Pathways Knowlegdes

Biological pathway database

Pathway DOIs Note
propene degradation

Accession ID: BioCyc:META_PWY-5534
  • 10.1146/annurev.biochem.72.121801.161820
 Ensign SA, Allen JR. Aliphatic epoxide carboxylation. Annu Rev Biochem. 2003;72():55–76. doi: 10.1146/annurev.biochem.72.121801.161820. PMID: 12524213.
C4 photosynthetic carbon assimilation cycle, PEPCK type

Accession ID: BioCyc:META_PWY-7117
  • 10.1006/abbi.1993.1524
  • 10.1007/978-94-007-7359-2_4
  • 10.1016/j.bmcl.2013.01.087
  • 10.1016/j.plaphy.2010.09.005
  • 10.1016/s0021-9258(19)75797-4
  • 10.1093/jxb/eru058
  • 10.1104/pp.106.093013
  • 10.1104/pp.107.098152
  • 10.1104/pp.114.237602
  • 10.1105/tpc.111.090324
  • 10.1111/j.1365-3040.2011.02364.x
 Studer AJ, Gandin A, Kolbe AR, Wang L, Cousins AB, Brutnell TP. A Limited Role for Carbonic Anhydrase in C4 Photosynthesis as Revealed by a ca1ca2 Double Mutant in Maize. Plant Physiol. 2014 Jun;165(2):608–17. PMID: 24706552; PMCID: PMC4044840.; Wang Y, Bräutigam A, Weber AP, Zhu XG. Three distinct biochemical subtypes of C4 photosynthesis? A modelling analysis. J Exp Bot. 2014 Jul;65(13):3567–78. PMID: 24609651; PMCID: PMC4085956.; Rowlett RS. Structure and catalytic mechanism of ß-carbonic anhydrases. Subcell Biochem. 2014;75():53–76. doi: 10.1007/978-94-007-7359-2_4. PMID: 24146374.; Monti SM, De Simone G, Dathan NA, Ludwig M, Vullo D, Scozzafava A, Capasso C, Supuran CT. Kinetic and anion inhibition studies of a ß-carbonic anhydrase (FbiCA 1) from the C4 plant Flaveria bidentis. Bioorganic & Medicinal Chemistry Letters. 2013 Mar;23(6):1626–30. doi: 10.1016/j.bmcl.2013.01.087.; Pick TR, Bräutigam A, Schlüter U, Denton AK, Colmsee C, Scholz U, Fahnenstich H, Pieruschka R, Rascher U, Sonnewald U, Weber AP. Systems analysis of a maize leaf developmental gradient redefines the current C4 model and provides candidates for regulation. Plant Cell. 2011 Dec;23(12):4208–20. PMID: 22186372; PMCID: PMC3269860.; LUDWIG M. Carbonic anhydrase and the molecular evolution of C4 photosynthesis. Plant Cell & Environment. 2011 Jul;35(1):22–37. doi: 10.1111/j.1365-3040.2011.02364.x.; Tems U, Burnell JN. Characterization and expression of the maize ß-carbonic anhydrase gene repeat regions. Plant Physiol Biochem. 2010 Dec;48(12):945–51. doi: 10.1016/j.plaphy.2010.09.005. PMID: 20933433.; Tetu SG, Tanz SK, Vella N, Burnell JN, Ludwig M. The Flaveria bidentis ß-Carbonic Anhydrase Gene Family Encodes Cytosolic and Chloroplastic Isoforms Demonstrating Distinct Organ-Specific Expression Patterns. Plant Physiol. 2007 May 11;144(3):1316–27. doi: 10.1104/pp.107.098152.; Bailey KJ, Gray JE, Walker RP, Leegood RC. Coordinate Regulation of Phosphoenolpyruvate Carboxylase and Phosphoenolpyruvate Carboxykinase by Light and CO2 during C4 Photosynthesis. Plant Physiol. 2007 Mar 02;144(1):479–86. doi: 10.1104/pp.106.093013.; Carnal NW, Agostino A, Hatch MD. Photosynthesis in Phosphoenolpyruvate Carboxykinase-Type C4 Plants: Mechanism and Regulation of C4 Acid Decarboxylation in Bundle Sheath Cells. Archives of Biochemistry and Biophysics. 1993 Nov;306(2):360–7. doi: 10.1006/abbi.1993.1524.; 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.
(S)-reticuline biosynthesis II

Accession ID: BioCyc:META_PWY-6133
  • 10.1073/pnas.0405430101
  • 10.1073/pnas.0503244102
 Boettcher C, Fellermeier M, Boettcher C, Dräger B, Zenk MH. How human neuroblastoma cells make morphine. Proc Natl Acad Sci U S A. 2005 Jun 14;102(24):8495–500. PMID: 15937106; PMCID: PMC1150847.; Poeaknapo C, Schmidt J, Brandsch M, Dräger B, Zenk MH. Endogenous formation of morphine in human cells. Proc. Natl. Acad. Sci. U.S.A. 2004 Sep 21;101(39):14091–6. doi: 10.1073/pnas.0405430101.
superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis

Accession ID: BioCyc:META_PWY-7211
  • 10.1146/annurev.arplant.57.032905.105421
 Zrenner R, Stitt M, Sonnewald U, Boldt R. Pyrimidine and purine biosynthesis and degradation in plants. Annu Rev Plant Biol. 2006;57():805–36. doi: 10.1146/annurev.arplant.57.032905.105421. PMID: 16669783.
coral bioluminescence

Accession ID: BioCyc:META_PWY-7914		 -
oxygenic photosynthesis

Accession ID: BioCyc:META_PHOTOALL-PWY
  • 10.1016/0005-2728(77)90041-x
  • 10.1038/nsmb.1559
 Guskov A, Kern J, Gabdulkhakov A, Broser M, Zouni A, Saenger W. Cyanobacterial photosystem II at 2.9-Å resolution and the role of quinones, lipids, channels and chloride. Nature Structural & Molecular Biology. 2009 Feb 15;16(3):334–42. doi: 10.1038/nsmb.1559.; Knaff DB, Malkin R, Clark Myron J, Stoller M. The role of plastoquinone and ß-carotene in the primary reaction of plant Photosystem II. Biochimica et Biophysica Acta (BBA) - Bioenergetics. 1977 Mar;459(3):402–11. doi: 10.1016/0005-2728(77)90041-x.
docosahexaenoate biosynthesis I (lower eukaryotes)

Accession ID: BioCyc:META_PWY-7053
  • 10.1074/jbc.m603022200
 Kaewsuwan S, Cahoon EB, Perroud PF, Wiwat C, Panvisavas N, Quatrano RS, Cove DJ, Bunyapraphatsara N. Identification and functional characterization of the moss Physcomitrella patens delta5-desaturase gene involved in arachidonic and eicosapentaenoic acid biosynthesis. J Biol Chem. 2006 Aug 04;281(31):21988–97. doi: 10.1074/jbc.m603022200. PMID: 16728405.
firefly bioluminescence

Accession ID: BioCyc:META_PWY-7913
  • 10.1371/journal.pone.0084023
  • 10.7717/peerj.2534
 Vongsangnak W, Chumnanpuen P, Sriboonlert A. Transcriptome analysis reveals candidate genes involved in luciferin metabolism in Luciola aquatilis (Coleoptera: Lampyridae). PeerJ. 2016;4():e2534. PMID: 27761329; PMCID: PMC5068357.; Oba Y, Yoshida N, Kanie S, Ojika M, Inouye S. Biosynthesis of Firefly Luciferin in Adult Lantern: Decarboxylation of ?-Cysteine is a Key Step for Benzothiazole Ring Formation in Firefly Luciferin Synthesis. PLoS ONE. 2013 Dec 31;8(12):e84023. doi: 10.1371/journal.pone.0084023.
gibberellin biosynthesis V

Accession ID: BioCyc:META_PWY-7232
  • 10.1042/bj20120245
  • 10.1073/pnas.141239398
  • 10.1146/annurev.arplant.59.032607.092804
 Hedden P, Thomas S. Gibberellin biosynthesis and its regulation. 2012 Apr 26;444(1):11–25. doi: 10.1042/bj20120245.; Yamaguchi S. Gibberellin metabolism and its regulation. Annu Rev Plant Biol. 2008;59():225–51. doi: 10.1146/annurev.arplant.59.032607.092804. PMID: 18173378.; Itoh H, Ueguchi-Tanaka M, Sentoku N, Kitano H, Matsuoka M, Kobayashi M. Cloning and functional analysis of two gibberellin 3 beta -hydroxylase genes that are differently expressed during the growth of rice. Proc Natl Acad Sci U S A. 2001 Jul 17;98(15):8909–14. PMID: 11438692; PMCID: PMC37534.
superpathway of L-methionine salvage and degradation

Accession ID: BioCyc:META_PWY-5328
  • 10.1016/0955-2863(90)90070-2
  • 10.1042/bj2340295
 Finkelstein JD. Methionine metabolism in mammals. The Journal of Nutritional Biochemistry. 1990 May;1(5):228–37. doi: 10.1016/0955-2863(90)90070-2.; Paxton R, Scislowski PW, Davis EJ, Harris RA. Role of branched-chain 2-oxo acid dehydrogenase and pyruvate dehydrogenase in 2-oxobutyrate metabolism. Biochem J. 1986 Mar 01;234(2):295–303. PMID: 3718468; PMCID: PMC1146565.
ethylene biosynthesis I (plants)

Accession ID: BioCyc:META_ETHYL-PWY
  • 10.1002/j.1460-2075.1991.tb07730.x
  • 10.1016/s0168-9452(00)00314-9
  • 10.1111/j.1365-313x.2012.04965.x
 Lyzenga WJ, Booth JK, Stone SL. The Arabidopsis RING-type E3 ligase XBAT32 mediates the proteasomal degradation of the ethylene biosynthetic enzyme, 1-aminocyclopropane-1-carboxylate synthase 7. Plant J. 2012 Jul;71(1):23–34. doi: 10.1111/j.1365-313x.2012.04965.x. PMID: 22339729.; Kosugi Y, Shibuya K, Tsuruno N, Iwazaki Y, Mochizuki A, Yoshioka T, Hashiba T, Satoh S. Expression of genes responsible for ethylene production and wilting are differently regulated in carnation (Dianthus caryophyllus L.) petals. Plant Science. 2000 Sep;158(1-2):139–45. doi: 10.1016/s0168-9452(00)00314-9.; Spanu P, Reinhardt D, Boller T. Analysis and cloning of the ethylene-forming enzyme from tomato by functional expression of its mRNA in Xenopus laevis oocytes. The EMBO Journal. 1991 Aug;10(8):2007–13. doi: 10.1002/j.1460-2075.1991.tb07730.x.
L-isoleucine biosynthesis IV

Accession ID: BioCyc:META_PWY-5104
  • 10.1016/s0021-9258(17)36404-9
 Buchanan BB. Role of Ferredoxin in the Synthesis of a-Ketobutyrate from Propionyl Coenzyme A and Carbon Dioxide by Enzymes from Photosynthetic and Nonphotosynthetic Bacteria. Journal of Biological Chemistry. 1969 Aug;244(15):4218–23. doi: 10.1016/s0021-9258(17)36404-9.
formate to trimethylamine N-oxide electron transfer

Accession ID: BioCyc:META_PWY0-1355		 -
phenylethanol biosynthesis

Accession ID: BioCyc:META_PWY-5751
  • 10.1016/j.phytochem.2007.06.005
  • 10.1073/pnas.0602469103
  • 10.1074/jbc.275.19.14659
  • 10.1074/jbc.m211914200
  • 10.1074/jbc.m602708200
  • 10.1271/bbb.70090
 Tieman DM, Loucas HM, Kim JY, Clark DG, Klee HJ. Tomato phenylacetaldehyde reductases catalyze the last step in the synthesis of the aroma volatile 2-phenylethanol. Phytochemistry. 2007 Nov;68(21):2660–9. doi: 10.1016/j.phytochem.2007.06.005. PMID: 17644147.; SAKAI M, HIRATA H, SAYAMA H, SEKIGUCHI K, ITANO H, ASAI T, DOHRA H, HARA M, WATANABE N. Production of 2-Phenylethanol in Roses as the Dominant Floral Scent Compound fromL-Phenylalanine by Two Key Enzymes, a PLP-Dependent Decarboxylase and a Phenylacetaldehyde Reductase. Bioscience, Biotechnology, and Biochemistry. 2007 Oct 23;71(10):2408–19. doi: 10.1271/bbb.70090.; Kaminaga Y, Schnepp J, Peel G, Kish CM, Ben-Nissan G, Weiss D, Orlova I, Lavie O, Rhodes D, Wood K, Porterfield DM, Cooper AJL, Schloss JV, Pichersky E, Vainstein A, Dudareva N. Plant Phenylacetaldehyde Synthase Is a Bifunctional Homotetrameric Enzyme That Catalyzes Phenylalanine Decarboxylation and Oxidation. Journal of Biological Chemistry. 2006 Aug;281(33):23357–66. doi: 10.1074/jbc.m602708200.; Tieman D, Taylor M, Schauer N, Fernie AR, Hanson AD, Klee HJ. Tomato aromatic amino acid decarboxylases participate in synthesis of the flavor volatiles 2-phenylethanol and 2-phenylacetaldehyde. Proc Natl Acad Sci U S A. 2006 May 23;103(21):8287–92. PMID: 16698923; PMCID: PMC1472464.; Dickinson JR, Salgado LEJ, Hewlins MJE. The Catabolism of Amino Acids to Long Chain and Complex Alcohols in Saccharomyces cerevisiae. Journal of Biological Chemistry. 2003 Mar;278(10):8028–34. doi: 10.1074/jbc.m211914200.; Wittstock U, Halkier BA. Cytochrome P450 CYP79A2 from Arabidopsis thaliana L. Catalyzes the Conversion of l-Phenylalanine to Phenylacetaldoxime in the Biosynthesis of Benzylglucosinolate. Journal of Biological Chemistry. 2000 May;275(19):14659–66. doi: 10.1074/jbc.275.19.14659.
chanoclavine I aldehyde biosynthesis

Accession ID: BioCyc:META_PWY-6493
  • 10.1099/mic.0.27759-0
 Unsöld IA, Li SM. Overproduction, purification and characterization of FgaPT2, a dimethylallyltryptophan synthase from Aspergillus fumigatus. Microbiology (Reading). 2005 May;151(Pt 5):1499–505. doi: 10.1099/mic.0.27759-0. PMID: 15870460.
taurine degradation IV

Accession ID: BioCyc:META_PWY0-981
  • 10.1074/jbc.272.37.23031
  • 10.1128/jb.178.18.5438-5446.1996
 Eichhorn E, van der Ploeg JR, Kertesz MA, Leisinger T. Characterization of alpha-ketoglutarate-dependent taurine dioxygenase from Escherichia coli. J Biol Chem. 1997 Sep 12;272(37):23031–6. doi: 10.1074/jbc.272.37.23031. PMID: 9287300.; van der Ploeg JR, Weiss MA, Saller E, Nashimoto H, Saito N, Kertesz MA, Leisinger T. Identification of sulfate starvation-regulated genes in Escherichia coli: a gene cluster involved in the utilization of taurine as a sulfur source. J Bacteriol. 1996 Sep;178(18):5438–46. doi: 10.1128/jb.178.18.5438-5446.1996.
superpathway of NAD biosynthesis in eukaryotes

Accession ID: BioCyc:META_PWY-3502
  • 10.1016/s0014-5793(02)02585-1
  • 10.1074/jbc.m200671200
 Jackson MD, Denu JM. Structural identification of 2'- and 3'-O-acetyl-ADP-ribose as novel metabolites derived from the Sir2 family of beta -NAD+-dependent histone/protein deacetylases. J Biol Chem. 2002 May 24;277(21):18535–44. doi: 10.1074/jbc.m200671200. PMID: 11893743.; Panozzo C, Nawara M, Suski C, Kucharczyk R, Skoneczny M, Bécam A, Rytka J, Herbert CJ. Aerobic and anaerobic NAD+ metabolism in Saccharomyces cerevisiae. FEBS Letters. 2002 Mar 22;517(1-3):97–102. doi: 10.1016/s0014-5793(02)02585-1.
2-oxoglutarate decarboxylation to succinyl-CoA

Accession ID: BioCyc:ECO_PWY-5084
  • 10.1021/bi200936n
  • 10.1042/bj20071119
  • 10.1099/00221287-75-1-197
 Shim DJ, Nemeria NS, Balakrishnan A, Patel H, Song J, Wang J, Jordan F, Farinas ET. Assignment of Function to Histidines 260 and 298 by Engineering the E1 Component of the Escherichia coli 2-Oxoglutarate Dehydrogenase Complex; Substitutions That Lead to Acceptance of Substrates Lacking the 5-Carboxyl Group. Biochemistry. 2011 Aug 10;50(35):7705–9. doi: 10.1021/bi200936n.; Jones D , Perham R. The role of loop and ß-turn residues as structural and functional determinants for the lipoyl domain from the Escherichia coli 2-oxoglutarate dehydrogenase complex. 2007 Dec 21;409(2):357–66. doi: 10.1042/bj20071119.; Guest JR, Creaghan IT. Gene-protein relationships of the alpha-keto acid dehydrogenase complexes of Escherichia coli K12: isolation and characterization of lipoamide dehydrogenase mutants. J Gen Microbiol. 1973 Mar;75(1):197–210. doi: 10.1099/00221287-75-1-197. PMID: 4578971.
L-leucine biosynthesis

Accession ID: BioCyc:ECO_LEUSYN-PWY
  • 10.1128/jb.173.12.3864-3871.1991
 Vartak NB, Liu L, Wang BM, Berg CM. A functional leuABCD operon is required for leucine synthesis by the tyrosine-repressible transaminase in Escherichia coli K-12. J Bacteriol. 1991 Jun;173(12):3864–71. doi: 10.1128/jb.173.12.3864-3871.1991.
2-carboxy-1,4-naphthoquinol biosynthesis

Accession ID: BioCyc:ECO_PWY-5837		 -