Pathways Knowlegdes
Biological pathway database
| Pathway | DOIs | Note |
|---|---|---|
| adenosine deoxyribonucleotides de novo biosynthesis Accession ID: BioCyc:META_PWY-7227 |
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| sulfur oxidation II (Fe+3-dependent) Accession ID: BioCyc:META_FESULFOX-PWY |
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Sugio T, Katagiri T, Moriyama M, Zh?n YL, Inagaki K, Tano T. Existence of a new type of sulfite oxidase which utilizes ferric ions as an electron acceptor in Thiobacillus ferrooxidans. Appl Environ Microbiol. 1988 Jan;54(1):153–7. doi: 10.1128/aem.54.1.153-157.1988. |
| superpathway of adenosine nucleotides de novo biosynthesis I Accession ID: BioCyc:META_PWY-7229 |
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| sulfide oxidation I (sulfide-quinone reductase) Accession ID: BioCyc:META_P222-PWY |
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Reinartz M, Tschäpe J, Brüser T, Trüper HG, Dahl C. Sulfide oxidation in the phototrophic sulfur bacterium Chromatium vinosum. Arch Microbiol. 1998 Jul;170(1):59–68. doi: 10.1007/s002030050615. PMID: 9639604. |
| abscisic acid degradation to neophaseic acid Accession ID: BioCyc:META_PWY-7640 |
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Vashegyi I, Marozsán-Tóth Z, Galiba G, Dobrev PI, Vankova R, Tóth B. Cold response of dedifferentiated barley cells at the gene expression, hormone composition, and freezing tolerance levels: studies on callus cultures. Mol Biotechnol. 2013 Jun;54(2):337–49. doi: 10.1007/s12033-012-9569-9. PMID: 22669585.; Kosová K, Prášil IT, Vítámvás P, Dobrev P, Motyka V, Floková K, Novák O, Turecková V, Rolcik J, Pešek B, Trávnicková A, Gaudinová A, Galiba G, Janda T, Vlasáková E, Prášilová P, Vanková R. Complex phytohormone responses during the cold acclimation of two wheat cultivars differing in cold tolerance, winter Samanta and spring Sandra. J Plant Physiol. 2012 Apr 15;169(6):567–76. doi: 10.1016/j.jplph.2011.12.013. PMID: 22304971.; Kepka M, Benson CL, Gonugunta VK, Nelson KM, Christmann A, Grill E, Abrams SR. Action of natural abscisic acid precursors and catabolites on abscisic acid receptor complexes. Plant Physiol. 2011 Dec;157(4):2108–19. PMID: 21976481; PMCID: PMC3327214.; Okamoto M, Kushiro T, Jikumaru Y, Abrams SR, Kamiya Y, Seki M, Nambara E. ABA 9'-hydroxylation is catalyzed by CYP707A in Arabidopsis. Phytochemistry. 2011 Jun;72(8):717–22. doi: 10.1016/j.phytochem.2011.02.004. PMID: 21414645.; Turecková V, Novák O, Strnad M. Profiling ABA metabolites in Nicotiana tabacum L. leaves by ultra-performance liquid chromatography-electrospray tandem mass spectrometry. Talanta. 2009 Nov 15;80(1):390–9. doi: 10.1016/j.talanta.2009.06.027. PMID: 19782241.; Jadhav AS, Taylor DC, Giblin M, Ferrie AM, Ambrose SJ, Ross AR, Nelson KM, Irina Zaharia L, Sharma N, Anderson M, Fobert PR, Abrams SR. Hormonal regulation of oil accumulation in Brassica seeds: metabolism and biological activity of ABA, 7'-, 8'- and 9'-hydroxy ABA in microspore derived embryos of B. napus. Phytochemistry. 2008 Nov;69(15):2678–88. doi: 10.1016/j.phytochem.2008.08.010. PMID: 18823922.; Yamaguchi-Shinozaki K, Shinozaki K. Transcriptional regulatory networks in cellular responses and tolerance to dehydration and cold stresses. Annu Rev Plant Biol. 2006;57():781–803. doi: 10.1146/annurev.arplant.57.032905.105444. PMID: 16669782.; Nambara E, Marion-Poll A. Abscisic acid biosynthesis and catabolism. Annu Rev Plant Biol. 2005;56():165–85. doi: 10.1146/annurev.arplant.56.032604.144046. PMID: 15862093.; Zhou R, Cutler AJ, Ambrose SJ, Galka MM, Nelson KM, Squires TM, Loewen MK, Jadhav AS, Ross AR, Taylor DC, Abrams SR. A new abscisic acid catabolic pathway. Plant Physiol. 2004 Jan;134(1):361–9. PMID: 14671016; PMCID: PMC316315. |
| abscisic acid degradation by glucosylation Accession ID: BioCyc:META_PWY-5272 |
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Dong T, Xu ZY, Park Y, Kim DH, Lee Y, Hwang I. Abscisic acid uridine diphosphate glucosyltransferases play a crucial role in abscisic acid homeostasis in Arabidopsis. Plant Physiol. 2014 May;165(1):277–89. PMID: 24676855; PMCID: PMC4012586.; Okamoto M, Kushiro T, Jikumaru Y, Abrams SR, Kamiya Y, Seki M, Nambara E. ABA 9'-hydroxylation is catalyzed by CYP707A in Arabidopsis. Phytochemistry. 2011 Jun;72(8):717–22. doi: 10.1016/j.phytochem.2011.02.004. PMID: 21414645.; Kato-Noguchi H, Tanaka Y. Effect of ABA-beta-D-glucopyranosyl ester and activity of ABA-beta-D-glucosidase in Arabidopsis thaliana. J Plant Physiol. 2008 May 05;165(7):788–90. doi: 10.1016/j.jplph.2007.04.005. PMID: 17923167.; Lee KH, Piao HL, Kim HY, Choi SM, Jiang F, Hartung W, Hwang I, Kwak JM, Lee IJ, Hwang I. Activation of glucosidase via stress-induced polymerization rapidly increases active pools of abscisic acid. Cell. 2006 Sep 22;126(6):1109–20. doi: 10.1016/j.cell.2006.07.034. PMID: 16990135.; Nambara E, Marion-Poll A. Abscisic acid biosynthesis and catabolism. Annu Rev Plant Biol. 2005;56():165–85. doi: 10.1146/annurev.arplant.56.032604.144046. PMID: 15862093.; Xu ZJ, Nakajima M, Suzuki Y, Yamaguchi I. Cloning and characterization of the abscisic acid-specific glucosyltransferase gene from adzuki bean seedlings. Plant Physiol. 2002 Jul;129(3):1285–95. PMID: 12114582; PMCID: PMC166522. |
| abscisic acid degradation to phaseic acid Accession ID: BioCyc:META_PWY-5271 |
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Nambara E, Marion-Poll A. Abscisic acid biosynthesis and catabolism. Annu Rev Plant Biol. 2005;56():165–85. doi: 10.1146/annurev.arplant.56.032604.144046. PMID: 15862093.; Saito S, Hirai N, Matsumoto C, Ohigashi H, Ohta D, Sakata K, Mizutani M. Arabidopsis CYP707As encode (+)-abscisic acid 8'-hydroxylase, a key enzyme in the oxidative catabolism of abscisic acid. Plant Physiol. 2004 Apr;134(4):1439–49. PMID: 15064374; PMCID: PMC419820.; Kushiro T, Okamoto M, Nakabayashi K, Yamagishi K, Kitamura S, Asami T, Hirai N, Koshiba T, Kamiya Y, Nambara E. The Arabidopsis cytochrome P450 CYP707A encodes ABA 8'-hydroxylases: key enzymes in ABA catabolism. EMBO J. 2004 Apr 07;23(7):1647–56. PMID: 15044947; PMCID: PMC391058.; Krochko, Abrams, Loewen, Abrams, Cutler. (+)-Abscisic acid 8'-hydroxylase is a cytochrome P450 monooxygenase . Plant Physiol. 1998 Nov;118(3):849–60. PMID: 9808729; PMCID: PMC34795. |
| citronellol degradation Accession ID: BioCyc:META_PWY-6670 |
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Förster-Fromme K, Jendrossek D. Catabolism of citronellol and related acyclic terpenoids in pseudomonads. Applied Microbiology and Biotechnology. 2010 May 20;87(3):859–69. doi: 10.1007/s00253-010-2644-x.; Förster-Fromme K, Chattopadhyay A, Jendrossek D. Biochemical characterization of AtuD from Pseudomonas aeruginosa, the first member of a new subgroup of acyl-CoA dehydrogenases with specificity for citronellyl-CoA. Microbiology (Reading). 2008 Mar;154(Pt 3):789–96. doi: 10.1099/mic.0.2007/014530-0. PMID: 18310025. |
| β myrcene degradation Accession ID: BioCyc:META_PWY-7136 |
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Lüddeke F, Wülfing A, Timke M, Germer F, Weber J, Dikfidan A, Rahnfeld T, Linder D, Meyerdierks A, Harder J. Geraniol and geranial dehydrogenases induced in anaerobic monoterpene degradation by Castellaniella defragrans. Appl Environ Microbiol. 2012 Apr;78(7):2128–36. PMID: 22286981; PMCID: PMC3302621.; Lüddeke F, Harder J. Enantiospecific (S)-(+)-linalool formation from beta-myrcene by linalool dehydratase-isomerase. Z Naturforsch C J Biosci. 2011 Jul;66(7-8):409–12. doi: 10.1515/znc-2011-7-813. PMID: 21950166.; Brodkorb D, Gottschall M, Marmulla R, Lüddeke F, Harder J. Linalool Dehydratase-Isomerase, a Bifunctional Enzyme in the Anaerobic Degradation of Monoterpenes. Journal of Biological Chemistry. 2010 Oct;285(40):30436–42. doi: 10.1074/jbc.m109.084244.; Vladimirova-Kitova L, Deneva T, Marinov B. Predictors of the intima-media thickness of carotid artery in asymptomatic newly detected severe hypercholesterolemic patients. Clin Physiol Funct Imaging. 2010 Jul;30(4):250–9. doi: 10.1111/j.1475-097x.2010.00935.x. PMID: 20662876.; Wolken WA, van der Werf MJ. Geraniol biotransformation-pathway in spores of Penicillium digitatum. Appl Microbiol Biotechnol. 2001 Dec;57(5-6):731–7. doi: 10.1007/s002530100821. PMID: 11778886. |
| cis-genanyl-CoA degradation Accession ID: BioCyc:META_PWY-6672 |
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Förster-Fromme K, Jendrossek D. Catabolism of citronellol and related acyclic terpenoids in pseudomonads. Applied Microbiology and Biotechnology. 2010 May 20;87(3):859–69. doi: 10.1007/s00253-010-2644-x. |
| L-alanine degradation IV Accession ID: BioCyc:META_PWY1-2 |
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CHOWDHURY EK, SAITOH T, NAGATA S, ASHIUCHI M, MISONO H. Alanine Dehydrogenase fromEnterobacter aerogenes: Purification, Characterization, and Primary Structure. Bioscience, Biotechnology, and Biochemistry. 1998 Jan;62(12):2357–63. doi: 10.1271/bbb.62.2357.; Siranosian KJ, Ireton K, Grossman AD. Alanine dehydrogenase (ald) is required for normal sporulation in Bacillus subtilis. J Bacteriol. 1993 Nov;175(21):6789–96. doi: 10.1128/jb.175.21.6789-6796.1993.; Porumb H, Vancea D, Muresan L, Presecan E, Lascu I, Petrescu I, Porumb T, Pop R, Bârzu O. Structural and catalytic properties of L-alanine dehydrogenase from Bacillus cereus. Journal of Biological Chemistry. 1987 Apr;262(10):4610–5. doi: 10.1016/s0021-9258(18)61237-2.; Nitta Y, Yasuda Y, Tochikubo K, Hachisuka Y. |
| L-alanine degradation II (to D-lactate) Accession ID: BioCyc:META_ALACAT2-PWY |
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Schweiger G, Buckel W. On the dehydration of (R)-lactate in the fermentation of alanine to propionate by Clostridium propionicum. FEBS Letters. 1984 Jun 04;171(1):79–84. doi: 10.1016/0014-5793(84)80463-9. |
| propane degradation I Accession ID: BioCyc:META_PWY-7774 |
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Kotani T, Yurimoto H, Kato N, Sakai Y. Novel acetone metabolism in a propane-utilizing bacterium, Gordonia sp. strain TY-5. J Bacteriol. 2007 Feb;189(3):886–93. PMID: 17071761; PMCID: PMC1797311.; Kotani T, Yamamoto T, Yurimoto H, Sakai Y, Kato N. PropaneMonooxygenase and NAD + -Dependent Secondary AlcoholDehydrogenase in Propane Metabolism by Gordonia sp.StrainTY-5. J Bacteriol. 2003 Dec 15;185(24):7120–8. doi: 10.1128/jb.185.24.7120-7128.2003.; Gidda SK, Miersch O, Levitin A, Schmidt J, Wasternack C, Varin L. Biochemical and Molecular Characterization of a Hydroxyjasmonate Sulfotransferase from Arabidopsis thaliana. Journal of Biological Chemistry. 2003 May;278(20):17895–900. doi: 10.1074/jbc.m211943200. |
| dTDP-L-daunosamine biosynthesis Accession ID: BioCyc:META_PWY-7814 |
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Niraula NP, Kim SH, Sohng JK, Kim ES. Biotechnological doxorubicin production: pathway and regulation engineering of strains for enhanced production. Appl Microbiol Biotechnol. 2010 Jul;87(4):1187–94. doi: 10.1007/s00253-010-2675-3. PMID: 20508927. |
| 3-chlorobenzoate degradation I (via chlorocatechol) Accession ID: BioCyc:META_PWY-6088 |
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Harayama S, Rekik M, Bairoch A, Neidle EL, Ornston LN. Potential DNA slippage structures acquired during evolutionary divergence of Acinetobacter calcoaceticus chromosomal benABC and Pseudomonas putida TOL pWW0 plasmid xylXYZ, genes encoding benzoate dioxygenases. J Bacteriol. 1991 Dec;173(23):7540–8. doi: 10.1128/jb.173.23.7540-7548.1991.; Dorn E, Hellwig M, Reineke W, Knackmuss HJ. Isolation and characterization of a 3-chlorobenzoate degrading pseudomonad. Arch Microbiol. 1974;99(1):61–70. doi: 10.1007/bf00696222. PMID: 4852581. |
| methylthiopropanoate degradation I (cleavage) Accession ID: BioCyc:META_PWY-6048 |
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Reisch CR, Stoudemayer MJ, Varaljay VA, Amster IJ, Moran MA, Whitman WB. Novel pathway for assimilation of dimethylsulphoniopropionate widespread in marine bacteria. Nature. 2011 May 12;473(7346):208–11. doi: 10.1038/nature10078. PMID: 21562561. |
| naphthalene degradation (anaerobic) Accession ID: BioCyc:META_PWY-7620 |
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Estelmann S, Blank I, Feldmann A, Boll M. Two distinct old yellow enzymes are involved in naphthyl ring reduction during anaerobic naphthalene degradation. Mol Microbiol. 2015 Jan;95(2):162–72. doi: 10.1111/mmi.12875. PMID: 25424741.; Eberlein C, Estelmann S, Seifert J, von Bergen M, Müller M, Meckenstock RU, Boll M. Identification and characterization of 2-naphthoyl-coenzyme A reductase, the prototype of a novel class of dearomatizing reductases. Mol Microbiol. 2013 Jun;88(5):1032–9. doi: 10.1111/mmi.12238. PMID: 23646996.; Mouttaki H, Johannes J, Meckenstock RU. Identification of naphthalene carboxylase as a prototype for the anaerobic activation of non-substituted aromatic hydrocarbons. Environ Microbiol. 2012 Oct;14(10):2770–4. doi: 10.1111/j.1462-2920.2012.02768.x. PMID: 22564331.; Bergmann FD, Selesi D, Meckenstock RU. Identification of new enzymes potentially involved in anaerobic naphthalene degradation by the sulfate-reducing enrichment culture N47. Arch Microbiol. 2011 Apr;193(4):241–50. doi: 10.1007/s00203-010-0667-4. PMID: 21221530. |
| styrene degradation Accession ID: BioCyc:META_PWY-6941 |
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Beltrametti F, Marconi AM, Bestetti G, Colombo C, Galli E, Ruzzi M, Zennaro E. Sequencing and functional analysis of styrene catabolism genes from Pseudomonas fluorescens ST. Appl Environ Microbiol. 1997 Jun;63(6):2232–9. doi: 10.1128/aem.63.6.2232-2239.1997.; Hartmans S, van der Werf MJ, de Bont JA. Bacterial degradation of styrene involving a novel flavin adenine dinucleotide-dependent styrene monooxygenase. Appl Environ Microbiol. 1990 May;56(5):1347–51. doi: 10.1128/aem.56.5.1347-1351.1990. |
| p-cymene degradation Accession ID: BioCyc:META_PWY-5266 |
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Eaton RW. p-Cumate catabolic pathway in Pseudomonas putida Fl: cloning and characterization of DNA carrying the cmt operon. J Bacteriol. 1996 Mar;178(5):1351–62. doi: 10.1128/jb.178.5.1351-1362.1996.; DeFrank JJ, Ribbons DW. p-cymene pathway in Pseudomonas putida: initial reactions. J Bacteriol. 1977 Mar;129(3):1356–64. doi: 10.1128/jb.129.3.1356-1364.1977.; DeFrank JJ, Ribbons DW. p-Cymene pathway in Pseudomonas putida: ring cleavage of 2,3-dihydroxy-p-cumate and subsequent reactions. J Bacteriol. 1977 Mar;129(3):1365–74. doi: 10.1128/jb.129.3.1365-1374.1977. |
| brassinosteroids inactivation Accession ID: BioCyc:META_PWY-6546 |
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Marsolais F, Boyd J, Paredes Y, Schinas AM, Garcia M, Elzein S, Varin L. Molecular and biochemical characterization of two brassinosteroid sulfotransferases from Arabidopsis, AtST4a (At2g14920) and AtST1 (At2g03760). Planta. 2007 Apr;225(5):1233–44. doi: 10.1007/s00425-006-0413-y. PMID: 17039368.; Poppenberger B, Fujioka S, Soeno K, George GL, Vaistij FE, Hiranuma S, Seto H, Takatsuto S, Adam G, Yoshida S, Bowles D. The UGT73C5 of Arabidopsis thaliana glucosylates brassinosteroids. Proc. Natl. Acad. Sci. U.S.A. 2005 Oct 07;102(42):15253–8. doi: 10.1073/pnas.0504279102.; Turk EM, Fujioka S, Seto H, Shimada Y, Takatsuto S, Yoshida S, Denzel MA, Torres QI, Neff MM. CYP72B1 inactivates brassinosteroid hormones: an intersection between photomorphogenesis and plant steroid signal transduction. Plant Physiol. 2003 Dec;133(4):1643–53. PMID: 14605216; PMCID: PMC300720. |