Pathways Knowlegdes
Necessitatibus eius consequatur ex aliquid fuga eum quidem sint consectetur velit
| Pathway | DOIs | Note |
|---|---|---|
| abscisic acid biosynthesis Accession ID: BioCyc:META_PWY-695 |
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Schwartz SH, Qin X, Zeevaart JA. Elucidation of the indirect pathway of abscisic acid biosynthesis by mutants, genes, and enzymes. Plant Physiol. 2003 Apr;131(4):1591–601. PMID: 12692318; PMCID: PMC1540303.; Milborrow BV. The pathway of biosynthesis of abscisic acid in vascular plants: a review of the present state of knowledge of ABA biosynthesis. 2001 Jun 01;52(359):1145–64. doi: 10.1093/jexbot/52.359.1145. |
| diadinoxanthin and fucoxanthin biosynthesis Accession ID: BioCyc:META_PWY-7950 |
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Dambek M, Eilers U, Breitenbach J, Steiger S, Buchel C, Sandmann G. Biosynthesis of fucoxanthin and diadinoxanthin and function of initial pathway genes in Phaeodactylum tricornutum. Journal of Experimental Botany. 2012 Aug 09;63(15):5607–12. doi: 10.1093/jxb/ers211.; Asai A, Sugawara T, Ono H, Nagao A. Biotransformation of fucoxanthinol into amarouciaxanthin A in mice and HepG2 cells: formation and cytotoxicity of fucoxanthin metabolites. Drug Metab Dispos. 2004 Feb;32(2):205–11. doi: 10.1124/dmd.32.2.205. PMID: 14744942. |
| neoxanthin biosynthesis Accession ID: BioCyc:META_PWY-6809 |
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Bouvier F, D’Harlingue A, Backhaus RA, Kumagai MH, Camara B. Identification of neoxanthin synthase as a carotenoid cyclase paralog. European Journal of Biochemistry. 2000 Nov;267(21):6346–52. doi: 10.1046/j.1432-1327.2000.01722.x. |
| superpathway of carotenoid biosynthesis in plants Accession ID: BioCyc:META_CAROTENOID-PWY |
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Maresca JA, Graham JE, Wu M, Eisen JA, Bryant DA. Identification of a fourth family of lycopene cyclases in photosynthetic bacteria. Proc Natl Acad Sci U S A. 2007 Jul 10;104(28):11784–9. PMID: 17606904; PMCID: PMC1905924.; Grotewold E. The genetics and biochemistry of floral pigments. Annu Rev Plant Biol. 2006;57():761–80. doi: 10.1146/annurev.arplant.57.032905.105248. PMID: 16669781.; Choi SK, Matsuda S, Hoshino T, Peng X, Misawa N. Characterization of bacterial beta-carotene 3,3'-hydroxylases, CrtZ, and P450 in astaxanthin biosynthetic pathway and adonirubin production by gene combination in Escherichia coli. Appl Microbiol Biotechnol. 2006 Oct;72(6):1238–46. doi: 10.1007/s00253-006-0426-2. PMID: 16614859.; Breitenbach J, Sandmann G. zeta-Carotene cis isomers as products and substrates in the plant poly-cis carotenoid biosynthetic pathway to lycopene. Planta. 2005 Mar;220(5):785–93. doi: 10.1007/s00425-004-1395-2. PMID: 15503129.; Stickforth P, Steiger S, Hess WR, Sandmann G. A novel type of lycopene epsilon-cyclase in the marine cyanobacterium Prochlorococcus marinus MED4. Arch Microbiol. 2003 Jun;179(6):409–15. doi: 10.1007/s00203-003-0545-4. PMID: 12712234.; Zhu C, Yamamura S, Nishihara M, Koiwa H, Sandmann G. cDNAs for the synthesis of cyclic carotenoids in petals of Gentiana lutea and their regulation during flower development. Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression. 2003 Feb;1625(3):305–8. doi: 10.1016/s0167-4781(03)00017-4.; Hornero-Méndez D, Britton G. Involvement of NADPH in the cyclization reaction of carotenoid biosynthesis. FEBS Lett. 2002 Mar 27;515(1-3):133–6. doi: 10.1016/s0014-5793(02)02453-5. PMID: 11943208.; Hirschberg J. Carotenoid biosynthesis in flowering plants. Curr Opin Plant Biol. 2001 Jun;4(3):210–8. doi: 10.1016/s1369-5266(00)00163-1. PMID: 11312131.; Cunningham FX, Gantt E. One ring or two? Determination of ring number in carotenoids by lycopene epsilon-cyclases. Proc Natl Acad Sci U S A. 2001 Feb 27;98(5):2905–10. PMID: 11226339; PMCID: PMC30238.; Josse EM, Simkin AJ, Gaffé J, Labouré AM, Kuntz M, Carol P. A plastid terminal oxidase associated with carotenoid desaturation during chromoplast differentiation. Plant Physiol. 2000 Aug;123(4):1427–36. PMID: 10938359; PMCID: PMC59099.; Breitenbach J, Kuntz M, Takaichi S, Sandmann G. Catalytic properties of an expressed and purified higher plant type?-carotene desaturase fromCapsicum annuum. European Journal of Biochemistry. 1999 Oct;265(1):376–83. doi: 10.1046/j.1432-1327.1999.00746.x.; Linden H. Carotenoid hydroxylase from Haematococcus pluvialis: cDNA sequence, regulation and functional complementation. Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression. 1999 Sep;1446(3):203–12. doi: 10.1016/s0167-4781(99)00088-3.; Bouvier F, Keller Y, d'Harlingue A, Camara B. Xanthophyll biosynthesis: molecular and functional characterization of carotenoid hydroxylases from pepper fruits (Capsicum annuum L.). Biochimica et Biophysica Acta (BBA) - Lipids and Lipid Metabolism. 1998 Apr;1391(3):320–8. doi: 10.1016/s0005-2760(98)00029-0.; Fraser PD, Shimada H, Misawa N. Enzymic confirmation of reactions involved in routes to astaxanthin formation, elucidated using a direct substrate in vitro assay. European Journal of Biochemistry. 1998 Mar;252(2):229–36. doi: 10.1046/j.1432-1327.1998.2520229.x.; Schneider C, Böger P, Sandmann G. Phytoene Desaturase: Heterologous Expression in an Active State, Purification, and Biochemical Properties. Protein Expression and Purification. 1997 Jul;10(2):175–9. doi: 10.1006/prep.1997.0730.; Fraser PD, Miura Y, Misawa N. In Vitro Characterization of Astaxanthin Biosynthetic Enzymes. Journal of Biological Chemistry. 1997 Mar;272(10):6128–35. doi: 10.1074/jbc.272.10.6128.; Sun Z, Gantt E, Cunningham FX. Cloning and functional analysis of the beta-carotene hydroxylase of Arabidopsis thaliana. J Biol Chem. 1996 Oct 04;271(40):24349–52. doi: 10.1074/jbc.271.40.24349. PMID: 8798688.; Albrecht M, Linden H, Sandmann G. Biochemical Characterization of Purified ?-Carotene Desaturase from Anabaena PCC 7120 after Expression in Escherichia coli. European Journal of Biochemistry. 1996 Feb;236(1):115–20. doi: 10.1111/j.1432-1033.1996.00115.x.; Pecker I, Gabbay R, Cunningham FX, Hirschberg J. Cloning and characterization of the cDNA for lycopene beta-cyclase from tomato reveals decrease in its expression during fruit ripening. Plant Mol Biol. 1996 Feb;30(4):807–19. doi: 10.1007/bf00019013. PMID: 8624411.; Hugueney P, Badillo A, Chen H, Klein A, Hirschberg J, Camara B, Kuntz M. Metabolism of cyclic carotenoids: a model for the alteration of this biosynthetic pathway in Capsicum annuum chromoplasts. The Plant Journal. 1995 Sep;8(3):417–24. doi: 10.1046/j.1365-313x.1995.08030417.x.; Cunningham FX, Sun Z, Chamovitz D, Hirschberg J, Gantt E. Molecular structure and enzymatic function of lycopene cyclase from the cyanobacterium Synechococcus sp strain PCC7942. Plant Cell. 1994 Aug;6(8):1107–21. PMID: 7919981; PMCID: PMC160505.; Cunningham FX, Chamovitz D, Misawa N, Gantt E, Hirschberg J. Cloning and functional expression in Escherichia coli of a cyanobacterial gene for lycopene cyclase, the enzyme that catalyzes the biosynthesis of beta-carotene. FEBS Lett. 1993 Aug 09;328(1-2):130–8. doi: 10.1016/0014-5793(93)80980-9. PMID: 8344419.; Fraser PD, Linden H, Sandmann G. Purification and reactivation of recombinant Synechococcus phytoene desaturase from an overexpressing strain of Escherichia coli. Biochem J. 1993 May 01;291 ( Pt 3)():687–92. PMID: 8489496; PMCID: PMC1132422. |
| Abscisic acid homeostasis Accession ID: Plant Reactome:R-OSA-9608520 |
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Liu Z, Yan JP, Li DK, Luo Q, Yan Q, Liu ZB, Ye LM, Wang JM, Li XF, Yang Y. UDP-glucosyltransferase71c5, a major glucosyltransferase, mediates abscisic acid homeostasis in Arabidopsis. Plant Physiol. 2015 Apr;167(4):1659–70. PMID: 25713337; PMCID: PMC4378179.; Dong T, Xu ZY, Park Y, Kim DH, Lee Y, Hwang I. Abscisic acid uridine diphosphate glucosyltransferases play a crucial role in abscisic acid homeostasis in Arabidopsis. Plant Physiol. 2014 May;165(1):277–89. PMID: 24676855; PMCID: PMC4012586.; Xu ZJ, Nakajima M, Suzuki Y, Yamaguchi I. Cloning and characterization of the abscisic acid-specific glucosyltransferase gene from adzuki bean seedlings. Plant Physiol. 2002 Jul;129(3):1285–95. PMID: 12114582; PMCID: PMC166522.; Bray EA, Zeevaart JA. The Compartmentation of Abscisic Acid and beta-d-Glucopyranosyl Abscisate in Mesophyll Cells. Plant Physiol. 1985 Nov;79(3):719–22. PMID: 16664479; PMCID: PMC1074958.; Boyer GL, Zeevaart JA. Isolation and Quantitation of beta-d-Glucopyranosyl Abscisate from Leaves of Xanthium and Spinach. Plant Physiol. 1982 Jul;70(1):227–31. PMID: 16662451; PMCID: PMC1067117. |
| Metabolism and regulation Accession ID: Plant Reactome:R-OSA-2744345 |
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Saqib A, Scheller HV, Fredslund F, Welner DH. Molecular characteristics of plant UDP-arabinopyranose mutases. Glycobiology. 2019 Nov 20;29(12):839–46. PMID: 31679023; PMCID: PMC6861824.; Perera I, Seneweera S, Hirotsu N. Manipulating the Phytic Acid Content of Rice Grain Toward Improving Micronutrient Bioavailability. Rice (N Y). 2018 Jan 11;11(1):4. PMID: 29327163; PMCID: PMC5764899.; Rautengarten C, Birdseye D, Pattathil S, McFarlane HE, Saez-Aguayo S, Orellana A, Persson S, Hahn MG, Scheller HV, Heazlewood JL, Ebert B. The elaborate route for UDP-arabinose delivery into the Golgi of plants. Proc Natl Acad Sci U S A. 2017 Apr 18;114(16):4261–6. PMID: 28373556; PMCID: PMC5402404.; Yu L, Liu Y, Lu L, Zhang Q, Chen Y, Zhou L, Chen H, Peng C. Ascorbic acid deficiency leads to increased grain chalkiness in transgenic rice for suppressed of L-GalLDH. J Plant Physiol. 2017 Apr;211():13–26. doi: 10.1016/j.jplph.2016.11.017. PMID: 28142093.; Qin H, Deng Z, Zhang C, Wang Y, Wang J, Liu H, Zhang Z, Huang R, Zhang Z. Rice GDP-mannose pyrophosphorylase OsVTC1-1 and OsVTC1-3 play different roles in ascorbic acid synthesis. Plant Mol Biol. 2016 Feb;90(3):317–27. doi: 10.1007/s11103-015-0420-0. PMID: 26715595.; Nozoye T, Nagasaka S, Kobayashi T, Sato Y, Uozumi N, Nakanishi H, Nishizawa NK. The Phytosiderophore Efflux Transporter TOM2 Is Involved in Metal Transport in Rice. Journal of Biological Chemistry. 2015 Nov;290(46):27688–99. doi: 10.1074/jbc.m114.635193.; Bennett T. PIN proteins and the evolution of plant development. Trends Plant Sci. 2015 Aug;20(8):498–507. doi: 10.1016/j.tplants.2015.05.005. PMID: 26051227.; Mohanta TK, Mohanta N, Bae H. Identification and Expression Analysis of PIN-Like (PILS) Gene Family of Rice Treated with Auxin and Cytokinin. Genes (Basel). 2015 Jul 16;6(3):622–40. PMID: 26193322; PMCID: PMC4584321.; 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.; Zhang G, Liu R, Zhang C, Tang K, Sun M, Yan G, Liu Q. Manipulation of the Rice L-Galactose Pathway: Evaluation of the Effects of Transgene Overexpression on Ascorbate Accumulation and Abiotic Stress Tolerance. PLoS ONE. 2015 May 04;10(5):e0125870. doi: 10.1371/journal.pone.0125870.; Seyfferth C, Tsuda K. Salicylic acid signal transduction: the initiation of biosynthesis, perception and transcriptional reprogramming. Front Plant Sci. 2014;5():697. PMID: 25538725; PMCID: PMC4260477.; Wang W, Bai M, Wang Z. The brassinosteroid signaling network — a paradigm of signal integration. Current Opinion in Plant Biology. 2014 Oct;21():147–53. doi: 10.1016/j.pbi.2014.07.012.; Balzan S, Johal GS, Carraro N. The role of auxin transporters in monocots development. Front Plant Sci. 2014;5():393. PMID: 25177324; PMCID: PMC4133927.; Bernardo-García S, de Lucas M, Martínez C, Espinosa-Ruiz A, Davière JM, Prat S. BR-dependent phosphorylation modulates PIF4 transcriptional activity and shapes diurnal hypocotyl growth. Genes Dev. 2014 Aug 01;28(15):1681–94. PMID: 25085420; PMCID: PMC4117943.; Oh E, Zhu J, Ryu H, Hwang I, Wang Z. TOPLESS mediates brassinosteroid-induced transcriptional repression through interaction with BZR1. Nature Communications. 2014 Jun 18;5(1):4140. doi: 10.1038/ncomms5140.; Lunn JE, Delorge I, Figueroa CM, Van Dijck P, Stitt M. Trehalose metabolism in plants. Plant J. 2014 Aug;79(4):544–67. doi: 10.1111/tpj.12509. PMID: 24645920.; 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.; Barberon M, Dubeaux G, Kolb C, Isono E, Zelazny E, Vert G. Polarization of IRON-REGULATED TRANSPORTER 1 (IRT1) to the plant-soil interface plays crucial role in metal homeostasis. Proc Natl Acad Sci U S A. 2014 Jun 03;111(22):8293–8. PMID: 24843126; PMCID: PMC4050562.; Lee C, Teng Q, Zhong R, Yuan Y, Ye Z. Functional roles of rice glycosyltransferase family GT43 in xylan biosynthesis. Plant Signaling & Behavior. 2014 Feb 13;9(3):e27809. doi: 10.4161/psb.27809.; Ma B, He SJ, Duan KX, Yin CC, Chen H, Yang C, Xiong Q, Song QX, Lu X, Chen HW, Zhang WK, Lu TG, Chen SY, Zhang JS. Identification of rice ethylene-response mutants and characterization of MHZ7/OsEIN2 in distinct ethylene response and yield trait regulation. Mol Plant. 2013 Nov;6(6):1830–48. doi: 10.1093/mp/sst087. PMID: 23718947.; Wang Q, Zhang W, Yin Z, Wen CK. Rice CONSTITUTIVE TRIPLE-RESPONSE2 is involved in the ethylene-receptor signalling and regulation of various aspects of rice growth and development. J Exp Bot. 2013 Nov;64(16):4863–75. PMID: 24006427; PMCID: PMC3830475.; Werner AK, Medina-Escobar N, Zulawski M, Sparkes IA, Cao FQ, Witte CP. The ureide-degrading reactions of purine ring catabolism employ three amidohydrolases and one aminohydrolase in Arabidopsis, soybean, and rice. Plant Physiol. 2013 Oct;163(2):672–81. PMID: 23940254; PMCID: PMC3793049.; Itai RN, Ogo Y, Kobayashi T, Nakanishi H, Nishizawa NK. Rice genes involved in phytosiderophore biosynthesis are synchronously regulated during the early stages of iron deficiency in roots. Rice (N Y). 2013 Jun 25;6(1):16. PMID: 24280375; PMCID: PMC4883707.; Flis VV, Daum G. Lipid Transport between the Endoplasmic Reticulum and Mitochondria. Cold Spring Harbor Perspectives in Biology. 2013 Jun 01;5(6):a013235. doi: 10.1101/cshperspect.a013235.; Bender RL, Fekete ML, Klinkenberg PM, Hampton M, Bauer B, Malecha M, Lindgren K, A. Maki J, Perera MADN, Nikolau BJ, Carter CJ. PIN6 is required for nectary auxin response and short stamen development. The Plant Journal. 2013 May 02;74(6):893–904. doi: 10.1111/tpj.12184.; Sawchuk MG, Edgar A, Scarpella E. Patterning of Leaf Vein Networks by Convergent Auxin Transport Pathways. PLoS Genet. 2013 Feb 21;9(2):e1003294. doi: 10.1371/journal.pgen.1003294.; Chiniquy D, Sharma V, Schultink A, Baidoo EE, Rautengarten C, Cheng K, Carroll A, Ulvskov P, Harholt J, Keasling JD, Pauly M, Scheller HV, Ronald PC. XAX1 from glycosyltransferase family 61 mediates xylosyltransfer to rice xylan. Proc Natl Acad Sci U S A. 2012 Oct 16;109(42):17117–22. PMID: 23027943; PMCID: PMC3479505.; Zhao B, Li J. Regulation of brassinosteroid biosynthesis and inactivation. J Integr Plant Biol. 2012 Oct;54(10):746–59. doi: 10.1111/j.1744-7909.2012.01168.x. PMID: 22963251.; Oh E, Zhu JY, Wang ZY. Interaction between BZR1 and PIF4 integrates brassinosteroid and environmental responses. Nat Cell Biol. 2012 Aug;14(8):802–9. PMID: 22820378; PMCID: PMC3703456.; Ding Z, Wang B, Moreno I, Dupláková N, Simon S, Carraro N, Reemmer J, Pencík A, Chen X, Tejos R, Skupa P, Pollmann S, Mravec J, Petrášek J, Zažímalová E, Honys D, Rolcík J, Murphy A, Orellana A, Geisler M, Friml J. ER-localized auxin transporter PIN8 regulates auxin homeostasis and male gametophyte development in Arabidopsis. Nat Commun. 2012 Jul 03;3():941. doi: 10.1038/ncomms1941. PMID: 22760640.; Kakei Y, Ishimaru Y, Kobayashi T, Yamakawa T, Nakanishi H, Nishizawa NK. OsYSL16 plays a role in the allocation of iron. Plant Molecular Biology. 2012 May 29;79(6):583–94. doi: 10.1007/s11103-012-9930-1.; Barbez E, Kubeš M, Rolcík J, Béziat C, Pencík A, Wang B, Rosquete MR, Zhu J, Dobrev PI, Lee Y, Zažímalovà E, Petrášek J, Geisler M, Friml J, Kleine-Vehn J. A novel putative auxin carrier family regulates intracellular auxin homeostasis in plants. Nature. 2012 Apr 15;485(7396):119–22. doi: 10.1038/nature11001. PMID: 22504182.; Mano Y, Nemoto K. The pathway of auxin biosynthesis in plants. Journal of Experimental Botany. 2012 Mar 23;63(8):2853–72. doi: 10.1093/jxb/ers091.; Wang P, Kong CH, Sun B, Xu XH. Distribution and function of allantoin (5-ureidohydantoin) in rice grains. J Agric Food Chem. 2012 Mar 21;60(11):2793–8. doi: 10.1021/jf2051043. PMID: 22369364.; Zhao Y. Auxin biosynthesis: a simple two-step pathway converts tryptophan to indole-3-acetic acid in plants. Mol Plant. 2012 Mar;5(2):334–8. PMID: 22155950; PMCID: PMC3309920.; Anders N, Wilkinson MD, Lovegrove A, Freeman J, Tryfona T, Pellny TK, Weimar T, Mortimer JC, Stott K, Baker JM, Defoin-Platel M, Shewry PR, Dupree P, Mitchell RAC. Glycosyl transferases in family 61 mediate arabinofuranosyl transfer onto xylan in grasses. Proc. Natl. Acad. Sci. U.S.A. 2012 Jan 03;109(3):989–93. doi: 10.1073/pnas.1115858109.; Lee S, Ryoo N, Jeon J, Guerinot ML, An G. Activation of rice Yellow Stripe1-Like 16 (OsYSL16) enhances iron efficiency. Molecules and Cells. 2012 Jan 03;33(2):117–26. doi: 10.1007/s10059-012-2165-9.; Saito M, Yoshida M. Expression analysis of the gene family associated with raffinose accumulation in rice seedlings under cold stress. J Plant Physiol. 2011 Dec 15;168(18):2268–71. doi: 10.1016/j.jplph.2011.07.002. PMID: 21824678.; Takahashi R, Ishimaru Y, Nakanishi H, Nishizawa NK. Role of the iron transporter OsNRAMP1 in cadmium uptake and accumulation in rice. Plant Signaling & Behavior. 2011 Nov;6(11):1813–6. doi: 10.4161/psb.6.11.17587.; Won C, Shen X, Mashiguchi K, Zheng Z, Dai X, Cheng Y, Kasahara H, Kamiya Y, Chory J, Zhao Y. Conversion of tryptophan to indole-3-acetic acid by TRYPTOPHAN AMINOTRANSFERASES OF ARABIDOPSIS and YUCCAs in Arabidopsis. Proc. Natl. Acad. Sci. U.S.A. 2011 Oct 24;108(45):18518–23. doi: 10.1073/pnas.1108436108.; Mashiguchi K, Tanaka K, Sakai T, Sugawara S, Kawaide H, Natsume M, Hanada A, Yaeno T, Shirasu K, Yao H, McSteen P, Zhao Y, Hayashi K, Kamiya Y, Kasahara H. The main auxin biosynthesis pathway in Arabidopsis. Proc. Natl. Acad. Sci. U.S.A. 2011 Oct 24;108(45):18512–7. doi: 10.1073/pnas.1108434108.; Nozoye T, Nagasaka S, Kobayashi T, Takahashi M, Sato Y, Sato Y, Uozumi N, Nakanishi H, Nishizawa NK. Phytosiderophore Efflux Transporters Are Crucial for Iron Acquisition in Graminaceous Plants. Journal of Biological Chemistry. 2011 Feb;286(7):5446–54. doi: 10.1074/jbc.m110.180026.; Ludwig-Müller J. Auxin conjugates: their role for plant development and in the evolution of land plants. J Exp Bot. 2011 Mar;62(6):1757–73. doi: 10.1093/jxb/erq412. PMID: 21307383.; Carroll A, Specht CD. Understanding Plant Cellulose Synthases through a Comprehensive Investigation of the Cellulose Synthase Family Sequences. Front Plant Sci. 2011;2():5. PMID: 22629257; PMCID: PMC3355508.; Lehmann T, Hoffmann M, Hentrich M, Pollmann S. Indole-3-acetamide-dependent auxin biosynthesis: A widely distributed way of indole-3-acetic acid production? European Journal of Cell Biology. 2010 Dec;89(12):895–905. doi: 10.1016/j.ejcb.2010.06.021.; Kotchoni SO, Jimenez-Lopez JC, Gao D, Edwards V, Gachomo EW, Margam VM, Seufferheld MJ. Modeling-Dependent Protein Characterization of the Rice Aldehyde Dehydrogenase (ALDH) Superfamily Reveals Distinct Functional and Structural Features. PLoS ONE. 2010 Jul 12;5(7):e11516. doi: 10.1371/journal.pone.0011516.; Wang L, Liu M, Lv YG, Zhang H. Purification of calmodulin from rice bran and activation of glutamate decarboxylase by Ca2+/calmodulin. J Sci Food Agric. 2010 Mar 15;90(4):669–75. doi: 10.1002/jsfa.3866. PMID: 20355097.; Kobayashi T, Itai RN, Ogo Y, Kakei Y, Nakanishi H, Takahashi M, Nishizawa NK. The rice transcription factor IDEF1 is essential for the early response to iron deficiency, and induces vegetative expression of late embryogenesis abundant genes. Plant J. 2009 Dec;60(6):948–61. doi: 10.1111/j.1365-313x.2009.04015.x. PMID: 19737364.; Mravec J, Skupa P, Bailly A, Hoyerová K, Krecek P, Bielach A, Petrásek J, Zhang J, Gaykova V, Stierhof YD, Dobrev PI, Schwarzerová K, Rolcík J, Seifertová D, Luschnig C, Benková E, Zazímalová E, Geisler M, Friml J. Subcellular homeostasis of phytohormone auxin is mediated by the ER-localized PIN5 transporter. Nature. 2009 Jun 25;459(7250):1136–40. doi: 10.1038/nature08066. PMID: 19506555.; Wuriyanghan H, Zhang B, Cao WH, Ma B, Lei G, Liu YF, Wei W, Wu HJ, Chen LJ, Chen HW, Cao YR, He SJ, Zhang WK, Wang XJ, Chen SY, Zhang JS. The ethylene receptor ETR2 delays floral transition and affects starch accumulation in rice. Plant Cell. 2009 May;21(5):1473–94. PMID: 19417056; PMCID: PMC2700534.; Inoue H, Kobayashi T, Nozoye T, Takahashi M, Kakei Y, Suzuki K, Nakazono M, Nakanishi H, Mori S, Nishizawa NK. Rice OsYSL15 Is an Iron-regulated Iron(III)-Deoxymugineic Acid Transporter Expressed in the Roots and Is Essential for Iron Uptake in Early Growth of the Seedlings. Journal of Biological Chemistry. 2009 Feb;284(6):3470–9. doi: 10.1074/jbc.m806042200.; Linster CL, Adler LN, Webb K, Christensen KC, Brenner C, Clarke SG. A second GDP-L-galactose phosphorylase in arabidopsis en route to vitamin C. Covalent intermediate and substrate requirements for the conserved reaction. J Biol Chem. 2008 Jul 04;283(27):18483–92. PMID: 18463094; PMCID: PMC2441562.; Vogel J. Unique aspects of the grass cell wall. Curr Opin Plant Biol. 2008 Jun;11(3):301–7. doi: 10.1016/j.pbi.2008.03.002. PMID: 18434239.; Suzuki M, Tanaka K, Kuwano M, Yoshida KT. Expression pattern of inositol phosphate-related enzymes in rice (Oryza sativa L.): implications for the phytic acid biosynthetic pathway. Gene. 2007 Dec 15;405(1-2):55–64. doi: 10.1016/j.gene.2007.09.006. PMID: 17961936.; Kobayashi T, Ogo Y, Itai RN, Nakanishi H, Takahashi M, Mori S, Nishizawa NK. The transcription factor IDEF1 regulates the response to and tolerance of iron deficiency in plants. Proc Natl Acad Sci U S A. 2007 Nov 27;104(48):19150–5. PMID: 18025467; PMCID: PMC2141923.; Shimura K, Okada A, Okada K, Jikumaru Y, Ko K, Toyomasu T, Sassa T, Hasegawa M, Kodama O, Shibuya N, Koga J, Nojiri H, Yamane H. Identification of a Biosynthetic Gene Cluster in Rice for Momilactones. Journal of Biological Chemistry. 2007 Nov;282(47):34013–8. doi: 10.1074/jbc.m703344200.; 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.; Baud S, Wuillème S, Dubreucq B, De Almeida A, Vuagnat C, Lepiniec L, Miquel M, Rochat C. Function of plastidial pyruvate kinases in seeds of Arabidopsis thaliana†. The Plant Journal. 2007 Sep 24;52(3):405–19. doi: 10.1111/j.1365-313x.2007.03232.x.; Linster CL, Gomez TA, Christensen KC, Adler LN, Young BD, Brenner C, Clarke SG. Arabidopsis VTC2 Encodes a GDP-l-Galactose Phosphorylase, the Last Unknown Enzyme in the Smirnoff-Wheeler Pathway to Ascorbic Acid in Plants. Journal of Biological Chemistry. 2007 Jun;282(26):18879–85. doi: 10.1074/jbc.m702094200.; Andre C, Froehlich JE, Moll MR, Benning C. A heteromeric plastidic pyruvate kinase complex involved in seed oil biosynthesis in Arabidopsis. Plant Cell. 2007 Jun;19(6):2006–22. PMID: 17557808; PMCID: PMC1955724.; Mustroph A, Sonnewald U, Biemelt S. Characterisation of the ATP-dependent phosphofructokinase gene family from Arabidopsis thaliana. FEBS Lett. 2007 May 29;581(13):2401–10. doi: 10.1016/j.febslet.2007.04.060. PMID: 17485088.; Kurakawa T, Ueda N, Maekawa M, Kobayashi K, Kojima M, Nagato Y, Sakakibara H, Kyozuka J. Direct control of shoot meristem activity by a cytokinin-activating enzyme. Nature. 2007 Feb 08;445(7128):652–5. doi: 10.1038/nature05504. PMID: 17287810.; Hofmann E, Zerbe P, Schaller F. The crystal structure of Arabidopsis thaliana allene oxide cyclase: insights into the oxylipin cyclization reaction. Plant Cell. 2006 Nov;18(11):3201–17. PMID: 17085685; PMCID: PMC1693953.; 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.; KANNO Y, OTOMO K, KENMOKU H, MITSUHASHI W, YAMANE H, OIKAWA H, TOSHIMA H, MATSUOKA M, SASSA T, TOYOMASU T. Characterization of a Rice Gene Family Encoding Type-A Diterpene Cyclases. Bioscience, Biotechnology, and Biochemistry. 2006 Jul 23;70(7):1702–10. doi: 10.1271/bbb.60044.; Nozu Y, Tsugita A, Kamijo K. Proteomic analysis of rice leaf, stem and root tissues during growth course. Proteomics. 2006 Jun;6(12):3665–70. doi: 10.1002/pmic.200600043. PMID: 16758443.; Mao C, Wang S, Jia Q, Wu P. OsEIL1, a rice homolog of the Arabidopsis EIN3 regulates the ethylene response as a positive component. Plant Mol Biol. 2006 May;61(1-2):141–52. doi: 10.1007/s11103-005-6184-1. PMID: 16786297.; Cho JI, Ryoo N, Ko S, Lee SK, Lee J, Jung KH, Lee YH, Bhoo SH, Winderickx J, An G, Hahn TR, Jeon JS. Structure, expression, and functional analysis of the hexokinase gene family in rice (Oryza sativa L.). Planta. 2006 Aug;224(3):598–611. doi: 10.1007/s00425-006-0251-y. PMID: 16552590.; Ytterberg AJ, Peltier JB, van Wijk KJ. Protein profiling of plastoglobules in chloroplasts and chromoplasts. A surprising site for differential accumulation of metabolic enzymes. Plant Physiol. 2006 Mar;140(3):984–97. PMID: 16461379; PMCID: PMC1400577.; Watanabe K, Suzuki K, Kitamura S. Characterization of a GDP-D-mannose 3'',5''-epimerase from rice. Phytochemistry. 2006 Feb;67(4):338–46. doi: 10.1016/j.phytochem.2005.12.003. PMID: 16413588.; Ishimaru Y, Suzuki M, Tsukamoto T, Suzuki K, Nakazono M, Kobayashi T, Wada Y, Watanabe S, Matsuhashi S, Takahashi M, Nakanishi H, Mori S, Nishizawa NK. Rice plants take up iron as an Fe3+-phytosiderophore and as Fe2+. The Plant Journal. 2006 Jan 10;45(3):335–46. doi: 10.1111/j.1365-313x.2005.02624.x.; Kotake T, Yamaguchi D, Ohzono H, Hojo S, Kaneko S, Ishida H, Tsumuraya Y. UDP-sugar Pyrophosphorylase with Broad Substrate Specificity Toward Various Monosaccharide 1-Phosphates from Pea Sprouts. Journal of Biological Chemistry. 2004 Oct;279(44):45728–36. doi: 10.1074/jbc.m408716200.; Koike S, Inoue H, Mizuno D, Takahashi M, Nakanishi H, Mori S, Nishizawa NK. OsYSL2 is a rice metal-nicotianamine transporter that is regulated by iron and expressed in the phloem. Plant J. 2004 Aug;39(3):415–24. doi: 10.1111/j.1365-313x.2004.02146.x. PMID: 15255870.; Sakamoto T, Miura K, Itoh H, Tatsumi T, Ueguchi-Tanaka M, Ishiyama K, Kobayashi M, Agrawal GK, Takeda S, Abe K, Miyao A, Hirochika H, Kitano H, Ashikari M, Matsuoka M. An overview of gibberellin metabolism enzyme genes and their related mutants in rice. Plant Physiol. 2004 Apr;134(4):1642–53. PMID: 15075394; PMCID: PMC419838.; 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.; Cahoon EB, Hall SE, Ripp KG, Ganzke TS, Hitz WD, Coughlan SJ. Metabolic redesign of vitamin E biosynthesis in plants for tocotrienol production and increased antioxidant content. Nat Biotechnol. 2003 Sep;21(9):1082–7. doi: 10.1038/nbt853. PMID: 12897790.; Springob K, Nakajima J, Yamazaki M, Saito K. Recent advances in the biosynthesis and accumulation of anthocyanins. Nat Prod Rep. 2003 Jun;20(3):288–303. doi: 10.1039/b109542k. PMID: 12828368.; Bouché N, Fait A, Bouchez D, Møller SG, Fromm H. Mitochondrial succinic-semialdehyde dehydrogenase of the gamma-aminobutyrate shunt is required to restrict levels of reactive oxygen intermediates in plants. Proc Natl Acad Sci U S A. 2003 May 27;100(11):6843–8. PMID: 12740438; PMCID: PMC164534.; Burget EG, Verma R, Mølhøj M, Reiter WD. The biosynthesis of L-arabinose in plants: molecular cloning and characterization of a Golgi-localized UDP-D-xylose 4-epimerase encoded by the MUR4 gene of Arabidopsis. Plant Cell. 2003 Feb;15(2):523–31. PMID: 12566589; PMCID: PMC141218.; Bughio N, Yamaguchi H, Nishizawa NK, Nakanishi H, Mori S. Cloning an iron-regulated metal transporter from rice. J Exp Bot. 2002 Jul;53(374):1677–82. doi: 10.1093/jxb/erf004. PMID: 12096107.; Gatzek S, Wheeler GL, Smirnoff N. Antisense suppression of |
| Hormone signaling, transport, and metabolism Accession ID: Plant Reactome:R-OSA-2744341 |
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Bennett T. PIN proteins and the evolution of plant development. Trends Plant Sci. 2015 Aug;20(8):498–507. doi: 10.1016/j.tplants.2015.05.005. PMID: 26051227.; Mohanta TK, Mohanta N, Bae H. Identification and Expression Analysis of PIN-Like (PILS) Gene Family of Rice Treated with Auxin and Cytokinin. Genes (Basel). 2015 Jul 16;6(3):622–40. PMID: 26193322; PMCID: PMC4584321.; Balzan S, Johal GS, Carraro N. The role of auxin transporters in monocots development. Front Plant Sci. 2014;5():393. PMID: 25177324; PMCID: PMC4133927.; Bender RL, Fekete ML, Klinkenberg PM, Hampton M, Bauer B, Malecha M, Lindgren K, A. Maki J, Perera MADN, Nikolau BJ, Carter CJ. PIN6 is required for nectary auxin response and short stamen development. The Plant Journal. 2013 May 02;74(6):893–904. doi: 10.1111/tpj.12184.; Sawchuk MG, Edgar A, Scarpella E. Patterning of Leaf Vein Networks by Convergent Auxin Transport Pathways. PLoS Genet. 2013 Feb 21;9(2):e1003294. doi: 10.1371/journal.pgen.1003294.; Ding Z, Wang B, Moreno I, Dupláková N, Simon S, Carraro N, Reemmer J, Pencík A, Chen X, Tejos R, Skupa P, Pollmann S, Mravec J, Petrášek J, Zažímalová E, Honys D, Rolcík J, Murphy A, Orellana A, Geisler M, Friml J. ER-localized auxin transporter PIN8 regulates auxin homeostasis and male gametophyte development in Arabidopsis. Nat Commun. 2012 Jul 03;3():941. doi: 10.1038/ncomms1941. PMID: 22760640.; Barbez E, Kubeš M, Rolcík J, Béziat C, Pencík A, Wang B, Rosquete MR, Zhu J, Dobrev PI, Lee Y, Zažímalovà E, Petrášek J, Geisler M, Friml J, Kleine-Vehn J. A novel putative auxin carrier family regulates intracellular auxin homeostasis in plants. Nature. 2012 Apr 15;485(7396):119–22. doi: 10.1038/nature11001. PMID: 22504182.; Mravec J, Skupa P, Bailly A, Hoyerová K, Krecek P, Bielach A, Petrásek J, Zhang J, Gaykova V, Stierhof YD, Dobrev PI, Schwarzerová K, Rolcík J, Seifertová D, Luschnig C, Benková E, Zazímalová E, Geisler M, Friml J. Subcellular homeostasis of phytohormone auxin is mediated by the ER-localized PIN5 transporter. Nature. 2009 Jun 25;459(7250):1136–40. doi: 10.1038/nature08066. PMID: 19506555. |
| ABA biosynthesis and mediated signaling Accession ID: Plant Reactome:R-OSA-3899368 |
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| Secondary metabolism Accession ID: Plant Reactome:R-OSA-2744344 |
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Perera I, Seneweera S, Hirotsu N. Manipulating the Phytic Acid Content of Rice Grain Toward Improving Micronutrient Bioavailability. Rice (N Y). 2018 Jan 11;11(1):4. PMID: 29327163; PMCID: PMC5764899.; 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.; 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.; Suzuki M, Tanaka K, Kuwano M, Yoshida KT. Expression pattern of inositol phosphate-related enzymes in rice (Oryza sativa L.): implications for the phytic acid biosynthetic pathway. Gene. 2007 Dec 15;405(1-2):55–64. doi: 10.1016/j.gene.2007.09.006. PMID: 17961936.; Shimura K, Okada A, Okada K, Jikumaru Y, Ko K, Toyomasu T, Sassa T, Hasegawa M, Kodama O, Shibuya N, Koga J, Nojiri H, Yamane H. Identification of a Biosynthetic Gene Cluster in Rice for Momilactones. Journal of Biological Chemistry. 2007 Nov;282(47):34013–8. doi: 10.1074/jbc.m703344200. |
| Carotenoid biosynthesis Accession ID: Plant Reactome:R-OSA-1119449 |
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| ABA synthesis Accession ID: Plant Reactome:R-OSA-1119374 |
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| superpathway of carotenoid biosynthesis in plants Accession ID: PlantCyc:SFALLAX_CAROTENOID-PWY |
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| superpathway of carotenoid biosynthesis in plants Accession ID: PlantCyc:VALLEYOAK_CAROTENOID-PWY |
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| superpathway of carotenoid biosynthesis in plants Accession ID: PlantCyc:PHALLII_CAROTENOID-PWY |
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| superpathway of carotenoid biosynthesis in plants Accession ID: PlantCyc:AHALLERI_CAROTENOID-PWY |
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| superpathway of carotenoid biosynthesis in plants Accession ID: PlantCyc:CACUMINATA_CAROTENOID-PWY |
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| superpathway of carotenoid biosynthesis in plants Accession ID: PlantCyc:DROTUNDATA_CAROTENOID-PWY |
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| superpathway of carotenoid biosynthesis in plants Accession ID: PlantCyc:EUROPEANPEAR_CAROTENOID-PWY |
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| superpathway of carotenoid biosynthesis in plants Accession ID: PlantCyc:BRACHYPODIUM_CAROTENOID-PWY |
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| superpathway of carotenoid biosynthesis in plants Accession ID: PlantCyc:POPLAR_CAROTENOID-PWY |
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