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Volumn 12, Issue 1, 2017, Pages

Reconstruction of biological pathways and metabolic networks from in silico labeled metabolites

Author keywords

Atom mapping; carbon labeling; metabolic networks

Indexed keywords

AUTOMATION; CARBON; COMPLEX NETWORKS; CONFORMAL MAPPING; ESCHERICHIA COLI; MAPPING; METABOLISM; METABOLITES;

EID: 85008869334     PISSN: 18606768     EISSN: 18607314     Source Type: Journal    
DOI: 10.1002/biot.201600464     Document Type: Article
Times cited : (11)

References (55)
  • 1
    • 0242574984 scopus 로고    scopus 로고
    • In silico atomic tracing by substrate-product relationships in Escherichia coli intermediary metabolism
    • Arita, M., In silico atomic tracing by substrate-product relationships in Escherichia coli intermediary metabolism. Genome Res. 2003, 13, 2455–2466.
    • (2003) Genome Res , vol.13 , pp. 2455-2466
    • Arita, M.1
  • 2
    • 47349099128 scopus 로고    scopus 로고
    • Automatic determination of reaction mappings anal reaction center information. 2. Validation on a biochemical reaction database
    • Apostolakis, J., Sacher, O., Korner, R., Gasteiger, J., Automatic determination of reaction mappings anal reaction center information. 2. Validation on a biochemical reaction database. J. Chem. Inf. Model. 2008, 48, 1190–1198.
    • (2008) J. Chem. Inf. Model , vol.48 , pp. 1190-1198
    • Apostolakis, J.1    Sacher, O.2    Korner, R.3    Gasteiger, J.4
  • 4
    • 77954188312 scopus 로고    scopus 로고
    • Finding metabolic pathways using atom tracking
    • Heath, A. P., Bennett, G. N., Kavraki, L. E., Finding metabolic pathways using atom tracking. Bioinformatics 2010, 26, 1548–1555.
    • (2010) Bioinformatics , vol.26 , pp. 1548-1555
    • Heath, A.P.1    Bennett, G.N.2    Kavraki, L.E.3
  • 5
    • 3142626457 scopus 로고    scopus 로고
    • Efficient extraction of mapping rules of atoms from enzymatic reaction data
    • Akutsu, T., Efficient extraction of mapping rules of atoms from enzymatic reaction data. J. Comput. Biol. 2004, 11, 449–462.
    • (2004) J. Comput. Biol , vol.11 , pp. 449-462
    • Akutsu, T.1
  • 6
    • 84882640384 scopus 로고    scopus 로고
    • Flux analysis and metabolomics for systematic metabolic engineering of microorganisms
    • Toya, Y., Shimizu, H., Flux analysis and metabolomics for systematic metabolic engineering of microorganisms. Biotechnol Adv 2013, 31, 818–826.
    • (2013) Biotechnol Adv , vol.31 , pp. 818-826
    • Toya, Y.1    Shimizu, H.2
  • 7
    • 78149407462 scopus 로고    scopus 로고
    • Metabolic fluxes and beyond-systems biology understanding and engineering of microbial metabolism
    • Kohlstedt, M., Becker, J., Wittmann, C., Metabolic fluxes and beyond-systems biology understanding and engineering of microbial metabolism. Appl. Microbiol. Biotechnol. 2010, 88, 1065–1075.
    • (2010) Appl. Microbiol. Biotechnol , vol.88 , pp. 1065-1075
    • Kohlstedt, M.1    Becker, J.2    Wittmann, C.3
  • 8
    • 64649089947 scopus 로고    scopus 로고
    • Cross-platform comparison of methods for quantitative metabolomics of primary metabolism
    • Buscher, J. M., Czernik, D., Ewald, J. C., Sauer, U., Zamboni, N., Cross-platform comparison of methods for quantitative metabolomics of primary metabolism. Anal. Chem. 2009, 81, 2135–2143.
    • (2009) Anal. Chem , vol.81 , pp. 2135-2143
    • Buscher, J.M.1    Czernik, D.2    Ewald, J.C.3    Sauer, U.4    Zamboni, N.5
  • 9
    • 84940106174 scopus 로고    scopus 로고
    • Application of isotope labeling experiments and (13)C flux analysis to enable rational pathway engineering
    • McAtee, A. G., Jazmin, L. J., Young, J. D., Application of isotope labeling experiments and (13)C flux analysis to enable rational pathway engineering. Curr. Opin. Biotechnol. 2015, 36, 50–56.
    • (2015) Curr. Opin. Biotechnol , vol.36 , pp. 50-56
    • McAtee, A.G.1    Jazmin, L.J.2    Young, J.D.3
  • 10
    • 84994908000 scopus 로고    scopus 로고
    • A scientific workflow framework for C metabolic flux analysis
    • Dalman, T., Wiechert, W., Noh, K., A scientific workflow framework for C metabolic flux analysis. J. Biotechnol. 2015, 232 12–24.
    • (2015) J. Biotechnol , vol.232 , pp. 12-24
    • Dalman, T.1    Wiechert, W.2    Noh, K.3
  • 11
    • 33846061120 scopus 로고    scopus 로고
    • Metabolic networks in motion: 13C-based flux analysis
    • Sauer, U., Metabolic networks in motion: 13C-based flux analysis. Mol. Syst. Biol. 2006, 2, 62.
    • (2006) Mol. Syst. Biol , vol.2 , pp. 62
    • Sauer, U.1
  • 12
    • 0031594984 scopus 로고    scopus 로고
    • 13C-NMR, MS and metabolic flux balancing in biotechnology research
    • 13C-NMR, MS and metabolic flux balancing in biotechnology research. Q Rev Biophys 1998, 31, 41–106.
    • (1998) Q Rev Biophys , vol.31 , pp. 41-106
    • Szyperski, T.1
  • 13
    • 84897433019 scopus 로고    scopus 로고
    • C-13-metabolic flux analysis in heterologous cellulase production by Bacillus subtilis genome-reduced strain
    • Toya, Y., Hirasawa, T., Morimoto, T., Masuda, K. et al., C-13-metabolic flux analysis in heterologous cellulase production by Bacillus subtilis genome-reduced strain. J. Biotechnol. 2014, 179, 42–49.
    • (2014) J. Biotechnol , vol.179 , pp. 42-49
    • Toya, Y.1    Hirasawa, T.2    Morimoto, T.3    Masuda, K.4
  • 14
    • 67649984571 scopus 로고    scopus 로고
    • Computer aided optimization of carbon atom labeling for tracer experiments
    • Menkuc, B. S., Gille, C., Holzhutter, H. G., Computer aided optimization of carbon atom labeling for tracer experiments. Genome Inform. 2008, 20, 270–276.
    • (2008) Genome Inform , vol.20 , pp. 270-276
    • Menkuc, B.S.1    Gille, C.2    Holzhutter, H.G.3
  • 16
  • 17
    • 84919681581 scopus 로고    scopus 로고
    • CLCA: Maximum common molecular substructure queries within the MetRxn Database
    • Kumar, A., Maranas, C. D., CLCA: Maximum common molecular substructure queries within the MetRxn Database. J. Chem. Inf. Model. 2014, 54, 3417–3438.
    • (2014) J. Chem. Inf. Model , vol.54 , pp. 3417-3438
    • Kumar, A.1    Maranas, C.D.2
  • 19
    • 84888614601 scopus 로고    scopus 로고
    • ReactionMap: An efficient atom-mapping algorithm for chemical reactions
    • Fooshee, D., Andronico, A., Baldi, P., ReactionMap: An efficient atom-mapping algorithm for chemical reactions. J. Chem. Inf. Model. 2013, 53, 2812–2819.
    • (2013) J. Chem. Inf. Model , vol.53 , pp. 2812-2819
    • Fooshee, D.1    Andronico, A.2    Baldi, P.3
  • 20
    • 84897387824 scopus 로고    scopus 로고
    • Refining carbon flux paths using atomic trace data
    • Pey, J., Planes, F. J., Beasley, J. E., Refining carbon flux paths using atomic trace data. Bioinformatics 2014, 30, 975–980.
    • (2014) Bioinformatics , vol.30 , pp. 975-980
    • Pey, J.1    Planes, F.J.2    Beasley, J.E.3
  • 21
    • 84903954626 scopus 로고    scopus 로고
    • Optimal metabolic route search based on atom mappings
    • Latendresse, M., Krummenacker, M., Karp, P. D., Optimal metabolic route search based on atom mappings. Bioinformatics 2014, 30, 2043–2050.
    • (2014) Bioinformatics , vol.30 , pp. 2043-2050
    • Latendresse, M.1    Krummenacker, M.2    Karp, P.D.3
  • 22
    • 84886290382 scopus 로고    scopus 로고
    • Automatic reaction mapping and reaction center detection
    • Chen, W. L., Chen, D. Z., Taylor, K. T., Automatic reaction mapping and reaction center detection. WIREs Comput. Mol. Sci. 2013, 3, 560–593.
    • (2013) WIREs Comput. Mol. Sci , vol.3 , pp. 560-593
    • Chen, W.L.1    Chen, D.Z.2    Taylor, K.T.3
  • 23
    • 0004678097 scopus 로고
    • Automatic detection of chemical-reaction sites
    • Lynch, M. F., Willett, P., Automatic detection of chemical-reaction sites. J. Chem. Inf. Comput. Sci. 1978, 18, 154–159.
    • (1978) J. Chem. Inf. Comput. Sci , vol.18 , pp. 154-159
    • Lynch, M.F.1    Willett, P.2
  • 24
    • 47349103512 scopus 로고    scopus 로고
    • Automatic determination of reaction mappings and reaction center information. 1. The imaginary transition state energy approach
    • Korner, R., Apostolakis, J., Automatic determination of reaction mappings and reaction center information. 1. The imaginary transition state energy approach. J. Chem. Inf. Model. 2008, 48, 1181–1189.
    • (2008) J. Chem. Inf. Model , vol.48 , pp. 1181-1189
    • Korner, R.1    Apostolakis, J.2
  • 25
    • 0242574984 scopus 로고    scopus 로고
    • In silico atomic tracing by substrate-product relationships in Escherichia coli intermediary metabolism
    • Arita, M., In silico atomic tracing by substrate-product relationships in Escherichia coli intermediary metabolism. Genome Res. 2003, 13, 2455–2466.
    • (2003) Genome Res , vol.13 , pp. 2455-2466
    • Arita, M.1
  • 26
    • 0036663707 scopus 로고    scopus 로고
    • Maximum common subgraph isomorphism algorithms for the matching of chemical structures
    • Raymond, J. W., Willett, P., Maximum common subgraph isomorphism algorithms for the matching of chemical structures. J. Comput.- Aided Mol. Des. 2002, 16, 521–533.
    • (2002) J. Comput.- Aided Mol. Des , vol.16 , pp. 521-533
    • Raymond, J.W.1    Willett, P.2
  • 27
    • 79954459893 scopus 로고    scopus 로고
    • Construction of an E. coli genome-scale atom mapping model for MFA calculations
    • Ravikirthi, P., Suthers, P. F., Maranas, C. D., Construction of an E. coli genome-scale atom mapping model for MFA calculations. Biotechnol. Bioeng. 2011, 108, 1372–1382.
    • (2011) Biotechnol. Bioeng , vol.108 , pp. 1372-1382
    • Ravikirthi, P.1    Suthers, P.F.2    Maranas, C.D.3
  • 28
    • 85008970761 scopus 로고
    • Applications of the principle of minimal chemical distance
    • 47-COMP
    • Ugi, I. K., Wochner, M., Applications of the principle of minimal chemical distance. Abstr. Pap. Am. Chem. Soc. 1988, 196, 47-COMP.
    • (1988) Abstr. Pap. Am. Chem. Soc , vol.196
    • Ugi, I.K.1    Wochner, M.2
  • 29
    • 77957237619 scopus 로고    scopus 로고
    • An Open-Source Java Platform for Automated Reaction Mapping
    • Crabtree, J. D., Mehta, D. P., Kouri, T. M., An Open-Source Java Platform for Automated Reaction Mapping. J. Chem. Inf. Model. 2010, 50, 1751–1756.
    • (2010) J. Chem. Inf. Model , vol.50 , pp. 1751-1756
    • Crabtree, J.D.1    Mehta, D.P.2    Kouri, T.M.3
  • 30
    • 78651301358 scopus 로고    scopus 로고
    • Computing atom mappings for biochemical reactions without subgraph isomorphism
    • Heinonen, M., Lappalainen, S., Mielikainen, T., Rousu, J., Computing atom mappings for biochemical reactions without subgraph isomorphism. J. Comput. Biol. 2011, 18, 43–58.
    • (2011) J. Comput. Biol , vol.18 , pp. 43-58
    • Heinonen, M.1    Lappalainen, S.2    Mielikainen, T.3    Rousu, J.4
  • 31
    • 84858009851 scopus 로고    scopus 로고
    • Stereochemically consistent reaction mapping and identification of multiple reaction mechanisms through integer linear optimization
    • First, E. L., Gounaris, C. E., Floudas, C. A., Stereochemically consistent reaction mapping and identification of multiple reaction mechanisms through integer linear optimization. J. Chem. Inf. Model. 2012, 52, 84–92.
    • (2012) J. Chem. Inf. Model , vol.52 , pp. 84-92
    • First, E.L.1    Gounaris, C.E.2    Floudas, C.A.3
  • 32
    • 84871569267 scopus 로고    scopus 로고
    • Models for identification of erroneous atom-to-atom mapping of reactions performed by automated algorithms
    • Muller, C., Marcou, G., Horvath, D., Aires-de-Sousa, J., Varnek, A., Models for identification of erroneous atom-to-atom mapping of reactions performed by automated algorithms. J. Chem. Inf. Model. 2012, 52, 3116–3122.
    • (2012) J. Chem. Inf. Model , vol.52 , pp. 3116-3122
    • Muller, C.1    Marcou, G.2    Horvath, D.3    Aires-de-Sousa, J.4    Varnek, A.5
  • 33
    • 84958290345 scopus 로고    scopus 로고
    • MapMaker and PathTracer for tracking carbon in genome-scale metabolic models
    • Tervo, C. J., Reed, J. L., MapMaker and PathTracer for tracking carbon in genome-scale metabolic models. Biotechnol. J. 2016, 11, 648–661.
    • (2016) Biotechnol. J , vol.11 , pp. 648-661
    • Tervo, C.J.1    Reed, J.L.2
  • 35
    • 17444382016 scopus 로고    scopus 로고
    • Exploring the diversity of complex metabolic networks
    • Hatzimanikatis, V., Li, C. H., Ionita, J. A., Henry, C. S. et al., Exploring the diversity of complex metabolic networks. Bioinformatics 2005, 21, 1603–1609.
    • (2005) Bioinformatics , vol.21 , pp. 1603-1609
    • Hatzimanikatis, V.1    Li, C.H.2    Ionita, J.A.3    Henry, C.S.4
  • 36
    • 0033982936 scopus 로고    scopus 로고
    • KEGG: Kyoto Encyclopedia of Genes and Genomes
    • Kanehisa, M., Goto, S., KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 2000, 28, 27–30.
    • (2000) Nucleic Acids Res , vol.28 , pp. 27-30
    • Kanehisa, M.1    Goto, S.2
  • 38
    • 0001708959 scopus 로고
    • Description of several chemical-structure file formats used by computer-programs developed at molecular design limited
    • Dalby, A., Nourse, J. G., Hounshell, W. D., Gushurst, A. K. I. et al., Description of several chemical-structure file formats used by computer-programs developed at molecular design limited. J. Chem. Inf. Comput. Sci. 1992, 32, 244–255.
    • (1992) J. Chem. Inf. Comput. Sci , vol.32 , pp. 244-255
    • Dalby, A.1    Nourse, J.G.2    Hounshell, W.D.3    Gushurst, A.K.I.4
  • 39
    • 84993958585 scopus 로고    scopus 로고
    • ATLAS of Biochemistry, A repository of all possible biochemical reactions for synthetic biology and metabolic engineering studies
    • Hadadi, N., Hafner, J., Zisaki, A., Hatzimanikatis, V., ATLAS of Biochemistry, A repository of all possible biochemical reactions for synthetic biology and metabolic engineering studies. ACS Synth. Biol. 2016, 5, 1155-1166.
    • (2016) ACS Synth. Biol , vol.5 , pp. 1155-1166
    • Hadadi, N.1    Hafner, J.2    Zisaki, A.3    Hatzimanikatis, V.4
  • 40
    • 0029016344 scopus 로고
    • Nomenclature Committee of the International Union of Biochemistry and Molecular-Biology (NC-IUBMB). A nomenclature of junctions and branchpoints in nucleic-acids. Recommendations 1994
    • Lilley, D. M. J., Clegg, R. M., Diekmann, S., Seeman, N. C. et al., Nomenclature Committee of the International Union of Biochemistry and Molecular-Biology (NC-IUBMB). A nomenclature of junctions and branchpoints in nucleic-acids. Recommendations 1994. Eur. J. Biochem. 1995, 230, 1–2.
    • (1995) Eur. J. Biochem , vol.230 , pp. 1-2
    • Lilley, D.M.J.1    Clegg, R.M.2    Diekmann, S.3    Seeman, N.C.4
  • 41
    • 53049109464 scopus 로고    scopus 로고
    • De novo biosynthetic pathways: Rational design of microbial chemical factories
    • Prather, K. L., Martin, C. H., De novo biosynthetic pathways: Rational design of microbial chemical factories. Curr. Opin. Biotechnol. 2008, 19, 468–474.
    • (2008) Curr. Opin. Biotechnol , vol.19 , pp. 468-474
    • Prather, K.L.1    Martin, C.H.2
  • 42
    • 77953329895 scopus 로고    scopus 로고
    • Prediction of novel synthetic pathways for the production of desired chemicals
    • Cho, A., Yun, H., Park, J. H., Lee, S. Y., Park, S., Prediction of novel synthetic pathways for the production of desired chemicals. BMC Syst Biol 2010, 4, 35.
    • (2010) BMC Syst Biol , vol.4 , pp. 35
    • Cho, A.1    Yun, H.2    Park, J.H.3    Lee, S.Y.4    Park, S.5
  • 43
    • 79959374585 scopus 로고    scopus 로고
    • Metabolic engineering of Escherichia coli for direct production of 1,4-butanediol
    • Yim, H., Haselbeck, R., Niu, W., Pujol-Baxley, C. et al., Metabolic engineering of Escherichia coli for direct production of 1,4-butanediol. Nat. Chem. Biol. 2011, 7, 445–452.
    • (2011) Nat. Chem. Biol , vol.7 , pp. 445-452
    • Yim, H.1    Haselbeck, R.2    Niu, W.3    Pujol-Baxley, C.4
  • 44
    • 84880780543 scopus 로고    scopus 로고
    • Retrosynthetic design of heterologous pathways
    • Carbonell, P., Planson, A. G., Faulon, J. L., Retrosynthetic design of heterologous pathways. Methods Mol. Biol. 2013, 985, 149–173.
    • (2013) Methods Mol. Biol , vol.985 , pp. 149-173
    • Carbonell, P.1    Planson, A.G.2    Faulon, J.L.3
  • 45
    • 84907350970 scopus 로고    scopus 로고
    • Generation of an atlas for commodity chemical production in Escherichia coli and a novel pathway prediction algorithm, GEM-Path
    • Campodonico, M. A., Andrews, B. A., Asenjo, J. A., Palsson, B. O., Feist, A. M., Generation of an atlas for commodity chemical production in Escherichia coli and a novel pathway prediction algorithm, GEM-Path. Metab. Eng. 2014, 25, 140–158.
    • (2014) Metab. Eng , vol.25 , pp. 140-158
    • Campodonico, M.A.1    Andrews, B.A.2    Asenjo, J.A.3    Palsson, B.O.4    Feist, A.M.5
  • 46
    • 77953578214 scopus 로고    scopus 로고
    • Discovery and analysis of novel metabolic pathways for the biosynthesis of industrial chemicals: 3-Hydroxypropanoate
    • Henry, C. S., Broadbelt, L. J., Hatzimanikatis, V., Discovery and analysis of novel metabolic pathways for the biosynthesis of industrial chemicals: 3-Hydroxypropanoate. Biotechnol. Bioeng. 2010, 106, 462–473.
    • (2010) Biotechnol. Bioeng , vol.106 , pp. 462-473
    • Henry, C.S.1    Broadbelt, L.J.2    Hatzimanikatis, V.3
  • 47
    • 84896872039 scopus 로고    scopus 로고
    • A computational framework for integration of lipidomics data into metabolic pathways
    • Hadadi, N., Soh, K. C., Seijo, M., Zisaki, A. et al., A computational framework for integration of lipidomics data into metabolic pathways. Metab. Eng, 2014, 23, 1–8.
    • (2014) Metab. Eng. , vol.23 , pp. 1-8
    • Hadadi, N.1    Soh, K.C.2    Seijo, M.3    Zisaki, A.4
  • 49
    • 84936966835 scopus 로고    scopus 로고
    • Design of computational retrobiosynthesis tools for the design of de novo synthetic pathways
    • Hadadi, N., Hatzimanikatis, V., Design of computational retrobiosynthesis tools for the design of de novo synthetic pathways. Curr. Opin. Chem. Biol. 2015, 28, 99–104.
    • (2015) Curr. Opin. Chem. Biol , vol.28 , pp. 99-104
    • Hadadi, N.1    Hatzimanikatis, V.2
  • 50
    • 25644458211 scopus 로고    scopus 로고
    • The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes
    • Overbeek, R., Begley, T., Butler, R. M., Choudhuri, J. V. et al., The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res. 2005, 33, 5691–5702.
    • (2005) Nucleic Acids Res , vol.33 , pp. 5691-5702
    • Overbeek, R.1    Begley, T.2    Butler, R.M.3    Choudhuri, J.V.4
  • 52
    • 0034816101 scopus 로고    scopus 로고
    • Review of EcoCyc and MetaCyc databases
    • Maranas, C. D., Burgard, A. P., Review of EcoCyc and MetaCyc databases. Metab. Eng. 2001, 3, 98–99.
    • (2001) Metab. Eng , vol.3 , pp. 98-99
    • Maranas, C.D.1    Burgard, A.P.2
  • 53
    • 11444249446 scopus 로고    scopus 로고
    • Computational assignment of the EC numbers for genomic-scale analysis of enzymatic reactions
    • Kotera, M., Okuno, Y., Hattori, M., Goto, S., Kanehisa, M., Computational assignment of the EC numbers for genomic-scale analysis of enzymatic reactions. J. Am. Chem. Soc. 2004, 126, 16487–16498.
    • (2004) J. Am. Chem. Soc , vol.126 , pp. 16487-16498
    • Kotera, M.1    Okuno, Y.2    Hattori, M.3    Goto, S.4    Kanehisa, M.5
  • 55
    • 80054069179 scopus 로고    scopus 로고
    • A comprehensive genome-scale reconstruction of Escherichia coli metabolism-2011
    • Orth, J. D., Conrad, T. M., Na, J., Lerman, J. A. et al., A comprehensive genome-scale reconstruction of Escherichia coli metabolism-2011. Mol. Syst. Biol. 2011, 7, 535.
    • (2011) Mol. Syst. Biol , vol.7 , pp. 535
    • Orth, J.D.1    Conrad, T.M.2    Na, J.3    Lerman, J.A.4


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