Pathways Knowlegdes

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Pathway DOIs Note
superpathway of aromatic compound degradation via 2-hydroxypentadienoate

Accession ID: BioCyc:META_PWY-6954
  • 10.1016/0378-1119(91)90470-v
  • 10.1093/genetics/66.2.245
  • 10.1111/j.1574-6968.2009.01699.x
  • 10.1128/jb.00430-12
  • 10.1128/jb.00840-09
  • 10.1128/jb.128.1.182-191.1976
  • 10.1128/jb.173.15.4587-4594.1991
  • 10.1146/annurev.micro.50.1.553
 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.; Kasai D, Fujinami T, Abe T, Mase K, Katayama Y, Fukuda M, Masai E. Uncovering the protocatechuate 2,3-cleavage pathway genes. J Bacteriol. 2009 Nov;191(21):6758–68. PMID: 19717587; PMCID: PMC2795304.; Takenaka S, Sato T, Koshiya J, Murakami S, Aoki K. Gene cloning and characterization of a deaminase from the 4-amino-3-hydroxybenzoate-assimilating Bordetella sp. strain 10d. FEMS Microbiol Lett. 2009 Sep;298(1):93–8. doi: 10.1111/j.1574-6968.2009.01699.x. PMID: 19594622.; Harwood CS, Parales RE. The beta-ketoadipate pathway and the biology of self-identity. Annu Rev Microbiol. 1996;50():553–90. doi: 10.1146/annurev.micro.50.1.553. PMID: 8905091.; 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.; Kishore G, Sugumaran M, Vaidyanathan CS. Metabolism of DL-(+/-)-phenylalanine by Aspergillus niger. J Bacteriol. 1976 Oct;128(1):182–91. doi: 10.1128/jb.128.1.182-191.1976.; Wheelis ML, Stanier RY. The genetic control of dissimilatory pathways in Pseudomonas putida. Genetics. 1970 Oct;66(2):245–66. PMID: 5525301; PMCID: PMC1212492.
naphthalene degradation (aerobic)

Accession ID: BioCyc:AGRO_PWY-5427		 -
salicin biosynthesis

Accession ID: BioCyc:META_PWY-6766
  • 10.1007/s10886-010-9757-7
  • 10.1016/s0021-9258(18)82062-2
 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.
naphthalene degradation (aerobic)

Accession ID: BioCyc:AURANTIMONAS_PWY-5427		 -
naphthalene degradation (aerobic)

Accession ID: BioCyc:META_PWY-5427
  • 10.1128/jb.174.23.7542-7554.1992
 Eaton RW, Chapman PJ. Bacterial metabolism of naphthalene: construction and use of recombinant bacteria to study ring cleavage of 1,2-dihydroxynaphthalene and subsequent reactions. J Bacteriol. 1992 Dec;174(23):7542–54. doi: 10.1128/jb.174.23.7542-7554.1992.
naphthalene degradation to acetyl-CoA

Accession ID: BioCyc:META_PWY-6956
  • 10.1128/jb.174.23.7542-7554.1992
 Eaton RW, Chapman PJ. Bacterial metabolism of naphthalene: construction and use of recombinant bacteria to study ring cleavage of 1,2-dihydroxynaphthalene and subsequent reactions. J Bacteriol. 1992 Dec;174(23):7542–54. doi: 10.1128/jb.174.23.7542-7554.1992.
salicin biosynthesis

Accession ID: PlantCyc:PLANT_PWY-6766
  • 10.1007/s10886-010-9757-7
  • 10.1016/s0021-9258(18)82062-2
 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.
salicortin biosynthesis

Accession ID: PlantCyc:POPLAR_PWY-6763
  • 10.1007/s10886-010-9757-7
  • 10.1016/s0021-9258(18)82062-2
 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.
salicin biosynthesis

Accession ID: PlantCyc:POPLAR_PWY-6766
  • 10.1007/s10886-010-9757-7
  • 10.1016/s0021-9258(18)82062-2
 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.