A systems biology approach to reconcile metabolic network models with application to: Synechocystis sp. PCC 6803 for biofuel production

Molecular BioSystems

Volumn 12, Issue 8, 2016, Pages 2552-2561

  Mohammadi, Reza ^a   Fallah Mehrabadi, Jalil ^b   Bidkhori, Gholamreza ^c   Zahiri, Javad ^d   Javad Niroomand, Mohammad ^a   Masoudi Nejad, Ali ^a  

^a UNIVERSITY OF TEHRAN   (Iran)

^b Lister Institute of Microbiology   (Iran)

^c VTT TECHNICAL RESEARCH CENTRE OF FINLAND   (Finland)

^d TARBIAT MODARES UNIVERSITY   (Iran)

Author keywords

[No Author keywords available]

Indexed keywords

BIOFUEL;

ALGORITHM; BIOLOGICAL MODEL; BIOMASS; BIOTECHNOLOGY; METABOLISM; PROCEDURES; SYNECHOCYSTIS; SYSTEMS BIOLOGY;

ALGORITHMS; BIOFUELS; BIOMASS; BIOTECHNOLOGY; METABOLIC NETWORKS AND PATHWAYS; MODELS, BIOLOGICAL; SYNECHOCYSTIS; SYSTEMS BIOLOGY;

EID: 84979208502     PISSN: 1742206X     EISSN: 17422051     Source Type: Journal    
DOI: 10.1039/c6mb00119j     Document Type: Article

References (71)

1. J. Fargione J. Hill D. Tilman S. Polasky P. Hawthorne Land clearing and the biofuel carbon debt Science 2008 319 1235 1238 10.1126/science.1152747
2. D. C. Ducat J. C. Way P. A. Silver Engineering cyanobacteria to generate high-value products Trends Biotechnol. 2011 29 95 103 10.1016/j.tibtech.2010.12.003
3. I. M. Machado S. Atsumi Cyanobacterial biofuel production J. Biotechnol. 2012 162 50 56 10.1016/j.jbiotec.2012.03.005
4. J. Zhou Y. Li Engineering cyanobacteria for fuels and chemicals production Protein Cell 2010 1 207 210 10.1007/s13238-010-0043-9
5. L. S. Gronenberg R. J. Marcheschi J. C. Liao Next generation biofuel engineering in prokaryotes Curr. Opin. Chem. Biol. 2013 17 462 471 10.1016/j.cbpa.2013.03.037
6. L. Rosgaard A. J. dePorcellinis J. H. Jacobsen N. U. Frigaard Y. Sakuragi Bioengineering of carbon fixation, biofuels, and biochemicals in cyanobacteria and plants J. Biotechnol. 2012 162 134 147 10.1016/j.jbiotec.2012.05.006
7. W. R. Hess Cyanobacterial genomics for ecology and biotechnology Curr. Opin. Microbiol. 2011 14 608 614 10.1016/j.mib.2011.07.024
8. P. Erdrich H. Knoop R. Steuer S. Klamt Cyanobacterial biofuels: new insights and strain design strategies revealed by computational modeling Microb. Cell Fact. 2014 13 128 10.1186/s12934-014-0128-x
9. H. Knoop M. Grundel Y. Zilliges R. Lehmann S. Hoffmann W. Lockau et al., Flux balance analysis of cyanobacterial metabolism: the metabolic network of Synechocystis sp. PCC 6803 PLoS Comput. Biol. 2013 9 e1003081 10.1371/journal.pcbi.1003081
10. S. Atsumi W. Higashide J. C. Liao Direct photosynthetic recycling of carbon dioxide to isobutyraldehyde Nat. Biotechnol. 2009 27 1177 1180 10.1038/nbt.1586
11. X. Liu J. Sheng R. Curtiss 3rd Fatty acid production in genetically modified cyanobacteria Proc. Natl. Acad. Sci. U. S. A. 2011 108 6899 6904 10.1073/pnas.1103014108
12. P. Lindberg S. Park A. Melis Engineering a platform for photosynthetic isoprene production in cyanobacteria, using Synechocystis as the model organism Metab. Eng. 2010 12 70 79 10.1016/j.ymben.2009.10.001
13. N. Quintana F. Van der Kooy M. D. Van de Rhee G. P. Voshol R. Verpoorte Renewable energy from Cyanobacteria: energy production optimization by metabolic pathway engineering Appl. Microbiol. Biotechnol. 2011 91 471 490 10.1007/s00253-011-3394-0
14. E. I. Lan J. C. Liao ATP drives direct photosynthetic production of 1-butanol in cyanobacteria Proc. Natl. Acad. Sci. U. S. A. 2012 109 6018 6023 10.1073/pnas.1200074109
15. K. Schutz T. Happe O. Troshina P. Lindblad E. Leitao P. Oliveira et al., Cyanobacterial H(2) production-a comparative analysis Planta 2004 218 350 359 10.1007/s00425-003-1113-5
16. D. Dutta D. De S. Chaudhuri S. K. Bhattacharya Hydrogen production by Cyanobacteria Microb. Cell Fact. 2005 4 36 10.1186/1475-2859-4-36
17. M. D. Deng J. R. Coleman Ethanol synthesis by genetic engineering in cyanobacteria Appl. Environ. Microbiol. 1999 65 523 528
18. R. Vidal L. Lopez-Maury M. G. Guerrero F. J. Florencio Characterization of an alcohol dehydrogenase from the Cyanobacterium Synechocystis sp. strain PCC 6803 that responds to environmental stress conditions via the Hik34-Rre1 two-component system J. Bacteriol. 2009 191 4383 4391 10.1128/jb.00183-09
19. H. Knoop R. Steuer A computational analysis of stoichiometric constraints and trade-offs in cyanobacterial biofuel production Front. Bioeng. Biotechnol. 2015 3 47 10.3389/fbioe.2015.00047
20. A. A. Shastri J. A. Morgan Flux balance analysis of photoautotrophic metabolism Biotechnol. Prog. 2005 21 1617 1626 10.1021/bp050246d
21. H. Knoop Y. Zilliges W. Lockau R. Steuer The Metabolic Network of Synechocystis sp. PCC 6803: Systemic Properties of Autotrophic Growth Plant Physiol. 2010 154 410 422 10.1104/pp.110.157198
22. J. Nogales S. Gudmundsson E. M. Knight B. O. Palsson I. Thiele Detailing the optimality of photosynthesis in cyanobacteria through systems biology analysis Proc. Natl. Acad. Sci. U. S. A. 2012 109 2678 2683 10.1073/pnas.1117907109
23. S. K. Lee H. Chou T. S. Ham T. S. Lee J. D. Keasling Metabolic engineering of microorganisms for biofuels production: from bugs to synthetic biology to fuels Curr. Opin. Biotechnol. 2008 19 556 563 10.1016/j.copbio.2008.10.014
24. Y. Yu L. You D. Liu W. Hollinshead Y. J. Tang F. Zhang Development of Synechocystis sp. PCC 6803 as a phototrophic cell factory Mar. Drugs 2013 11 2894 2916 10.3390/md11082894
25. R. Steuer H. Knoop R. Machne Modelling cyanobacteria: from metabolism to integrative models of phototrophic growth J. Exp. Bot. 2012 63 2259 2274 10.1093/jxb/ers018
26. N. Tepper T. Shlomi Predicting metabolic engineering knockout strategies for chemical production: accounting for competing pathways Bioinformatics 2010 26 536 543 10.1093/bioinformatics/btp704
27. A. M. Feist M. J. Herrgard I. Thiele J. L. Reed B. O. Palsson Reconstruction of biochemical networks in microorganisms Nat. Rev. Microbiol. 2009 7 129 143 10.1038/nrmicro1949
28. A. M. Feist H. Nagarajan A. E. Rotaru P. L. Tremblay T. Zhang K. P. Nevin et al., Constraint-based modeling of carbon fixation and the energetics of electron transfer in Geobacter metallireducens PLoS Comput. Biol. 2014 10 e1003575 10.1371/journal.pcbi.1003575
29. R. A. Notebaart F. H. van Enckevort C. Francke R. J. Siezen B. Teusink Accelerating the reconstruction of genome-scale metabolic networks BMC Bioinf. 2006 7 296 10.1186/1471-2105-7-296
30. M. A. Oberhardt B. O. Palsson J. A. Papin Applications of genome-scale metabolic reconstructions Mol. Syst. Biol. 2009 5 320 10.1038/msb.2009.77
31. P. Fu Genome-scale modeling of Synechocystis sp. PCC 6803 and prediction of pathway insertion J. Chem. Technol. Biotechnol. 2009 84 473 483 10.1002/jctb.2065
32. A. Montagud E. Navarro P. Fernandez de Cordoba J. F. Urchueguia K. R. Patil Reconstruction and analysis of genome-scale metabolic model of a photosynthetic bacterium BMC Syst. Biol. 2010 4 156 10.1186/1752-0509-4-156
33. K. Yoshikawa Y. Kojima T. Nakajima C. Furusawa T. Hirasawa H. Shimizu Reconstruction and verification of a genome-scale metabolic model for Synechocystis sp. PCC6803 Appl. Microbiol. Biotechnol. 2011 92 347 358 10.1007/s00253-011-3559-x
34. A. Montagud A. Zelezniak E. Navarro P. F. de Cordoba J. F. Urchueguia K. R. Patil Flux coupling and transcriptional regulation within the metabolic network of the photosynthetic bacterium Synechocystis sp. PCC6803 Biotechnol. J. 2011 6 330 342 10.1002/biot.201000109
35. R. Saha A. T. Verseput B. M. Berla T. J. Mueller H. B. Pakrasi C. D. Maranas Reconstruction and comparison of the metabolic potential of cyanobacteria Cyanothece sp. ATCC 51-142 and Synechocystis sp. PCC 6803 PLoS One 2012 7 e48285 10.1371/journal.pone.0048285
36. N. Swainston K. Smallbone P. Mendes D. Kell N. Paton The SuBliMinaL Toolbox: automating steps in the reconstruction of metabolic networks J. Integr. Bioinf. 2011 8 186 10.2390/biecoll-jib-2011-186
37. A. Ravikrishnan K. Raman Critical assessment of genome-scale metabolic networks: the need for a unified standard Briefings Bioinf. 2015 10.1093/bib/bbv003
38. A. P. Burgard P. Pharkya C. D. Maranas Optknock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization Biotechnol. Bioeng. 2003 84 647 657 10.1002/bit.10803
39. P. Pharkya A. P. Burgard C. D. Maranas OptStrain: a computational framework for redesign of microbial production systems Genome Res. 2004 14 2367 2376 10.1101/gr.2872004
40. J. W. Pinney M. W. Shirley G. A. McConkey D. R. Westhead metaSHARK: software for automated metabolic network prediction from DNA sequence and its application to the genomes of Plasmodium falciparum and Eimeria tenella Nucleic Acids Res. 2005 33 1399 1409 10.1093/nar/gki285
41. L. Chindelevitch S. Stanley D. Hung A. Regev B. Berger MetaMerge: scaling up genome-scale metabolic reconstructions with application to Mycobacterium tuberculosis Genome Biol. 2012 13 r6 10.1186/gb-2012-13-1-r6
42. E. Vitkin T. Shlomi MIRAGE: a functional genomics-based approach for metabolic network model reconstruction and its application to cyanobacteria networks Genome Biol. 2012 13 R111 10.1186/gb-2012-13-11-r111
43. O. Hadicke S. Klamt CASOP: a computational approach for strain optimization aiming at high productivity J. Biotechnol. 2010 147 88 101 10.1016/j.jbiotec.2010.03.006
44. L. Yang W. R. Cluett R. Mahadevan EMILiO: a fast algorithm for genome-scale strain design Metab. Eng. 2011 13 272 281 10.1016/j.ymben.2011.03.002
45. J. Kim J. L. Reed OptORF: Optimal metabolic and regulatory perturbations for metabolic engineering of microbial strains BMC Syst. Biol. 2010 4 53 10.1186/1752-0509-4-53
46. M. Hucka A. Finney H. M. Sauro H. Bolouri J. C. Doyle H. Kitano et al., The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models Bioinformatics 2003 19 524 531
47. The Systems Biology Markup Language 2015. http://sbml.org/Main-Page
48. D. Maglott J. Ostell K. D. Pruitt T. Tatusova Entrez Gene: gene-centered information at NCBI Nucleic Acids Res. 2011 39 D52 D57 10.1093/nar/gkq1237
49. G. R. Brown V. Hem K. S. Katz M. Ovetsky C. Wallin O. Ermolaeva et al., Gene: a gene-centered information resource at NCBI Nucleic Acids Res. 2015 43 D36 D42 10.1093/nar/gku1055
50. A. Bairoch The ENZYME database in 2000 Nucleic Acids Res. 2000 28 304 305 10.1093/nar/28.1.304
51. M. Kanehisa S. Goto KEGG: kyoto encyclopedia of genes and genomes Nucleic Acids Res. 2000 28 27 30
52. The UniProt Consortium, Ongoing and future developments at the Universal Protein Resource Nucleic Acids Res. 2011 39 D214 D219 10.1093/nar/gkq1020
53. CAS, Chemical Abstracts Service Home Page n.d. https://www.cas.org/ (accessed December 9, 2015)
54. K. Degtyarenko P. de Matos M. Ennis J. Hastings M. Zbinden A. McNaught et al., ChEBI: a database and ontology for chemical entities of biological interest Nucleic Acids Res. 2008 36 D344 D350 10.1093/nar/gkm791
55. M. A. Jaro Advances in Record-Linkage Methodology as Applied to Matching the 1985 Census of Tampa, Florida J. Am. Stat. Assoc. 2012 414 420 10.1080/01621459.1989.10478785
56. Division UCB-SR. ABSTRACT: The State of Record Linkage and Current Research Problems n.d
57. J. D. Orth I. Thiele B. O. Palsson What is flux balance analysis? Nat. Biotechnol. 2010 28 245 248 10.1038/nbt.1614
58. N. E. Lewis H. Nagarajan B. O. Palsson Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods Nat. Rev. Microbiol. 2012 10 291 305 10.1038/nrmicro2737
59. J. Schellenberger R. Que R. M. Fleming I. Thiele J. D. Orth A. M. Feist et al., Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0 Nat. Protoc. 2011 6 1290 1307 10.1038/nprot.2011.308
60. F. Llaneras J. Pico Stoichiometric modelling of cell metabolism J. Biosci. Bioeng. 2008 105 1 11 10.1263/jbb.105.1
61. J. S. Edwards R. U. Ibarra B. O. Palsson In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data Nat. Biotechnol. 2001 19 125 130 10.1038/84379
62. R. U. Ibarra J. S. Edwards B. O. Palsson Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth Nature 2002 420 186 189 10.1038/nature01149
63. J. S. Edwards R. Ramakrishna B. O. Palsson Characterizing the metabolic phenotype: a phenotype phase plane analysis Biotechnol. Bioeng. 2002 77 27 36
64. J. W. Cooley C. A. Howitt W. F. Vermaas Succinate:quinol oxidoreductases in the cyanobacterium Synechocystis sp. strain PCC 6803: presence and function in metabolism and electron transport J. Bacteriol. 2000 182 714 722
65. J. Zahiri G. Mahdevar A. Nowzari-Dalini H. Ahrabian M. Sadeghi A novel efficient dynamic programming algorithm for haplotype block partitioning J. Theor. Biol. 2010 267 164 170 10.1016/j.jtbi.2010.08.019
66. J. A. Capra K. S. Pollard M. Singh Novel genes exhibit distinct patterns of function acquisition and network integration Genome Biol. 2010 11 R127 10.1186/gb-2010-11-12-r127
67. S. S. Shen-Orr R. Milo S. Mangan U. Alon Network motifs in the transcriptional regulation network of Escherichia coli Nat. Genet. 2002 31 64 68 10.1038/ng881
68. A. Tanay R. Sharan R. Shamir Discovering statistically significant biclusters in gene expression data Bioinformatics 2002 18 S136 S144 10.1093/bioinformatics/18.suppl-1.S136
69. L. Tian S. A. Greenberg S. W. Kong J. Altschuler I. S. Kohane P. J. Park Discovering statistically significant pathways in expression profiling studies Proc. Natl. Acad. Sci. U. S. A. 2005 102 13544 13549 10.1073/pnas.0506577102
70. Wilcoxon Signed-Rank Test-R Tutorial n.d. http://www.r-tutor.com/elementary-statistics/non-parametric-methods/wilcoxon-signed-rank-test (accessed February 9, 2016)
71. I. Thiele B. O. Palsson A protocol for generating a high-quality genome-scale metabolic reconstruction Nat. Protoc. 2010 5 93 121 10.1038/nprot.2009.203