Pathways Knowlegdes
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| Pathway | DOIs | Note |
|---|---|---|
| cardiolipin biosynthesis I Accession ID: BioCyc:ECO_PWY-5668 |
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| glycerophosphodiester degradation Accession ID: BioCyc:ECO_PWY-6952 |
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| glycerol and glycerophosphodiester degradation Accession ID: BioCyc:ECO_PWY0-381 |
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| glycerol degradation V Accession ID: BioCyc:ECO_GLYCEROLMETAB-PWY |
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Wong MS, Li M, Black RW, Le TQ, Puthli S, Campbell P, Monticello DJ. Microaerobic conversion of glycerol to ethanol in Escherichia coli. Appl Environ Microbiol. 2014 May;80(10):3276–82. PMID: 24584248; PMCID: PMC4018910.; Cintolesi A, Clomburg JM, Rigou V, Zygourakis K, Gonzalez R. Quantitative analysis of the fermentative metabolism of glycerol in Escherichia coli. Biotech & Bioengineering. 2011 Aug 31;109(1):187–98. doi: 10.1002/bit.23309.; Durnin G, Clomburg J, Yeates Z, Alvarez PJ, Zygourakis K, Campbell P, Gonzalez R. Understanding and harnessing the microaerobic metabolism of glycerol in Escherichia coli. Biotechnol Bioeng. 2009 May 01;103(1):148–61. doi: 10.1002/bit.22246. PMID: 19189409.; Jin RZ, Lin EC. An inducible phosphoenolpyruvate: dihydroxyacetone phosphotransferase system in Escherichia coli. J Gen Microbiol. 1984 Jan;130(1):83–8. doi: 10.1099/00221287-130-1-83. PMID: 6368745.; Jin RZ, Tang JC-, Lin ECC. Experimental evolution of a novel pathway for glycerol dissimilation inEscherichia coli. Journal of Molecular Evolution. 1983 Nov;19(6):429–36. doi: 10.1007/bf02102318. |
| superpathway of glyoxylate bypass and TCA Accession ID: BioCyc:ECO_TCA-GLYOX-BYPASS |
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| gluconeogenesis I Accession ID: BioCyc:ECO_GLUCONEO-PWY |
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Hines JK, Fromm HJ, Honzatko RB. Novel Allosteric Activation Site in Escherichia coli Fructose-1,6-bisphosphatase. Journal of Biological Chemistry. 2006 Jul;281(27):18386–93. doi: 10.1074/jbc.m602553200.; Sauer U, Eikmanns BJ. The PEP—pyruvate—oxaloacetate node as the switch point for carbon flux distribution in bacteria: We dedicate this paper to Rudolf K. Thauer, Director of the Max-Planck-Institute for Terrestrial Microbiology in Marburg, Germany, on the occasion of his 65th birthday. FEMS Microbiol Rev. 2005 Sep;29(4):765–94. doi: 10.1016/j.femsre.2004.11.002.; Peng L, Shimizu K. Global metabolic regulation analysis for Escherichia coli K12 based on protein expression by 2-dimensional electrophoresis and enzyme activity measurement. Applied Microbiology and Biotechnology. 2003 Jan 09;61(2):163–78. doi: 10.1007/s00253-002-1202-6.; Chao YP, Patnaik R, Roof WD, Young RF, Liao JC. Control of gluconeogenic growth by pps and pck in Escherichia coli. J Bacteriol. 1993 Nov;175(21):6939–44. doi: 10.1128/jb.175.21.6939-6944.1993. |
| superpathway of polyamine biosynthesis I Accession ID: BioCyc:ECO_POLYAMSYN-PWY |
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Soksawatmaekhin W, Kuraishi A, Sakata K, Kashiwagi K, Igarashi K. Excretion and uptake of cadaverine by CadB and its physiological functions in Escherichia coli. Molecular Microbiology. 2004 Jan 13;51(5):1401–12. doi: 10.1046/j.1365-2958.2003.03913.x.; Igarashi K, Kashiwagi K, Hamasaki H, Miura A, Kakegawa T, Hirose S, Matsuzaki S. Formation of a compensatory polyamine by Escherichia coli polyamine-requiring mutants during growth in the absence of polyamines. J Bacteriol. 1986 Apr;166(1):128–34. doi: 10.1128/jb.166.1.128-134.1986.; Dion AS, Cohen SS. Polyamine stimulation of nucleic acid synthesis in an uninfected and phage-infected polyamine auxotroph of Escherichia coli K12 (arginine-agmatine ureohydrolase-putrescine-spermidine-lysine-cadaverine). Proc Natl Acad Sci U S A. 1972 Jan;69(1):213–7. PMID: 4550506; PMCID: PMC427578. |
| superpathway of tetrahydrofolate biosynthesis Accession ID: BioCyc:ECO_PWY-6612 |
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| GDP-L-fucose biosynthesis I (from GDP-D-mannose) Accession ID: BioCyc:ECO_PWY-66 |
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Lau ST, Tanner ME. Mechanism and active site residues of GDP-fucose synthase. J Am Chem Soc. 2008 Dec 24;130(51):17593–602. doi: 10.1021/ja807799k. PMID: 19053199.; Andrianopoulos K, Wang L, Reeves PR. Identification of the Fucose Synthetase Gene in the Colanic Acid Gene Cluster of Escherichia coli K-12. J Bacteriol. 1998 Feb 15;180(4):998–1001. doi: 10.1128/jb.180.4.998-1001.1998.; Sturla L, Bisso A, Zanardi D, Benatti U, De Flora A, Tonetti M. Expression, purification and characterization of GDP- |
| protein N-glycosylation (yeast) processing in the ER Accession ID: BioCyc:YEAST_PWY-7918 |
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| triacylglycerol biosynthesis Accession ID: BioCyc:YEAST_TRIGLSYN-PWY |
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Pascual F, Carman GM. Phosphatidate phosphatase, a key regulator of lipid homeostasis. Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids. 2013 Mar;1831(3):514–22. doi: 10.1016/j.bbalip.2012.08.006.; Kurat CF, Wolinski H, Petschnigg J, Kaluarachchi S, Andrews B, Natter K, Kohlwein SD. Cdk1/Cdc28-Dependent Activation of the Major Triacylglycerol Lipase Tgl4 in Yeast Links Lipolysis to Cell-Cycle Progression. Molecular Cell. 2009 Jan;33(1):53–63. doi: 10.1016/j.molcel.2008.12.019.; Athenstaedt K, Daum G. Tgl4p and Tgl5p, Two Triacylglycerol Lipases of the Yeast Saccharomyces cerevisiae Are Localized to Lipid Particles. Journal of Biological Chemistry. 2005 Nov;280(45):37301–9. doi: 10.1074/jbc.m507261200.; Zheng Z, Zou J. The initial step of the glycerolipid pathway: identification of glycerol 3-phosphate/dihydroxyacetone phosphate dual substrate acyltransferases in Saccharomyces cerevisiae. J Biol Chem. 2001 Nov 09;276(45):41710–6. doi: 10.1074/jbc.m104749200. PMID: 11544256.; Lin YP, Carman GM. Purification and Characterization of Phosphatidate Phosphatase from Saccharomyces cerevisiae. Journal of Biological Chemistry. 1989 May;264(15):8641–5. doi: 10.1016/s0021-9258(18)81840-3. |
| superpathway of purine nucleotides de novo biosynthesis I Accession ID: BioCyc:YEAST_PWY-841 |
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Hyle JW, Shaw RJ, Reines D. Functional Distinctions between IMP Dehydrogenase Genes in Providing Mycophenolate Resistance and Guanine Prototrophy to Yeast. Journal of Biological Chemistry. 2003 Aug;278(31):28470–8. doi: 10.1074/jbc.m303736200. |
| NAD/NADP-NADH/NADPH mitochondrial interconversion (yeast) Accession ID: BioCyc:YEAST_PWY-7269 |
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| phospholipid remodeling (phosphatidylethanolamine) Accession ID: BioCyc:YEAST_PWY-7409 |
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Henry SA, Kohlwein SD, Carman GM. Metabolism and regulation of glycerolipids in the yeast Saccharomyces cerevisiae. Genetics. 2012 Feb;190(2):317–49. PMID: 22345606; PMCID: PMC3276621.; Ayciriex S, Le Guédard M, Camougrand N, Velours G, Schoene M, Leone S, Wattelet-Boyer V, Dupuy JW, Shevchenko A, Schmitter JM, Lessire R, Bessoule JJ, Testet E. YPR139c/LOA1 encodes a novel lysophosphatidic acid acyltransferase associated with lipid droplets and involved in TAG homeostasis. Mol Biol Cell. 2012 Jan;23(2):233–46. PMID: 22090344; PMCID: PMC3258169.; Rajakumari S, Daum G. Multiple Functions as Lipase, Steryl Ester Hydrolase, Phospholipase, and Acyltransferase of Tgl4p from the Yeast Saccharomyces cerevisiae. Journal of Biological Chemistry. 2010 May;285(21):15769–76. doi: 10.1074/jbc.m109.076331.; Petschnigg J, Wolinski H, Kolb D, Zellnig G, Kurat CF, Natter K, Kohlwein SD. Good Fat, Essential Cellular Requirements for Triacylglycerol Synthesis to Maintain Membrane Homeostasis in Yeast. Journal of Biological Chemistry. 2009 Nov;284(45):30981–93. doi: 10.1074/jbc.m109.024752.; Chen Q, Kazachkov M, Zheng Z, Zou J. The yeast acylglycerol acyltransferase LCA1 is a key component of Lands cycle for phosphatidylcholine turnover. FEBS Lett. 2007 Nov 27;581(28):5511–6. doi: 10.1016/j.febslet.2007.10.061. PMID: 17996202.; Jain S, Stanford N, Bhagwat N, Seiler B, Costanzo M, Boone C, Oelkers P. Identification of a Novel Lysophospholipid Acyltransferase in Saccharomyces cerevisiae. Journal of Biological Chemistry. 2007 Oct;282(42):30562–9. doi: 10.1074/jbc.m706326200.; Riekhof WR, Wu J, Jones JL, Voelker DR. Identification and Characterization of the Major Lysophosphatidylethanolamine Acyltransferase in Saccharomyces cerevisiae. Journal of Biological Chemistry. 2007 Sep;282(39):28344–52. doi: 10.1074/jbc.m705256200.; Boumann HA, Gubbens J, Koorengevel MC, Oh CS, Martin CE, Heck AJ, Patton-Vogt J, Henry SA, de Kruijff B, de Kroon AI. Depletion of phosphatidylcholine in yeast induces shortening and increased saturation of the lipid acyl chains: evidence for regulation of intrinsic membrane curvature in a eukaryote. Mol Biol Cell. 2006 Feb;17(2):1006–17. PMID: 16339082; PMCID: PMC1356607.; Kurat CF, Natter K, Petschnigg J, Wolinski H, Scheuringer K, Scholz H, Zimmermann R, Leber R, Zechner R, Kohlwein SD. Obese Yeast: Triglyceride Lipolysis Is Functionally Conserved from Mammals to Yeast. Journal of Biological Chemistry. 2006 Jan;281(1):491–500. doi: 10.1074/jbc.m508414200.; Athenstaedt K, Daum G. Tgl4p and Tgl5p, Two Triacylglycerol Lipases of the Yeast Saccharomyces cerevisiae Are Localized to Lipid Particles. Journal of Biological Chemistry. 2005 Nov;280(45):37301–9. doi: 10.1074/jbc.m507261200.; Fisher E, Almaguer C, Holic R, Griac P, Patton-Vogt J. Glycerophosphocholine-dependent Growth Requires Gde1p (YPL110c) and Git1p in Saccharomyces cerevisiae. Journal of Biological Chemistry. 2005 Oct;280(43):36110–7. doi: 10.1074/jbc.m507051200.; Merkel O, Oskolkova OV, Raab F, El-Toukhy R, Paltauf F. Regulation of activity in vitro and in vivo of three phospholipases B from Saccharomyces cerevisiae. Biochem J. 2005 Apr 15;387(Pt 2):489–96. PMID: 15588231; PMCID: PMC1134978.; Merkel O, Fido M, Mayr JA, Prüger H, Raab F, Zandonella G, Kohlwein SD, Paltauf F. Characterization and Function in Vivo of Two Novel Phospholipases B/Lysophospholipases fromSaccharomyces cerevisiae. Journal of Biological Chemistry. 1999 Oct;274(40):28121–7. doi: 10.1074/jbc.274.40.28121.; Fyrst H, Oskouian B, Kuypers FA, Saba JD. The PLB2 gene of Saccharomyces cerevisiae confers resistance to lysophosphatidylcholine and encodes a phospholipase B/lysophospholipase. Biochemistry. 1999 May 04;38(18):5864–71. doi: 10.1021/bi9824590. PMID: 10231538.; Wagner S, Paltauf F. Generation of glycerophospholipid molecular species in the yeast Saccharomyces cerevisiae. Fatty acid pattern of phospholipid classes and selective acyl turnover at sn-1 and sn-2 positions. Yeast. 1994 Nov;10(11):1429–37. doi: 10.1002/yea.320101106.; Lee KS, Patton JL, Fido M, Hines LK, Kohlwein SD, Paltauf F, Henry SA, Levin DE. The Saccharomyces cerevisiae PLB1 gene encodes a protein required for lysophospholipase and phospholipase B activity. Journal of Biological Chemistry. 1994 Aug;269(31):19725–30. doi: 10.1016/s0021-9258(17)32081-1.; Cullis PR, De Kruijff B. The polymorphic phase behaviour of phosphatidylethanolamines of natural and synthetic origin. A 31P NMR study. Biochimica et Biophysica Acta (BBA) - Biomembranes. 1978 Oct;513(1):31–42. doi: 10.1016/0005-2736(78)90109-8.; LANDS WE. LIPID METABOLISM. Annu Rev Biochem. 1965;34():313–46. doi: 10.1146/annurev.bi.34.070165.001525. PMID: 14321173.; LANDS WE. Metabolism of glycerolipids. 2. The enzymatic acylation of lysolecithin. J Biol Chem. 1960 Aug;235():2233–7. PMID: 14413818. |
| protein N-glycosylation (eukaryotic) initial steps Accession ID: BioCyc:YEAST_MANNOSYL-CHITO-DOLICHOL-BIOSYNTHESIS |
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Bickel T, Lehle L, Schwarz M, Aebi M, Jakob CA. Biosynthesis of lipid-linked oligosaccharides in Saccharomyces cerevisiae: Alg13p and Alg14p form a complex required for the formation of GlcNAc(2)-PP-dolichol. J Biol Chem. 2005 Oct 14;280(41):34500–6. doi: 10.1074/jbc.m506358200. PMID: 16100113.; Chantret I, Dancourt J, Barbat A, Moore SEH. Two Proteins Homologous to the N- and C-terminal Domains of the Bacterial Glycosyltransferase Murg Are Required for the Second Step of Dolichyl-linked Oligosaccharide Synthesis in Saccharomyces cerevisiae. Journal of Biological Chemistry. 2005 Mar;280(10):9236–42. doi: 10.1074/jbc.m413941200.; Cipollo JF, Trimble RB, Chi JH, Yan Q, Dean N. The yeast ALG11 gene specifies addition of the terminal alpha 1,2-Man to the Man5GlcNAc2-PP-dolichol N-glycosylation intermediate formed on the cytosolic side of the endoplasmic reticulum. J Biol Chem. 2001 Jun 15;276(24):21828–40. doi: 10.1074/jbc.m010896200. PMID: 11278778.; Burda P, Jakob CA, Beinhauer J, Hegemann JH, Aebi M. Ordered assembly of the asymmetrically branched lipid-linked oligosaccharide in the endoplasmic reticulum is ensured by the substrate specificity of the individual glycosyltransferases. Glycobiology. 1999 Jun;9(6):617–25. doi: 10.1093/glycob/9.6.617. PMID: 10336995.; Burda P, Aebi M. The dolichol pathway of N-linked glycosylation. Biochimica et Biophysica Acta (BBA) - General Subjects. 1999 Jan;1426(2):239–57. doi: 10.1016/s0304-4165(98)00127-5.; Herscovics A, Orlean P. Glycoprotein biosynthesis in yeast. FASEB J. 1993 Apr 01;7(6):540–50. doi: 10.1096/fasebj.7.6.8472892. PMID: 8472892.; Kornfeld R, Kornfeld S. Assembly of asparagine-linked oligosaccharides. Annu Rev Biochem. 1985;54():631–64. doi: 10.1146/annurev.bi.54.070185.003215. PMID: 3896128. |
| phosphatidylcholine biosynthesis V Accession ID: BioCyc:YEAST_PWY-6825 |
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| UDP-sugars interconversion Accession ID: BioCyc:ARA_PWY-5114 |
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| phosphatidylglycerol biosynthesis II (non-plastidic) Accession ID: BioCyc:ARA_PWY4FS-8 |
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| citrulline-nitric oxide cycle Accession ID: BioCyc:HUMAN_PWY-4983 |
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Nussler AK, Billiar TR, Liu ZZ, Morris SM. Coinduction of nitric oxide synthase and argininosuccinate synthetase in a murine macrophage cell line. Implications for regulation of nitric oxide production. Journal of Biological Chemistry. 1994 Jan;269(2):1257–61. doi: 10.1016/s0021-9258(17)42251-4. |
| formaldehyde oxidation Accession ID: BioCyc:HUMAN_PWY-1801 |
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Engeland K, Höög JO, Holmquist B, Estonius M, Jörnvall H, Vallee BL. Mutation of Arg-115 of human class III alcohol dehydrogenase: a binding site required for formaldehyde dehydrogenase activity and fatty acid activation. Proc. Natl. Acad. Sci. U.S.A. 1993 Mar 15;90(6):2491–4. doi: 10.1073/pnas.90.6.2491. |