메뉴 건너뛰기




Volumn 6, Issue , 2016, Pages

Principles of proteome allocation are revealed using proteomic data and genome-scale models

Author keywords

[No Author keywords available]

Indexed keywords

PROTEOME;

EID: 84995959470     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep36734     Document Type: Article
Times cited : (34)

References (38)
  • 1
    • 84900303762 scopus 로고    scopus 로고
    • Optimizing genome-scale network reconstructions
    • Monk, J., Nogales, J., Palsson, B. O. Optimizing genome-scale network reconstructions. Nature Biotechnology 32, 447-452 (2014).
    • (2014) Nature Biotechnology , vol.32 , pp. 447-452
    • Monk, J.1    Nogales, J.2    Palsson, B.O.3
  • 2
    • 84858439602 scopus 로고    scopus 로고
    • Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods
    • Lewis, N. E., Nagarajan, H., Palsson, B. O. Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods. Nat Rev Microbiol 10, 291-305 (2012).
    • (2012) Nat Rev Microbiol , vol.10 , pp. 291-305
    • Lewis, N.E.1    Nagarajan, H.2    Palsson, B.O.3
  • 3
    • 84866128045 scopus 로고    scopus 로고
    • Shrinking the metabolic solution space using experimental datasets
    • Reed, J. L. Shrinking the metabolic solution space using experimental datasets. PLoS Comput Biol 8, e1002662 (2012).
    • (2012) PLoS Comput Biol , vol.8 , pp. e1002662
    • Reed, J.L.1
  • 4
    • 84928412434 scopus 로고    scopus 로고
    • Methods for integration of transcriptomic data in genome-scale metabolic models
    • Kim, M. K., Lun, D. S. Methods for integration of transcriptomic data in genome-scale metabolic models. Comput Struct Biotechnol J 11, 59-65 (2014).
    • (2014) Comput Struct Biotechnol J , vol.11 , pp. 59-65
    • Kim, M.K.1    Lun, D.S.2
  • 5
    • 84901306814 scopus 로고    scopus 로고
    • Systematic evaluation of methods for integration of transcriptomic data into constraint-based models of metabolism
    • Machado, D., Herrgård, M. Systematic evaluation of methods for integration of transcriptomic data into constraint-based models of metabolism. PLoS Comput Biol 10, e1003580 (2014).
    • (2014) PLoS Comput Biol , vol.10 , pp. e1003580
    • MacHado, D.1    Herrgård, M.2
  • 7
    • 84955660244 scopus 로고    scopus 로고
    • Transcriptomics-based strain optimization tool for designing secondary metabolite overproducing strains of streptomyces coelicolor
    • Kim, M., Yi, J. S., Lakshmanan, M., Lee, D.-Y., Kim, B.-G. Transcriptomics-based strain optimization tool for designing secondary metabolite overproducing strains of streptomyces coelicolor. Biotechnol Bioeng 113, 651-660 (2016).
    • (2016) Biotechnol Bioeng , vol.113 , pp. 651-660
    • Kim, M.1    Yi, J.S.2    Lakshmanan, M.3    Lee, D.-Y.4    Kim, B.-G.5
  • 8
    • 84864843180 scopus 로고    scopus 로고
    • In silico method for modelling metabolism and gene product expression at genome scale
    • Lerman, J. A. et al. In silico method for modelling metabolism and gene product expression at genome scale. Nature Communications 3, 929 (2012).
    • (2012) Nature Communications , vol.3 , pp. 929
    • Lerman, J.A.1
  • 9
    • 84866975246 scopus 로고    scopus 로고
    • Multiscale modeling of metabolism and macromolecular synthesis in E. Coli and its application to the evolution of codon usage
    • Thiele, I. et al. Multiscale modeling of metabolism and macromolecular synthesis in E. coli and its application to the evolution of codon usage. PloS ONE 7, e45635 (2012).
    • (2012) PloS ONE , vol.7 , pp. e45635
    • Thiele, I.1
  • 10
    • 84885367114 scopus 로고    scopus 로고
    • Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction
    • O'Brien, E. J., Lerman, J. A., Chang, R. L., Hyduke, D. R., Palsson, B. O. Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction. Mol Syst Biol 9, 1 (2013).
    • (2013) Mol Syst Biol , vol.9 , pp. 1
    • O'Brien, E.J.1    Lerman, J.A.2    Chang, R.L.3    Hyduke, D.R.4    Palsson, B.O.5
  • 11
    • 84907272917 scopus 로고    scopus 로고
    • Reconstruction and modeling protein translocation and compartmentalization in Escherichia coli at the genome-scale
    • Liu, J. K. et al. Reconstruction and modeling protein translocation and compartmentalization in Escherichia coli at the genome-scale. BMC Syst Biol 8, 110 (2014).
    • (2014) BMC Syst Biol , vol.8 , pp. 110
    • Liu, J.K.1
  • 12
    • 84978861815 scopus 로고    scopus 로고
    • Quantification and classification of e. Coli proteome utilization and unused protein costs across environments
    • O'Brien, E., Utrilla, J., Palsson, B. Quantification and classification of e. coli proteome utilization and unused protein costs across environments. PLoS Comput Biol 12, e1004998 (2016).
    • (2016) PLoS Comput Biol , vol.12 , pp. e1004998
    • O'Brien, E.1    Utrilla, J.2    Palsson, B.3
  • 13
    • 84953737483 scopus 로고    scopus 로고
    • The quantitative and condition-dependent Escherichia coli proteome
    • Schmidt, A. et al. The quantitative and condition-dependent escherichia coli proteome. Nature Biotechnology 34, 104-110 (2016).
    • (2016) Nature Biotechnology , vol.34 , pp. 104-110
    • Schmidt, A.1
  • 14
    • 84967180536 scopus 로고    scopus 로고
    • Global rebalancing of cellular resources by pleiotropic point mutations illustrates a multi-scale mechanism of adaptive evolution
    • Utrilla, J. et al. Global rebalancing of cellular resources by pleiotropic point mutations illustrates a multi-scale mechanism of adaptive evolution. Cell Systems 2, 260-271 (2016).
    • (2016) Cell Systems , vol.2 , pp. 260-271
    • Utrilla, J.1
  • 16
    • 69149110444 scopus 로고    scopus 로고
    • Multiobjective flux balancing using the NISE Method for metabolic network analysis
    • Oh, Y. G., Lee, D. Y., Lee, S. Y., Park, S. Multiobjective Flux Balancing Using the NISE Method for Metabolic Network Analysis. Biomolecular Engineering 25, 999-1008 (2009).
    • (2009) Biomolecular Engineering , vol.25 , pp. 999-1008
    • Oh, Y.G.1    Lee, D.Y.2    Lee, S.Y.3    Park, S.4
  • 17
    • 85027924722 scopus 로고    scopus 로고
    • Hierarchy of non-glucose sugars in Escherichia coli
    • Aidelberg, G. et al. Hierarchy of non-glucose sugars in escherichia coli. BMC Syst Biol 8, 133, 2014.
    • (2014) BMC Syst Biol , vol.8 , pp. 133
    • Aidelberg, G.1
  • 18
    • 84923658662 scopus 로고    scopus 로고
    • Quantitative proteomic analysis reveals a simple strategy of global resource allocation in bacteria
    • Hui, S. et al. Quantitative proteomic analysis reveals a simple strategy of global resource allocation in bacteria. Mol Syst Biol 11, 784 (2015).
    • (2015) Mol Syst Biol , vol.11 , pp. 784
    • Hui, S.1
  • 19
    • 84941067064 scopus 로고    scopus 로고
    • Expanded microbial genome coverage and improved protein family annotation in the cog database
    • Galperin, M. Y., Makarova, K. S., Wolf, Y. I., Koonin, E. V. Expanded microbial genome coverage and improved protein family annotation in the cog database. Nucleic Acids Research 43, D261-D269 (2014).
    • (2014) Nucleic Acids Research , vol.43 , pp. D261-D269
    • Galperin, M.Y.1    Makarova, K.S.2    Wolf, Y.I.3    Koonin, E.V.4
  • 20
    • 18144396807 scopus 로고    scopus 로고
    • Global transcriptional programs reveal a carbon source foraging strategy by Escherichia coli
    • Liu, M. et al. Global transcriptional programs reveal a carbon source foraging strategy by escherichia coli. Journal of Biological Chemistry 280, 15921-15927 (2005).
    • (2005) Journal of Biological Chemistry , vol.280 , pp. 15921-15927
    • Liu, M.1
  • 21
    • 84893398632 scopus 로고    scopus 로고
    • Bacterial growth: Global effects on gene expression, growth feedback and proteome partition
    • Klumpp, S., Hwa, T. Bacterial growth: global effects on gene expression, growth feedback and proteome partition. Curr Opin in Biotechnol 28, 96-102 (2014).
    • (2014) Curr Opin in Biotechnol , vol.28 , pp. 96-102
    • Klumpp, S.1    Hwa, T.2
  • 22
    • 0037335931 scopus 로고    scopus 로고
    • Metabolic flux profiling of Escherichia coli mutants in central carbon metabolism using gc-ms
    • Fischer, E., Sauer, U. Metabolic flux profiling of Escherichia coli mutants in central carbon metabolism using gc-ms. European Journal of Biochemistry 270, 880-891 (2003).
    • (2003) European Journal of Biochemistry , vol.270 , pp. 880-891
    • Fischer, E.1    Sauer, U.2
  • 23
    • 0037079023 scopus 로고    scopus 로고
    • Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth
    • Ibarra, R. U., Edwards, J. S., Palsson, B. O. Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth. Nature 420, 186-189 (2002).
    • (2002) Nature , vol.420 , pp. 186-189
    • Ibarra, R.U.1    Edwards, J.S.2    Palsson, B.O.3
  • 24
    • 84951061481 scopus 로고    scopus 로고
    • Pseudo-transition analysis identifies the key regulators of dynamic metabolic adaptations from steady-state data
    • Gerosa, L. et al. Pseudo-transition analysis identifies the key regulators of dynamic metabolic adaptations from steady-state data. Cell Systems 1, 270-282 (2015).
    • (2015) Cell Systems , vol.1 , pp. 270-282
    • Gerosa, L.1
  • 25
    • 79953317811 scopus 로고    scopus 로고
    • Large-scale 13c-flux analysis reveals distinct transcriptional control of respiratory and fermentative metabolism in Escherichia coli
    • van Rijsewijk, B. R. H., Nanchen, A., Nallet, S., Kleijn, R. J., Sauer, U. Large-scale 13c-flux analysis reveals distinct transcriptional control of respiratory and fermentative metabolism in escherichia coli. Mol Syst Biol 7, 477 (2011).
    • (2011) Mol Syst Biol , vol.7 , pp. 477
    • Van Rijsewijk, B.R.H.1    Nanchen, A.2    Nallet, S.3    Kleijn, R.J.4    Sauer, U.5
  • 26
    • 84995608089 scopus 로고    scopus 로고
    • SolveME: Fast and reliable solution of nonlinear ME models
    • Yang, L. et al. solveME: fast and reliable solution of nonlinear ME models. BMC Bioinform 17, 391 (2016).
    • (2016) BMC Bioinform , vol.17 , pp. 391
    • Yang, L.1
  • 27
    • 84920923824 scopus 로고    scopus 로고
    • Computing the functional proteome: Recent progress and future prospects for genome-scale models
    • O'Brien, E. J., Palsson, B. O. Computing the functional proteome: recent progress and future prospects for genome-scale models. Curr Opin Biotechnol 34, 125-134 (2015).
    • (2015) Curr Opin Biotechnol , vol.34 , pp. 125-134
    • O'Brien, E.J.1    Palsson, B.O.2
  • 28
    • 84917705874 scopus 로고    scopus 로고
    • Use of adaptive laboratory evolution to discover key mutations enabling rapid growth of Escherichia coli K-12 MG1655 on glucose minimal medium
    • LaCroix, R. A. et al. Use of adaptive laboratory evolution to discover key mutations enabling rapid growth of Escherichia coli K-12 MG1655 on glucose minimal medium. Appl Environ Microbiol 81, 17-30 (2015).
    • (2015) Appl Environ Microbiol , vol.81 , pp. 17-30
    • LaCroix, R.A.1
  • 29
    • 79959374585 scopus 로고    scopus 로고
    • Metabolic engineering of Escherichia coli for direct production of 1, 4-butanediol
    • Yim, H. et al. Metabolic engineering of Escherichia coli for direct production of 1, 4-butanediol. Nature Chemical Biology 7, 445-452 (2011).
    • (2011) Nature Chemical Biology , vol.7 , pp. 445-452
    • Yim, H.1
  • 30
    • 84867322381 scopus 로고    scopus 로고
    • Current knowledge of the Escherichia coli phosphoenolpyruvate-carbohydrate phosphotransferase system: Peculiarities of regulation and impact on growth and product formation
    • Escalante, A., Cervantes, A. S., Gosset, G., Bolvar, F. Current knowledge of the Escherichia coli phosphoenolpyruvate-carbohydrate phosphotransferase system: peculiarities of regulation and impact on growth and product formation. Applied Microbiology and Biotechnology 94, 1483-1494 (2012).
    • (2012) Applied Microbiology and Biotechnology , vol.94 , pp. 1483-1494
    • Escalante, A.1    Cervantes, A.S.2    Gosset, G.3    Bolvar, F.4
  • 31
    • 84938936390 scopus 로고    scopus 로고
    • Decoding genome-wide gadewx-transcriptional regulatory networks reveals multifaceted cellular responses to acid stress in Escherichia coli
    • Seo, S. W., Kim, D., O'Brien, E. J., Szubin, R., Palsson, B. O. Decoding genome-wide gadewx-transcriptional regulatory networks reveals multifaceted cellular responses to acid stress in escherichia coli. Nat Commun 6, 7970 (2015).
    • (2015) Nat Commun , vol.6 , pp. 7970
    • Seo, S.W.1    Kim, D.2    O'Brien, E.J.3    Szubin, R.4    Palsson, B.O.5
  • 32
    • 84920906247 scopus 로고    scopus 로고
    • Deciphering fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli
    • Seo, S. W. et al. Deciphering Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli. Nat Commun 5, 4910 (2014).
    • (2014) Nat Commun , vol.5 , pp. 4910
    • Seo, S.W.1
  • 33
    • 84939798405 scopus 로고    scopus 로고
    • Genome-wide reconstruction of oxyr and soxrs transcriptional regulatory networks under oxidative stress in Escherichia coli k-12 mg1655
    • Seo, S. W., Kim, D., Szubin, R., Palsson, B. O. Genome-wide reconstruction of oxyr and soxrs transcriptional regulatory networks under oxidative stress in escherichia coli k-12 mg1655. Cell Reports 12, 1289-1299 (2015).
    • (2015) Cell Reports , vol.12 , pp. 1289-1299
    • Seo, S.W.1    Kim, D.2    Szubin, R.3    Palsson, B.O.4
  • 34
    • 84880860962 scopus 로고    scopus 로고
    • Robust flux balance analysis of multiscale biochemical reaction networks
    • Sun, Y., Fleming, R. M., Thiele, I., Saunders, M. A. Robust flux balance analysis of multiscale biochemical reaction networks. BMC Bioinformatics 14, 240 (2013).
    • (2013) BMC Bioinformatics , vol.14 , pp. 240
    • Sun, Y.1    Fleming, R.M.2    Thiele, I.3    Saunders, M.A.4
  • 35
    • 84947073615 scopus 로고    scopus 로고
    • Solving multiscale linear programs using the simplex method in quadruple precision
    • Ma, D., Saunders, M. A. Solving multiscale linear programs using the simplex method in quadruple precision. In Numerical Analysis and Optimization, 223-235 (2015).
    • (2015) Numerical Analysis and Optimization , pp. 223-235
    • Ma, D.1    Saunders, M.A.2
  • 37
    • 0004027076 scopus 로고    scopus 로고
    • Ph. D. thesis, Technische Universität Berlin Retrieved September 19, 2016
    • Wunderling, R. Paralleler und objektorientierter Simplex-Algorithmus. Ph. D. thesis, Technische Universität Berlin (1996). https://opus4. kobv. de/opus4-zib/frontdoor/index/index/docId/538. Retrieved September 19, 2016.
    • (1996) Paralleler und Objektorientierter Simplex-Algorithmus
    • Wunderling, R.1
  • 38
    • 79960930689 scopus 로고    scopus 로고
    • Condition-dependent cell volume and concentration of Escherichia coli to facilitate data conversion for systems biology modeling
    • Volkmer, B., Heinemann, M. Condition-dependent cell volume and concentration of Escherichia coli to facilitate data conversion for systems biology modeling. PloS ONE 6, e23126 (2011).
    • (2011) PloS ONE , vol.6 , pp. e23126
    • Volkmer, B.1    Heinemann, M.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.