OR, Yang H, Bedgar DL, Laskar DD, Anterola AM, Moog-Anterola FA, Hood RL, Kohalmi SE, Bernards MA, Kang C, Davin LB, Lewis NG. Phenylalanine biosynthesis in Arabidopsis thaliana. Identification and characterization of arogenate dehydratases. J Biol Chem. 2007 Oct 19;282(42):30827–35. doi: 10.1074/jbc.m702662200. PMID: 17726025.; Prakash P, Pathak N, Hasnain SE. pheA (Rv3838c) of Mycobacterium tuberculosis Encodes an Allosterically Regulated Monofunctional Prephenate Dehydratase That Requires Both Catalytic and Regulatory Domains for Optimum Activity. Journal of Biological Chemistry. 2005 May;280(21):20666–71. doi: 10.1074/jbc.m502107200.; Dixon RA, Sumner LW. Legume natural products: understanding and manipulating complex pathways for human and animal health. Plant Physiol. 2003 Mar;131(3):878–85. PMID: 12644640; PMCID: PMC1540287.; Winkel-Shirley B. It takes a garden. How work on diverse plant species has contributed to an understanding of flavonoid metabolism. Plant Physiol. 2001 Dec;127(4):1399–404. PMID: 11743081; PMCID: PMC1540170.
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.
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.
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.
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.
coenzyme M biosynthesis II

Accession ID: BioCyc:META_PWY-6643
  • 10.1042/bj20090999
 Graham DE, Taylor SM, Wolf RZ, Namboori SC. Convergent evolution of coenzyme M biosynthesis in the Methanosarcinales: cysteate synthase evolved from an ancestral threonine synthase. Biochem J. 2009 Dec 10;424(3):467–78. doi: 10.1042/bj20090999. PMID: 19761441.
L-lysine degradation VII

Accession ID: BioCyc:META_PWY-5311
  • 10.1016/s0021-9258(19)86128-8
  • 10.1023/a:1020967408229
 Lukasheva EV, Berezov TT. L-Lysine alpha-oxidase: physicochemical and biological properties. Biochemistry (Mosc). 2002 Oct;67(10):1152–8. doi: 10.1023/a:1020967408229. PMID: 12460113.; Kusakabe H, Kodama K, Kuninaka A, Yoshino H, Misono H, Soda K. A new antitumor enzyme, L-lysine alpha-oxidase from Trichoderma viride. Purification and enzymological properties. Journal of Biological Chemistry. 1980 Feb;255(3):976–81. doi: 10.1016/s0021-9258(19)86128-8.
γ-butyrobetaine degradation

Accession ID: BioCyc:META_PWY-3621
  • 10.1128/jb.101.3.1094-1095.1970
 Lindstedt G, Lindstedt S, Midtvedt T, Tofft M. Inducible ?-Butyrobetaine-Degrading Enzymes in Pseudomonas Species AK 1. J Bacteriol. 1970 Mar;101(3):1094–5. doi: 10.1128/jb.101.3.1094-1095.1970.
L-lysine degradation XI (mammalian)

Accession ID: BioCyc:META_LYSINE-DEG1-PWY
  • 10.1146/annurev.nu.11.070191.002251
 Broquist HP. Lysine-pipecolic acid metabolic relationships in microbes and mammals. Annu Rev Nutr. 1991;11():435–48. doi: 10.1146/annurev.nu.11.070191.002251. PMID: 1909881.
L-lysine degradation I

Accession ID: BioCyc:META_PWY0-461
  • 10.1128/jb.182.23.6732-6741.2000
 Takatsuka Y, Yamaguchi Y, Ono M, Kamio Y. Gene Cloning and Molecular Characterization of Lysine Decarboxylase from Selenomonas ruminantium Delineate Its Evolutionary Relationship to Ornithine Decarboxylases from Eukaryotes. J Bacteriol. 2000 Dec;182(23):6732–41. doi: 10.1128/jb.182.23.6732-6741.2000.
L-tyrosine degradation I

Accession ID: BioCyc:META_TYRFUMCAT-PWY
  • 10.1006/fgbi.2001.1284
  • 10.1016/j.abb.2004.08.015
  • 10.1016/s0305-0491(98)00028-5
  • 10.1073/pnas.92.20.9132
  • 10.1128/jb.186.15.5062-5077.2004
 Moran GR. 4-Hydroxyphenylpyruvate dioxygenase. Archives of Biochemistry and Biophysics. 2005 Jan;433(1):117–28. doi: 10.1016/j.abb.2004.08.015.; Arias-Barrau E, Olivera ER, Luengo JM, Ferna´ndez C, Gala´n B, Garci´a JL, Di´az E, Min~ambres B. The Homogentisate Pathway: a Central Catabolic Pathway Involved in the Degradation of l -Phenylalanine, l -Tyrosine, and 3-Hydroxyphenylacetate in Pseudomonas putida. J Bacteriol. 2004 Aug;186(15):5062–77. doi: 10.1128/jb.186.15.5062-5077.2004.; Peñalva MA. A fungal perspective on human inborn errors of metabolism: alkaptonuria and beyond. Fungal Genet Biol. 2001 Oct;34(1):1–10. doi: 10.1006/fgbi.2001.1284. PMID: 11567547.; Sanchez-Amat A, Ruzafa C, Solano F. Comparative tyrosine degradation in Vibrio cholerae strains. The strain ATCC 14035 as a prokaryotic melanogenic model of homogentisate-releasing cell. Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology. 1998 Mar;119(3):557–62. doi: 10.1016/s0305-0491(98)00028-5.; Fernández-Cañón JM, Peñalva MA. Fungal metabolic model for human type I hereditary tyrosinaemia. Proc. Natl. Acad. Sci. U.S.A. 1995 Sep 26;92(20):9132–6. doi: 10.1073/pnas.92.20.9132.
pyruvate fermentation to hexanol (engineered)

Accession ID: BioCyc:META_PWY-6863
  • 10.1021/ja203814d
  • 10.1093/oxfordjournals.jbchem.a121813
 Dekishima Y, Lan EI, Shen CR, Cho KM, Liao JC. Extending carbon chain length of 1-butanol pathway for 1-hexanol synthesis from glucose by engineered Escherichia coli. J Am Chem Soc. 2011 Aug 03;133(30):11399–401. doi: 10.1021/ja203814d. PMID: 21707101.; Inui H, Miyatake K, Nakano Y, Kitaoka S. Purification and some properties of short chain-length specific trans-2-enoyl-CoA reductase in mitochondria of Euglena gracilis. J Biochem. 1986 Oct;100(4):995–1000. doi: 10.1093/oxfordjournals.jbchem.a121813. PMID: 3102464.
L-tyrosine degradation IV (to 4-methylphenol)

Accession ID: BioCyc:META_PWY-7514
  • 10.1128/jb.127.1.362-366.1976
  • 10.1139/m77-169
 Blakley ER. The catabolism of L-tyrosine by an Arthrobacter sp. Can. J. Microbiol. 1977 Sep 01;23(9):1128–39. doi: 10.1139/m77-169.; Sparnins VL, Chapman PJ. Catabolism of L-tyrosine by the homoprotocatechuate pathway in gram-positive bacteria. J Bacteriol. 1976 Jul;127(1):362–6. doi: 10.1128/jb.127.1.362-366.1976.
2-aminoethylphosphonate biosynthesis

Accession ID: BioCyc:META_PWY-6839
  • 10.1016/0304-4165(72)90319-4
  • 10.1016/s0006-291x(88)81205-1
  • 10.1021/bi00482a016
  • 10.1021/bi952944k
 Kim J, Dunaway-Mariano D. Phosphoenolpyruvate mutase catalysis of phosphoryl transfer in phosphoenolpyruvate: kinetics and mechanism of phosphorus-carbon bond formation. Biochemistry. 1996 Apr 09;35(14):4628–35. doi: 10.1021/bi952944k. PMID: 8605214.; Bowman ED, McQueney MS, Scholten JD, Dunaway-Mariano D. Purification and characterization of the Tetrahymena pyriformis P-C bond forming enzyme phosphoenolpyruvate phosphomutase. Biochemistry. 1990 Jul 31;29(30):7059–63. doi: 10.1021/bi00482a016. PMID: 2121271.; Barry RJ, Bowman E, McQueney M, Dunaway-Mariano D. Elucidation of the 2-aminoethylphosphonate biosynthetic pathway in Tetrahymena pyriformis. Biochemical and Biophysical Research Communications. 1988 May;153(1):177–82. doi: 10.1016/s0006-291x(88)81205-1.; Horiguchi M. Biosynthesis of 2-aminoethylphosphonic acid in cell-free preparations from tetrahymena. Biochimica et Biophysica Acta (BBA) - General Subjects. 1972 Jan;261(1):102–13. doi: 10.1016/0304-4165(72)90319-4.
aflatoxins B2 and G2 biosynthesis

Accession ID: BioCyc:META_PWY-5960
  • 10.1007/s00253-004-1566-x
 Yabe K, Nakajima H. Enzyme reactions and genes in aflatoxin biosynthesis. Applied Microbiology and Biotechnology. 2004 Jun 01;64(6):745–55. doi: 10.1007/s00253-004-1566-x.
L-glutamine biosynthesis III

Accession ID: BioCyc:META_PWY-6549
  • 10.1111/j.1365-313x.2010.04179.x
 Taylor L, Nunes-Nesi A, Parsley K, Leiss A, Leach G, Coates S, Wingler A, Fernie AR, Hibberd JM. Cytosolic pyruvate,orthophosphate dikinase functions in nitrogen remobilization during leaf senescence and limits individual seed growth and nitrogen content. Plant J. 2010 May 01;62(4):641–52. doi: 10.1111/j.1365-313x.2010.04179.x. PMID: 20202167.
4-hydroxycoumarin and dicoumarol biosynthesis

Accession ID: BioCyc:META_PWY-6418
  • 10.1007/s11103-009-9548-0
 Liu B, Raeth T, Beuerle T, Beerhues L. A novel 4-hydroxycoumarin biosynthetic pathway. Plant Mol Biol. 2010 Jan;72(1-2):17–25. doi: 10.1007/s11103-009-9548-0. PMID: 19757094.
cyanate degradation

Accession ID: BioCyc:META_CYANCAT-PWY
  • 10.1016/s0003-9861(02)00243-6
  • 10.1016/s0021-9258(19)75797-4
  • 10.1104/pp.105.2.707
  • 10.1371/journal.pone.0018300
 Qian D, Jiang L, Lu L, Wei C, Li Y. Biochemical and Structural Properties of Cyanases from Arabidopsis thaliana and Oryza sativa. PLoS ONE. 2011 Mar 31;6(3):e18300. doi: 10.1371/journal.pone.0018300.; Rowlett RS, Tu C, McKay MM, Preiss JR, Loomis RJ, Hicks KA, Marchione RJ, Strong JA, Donovan GS, Chamberlin JE. Kinetic characterization of wild-type and proton transfer-impaired variants of beta-carbonic anhydrase from Arabidopsis thaliana. Arch Biochem Biophys. 2002 Aug 15;404(2):197–209. doi: 10.1016/s0003-9861(02)00243-6. PMID: 12147257.; Fett JP, Coleman JR. Characterization and expression of two cDNAs encoding carbonic anhydrase in Arabidopsis thaliana. Plant Physiol. 1994 Jun;105(2):707–13. PMID: 7520589; PMCID: PMC159412.; Murakami H, Sly WS. Purification and characterization of human salivary carbonic anhydrase. Journal of Biological Chemistry. 1987 Jan;262(3):1382–8. doi: 10.1016/s0021-9258(19)75797-4.
ellagic acid degradation to urolithins

Accession ID: BioCyc:META_PWY-7951
  • 10.3389/fmicb.2017.01521
 Selma MV, Beltrán D, Luna MC, Romo-Vaquero M, García-Villalba R, Mira A, Espín JC, Tomás-Barberán FA. Isolation of Human Intestinal Bacteria Capable of Producing the Bioactive Metabolite Isourolithin A from Ellagic Acid. Front Microbiol. 2017;8():1521. PMID: 28824607; PMCID: PMC5545574.