메뉴 건너뛰기




Volumn 228, Issue 1, 2010, Pages 78-89

Mathematical modeling of monolignol biosynthesis in Populus xylem

Author keywords

Biochemical systems theory; Flux balance analysis; Monolignol biosynthesis; Optimization; Parameter estimation; Populus

Indexed keywords

BIOCHEMICAL SYSTEMS THEORY; CONTRIBUTING FACTOR; EFFECTIVE TOOL; ENERGY SOURCE; EXPERIMENTAL DATA; FERMENTABLE SUGARS; FLUX BALANCE ANALYSIS; GENETICALLY ENGINEERED CROPS; GENOMICS; GUAIACYL; HIGHER YIELD; IN-VIVO; LIGNIN BIOSYNTHESIS; LIGNIN CONTENTS; LIGNOCELLULOSIC BIOMASS; MATHEMATICAL METHOD; MATHEMATICAL MODELING; METABOLIC ENGINEERING; METABOLIC NETWORK; METABOLITE PROFILING; MODEL CONSTRUCTION; MODEL PREDICTION; MODEL RESULTS; MONOLIGNOL BIOSYNTHESIS; MONOLIGNOLS; MONOMER COMPOSITIONS; NONLINEAR DYNAMIC MODELING; ORGANIZATIONAL LEVELS; POPULUS; PRELIMINARY MODEL; SINAPYL ALCOHOLS; SUBSTRATE SATURATION; SYSTEMS BIOLOGY; TRANSGENIC APPROACHES; TRANSGENICS;

EID: 77957687260     PISSN: 00255564     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mbs.2010.08.009     Document Type: Article
Times cited : (24)

References (70)
  • 2
    • 13444280500 scopus 로고    scopus 로고
    • Ethanol from lignocellulosic biomass: techno-economic performance in short-, middle-, and long-term
    • Hamelinck C.N., Hooijdonk G., Faaij A.P.C. Ethanol from lignocellulosic biomass: techno-economic performance in short-, middle-, and long-term. Biomass and Bioenergy 2005, 28:384.
    • (2005) Biomass and Bioenergy , vol.28 , pp. 384
    • Hamelinck, C.N.1    Hooijdonk, G.2    Faaij, A.P.C.3
  • 3
    • 33744903388 scopus 로고    scopus 로고
    • Plant genetic engineering to improve biomass characteristics for biofuels
    • Sticklen M. Plant genetic engineering to improve biomass characteristics for biofuels. Current Opinion in Biotechnology 2006, 17:315.
    • (2006) Current Opinion in Biotechnology , vol.17 , pp. 315
    • Sticklen, M.1
  • 4
    • 34447319626 scopus 로고    scopus 로고
    • Lignin modification improves fermentable sugar yields for biofuel production
    • Chen F., Dixon R.A. Lignin modification improves fermentable sugar yields for biofuel production. Nature Biotechnology 2007, 25:759.
    • (2007) Nature Biotechnology , vol.25 , pp. 759
    • Chen, F.1    Dixon, R.A.2
  • 5
    • 0034649566 scopus 로고    scopus 로고
    • TheArabidopsis Genome Initiative, Analysis of the genome sequence of the flowering plant Arabidopsis thaliana, Nature,
    • TheArabidopsis Genome Initiative, Analysis of the genome sequence of the flowering plant Arabidopsis thaliana, Nature, 408, 2000, pp. 796-815.
    • (2000) , vol.408 , pp. 796-815
  • 7
    • 0033575387 scopus 로고    scopus 로고
    • Plant functional genomics
    • Somerville C., Somerville S. Plant functional genomics. Science 1999, 285:380.
    • (1999) Science , vol.285 , pp. 380
    • Somerville, C.1    Somerville, S.2
  • 8
    • 37849044667 scopus 로고    scopus 로고
    • Downregulation of cinnamoyl-coenzyme a reductase in poplar: multiple-level phenotyping reveals effects on cell wall polymer metabolism and structure
    • Leplé J.C., Dauwe R., Morreel K., Storme V., Lapierre C., Pollet B., Naumann A., Kang K.Y., Kim H., Ruel K. Downregulation of cinnamoyl-coenzyme a reductase in poplar: multiple-level phenotyping reveals effects on cell wall polymer metabolism and structure. The Plant Cell 2007, 19:3669.
    • (2007) The Plant Cell , vol.19 , pp. 3669
    • Leplé, J.C.1    Dauwe, R.2    Morreel, K.3    Storme, V.4    Lapierre, C.5    Pollet, B.6    Naumann, A.7    Kang, K.Y.8    Kim, H.9    Ruel, K.10
  • 10
    • 0142121364 scopus 로고    scopus 로고
    • Profiling phenolic metabolites in transgenic alfalfa modified in lignin biosynthesis
    • Chen F., Duran A.L., Blount J.W., Sumner L.W., Dixon R.A. Profiling phenolic metabolites in transgenic alfalfa modified in lignin biosynthesis. Phytochemistry 2003, 64:1013.
    • (2003) Phytochemistry , vol.64 , pp. 1013
    • Chen, F.1    Duran, A.L.2    Blount, J.W.3    Sumner, L.W.4    Dixon, R.A.5
  • 11
    • 0344824417 scopus 로고    scopus 로고
    • Saccharomyces cerevisiae phenotypes can be predicted by using constraint-based analysis of a genome-scale reconstructed metabolic network
    • Famili I., Forster J., Nielsen J., Palsson B.Ø. Saccharomyces cerevisiae phenotypes can be predicted by using constraint-based analysis of a genome-scale reconstructed metabolic network. Proceedings of the National Academy of Sciences 2003, 100:13134.
    • (2003) Proceedings of the National Academy of Sciences , vol.100 , pp. 13134
    • Famili, I.1    Forster, J.2    Nielsen, J.3    Palsson, B.Ø.4
  • 12
    • 0037313750 scopus 로고    scopus 로고
    • Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network
    • Förster J., Famili I., Fu P., Palsson B.Ø., Nielsen J. Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. Genome Research 2003, 13:244.
    • (2003) Genome Research , vol.13 , pp. 244
    • Förster, J.1    Famili, I.2    Fu, P.3    Palsson, B.Ø.4    Nielsen, J.5
  • 13
    • 0028108519 scopus 로고
    • Metabolic flux balancing: basic concepts, scientific and practical use
    • Varma A., Palsson B.Ø. Metabolic flux balancing: basic concepts, scientific and practical use. Biotechnology 1994, 12:994.
    • (1994) Biotechnology , vol.12 , pp. 994
    • Varma, A.1    Palsson, B.Ø.2
  • 18
    • 42949164125 scopus 로고    scopus 로고
    • Formulating genome-scale kinetic models in the post-genome era
    • Jamshidi N., Palsson B.Ø. Formulating genome-scale kinetic models in the post-genome era. Molecular Systems Biology 2008, 4:171.
    • (2008) Molecular Systems Biology , vol.4 , pp. 171
    • Jamshidi, N.1    Palsson, B.Ø.2
  • 22
    • 0014649230 scopus 로고
    • Biochemical systems analysis. I. Some mathematical properties of the rate law for the component enzymatic reactions
    • Savageau M.A. Biochemical systems analysis. I. Some mathematical properties of the rate law for the component enzymatic reactions. Journal of Theoretical Biology 1969, 25:365.
    • (1969) Journal of Theoretical Biology , vol.25 , pp. 365
    • Savageau, M.A.1
  • 23
    • 0014658880 scopus 로고
    • Biochemical systems analysis. II. The steady-state solutions for an n-pool system using a power-law approximation
    • Savageau M.A. Biochemical systems analysis. II. The steady-state solutions for an n-pool system using a power-law approximation. Journal of Theoretical Biology 1969, 25:370.
    • (1969) Journal of Theoretical Biology , vol.25 , pp. 370
    • Savageau, M.A.1
  • 26
    • 0141684666 scopus 로고    scopus 로고
    • Dynamic simulation and metabolic re-design of a branched pathway using linlog kinetics
    • Visser D., Heijnen J.J. Dynamic simulation and metabolic re-design of a branched pathway using linlog kinetics. Metabolic Engineering 2003, 5:164.
    • (2003) Metabolic Engineering , vol.5 , pp. 164
    • Visser, D.1    Heijnen, J.J.2
  • 27
    • 0015824267 scopus 로고
    • The control of flux, in: Symposia of the Society for Experimental Biology,
    • H. Kascer, J.A. Burns, The control of flux, in: Symposia of the Society for Experimental Biology, 1973, pp. 65-104.
    • (1973) , pp. 65-104
    • Kascer, H.1    Burns, J.A.2
  • 28
    • 0015949374 scopus 로고
    • A linear steady-state treatment of enzymatic chains. Critique of the crossover theorem and a general procedure to identify interaction sites with an effector
    • Heinrich R., Rapoport T.A. A linear steady-state treatment of enzymatic chains. Critique of the crossover theorem and a general procedure to identify interaction sites with an effector. European Journal of Biochemistry 1974, 42:97.
    • (1974) European Journal of Biochemistry , vol.42 , pp. 97
    • Heinrich, R.1    Rapoport, T.A.2
  • 30
    • 35448974147 scopus 로고    scopus 로고
    • Something from nothing-bridging the gap between constraint-based and kinetic modelling
    • Smallbone K., Simeonidis E., Broomhead D.S., Kell D.B. Something from nothing-bridging the gap between constraint-based and kinetic modelling. FEBS Journal 2007, 274:5576.
    • (2007) FEBS Journal , vol.274 , pp. 5576
    • Smallbone, K.1    Simeonidis, E.2    Broomhead, D.S.3    Kell, D.B.4
  • 32
    • 0030021535 scopus 로고    scopus 로고
    • Variation in lignin content and composition (mechanisms of control and implications for the genetic improvement of plants)
    • Campbell M.M., Sederoff R.R. Variation in lignin content and composition (mechanisms of control and implications for the genetic improvement of plants). Plant Physiology 1996, 110:3.
    • (1996) Plant Physiology , vol.110 , pp. 3
    • Campbell, M.M.1    Sederoff, R.R.2
  • 35
    • 0034054073 scopus 로고    scopus 로고
    • 5-hydroxyconiferyl aldehyde modulates enzymatic methylation for syringyl monolignol formation, a new view of monolignol biosynthesis in angiosperms
    • Li L., Popko J.L., Umezawa T., Chiang V.L. 5-hydroxyconiferyl aldehyde modulates enzymatic methylation for syringyl monolignol formation, a new view of monolignol biosynthesis in angiosperms. Journal of Biological Chemistry 2000, 275:6537.
    • (2000) Journal of Biological Chemistry , vol.275 , pp. 6537
    • Li, L.1    Popko, J.L.2    Umezawa, T.3    Chiang, V.L.4
  • 36
    • 85047681876 scopus 로고    scopus 로고
    • Differential substrate inhibition couples kinetically distinct 4-coumarate: coenzyme A ligases with spatially distinct metabolic roles in quaking aspen
    • Harding S.A., Leshkevich J., Chiang V.L., Tsai C.-J. Differential substrate inhibition couples kinetically distinct 4-coumarate: coenzyme A ligases with spatially distinct metabolic roles in quaking aspen. Plant Physiology 2002, 128:428.
    • (2002) Plant Physiology , vol.128 , pp. 428
    • Harding, S.A.1    Leshkevich, J.2    Chiang, V.L.3    Tsai, C.-J.4
  • 37
    • 33748696780 scopus 로고    scopus 로고
    • 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.)
    • Chen F., Srinivasa Reddy M.S., Temple S., Jackson L., Shadle G., Dixon R.A. 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.). The Plant Journal 2006, 48:113.
    • (2006) The Plant Journal , vol.48 , pp. 113
    • Chen, F.1    Srinivasa Reddy, M.S.2    Temple, S.3    Jackson, L.4    Shadle, G.5    Dixon, R.A.6
  • 40
  • 41
    • 33646944861 scopus 로고    scopus 로고
    • Variation of S/G ratio and lignin content in a Populus family influences the release of xylose by dilute acid hydrolysis
    • Davison B.H., Drescher S.R., Tuskan G.A., Davis M.F., Nghiem N.P. Variation of S/G ratio and lignin content in a Populus family influences the release of xylose by dilute acid hydrolysis. Applied Biochemistry and Biotechnology 2006, 130:427.
    • (2006) Applied Biochemistry and Biotechnology , vol.130 , pp. 427
    • Davison, B.H.1    Drescher, S.R.2    Tuskan, G.A.3    Davis, M.F.4    Nghiem, N.P.5
  • 43
    • 0026947812 scopus 로고
    • An Arabidopsis mutant defective in the general phenylpropanoid pathway
    • Chapple C.C.S., Vogt T., Ellis B.E., Somerville C.R. An Arabidopsis mutant defective in the general phenylpropanoid pathway. The Plant Cell 1992, 4:1413.
    • (1992) The Plant Cell , vol.4 , pp. 1413
    • Chapple, C.C.S.1    Vogt, T.2    Ellis, B.E.3    Somerville, C.R.4
  • 45
    • 9544253891 scopus 로고    scopus 로고
    • Genome-scale models of microbial cells: evaluating the consequences of constraints
    • Price N.D., Reed J.L., Palsson B.Ø. Genome-scale models of microbial cells: evaluating the consequences of constraints. Nature Reviews Microbiology 2004, 2:886.
    • (2004) Nature Reviews Microbiology , vol.2 , pp. 886
    • Price, N.D.1    Reed, J.L.2    Palsson, B.Ø.3
  • 46
    • 0001809741 scopus 로고    scopus 로고
    • Diversity, redundancy and multiplicity in chemical defense systems of aspen
    • Plenum Press, New York, NY, USA, J.T. Romeo, J.A. Saunders, P. Barbosa (Eds.)
    • Lindroth R.L., Hwang S.Y. Diversity, redundancy and multiplicity in chemical defense systems of aspen. Phytochemical Diversity and Redundancy in Ecological Interactions 1996, 25. Plenum Press, New York, NY, USA. J.T. Romeo, J.A. Saunders, P. Barbosa (Eds.).
    • (1996) Phytochemical Diversity and Redundancy in Ecological Interactions , pp. 25
    • Lindroth, R.L.1    Hwang, S.Y.2
  • 47
    • 41949114062 scopus 로고    scopus 로고
    • RNAi-mediated suppression of p-coumaroyl-CoA 3'-hydroxylase in hybrid poplar impacts lignin deposition and soluble secondary metabolism
    • Coleman H.D., Park J.-Y., Nair R., Chapple C.C.S., Mansfield S.D. RNAi-mediated suppression of p-coumaroyl-CoA 3'-hydroxylase in hybrid poplar impacts lignin deposition and soluble secondary metabolism. Proceedings of the National Academy of Sciences 2008, 105:4501.
    • (2008) Proceedings of the National Academy of Sciences , vol.105 , pp. 4501
    • Coleman, H.D.1    Park, J.-Y.2    Nair, R.3    Chapple, C.C.S.4    Mansfield, S.D.5
  • 48
    • 0029661277 scopus 로고    scopus 로고
    • Modeling forest growth. I. Canonical approach
    • Voit E.O., Sands P.J. Modeling forest growth. I. Canonical approach. Ecological Modeling 1996, 86:51.
    • (1996) Ecological Modeling , vol.86 , pp. 51
    • Voit, E.O.1    Sands, P.J.2
  • 49
    • 0029661281 scopus 로고    scopus 로고
    • Modeling forest growth. II. Biomass partitioning in Scots pine
    • Voit E.O., Sands P.J. Modeling forest growth. II. Biomass partitioning in Scots pine. Ecological Modeling 1996, 86:73.
    • (1996) Ecological Modeling , vol.86 , pp. 73
    • Voit, E.O.1    Sands, P.J.2
  • 50
    • 0002239988 scopus 로고
    • Dynamics of self-thinning plant stands
    • Voit E.O. Dynamics of self-thinning plant stands. Annals of Botany 1988, 62:67.
    • (1988) Annals of Botany , vol.62 , pp. 67
    • Voit, E.O.1
  • 51
    • 65649102679 scopus 로고    scopus 로고
    • Recent developments in parameter estimation and structure identification of biochemical and genomic systems
    • Chou I.-C., Voit E.O. Recent developments in parameter estimation and structure identification of biochemical and genomic systems. Mathematical Biosciences 2009, 219:57.
    • (2009) Mathematical Biosciences , vol.219 , pp. 57
    • Chou, I.-C.1    Voit, E.O.2
  • 55
    • 34948840834 scopus 로고    scopus 로고
    • Ensemble modeling for analysis of cell signaling dynamics
    • Kuepfer L., Peter M., Sauer U. Ensemble modeling for analysis of cell signaling dynamics. Nature Biotechnology 2007, 25:1001.
    • (2007) Nature Biotechnology , vol.25 , pp. 1001
    • Kuepfer, L.1    Peter, M.2    Sauer, U.3
  • 56
    • 77957682547 scopus 로고    scopus 로고
    • Power Law Analysis and Simulation (PLAS).
    • A. Ferreira, Power Law Analysis and Simulation (PLAS). , 2000. http://www.dqb.fc.ul.pt/docentes/aferreira/plas.html.
    • (2000)
    • Ferreira, A.1
  • 58
    • 0031554875 scopus 로고    scopus 로고
    • An indirect optimization method for biochemical systems: description of method and application to the maximization of the rate of ethanol, glycerol, and carbohydrate production in Saccharomyces cerevisiae
    • Torres N.V., Voit E.O., Glez-Alcón C., Rodriguez F. An indirect optimization method for biochemical systems: description of method and application to the maximization of the rate of ethanol, glycerol, and carbohydrate production in Saccharomyces cerevisiae. Biotechnology and Bioengineering 1997, 55:758.
    • (1997) Biotechnology and Bioengineering , vol.55 , pp. 758
    • Torres, N.V.1    Voit, E.O.2    Glez-Alcón, C.3    Rodriguez, F.4
  • 59
    • 1542288938 scopus 로고    scopus 로고
    • Global organization of metabolic fluxes in the bacterium Escherichia coli
    • Almaas E., Kovacs B., Vicsek T., Oltvai Z.N., Barabasi A.L. Global organization of metabolic fluxes in the bacterium Escherichia coli. Nature 2004, 427:839.
    • (2004) Nature , vol.427 , pp. 839
    • Almaas, E.1    Kovacs, B.2    Vicsek, T.3    Oltvai, Z.N.4    Barabasi, A.L.5
  • 60
    • 0742305866 scopus 로고    scopus 로고
    • Network biology: understanding the cell's functional organization
    • Barabasi A.L., Oltvai Z.N. Network biology: understanding the cell's functional organization. Nature Reviews Genetics 2004, 5:101.
    • (2004) Nature Reviews Genetics , vol.5 , pp. 101
    • Barabasi, A.L.1    Oltvai, Z.N.2
  • 61
    • 38149033365 scopus 로고    scopus 로고
    • Biological systems modeling and analysis: a biomolecular technique of the twenty-first century
    • Goel G., Chou I.-C., Voit E.O. Biological systems modeling and analysis: a biomolecular technique of the twenty-first century. Journal of Biomolecular Techniques 2006, 17:252.
    • (2006) Journal of Biomolecular Techniques , vol.17 , pp. 252
    • Goel, G.1    Chou, I.-C.2    Voit, E.O.3
  • 62
    • 3042728023 scopus 로고    scopus 로고
    • Predictive reconstruction of the mitochondrial iron-sulfur cluster assembly metabolism: I. The role of the protein pair ferredoxin-ferredoxin reductase (Yah1-Arh1)
    • Alves R., Herrero E., Sorribas A. Predictive reconstruction of the mitochondrial iron-sulfur cluster assembly metabolism: I. The role of the protein pair ferredoxin-ferredoxin reductase (Yah1-Arh1). Proteins: Structure, Function, and Bioinformatics 2004, 56:354.
    • (2004) Proteins: Structure, Function, and Bioinformatics , vol.56 , pp. 354
    • Alves, R.1    Herrero, E.2    Sorribas, A.3
  • 63
    • 27744464483 scopus 로고    scopus 로고
    • Gene stacking in transgenic plants - the challenge for 21st century plant biotechnology
    • Halpin C. Gene stacking in transgenic plants - the challenge for 21st century plant biotechnology. Plant Biotechnology Journal 2005, 3:141.
    • (2005) Plant Biotechnology Journal , vol.3 , pp. 141
    • Halpin, C.1
  • 64
    • 33644853940 scopus 로고    scopus 로고
    • Measuring multiple fluxes through plant metabolic networks
    • Ratcliffe R.G., Shachar-Hill Y. Measuring multiple fluxes through plant metabolic networks. The Plant Journal 2006, 45:490.
    • (2006) The Plant Journal , vol.45 , pp. 490
    • Ratcliffe, R.G.1    Shachar-Hill, Y.2
  • 69
    • 0033759391 scopus 로고    scopus 로고
    • Altering expression of cinnamic acid 4-hydroxylase in transgenic plants provides evidence for a feedback loop at the entry point into the phenylpropanoid pathway
    • Blount J.W., Korth K.L., Masoud S.A., Rasmussen S., Lamb C., Dixon R.A. Altering expression of cinnamic acid 4-hydroxylase in transgenic plants provides evidence for a feedback loop at the entry point into the phenylpropanoid pathway. Plant Physiology 2000, 122:107.
    • (2000) Plant Physiology , vol.122 , pp. 107
    • Blount, J.W.1    Korth, K.L.2    Masoud, S.A.3    Rasmussen, S.4    Lamb, C.5    Dixon, R.A.6
  • 70
    • 25444453719 scopus 로고    scopus 로고
    • Clarification of cinnamoyl co-enzyme A reductase catalysis in monolignol biosynthesis of aspen
    • Li L., Cheng X., Lu S., Nakatsubo T., Umezawa T., Chiang V.L. Clarification of cinnamoyl co-enzyme A reductase catalysis in monolignol biosynthesis of aspen. Plant & Cell Physiology 2005, 46:1073.
    • (2005) Plant & Cell Physiology , vol.46 , pp. 1073
    • Li, L.1    Cheng, X.2    Lu, S.3    Nakatsubo, T.4    Umezawa, T.5    Chiang, V.L.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.