Pathways Knowlegdes

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Pathway DOIs Note
thiamine salvage IV (yeast)

Accession ID: BioCyc:ARA_PWY-7356
  • 10.1016/0167-4838(90)90160-h
 Nosaka K. High affinity of acid phosphatase encoded by PHO3 gene in Saccharomyces cerevisiae for thiamin phosphates. Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology. 1990 Feb;1037(2):147–54. doi: 10.1016/0167-4838(90)90160-h.
hydroxymethylpyrimidine salvage

Accession ID: BioCyc:ARA_PWY-6910
  • 10.1016/j.bioorg.2007.10.005
  • 10.1038/nchembio.2007.13
 Jenkins AL, Zhang Y, Ealick SE, Begley TP. Mutagenesis studies on TenA: A thiamin salvage enzyme from Bacillus subtilis. Bioorganic Chemistry. 2008 Feb;36(1):29–32. doi: 10.1016/j.bioorg.2007.10.005.; Jenkins AH, Schyns G, Potot S, Sun G, Begley TP. A new thiamin salvage pathway. Nat Chem Biol. 2007 Aug;3(8):492–7. doi: 10.1038/nchembio.2007.13. PMID: 17618314.
pyrimidine ribonucleotides interconversion

Accession ID: BioCyc:ARA_PWY-5687
  • 10.1146/annurev.arplant.57.032905.105421
 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.
4-amino-2-methyl-5-diphosphomethylpyrimidine biosynthesis

Accession ID: BioCyc:ARA_PWY-6890
  • 10.1016/j.abb.2006.11.011
 Ajjawi I, Tsegaye Y, Shintani D. Determination of the genetic, molecular, and biochemical basis of the Arabidopsis thaliana thiamin auxotroph th1. Archives of Biochemistry and Biophysics. 2007 Mar;459(1):107–14. doi: 10.1016/j.abb.2006.11.011.
lipid-dependent phytate biosynthesis II (via Ins(1,3,4)P3)

Accession ID: BioCyc:ARA_PWY-4562
  • 10.1073/pnas.0504172102
 Stevenson-Paulik J, Bastidas RJ, Chiou S, Frye RA, York JD. Generation of phytate-free seeds in Arabidopsis through disruption of inositol polyphosphate kinases. Proc. Natl. Acad. Sci. U.S.A. 2005 Aug 17;102(35):12612–7. doi: 10.1073/pnas.0504172102.
superpathway of L-threonine biosynthesis

Accession ID: BioCyc:ARA_THRESYN-PWY		 -
lipid-dependent phytate biosynthesis I (via Ins(1,4,5)P3)

Accession ID: BioCyc:ARA_PWY-4541
  • 10.1073/pnas.0504172102
 Stevenson-Paulik J, Bastidas RJ, Chiou S, Frye RA, York JD. Generation of phytate-free seeds in Arabidopsis through disruption of inositol polyphosphate kinases. Proc. Natl. Acad. Sci. U.S.A. 2005 Aug 17;102(35):12612–7. doi: 10.1073/pnas.0504172102.
superpathway of pyrimidine ribonucleosides salvage

Accession ID: BioCyc:ARA_PWY-7196
  • 10.1007/s00294-002-0296-9
  • 10.1007/s002940050482
 Kurtz JE, Exinger F, Erbs P, Jund R. The URH1 uridine ribohydrolase of Saccharomyces cerevisiae. Curr Genet. 2002 Jun;41(3):132–41. doi: 10.1007/s00294-002-0296-9. PMID: 12111094.; Kurtz JE, Exinger F, Erbs P, Jund R. New insights into the pyrimidine salvage pathway of Saccharomyces cerevisiae: requirement of six genes for cytidine metabolism. Curr Genet. 1999 Sep;36(3):130–6. doi: 10.1007/s002940050482. PMID: 10501935.
D-galactose degradation III

Accession ID: BioCyc:ARA_PWY-3821
  • 10.1016/j.pbi.2004.03.004
  • 10.1016/s0960-9822(02)01260-5
 Seifert GJ. Nucleotide sugar interconversions and cell wall biosynthesis: how to bring the inside to the outside. Curr Opin Plant Biol. 2004 Jun;7(3):277–84. doi: 10.1016/j.pbi.2004.03.004. PMID: 15134748.; Seifert GJ, Barber C, Wells B, Dolan L, Roberts K. Galactose biosynthesis in Arabidopsis: genetic evidence for substrate channeling from UDP-D-galactose into cell wall polymers. Curr Biol. 2002 Oct 29;12(21):1840–5. doi: 10.1016/s0960-9822(02)01260-5. PMID: 12419184.
folate polyglutamylation II

Accession ID: BioCyc:ARA_PWY-2161B-PMN
  • 10.1006/bbrc.1996.1608
  • 10.1016/s1369-5266(02)00249-2
  • 10.1073/pnas.261585098
  • 10.1074/jbc.m504306200
  • 10.1146/annurev.arplant.52.1.119
  • 10.18388/abp.2000_3992
 Orsomando G, de la Garza RD, Green BJ, Peng M, Rea PA, Ryan TJ, Gregory JF, Hanson AD. Plant gamma-glutamyl hydrolases and folate polyglutamates: characterization, compartmentation, and co-occurrence in vacuoles. J Biol Chem. 2005 Aug 12;280(32):28877–84. doi: 10.1074/jbc.m504306200. PMID: 15961386.; 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. ONE-CARBONMETABOLISM INHIGHERPLANTS. Annu. Rev. Plant. Physiol. Plant. Mol. Biol. 2001 Jun;52(1):119–37. doi: 10.1146/annurev.arplant.52.1.119.; Brzezinska A, Winska P, Balinska M. Cellular aspects of folate and antifolate membrane transport. Acta Biochim Pol. 2000 Sep 30;47(3):735–49. doi: 10.18388/abp.2000_3992.; Huangpu J, Pak JH, Graham MC, Rickle SA, Graham JS. Purification and Molecular Analysis of an Extracellular ?-Glutamyl Hydrolase Present in Young Tissues of the Soybean Plant. Biochemical and Biophysical Research Communications. 1996 Nov;228(1):1–6. doi: 10.1006/bbrc.1996.1608.
L-ornithine biosynthesis I

Accession ID: BioCyc:ARA_GLUTORN-PWY
  • 10.1016/j.plaphy.2005.06.007
 Slocum RD. Genes, enzymes and regulation of arginine biosynthesis in plants. Plant Physiol Biochem. 2005 Aug;43(8):729–45. doi: 10.1016/j.plaphy.2005.06.007. PMID: 16122935.
adenosine deoxyribonucleotides de novo biosynthesis

Accession ID: BioCyc:ARA_PWY-7227		 -
sorbitol biosynthesis II

Accession ID: BioCyc:ARA_PWY-5530		 -
L-homoserine biosynthesis

Accession ID: BioCyc:ARA_HOMOSERSYN-PWY
  • 10.1074/jbc.m509324200
 Curien G, Ravanel S, Robert M, Dumas R. Identification of six novel allosteric effectors of Arabidopsis thaliana aspartate kinase-homoserine dehydrogenase isoforms. Physiological context sets the specificity. J Biol Chem. 2005 Dec 16;280(50):41178–83. doi: 10.1074/jbc.m509324200. PMID: 16216875.
TCA cycle variation V (plant)

Accession ID: BioCyc:ARA_PWYQT-4481
  • 10.1016/0003-9861(81)90297-6
  • 10.1042/bj20100497
  • 10.1074/jbc.m109.097477
  • 10.1104/pp.107.114975
  • 10.1104/pp.59.4.630
  • 10.1111/j.1432-1033.1970.tb01058.x
  • 10.1111/j.1432-1033.1972.tb01792.x
 Tronconi MA, Gerrard Wheeler MC, Maurino VG, Drincovich MF, Andreo CS. NAD-malic enzymes of Arabidopsis thaliana display distinct kinetic mechanisms that support differences in physiological control. Biochem J. 2010 Sep 01;430(2):295–303. doi: 10.1042/bj20100497. PMID: 20528775.; Tronconi MA, Maurino VG, Andreo CS, Drincovich MF. Three Different and Tissue-specific NAD-Malic Enzymes Generated by Alternative Subunit Association in Arabidopsis thaliana. Journal of Biological Chemistry. 2010 Apr;285(16):11870–9. doi: 10.1074/jbc.m109.097477.; Tronconi MA, Fahnenstich H, Gerrard Weehler MC, Andreo CS, Flügge UI, Drincovich MF, Maurino VG. Arabidopsis NAD-malic enzyme functions as a homodimer and heterodimer and has a major impact on nocturnal metabolism. Plant Physiol. 2008 Apr;146(4):1540–52. PMID: 18223148; PMCID: PMC2287332.; Grover SD, Canellas PF, Wedding RT. Purification of NAD malic enzyme from potato and investigation of some physical and kinetic properties. Archives of Biochemistry and Biophysics. 1981 Jul;209(2):396–407. doi: 10.1016/0003-9861(81)90297-6.; Day DA, Hanson JB. Pyruvate and malate transport and oxidation in corn mitochondria. Plant Physiol. 1977 Apr;59(4):630–5. PMID: 16659908; PMCID: PMC542463.; Coleman JOD, Palmer JM. The Oxidation of Malate by Isolated Plant Mitochondria. European Journal of Biochemistry. 1972 Apr;26(4):499–509. doi: 10.1111/j.1432-1033.1972.tb01792.x.; Macrae AR, Moorhouse R. The Oxidation of Malate by Mitochondria Isolated from Cauliflower Buds. European Journal of Biochemistry. 1970 Sep;16(1):96–102. doi: 10.1111/j.1432-1033.1970.tb01058.x.
L-ornithine biosynthesis II

Accession ID: BioCyc:ARA_ARGININE-SYN4-PWY		 -
formate assimilation into 5,10-methylenetetrahydrofolate

Accession ID: BioCyc:ARA_PWY-1722
  • 10.1128/jb.185.24.7169-7175.2003
 Marx CJ, Laukel M, Vorholt JA, Lidstrom ME. Purification of the Formate-Tetrahydrofolate Ligasefrom Methylobacterium extorquens AM1 and Demonstrationof Its Requirement for MethylotrophicGrowth. J Bacteriol. 2003 Dec 15;185(24):7169–75. doi: 10.1128/jb.185.24.7169-7175.2003.
UDP-D-galacturonate biosynthesis II (from D-galacturonate)

Accession ID: BioCyc:ARA_PWY-4
  • 10.1016/0006-3002(61)90223-2
  • 10.1016/s0021-9258(18)64358-3
  • 10.1016/s0021-9258(18)93978-5
 Neufeld EF, Feingold DS, Ilves SM, Kessler G, Hassid WZ. Phosphorylation of d-Galacturonic Acid by Extracts from Germinating Seeds of Phaseolus aureus. Journal of Biological Chemistry. 1961 Dec;236(12):3102–5. doi: 10.1016/s0021-9258(18)93978-5.; NEUFELD EF, FEINGOLD DS. Isolation of uridine diphosphate-galacturonic acid from seedlings of Phaseolus aureus. Biochim Biophys Acta. 1961 Nov 11;53():589–90. doi: 10.1016/0006-3002(61)90223-2. PMID: 14479162.; Kessler G, Neufeld EF, Feingold DS, Hassid WZ. Metabolism of d-Glucuronic Acid and d-Galacturonic Acid by Phaseolus aureus Seedlings. Journal of Biological Chemistry. 1961 Feb;236(2):308–12. doi: 10.1016/s0021-9258(18)64358-3.
adenine and adenosine salvage VI

Accession ID: BioCyc:ARA_PWY-6619
  • 10.1034/j.1399-3054.2002.1150106.x
  • 10.1104/pp.124.4.1775
 Allen M, Qin W, Moreau F, Moffatt B. Adenine phosphoribosyltransferase isoforms of Arabidopsis and their potential contributions to adenine and cytokinin metabolism. Physiol Plant. 2002 May;115(1):56–68. doi: 10.1034/j.1399-3054.2002.1150106.x. PMID: 12010467.; Moffatt BA, Wang L, Allen MS, Stevens YY, Qin W, Snider J, von Schwartzenberg K. Adenosine kinase of Arabidopsis. Kinetic properties and gene expression. Plant Physiol. 2000 Dec;124(4):1775–85. PMID: 11115893; PMCID: PMC59874.
glycerol degradation I

Accession ID: BioCyc:ARA_PWY-4261
  • 10.1016/s0014-5793(03)00033-4
  • 10.1111/j.1365-313x.2003.01989.x
 Eastmond PJ. Glycerol-insensitive Arabidopsis mutants: gli1 seedlings lack glycerol kinase, accumulate glycerol and are more resistant to abiotic stress. The Plant Journal. 2004 Jan 26;37(4):617–25. doi: 10.1111/j.1365-313x.2003.01989.x.; Shen W, Wei Y, Dauk M, Zheng Z, Zou J. Identification of a mitochondrial glycerol-3-phosphate dehydrogenase from Arabidopsis thaliana: evidence for a mitochondrial glycerol-3-phosphate shuttle in plants. FEBS Lett. 2003 Feb 11;536(1-3):92–6. doi: 10.1016/s0014-5793(03)00033-4. PMID: 12586344.