Pathways Knowlegdes
Necessitatibus eius consequatur ex aliquid fuga eum quidem sint consectetur velit
| Pathway | DOIs | Note |
|---|---|---|
| toluene degradation to benzoate Accession ID: BioCyc:META_TOLUENE-DEG-CATECHOL-PWY |
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Inoue J, Shaw JP, Rekik M, Harayama S. Overlapping substrate specificities of benzaldehyde dehydrogenase (the xylC gene product) and 2-hydroxymuconic semialdehyde dehydrogenase (the xylG gene product) encoded by TOL plasmid pWW0 of Pseudomonas putida. J Bacteriol. 1995 Mar;177(5):1196–201. doi: 10.1128/jb.177.5.1196-1201.1995.; Shaw JP, Rekik M, Schwager F, Harayama S. Kinetic studies on benzyl alcohol dehydrogenase encoded by TOL plasmid pWWO. A member of the zinc-containing long chain alcohol dehydrogenase family. Journal of Biological Chemistry. 1993 May;268(15):10842–50. doi: 10.1016/s0021-9258(18)82062-2.; SHAW JP, HARAYAMA S. Purification and characterisation of TOL plasmid-encoded benzyl alcohol dehydrogenase and benzaldehyde dehydrogenase of Pseudomonas putida. European Journal of Biochemistry. 1990 Aug;191(3):705–14. doi: 10.1111/j.1432-1033.1990.tb19179.x.; Harayama S, Rekik M, Wubbolts M, Rose K, Leppik RA, Timmis KN. Characterization of five genes in the upper-pathway operon of TOL plasmid pWW0 from Pseudomonas putida and identification of the gene products. J Bacteriol. 1989 Sep;171(9):5048–55. doi: 10.1128/jb.171.9.5048-5055.1989.; Worsey MJ, Williams PA. Metabolism of toluene and xylenes by Pseudomonas (putida (arvilla) mt-2: evidence for a new function of the TOL plasmid. J Bacteriol. 1975 Oct;124(1):7–13. doi: 10.1128/jb.124.1.7-13.1975. |
| toluene degradation IV (aerobic) (via catechol) Accession ID: BioCyc:META_PWY-5178 |
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Marín M, Plumeier I, Pieper DH. Degradation of 2,3-dihydroxybenzoate by a novel meta-cleavage pathway. J Bacteriol. 2012 Aug;194(15):3851–60. PMID: 22609919; PMCID: PMC3416551.; Johnson DR, Park J, Kukor JJ, Abriola LM. Effect of carbon starvation on toluene degradation activity by toluene monooxygenase-expressing bacteria. Biodegradation. 2006 Oct;17(5):437–45. doi: 10.1007/s10532-005-9014-x. PMID: 16477358.; Shaw JP, Rekik M, Schwager F, Harayama S. Kinetic studies on benzyl alcohol dehydrogenase encoded by TOL plasmid pWWO. A member of the zinc-containing long chain alcohol dehydrogenase family. Journal of Biological Chemistry. 1993 May;268(15):10842–50. doi: 10.1016/s0021-9258(18)82062-2. |
| superpathway of aerobic toluene degradation Accession ID: BioCyc:META_PWY-5183 |
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Marín M, Plumeier I, Pieper DH. Degradation of 2,3-dihydroxybenzoate by a novel meta-cleavage pathway. J Bacteriol. 2012 Aug;194(15):3851–60. PMID: 22609919; PMCID: PMC3416551.; Johnson DR, Park J, Kukor JJ, Abriola LM. Effect of carbon starvation on toluene degradation activity by toluene monooxygenase-expressing bacteria. Biodegradation. 2006 Oct;17(5):437–45. doi: 10.1007/s10532-005-9014-x. PMID: 16477358.; Fishman A, Tao Y, Wood TK. Toluene 3-Monooxygenase of Ralstonia pickettii PKO1 Is a para -Hydroxylating Enzyme. J Bacteriol. 2004 May 15;186(10):3117–23. doi: 10.1128/jb.186.10.3117-3123.2004.; Newman LM, Wackett LP. Purification and characterization of toluene 2-monooxygenase from Burkholderia cepacia G4. Biochemistry. 1995 Oct 31;34(43):14066–76. doi: 10.1021/bi00043a012. PMID: 7578004.; Inoue J, Shaw JP, Rekik M, Harayama S. Overlapping substrate specificities of benzaldehyde dehydrogenase (the xylC gene product) and 2-hydroxymuconic semialdehyde dehydrogenase (the xylG gene product) encoded by TOL plasmid pWW0 of Pseudomonas putida. J Bacteriol. 1995 Mar;177(5):1196–201. doi: 10.1128/jb.177.5.1196-1201.1995.; Olsen RH, Kukor JJ, Kaphammer B. A novel toluene-3-monooxygenase pathway cloned from Pseudomonas pickettii PKO1. J Bacteriol. 1994 Jun;176(12):3749–56. doi: 10.1128/jb.176.12.3749-3756.1994.; Shaw JP, Rekik M, Schwager F, Harayama S. Kinetic studies on benzyl alcohol dehydrogenase encoded by TOL plasmid pWWO. A member of the zinc-containing long chain alcohol dehydrogenase family. Journal of Biological Chemistry. 1993 May;268(15):10842–50. doi: 10.1016/s0021-9258(18)82062-2.; Yen KM, Karl MR, Blatt LM, Simon MJ, Winter RB, Fausset PR, Lu HS, Harcourt AA, Chen KK. Cloning and characterization of a Pseudomonas mendocina KR1 gene cluster encoding toluene-4-monooxygenase. J Bacteriol. 1991 Sep;173(17):5315–27. doi: 10.1128/jb.173.17.5315-5327.1991.; Kukor JJ, Olsen RH. Genetic organization and regulation of a meta cleavage pathway for catechols produced from catabolism of toluene, benzene, phenol, and cresols by Pseudomonas pickettii PKO1. J Bacteriol. 1991 Aug;173(15):4587–94. doi: 10.1128/jb.173.15.4587-4594.1991.; Menn FM, Zylstra GJ, Gibson DT. Location and sequence of the todF gene encoding 2-hydroxy-6-oxohepta-2,4-dienoate hydrolase in Pseudomonas putida F1. Gene. 1991 Jul 31;104(1):91–4. doi: 10.1016/0378-1119(91)90470-v. PMID: 1916282. |
| tea aroma glycosidic precursor bioactivation Accession ID: BioCyc:META_PWY-7114 |
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Saino H, Mizutani M, Hiratake J, Sakata K. Expression and biochemical characterization of beta-primeverosidase and application of beta-primeverosylamidine to affinity purification. Biosci Biotechnol Biochem. 2008 Feb;72(2):376–83. doi: 10.1271/bbb.70447. PMID: 18256510.; Mizutani M, Nakanishi H, Ema J, Ma SJ, Noguchi E, Inohara-Ochiai M, Fukuchi-Mizutani M, Nakao M, Sakata K. Cloning of beta-primeverosidase from tea leaves, a key enzyme in tea aroma formation. Plant Physiol. 2002 Dec;130(4):2164–76. PMID: 12481100; PMCID: PMC166728.; Pichersky E, Gershenzon J. The formation and function of plant volatiles: perfumes for pollinator attraction and defense. Curr Opin Plant Biol. 2002 Jun;5(3):237–43. doi: 10.1016/s1369-5266(02)00251-0. PMID: 11960742.; Ma SJ, Watanabe N, Yagi A, Sakata K. The (3R,9R)-3-hydroxy-7,8-dihydro-beta-ionol disaccharide glycoside is an aroma precursor in tea leaves. Phytochemistry. 2001 Apr;56(8):819–25. doi: 10.1016/s0031-9422(00)00361-7. PMID: 11324911.; Wang D, Kurasawa E, Yamaguchi Y, Kubota K, Kobayashi A. Analysis of glycosidically bound aroma precursors in tea leaves. 2. Changes in glycoside contents and glycosidase activities in tea leaves during the black tea manufacturing process. J Agric Food Chem. 2001 Apr;49(4):1900–3. doi: 10.1021/jf001077+. PMID: 11308343.; Ma SJ, Mizutani M, Hiratake J, Hayashi K, Yagi K, Watanabe N, Sakata K. Substrate specificity of beta-primeverosidase, a key enzyme in aroma formation during oolong tea and black tea manufacturing. Biosci Biotechnol Biochem. 2001 Dec;65(12):2719–29. doi: 10.1271/bbb.65.2719. PMID: 11826969.; Wang D, Yoshimura T, Kubota K, Kobayashi A. Analysis of glycosidically bound aroma precursors in tea leaves. 1. Qualitative and quantitative analyses of glycosides with aglycons as aroma compounds. J Agric Food Chem. 2000 Nov;48(11):5411–8. doi: 10.1021/jf000443m. PMID: 11087494.; Pare, Tumlinson. Plant volatiles as a defense against insect herbivores. Plant Physiol. 1999 Oct;121(2):325–32. PMID: 10517823; PMCID: PMC1539229.; Pattnaik S, Subramanyam VR, Bapaji M, Kole CR. Antibacterial and antifungal activity of aromatic constituents of essential oils. Microbios. 1997;89(358):39–46. PMID: 9218354.; Moon J, Watanabe N, Ijima Y, Yagi A, Sakata K. cis- andtrans-Linalool 3,7-Oxides and Methyl Salicylate Glycosides and (Z)-3-Hexenylß- |
| volatile esters biosynthesis (during fruit ripening) Accession ID: BioCyc:META_PWY-6801 |
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Günther CS, Chervin C, Marsh KB, Newcomb RD, Souleyre EJ. Characterisation of two alcohol acyltransferases from kiwifruit (Actinidia spp.) reveals distinct substrate preferences. Phytochemistry. 2011 Jun;72(8):700–10. doi: 10.1016/j.phytochem.2011.02.026. PMID: 21450321.; Boatright J, Negre F, Chen X, Kish CM, Wood B, Peel G, Orlova I, Gang D, Rhodes D, Dudareva N. Understanding in vivo benzenoid metabolism in petunia petal tissue. Plant Physiol. 2004 Aug;135(4):1993–2011. PMID: 15286288; PMCID: PMC520771.; D'Auria JC, Chen F, Pichersky E. Characterization of an acyltransferase capable of synthesizing benzylbenzoate and other volatile esters in flowers and damaged leaves of Clarkia breweri. Plant Physiol. 2002 Sep;130(1):466–76. PMID: 12226525; PMCID: PMC166578. |
| tRNA charging Accession ID: BioCyc:ECO_TRNA-CHARGING-PWY |
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| volatile benzenoid biosynthesis I (ester formation) Accession ID: BioCyc:ARA_PWY-4203 |
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Dudareva N, Pichersky E, Gershenzon J. Biochemistry of plant volatiles. Plant Physiol. 2004 Aug;135(4):1893–902. PMID: 15326281; PMCID: PMC520761.; Chen F, D'Auria JC, Tholl D, Ross JR, Gershenzon J, Noel JP, Pichersky E. An Arabidopsis thaliana gene for methylsalicylate biosynthesis, identified by a biochemical genomics approach, has a role in defense. The Plant Journal. 2003 Nov 18;36(5):577–88. doi: 10.1046/j.1365-313x.2003.01902.x.; Degenhardt J, Gershenzon J, Baldwin IT, Kessler A. Attracting friends to feast on foes: engineering terpene emission to make crop plants more attractive to herbivore enemies. Curr Opin Biotechnol. 2003 Apr;14(2):169–76. doi: 10.1016/s0958-1669(03)00025-9. PMID: 12732318.; D'Auria JC, Chen F, Pichersky E. Characterization of an acyltransferase capable of synthesizing benzylbenzoate and other volatile esters in flowers and damaged leaves of Clarkia breweri. Plant Physiol. 2002 Sep;130(1):466–76. PMID: 12226525; PMCID: PMC166578.; Dudareva N, Raguso RA, Wang J, Ross JR, Pichersky E. Floral scent production in Clarkia breweri. III. Enzymatic synthesis and emission of benzenoid esters. Plant Physiol. 1998 Feb;116(2):599–604. PMID: 9489012; PMCID: PMC35117. |
| benzoate biosynthesis I (CoA-dependent, β-oxidative) Accession ID: BioCyc:ARA_PWY-6443 |
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| volatile benzenoid biosynthesis I (ester formation) Accession ID: BioCyc:META_PWY-4203 |
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Dudareva N, Pichersky E, Gershenzon J. Biochemistry of plant volatiles. Plant Physiol. 2004 Aug;135(4):1893–902. PMID: 15326281; PMCID: PMC520761.; Boatright J, Negre F, Chen X, Kish CM, Wood B, Peel G, Orlova I, Gang D, Rhodes D, Dudareva N. Understanding in vivo benzenoid metabolism in petunia petal tissue. Plant Physiol. 2004 Aug;135(4):1993–2011. PMID: 15286288; PMCID: PMC520771.; Chen F, D'Auria JC, Tholl D, Ross JR, Gershenzon J, Noel JP, Pichersky E. An Arabidopsis thaliana gene for methylsalicylate biosynthesis, identified by a biochemical genomics approach, has a role in defense. The Plant Journal. 2003 Nov 18;36(5):577–88. doi: 10.1046/j.1365-313x.2003.01902.x.; Degenhardt J, Gershenzon J, Baldwin IT, Kessler A. Attracting friends to feast on foes: engineering terpene emission to make crop plants more attractive to herbivore enemies. Curr Opin Biotechnol. 2003 Apr;14(2):169–76. doi: 10.1016/s0958-1669(03)00025-9. PMID: 12732318.; D'Auria JC, Chen F, Pichersky E. Characterization of an acyltransferase capable of synthesizing benzylbenzoate and other volatile esters in flowers and damaged leaves of Clarkia breweri. Plant Physiol. 2002 Sep;130(1):466–76. PMID: 12226525; PMCID: PMC166578.; Dudareva N, Raguso RA, Wang J, Ross JR, Pichersky E. Floral scent production in Clarkia breweri. III. Enzymatic synthesis and emission of benzenoid esters. Plant Physiol. 1998 Feb;116(2):599–604. PMID: 9489012; PMCID: PMC35117. |
| benzoate biosynthesis I (CoA-dependent, β-oxidative) Accession ID: BioCyc:META_PWY-6443 |
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Van Moerkercke A, Schauvinhold I, Pichersky E, Haring MA, Schuurink RC. A plant thiolase involved in benzoic acid biosynthesis and volatile benzenoid production. Plant J. 2009 Oct;60(2):292–302. doi: 10.1111/j.1365-313x.2009.03953.x. PMID: 19659733.; Boatright J, Negre F, Chen X, Kish CM, Wood B, Peel G, Orlova I, Gang D, Rhodes D, Dudareva N. Understanding in vivo benzenoid metabolism in petunia petal tissue. Plant Physiol. 2004 Aug;135(4):1993–2011. PMID: 15286288; PMCID: PMC520771.; D'Auria JC, Chen F, Pichersky E. Characterization of an acyltransferase capable of synthesizing benzylbenzoate and other volatile esters in flowers and damaged leaves of Clarkia breweri. Plant Physiol. 2002 Sep;130(1):466–76. PMID: 12226525; PMCID: PMC166578.; Jarvis AP, Schaaf O, Oldham NJ. 3-hydroxy-3-phenylpropanoic acid is an intermediate in the biosynthesis of benzoic acid and salicylic acid but benzaldehyde is not. Planta. 2000 Dec;212(1):119–26. doi: 10.1007/s004250000377. PMID: 11219576.; Ribnicky, Shulaev, Raskin. Intermediates of salicylic acid biosynthesis in tobacco . Plant Physiol. 1998 Oct;118(2):565–72. PMID: 9765542; PMCID: PMC34832. |
| salicin biosynthesis Accession ID: BioCyc:META_PWY-6766 |
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Babst BA, Harding SA, Tsai C. Biosynthesis of Phenolic Glycosides from Phenylpropanoid and Benzenoid Precursors in Populus. Journal of Chemical Ecology. 2010 Feb 23;36(3):286–97. doi: 10.1007/s10886-010-9757-7.; Shaw JP, Rekik M, Schwager F, Harayama S. Kinetic studies on benzyl alcohol dehydrogenase encoded by TOL plasmid pWWO. A member of the zinc-containing long chain alcohol dehydrogenase family. Journal of Biological Chemistry. 1993 May;268(15):10842–50. doi: 10.1016/s0021-9258(18)82062-2. |
| toluene degradation to benzoate Accession ID: BioCyc:SCO_TOLUENE-DEG-CATECHOL-PWY |
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| salicortin biosynthesis Accession ID: BioCyc:META_PWY-6763 |
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Babst BA, Harding SA, Tsai C. Biosynthesis of Phenolic Glycosides from Phenylpropanoid and Benzenoid Precursors in Populus. Journal of Chemical Ecology. 2010 Feb 23;36(3):286–97. doi: 10.1007/s10886-010-9757-7.; Boatright J, Negre F, Chen X, Kish CM, Wood B, Peel G, Orlova I, Gang D, Rhodes D, Dudareva N. Understanding in vivo benzenoid metabolism in petunia petal tissue. Plant Physiol. 2004 Aug;135(4):1993–2011. PMID: 15286288; PMCID: PMC520771.; D'Auria JC, Chen F, Pichersky E. Characterization of an acyltransferase capable of synthesizing benzylbenzoate and other volatile esters in flowers and damaged leaves of Clarkia breweri. Plant Physiol. 2002 Sep;130(1):466–76. PMID: 12226525; PMCID: PMC166578.; Shaw JP, Rekik M, Schwager F, Harayama S. Kinetic studies on benzyl alcohol dehydrogenase encoded by TOL plasmid pWWO. A member of the zinc-containing long chain alcohol dehydrogenase family. Journal of Biological Chemistry. 1993 May;268(15):10842–50. doi: 10.1016/s0021-9258(18)82062-2. |
| tRNA charging Accession ID: BioCyc:META_TRNA-CHARGING-PWY |
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| amygdalin and prunasin degradation Accession ID: BioCyc:META_PWY-6011 |
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Swain E, Poulton JE. Utilization of Amygdalin during Seedling Development of Prunus serotina. Plant Physiol. 1994 Oct;106(2):437–45. PMID: 12232341; PMCID: PMC159548. |
| toluene degradation VI (anaerobic) Accession ID: BioCyc:META_PWY-5184 |
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Kung JW, Baumann S, von Bergen M, Müller M, Hagedoorn PL, Hagen WR, Boll M. Reversible biological Birch reduction at an extremely low redox potential. J Am Chem Soc. 2010 Jul 21;132(28):9850–6. doi: 10.1021/ja103448u. PMID: 20578740.; Beller HR, Spormann AM. Anaerobic activation of toluene and o-xylene by addition to fumarate in denitrifying strain T. J Bacteriol. 1997 Feb;179(3):670–6. doi: 10.1128/jb.179.3.670-676.1997.; Biegert T, Fuchs G, Heider J. Evidence That Anaerobic Oxidation of Toluene in the Denitrifying Bacterium Thauera aromatica is Initiated by Formation of Benzylsuccinate from Toluene and Fumarate. European Journal of Biochemistry. 1996 Jun;238(3):661–8. doi: 10.1111/j.1432-1033.1996.0661w.x.; Boll M, Fuchs G. Benzoyl-coenzyme A reductase (dearomatizing), a key enzyme of anaerobic aromatic metabolism. ATP dependence of the reaction, purification and some properties of the enzyme from Thauera aromatica strain K172. Eur J Biochem. 1995 Dec 15;234(3):921–33. doi: 10.1111/j.1432-1033.1995.921_a.x. PMID: 8575453. |
| toluene degradation to benzoyl-CoA (anaerobic) Accession ID: BioCyc:META_PWY-81 |
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Leuthner B, Heider J. Anaerobic Toluene Catabolism of Thauera aromatica : the bbs Operon Codes for Enzymes of ß Oxidation of the Intermediate Benzylsuccinate. J Bacteriol. 2000 Jan 15;182(2):272–7. doi: 10.1128/jb.182.2.272-277.2000. |
| Hexuronide and Hexuronate Degradation Accession ID: PathBank:SMP0000854 |
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| Glycerol Metabolism II Accession ID: PathBank:SMP0000932 |
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| Glycerol Metabolism III (sn-Glycero-3-Phosphoethanolamine) Accession ID: PathBank:SMP0000933 |
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