Pathways Knowlegdes

Biological pathway database

Pathway DOIs Note
superpathway of tryptophan utilization

Accession ID: BioCyc:HUMAN_PWY66-401		 -
L-tyrosine biosynthesis IV

Accession ID: BioCyc:META_PWY-6134
  • 10.1042/bj1270675
 McGee MM, Greengard O, Knox WE. Liver phenylalanine hydroxylase activity in relation to blood concentrations of tyrosine and phenylalanine in the rat. Biochem J. 1972 May;127(4):675–80. PMID: 4265522; PMCID: PMC1178765.
phenylalanine degradation/tyrosine biosynthesis

Accession ID: BioCyc:HUMAN_PHENYLALANINE-DEG1-PWY
  • 10.1021/bi035656u
 Fitzpatrick PF. Mechanism of aromatic amino acid hydroxylation. Biochemistry. 2003 Dec 09;42(48):14083–91. PMID: 14640675; PMCID: PMC1635487.
catecholamine biosynthesis

Accession ID: BioCyc:META_PWY66-301
  • 10.1016/s0031-6997(25)07406-x
 Blaschko H. THE DEVELOPMENT OF CURRENT CONCEPTS OF CATECHOLAMINE FORMATION. Pharmacological Reviews. 1959 Jun;11(2):307–16. doi: 10.1016/s0031-6997(25)07406-x.
L-phenylalanine degradation I (aerobic)

Accession ID: BioCyc:META_PHENYLALANINE-DEG1-PWY
  • 10.1021/bi035656u
 Fitzpatrick PF. Mechanism of aromatic amino acid hydroxylation. Biochemistry. 2003 Dec 09;42(48):14083–91. PMID: 14640675; PMCID: PMC1635487.
betalamic acid biosynthesis

Accession ID: BioCyc:META_PWY-5394
  • 10.1007/bf02157931
  • 10.1007/s00425-010-1191-0
  • 10.1007/s00425-012-1593-2
  • 10.1016/s0031-9422(02)00564-2
  • 10.1021/jf000523q
  • 10.1021/jf010456f
  • 10.1021/jf025696p
  • 10.1038/437334a
  • 10.1038/ng.3163
  • 10.1038/ng.3174
  • 10.1080/1071576031000097490
  • 10.1093/chromsci/43.9.454
  • 10.1104/pp.103.031914
  • 10.1104/pp.43.3.457
  • 10.1146/annurev.arplant.57.032905.105248
 Davies KM. Swapping one red pigment for another. Nat Genet. 2015 Jan;47(1):5–6. doi: 10.1038/ng.3174. PMID: 25547597.; Hatlestad GJ, Akhavan NA, Sunnadeniya RM, Elam L, Cargile S, Hembd A, Gonzalez A, McGrath JM, Lloyd AM. The beet Y locus encodes an anthocyanin MYB-like protein that activates the betalain red pigment pathway. Nat Genet. 2015 Jan;47(1):92–6. doi: 10.1038/ng.3163. PMID: 25436858.; Gandía-Herrero F, García-Carmona F. Characterization of recombinant Beta vulgaris 4,5-DOPA-extradiol-dioxygenase active in the biosynthesis of betalains. Planta. 2012 Jul;236(1):91–100. doi: 10.1007/s00425-012-1593-2. PMID: 22270561.; Gandía-Herrero F, Escribano J, García-Carmona F. Structural implications on color, fluorescence, and antiradical activity in betalains. Planta. 2010 Jul;232(2):449–60. doi: 10.1007/s00425-010-1191-0. PMID: 20467875.; Grotewold E. The genetics and biochemistry of floral pigments. Annu Rev Plant Biol. 2006;57():761–80. doi: 10.1146/annurev.arplant.57.032905.105248. PMID: 16669781.; 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.; Gandía-Herrero F, García-Carmona F, Escribano J. Botany: floral fluorescence effect. Nature. 2005 Sep 15;437(7057):334. doi: 10.1038/437334a. PMID: 16163341.; Christinet L, Burdet FX, Zaiko M, Hinz U, Zrÿd JP. Characterization and functional identification of a novel plant 4,5-extradiol dioxygenase involved in betalain pigment biosynthesis in Portulaca grandiflora. Plant Physiol. 2004 Jan;134(1):265–74. PMID: 14730069; PMCID: PMC316306.; Tesoriere L, Butera D, D'Arpa D, Di Gaudio F, Allegra M, Gentile C, Livrea MA. Increased resistance to oxidation of betalain-enriched human low density lipoproteins. Free Radic Res. 2003 Jun;37(6):689–96. doi: 10.1080/1071576031000097490. PMID: 12868496.; 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.; Butera D, Tesoriere L, Di Gaudio F, Bongiorno A, Allegra M, Pintaudi AM, Kohen R, Livrea MA. Antioxidant activities of sicilian prickly pear (Opuntia ficus indica) fruit extracts and reducing properties of its betalains: betanin and indicaxanthin. J Agric Food Chem. 2002 Nov 06;50(23):6895–901. doi: 10.1021/jf025696p. PMID: 12405794.; Kanner J, Harel S, Granit R. Betalains--a new class of dietary cationized antioxidants. J Agric Food Chem. 2001 Nov;49(11):5178–85. doi: 10.1021/jf010456f. PMID: 11714300.; Kujala TS, Loponen JM, Klika KD, Pihlaja K. Phenolics and Betacyanins in Red Beetroot (Beta vulgaris) Root: Distribution and Effect of Cold Storage on the Content of Total Phenolics and Three Individual Compounds. J. Agric. Food Chem. 2000 Oct 07;48(11):5338–42. doi: 10.1021/jf000523q.; Wohlpart A, Mabry TJ. On the light requirement for betalain biogenesis. Plant Physiol. 1968 Mar;43(3):457–9. PMID: 16656788; PMCID: PMC1086865.; WYLER H, DREIDING AS. [On betacyanins, the nitrogen containing pigment of Centrospermae. Preliminary report]. Experientia. 1961 Jan 15;17():23–5. doi: 10.1007/bf02157931. PMID: 13831375.
erythro-tetrahydrobiopterin biosynthesis II

Accession ID: BioCyc:META_PWY-5664
  • 10.1016/s0021-9258(18)83151-9
 Milstien S, Kaufman S. The biosynthesis of tetrahydrobiopterin in rat brain. Purification and characterization of 6-pyruvoyl tetrahydropterin (2'-oxo)reductase. J Biol Chem. 1989 May 15;264(14):8066–73. PMID: 2656673.
L-phenylalanine degradation I (aerobic)

Accession ID: BioCyc:VCHO_PHENYLALANINE-DEG1-PWY		 -
L-phenylalanine degradation I (aerobic)

Accession ID: BioCyc:MTBH37RV_PHENYLALANINE-DEG1-PWY		 -
tetrahydrobiopterin de novo biosynthesis

Accession ID: BioCyc:HUMAN_PWY-5663
  • 10.2174/1389200024605073
 Werner-Felmayer G, Golderer G, Werner ER. Tetrahydrobiopterin biosynthesis, utilization and pharmacological effects. Curr Drug Metab. 2002 Apr;3(2):159–73. doi: 10.2174/1389200024605073. PMID: 12003348.
catecholamine biosynthesis

Accession ID: BioCyc:HUMAN_PWY66-301		 -
superpathway of rosmarinic acid biosynthesis

Accession ID: BioCyc:META_PWY-5071
  • 10.1007/s00425-002-0960-9
  • 10.1016/s0014-5793(02)02368-2
  • 10.1016/s0031-9422(02)00513-7
  • 10.1023/b:plan.0000036367.03056.b2
  • 10.1042/bj1180291
 Kim KH, Janiak V, Petersen M. Purification, cloning and functional expression of hydroxyphenylpyruvate reductase involved in rosmarinic acid biosynthesis in cell cultures of Coleus blumei. Plant Mol Biol. 2004 Feb;54(3):311–23. doi: 10.1023/b:plan.0000036367.03056.b2. PMID: 15284489.; Petersen M. Cinnamic acid 4-hydroxylase from cell cultures of the hornwort Anthoceros agrestis. Planta. 2003 May;217(1):96–101. doi: 10.1007/s00425-002-0960-9. PMID: 12721853.; Petersen M, Simmonds MS. Rosmarinic acid. Phytochemistry. 2003 Jan;62(2):121–5. doi: 10.1016/s0031-9422(02)00513-7. PMID: 12482446.; Matsuno M, Nagatsu A, Ogihara Y, Ellis BE, Mizukami H. CYP98A6 from Lithospermum erythrorhizon encodes 4-coumaroyl-4'-hydroxyphenyllactic acid 3-hydroxylase involved in rosmarinic acid biosynthesis1. FEBS Letters. 2002 Mar 13;514(2-3):219–24. doi: 10.1016/s0014-5793(02)02368-2.; Ellis BE, Towers GH. Biogenesis of rosmarinic acid in Mentha. Biochem J. 1970 Jun;118(2):291–7. PMID: 5484678; PMCID: PMC1179116.
tetrahydrobiopterin biosynthesis II

Accession ID: BioCyc:FLY_PWY-5664		 -
serotonin and melatonin biosynthesis

Accession ID: BioCyc:HUMAN_PWY-6030
  • 10.1016/s0014-5793(01)03319-1
 Slominski A, Semak I, Pisarchik A, Sweatman T, Szczesniewski A, Wortsman J. Conversion of L-tryptophan to serotonin and melatonin in human melanoma cells. FEBS Lett. 2002 Jan 30;511(1-3):102–6. doi: 10.1016/s0014-5793(01)03319-1. PMID: 11821057.
rosmarinic acid biosynthesis II

Accession ID: BioCyc:META_PWY-5049
  • 10.1007/bf00039560
  • 10.1007/s00425-002-0960-9
  • 10.1016/s0031-9422(02)00513-7
  • 10.1023/b:plan.0000036367.03056.b2
  • 10.1042/bj1180291
 Kim KH, Janiak V, Petersen M. Purification, cloning and functional expression of hydroxyphenylpyruvate reductase involved in rosmarinic acid biosynthesis in cell cultures of Coleus blumei. Plant Mol Biol. 2004 Feb;54(3):311–23. doi: 10.1023/b:plan.0000036367.03056.b2. PMID: 15284489.; Petersen M. Cinnamic acid 4-hydroxylase from cell cultures of the hornwort Anthoceros agrestis. Planta. 2003 May;217(1):96–101. doi: 10.1007/s00425-002-0960-9. PMID: 12721853.; Petersen M, Simmonds MS. Rosmarinic acid. Phytochemistry. 2003 Jan;62(2):121–5. doi: 10.1016/s0031-9422(02)00513-7. PMID: 12482446.; Dry IB, Robinson SP. Molecular cloning and characterisation of grape berry polyphenol oxidase. Plant Mol Biol. 1994 Oct;26(1):495–502. doi: 10.1007/bf00039560. PMID: 7948897.; Ellis BE, Towers GH. Biogenesis of rosmarinic acid in Mentha. Biochem J. 1970 Jun;118(2):291–7. PMID: 5484678; PMCID: PMC1179116.
serotonin and melatonin biosynthesis

Accession ID: BioCyc:META_PWY-6030
  • 10.1016/s0014-5793(01)03319-1
  • 10.1111/j.1600-079x.2010.00783.x
  • 10.1126/science.3941912
 Kang K, Lee K, Park S, Kim YS, Back K. Enhanced production of melatonin by ectopic overexpression of human serotonin N-acetyltransferase plays a role in cold resistance in transgenic rice seedlings. J Pineal Res. 2010 Sep;49(2):176–82. doi: 10.1111/j.1600-079x.2010.00783.x. PMID: 20586889.; Slominski A, Semak I, Pisarchik A, Sweatman T, Szczesniewski A, Wortsman J. Conversion of L-tryptophan to serotonin and melatonin in human melanoma cells. FEBS Lett. 2002 Jan 30;511(1-3):102–6. doi: 10.1016/s0014-5793(01)03319-1. PMID: 11821057.; Ebihara S, Marks T, Hudson DJ, Menaker M. Genetic control of melatonin synthesis in the pineal gland of the mouse. Science. 1986 Jan 31;231(4737):491–3. doi: 10.1126/science.3941912. PMID: 3941912.
superpathway of betalain biosynthesis

Accession ID: BioCyc:META_PWY-5405
  • 10.1007/s00425-001-0685-1
  • 10.1007/s00425-005-1526-4
  • 10.1007/s10265-005-0237-z
  • 10.1016/s0021-9258(18)47073-1
  • 10.1016/s0031-9422(02)00564-2
  • 10.1021/jf0514120
  • 10.1046/j.1365-313x.1999.00540.x
  • 10.1093/chromsci/43.9.454
  • 10.1104/pp.103.031914
  • 10.1104/pp.104.057992
  • 10.1104/pp.119.4.1217
  • 10.1105/tpc.7.11.1811
  • 10.1146/annurev.arplant.57.032905.105248
 Grotewold E. The genetics and biochemistry of floral pigments. Annu Rev Plant Biol. 2006;57():761–80. doi: 10.1146/annurev.arplant.57.032905.105248. PMID: 16669781.; Sasaki N, Abe Y, Wada K, Koda T, Goda Y, Adachi T, Ozeki Y. Amaranthin in feather cockscombs is synthesized via glucuronylation at the cyclo-DOPA glucoside step in the betacyanin biosynthetic pathway. Journal of Plant Research. 2005 Oct 25;118(6):439–42. doi: 10.1007/s10265-005-0237-z.; Gandía-Herrero F, Escribano J, García-Carmona F. Characterization of the activity of tyrosinase on betaxanthins derived from (R)-amino acids. J Agric Food Chem. 2005 Nov 16;53(23):9207–12. doi: 10.1021/jf0514120. PMID: 16277424.; 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.; Gandía-Herrero F, Escribano J, García-Carmona F. Characterization of the monophenolase activity of tyrosinase on betaxanthins: the tyramine-betaxanthin/dopamine-betaxanthin pair. Planta. 2005 Oct;222(2):307–18. doi: 10.1007/s00425-005-1526-4. PMID: 15968512.; Gandía-Herrero F, Escribano J, García-Carmona F. Betaxanthins as substrates for tyrosinase. An approach to the role of tyrosinase in the biosynthetic pathway of betalains. Plant Physiol. 2005 May;138(1):421–32. PMID: 15805475; PMCID: PMC1104195.; Christinet L, Burdet FX, Zaiko M, Hinz U, Zrÿd JP. Characterization and functional identification of a novel plant 4,5-extradiol dioxygenase involved in betalain pigment biosynthesis in Portulaca grandiflora. Plant Physiol. 2004 Jan;134(1):265–74. PMID: 14730069; PMCID: PMC316306.; 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.; Vogt T. Substrate specificity and sequence analysis define a polyphyletic origin of betanidin 5- and 6-O-glucosyltransferase from Dorotheanthus bellidiformis. Planta. 2002 Jan;214(3):492–5. doi: 10.1007/s00425-001-0685-1. PMID: 11855654.; Vogt T, Grimm R, Strack D. Cloning and expression of a cDNA encoding betanidin 5-O-glucosyltransferase, a betanidin- and flavonoid-specific enzyme with high homology to inducible glucosyltransferases from the Solanaceae. Plant J. 1999 Sep;19(5):509–19. doi: 10.1046/j.1365-313x.1999.00540.x. PMID: 10504573.; 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.
erythro-tetrahydrobiopterin biosynthesis I

Accession ID: BioCyc:META_PWY-5663
  • 10.1016/j.femsle.2004.10.044
  • 10.2174/1389200024605073
 Choi YK, Jun SR, Cha EY, Park JS, Park YS. Sepiapterin reductases from Chlorobium tepidum and Chlorobium limicola catalyze the synthesis of L-threo-tetrahydrobiopterin from 6-pyruvoyltetrahydropterin. FEMS Microbiol Lett. 2005 Jan 01;242(1):95–9. doi: 10.1016/j.femsle.2004.10.044. PMID: 15621425.; Werner-Felmayer G, Golderer G, Werner ER. Tetrahydrobiopterin biosynthesis, utilization and pharmacological effects. Curr Drug Metab. 2002 Apr;3(2):159–73. doi: 10.2174/1389200024605073. PMID: 12003348.
tetrahydrobiopterin biosynthesis I

Accession ID: BioCyc:FLY_PWY-5663		 -
tetrahydrobiopterin biosynthesis I

Accession ID: BioCyc:SYNEL_PWY-5663		 -