Pathways Knowlegdes

Biological pathway database

Pathway DOIs Note
Ethene biosynthesis from methionine

Accession ID: Plant Reactome:R-JCU-1119334
  • 10.1111/nph.13209
 Voesenek LACJ, Bailey-Serres J. Flood adaptive traits and processes: an overview. New Phytol. 2015 Apr;206(1):57–73. doi: 10.1111/nph.13209. PMID: 25580769.
Tricin biosynthesis

Accession ID: Plant Reactome:R-JCU-9609573
  • 10.1007/s00280-006-0368-5
  • 10.1007/s00425-008-0806-1
  • 10.1016/j.foodchem.2012.09.129
  • 10.1016/j.intimp.2012.06.005
  • 10.1016/j.phytochem.2004.02.017
  • 10.1016/j.phytochem.2005.11.022
  • 10.1016/j.phytochem.2007.01.015
  • 10.1016/j.phytochem.2009.09.025
  • 10.1021/jf0703912
  • 10.1104/pp.114.239723
  • 10.1104/pp.114.253757
  • 10.1104/pp.15.00566
 Lam PY, Liu H, Lo C. Completion of Tricin Biosynthesis Pathway in Rice: Cytochrome P450 75B4 Is a Unique Chrysoeriol 5'-Hydroxylase. Plant Physiol. 2015 Aug;168(4):1527–36. PMID: 26082402; PMCID: PMC4528758.; Lan W, Lu F, Regner M, Zhu Y, Rencoret J, Ralph SA, Zakai UI, Morreel K, Boerjan W, Ralph J. Tricin, a flavonoid monomer in monocot lignification. Plant Physiol. 2015 Apr;167(4):1284–95. PMID: 25667313; PMCID: PMC4378158.; Lam PY, Zhu FY, Chan WL, Liu H, Lo C. Cytochrome P450 93G1 Is a Flavone Synthase II That Channels Flavanones to the Biosynthesis of Tricin O-Linked Conjugates in Rice. Plant Physiol. 2014 Jul;165(3):1315–27. PMID: 24843076; PMCID: PMC4081339.; Moheb A, Grondin M, Ibrahim RK, Roy R, Sarhan F. Winter wheat hull (husk) is a valuable source for tricin, a potential selective cytotoxic agent. Food Chem. 2013 Jun 01;138(2-3):931–7. doi: 10.1016/j.foodchem.2012.09.129. PMID: 23411198.; Shalini V, Bhaskar S, Kumar KS, Mohanlal S, Jayalekshmy A, Helen A. Molecular mechanisms of anti-inflammatory action of the flavonoid, tricin from Njavara rice (Oryza sativa L.) in human peripheral blood mononuclear cells: possible role in the inflammatory signaling. Int Immunopharmacol. 2012 Sep;14(1):32–8. doi: 10.1016/j.intimp.2012.06.005. PMID: 22705359.; Chang CL, Wang GJ, Zhang LJ, Tsai WJ, Chen RY, Wu YC, Kuo YH. Cardiovascular protective flavonolignans and flavonoids from Calamus quiquesetinervius. Phytochemistry. 2010 Feb;71(2-3):271–9. doi: 10.1016/j.phytochem.2009.09.025. PMID: 20006366.; Shih CH, Chu H, Tang LK, Sakamoto W, Maekawa M, Chu IK, Wang M, Lo C. Functional characterization of key structural genes in rice flavonoid biosynthesis. Planta. 2008 Nov;228(6):1043–54. doi: 10.1007/s00425-008-0806-1. PMID: 18726614.; Kong CH, Zhao H, Xu XH, Wang P, Gu Y. Activity and allelopathy of soil of flavone o-glycosides from rice. J Agric Food Chem. 2007 Jul 25;55(15):6007–12. doi: 10.1021/jf0703912. PMID: 17602647.; Duarte-Almeida JM, Negri G, Salatino A, de Carvalho JE, Lajolo FM. Antiproliferative and antioxidant activities of a tricin acylated glycoside from sugarcane (Saccharum officinarum) juice. Phytochemistry. 2007 Apr;68(8):1165–71. doi: 10.1016/j.phytochem.2007.01.015. PMID: 17350657.; Cai H, Boocock DJ, Steward WP, Gescher AJ. Tissue distribution in mice and metabolism in murine and human liver of apigenin and tricin, flavones with putative cancer chemopreventive properties. Cancer Chemother Pharmacol. 2007 Jul;60(2):257–66. doi: 10.1007/s00280-006-0368-5. PMID: 17089164.; Kim BG, Lee Y, Hur HG, Lim Y, Ahn JH. Flavonoid 3'-O-methyltransferase from rice: cDNA cloning, characterization and functional expression. Phytochemistry. 2006 Feb;67(4):387–94. doi: 10.1016/j.phytochem.2005.11.022. PMID: 16412485.; Kong C, Xu X, Zhou B, Hu F, Zhang C, Zhang M. Two compounds from allelopathic rice accession and their inhibitory activity on weeds and fungal pathogens. Phytochemistry. 2004 Apr;65(8):1123–8. doi: 10.1016/j.phytochem.2004.02.017. PMID: 15110693.
Response to iron deficiency

Accession ID: Plant Reactome:R-JCU-9025714		 -
Amino acid biosynthesis

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

Accession ID: Plant Reactome:R-PAB-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.
Cofactor biosyntheses

Accession ID: Plant Reactome:R-PAB-2867929		 -
Ethene biosynthesis from methionine

Accession ID: Plant Reactome:R-PAB-1119334
  • 10.1111/nph.13209
 Voesenek LACJ, Bailey-Serres J. Flood adaptive traits and processes: an overview. New Phytol. 2015 Apr;206(1):57–73. doi: 10.1111/nph.13209. PMID: 25580769.
Fatty acid and lipid metabolism

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

Accession ID: Plant Reactome:R-PAB-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-PAB-5368291		 -
Amino acid biosynthesis

Accession ID: Plant Reactome:R-SIT-5655122		 -
Tricin biosynthesis

Accession ID: Plant Reactome:R-SIT-9609573
  • 10.1007/s00280-006-0368-5
  • 10.1007/s00425-008-0806-1
  • 10.1016/j.foodchem.2012.09.129
  • 10.1016/j.intimp.2012.06.005
  • 10.1016/j.phytochem.2004.02.017
  • 10.1016/j.phytochem.2005.11.022
  • 10.1016/j.phytochem.2007.01.015
  • 10.1016/j.phytochem.2009.09.025
  • 10.1021/jf0703912
  • 10.1104/pp.114.239723
  • 10.1104/pp.114.253757
  • 10.1104/pp.15.00566
 Lam PY, Liu H, Lo C. Completion of Tricin Biosynthesis Pathway in Rice: Cytochrome P450 75B4 Is a Unique Chrysoeriol 5'-Hydroxylase. Plant Physiol. 2015 Aug;168(4):1527–36. PMID: 26082402; PMCID: PMC4528758.; Lan W, Lu F, Regner M, Zhu Y, Rencoret J, Ralph SA, Zakai UI, Morreel K, Boerjan W, Ralph J. Tricin, a flavonoid monomer in monocot lignification. Plant Physiol. 2015 Apr;167(4):1284–95. PMID: 25667313; PMCID: PMC4378158.; Lam PY, Zhu FY, Chan WL, Liu H, Lo C. Cytochrome P450 93G1 Is a Flavone Synthase II That Channels Flavanones to the Biosynthesis of Tricin O-Linked Conjugates in Rice. Plant Physiol. 2014 Jul;165(3):1315–27. PMID: 24843076; PMCID: PMC4081339.; Moheb A, Grondin M, Ibrahim RK, Roy R, Sarhan F. Winter wheat hull (husk) is a valuable source for tricin, a potential selective cytotoxic agent. Food Chem. 2013 Jun 01;138(2-3):931–7. doi: 10.1016/j.foodchem.2012.09.129. PMID: 23411198.; Shalini V, Bhaskar S, Kumar KS, Mohanlal S, Jayalekshmy A, Helen A. Molecular mechanisms of anti-inflammatory action of the flavonoid, tricin from Njavara rice (Oryza sativa L.) in human peripheral blood mononuclear cells: possible role in the inflammatory signaling. Int Immunopharmacol. 2012 Sep;14(1):32–8. doi: 10.1016/j.intimp.2012.06.005. PMID: 22705359.; Chang CL, Wang GJ, Zhang LJ, Tsai WJ, Chen RY, Wu YC, Kuo YH. Cardiovascular protective flavonolignans and flavonoids from Calamus quiquesetinervius. Phytochemistry. 2010 Feb;71(2-3):271–9. doi: 10.1016/j.phytochem.2009.09.025. PMID: 20006366.; Shih CH, Chu H, Tang LK, Sakamoto W, Maekawa M, Chu IK, Wang M, Lo C. Functional characterization of key structural genes in rice flavonoid biosynthesis. Planta. 2008 Nov;228(6):1043–54. doi: 10.1007/s00425-008-0806-1. PMID: 18726614.; Kong CH, Zhao H, Xu XH, Wang P, Gu Y. Activity and allelopathy of soil of flavone o-glycosides from rice. J Agric Food Chem. 2007 Jul 25;55(15):6007–12. doi: 10.1021/jf0703912. PMID: 17602647.; Duarte-Almeida JM, Negri G, Salatino A, de Carvalho JE, Lajolo FM. Antiproliferative and antioxidant activities of a tricin acylated glycoside from sugarcane (Saccharum officinarum) juice. Phytochemistry. 2007 Apr;68(8):1165–71. doi: 10.1016/j.phytochem.2007.01.015. PMID: 17350657.; Cai H, Boocock DJ, Steward WP, Gescher AJ. Tissue distribution in mice and metabolism in murine and human liver of apigenin and tricin, flavones with putative cancer chemopreventive properties. Cancer Chemother Pharmacol. 2007 Jul;60(2):257–66. doi: 10.1007/s00280-006-0368-5. PMID: 17089164.; Kim BG, Lee Y, Hur HG, Lim Y, Ahn JH. Flavonoid 3'-O-methyltransferase from rice: cDNA cloning, characterization and functional expression. Phytochemistry. 2006 Feb;67(4):387–94. doi: 10.1016/j.phytochem.2005.11.022. PMID: 16412485.; Kong C, Xu X, Zhou B, Hu F, Zhang C, Zhang M. Two compounds from allelopathic rice accession and their inhibitory activity on weeds and fungal pathogens. Phytochemistry. 2004 Apr;65(8):1123–8. doi: 10.1016/j.phytochem.2004.02.017. PMID: 15110693.
Mugineic acid biosynthesis

Accession ID: Plant Reactome:R-SIT-9025754
  • 10.1007/s11103-007-9262-8
  • 10.1046/j.1365-313x.2003.01878.x
  • 10.1074/jbc.m604133200
  • 10.1104/pp.107.107912
  • 10.1104/pp.121.3.947
  • 10.2183/pjab.86.900
 Kobayashi T, Nakanishi H, Nishizawa NK. Recent insights into iron homeostasis and their application in graminaceous crops. Proc Jpn Acad Ser B Phys Biol Sci. 2010;86(9):900–13. PMID: 21084773; PMCID: PMC3035920.; Inoue H, Takahashi M, Kobayashi T, Suzuki M, Nakanishi H, Mori S, Nishizawa NK. Identification and localisation of the rice nicotianamine aminotransferase gene OsNAAT1 expression suggests the site of phytosiderophore synthesis in rice. Plant Mol Biol. 2008 Jan;66(1-2):193–203. doi: 10.1007/s11103-007-9262-8. PMID: 18034312.; Cheng L, Wang F, Shou H, Huang F, Zheng L, He F, Li J, Zhao FJ, Ueno D, Ma JF, Wu P. Mutation in nicotianamine aminotransferase stimulated the Fe(II) acquisition system and led to iron accumulation in rice. Plant Physiol. 2007 Dec;145(4):1647–57. PMID: 17951455; PMCID: PMC2151683.; Bashir K, Inoue H, Nagasaka S, Takahashi M, Nakanishi H, Mori S, Nishizawa NK. Cloning and Characterization of Deoxymugineic Acid Synthase Genes from Graminaceous Plants. Journal of Biological Chemistry. 2006 Oct;281(43):32395–402. doi: 10.1074/jbc.m604133200.; Inoue H, Higuchi K, Takahashi M, Nakanishi H, Mori S, Nishizawa NK. Three rice nicotianamine synthase genes, OsNAS1, OsNAS2, and OsNAS3 are expressed in cells involved in long-distance transport of iron and differentially regulated by iron. The Plant Journal. 2003 Oct 13;36(3):366–81. doi: 10.1046/j.1365-313x.2003.01878.x.; Takahashi M, Yamaguchi H, Nakanishi H, Shioiri T, Nishizawa NK, Mori S. Cloning two genes for nicotianamine aminotransferase, a critical enzyme in iron acquisition (Strategy II) in graminaceous plants. Plant Physiol. 1999 Nov;121(3):947–56. PMID: 10557244; PMCID: PMC59459.
Metabolism and regulation

Accession ID: Plant Reactome:R-CSI-2744345		 -
Amino acid metabolism

Accession ID: Plant Reactome:R-CSI-2744343		 -
SMM cycle

Accession ID: Plant Reactome:R-CSI-1119349		 -
Methionine biosynthesis II

Accession ID: Plant Reactome:R-CSI-1119400		 -
Amine and polyamine biosynthesis

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

Accession ID: Plant Reactome:R-CSI-1119610		 -