Reconstruction and analysis of genome-scale metabolic model of a photosynthetic bacterium

被引:86
作者
Montagud, Arnau [1 ,3 ]
Navarro, Emilio [2 ]
Fernandez de Cordoba, Pedro [1 ]
Urchueguia, Javier F. [1 ]
Patil, Kiran Raosaheb [3 ]
机构
[1] Univ Politecn Valencia, Inst Univ Matemat Pura & Aplicada, Valencia 46022, Spain
[2] Univ Malaga, Dept Lenguajes & Ciencias Computac, E-29071 Malaga, Spain
[3] European Mol Biol Lab, Struct & Computat Biol Unit, D-69117 Heidelberg, Germany
关键词
ESCHERICHIA-COLI; SYNECHOCYSTIS; CYANOBACTERIUM; HYDROGENASES; SYSTEM; GROWTH;
D O I
10.1186/1752-0509-4-156
中图分类号
Q [生物科学];
学科分类号
07 ; 0710 ; 09 ;
摘要
Background: Synechocystis sp. PCC6803 is a cyanobacterium considered as a candidate photo-biological production platform - an attractive cell factory capable of using CO2 and light as carbon and energy source, respectively. In order to enable efficient use of metabolic potential of Synechocystis sp. PCC6803, it is of importance to develop tools for uncovering stoichiometric and regulatory principles in the Synechocystis metabolic network. Results: We report the most comprehensive metabolic model of Synechocystis sp. PCC6803 available, iSyn669, which includes 882 reactions, associated with 669 genes, and 790 metabolites. The model includes a detailed biomass equation which encompasses elementary building blocks that are needed for cell growth, as well as a detailed stoichiometric representation of photosynthesis. We demonstrate applicability of iSyn669 for stoichiometric analysis by simulating three physiologically relevant growth conditions of Synechocystis sp. PCC6803, and through in silico metabolic engineering simulations that allowed identification of a set of gene knock-out candidates towards enhanced succinate production. Gene essentiality and hydrogen production potential have also been assessed. Furthermore, iSyn669 was used as a transcriptomic data integration scaffold and thereby we found metabolic hot-spots around which gene regulation is dominant during light-shifting growth regimes. Conclusions: iSyn669 provides a platform for facilitating the development of cyanobacteria as microbial cell factories.
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页数:16
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