Pathways Knowlegdes
Necessitatibus eius consequatur ex aliquid fuga eum quidem sint consectetur velit
| Pathway | DOIs | Note |
|---|---|---|
| pyridine nucleotide cycling (plants) Accession ID: BioCyc:ARA_PWY-5381 |
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Noctor G, Queval G, Gakière B. NAD(P) synthesis and pyridine nucleotide cycling in plants and their potential importance in stress conditions. J Exp Bot. 2006;57(8):1603–20. doi: 10.1093/jxb/erj202. PMID: 16714307.; Zheng XQ, Hayashibe E, Ashihara H. Changes in trigonelline (N-methylnicotinic acid) content and nicotinic acid metabolism during germination of mungbean (Phaseolus aureus) seeds. J Exp Bot. 2005 Jun;56(416):1615–23. doi: 10.1093/jxb/eri156. PMID: 15837705.; Sinclair SJ, Murphy KJ, Birch CD, Hamill JD. Molecular characterization of quinolinate phosphoribosyltransferase (QPRtase) in Nicotiana. Plant Mol Biol. 2000 Nov;44(5):603–17. doi: 10.1023/a:1026590521318. PMID: 11198422.; Eastwell KC, Stumpf PK. The presence of 5'-nucleotidase in Swiss chard chloroplasts. Biochemical and Biophysical Research Communications. 1982 Oct;108(4):1690–4. doi: 10.1016/s0006-291x(82)80105-8.; Mann DF, Byerrum RU. Activation of the de Novo Pathway for Pyridine Nucleotide Biosynthesis Prior to Ricinine Biosynthesis in Castor Beans. Plant Physiol. 1974 Apr 01;53(4):603–9. doi: 10.1104/pp.53.4.603.; Gholson RK. The pyridine nucleotide cycle. Nature. 1966 Nov 26;212(5065):933–5. doi: 10.1038/212933a0. PMID: 4306794.; Joshi JG, Handler P. Biosynthesis of Trigonelline. Journal of Biological Chemistry. 1960 Oct;235(10):2981–3. doi: 10.1016/s0021-9258(18)64575-2. |
| pyrimidine deoxyribonucleotides de novo biosynthesis I Accession ID: BioCyc:ARA_PWY-7184 |
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Zrenner R, Stitt M, Sonnewald U, Boldt R. Pyrimidine and purine biosynthesis and degradation in plants. Annu Rev Plant Biol. 2006;57():805–36. doi: 10.1146/annurev.arplant.57.032905.105421. PMID: 16669783. |
| 5-aminoimidazole ribonucleotide biosynthesis II Accession ID: BioCyc:ARA_PWY-6122 |
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| choline biosynthesis I Accession ID: BioCyc:ARA_PWY-3385 |
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Rontein D, Rhodes D, Hanson AD. Evidence from engineering that decarboxylation of free serine is the major source of ethanolamine moieties in plants. Plant Cell Physiol. 2003 Nov;44(11):1185–91. doi: 10.1093/pcp/pcg144. PMID: 14634155.; Mou Z, Wang X, Fu Z, Dai Y, Han C, Ouyang J, Bao F, Hu Y, Li J. Silencing of Phosphoethanolamine N-Methyltransferase Results in Temperature-Sensitive Male Sterility and Salt Hypersensitivity in Arabidopsis. Plant Cell. 2002 Aug 23;14(9):2031–43. doi: 10.1105/tpc.001701.; Rontein D, Nishida I, Tashiro G, Yoshioka K, Wu W, Voelker DR, Basset G, Hanson AD. Plants Synthesize Ethanolamine by Direct Decarboxylation of Serine Using a Pyridoxal Phosphate Enzyme. Journal of Biological Chemistry. 2001 Sep;276(38):35523–9. doi: 10.1074/jbc.m106038200.; McNeil SD, Nuccio ML, Ziemak MJ, Hanson AD. Enhanced synthesis of choline and glycine betaine in transgenic tobacco plants that overexpress phosphoethanolamine N -methyltransferase. Proc. Natl. Acad. Sci. U.S.A. 2001 Jul 31;98(17):10001–5. doi: 10.1073/pnas.171228998.; Nuccio ML, Ziemak MJ, Henry SA, Weretilnyk EA, Hanson AD. cDNA cloning of phosphoethanolamine N-methyltransferase from spinach by complementation in Schizosaccharomyces pombe and characterization of the recombinant enzyme. J Biol Chem. 2000 May 12;275(19):14095–101. doi: 10.1074/jbc.275.19.14095. PMID: 10799484.; McNeil SD, Nuccio ML, Rhodes D, Shachar-Hill Y, Hanson AD. Radiotracer and computer modeling evidence that phospho-base methylation is the main route of choline synthesis in tobacco. Plant Physiol. 2000 May;123(1):371–80. PMID: 10806254; PMCID: PMC59011.; Weretilnyk EA, Smith DD, Wilch GA, Summers PS. Enzymes of Choline Synthesis in Spinach (Response of Phospho-Base N-Methyltransferase Activities to Light and Salinity). Plant Physiol. 1995 Nov;109(3):1085–91. PMID: 12228655; PMCID: PMC161412.; Summers PS, Weretilnyk EA. Choline Synthesis in Spinach in Relation to Salt Stress. Plant Physiol. 1993 Dec;103(4):1269–76. PMID: 12232019; PMCID: PMC159115. |
| L-citrulline biosynthesis Accession ID: BioCyc:ARA_CITRULBIO-PWY |
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| L-proline biosynthesis I Accession ID: BioCyc:ARA_PROSYN-PWY |
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| folate transformations II Accession ID: BioCyc:ARA_PWY-3841 |
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Goyer A, Collakova E, Díaz de la Garza R, Quinlivan EP, Williamson J, Gregory JF, Shachar-Hill Y, Hanson AD. 5-Formyltetrahydrofolate is an inhibitory but well tolerated metabolite in Arabidopsis leaves. J Biol Chem. 2005 Jul 15;280(28):26137–42. doi: 10.1074/jbc.m503106200. PMID: 15888445.; Basset GJC, Ravanel S, Quinlivan EP, White R, Giovannoni JJ, Rébeillé F, Nichols BP, Shinozaki K, Seki M, Gregory JF, Hanson AD. Folate synthesis in plants: the last step of the p-aminobenzoate branch is catalyzed by a plastidial aminodeoxychorismate lyase. The Plant Journal. 2004 Sep 27;40(4):453–61. doi: 10.1111/j.1365-313x.2004.02231.x.; Basset GJC, Quinlivan EP, Ravanel S, Rébeillé F, Nichols BP, Shinozaki K, Seki M, Adams-Phillips LC, Giovannoni JJ, Gregory JF, Hanson AD. Folate synthesis in plants: The p -aminobenzoate branch is initiated by a bifunctional PabA-PabB protein that is targeted to plastids. Proc. Natl. Acad. Sci. U.S.A. 2004 Jan 26;101(6):1496–501. doi: 10.1073/pnas.0308331100.; Jabrin S, Ravanel S, Gambonnet B, Douce R, Rébeillé F. One-carbon metabolism in plants. Regulation of tetrahydrofolate synthesis during germination and seedling development. Plant Physiol. 2003 Mar;131(3):1431–9. PMID: 12644692; PMCID: PMC166902.; Roje S, Janave MT, Ziemak MJ, Hanson AD. Cloning and Characterization of Mitochondrial 5-Formyltetrahydrofolate Cycloligase from Higher Plants. Journal of Biological Chemistry. 2002 Nov;277(45):42748–54. doi: 10.1074/jbc.m205632200.; Hanson AD, Gregory III JF. Synthesis and turnover of folates in plants. Current Opinion in Plant Biology. 2002 Jun;5(3):244–9. doi: 10.1016/s1369-5266(02)00249-2.; Ravanel S, Cherest H, Jabrin S, Grunwald D, Surdin-Kerjan Y, Douce R, Rébeillé F. Tetrahydrofolate biosynthesis in plants: Molecular and functional characterization of dihydrofolate synthetase and three isoforms of folylpolyglutamate synthetase in Arabidopsis thaliana. Proc. Natl. Acad. Sci. U.S.A. 2001 Dec 18;98(26):15360–5. doi: 10.1073/pnas.261585098.; Hanson AD, Roje S. O |
| trehalose degradation II (trehalase) Accession ID: BioCyc:ARA_PWY0-1182 |
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Avonce N, Leyman B, Thevelein J, Iturriaga G. Trehalose metabolism and glucose sensing in plants. Biochem Soc Trans. 2005 Feb;33(Pt 1):276–9. doi: 10.1042/bst0330276. PMID: 15667325.; Brodmann A, Schuller A, Ludwig-Müller J, Aeschbacher RA, Wiemken A, Boller T, Wingler A. Induction of trehalase in Arabidopsis plants infected with the trehalose-producing pathogen Plasmodiophora brassicae. Mol Plant Microbe Interact. 2002 Jul;15(7):693–700. doi: 10.1094/mpmi.2002.15.7.693. PMID: 12118885.; Müller J, Aeschbacher RA, Wingler A, Boller T, Wiemken A. Trehalose and trehalase in Arabidopsis. Plant Physiol. 2001 Feb;125(2):1086–93. PMID: 11161063; PMCID: PMC64907.; Goddijn OJ, Verwoerd TC, Voogd E, Krutwagen RW, de Graaf PT, van Dun K, Poels J, Ponstein AS, Damm B, Pen J. Inhibition of trehalase activity enhances trehalose accumulation in transgenic plants. Plant Physiol. 1997 Jan;113(1):181–90. PMID: 9008394; PMCID: PMC158129. |
| UTP and CTP dephosphorylation I Accession ID: BioCyc:ARA_PWY-7185 |
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Zrenner R, Stitt M, Sonnewald U, Boldt R. Pyrimidine and purine biosynthesis and degradation in plants. Annu Rev Plant Biol. 2006;57():805–36. doi: 10.1146/annurev.arplant.57.032905.105421. PMID: 16669783. |
| GDP-glucose biosynthesis Accession ID: BioCyc:ARA_PWY-5661 |
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Carlson DM, Hansen RG. The Isolation and Synthesis of Guanosine Diphosphate Glucose. Journal of Biological Chemistry. 1962 Apr;237(4):1260–5. doi: 10.1016/s0021-9258(18)60318-7. |
| 3-phosphoinositide biosynthesis Accession ID: BioCyc:ARA_PWY-6352 |
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| folate polyglutamylation Accession ID: BioCyc:ARA_PWY-2161 |
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Li R, Moore M, King J. Investigating the regulation of one-carbon metabolism in Arabidopsis thaliana. Plant Cell Physiol. 2003 Mar;44(3):233–41. doi: 10.1093/pcp/pcg029. PMID: 12668769.; Hanson AD, Gregory III JF. Synthesis and turnover of folates in plants. Current Opinion in Plant Biology. 2002 Jun;5(3):244–9. doi: 10.1016/s1369-5266(02)00249-2.; Ravanel S, Cherest H, Jabrin S, Grunwald D, Surdin-Kerjan Y, Douce R, Rébeillé F. Tetrahydrofolate biosynthesis in plants: Molecular and functional characterization of dihydrofolate synthetase and three isoforms of folylpolyglutamate synthetase in Arabidopsis thaliana. Proc. Natl. Acad. Sci. U.S.A. 2001 Dec 18;98(26):15360–5. doi: 10.1073/pnas.261585098.; Hanson AD, Roje S. O |
| [2Fe-2S] iron-sulfur cluster biosynthesis Accession ID: BioCyc:ARA_PWY-7250 |
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| glycolysis II (from fructose 6-phosphate) Accession ID: BioCyc:ARA_PWY-5484 |
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Mustroph A, Sonnewald U, Biemelt S. Characterisation of the ATP-dependent phosphofructokinase gene family from Arabidopsis thaliana. FEBS Lett. 2007 May 29;581(13):2401–10. doi: 10.1016/j.febslet.2007.04.060. PMID: 17485088.; Ito H, Iwabuchi M, Ogawa K. The sugar-metabolic enzymes aldolase and triose-phosphate isomerase are targets of glutathionylation in Arabidopsis thaliana: detection using biotinylated glutathione. Plant Cell Physiol. 2003 Jul;44(7):655–60. doi: 10.1093/pcp/pcg098. PMID: 12881492. |
| glutathione biosynthesis Accession ID: BioCyc:ARA_GLUTATHIONESYN-PWY |
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Jez JM, Cahoon RE. Kinetic Mechanism of Glutathione Synthetase from Arabidopsis thaliana. Journal of Biological Chemistry. 2004 Oct;279(41):42726–31. doi: 10.1074/jbc.m407961200.; Jez JM, Cahoon RE, Chen S. Arabidopsis thaliana glutamate-cysteine ligase: functional properties, kinetic mechanism, and regulation of activity. J Biol Chem. 2004 Aug 06;279(32):33463–70. doi: 10.1074/jbc.m405127200. PMID: 15180996.; Meyer AJ, Fricker MD. Control of demand-driven biosynthesis of glutathione in green Arabidopsis suspension culture cells. Plant Physiol. 2002 Dec;130(4):1927–37. PMID: 12481075; PMCID: PMC166703.; Noctor G, Gomez L, Vanacker H, Foyer CH. Interactions between biosynthesis, compartmentation and transport in the control of glutathione homeostasis and signalling. J Exp Bot. 2002 May;53(372):1283–304. doi: 10.1093/jexbot/53.372.1283. PMID: 11997376.; Meyer AJ, May MJ, Fricker M. Quantitative in vivo measurement of glutathione in Arabidopsis cells. The Plant Journal. 2001 Jul;27(1):67–78. doi: 10.1046/j.1365-313x.2001.01071.x.; Xiang C, Werner BL, Christensen EM, Oliver DJ. The biological functions of glutathione revisited in arabidopsis transgenic plants with altered glutathione levels. Plant Physiol. 2001 Jun;126(2):564–74. PMID: 11402187; PMCID: PMC111149.; Wang CL, Oliver DJ. Cloning of the cDNA and genomic clones for glutathione synthetase from Arabidopsis thaliana and complementation of a gsh2 mutant in fission yeast. Plant Mol Biol. 1996 Sep;31(6):1093–104. doi: 10.1007/bf00040827. PMID: 8914526.; Marrs KA. THE FUNCTIONS AND REGULATION OF GLUTATHIONE S-TRANSFERASES IN PLANTS. Annu Rev Plant Physiol Plant Mol Biol. 1996 Jun;47():127–58. doi: 10.1146/annurev.arplant.47.1.127. PMID: 15012285.; Ullmann P, Gondet L, Potier S, Bach TJ. Cloning of Arabidopsis thaliana Glutathione Synthetase (GSH2) by Functional Complementation of a Yeast Gsh2 Mutant. European Journal of Biochemistry. 1996 Mar;236(2):662–9. doi: 10.1111/j.1432-1033.1996.00662.x.; May MJ, Leaver CJ. Arabidopsis thaliana gamma-glutamylcysteine synthetase is structurally unrelated to mammalian, yeast, and Escherichia coli homologs. Proc. Natl. Acad. Sci. U.S.A. 1994 Oct 11;91(21):10059–63. doi: 10.1073/pnas.91.21.10059.; Metroka CE, Lewis NJ, Jacobus DP. Desensitization to dapsone in HIV-positive patients. JAMA. 1992 Jan;267(4):512. doi: 10.1001/jama.267.4.512. PMID: 1530873.; Madamanchi NR, Alscher RG. Metabolic bases for differences in sensitivity of two pea cultivars to sulfur dioxide. Plant Physiol. 1991 Sep;97(1):88–93. PMID: 16668420; PMCID: PMC1080967.; Grill E, Löffler S, Winnacker EL, Zenk MH. Phytochelatins, the heavy-metal-binding peptides of plants, are synthesized from glutathione by a specific gamma-glutamylcysteine dipeptidyl transpeptidase (phytochelatin synthase). Proc Natl Acad Sci U S A. 1989 Sep;86(18):6838–42. PMID: 16594069; PMCID: PMC297945.; Matringe M, Scalla R. Studies on the mode of action of acifluorfen-methyl in nonchlorophyllous soybean cells : accumulation of tetrapyrroles. Plant Physiol. 1988 Feb;86(2):619–22. PMID: 16665956; PMCID: PMC1054533.; Richman PG, Meister A. Regulation of gamma-glutamyl-cysteine synthetase by nonallosteric feedback inhibition by glutathione. Journal of Biological Chemistry. 1975 Feb;250(4):1422–6. doi: 10.1016/s0021-9258(19)41830-9. |
| sulfate activation for sulfonation Accession ID: BioCyc:ARA_PWY-5340 |
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| Calvin-Benson-Bassham cycle Accession ID: BioCyc:ARA_CALVIN-PWY |
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Takahashi H, Takahara K, Hashida SN, Hirabayashi T, Fujimori T, Kawai-Yamada M, Yamaya T, Yanagisawa S, Uchimiya H. Pleiotropic modulation of carbon and nitrogen metabolism in Arabidopsis plants overexpressing the NAD kinase2 gene. Plant Physiol. 2009 Sep;151(1):100–13. PMID: 19587098; PMCID: PMC2735975.; Cleland WW, Andrews TJ, Gutteridge S, Hartman FC, Lorimer GH. Mechanism of Rubisco: The Carbamate as General Base. Chem Rev. 1998 Apr 02;98(2):549–62. doi: 10.1021/cr970010r. PMID: 11848907. |
| superpathway of sucrose and starch metabolism I (non-photosynthetic tissue) Accession ID: BioCyc:ARA_PWYQT-4466 |
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Dai N, Petreikov M, Portnoy V, Katzir N, Pharr DM, Schaffer AA. Cloning and expression analysis of a UDP-galactose/glucose pyrophosphorylase from melon fruit provides evidence for the major metabolic pathway of galactose metabolism in raffinose oligosaccharide metabolizing plants. Plant Physiol. 2006 Sep;142(1):294–304. PMID: 16829585; PMCID: PMC1557607. |
| 3,8-divinyl-chlorophyllide a biosynthesis I (aerobic, light-dependent) Accession ID: BioCyc:ARA_CHLOROPHYLL-SYN |
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Nagata N, Tanaka R, Satoh S, Tanaka A. Identification of a Vinyl Reductase Gene for Chlorophyll Synthesis in Arabidopsis thaliana and Implications for the Evolution of Prochlorococcus Species. Plant Cell. 2005 Jan;17(1):233–40. doi: 10.1105/tpc.104.027276.; Walker CJ, Mansfield KE, Rezzano IN, Hanamoto CM, Smith KM, Castelfranco PA. The magnesium-protoporphyrin IX (oxidative) cyclase system. Studies on the mechanism and specificity of the reaction sequence. Biochem J. 1988 Oct 15;255(2):685–92. PMID: 3202840; PMCID: PMC1135280. |
| superpathway of central carbon metabolism Accession ID: BioCyc:LEISH_PWY3IU-99 |
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Sernee MF, Ralton JE, Dinev Z, Khairallah GN, O’Hair RA, Williams SJ, McConville MJ. Leishmania ß-1,2-mannan is assembled on a mannose-cyclic phosphate primer. Proc. Natl. Acad. Sci. U.S.A. 2006 Jun 20;103(25):9458–63. doi: 10.1073/pnas.0603539103. |