Pathways Knowlegdes

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Pathway DOIs Note
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.
formate to trimethylamine N-oxide electron transfer

Accession ID: BioCyc:META_PWY0-1355		 -
nitrifier denitrification

Accession ID: BioCyc:META_PWY-7084
  • 10.1042/bj1261181
  • 10.1128/aem.49.5.1134-1141.1985
 Poth M, Focht DD. 15 N Kinetic Analysis of N 2 O Production by Nitrosomonas europaea : an Examination of Nitrifier Denitrification. Appl Environ Microbiol. 1985 May;49(5):1134–41. doi: 10.1128/aem.49.5.1134-1141.1985.; Ritchie GA, Nicholas DJ. Identification of the sources of nitrous oxide produced by oxidative and reductive processes in Nitrosomonas europaea. Biochem J. 1972 Mar;126(5):1181–91. PMID: 5073730; PMCID: PMC1178541.
nitrate reduction I (denitrification)

Accession ID: BioCyc:META_DENITRIFICATION-PWY
  • 10.1128/mmbr.46.1.43-70.1982
  • 10.1146/annurev.mi.30.100176.001325
 Knowles R. Denitrification. Microbiol Rev. 1982 Mar;46(1):43–70. doi: 10.1128/mr.46.1.43-70.1982.; Delwiche CC, Bryan BA. Denitrification. Annu Rev Microbiol. 1976;30():241–62. doi: 10.1146/annurev.mi.30.100176.001325. PMID: 10827.
D-galactarate degradation I

Accession ID: BioCyc:ECO_GALACTARDEG-PWY		 -
formate to nitrite electron transfer

Accession ID: BioCyc:ECO_PWY0-1585
  • 10.1007/s002030050515
  • 10.1016/s0168-6445(02)00111-0
  • 10.1099/00221287-128-1-219
  • 10.1111/j.1432-1033.1979.tb12966.x
 Simon J. Enzymology and bioenergetics of respiratory nitrite ammonification. FEMS Microbiol Rev. 2002 Aug;26(3):285–309. doi: 10.1111/j.1574-6976.2002.tb00616.x. PMID: 12165429.; Tyson K, Metheringham R, Griffiths L, Cole J. Characterisation of Escherichia coli K-12 mutants defective in formate-dependent nitrite reduction: essential roles for hemN and the menFDBCE operon. Arch Microbiol. 1997 Nov;168(5):403–11. doi: 10.1007/s002030050515. PMID: 9325429.; Pope NR, Cole JA. Generation of a membrane potential by one of two independent pathways for nitrite reduction by Escherichia coli. J Gen Microbiol. 1982 Jan;128(1):219–22. doi: 10.1099/00221287-128-1-219. PMID: 6283015.; Abou-Jaoudé A, Chippaux M, Pascal MC. Formate-nitrite reduction in Escherchia coli K12. 1. Physiological study of the system. Eur J Biochem. 1979 Apr 02;95(2):309–14. doi: 10.1111/j.1432-1033.1979.tb12966.x. PMID: 37075.
cyanide detoxification I

Accession ID: BioCyc:ARA_ASPSYNII-PWY
  • 10.1007/s11103-005-6217-9
  • 10.1074/jbc.m007890200
  • 10.1104/pp.123.3.1163
 Piotrowski M, Volmer JJ. Cyanide metabolism in higher plants: cyanoalanine hydratase is a NIT4 homolog. Plant Mol Biol. 2006 May;61(1-2):111–22. doi: 10.1007/s11103-005-6217-9. PMID: 16786295.; Piotrowski M, Schönfelder S, Weiler EW. The Arabidopsis thaliana isogene NIT4 and its orthologs in tobacco encode beta-cyano-L-alanine hydratase/nitrilase. J Biol Chem. 2001 Jan 26;276(4):2616–21. doi: 10.1074/jbc.m007890200. PMID: 11060302.; Hatzfeld Y, Maruyama A, Schmidt A, Noji M, Ishizawa K, Saito K. beta-Cyanoalanine synthase is a mitochondrial cysteine synthase-like protein in spinach and Arabidopsis. Plant Physiol. 2000 Jul;123(3):1163–71. PMID: 10889265; PMCID: PMC59079.
fatty acid α-oxidation I

Accession ID: BioCyc:ARA_PWY-2501
  • 10.1016/s0090-6980(02)00040-0
  • 10.1046/j.1365-313x.2002.01195.x
  • 10.1074/jbc.274.35.24503
  • 10.1074/jbc.m310514200
  • 10.1104/pp.123.4.1545
 Hamberg M, Sanz A, Rodriguez MJ, Calvo AP, Castresana C. Activation of the fatty acid alpha-dioxygenase pathway during bacterial infection of tobacco leaves. Formation of oxylipins protecting against cell death. J Biol Chem. 2003 Dec 19;278(51):51796–805. doi: 10.1074/jbc.m310514200. PMID: 14522973.; Hamberg M, Ponce de León I, Sanz A, Castresana C. Fatty acid alpha-dioxygenases. Prostaglandins Other Lipid Mediat. 2002 Aug;68-69():363–74. doi: 10.1016/s0090-6980(02)00040-0. PMID: 12432929.; De León IP, Sanz A, Hamberg M, Castresana C. Involvement of the Arabidopsis alpha-DOX1 fatty acid dioxygenase in protection against oxidative stress and cell death. Plant J. 2002 Jan;29(1):61–2. doi: 10.1046/j.1365-313x.2002.01195.x. PMID: 12060227.; Saffert A, Hartmann-Schreier J, Schön A, Schreier P. A dual function alpha-dioxygenase-peroxidase and NAD(+) oxidoreductase active enzyme from germinating pea rationalizing alpha-oxidation of fatty acids in plants. Plant Physiol. 2000 Aug;123(4):1545–52. PMID: 10938370; PMCID: PMC59111.; Hamberg M, Sanz A, Castresana C. alpha-oxidation of fatty acids in higher plants. Identification of a pathogen-inducible oxygenase (piox) as an alpha-dioxygenase and biosynthesis of 2-hydroperoxylinolenic acid. J Biol Chem. 1999 Aug 27;274(35):24503–13. doi: 10.1074/jbc.274.35.24503. PMID: 10455113.
thiosulfate disproportionation IV (rhodanese)

Accession ID: BioCyc:ARA_PWY-5350
  • 10.1016/j.plaphy.2007.02.005
  • 10.1016/s0014-5793(02)03723-7
 Bartels A, Mock HP, Papenbrock J. Differential expression of Arabidopsis sulfurtransferases under various growth conditions. Plant Physiol Biochem. 2007 Mar;45(3-4):178–87. doi: 10.1016/j.plaphy.2007.02.005. PMID: 17408957.; Bauer M, Papenbrock J. Identification and characterization of single-domain thiosulfate sulfurtransferases from Arabidopsis thaliana. FEBS Lett. 2002 Dec 18;532(3):427–31. doi: 10.1016/s0014-5793(02)03723-7. PMID: 12482606.
thiosulfate disproportionation IV (rhodanese)

Accession ID: BioCyc:VCHO_PWY-5350		 -
thiosulfate disproportionation III (rhodanese)

Accession ID: BioCyc:CAULO_PWY-5350		 -
L-cysteine degradation III

Accession ID: BioCyc:MOUSE_PWY-5329		 -
thiosulfate disproportionation III (rhodanese)

Accession ID: BioCyc:FLY_PWY-5350		 -
thiosulfate disproportionation III (rhodanese)

Accession ID: BioCyc:PCHR_PWY-5350		 -
L-cysteine degradation III

Accession ID: BioCyc:THAPS_PWY-5329		 -
taxiphyllin bioactivation

Accession ID: BioCyc:CLOSSAC_PWY-7089		 -
formate to nitrite electron transfer

Accession ID: BioCyc:META_PWY0-1585
  • 10.1007/s002030050515
  • 10.1016/s0168-6445(02)00111-0
  • 10.1099/00221287-128-1-219
  • 10.1111/j.1432-1033.1979.tb12966.x
 Simon J. Enzymology and bioenergetics of respiratory nitrite ammonification. FEMS Microbiol Rev. 2002 Aug;26(3):285–309. doi: 10.1111/j.1574-6976.2002.tb00616.x. PMID: 12165429.; Tyson K, Metheringham R, Griffiths L, Cole J. Characterisation of Escherichia coli K-12 mutants defective in formate-dependent nitrite reduction: essential roles for hemN and the menFDBCE operon. Arch Microbiol. 1997 Nov;168(5):403–11. doi: 10.1007/s002030050515. PMID: 9325429.; Pope NR, Cole JA. Generation of a membrane potential by one of two independent pathways for nitrite reduction by Escherichia coli. J Gen Microbiol. 1982 Jan;128(1):219–22. doi: 10.1099/00221287-128-1-219. PMID: 6283015.; Abou-Jaoudé A, Chippaux M, Pascal MC. Formate-nitrite reduction in Escherchia coli K12. 1. Physiological study of the system. Eur J Biochem. 1979 Apr 02;95(2):309–14. doi: 10.1111/j.1432-1033.1979.tb12966.x. PMID: 37075.
formate oxidation to CO2

Accession ID: BioCyc:META_PWY-1881
  • 10.1046/j.1432-1033.2003.03391.x
  • 10.1128/jb.186.1.22-28.2004
 Chistoserdova L, Laukel M, Portais J, Vorholt JA, Lidstrom ME. Multiple Formate Dehydrogenase Enzymes in the Facultative Methylotroph Methylobacterium extorquens AM1 Are Dispensable for Growth on Methanol. J Bacteriol. 2004 Jan;186(1):22–8. doi: 10.1128/jb.186.1.22-28.2004.; Laukel M, Chistoserdova L, Lidstrom ME, Vorholt JA. The tungsten-containing formate dehydrogenase from Methylobacterium extorquens AM1: Purification and properties. European Journal of Biochemistry. 2002 Dec 19;270(2):325–33. doi: 10.1046/j.1432-1033.2003.03391.x.
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation

Accession ID: BioCyc:META_PWY-6604
  • 10.1016/s0021-9258(18)65732-1
  • 10.1016/s0021-9258(18)71290-8
  • 10.1016/s0021-9258(18)71291-x
  • 10.1096/fasebj.9.9.7601336
 Thorpe C, Kim JP. Structure and mechanism of action of the Acyl-CoA dehydrogenases 1. The FASEB Journal. 1995 Jun;9(9):718–25. doi: 10.1096/fasebj.9.9.7601336.; Hauge JG, Crane FL, Beinert H. ON THE MECHANISM OF DEHYDROGENATION OF FATTY ACYL DERIVATIVES OF COENZYME A. Journal of Biological Chemistry. 1956 Apr;219(2):727–33. doi: 10.1016/s0021-9258(18)65732-1.; Green DE, Mii S, Mahler HR, Bock RM. STUDIES ON THE FATTY ACID OXIDIZING SYSTEM OF ANIMAL TISSUES. Journal of Biological Chemistry. 1954 Jan;206(1):1–12. doi: 10.1016/s0021-9258(18)71290-8.; MAHLER HR. Studies on the fatty acid oxidizing system of animal tissues. IV. The prosthetic group of butyryl coenzyme A dehydrogenase. J Biol Chem. 1954 Jan;206(1):13–26. PMID: 13130522.
pyruvate fermentation to acetone

Accession ID: BioCyc:META_PWY-6588
  • 10.1128/mmbr.50.4.484-524.1986
 Jones DT, Woods DR. Acetone-butanol fermentation revisited. Microbiol Rev. 1986 Dec;50(4):484–524. doi: 10.1128/mr.50.4.484-524.1986.