Pathways Knowlegdes

Biological pathway database

Pathway DOIs Note
Secondary Metabolites: Leucine Biosynthesis

Accession ID: PathBank:SMP0000996		 -
Secondary Metabolites: Histidine Biosynthesis

Accession ID: PathBank:SMP0001000		 -
Lipopolysaccharide Biosynthesis II

Accession ID: PathBank:SMP0001919		 -
Tryptophan Metabolism II

Accession ID: PathBank:SMP0001930		 -
Glutathione Metabolism II

Accession ID: PathBank:SMP0001941		 -
Glutathione Metabolism III

Accession ID: PathBank:SMP0002032		 -
Thiamin Diphosphate Biosynthesis

Accession ID: PathBank:SMP0002042		 -
Purine Nucleotides De Novo Biosynthesis 2

Accession ID: PathBank:SMP0002047		 -
Secondary Metabolites: Enterobacterial Common Antigen Biosynthesis 2

Accession ID: PathBank:SMP0002059		 -
Secondary Metabolites: Enterobacterial Common Antigen Biosynthesis 3

Accession ID: PathBank:SMP0002060		 -
Polymyxin Resistance

Accession ID: PathBank:SMP0002065		 -
Putrescine Degradation II

Accession ID: PathBank:SMP0002067		 -
Lipopolysaccharide Biosynthesis III

Accession ID: PathBank:SMP0002071		 -
Peptidoglycan Biosynthesis II

Accession ID: PathBank:SMP0002074		 -
Hydrogen Sulfide Biosynthesis I

Accession ID: PathBank:SMP0002078		 -
4-Aminobutanoate Degradation I

Accession ID: PathBank:SMP0002080		 -
O-Antigen Building Blocks Biosynthesis

Accession ID: PathBank:SMP0002101		 -
PCO cycle

Accession ID: Plant Reactome:R-HVU-1119312
  • 10.1016/j.jphotobiol.2014.11.009
  • 10.1016/j.molp.2016.02.002
  • 10.1093/jxb/erp056
  • 10.1093/jxb/erq028
  • 10.1093/jxb/ers398
  • 10.1104/pp.106.085514
  • 10.1104/pp.112.201459
  • 10.1111/j.1365-3040.2009.01937.x
  • 10.1111/j.1438-8677.2012.00723.x
  • 10.1111/jipb.12125
  • 10.1111/jipb.12336
  • 10.1111/pce.12078
  • 10.1111/ppl.12104
  • 10.1371/journal.pone.0039658
  • 10.3389/fpls.2016.01165
  • 10.7717/peerj.28
 Cui LL, Lu YS, Li Y, Yang C, Peng XX. Overexpression of Glycolate Oxidase Confers Improved Photosynthesis under High Light and High Temperature in Rice. Front Plant Sci. 2016;7():1165. PMID: 27540387; PMCID: PMC4972838.; Zhang Z, Xu Y, Xie Z, Li X, He ZH, Peng XX. Association-Dissociation of Glycolate Oxidase with Catalase in Rice: A Potential Switch to Modulate Intracellular H2O2 Levels. Mol Plant. 2016 May 02;9(5):737–48. doi: 10.1016/j.molp.2016.02.002. PMID: 26900141.; Wang D, Liu H, Li S, Zhai G, Shao J, Tao Y. Characterization and molecular cloning of a serine hydroxymethyltransferase 1 (OsSHM1) in rice. J Integr Plant Biol. 2015 Sep;57(9):745–56. doi: 10.1111/jipb.12336. PMID: 25641188.; Zhang Z, Mao X, Ou J, Ye N, Zhang J, Peng X. Distinct photorespiratory reactions are preferentially catalyzed by glutamate:glyoxylate and serine:glyoxylate aminotransferases in rice. Journal of Photochemistry and Photobiology B: Biology. 2015 Jan;142():110–7. doi: 10.1016/j.jphotobiol.2014.11.009.; Ye N, Yang G, Chen Y, Zhang C, Zhang J, Peng X. Two hydroxypyruvate reductases encoded by OsHPR1 and OsHPR2 are involved in photorespiratory metabolism in rice. J Integr Plant Biol. 2014 Feb;56(2):170–80. doi: 10.1111/jipb.12125. PMID: 24401104.; Lu Y, Li Y, Yang Q, Zhang Z, Chen Y, Zhang S, Peng XX. Suppression of glycolate oxidase causes glyoxylate accumulation that inhibits photosynthesis through deactivating Rubisco in rice. Physiol Plant. 2014 Mar;150(3):463–76. doi: 10.1111/ppl.12104. PMID: 24102419.; Sørhagen K, Laxa M, Peterhänsel C, Reumann S. The emerging role of photorespiration and non-photorespiratory peroxisomal metabolism in pathogen defence. Plant Biol (Stuttg). 2013 Jul;15(4):723–36. doi: 10.1111/j.1438-8677.2012.00723.x. PMID: 23506300.; ZHOU Q, YU Q, WANG Z, PAN Y, LV W, ZHU L, CHEN R, HE G. Knockdown of GDCH gene reveals reactive oxygen species-induced leaf senescence in rice. Plant Cell & Environment. 2013 Mar 12;36(8):1476–89. doi: 10.1111/pce.12078.; Chern M, Bai W, Chen X, Canlas PE, Ronald PC. Reduced expression of glycolate oxidase leads to enhanced disease resistance in rice. PeerJ. 2013;1():e28. PMID: 23638363; PMCID: PMC3628735.; Suzuki Y, Makino A. Translational downregulation of RBCL is operative in the coordinated expression of Rubisco genes in senescent leaves in rice. J Exp Bot. 2013 Feb;64(4):1145–52. PMID: 23349140; PMCID: PMC3580822.; Suzuki Y, Makino A. Availability of Rubisco small subunit up-regulates the transcript levels of large subunit for stoichiometric assembly of its holoenzyme in rice. Plant Physiol. 2012 Sep;160(1):533–40. PMID: 22811433; PMCID: PMC3440226.; Zhang Z, Lu Y, Zhai L, Deng R, Jiang J, Li Y, He Z, Peng X. Glycolate Oxidase Isozymes Are Coordinately Controlled by GLO1 and GLO4 in Rice. PLoS ONE. 2012 Jun 26;7(6):e39658. doi: 10.1371/journal.pone.0039658.; Yu L, Jiang J, Zhang C, Jiang L, Ye N, Lu Y, Yang G, Liu E, Peng C, He Z, Peng X. Glyoxylate rather than ascorbate is an efficient precursor for oxalate biosynthesis in rice. J Exp Bot. 2010 Jun;61(6):1625–34. PMID: 20194922; PMCID: PMC2914580.; Xu H, Zhang J, Zeng J, Jiang L, Liu E, Peng C, He Z, Peng X. Inducible antisense suppression of glycolate oxidase reveals its strong regulation over photosynthesis in rice. J Exp Bot. 2009;60(6):1799–809. doi: 10.1093/jxb/erp056. PMID: 19264754.; SUZUKI Y, MIYAMOTO T, YOSHIZAWA R, MAE T, MAKINO A. Rubisco content and photosynthesis of leaves at different positions in transgenic rice with an overexpression of RBCS. Plant Cell & Environment. 2009 Mar 05;32(4):417–27. doi: 10.1111/j.1365-3040.2009.01937.x.; Igarashi D, Tsuchida H, Miyao M, Ohsumi C. Glutamate:glyoxylate aminotransferase modulates amino acid content during photorespiration. Plant Physiol. 2006 Nov;142(3):901–10. PMID: 16950862; PMCID: PMC1630728.
Metabolism and regulation

Accession ID: Plant Reactome:R-OAU-2744345		 -
PCO cycle

Accession ID: Plant Reactome:R-TAE-1119312
  • 10.1016/j.jphotobiol.2014.11.009
  • 10.1016/j.molp.2016.02.002
  • 10.1093/jxb/erp056
  • 10.1093/jxb/erq028
  • 10.1093/jxb/ers398
  • 10.1104/pp.106.085514
  • 10.1104/pp.112.201459
  • 10.1111/j.1365-3040.2009.01937.x
  • 10.1111/j.1438-8677.2012.00723.x
  • 10.1111/jipb.12125
  • 10.1111/jipb.12336
  • 10.1111/pce.12078
  • 10.1111/ppl.12104
  • 10.1371/journal.pone.0039658
  • 10.3389/fpls.2016.01165
  • 10.7717/peerj.28
 Cui LL, Lu YS, Li Y, Yang C, Peng XX. Overexpression of Glycolate Oxidase Confers Improved Photosynthesis under High Light and High Temperature in Rice. Front Plant Sci. 2016;7():1165. PMID: 27540387; PMCID: PMC4972838.; Zhang Z, Xu Y, Xie Z, Li X, He ZH, Peng XX. Association-Dissociation of Glycolate Oxidase with Catalase in Rice: A Potential Switch to Modulate Intracellular H2O2 Levels. Mol Plant. 2016 May 02;9(5):737–48. doi: 10.1016/j.molp.2016.02.002. PMID: 26900141.; Wang D, Liu H, Li S, Zhai G, Shao J, Tao Y. Characterization and molecular cloning of a serine hydroxymethyltransferase 1 (OsSHM1) in rice. J Integr Plant Biol. 2015 Sep;57(9):745–56. doi: 10.1111/jipb.12336. PMID: 25641188.; Zhang Z, Mao X, Ou J, Ye N, Zhang J, Peng X. Distinct photorespiratory reactions are preferentially catalyzed by glutamate:glyoxylate and serine:glyoxylate aminotransferases in rice. Journal of Photochemistry and Photobiology B: Biology. 2015 Jan;142():110–7. doi: 10.1016/j.jphotobiol.2014.11.009.; Ye N, Yang G, Chen Y, Zhang C, Zhang J, Peng X. Two hydroxypyruvate reductases encoded by OsHPR1 and OsHPR2 are involved in photorespiratory metabolism in rice. J Integr Plant Biol. 2014 Feb;56(2):170–80. doi: 10.1111/jipb.12125. PMID: 24401104.; Lu Y, Li Y, Yang Q, Zhang Z, Chen Y, Zhang S, Peng XX. Suppression of glycolate oxidase causes glyoxylate accumulation that inhibits photosynthesis through deactivating Rubisco in rice. Physiol Plant. 2014 Mar;150(3):463–76. doi: 10.1111/ppl.12104. PMID: 24102419.; Sørhagen K, Laxa M, Peterhänsel C, Reumann S. The emerging role of photorespiration and non-photorespiratory peroxisomal metabolism in pathogen defence. Plant Biol (Stuttg). 2013 Jul;15(4):723–36. doi: 10.1111/j.1438-8677.2012.00723.x. PMID: 23506300.; ZHOU Q, YU Q, WANG Z, PAN Y, LV W, ZHU L, CHEN R, HE G. Knockdown of GDCH gene reveals reactive oxygen species-induced leaf senescence in rice. Plant Cell & Environment. 2013 Mar 12;36(8):1476–89. doi: 10.1111/pce.12078.; Chern M, Bai W, Chen X, Canlas PE, Ronald PC. Reduced expression of glycolate oxidase leads to enhanced disease resistance in rice. PeerJ. 2013;1():e28. PMID: 23638363; PMCID: PMC3628735.; Suzuki Y, Makino A. Translational downregulation of RBCL is operative in the coordinated expression of Rubisco genes in senescent leaves in rice. J Exp Bot. 2013 Feb;64(4):1145–52. PMID: 23349140; PMCID: PMC3580822.; Suzuki Y, Makino A. Availability of Rubisco small subunit up-regulates the transcript levels of large subunit for stoichiometric assembly of its holoenzyme in rice. Plant Physiol. 2012 Sep;160(1):533–40. PMID: 22811433; PMCID: PMC3440226.; Zhang Z, Lu Y, Zhai L, Deng R, Jiang J, Li Y, He Z, Peng X. Glycolate Oxidase Isozymes Are Coordinately Controlled by GLO1 and GLO4 in Rice. PLoS ONE. 2012 Jun 26;7(6):e39658. doi: 10.1371/journal.pone.0039658.; Yu L, Jiang J, Zhang C, Jiang L, Ye N, Lu Y, Yang G, Liu E, Peng C, He Z, Peng X. Glyoxylate rather than ascorbate is an efficient precursor for oxalate biosynthesis in rice. J Exp Bot. 2010 Jun;61(6):1625–34. PMID: 20194922; PMCID: PMC2914580.; Xu H, Zhang J, Zeng J, Jiang L, Liu E, Peng C, He Z, Peng X. Inducible antisense suppression of glycolate oxidase reveals its strong regulation over photosynthesis in rice. J Exp Bot. 2009;60(6):1799–809. doi: 10.1093/jxb/erp056. PMID: 19264754.; SUZUKI Y, MIYAMOTO T, YOSHIZAWA R, MAE T, MAKINO A. Rubisco content and photosynthesis of leaves at different positions in transgenic rice with an overexpression of RBCS. Plant Cell & Environment. 2009 Mar 05;32(4):417–27. doi: 10.1111/j.1365-3040.2009.01937.x.; Igarashi D, Tsuchida H, Miyao M, Ohsumi C. Glutamate:glyoxylate aminotransferase modulates amino acid content during photorespiration. Plant Physiol. 2006 Nov;142(3):901–10. PMID: 16950862; PMCID: PMC1630728.