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N Use By Plants
Nitrate Assimilation
Ammonia Assimilation
Glu, Gln, Asn, Gly, Ser
Aminotransferases
Asp, Ala, GABA
Val, Leu, Ileu, Thr, Lys
Pro, Arg, Orn
Polyamines
Non-protein AAs
Alkaloids
Sulfate Assimilation
Cys, Met, AdoMet, ACC
His, Phe, Tyr, Tryp
Secondary Products
Onium Compounds
Enzymes
Methods
Simulation
References
HORT640 - Metabolic Plant Physiology

References, lignin or lignification

Abbott JC, Barakate A, Pincon G, Legrand M, Lapierre C, Mila I, Schuch W, Halpin C. Simultaneous suppression of multiple genes by single transgenes. Down-regulation of three unrelated lignin biosynthetic genes in tobacco. Plant Physiol. 128: 844-853 (2002).

Abdulrazzak N, Pollet B, Ehlting J, Larsen K, Asnaghi C, Ronseau S, Proux C, Erhardt M, Seltzer V, Renou JP, Ullmann P, Pauly M, Lapierre C, Werck-Reichhart D. A coumaroyl-ester-3-hydroxylase insertion mutant reveals the existence of nonredundant meta-hydroxylation pathways and essential roles for phenolic precursors in cell expansion and plant growth. Plant Physiol. 140: 30-48 (2006).

Agarwal UP. Raman imaging to investigate ultrastructure and composition of plant cell walls: distribution of lignin and cellulose in black spruce wood (Picea mariana). Planta 224: 1141-1153 (2006).

Agusti J, Merelo P, Cercos M, Tadeo FR, Talon M. Ethylene-induced differential gene expression during abscission of citrus leaves. J. Exp. Bot. 59: 2717-2733 (2008).

Aharoni A, Keizer LC, Van Den Broeck HC, Blanco-Portales R, Munoz-Blanco J, Bois G, Smit P, De Vos RC, O'Connell AP. Novel insight into vascular, stress, and auxin-dependent and -independent gene expression programs in strawberry, a non-climacteric fruit. Plant Physiol. 129: 1019-1031 (2002).

Allerdings E, Ralph J, Steinhart H, Bunzel M. Isolation and structural identification of complex feruloylated heteroxylan side-chains from maize bran. Phytochemistry 67: 1276-1286 (2006).

Almagro L, Gomez Ros LV, Belchi-Navarro S, Bru R, Ros Barcelo A, Pedreno MA. Class III peroxidases in plant defence reactions. J. Exp. Bot. 60: 377-390 (2009).

Alvarez S, Marsh EL, Schroeder SG, Schachtman DP. Metabolomic and proteomic changes in the xylem sap of maize under drought. Plant Cell Environ. 31: 325-340 (2008).

Amrhein N, Frank G, Lemm G, Luhmann HB. Inhibition of lignin formation by L-alpha-aminooxy-beta-phenylpropionic acid, an inhibitor of phenylalanine ammonia-lyase. Eur. J. Cell Biol. 29: 139-144 (1983).

Amthor JS. Efficiency of lignin biosynthesis: a quantitative analysis. Ann. Bot. (Lond.) 91: 673-695 (2003).

Andersen JR, Zein I, Wenzel G, Krutzfeldt B, Eder J, Ouzunova M, Lubberstedt T. High levels of linkage disequilibrium and associations with forage quality at a phenylalanine ammonia-lyase locus in European maize (Zea mays L.) inbreds. Theor. Appl. Genet. 114: 307-319 (2007).

Andersson-Gunneras S, Mellerowicz EJ, Love J, Segerman B, Ohmiya Y, Coutinho PM, Nilsson P, Henrissat B, Moritz T, Sundberg B. Biosynthesis of cellulose-enriched tension wood in Populus: global analysis of transcripts and metabolites identifies biochemical and developmental regulators in secondary wall biosynthesis. Plant J. 45: 144-165 (2006).

Andrews J, Adams SR, Burton KS, Evered CE. Subcellular localization of peroxidase in tomato fruit skin and the possible implications for the regulation of fruit growth. J. Exp. Bot. 53: 2185-2191 (2002).

Anterola AM, Jeon JH, Davin LB, Lewis NG. Transcriptional control of monolignol biosynthesis in Pinus taeda - Factors affecting monolignol ratios and carbon allocation in phenylpropanoid metabolism. J. Biol. Chem. 277: 18272-18280 (2002).

Anterola AM, Lewis NG. Trends in lignin modification: a comprehensive analysis of the effects of genetic manipulations/mutations on lignification and vascular integrity. Phytochemistry 61: 221-294 (2002).

Aristidou A, Penttila M. Metabolic engineering applications to renewable resource utilization. Curr. Opin. Biotechnol. 11: 187-198 (2000).

Aspeborg H, Schrader J, Coutinho PM, Stam M, Kallas A, Djerbi S, Nilsson P, Denman S, Amini B, Sterky F, Master E, Sandberg G, Mellerowicz E, Sundberg B, Henrissat B, Teeri TT. Carbohydrate-active enzymes involved in the secondary cell wall biogenesis in hybrid aspen. Plant Physiol. 137: 983-997 (2005).

Aston C, Mishra B, Schwartz DC. Optical mapping and its potential for large-scale sequencing projects. Trends Biotechnol. 17: 297-302 (1999).

Baldridge GD, O'Neill NR, Samac DA. Alfalfa (Medicago sativa L.) resistance to the root-lesion nematode, Pratylenchus penetrans: defense-response gene mRNA and isoflavonoid phytoalexin levels in roots. Plant Mol. Biol. 38: 999-1010 (1998).

Balsamo RA, Vander Willigen C, Boyko W, Farrant J. Retention of mobile water during dehydration in the desiccation-tolerant grass Eragrostis nindensis. Physiol. Plant. 124: 336-342 (2005).

Balsamo RA, Willigen CV, Bauer AM, Farrant J. Drought tolerance of selected Eragrostis species correlates with leaf tensile properties. Ann. Bot. (Lond.) 97: 985-991 (2006).

Banu MN, Hoque MA, Watanabe-Sugimoto M, Matsuoka K, Nakamura Y, Shimoishi Y, Murata Y. Proline and glycinebetaine induce antioxidant defense gene expression and suppress cell death in cultured tobacco cells under salt stress. J. Plant Physiol. 166: 146-156 (2009).

Barakat A, Chabbert B, Cathala B. Effect of reaction media concentration on the solubility and the chemical structure of lignin model compounds. Phytochemistry 68: 2118-2125 (2007).

Barakat A, Winter H, Rondeau-Mouro C, Saake B, Chabbert B, Cathala B. Studies of xylan interactions and cross-linking to synthetic lignins formed by bulk and end-wise polymerization: a model study of lignin carbohydrate complex formation. Planta 226: 267-281 (2007).

Barbour MM, Andrews TJ, Farquhar GD. Correlations between oxygen isotope ratios of wood constituents of Quercus and Pinus samples from around the world. Aust. J. Plant Physiol. 28: 335-348 (2001).

Baskin TI, Beemster GT, Judy-March JE, Marga F. Disorganization of cortical microtubules stimulates tangential expansion and reduces the uniformity of cellulose microfibril alignment among cells in the root of Arabidopsis. Plant Physiol. 135: 2279-2290 (2004).

Bate NJ, Orr J, Ni W, Meromi A, Nadler-Hassar T, Doerner PW, Dixon RA, Lamb CJ, Elkind Y. Quantitative relationship between phenylalanine ammonia-lyase levels and phenylpropanoid accumulation in transgenic tobacco identifies a rate-determining step in natural product synthesis. Proc. Natl. Acad. Sci. U.S.A. 91: 7608-7612 (1994).

Baucher M, Bernard-Vailhe MA, Chabbert B, Besle JM, Opsomer C, Van Montagu M, Botterman J. Down-regulation of cinnamyl alcohol dehydrogenase in transgenic alfalfa (Medicago sativa L.) and the effect on lignin composition and digestibility. Plant Mol. Biol. 39: 437-447 (1999).

Baucher M, Chabbert B, Pilate G, Van Doorsselaere J, Tollier MT, Petit-Conil M, Cornu D, Monties B, Van Montagu M, Inze D, Jouanin L, Boerjan W. Red xylem and higher lignin extractability by down-regulating a cinnamyl alcohol dehydrogenase in poplar. Plant Physiol. 112: 1479-1490 (1996).

Bedon F, Levasseur C, Grima-Pettenati J, Seguin A, MacKay J. Sequence analysis and functional characterization of the promoter of the Picea glauca cinnamyl alcohol dehydrogenase gene in transgenic white spruce plants. Plant Cell Rep. 28: 787-800 (2009).

Bell-Lelong DA, Cusumano JC, Meyer K, Chapple C. Cinnamate-4-hydroxylase expression in Arabidopsis. Regulation in response to development and the environment. Plant Physiol. 113: 729-738 (1997).

Bernards MA, Susag LM, Bedgar DL, Anterola AM, Lewis NG. Induced phenylpropanoid metabolism during suberization and lignification: a comparative analysis. J. Plant Physiol. 157: 601-607 (2000).

Bertea CM, Luciano P, Bossi S, Leoni F, Baiocchi C, Medana C, Azzolin CM, Temporale G, Lombardozzi MA, Maffei ME. PCR and PCR-RFLP of the 5S-rRNA-NTS region and salvinorin A analyses for the rapid and unequivocal determination of Salvia divinorum. Phytochemistry 67: 371-378 (2006).

Bevan M, Shufflebottom D, Edwards K, Jefferson R, Schuch W. Tissue- and cell-specific activity of a phenylalanine ammonia-lyase promoter in transgenic plants. EMBO J. 8: 1899-1906 (1989).

Bharti AK, Khurana JP. Mutants of Arabidopsis as tools to understand the regulation of phenylpropanoid pathway and UVB protection mechanisms. Photochem. Photobiol. 65: 765-776 (1997).

Bhuiyan NH, Liu W, Liu G, Selvaraj G, Wei Y, King J. Transcriptional regulation of genes involved in the pathways of biosynthesis and supply of methyl units in response to powdery mildew attack and abiotic stresses in wheat. Plant Mol. Biol. 64: 305-318 (2007).

Bhuiyan NH, Selvaraj G, Wei Y, King J. Gene expression profiling and silencing reveal that monolignol biosynthesis plays a critical role in penetration defence in wheat against powdery mildew invasion. J. Exp. Bot. 60: 509-521 (2009).

Bianchi MW, Damerval C, Vartanian N. Identification of proteins regulated by cross-talk between drought and hormone pathways in Arabidopsis wild-type and auxin-insensitive mutants, axr1 and axf2. Funct. Plant Biol. 29: 55-61 (2002).

Biemelt S, Tschiersch H, Sonnewald U. Impact of altered gibberellin metabolism on biomass accumulation, lignin biosynthesis, and photosynthesis in transgenic tobacco plants. Plant Physiol. 135: 254-265 (2004).

Bindschedler LV, Tuerck J, Maunders M, Ruel K, Petit-Conil M, Danoun S, Boudet AM, Joseleau JP, Bolwell GP. Modification of hemicellulose content by antisense down-regulation of UDP-glucuronate decarboxylase in tobacco and its consequences for cellulose extractability. Phytochemistry 68: 2635-2648 (2007).

Bischoff V, Cookson SJ, Wu S, Scheible WR. Thaxtomin A affects CESA-complex density, expression of cell wall genes, cell wall composition, and causes ectopic lignification in Arabidopsis thaliana seedlings. J. Exp. Bot. 60: 955-965 (2009).

Blanco-Portales R, Medina-Escobar N, Lopez-Raez JA, Gonzalez-Reyes JA, Villalba JM, Moyano E, Caballero JL, Munoz-Blanco J. Cloning, expression and immunolocalization pattern of a cinnamyl alcohol dehydrogenase gene from strawberry (Fragaria x ananassa cv. Chandler). J. Exp. Bot. 53: 1723-1734 (2002).

Blaschke L, Legrand M, Mai C, Polle A. Lignification and structural biomass production in tobacco with suppressed caffeic/5-hydroxy ferulic acid-O-methyl transferase activity under ambient and elevated CO concentrations. Physiol. Plant. 121: 75-83 (2004).

Blee K, Choi JW, O'Connell AP, Jupe SC, Schuch W, Lewis NG, Bolwell GP. Antisense and sense expression of cDNA coding for CYP73A15, a class II cinnamate 4-hydroxylase, leads to a delayed and reduced production of lignin in tobacco. Phytochemistry 57: 1159-1166 (2001).

Blokhina O, Virolainen E, Fagerstedt KV. Antioxidants, oxidative damage and oxygen deprivation stress: a review. Ann. Bot. (Lond.) 91: 179-194 (2003).

Blount JW, Masoud S, Sumner LW, Huhman D, Dixon RA. Over-expression of cinnamate 4-hydroxylase leads to increased accumulation of acetosyringone in elicited tobacco cell-suspension cultures. Planta 214: 902-910 (2002).

Boerjan W, Ralph J, Baucher M. Lignin biosynthesis. Annu. Rev. Plant Biol. 54: 519-546 (2003).

Bomal C, Bedon F, Caron S, Mansfield SD, Levasseur C, Cooke JE, Blais S, Tremblay L, Morency MJ, Pavy N, Grima-Pettenati J, Séguin A, Mackay J. Involvement of Pinus taeda MYB1 and MYB8 in phenylpropanoid metabolism and secondary cell wall biogenesis: a comparative in planta analysis. J. Exp. Bot. 59: 3925-3939 (2008).

Booker FL. Influence of carbon dioxide enrichment, ozone and nitrogen fertilization on cotton (Gossypium hirsutum L.) leaf and root composition. Plant Cell Environ. 23: 573-583 (2000).

Borevitz JO, Xia Y, Blount J, Dixon RA, Lamb C. Activation tagging identifies a conserved MYB regulator of phenylpropanoid biosynthesis. Plant Cell 12: 2383-2394 (2000).

Boudet AM. Evolution and current status of research in phenolic compounds. Phytochemistry 68: 2722-2735 (2007).

Boudet AM, Kajita S, Grima-Pettenati J, Goffner D. Lignins and lignocellulosics: a better control of synthesis for new and improved uses. Trends Plant Sci. 8: 576-581 (2003).

Bouranis DL, Chorianopoulou SN, Kollias C, Maniou P, Protonotarios VE, Siyiannis VF, Hawkesford MJ. Dynamics of aerenchyma distribution in the cortex of sulfate-deprived adventitious roots of maize. Ann. Bot. (Lond.) 97: 695-704 (2006).

Brazier-Hicks M, Edwards LA, Edwards R. Selection of plants for roles in phytoremediation: the importance of glucosylation. Plant Biotechnol. J. 5: 627-635 (2007).

Brazier-Hicks M, Edwards R. Functional importance of the family 1 glucosyltransferase UGT72B1 in the metabolism of xenobiotics in Arabidopsis thaliana. Plant J. 42: 556-566 (2005).

Briggs CL, Morris EC. Seed-coat dormancy in Grevillea linearifolia: little change in permeability to an apoplastic tracer after treatment with smoke and heat. Ann. Bot. (Lond.) 101: 623-632 (2008).

Brill EM, Abrahams S, Hayes CM, Jenkins CL, Watson JM. Molecular characterisation and expression of a wound-inducible cDNA encoding a novel cinnamyl-alcohol dehydrogenase enzyme in lucerne (Medicago sativa L.) Plant Mol. Biol. 41: 279-291 (1999).

Burlat V, Kwon M, Davin LB, Lewis NG. Dirigent proteins and dirigent sites in lignifying tissues. Phytochemistry 57: 883-897 (2001).

Busam G, Junghanns KT, Kneusel RE, Kassemeyer HH, Matern U. Characterization and expression of caffeoyl-coenzyme A 3-O-methyltransferase proposed for the induced resistance response of Vitis vinifera L. Plant Physiol. 115: 1039-1048 (1997).

Busov V, Meilan R, Pearce DW, Rood SB, Ma C, Tschaplinski TJ, Strauss SH. Transgenic modification of gai or rgl1 causes dwarfing and alters gibberellins, root growth, and metabolite profiles in Populus. Planta 224: 288-299 (2006).

Cabane M, Pireaux JC, Leger E, Weber E, Dizengremel P, Pollet B, Lapierre C. Condensed lignins are synthesized in poplar leaves exposed to ozone. Plant Physiol. 134: 586-594 (2004).

Cai K, Gao D, Luo S, Zeng R, Yang J, Zhu X. Physiological and cytological mechanisms of silicon induced resistance in rice against blast disease. Physiol. Plant. 134: 324-333 (2008).

Cai S, Lashbrook CC. Laser capture microdissection of plant cells from tape-transferred paraffin sections promotes recovery of structurally intact RNA for global gene profiling. Plant J. 48: 628-637 (2006).

Cameron DD, Coats AM, Seel WE. Differential resistance among host and non-host species underlies the variable success of the hemi-parasitic plant Rhinanthus minor. Ann. Bot. (Lond.) 98: 1289-1299 (2006).

Cano-Delgado A, Penfield S, Smith C, Catley M, Bevan M. Reduced cellulose synthesis invokes lignification and defense responses in Arabidopsis thaliana. Plant J. 34: 351-362 (2003).

Canton FR, Suarez MF, Canovas FM. Molecular aspects of nitrogen mobilization and recycling in trees. Photosynth. Res. 83: 265-278 (2005).

Cao Y, Shen D, Lu Y, Huang Y. A Raman-scattering study on the net orientation of biomacromolecules in the outer epidermal walls of mature wheat stems (Triticum aestivum). Ann. Bot. (Lond.) 97: 1091-1094 (2006).

Capellades M, Torres MA, Bastisch I, Stiefel V, Vignols F, Bruce WB, Peterson D, Puigdomenech P, Rigau J. The maize caffeic acid O-methyltransferase gene promoter is active in transgenic tobacco and maize plant tissues. Plant Mol. Biol. 31: 307-322 (1996).

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Chabannes M, Barakate A, Lapierre C, Marita JM, Ralph J, Pean M, Danoun S, Halpin C, Grima-Pettenati J, Boudet AM. Strong decrease in lignin content without significant alteration of plant development is induced by simultaneous down-regulation of cinnamoyl CoA reductase (CCR) and cinnamyl alcohol dehydrogenase (CAD) in tobacco plants. Plant J. 28: 257-270 (2001).

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Chapple C, Ladisch M, Meilan R. Loosening lignin's grip on biofuel production. Nat. Biotechnol. 25: 746-748 (2007).

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Chen C, Meyermans H, Burggraeve B, De Rycke RM, Inoue K, De Vleesschauwer V, Steenackers M, Van Montagu MC, Engler GJ, Boerjan WA. Cell-specific and conditional expression of caffeoyl-coenzyme A-3-O-methyltransferase in poplar. Plant Physiol. 123: 853-868 (2000).

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Chen F, Srinivasa Reddy MS, Temple S, Jackson L, Shadle G, Dixon RA. Multi-site genetic modulation of monolignol biosynthesis suggests new routes for formation of syringyl lignin and wall-bound ferulic acid in alfalfa (Medicago sativa L.). Plant J. 48: 113-124 (2006).

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Davin LB, Lewis NG. Dirigent proteins and dirigent sites explain the mystery of specificity of radical precursor coupling in lignan and lignin biosynthesis. Plant Physiol. 123: 453-62 (2000).

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Dubos C, Willment J, Huggins D, Grant GH, Campbell MM. Kanamycin reveals the role played by glutamate receptors in shaping plant resource allocation. Plant J. 43: 348-355 (2005).

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Ehlting J, Buttner D, Wang Q, Douglas CJ, Somssich IE, Kombrink E. Three 4-coumarate:coenzyme A ligases in Arabidopsis thaliana represent two evolutionarily divergent classes in angiosperms. Plant J. 19: 9-20 (1999).

Ehlting J, Mattheus N, Aeschliman DS, Li E, Hamberger B, Cullis IF, Zhuang J, Kaneda M, Mansfield SD, Samuels L, Ritland K, Ellis BE, Bohlmann J, Douglas CJ. Global transcript profiling of primary stems from Arabidopsis thaliana identifies candidate genes for missing links in lignin biosynthesis and transcriptional regulators of fiber differentiation. Plant J. 42: 618-640 (2005).

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Ellerstrom M, Reidt W, Ivanov R, Tiedemann J, Melzer M, Tewes A, Moritz T, Mock HP, Sitbon F, Rask L, Baumlein H. Ectopic expression of EFFECTOR OF TRANSCRIPTION perturbs gibberellin-mediated plant developmental processes. Plant Mol. Biol. 59: 663-681 (2005).

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David Rhodes
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