Reconstruction and verification of a genome-scale metabolic model for Synechocystis sp. PCC6803

Abstract

In terms of generating sustainable energy resources, the prospect of producing energy and other useful materials using cyanobacteria has been attracting increasing attention since these processes require only carbon dioxide and solar energy. To establish production processes with a high productivity, in silico models to predict the metabolic activity of cyanobacteria are highly desired. In this study, we reconstructed a genome-scale metabolic model of the cyanobacterium Synechocystis sp. PCC6803, which included 465 metabolites and 493 metabolic reactions. Using this model, we performed constraint-based metabolic simulations to obtain metabolic flux profiles under various environmental conditions. We evaluated the simulated results by comparing these with experimental results from (13)C-tracer metabolic flux analyses, which were obtained under heterotrophic and mixotrophic conditions. There was a good agreement of simulation and experimental results under both conditions. Furthermore, using our model, we evaluated the production of ethanol by Synechocystis sp. PCC6803, which enabled us to estimate quantitatively how its productivity depends on the environmental conditions. The genome-scale metabolic model provides useful information for the evaluation of the metabolic capabilities, and prediction of the metabolic characteristics, of Synechocystis sp. PCC6803.

Mathematical modeling of unicellular microalgae and cyanobacteria metabolism for biofuel production

“…When several metabolic states were simulated, the parameters were counted for only one state since the same parameter was estimated several times. For [38][39][40], the parameters to estimate were inherited by the use of Shastri et al [8] biomass equation, which includes a maintenance term. For [29], the parameters to estimate were inherited by the use of the model of Cogne et al [13].…”

Advances in metabolic modeling of oleaginous microalgae

“…PCC 6803 GSM ( i Syn811)FBA811956911259 [43] Synechocystis sp. PCC 6803 GSMFBA/ 13 C MFA–493465251 [42] Synechocystis sp. PCC 6803 GSM ( i JN678)FBA6788637953206 [46] Synechocystis sp.…”

“…A few other approaches have been used as an alternative or complement, such as 13 C-MFA [22, 31, 34, 42] or EM [50]. Figure 1b, c highlights existing models and methods used to interrogate these models.…”

“…Currently, large-scale metabolic networks are analyzed mainly in silico using FBA. Analysis of dynamic data obtained by experimentally intensive strategies like 13 C-MFA rely on simplified metabolic models, e.g., representing only central metabolism [22, 31, 34, 42]. …”

Modelling and analysis of biological systems to obtain biofuels

“…Genome-wide transcriptional microarrays, first used to study stress responses in Saccharomyces cerevisiae in 2000 (Gasch et al, 2000), were developed in 2001 for this cyanobacterium (Hihara et al, 2001;Suzuki et al, 2001) and works have been published since then using this transcriptomic technique (Foster et al, 2007;Gill et al, 2002;Hihara et al, 2003;Huang et al, 2002b;Hübschmann et al, 2005;Kanesaki et al, 2002;Schmitt and Stephanopoulos, 2003;Singh et al, 2009Singh et al, , 2003Summerfield and Sherman, 2008;Suzuki et al, 2006;Wang et al, 2004;Yamaguchi et al, 2002;Zhang et al, 2008). Finally, and following the work of pioneering metabolic studies of Haemophilus influenzae Rd , Escherichia coli (Edwards and Palsson, 2000b;Palsson, 1993a, 1993b) and Saccharomyces cerevisiae (Förster et al, 2003), several groups have developed metabolic models for this organism (Knoop et al, 2010;Kun et al, 2008;Montagud et al, 2010Montagud et al, , 2011Navarro et al, 2009;Shastri and Morgan, 2005;Yang et al, 2002b;Yoshikawa et al, 2011). Chapter 2, devoted to the reconstruction of genome-scale metabolic models, bears a comparison of all the metabolic models developed up to date for Synechocystis sp.…”