Pathways Knowlegdes
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| Pathway | DOIs | Note |
|---|---|---|
| bacterioruberin biosynthesis Accession ID: BioCyc:META_PWY-7944 |
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Yang Y, Yatsunami R, Ando A, Miyoko N, Fukui T, Takaichi S, Nakamura S. Complete Biosynthetic Pathway of the C50Carotenoid Bacterioruberin from Lycopene in the Extremely Halophilic Archaeon Haloarcula japonica. J. Bacteriol. 2015 Feb 23;197(9):1614–23. doi: 10.1128/jb.02523-14. |
| (S)-propane-1,2-diol degradation Accession ID: BioCyc:META_PWY-7013 |
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Cheng S, Liu Y, Crowley CS, Yeates TO, Bobik TA. Bacterial microcompartments: their properties and paradoxes. BioEssays. 2008 Oct 20;30(11-12):1084–95. doi: 10.1002/bies.20830.; Liu Y, Leal NA, Sampson EM, Johnson CLV, Havemann GD, Bobik TA. PduL Is an Evolutionarily Distinct Phosphotransacylase Involved in B 12 -Dependent 1,2-Propanediol Degradation by Salmonella enterica Serovar Typhimurium LT2. J Bacteriol. 2007 Mar;189(5):1589–96. doi: 10.1128/jb.01151-06. |
| cyclohexanol degradation Accession ID: BioCyc:META_CYCLOHEXANOL-OXIDATION-PWY |
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DONOGHUE NA, TRUDGILL PW. The Metabolism of Cyclohexanol by Acinetobacter NCIB 9871. European Journal of Biochemistry. 1975 Dec;60(1):1–7. doi: 10.1111/j.1432-1033.1975.tb20968.x. |
| nitrate reduction IX (dissimilatory) Accession ID: BioCyc:META_PWY0-1581 |
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Garland PB, Downie JA, Haddock BA. Proton translocation and the respiratory nitrate reductase of Escherichia coli. Biochem J. 1975 Dec;152(3):547–59. PMID: 5996; PMCID: PMC1172508.; Miki K, Lin EC. Electron transport chain from glycerol 3-phosphate to nitrate in Escherichia coli. J Bacteriol. 1975 Dec;124(3):1288–94. doi: 10.1128/jb.124.3.1288-1294.1975. |
| protein N-glycosylation processing phase (yeast) Accession ID: BioCyc:META_PWY-7918 |
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Herscovics A. Processing glycosidases of Saccharomyces cerevisiae. Biochimica et Biophysica Acta (BBA) - General Subjects. 1999 Jan;1426(2):275–85. doi: 10.1016/s0304-4165(98)00129-9.; Daniel PF, Winchester B, Warren CD. Mammalian alpha-mannosidases--multiple forms but a common purpose? Glycobiology. 1994 Oct;4(5):551–66. doi: 10.1093/glycob/4.5.551. PMID: 7881169. |
| alginate biosynthesis II (bacterial) Accession ID: BioCyc:META_PWY-6082 |
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Rehman ZU, Wang Y, Moradali MF, Hay ID, Rehm BH. Insights into the assembly of the alginate biosynthesis machinery in Pseudomonas aeruginosa. Appl Environ Microbiol. 2013 May;79(10):3264–72. PMID: 23503314; PMCID: PMC3685254. |
| putrescine biosynthesis III Accession ID: BioCyc:META_PWY-46 |
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Gupta R, Hamasaki-Katagiri N, Tabor CW, Tabor H. Effect of spermidine on the in vivo degradation of ornithine decarboxylase in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. U.S.A. 2001 Sep 04;98(19):10620–3. doi: 10.1073/pnas.181341298.; Schwartz B, Hittelman A, Daneshvar L, Basu HS, Marton LJ, Feuerstein BG. A new model for disruption of the ornithine decarboxylase gene, SPE1, in Saccharomyces cerevisiae exhibits growth arrest and genetic instability at the MAT locus. Biochem J. 1995 Nov 15;312 ( Pt 1)():83–90. PMID: 7492339; PMCID: PMC1136230.; Balasundaram D, Xie QW, Tabor CW, Tabor H. The presence of an active S-adenosylmethionine decarboxylase gene increases the growth defect observed in Saccharomyces cerevisiae mutants unable to synthesize putrescine, spermidine, and spermine. J Bacteriol. 1994 Oct;176(20):6407–9. doi: 10.1128/jb.176.20.6407-6409.1994.; Morris DR, Jorstad CM. Isolation of Conditionally Putrescine-Deficient Mutants ofEscherichia coli. J Bacteriol. 1970 Mar;101(3):731–7. doi: 10.1128/jb.101.3.731-737.1970. |
| 2-chloroacrylate degradation II Accession ID: BioCyc:META_PWY-7428 |
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KURIHARA T. A Mechanistic Analysis of Enzymatic Degradation of Organohalogen Compounds. Bioscience, Biotechnology, and Biochemistry. 2011 Feb 23;75(2):189–98. doi: 10.1271/bbb.100746.; Mowafy AM, Kurihara T, Kurata A, Uemura T, Esaki N. 2-haloacrylate hydratase, a new class of flavoenzyme that catalyzes the addition of water to the substrate for dehalogenation. Appl Environ Microbiol. 2010 Sep;76(18):6032–7. PMID: 20656877; PMCID: PMC2937477. |
| homogalacturonan biosynthesis Accession ID: BioCyc:META_PWY-1061 |
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Sterling JD, Quigley HF, Orellana A, Mohnen D. The catalytic site of the pectin biosynthetic enzyme alpha-1,4-galacturonosyltransferase is located in the lumen of the Golgi. Plant Physiol. 2001 Sep;127(1):360–71. PMID: 11553763; PMCID: PMC117991.; Ishikawa M, Kuroyama H, Takeuchi Y, Tsumuraya Y. Characterization of pectin methyltransferase from soybean hypocotyls. Planta. 2000 Apr;210(5):782–91. doi: 10.1007/s004250050680. PMID: 10805450.; Goubet F, Mohnen D. Solubilization and partial characterization of homogalacturonan-methyltransferase from microsomal membranes of suspension-cultured tobacco cells. Plant Physiol. 1999 Sep;121(1):281–90. PMID: 10482684; PMCID: PMC59378. |
| fructan biosynthesis Accession ID: BioCyc:META_PWY-822 |
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Vijn I, Van Dijken A, Sprenger N, Van Dun K, Weisbeek P, Wiemken A, Smeekens S. Fructan of the inulin neoseries is synthesized in transgenic chicory plants (Cichorium intybus L.) harbouring onion (Allium cepa L.) fructan:fructan 6G-fructosyltransferase. The Plant Journal. 1997 Mar;11(3):387–98. doi: 10.1046/j.1365-313x.1997.11030387.x. |
| acetan biosynthesis Accession ID: BioCyc:META_PWY-6658 |
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Barreras M, Salinas SR, Abdian PL, Kampel MA, Ielpi L. Structure and Mechanism of GumK, a Membrane-associated Glucuronosyltransferase. Journal of Biological Chemistry. 2008 Sep;283(36):25027–35. doi: 10.1074/jbc.m801227200.; Barreras M, Bianchet MA, Ielpi L. Crystallization and preliminary crystallographic characterization of GumK, a membrane-associated glucuronosyltransferase from Xanthomonas campestris required for xanthan polysaccharide synthesis. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2006 Sep 01;62(Pt 9):880–3. PMID: 16946469; PMCID: PMC2242869.; Ishida T, Sugano Y, Shoda M. Novel glycosyltransferase genes involved in the acetan biosynthesis of Acetobacter xylinum. Biochemical and Biophysical Research Communications. 2002 Jul;295(2):230–5. doi: 10.1016/s0006-291x(02)00663-0.; Colquhoun IJ, Defernez M, Morris VJ. NMR studies of acetan and the related bacterial polysaccharide, CR1/4, produced by a mutant strain of Acetobacter xylinum. Carbohydr Res. 1995 Apr 19;269(2):319–31. doi: 10.1016/0008-6215(94)00367-o. PMID: 7780996.; Griffin AM, Morris VJ, Gasson MJ. Genetic analysis of the acetan biosynthetic pathway in Acetobacter xylinum. International Journal of Biological Macromolecules. 1994 Dec;16(6):287–9. doi: 10.1016/0141-8130(94)90057-4. |
| L-homophenylalanine biosynthesis Accession ID: BioCyc:META_PWY-7275 |
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Koketsu K, Mitsuhashi S, Tabata K. Identification of homophenylalanine biosynthetic genes from the cyanobacterium Nostoc punctiforme PCC73102 and application to its microbial production by Escherichia coli. Appl Environ Microbiol. 2013 Apr;79(7):2201–8. PMID: 23354699; PMCID: PMC3623235. |
| superpathway of 5-aminoimidazole ribonucleotide biosynthesis Accession ID: BioCyc:META_PWY-6277 |
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Nygaard P, Smith JM. Evidence for a novel glycinamide ribonucleotide transformylase in Escherichia coli. J Bacteriol. 1993 Jun;175(11):3591–7. doi: 10.1128/jb.175.11.3591-3597.1993. |
| xylogalacturonan biosynthesis Accession ID: BioCyc:META_PWY-5980 |
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Jensen JK, Sørensen SO, Harholt J, Geshi N, Sakuragi Y, Møller I, Zandleven J, Bernal AJ, Jensen NB, Sørensen C, Pauly M, Beldman G, Willats WG, Scheller HV. Identification of a xylogalacturonan xylosyltransferase involved in pectin biosynthesis in Arabidopsis. Plant Cell. 2008 May;20(5):1289–302. PMID: 18460606; PMCID: PMC2438468. |
| 4-methyl-proline biosynthesis Accession ID: BioCyc:META_PWY-7648 |
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Bills G, Li Y, Chen L, Yue Q, Niu XM, An Z. New insights into the echinocandins and other fungal non-ribosomal peptides and peptaibiotics. Nat Prod Rep. 2014 Oct;31(10):1348–75. doi: 10.1039/c4np00046c. PMID: 25156669.; Jiang W, Cacho RA, Chiou G, Garg NK, Tang Y, Walsh CT. EcdGHK are three tailoring iron oxygenases for amino acid building blocks of the echinocandin scaffold. J Am Chem Soc. 2013 Mar 20;135(11):4457–66. PMID: 23451921; PMCID: PMC3628723.; Emri T, Majoros L, Tóth V, Pócsi I. Echinocandins: production and applications. Applied Microbiology and Biotechnology. 2013 Mar 06;97(8):3267–84. doi: 10.1007/s00253-013-4761-9.; Hibi M, Kawashima T, Sokolov PM, Smirnov SV, Kodera T, Sugiyama M, Shimizu S, Yokozeki K, Ogawa J. l-Leucine 5-hydroxylase of Nostoc punctiforme is a novel type of Fe(II)/a-ketoglutarate-dependent dioxygenase that is useful as a biocatalyst. Applied Microbiology and Biotechnology. 2012 May 16;97(6):2467–72. doi: 10.1007/s00253-012-4136-7.; Zambias RA, Hammond ML, Heck JV, Bartizal K, Trainor C, Abruzzo G, Schmatz DM, Nollstadt KM. Preparation and structure-activity relationships of simplified analogues of the antifungal agent cilofungin: a total synthesis approach. J Med Chem. 1992 Jul 24;35(15):2843–55. doi: 10.1021/jm00093a018. PMID: 1495015. |
| terminal O-glycans residues modification (via type 2 precursor disaccharide) Accession ID: BioCyc:META_PWY-7434 |
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Amado M, Almeida R, Schwientek T, Clausen H. Identification and characterization of large galactosyltransferase gene families: galactosyltransferases for all functions. Biochimica et Biophysica Acta (BBA) - General Subjects. 1999 Dec;1473(1):35–53. doi: 10.1016/s0304-4165(99)00168-3. |
| L-alanine biosynthesis II Accession ID: BioCyc:META_ALANINE-SYN2-PWY |
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Wang MD, Buckley L, Berg CM. Cloning of genes that suppress an Escherichia coli K-12 alanine auxotroph when present in multicopy plasmids. J Bacteriol. 1987 Dec;169(12):5610–4. doi: 10.1128/jb.169.12.5610-5614.1987. |
| adenosine 5'-phosphoramidate biosynthesis Accession ID: BioCyc:META_PWY-6794 |
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Fankhauser H, Schiff JA, Garber LJ. Purification and properties of adenylyl sulphate:ammonia adenylyltransferase from Chlorella catalysing the formation of adenosine 5' -phosphoramidate from adenosine 5' -phosphosulphate and ammonia. Biochem J. 1981 Jun 01;195(3):545–60. PMID: 6274307; PMCID: PMC1162926. |
| xanthan biosynthesis Accession ID: BioCyc:META_PWY-6655 |
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Barreras M, Salinas SR, Abdian PL, Kampel MA, Ielpi L. Structure and Mechanism of GumK, a Membrane-associated Glucuronosyltransferase. Journal of Biological Chemistry. 2008 Sep;283(36):25027–35. doi: 10.1074/jbc.m801227200.; Vorhölter FJ, Schneiker S, Goesmann A, Krause L, Bekel T, Kaiser O, Linke B, Patschkowski T, Rückert C, Schmid J, Sidhu VK, Sieber V, Tauch A, Watt SA, Weisshaar B, Becker A, Niehaus K, Pühler A. The genome of Xanthomonas campestris pv. campestris B100 and its use for the reconstruction of metabolic pathways involved in xanthan biosynthesis. J Biotechnol. 2008 Mar 20;134(1-2):33–45. doi: 10.1016/j.jbiotec.2007.12.013. PMID: 18304669.; Barreras M, Bianchet MA, Ielpi L. Crystallization and preliminary crystallographic characterization of GumK, a membrane-associated glucuronosyltransferase from Xanthomonas campestris required for xanthan polysaccharide synthesis. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2006 Sep 01;62(Pt 9):880–3. PMID: 16946469; PMCID: PMC2242869.; Katzen F, Ferreiro DU, Oddo CG, Ielmini MV, Becker A, Pu¨hler A, Ielpi L. Xanthomonas campestris pv. campestris gum Mutants: Effects on Xanthan Biosynthesis and Plant Virulence. J Bacteriol. 1998 Apr;180(7):1607–17. doi: 10.1128/jb.180.7.1607-1617.1998.; Ielpi L, Couso RO, Dankert MA. Sequential assembly and polymerization of the polyprenol-linked pentasaccharide repeating unit of the xanthan polysaccharide in Xanthomonas campestris. J Bacteriol. 1993 May;175(9):2490–500. doi: 10.1128/jb.175.9.2490-2500.1993.; Stankowski JD, Mueller BE, Zeller SG. Location of a second O-acetyl group in xanthan gum by the reductive-cleavage method. Carbohydr Res. 1993 Mar 17;241():321–6. doi: 10.1016/0008-6215(93)80123-v. PMID: 8472258.; Marzocca MP, Harding NE, Petroni EA, Cleary JM, Ielpi L. Location and cloning of the ketal pyruvate transferase gene of Xanthomonas campestris. J Bacteriol. 1991 Dec;173(23):7519–24. doi: 10.1128/jb.173.23.7519-7524.1991. |
| glucuronoarabinoxylan degradation Accession ID: BioCyc:META_PWY-6813 |
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de Vries RP, Visser J. Aspergillus enzymes involved in degradation of plant cell wall polysaccharides. Microbiol Mol Biol Rev. 2001 Dec;65(4):497–522, table of contents. PMID: 11729262; PMCID: PMC99039.; Nishitani K, Nevins DJ. Glucuronoxylan xylanohydrolase. A unique xylanase with the requirement for appendant glucuronosyl units. Journal of Biological Chemistry. 1991 Apr;266(10):6539–43. doi: 10.1016/s0021-9258(18)38151-1. |