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Volumn 4, Issue DEC, 2013, Pages

A workflow for mathematical modeling of subcellular metabolic pathways in leaf metabolism of Arabidopsis thaliana

Author keywords

Genome scale models; Inverse calculation; Mathematical modeling; Metabolomics; Plant systems biology; Subcellular compartmentation

Indexed keywords


EID: 84901025382     PISSN: None     EISSN: 1664462X     Source Type: Journal    
DOI: 10.3389/fpls.2013.00541     Document Type: Article
Times cited : (11)

References (34)
  • 1
    • 84866487453 scopus 로고    scopus 로고
    • Integration of expression data in genome-scale metabolic network reconstructions
    • doi: 10.3389/fphys.2012.00299
    • Blazier, A. S., and Papin, J. A. (2012). Integration of expression data in genome-scale metabolic network reconstructions. Front. Physiol. 3:299. doi: 10.3389/fphys.2012.00299
    • (2012) Front. Physiol , vol.3 , pp. 299
    • Blazier, A.S.1    Papin, J.A.2
  • 2
    • 84861165967 scopus 로고    scopus 로고
    • Are we ready for genome-scale modeling in plants?
    • doi: 10.1016/j.plantsci.2012.04.010
    • Collakova, E., Yen, J. Y., and Senger, R. S. (2012). Are we ready for genome-scale modeling in plants? Plant Sci. 191-192, 53-70. doi: 10.1016/j.plantsci.2012.04.010
    • (2012) Plant Sci , vol.191-192 , pp. 53-70
    • Collakova, E.1    Yen, J.Y.2    Senger, R.S.3
  • 4
    • 84877605157 scopus 로고    scopus 로고
    • Granger causality in integrated GC-MS and LC-MS metabolomics data reveals the interface of primary and secondary metabolism
    • doi: 10.1007/s11306-012-0470-0
    • Doerfler, H., Lyon, D., Nagele, T., Sun, X., Fragner, L., Hadacek, F., et al. (2013). Granger causality in integrated GC-MS and LC-MS metabolomics data reveals the interface of primary and secondary metabolism. Metabolomics 9, 564-574. doi: 10.1007/s11306-012-0470-0
    • (2013) Metabolomics , vol.9 , pp. 564-574
    • Doerfler, H.1    Lyon, D.2    Nagele, T.3    Sun, X.4    Fragner, L.5    Hadacek, F.6
  • 5
    • 45149111660 scopus 로고    scopus 로고
    • The growing scope of applications of genome-scale metabolic reconstructions using
    • doi: 10.1038/nbt1401
    • Feist, A. M., and Palsson, B. O. (2008). The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli. Nat. Biotechnol. 26, 659-667. doi: 10.1038/nbt1401
    • (2008) Escherichia Coli. Nat. Biotechnol , vol.26 , pp. 659-667
    • Feist, A.M.1    Palsson, B.O.2
  • 6
    • 9444266171 scopus 로고    scopus 로고
    • CellDesigner: A process diagram editor for gene-regulatory and biochemical networks
    • doi: 10.1016/S1478-5382(03)02370-9
    • Funahashi, A., Morohashi, M., Kitano, H., and Tanimura, N. (2003). CellDesigner: a process diagram editor for gene-regulatory and biochemical networks. BIOSILICO 1, 159-162. doi: 10.1016/S1478-5382(03)02370-9
    • (2003) BIOSILICO , vol.1 , pp. 159-162
    • Funahashi, A.1    Morohashi, M.2    Kitano, H.3    Tanimura, N.4
  • 7
    • 14744280370 scopus 로고    scopus 로고
    • A robot-based platform to measure multiple enzyme activities in Arabidopsis using a set of cycling assays: Comparison of changes of enzyme activities and transcript levels during diurnal cycles and in prolonged darkness
    • doi: 10.1105/tpc.104.025973
    • Gibon, Y., Blaesing, O. E., Hannemann, J., Carillo, P., Hohne, M., Hendriks, J. H. M., et al. (2004). A robot-based platform to measure multiple enzyme activities in Arabidopsis using a set of cycling assays: comparison of changes of enzyme activities and transcript levels during diurnal cycles and in prolonged darkness. PlantCell 16, 3304-3325. doi: 10.1105/tpc.104.025973
    • (2004) PlantCell , vol.16 , pp. 3304-3325
    • Gibon, Y.1    Blaesing, O.E.2    Hannemann, J.3    Carillo, P.4    Hohne, M.5    Hendriks, J.H.M.6
  • 8
    • 33845368513 scopus 로고    scopus 로고
    • COPASI - a COmplex PAthway SImulator
    • doi: 10.1093/bioinformatics/btl485
    • Hoops, S., Sahle, S., Gauges, R., Lee, C., Pahle, J., Simus, N., et al. (2006). COPASI - a COmplex PAthway SImulator. Bioinformatics 22, 3067-3074. doi: 10.1093/bioinformatics/btl485
    • (2006) Bioinformatics , vol.22 , pp. 3067-3074
    • Hoops, S.1    Sahle, S.2    Gauges, R.3    Lee, C.4    Pahle, J.5    Simus, N.6
  • 9
    • 34548841428 scopus 로고    scopus 로고
    • The golm metabolome database: A database for GC-MS based metabolite profiling
    • , eds J. Nielsen and M. Jewett (Berlin; Heidelberg: Springer)
    • Hummel, J., Selbig, J., Walther, D., and Kopka, J. (2007). "The golm metabolome database: a database for GC-MS based metabolite profiling, in Metabolomics, eds J. Nielsen and M. Jewett (Berlin; Heidelberg: Springer), 75-95.
    • (2007) Metabolomics , pp. 75-95
    • Hummel, J.1    Selbig, J.2    Walther, D.3    Kopka, J.4
  • 10
    • 84872754613 scopus 로고    scopus 로고
    • Analysis of the compartmentalized metabolome - a validation of the non-aqueous fractionation technique
    • doi: 10.3389/fpls.2011.00055
    • Klie, S., Krueger, S., Krall, L., Giavalisco, P., Flugge, U. I., Willmitzer, L., et al. (2011). Analysis of the compartmentalized metabolome - a validation of the non-aqueous fractionation technique. Front. Plant Sci. 2:55. doi: 10.3389/fpls.2011.00055
    • (2011) Front. Plant Sci , vol.2 , pp. 55
    • Klie, S.1    Krueger, S.2    Krall, L.3    Giavalisco, P.4    Flugge, U.I.5    Willmitzer, L.6
  • 11
    • 80052058127 scopus 로고    scopus 로고
    • Evidence for arole of raffinose in stabilizing photosystem II during freeze-thaw cycles
    • doi: 10.1007/s00425-011-1413-0
    • Knaupp, M., Mishra, K. B., Nedbal, L., and Heyer, A. G. (2011). Evidence for arole of raffinose in stabilizing photosystem II during freeze-thaw cycles. Planta 234, 477-486. doi: 10.1007/s00425-011-1413-0
    • (2011) Planta , vol.234 , pp. 477-486
    • Knaupp, M.1    Mishra, K.B.2    Nedbal, L.3    Heyer, A.G.4
  • 12
    • 79952672684 scopus 로고    scopus 로고
    • A topological map of the compartmentalized Arabidopsis thaliana leaf metabolome
    • doi: 10.1371/journal.pone.0017806
    • Krueger, S., Giavalisco, P., Krall, L., Steinhauser, M.-C., Bussis, D., Usadel, B., et al.A topological map of the compartmentalized Arabidopsis thaliana leaf metabolome. PLoS ONE 6:e17806. doi: 10.1371/journal.pone.0017806
    • PLoS ONE , vol.6
    • Krueger, S.1    Giavalisco, P.2    Krall, L.3    Steinhauser, M.-C.4    Bussis, D.5    Usadel, B.6
  • 13
    • 33845874376 scopus 로고    scopus 로고
    • Compartmentation in plant metabolism
    • doi: 10.1093/jxb/erl134
    • Lunn, J. E. (2007). Compartmentation in plant metabolism. J. Exp. Bot. 58, 35-47. doi: 10.1093/jxb/erl134
    • (2007) J. Exp. Bot , vol.58 , pp. 35-47
    • Lunn, J.E.1
  • 15
    • 72849144434 scopus 로고    scopus 로고
    • Sequencing technologies - the next generation
    • doi: 10.1038/nrg2626
    • Metzker, M. L. (2010). Sequencing technologies - the next generation. Nat. Rev. Genet. 11, 31-46. doi: 10.1038/nrg2626
    • (2010) Nat. Rev. Genet , vol.11 , pp. 31-46
    • Metzker, M.L.1
  • 16
    • 84856015478 scopus 로고    scopus 로고
    • Reconstruction of Arabidopsis metabolic network models accounting for subcellular compartmentalization and tissue-specificity
    • doi: 10.1073/pnas.1100358109
    • Mintz-Oron, S., Meir, S., Malitsky, S., Ruppin, E., Aharoni, A., and Shlomi, T.Reconstruction of Arabidopsis metabolic network models accounting for subcellular compartmentalization and tissue-specificity. Proc. Natl. Acad. Sci. U.S.A. 109,339-344. doi: 10.1073/pnas.1100358109
    • Proc. Natl. Acad. Sci. U.S.A , vol.109 , pp. 339-344
    • Mintz-Oron, S.1    Meir, S.2    Malitsky, S.3    Ruppin, E.4    Aharoni, A.5    Shlomi, T.6
  • 17
    • 84894419393 scopus 로고    scopus 로고
    • Eigenvalues of Jacobian matrices report on steps of metabolic reprogramming in a complex plant-environment interaction
    • doi: 10.4236/am.2013.48A007
    • Nagele, T., and Weckwerth, W. (2013). Eigenvalues of Jacobian matrices report on steps of metabolic reprogramming in a complex plant-environment interaction. Appl. Math. 4, 44-49. doi: 10.4236/am.2013.48A007
    • (2013) Appl. Math , vol.4 , pp. 44-49
    • Nagele, T.1    Weckwerth, W.2
  • 18
    • 84876413945 scopus 로고    scopus 로고
    • Approximating subcellular organisation of carbohydrate metabolism during cold acclimation in different natural accessions of
    • doi: 10.1111/nph.12201
    • Nagele, T., and Heyer, A. G. (2013). Approximating subcellular organisation of carbohydrate metabolism during cold acclimation in different natural accessions of Arabidopsis thaliana. New Phytol. 198, 777-787. doi: 10.1111/nph.12201
    • (2013) Arabidopsis Thaliana. New Phytol , vol.198 , pp. 777-787
    • Nagele, T.1    Heyer, A.G.2
  • 19
    • 84866739110 scopus 로고    scopus 로고
    • Identification of a metabolic bottleneck for cold acclimation in Arabidopsis thaliana
    • doi: 10.1111/j.1365-313X.2012.05064.x
    • Nagele, T., Stutz, S., Hormiller, I. I., and Heyer, A. G. (2012). Identification of a metabolic bottleneck for cold acclimation in Arabidopsis thaliana. Plant J. 72, 102-114. doi: 10.1111/j.1365-313X.2012.05064.x
    • (2012) Plant J , vol.72 , pp. 102-114
    • Nagele, T.1    Stutz, S.2    Hormiller, I.I.3    Heyer, A.G.4
  • 20
    • 84877595714 scopus 로고    scopus 로고
    • Mathematical modeling of plant metabolismrfrom reconstruction to prediction
    • doi: 10.3390/metabo2030553
    • Nagele, T., and Weckwerth, W. (2012). Mathematical modeling of plant metabolismrfrom reconstruction to prediction. Metabolites 2, 553-566. doi: 10.3390/metabo2030553
    • (2012) Metabolites , vol.2 , pp. 553-566
    • Nagele, T.1    Weckwerth, W.2
  • 21
    • 70350676551 scopus 로고    scopus 로고
    • A genome-scale metabolic model of Arabidopsis and some of its properties
    • doi: 10.1104/pp.109.141267
    • Poolman, M. G., Miguet, L., Sweetlove, L. J., and Fell, D. A. (2009). A genome-scale metabolic model of Arabidopsis and some of its properties. Plant Physiol. 151, 1570-1581. doi: 10.1104/pp.109.141267
    • (2009) Plant Physiol , vol.151 , pp. 1570-1581
    • Poolman, M.G.1    Miguet, L.2    Sweetlove, L.J.3    Fell, D.A.4
  • 22
    • 84859355304 scopus 로고    scopus 로고
    • Kinetic modelling of plant metabolic pathways
    • doi: 10.1093/jxb/ers080
    • Rohwer, J. M. (2012). Kinetic modelling of plant metabolic pathways. J. Exp. Bot. 63,2275-2292. doi: 10.1093/jxb/ers080
    • (2012) J. Exp. Bot , vol.63 , pp. 2275-2292
    • Rohwer, J.M.1
  • 23
    • 58849118519 scopus 로고    scopus 로고
    • Nested uncertainties in biochemical models
    • doi: 10.1049/iet-syb:20070042
    • Schaber, J., Liebermeister, W., and Klipp, E. (2009). Nested uncertainties in biochemical models. IET Syst. Biol. 3, 1-9. doi: 10.1049/iet-syb:20070042
    • (2009) IET Syst. Biol , vol.3 , pp. 1-9
    • Schaber, J.1    Liebermeister, W.2    Klipp, E.3
  • 24
    • 84856264733 scopus 로고    scopus 로고
    • Cold acclimation induces changes in Arabidopsis tonoplast protein abundance and activity and alters phosphorylation of tonoplast monosaccharide transporters
    • doi: 10.1111/j.1365-313X.2011. 04812.x
    • Schulze, W. X., Schneider, T., Starck, S., Martinoia, E., and Trentmann, O. (2012). Cold acclimation induces changes in Arabidopsis tonoplast protein abundance and activity and alters phosphorylation of tonoplast monosaccharide transporters. Plant J. 69, 529-541. doi: 10.1111/j.1365-313X.2011. 04812.x
    • (2012) Plant J , vol.69 , pp. 529-541
    • Schulze, W.X.1    Schneider, T.2    Starck, S.3    Martinoia, E.4    Trentmann, O.5
  • 25
    • 34547684426 scopus 로고    scopus 로고
    • Computational approaches to the topology, stability and dynamics of metabolic networks
    • doi: 10.1016/j.phytochem.2007.04.041
    • Steuer, R. (2007). Computational approaches to the topology, stability and dynamics of metabolic networks. Phytochemistry 68, 2139-2151. doi: 10.1016/j.phytochem.2007.04.041
    • (2007) Phytochemistry , vol.68 , pp. 2139-2151
    • Steuer, R.1
  • 26
    • 0038281453 scopus 로고    scopus 로고
    • Observing and interpreting correlations in metabolomic networks
    • doi: 10.1093/bioinformatics/btg120
    • Steuer, R., Kurths, J., Fiehn, O., and Weckwerth, W. (2003). Observing and interpreting correlations in metabolomic networks. Bioinformatics 19, 1019-1026. doi: 10.1093/bioinformatics/btg120
    • (2003) Bioinformatics , vol.19 , pp. 1019-1026
    • Steuer, R.1    Kurths, J.2    Fiehn, O.3    Weckwerth, W.4
  • 28
    • 84862802794 scopus 로고    scopus 로고
    • COVAIN: Atoolboxfor uni- andmultivariate statistics, time-series and correlation network analysis and inverse estimation of the differential Jacobian from metabolomics covariance data
    • doi: 10.1007/s11306-012-0399-3
    • Sun, X. L., and Weckwerth, W. (2012). COVAIN: atoolboxfor uni- andmultivariate statistics, time-series and correlation network analysis and inverse estimation of the differential Jacobian from metabolomics covariance data. Metabolomics 8, S81-S93. doi: 10.1007/s11306-012-0399-3
    • (2012) Metabolomics , vol.8
    • Sun, X.L.1    Weckwerth, W.2
  • 29
    • 75149129569 scopus 로고    scopus 로고
    • A protocol for generating a high- quality genome-scale metabolic reconstruction
    • doi: 10.1038/nprot.2009.203
    • Thiele, I., and Palsson, B. O. (2010). A protocol for generating a high- quality genome-scale metabolic reconstruction. Nat. Protoc. 5, 93-121. doi: 10.1038/nprot.2009.203
    • (2010) Nat. Protoc , vol.5 , pp. 93-121
    • Thiele, I.1    Palsson, B.O.2
  • 30
    • 84881111872 scopus 로고    scopus 로고
    • Systemic cold stress adaptation of Chlamydomonas reinhardtii
    • doi: 10.1074/mcp.M112.026765
    • Valledor, L., Furuhashi, T., Hanak, A. M., and Weckwerth, W. (2013). Systemic cold stress adaptation of Chlamydomonas reinhardtii. Mol. Cell. Proteomics 12, 2032-2047. doi: 10.1074/mcp.M112.026765
    • (2013) Mol. Cell. Proteomics , vol.12 , pp. 2032-2047
    • Valledor, L.1    Furuhashi, T.2    Hanak, A.M.3    Weckwerth, W.4
  • 31
    • 84858718127 scopus 로고    scopus 로고
    • Green systems biology - from single genomes, proteomes and metabolomes to ecosystems research and biotechnology
    • doi: 10.1016/j.jprot.2011.07.010
    • Weckwerth, W. (2011a). Green systems biology - from single genomes, proteomes and metabolomes to ecosystems research and biotechnology. J. Proteomics 75, 284-305. doi: 10.1016/j.jprot.2011.07.010
    • (2011) J. Proteomics , vol.75 , pp. 284-305
    • Weckwerth, W.1
  • 32
    • 79956281118 scopus 로고    scopus 로고
    • Unpredictability of metabolism-the key role of metabolomics science in combination with next-generation genome sequencing
    • doi: 10.1007/s00216-011- 4948-9
    • Weckwerth, W. (2011b). Unpredictability of metabolism-the key role of metabolomics science in combination with next-generation genome sequencing. Anal. Bioanal. Chem. 400, 1967-1978. doi: 10.1007/s00216-011- 4948-9
    • (2011) Anal. Bioanal. Chem , vol.400 , pp. 1967-1978
    • Weckwerth, W.1
  • 33
    • 77952528150 scopus 로고    scopus 로고
    • Targeted proteomics for Chlamydomonas reinhardtii combined with rapid subcellular protein fractionation, metabolomics and metabolic flux analyses
    • doi: 10.1039/b920913a
    • Wienkoop, S., Weiss, J., May, P., Kempa, S., Irgang, S., Recuenco-Munoz, L., et al. (2010). Targeted proteomics for Chlamydomonas reinhardtii combined with rapid subcellular protein fractionation, metabolomics and metabolic flux analyses. Mol. Biosyst. 6, 1018-1031. doi: 10.1039/b920913a
    • (2010) Mol. Biosyst , vol.6 , pp. 1018-1031
    • Wienkoop, S.1    Weiss, J.2    May, P.3    Kempa, S.4    Irgang, S.5    Recuenco-Munoz, L.6
  • 34
    • 33947507541 scopus 로고    scopus 로고
    • Molecular identification and physiological characterization of a novel monosaccharide transporter from Arabidopsis involved in vacuolar sugar transport
    • doi: 10.1105/tpc.106. 047290
    • Wormit, A., Trentmann, O., Feifer, I., Lohr, C., Tjaden, J., Meyer, S., et al. (2006). Molecular identification and physiological characterization of a novel monosaccharide transporter from Arabidopsis involved in vacuolar sugar transport. Plant Cell 18, 3476-3490. doi: 10.1105/tpc.106. 047290
    • (2006) Plant Cell , vol.18 , pp. 3476-3490
    • Wormit, A.1    Trentmann, O.2    Feifer, I.3    Lohr, C.4    Tjaden, J.5    Meyer, S.6


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