Pathways Knowlegdes

Biological pathway database

Pathway DOIs Note
SMM cycle

Accession ID: Plant Reactome:R-TDI-1119349		 -
Amine and polyamine biosynthesis

Accession ID: Plant Reactome:R-TDI-5096066
  • 10.1016/j.plaphy.2010.02.008
 Fuell C, Elliott KA, Hanfrey CC, Franceschetti M, Michael AJ. Polyamine biosynthetic diversity in plants and algae. Plant Physiol Biochem. 2010 Jul;48(7):513–20. doi: 10.1016/j.plaphy.2010.02.008. PMID: 20227886.
Spermidine biosynthesis

Accession ID: Plant Reactome:R-TDI-1119343		 -
Biotin biosynthesis II

Accession ID: Plant Reactome:R-TDI-1119610		 -
Ethylene biosynthesis and signaling

Accession ID: Plant Reactome:R-TDI-5225808		 -
Fatty acid and lipid metabolism

Accession ID: Plant Reactome:R-TDI-3906998		 -
Choline biosynthesis I

Accession ID: Plant Reactome:R-TDI-1119556
  • 10.1073/pnas.171228998
  • 10.1074/jbc.m704939200
  • 10.1104/pp.103.4.1269
  • 10.1105/tpc.15.00207
 Lin YC, Liu YC, Nakamura Y. The Choline/Ethanolamine Kinase Family in Arabidopsis: Essential Role of CEK4 in Phospholipid Biosynthesis and Embryo Development. Plant Cell. 2015 May;27(5):1497–511. PMID: 25966764; PMCID: PMC4456650.; Waditee R, Bhuiyan NH, Hirata E, Hibino T, Tanaka Y, Shikata M, Takabe T. Metabolic Engineering for Betaine Accumulation in Microbes and Plants. Journal of Biological Chemistry. 2007 Nov;282(47):34185–93. doi: 10.1074/jbc.m704939200.; 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.; 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.
Inorganic nutrients metabolism

Accession ID: Plant Reactome:R-TDI-5368291		 -
Metabolism and regulation

Accession ID: Plant Reactome:R-DRO-2744345		 -
Amino acid biosynthesis

Accession ID: Plant Reactome:R-DRO-5655122		 -
Beta-alanine betaine biosynthesis

Accession ID: Plant Reactome:R-DRO-1119528
  • 10.1046/j.1365-313x.1997.12010133.x
  • 10.1046/j.1365-313x.1998.00316.x
  • 10.1093/jexbot/51.342.81
  • 10.1104/pp.103.020453
  • 10.1104/pp.120.4.945
  • 10.1104/pp.122.3.747
  • 10.1104/pp.126.3.1241
 Raman SB, Rathinasabapathi B. beta-alanine N-methyltransferase of Limonium latifolium. cDNA cloning and functional expression of a novel N-methyltransferase implicated in the synthesis of the osmoprotectant beta-alanine betaine. Plant Physiol. 2003 Jul;132(3):1642–51. PMID: 12857843; PMCID: PMC167101.; Rathinasabapathi B, Fouad WM, Sigua CA. ß-Alanine Betaine Synthesis in the Plumbaginaceae. Purification and Characterization of a Trifunctional,S-Adenosyl-l-Methionine-DependentN-Methyltransferase from Limonium latifoliumLeaves. 2001 Jul 01;126(3):1241–9. doi: 10.1104/pp.126.3.1241.; Huang J, Hirji R, Adam L, Rozwadowski KL, Hammerlindl JK, Keller WA, Selvaraj G. Genetic engineering of glycinebetaine production toward enhancing stress tolerance in plants: metabolic limitations. Plant Physiol. 2000 Mar;122(3):747–56. PMID: 10712538; PMCID: PMC58910.; Sakamoto A, Murata N. Genetic engineering of glycinebetaine synthesis in plants: current status and implications for enhancement of stress tolerance. 2000 Jan;51(342):81–8. doi: 10.1093/jexbot/51.342.81.; McNeil, Nuccio, Hanson. Betaines and related osmoprotectants. Targets for metabolic engineering of stress resistance . Plant Physiol. 1999 Aug;120(4):945–50. PMID: 10444077; PMCID: PMC1539222.; Nuccio ML, Russell BL, Nolte KD, Rathinasabapathi B, Gage DA, Hanson A. The endogenous choline supply limits glycine betaine synthesis in transgenic tobacco expressing choline monooxygenase. The Plant Journal. 1998 Nov;16(4):487–96. doi: 10.1046/j.1365-313x.1998.00316.x.; Hayashi H, Alia, Mustardy L, Deshnium P, Ida M, Murata N. Transformation of Arabidopsis thaliana with the codA gene for choline oxidase; accumulation of glycinebetaine and enhanced tolerance to salt and cold stress. The Plant Journal. 1997 Jul;12(1):133–42. doi: 10.1046/j.1365-313x.1997.12010133.x.
Biotin biosynthesis II

Accession ID: Plant Reactome:R-DRO-1119610		 -
Sterol biosynthesis

Accession ID: Plant Reactome:R-DRO-1119370		 -
SAM cycle

Accession ID: Plant Reactome:R-OGU-1119501		 -
Amine and polyamine biosynthesis

Accession ID: Plant Reactome:R-OGU-5096066
  • 10.1016/j.plaphy.2010.02.008
 Fuell C, Elliott KA, Hanfrey CC, Franceschetti M, Michael AJ. Polyamine biosynthetic diversity in plants and algae. Plant Physiol Biochem. 2010 Jul;48(7):513–20. doi: 10.1016/j.plaphy.2010.02.008. PMID: 20227886.
Spermidine biosynthesis

Accession ID: Plant Reactome:R-OGU-1119343		 -
Biotin biosynthesis II

Accession ID: Plant Reactome:R-OGU-1119610		 -
Hormone signaling, transport, and metabolism

Accession ID: Plant Reactome:R-OGU-2744341		 -
Fatty acid and lipid metabolism

Accession ID: Plant Reactome:R-OGU-3906998		 -
Choline biosynthesis I

Accession ID: Plant Reactome:R-OGU-1119556
  • 10.1073/pnas.171228998
  • 10.1074/jbc.m704939200
  • 10.1104/pp.103.4.1269
  • 10.1105/tpc.15.00207
 Lin YC, Liu YC, Nakamura Y. The Choline/Ethanolamine Kinase Family in Arabidopsis: Essential Role of CEK4 in Phospholipid Biosynthesis and Embryo Development. Plant Cell. 2015 May;27(5):1497–511. PMID: 25966764; PMCID: PMC4456650.; Waditee R, Bhuiyan NH, Hirata E, Hibino T, Tanaka Y, Shikata M, Takabe T. Metabolic Engineering for Betaine Accumulation in Microbes and Plants. Journal of Biological Chemistry. 2007 Nov;282(47):34185–93. doi: 10.1074/jbc.m704939200.; 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.; 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.