메뉴 건너뛰기




Volumn 5, Issue JUN, 2014, Pages

Reconstruction of gene regulatory network related to photosynthesis in Arabidopsis thaliana

Author keywords

Coordination; Photosynthesis; Regulatory network; Small world; Transcription factors

Indexed keywords


EID: 84979561805     PISSN: None     EISSN: 1664462X     Source Type: Journal    
DOI: 10.3389/fpls.2014.00273     Document Type: Article
Times cited : (21)

References (37)
  • 1
    • 0036154803 scopus 로고    scopus 로고
    • Overexpression of C4 PEPC caused O2-insensitive photosynthesis in transgenic rice plants
    • Agarie, S., Miura, A., Sumikura, R., Tsukamoto, S., Nose, A., Arima, S., et al. (2002). Overexpression of C4 PEPC caused O2-insensitive photosynthesis in transgenic rice plants. Plant Sci. 162, 257-265. doi:10.1016/S0168-9452(01)00572-6
    • (2002) Plant Sci , vol.162 , pp. 257-265
    • Agarie, S.1    Miura, A.2    Sumikura, R.3    Tsukamoto, S.4    Nose, A.5    Arima, S.6
  • 2
    • 0026857990 scopus 로고
    • Homodimeric and heterodimeric leucine zipper proteins and nuclear factors from parsley recognize diverse promoter elements with ACGT cores
    • Armstrong, G. A., Weisshaar, B., and Hahlbrock, K. (1992). Homodimeric and heterodimeric leucine zipper proteins and nuclear factors from parsley recognize diverse promoter elements with ACGT cores. Plant Cell 4, 525-537. doi:10.1105/tpc.4.5.525
    • (1992) Plant Cell , vol.4 , pp. 525-537
    • Armstrong, G.A.1    Weisshaar, B.2    Hahlbrock, K.3
  • 3
    • 38349164409 scopus 로고    scopus 로고
    • Computing topological parameters of biological networks
    • Assenov, Y., Ramirez, F., Schelhorn, S. E., Lengauer, T., and Albrecht, M. (2008). Computing topological parameters of biological networks. Bioinformatics 24, 282-284. doi:10.1093/bioinformatics/btm554
    • (2008) Bioinformatics , vol.24 , pp. 282-284
    • Assenov, Y.1    Ramirez, F.2    Schelhorn, S.E.3    Lengauer, T.4    Albrecht, M.5
  • 5
    • 18144410184 scopus 로고    scopus 로고
    • Topology of large-scale engineering problem-solving networks
    • Braha, D., and Bar-Yam, Y. (2004). Topology of large-scale engineering problem-solving networks. Phys. Rev. E. Stat. Nonlin. Soft Matter Phys. 69:016113. doi:10.1103/Physreve.69.016113
    • (2004) Phys. Rev. E. Stat. Nonlin. Soft Matter Phys , vol.69
    • Braha, D.1    Bar-Yam, Y.2
  • 6
    • 0033213236 scopus 로고    scopus 로고
    • The maize EmBP-1 orthologue differentially regulates opaque2-dependent gene expression in yeast and cultured maize endosperm cells
    • Carlini, L. E., Ketudat, M., Parsons, R. L., Prabhakar, S., Schmidt, R. J., and Guiltinan, M. J. (1999). The maize EmBP-1 orthologue differentially regulates opaque2-dependent gene expression in yeast and cultured maize endosperm cells. Plant Mol. Biol. 41, 339-349. doi:10.1023/A:1006338727053
    • (1999) Plant Mol. Biol , vol.41 , pp. 339-349
    • Carlini, L.E.1    Ketudat, M.2    Parsons, R.L.3    Prabhakar, S.4    Schmidt, R.J.5    Guiltinan, M.J.6
  • 7
    • 25444489576 scopus 로고    scopus 로고
    • Photosynthetic acclimation in rice leaves to free-air CO2 enrichment related to both ribulose-1,5-bisphosphate carboxylation limitation and ribulose-1,5-bisphosphate regeneration limitation
    • Chen, G. Y., Yong, Z. H., Liao, Y., Zhang, D. Y., Chen, Y., Zhang, H. B., et al. (2005). Photosynthetic acclimation in rice leaves to free-air CO2 enrichment related to both ribulose-1,5-bisphosphate carboxylation limitation and ribulose-1,5-bisphosphate regeneration limitation. Plant Cell Physiol. 46, 1036-1045. doi:10.1093/pcp/pci113
    • (2005) Plant Cell Physiol , vol.46 , pp. 1036-1045
    • Chen, G.Y.1    Yong, Z.H.2    Liao, Y.3    Zhang, D.Y.4    Chen, Y.5    Zhang, H.B.6
  • 8
    • 48549098736 scopus 로고    scopus 로고
    • Deregulation of maize C4 photosynthetic development in a mesophyll cell-defective mutant
    • Covshoff, S., Majeran, W., Liu, P., Kolkman, J. M., van Wijk, K. J., and Brutnell, T. P. (2008). Deregulation of maize C4 photosynthetic development in a mesophyll cell-defective mutant. Plant Physiol. 146, 1469-1481. doi:10.1104/pp.107.113423
    • (2008) Plant Physiol , vol.146 , pp. 1469-1481
    • Covshoff, S.1    Majeran, W.2    Liu, P.3    Kolkman, J.M.4    Van Wijk, K.J.5    Brutnell, T.P.6
  • 9
  • 10
    • 78651444472 scopus 로고    scopus 로고
    • The Zea mays mutants opaque-2 and opaque-7 disclose extensive changes in endosperm metabolism as revealed by protein, amino acid, and transcriptome-wide analyses
    • Hartings, H., Lauria, M., Lazzaroni, N., Pirona, R., and Motto, M. (2011). The Zea mays mutants opaque-2 and opaque-7 disclose extensive changes in endosperm metabolism as revealed by protein, amino acid, and transcriptome-wide analyses. BMC Genomics 12:41. doi:10.1186/1471-2164-12-41
    • (2011) BMC Genomics , vol.12 , pp. 41
    • Hartings, H.1    Lauria, M.2    Lazzaroni, N.3    Pirona, R.4    Motto, M.5
  • 11
    • 0000467650 scopus 로고
    • Reduction of ribulose-1,5-bisphosphate carboxylase/oxygenase content by antisense RNA reduces photosynthesis in transgenic tobacco plants
    • Hudson, G. S., Evans, J. R., von Caemmerer, S., Arvidsson, Y. B., and Andrews, T. J. (1992). Reduction of ribulose-1,5-bisphosphate carboxylase/oxygenase content by antisense RNA reduces photosynthesis in transgenic tobacco plants. Plant Physiol. 98, 294-302. doi:10.1104/pp.98.1.294
    • (1992) Plant Physiol , vol.98 , pp. 294-302
    • Hudson, G.S.1    Evans, J.R.2    Von Caemmerer, S.3    Arvidsson, Y.B.4    Andrews, T.J.5
  • 12
    • 33846818896 scopus 로고    scopus 로고
    • Regulatory network construction in Arabidopsis by using genome-wide gene expression quantitative trait loci
    • Keurentjes, J. J., Fu, J., Terpstra, I. R., Garcia, J. M., van den Ackerveken, G., Snoek, L. B., et al. (2007). Regulatory network construction in Arabidopsis by using genome-wide gene expression quantitative trait loci. Proc. Natl. Acad. Sci. U.S.A. 104, 1708-1713. doi:10.1073/pnas.0610429104
    • (2007) Proc. Natl. Acad. Sci. U.S.A. , vol.104 , pp. 1708-1713
    • Keurentjes, J.J.1    Fu, J.2    Terpstra, I.R.3    Garcia, J.M.4    Van Den Ackerveken, G.5    Snoek, L.B.6
  • 13
    • 76349125292 scopus 로고    scopus 로고
    • Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana
    • Lee, I., Ambaru, B., Thakkar, P., Marcotte, E. M., and Rhee, S. Y. (2010). Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana. Nat. Biotechnol. 28, 149-156. doi:10.1038/nbt.1603
    • (2010) Nat. Biotechnol , vol.28 , pp. 149-156
    • Lee, I.1    Ambaru, B.2    Thakkar, P.3    Marcotte, E.M.4    Rhee, S.Y.5
  • 14
    • 27244458411 scopus 로고    scopus 로고
    • Increased sedoheptulose-1,7-bisphosphatase activity in transgenic tobacco plants stimulates photosynthesis and growth from an early stage in development
    • Lefebvre, S., Lawson, T., Zakhleniuk, O. V., Lloyd, J. C., Raines, C. A., and Fryer, M. (2005). Increased sedoheptulose-1,7-bisphosphatase activity in transgenic tobacco plants stimulates photosynthesis and growth from an early stage in development. Plant Physiol. 138, 451-460. doi:10.1104/pp.104.055046
    • (2005) Plant Physiol , vol.138 , pp. 451-460
    • Lefebvre, S.1    Lawson, T.2    Zakhleniuk, O.V.3    Lloyd, J.C.4    Raines, C.A.5    Fryer, M.6
  • 15
    • 3242739404 scopus 로고    scopus 로고
    • Rising atmospheric carbon dioxide: Plants face the future
    • Long, S. P., Ainsworth, E. A., Rogers, A., and Ort, D. R. (2004). Rising atmospheric carbon dioxide: plants face the future. Annu. Rev. Plant Biol. 55, 591-628. doi:10.1146/annurev.arplant.55.031903.141610
    • (2004) Annu. Rev. Plant Biol , vol.55 , pp. 591-628
    • Long, S.P.1    Ainsworth, E.A.2    Rogers, A.3    Ort, D.R.4
  • 16
    • 55849151275 scopus 로고    scopus 로고
    • Systems approaches to identifying gene regulatory networks in plants
    • Long, T. A., Rady, S. M., and Benfey, P. N. (2008). Systems approaches to identifying gene regulatory networks in plants. Ann. Rev. Cell Dev. Biol. 24, 81-103. doi:10.1146/annurev.cellbio.24.110707.175408
    • (2008) Ann. Rev. Cell Dev. Biol , vol.24 , pp. 81-103
    • Long, T.A.1    Rady, S.M.2    Benfey, P.N.3
  • 17
    • 35948931439 scopus 로고    scopus 로고
    • An Arabidopsis gene network based on the graphical Gaussian model
    • Ma, S., Gong, Q., and Bohnert, H. J. (2007). An Arabidopsis gene network based on the graphical Gaussian model. Genome Res. 17, 1614-1625. doi:10.1101/gr.6911207
    • (2007) Genome Res , vol.17 , pp. 1614-1625
    • Ma, S.1    Gong, Q.2    Bohnert, H.J.3
  • 18
    • 0029917687 scopus 로고    scopus 로고
    • The transcriptional activator Opaque-2 controls the expression of a cytosolic form of pyruvate orthophosphate dikinase-1 in maize endosperms
    • Maddaloni, M., Donini, G., Balconi, C., Rizzi, E., Gallusci, P., Forlani, F., et al. (1996). The transcriptional activator Opaque-2 controls the expression of a cytosolic form of pyruvate orthophosphate dikinase-1 in maize endosperms. Mol. Gen. Genet. 250, 647-654.
    • (1996) Mol. Gen. Genet , vol.250 , pp. 647-654
    • Maddaloni, M.1    Donini, G.2    Balconi, C.3    Rizzi, E.4    Gallusci, P.5    Forlani, F.6
  • 19
    • 52649096494 scopus 로고    scopus 로고
    • Consequences of C4 differentiation for chloroplast membrane proteomes in maize mesophyll and bundle sheath cells
    • Majeran, W., Zybailov, B., Ytterberg, A. J., Dunsmore, J., Sun, Q., and van Wijk, K. J. (2008). Consequences of C4 differentiation for chloroplast membrane proteomes in maize mesophyll and bundle sheath cells. Mol. Cell. Proteomics 7, 1609-1638. doi:10.1074/mcp.M800016-MCP200
    • (2008) Mol. Cell. Proteomics , vol.7 , pp. 1609-1638
    • Majeran, W.1    Zybailov, B.2    Ytterberg, A.J.3    Dunsmore, J.4    Sun, Q.5    Van Wijk, K.J.6
  • 21
    • 0037208166 scopus 로고    scopus 로고
    • TRANSFAC: Transcriptional regulation, from patterns to profiles
    • Matys, V., Fricke, E., Geffers, R., Gossling, E., Haubrock, M., Hehl, R., et al. (2003). TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic Acids Res. 31, 374-378. doi:10.1093/nar/gkg108
    • (2003) Nucleic Acids Res , vol.31 , pp. 374-378
    • Matys, V.1    Fricke, E.2    Geffers, R.3    Gossling, E.4    Haubrock, M.5    Hehl, R.6
  • 22
    • 48249094269 scopus 로고    scopus 로고
    • PIF1 directly and indirectly regulates chlorophyll biosynthesis to optimize the greening process in Arabidopsis
    • Moon, J., Zhu, L., Shen, H., and Huq, E. (2008). PIF1 directly and indirectly regulates chlorophyll biosynthesis to optimize the greening process in Arabidopsis. Proc. Natl. Acad. Sci. U.S.A. 105, 9433-9438. doi:10.1073/pnas.0803611105
    • (2008) Proc. Natl. Acad. Sci. U.S.A. , vol.105 , pp. 9433-9438
    • Moon, J.1    Zhu, L.2    Shen, H.3    Huq, E.4
  • 23
    • 0038054341 scopus 로고    scopus 로고
    • PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes
    • Mootha, V. K., Lindgren, C. M., Eriksson, K. F., Subramanian, A., Sihag, S., Lehar, J., et al. (2003). PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat. Genet. 34, 267-273. doi:10.1038/ng1180
    • (2003) Nat. Genet , vol.34 , pp. 267-273
    • Mootha, V.K.1    Lindgren, C.M.2    Eriksson, K.F.3    Subramanian, A.4    Sihag, S.5    Lehar, J.6
  • 24
    • 0031828646 scopus 로고    scopus 로고
    • Photosynthesis is strongly reduced by antisense suppression of chloroplastic cytochrome bf complex in transgenic tobacco
    • Price, G. D., Caemmerer, S. V., Evans, J. R., Siebke, K., Anderson, J. M., and Badger, M. R. (1998). Photosynthesis is strongly reduced by antisense suppression of chloroplastic cytochrome bf complex in transgenic tobacco. Funct. Plant Biol. 25, 445-452.
    • (1998) Funct. Plant Biol , vol.25 , pp. 445-452
    • Price, G.D.1    Caemmerer, S.V.2    Evans, J.R.3    Siebke, K.4    Erson, J.M.5    Badger, M.R.6
  • 25
    • 33846700587 scopus 로고    scopus 로고
    • Predicting transcription factor affinities to DNA from a biophysical model
    • Roider, H. G., Kanhere, A., Manke, T., and Vingron, M. (2007). Predicting transcription factor affinities to DNA from a biophysical model. Bioinformatics 23, 134-141. doi:10.1093/bioinformatics/btl565
    • (2007) Bioinformatics , vol.23 , pp. 134-141
    • Roider, H.G.1    Kanhere, A.2    Manke, T.3    Vingron, M.4
  • 26
    • 59849097652 scopus 로고    scopus 로고
    • Transcription factors and regulation of photosynthetic and related metabolism under environmental stresses
    • Saibo, N. J. M., Lourenco, T., and Oliveira, M. M. (2009). Transcription factors and regulation of photosynthetic and related metabolism under environmental stresses. Ann. Bot. 103, 609-623. doi:10.1093/aob/mcn227
    • (2009) Ann. Bot , vol.103 , pp. 609-623
    • Saibo, N.J.M.1    Lourenco, T.2    Oliveira, M.M.3
  • 27
    • 0035165481 scopus 로고    scopus 로고
    • Plant bZIP G-box binding factors. Modular structure and activation mechanisms
    • Siberil, Y., Doireau, P., and Gantet, P. (2001). Plant bZIP G-box binding factors. Modular structure and activation mechanisms. Eur. J. Biochem. 268, 5655-5666. doi:10.1046/j.0014-2956.2001.02552.x
    • (2001) Eur. J. Biochem , vol.268 , pp. 5655-5666
    • Siberil, Y.1    Doireau, P.2    Gantet, P.3
  • 28
    • 84864381294 scopus 로고    scopus 로고
    • Molecular Interactions of GBF1 with HY5 and HYH Proteins during Light-mediated Seedling Development in Arabidopsis thaliana
    • Singh, A., Ram, H., Abbas, N., and Chattopadhyay, S. (2012). Molecular Interactions of GBF1 with HY5 and HYH Proteins during Light-mediated Seedling Development in Arabidopsis thaliana. J. Biol. Chem. 287, 25995-26009. doi:10.1074/jbc.M111.333906
    • (2012) J. Biol. Chem , vol.287 , pp. 25995-26009
    • Singh, A.1    Ram, H.2    Abbas, N.3    Chattopadhyay, S.4
  • 29
    • 33644872577 scopus 로고    scopus 로고
    • Limma: Linear models for microarray data
    • eds R. Gentleman, V. Carey, W. Huber, R. Irizarry, and S. Dudo it(NewYork,NY:Springer)
    • Smyth, G. K. (2005). “Limma: linear models for microarray data,” in Bioinformatics and Computational Biology Solutions Using R and Bioconductor, eds R. Gentleman, V. Carey, W. Huber, R. Irizarry, and S. Dudoit(NewYork,NY:Springer),397-420.doi:10.1007/0-387-29362-0_23
    • (2005) Bioinformatics and Computational Biology Solutions Using R and Bioconductor , pp. 397-420
    • Smyth, G.K.1
  • 30
    • 27344435774 scopus 로고    scopus 로고
    • Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
    • Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S., Ebert, B. L., Gillette, M. A., et al. (2005). Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl. Acad. Sci. U.S.A. 102, 15545-15550. doi:10.1073/pnas.0506580102
    • (2005) Proc. Natl. Acad. Sci. U.S.A. , vol.102 , pp. 15545-15550
    • Subramanian, A.1    Tamayo, P.2    Mootha, V.K.3    Mukherjee, S.4    Ebert, B.L.5    Gillette, M.A.6
  • 31
    • 0036008348 scopus 로고    scopus 로고
    • Arabidopsis GARP transcriptional activators interact with the Pro-rich activation domain shared by G-box-binding bZIP factors
    • Tamai, H., Iwabuchi, M., and Meshi, T. (2002). Arabidopsis GARP transcriptional activators interact with the Pro-rich activation domain shared by G-box-binding bZIP factors. Plant Cell Physiol. 43, 99-107. doi:10.1093/pcp/pcf011
    • (2002) Plant Cell Physiol , vol.43 , pp. 99-107
    • Tamai, H.1    Iwabuchi, M.2    Meshi, T.3
  • 32
    • 33845305028 scopus 로고    scopus 로고
    • Genetic networks: Processing data, regulatory network modelling and their analysis
    • Thai, M. T., Cai, Z., and Du, D. Z. (2007). Genetic networks: processing data, regulatory network modelling and their analysis. Optim. Methods Softw. 22, 169-185. doi:10.1080/10556780600881860
    • (2007) Optim. Methods Softw , vol.22 , pp. 169-185
    • Thai, M.T.1    Cai, Z.2    Du, D.Z.3
  • 33
    • 0026842362 scopus 로고
    • Sequences flanking the hexameric G-box core CACGTG affect the specificity of protein binding
    • Williams, M. E., Foster, R., and Chua, N. H. (1992). Sequences flanking the hexameric G-box core CACGTG affect the specificity of protein binding. Plant Cell 4, 485-496. doi:10.1105/tpc.4.4.485
    • (1992) Plant Cell , vol.4 , pp. 485-496
    • Williams, M.E.1    Foster, R.2    Chua, N.H.3
  • 34
    • 77954901952 scopus 로고
    • Biochemical limitations to carbon assimilation in C(3) plants-a retrospective analysis of the a/Ci curves from 109 species
    • Wullschleger, S. D. (1993). Biochemical limitations to carbon assimilation in C(3) plants-a retrospective analysis of the a/Ci curves from 109 species. J. Exp. Bot. 44, 907-920. doi:10.1093/Jxb/44.5.907
    • (1993) J. Exp. Bot , vol.44 , pp. 907-920
    • Wullschleger, S.D.1
  • 35
    • 35348928051 scopus 로고    scopus 로고
    • Optimizing the distribution of resources between enzymes of carbon metabolism can dramatically increase photosynthetic rate: A numerical simulation using an evolutionary algorithm
    • Zhu, X. G., de Sturler, E., and Long, S. P. (2007). Optimizing the distribution of resources between enzymes of carbon metabolism can dramatically increase photosynthetic rate: a numerical simulation using an evolutionary algorithm. Plant Physiol. 145, 513-526. doi:10.1104/pp.107.103713
    • (2007) Plant Physiol , vol.145 , pp. 513-526
    • Zhu, X.G.1    De Sturler, E.2    Long, S.P.3
  • 36
    • 77952533806 scopus 로고    scopus 로고
    • Improving photosynthetic efficiency for greater yield
    • Zhu, X. G., Long, S. P., and Ort, D. R. (2010). Improving photosynthetic efficiency for greater yield. Annu Rev. Plant Biol. 61, 235-261. doi:10.1146/annurev-arplant-042809-112206
    • (2010) Annu Rev. Plant Biol , vol.61 , pp. 235-261
    • Zhu, X.G.1    Long, S.P.2    Ort, D.R.3
  • 37
    • 2942592222 scopus 로고    scopus 로고
    • The slow reversibility of photosystem II thermal energy dissipation on transfer from high to low light may cause large losses in carbon gain by crop canopies: A theoretical analysis
    • Zhu, X. G., Ort, D. R., Whitmarsh, J., and Long, S. P. (2004). The slow reversibility of photosystem II thermal energy dissipation on transfer from high to low light may cause large losses in carbon gain by crop canopies: a theoretical analysis. J. Exp. Bot. 55, 1167-1175. doi:10.1093/jxb/erh141
    • (2004) J. Exp. Bot , vol.55 , pp. 1167-1175
    • Zhu, X.G.1    Ort, D.R.2    Whitmarsh, J.3    Long, S.P.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.