Pathways Knowlegdes

Biological pathway database

Pathway DOIs Note
NAD/NADH phosphorylation and dephosphorylation

Accession ID: BioCyc:META_PWY-5083
  • 10.1006/bbrc.1999.1627
  • 10.1016/s0005-2728(03)00045-8
  • 10.1042/bj20040292
  • 10.1046/j.1365-2958.2000.01829.x
  • 10.1093/jexbot/51.349.1389
  • 10.1104/pp.104.040428
  • 10.1104/pp.54.2.136
  • 10.1128/jb.183.13.3974-3981.2001
  • 10.1146/annurev.arplant.52.1.561
  • 10.3109/10409238509113625
 Turner WL, Waller JC, Snedden WA. Identification, molecular cloning and functional characterization of a novel NADH kinase from Arabidopsis thaliana (thale cress). Biochem J. 2005 Jan 01;385(Pt 1):217–23. PMID: 15347288; PMCID: PMC1134690.; Turner WL, Waller JC, Vanderbeld B, Snedden WA. Cloning and characterization of two NAD kinases from Arabidopsis. identification of a calmodulin binding isoform. Plant Physiol. 2004 Jul;135(3):1243–55. PMID: 15247403; PMCID: PMC519044.; Heazlewood JL, Howell KA, Millar AH. Mitochondrial complex I from Arabidopsis and rice: orthologs of mammalian and fungal components coupled with plant-specific subunits. Biochimica et Biophysica Acta (BBA) - Bioenergetics. 2003 Jul;1604(3):159–69. doi: 10.1016/s0005-2728(03)00045-8.; Kemmer G, Reilly TJ, Schmidt-Brauns J, Zlotnik GW, Green BA, Fiske MJ, Herbert M, Kraiß A, Schlo¨r S, Smith A, Reidl J. NadN and e (P4) Are Essential for Utilization of NAD and Nicotinamide Mononucleotide but Not Nicotinamide Riboside in Haemophilus influenzae. J Bacteriol. 2001 Jul;183(13):3974–81. doi: 10.1128/jb.183.13.3974-3981.2001.; Møller IM. PLANT MITOCHONDRIA AND OXIDATIVE STRESS: Electron Transport, NADPH Turnover, and Metabolism of Reactive Oxygen Species. Annu. Rev. Plant. Physiol. Plant. Mol. Biol. 2001 Jun;52(1):561–91. doi: 10.1146/annurev.arplant.52.1.561.; Gallais S, de Crescenzo MP, Laval-Martin DL. Evidence of active NADP+ phosphatase in dormant seeds of Avena sativa L. 2000 Aug;51(349):1389–94. doi: 10.1093/jexbot/51.349.1389.; Reidl J, Schlör S, Kraiss A, Schmidt-Brauns J, Kemmer G, Soleva E. NADP and NAD utilization in Haemophilus influenzae. Mol Microbiol. 2000 Mar;35(6):1573–81. doi: 10.1046/j.1365-2958.2000.01829.x. PMID: 10760156.; Bykova NV, Rasmusson AG, Igamberdiev AU, Gardeström P, Møller IM. Two Separate Transhydrogenase Activities Are Present in Plant Mitochondria. Biochemical and Biophysical Research Communications. 1999 Nov;265(1):106–11. doi: 10.1006/bbrc.1999.1627.; You K, Oppenheimer NJ. Stereospecificity for Nicotinamide Nucleotides in Enzymatic and Chemical Hydride Transfer Reaction. Critical Reviews in Biochemistry. 1985 Jan;17(4):313–451. doi: 10.3109/10409238509113625.; Wells GN, Hageman RH. Specificity for nicotinamide adenine dinucleotide by nitrate reductase from leaves. Plant Physiol. 1974 Aug;54(2):136–41. PMID: 16658848; PMCID: PMC541519.
rotenoid biosynthesis II

Accession ID: BioCyc:META_PWY-6425
  • 10.1016/s0031-9422(98)00178-2
 Crombie L, Whiting DA. Review article number 135 biosynthesis in the rotenoid group of natural products: applications of isotope methodology. Phytochemistry. 1998 Nov 20;49(6):1479–507. doi: 10.1016/s0031-9422(98)00178-2. PMID: 11711058.
rotenoid biosynthesis I

Accession ID: BioCyc:META_PWY-5775
  • 10.1016/s0031-9422(98)00178-2
 Crombie L, Whiting DA. Review article number 135 biosynthesis in the rotenoid group of natural products: applications of isotope methodology. Phytochemistry. 1998 Nov 20;49(6):1479–507. doi: 10.1016/s0031-9422(98)00178-2. PMID: 11711058.
aerobic respiration III (alternative oxidase pathway)

Accession ID: BioCyc:META_PWY-4302
  • 10.1016/s0378-1119(97)00502-7
  • 10.1023/a:1005818507743
  • 10.1073/pnas.89.22.10842
  • 10.1074/jbc.m206724200
  • 10.1146/annurev.arplant.48.1.703
 Berthold DA, Voevodskaya N, Stenmark P, Gräslund A, Nordlund P. EPR studies of the mitochondrial alternative oxidase. Evidence for a diiron carboxylate center. J Biol Chem. 2002 Nov 15;277(46):43608–14. doi: 10.1074/jbc.m206724200. PMID: 12215444.; Ito Y, Saisho D, Nakazono M, Tsutsumi N, Hirai A. Transcript levels of tandem-arranged alternative oxidase genes in rice are increased by low temperature. Gene. 1997 Dec 12;203(2):121–9. doi: 10.1016/s0378-1119(97)00502-7. PMID: 9426242.; Saisho D, Nambara E, Naito S, Tsutsumi N, Hirai A, Nakazono M. Characterization of the gene family for alternative oxidase from Arabidopsis thaliana. Plant Mol Biol. 1997 Nov;35(5):585–96. doi: 10.1023/a:1005818507743. PMID: 9349280.; Vanlerberghe GC, McIntosh L. ALTERNATIVE OXIDASE: From Gene to Function. Annu Rev Plant Physiol Plant Mol Biol. 1997 Jun;48():703–34. doi: 10.1146/annurev.arplant.48.1.703. PMID: 15012279.; Kumar AM, Söll D. Arabidopsis alternative oxidase sustains Escherichia coli respiration. Proc. Natl. Acad. Sci. U.S.A. 1992 Nov 15;89(22):10842–6. doi: 10.1073/pnas.89.22.10842.
aerobic respiration I (cytochrome c)

Accession ID: BioCyc:META_PWY-3781
  • 10.1038/nature11541
  • 10.1074/jbc.273.38.24529
  • 10.1111/j.1432-1033.1991.tb15775.x
  • 10.1128/jb.180.16.4051-4055.1998
 Feng Y, Li W, Li J, Wang J, Ge J, Xu D, Liu Y, Wu K, Zeng Q, Wu JW, Tian C, Zhou B, Yang M. Structural insight into the type-II mitochondrial NADH dehydrogenases. Nature. 2012 Nov 15;491(7424):478–82. doi: 10.1038/nature11541. PMID: 23086143.; Luttik MAH, Overkamp KM, Kötter P, de Vries S, van Dijken JP, Pronk JT. The Saccharomyces cerevisiae NDE1 and NDE2 Genes Encode Separate Mitochondrial NADH Dehydrogenases Catalyzing the Oxidation of Cytosolic NADH. Journal of Biological Chemistry. 1998 Sep;273(38):24529–34. doi: 10.1074/jbc.273.38.24529.; Small WC, McAlister-Henn L. Identification of a Cytosolically Directed NADH Dehydrogenase in Mitochondria of Saccharomyces cerevisiae. J Bacteriol. 1998 Aug 15;180(16):4051–5. doi: 10.1128/jb.180.16.4051-4055.1998.; MARRES CAM, de VRIES S, GRIVELL LA. Isolation and inactivation of the nuclear gene encoding the rotenone-insensitive internal NADH: ubiquinone oxidoreductase of mitochondria from Saccharomyces cerevisiae. European Journal of Biochemistry. 1991 Feb;195(3):857–62. doi: 10.1111/j.1432-1033.1991.tb15775.x.
rotenoid biosynthesis II

Accession ID: PlantCyc:PLANT_PWY-6425
  • 10.1016/s0031-9422(98)00178-2
 Crombie L, Whiting DA. Review article number 135 biosynthesis in the rotenoid group of natural products: applications of isotope methodology. Phytochemistry. 1998 Nov 20;49(6):1479–507. doi: 10.1016/s0031-9422(98)00178-2. PMID: 11711058.
rotenoid biosynthesis I

Accession ID: PlantCyc:PLANT_PWY-5775
  • 10.1016/s0031-9422(98)00178-2
 Crombie L, Whiting DA. Review article number 135 biosynthesis in the rotenoid group of natural products: applications of isotope methodology. Phytochemistry. 1998 Nov 20;49(6):1479–507. doi: 10.1016/s0031-9422(98)00178-2. PMID: 11711058.
4-hydroxytamoxifen, dexamethasone, and retinoic acids regulation of p27 expression

Accession ID: WikiPathways:WP3879
  • 10.1186/1475-2867-10-3
 Eto I. Upstream molecular signaling pathways of p27 (Kip1) expression: Effects of 4-hydroxytamoxifen, dexamethasone, and retinoic acids. Cancer Cell International. 2010 Feb 19;10(1):3. doi: 10.1186/1475-2867-10-3.