Pathways Knowlegdes

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Pathway DOIs Note
pyruvate fermentation to butanol II (engineered)

Accession ID: BioCyc:META_PWY-6883
  • 10.1016/j.ymben.2011.04.004
  • 10.1093/oxfordjournals.jbchem.a121813
 Lan EI, Liao JC. Metabolic engineering of cyanobacteria for 1-butanol production from carbon dioxide. Metab Eng. 2011 Jul;13(4):353–63. doi: 10.1016/j.ymben.2011.04.004. PMID: 21569861.; Inui H, Miyatake K, Nakano Y, Kitaoka S. Purification and some properties of short chain-length specific trans-2-enoyl-CoA reductase in mitochondria of Euglena gracilis. J Biochem. 1986 Oct;100(4):995–1000. doi: 10.1093/oxfordjournals.jbchem.a121813. PMID: 3102464.
1-butanol autotrophic biosynthesis (engineered)

Accession ID: BioCyc:META_PWY-6886
  • 10.1016/0005-2728(77)90041-x
  • 10.1016/j.ymben.2011.04.004
  • 10.1038/nsmb.1559
  • 10.1093/oxfordjournals.jbchem.a121813
 Lan EI, Liao JC. Metabolic engineering of cyanobacteria for 1-butanol production from carbon dioxide. Metab Eng. 2011 Jul;13(4):353–63. doi: 10.1016/j.ymben.2011.04.004. PMID: 21569861.; 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.; Inui H, Miyatake K, Nakano Y, Kitaoka S. Purification and some properties of short chain-length specific trans-2-enoyl-CoA reductase in mitochondria of Euglena gracilis. J Biochem. 1986 Oct;100(4):995–1000. doi: 10.1093/oxfordjournals.jbchem.a121813. PMID: 3102464.; 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.
butane degradation

Accession ID: BioCyc:META_PWY-7780
  • 10.1099/13500872-145-5-1173
 Arp DJ. Butane metabolism by butane-grown 'Pseudomonas butanovora'. Microbiology (Reading). 1999 May;145 ( Pt 5)():1173–80. doi: 10.1099/13500872-145-5-1173. PMID: 10376833.
glycerol degradation to butanol

Accession ID: BioCyc:ECOO157_PWY-7003		 -
glycerol degradation to butanol

Accession ID: BioCyc:10403S_RAST_PWY-7003		 -
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.
superpathway of Clostridium acetobutylicum solventogenic fermentation

Accession ID: BioCyc:META_PWY-6594
  • 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
  • 10.1128/mmbr.50.4.484-524.1986
 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.; 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.; 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.
butanol and isobutanol biosynthesis (engineered)

Accession ID: BioCyc:META_PWY-7396
  • 10.1016/j.femsyr.2005.03.001
  • 10.1186/1754-6834-6-68
 Branduardi P, Longo V, Berterame NM, Rossi G, Porro D. A novel pathway to produce butanol and isobutanol in Saccharomyces cerevisiae. Biotechnology for Biofuels and Bioproducts. 2013 May 04;6(1):68. doi: 10.1186/1754-6834-6-68.; Villas-Bôas SG, Kesson M, Nielsen J. Biosynthesis of glyoxylate from glycine in Saccharomyces cerevisiae. FEMS Yeast Res. 2005 May;5(8):703–9. doi: 10.1016/j.femsyr.2005.03.001. PMID: 15851099.
glycerol degradation to butanol

Accession ID: BioCyc:META_PWY-7003
  • 10.1007/s00253-011-3629-0
  • 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
 Malaviya A, Jang YS, Lee SY. Continuous butanol production with reduced byproducts formation from glycerol by a hyper producing mutant of Clostridium pasteurianum. Appl Microbiol Biotechnol. 2012 Feb;93(4):1485–94. doi: 10.1007/s00253-011-3629-0. PMID: 22052388.; 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.
butachlor degradation

Accession ID: BioCyc:META_PWY-7771
  • 10.1021/acs.jafc.5b03326
  • 10.1021/jf104695g
 Gao Y, Jin L, Shi H, Chu Z. Characterization of a Novel Butachlor Biodegradation Pathway and Cloning of the Debutoxylase (Dbo) Gene Responsible for Debutoxylation of Butachlor in Bacillus sp. hys-1. J Agric Food Chem. 2015 Sep 30;63(38):8381–90. doi: 10.1021/acs.jafc.5b03326. PMID: 26368393.; Zhang J, Zheng JW, Liang B, Wang CH, Cai S, Ni YY, He J, Li SP. Biodegradation of chloroacetamide herbicides by Paracoccus sp. FLY-8 in vitro. J Agric Food Chem. 2011 May 11;59(9):4614–21. doi: 10.1021/jf104695g. PMID: 21417467.
volatile esters biosynthesis (during fruit ripening)

Accession ID: BioCyc:META_PWY-6801
  • 10.1016/j.phytochem.2011.02.026
  • 10.1104/pp.006460
  • 10.1104/pp.104.045468
 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.
pyruvate fermentation to butanol I

Accession ID: BioCyc:META_PWY-6583
  • 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
  • 10.1128/mmbr.50.4.484-524.1986
 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.; 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.; 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.
glycerol degradation to butanol

Accession ID: BioCyc:CLOSSAC_PWY-7003		 -
volatile esters biosynthesis (during fruit ripening)

Accession ID: PlantCyc:SUNFLOWER_PWY-6801		 -
volatile esters biosynthesis (during fruit ripening)

Accession ID: PlantCyc:ASPARAGUS_PWY-6801		 -
volatile esters biosynthesis (during fruit ripening)

Accession ID: PlantCyc:WHEATA_PWY-6801		 -
volatile esters biosynthesis (during fruit ripening)

Accession ID: PlantCyc:BANANA_PWY-6801		 -
volatile esters biosynthesis (during fruit ripening)

Accession ID: PlantCyc:BARLEY_PWY-6801		 -
volatile esters biosynthesis (during fruit ripening)

Accession ID: PlantCyc:ZMARINA_PWY-6801		 -