IN SILICO GENOME-SCALE RECONSTRUCTION AND ANALYSIS OF THE SHEWANELLA LOIHICA PV-4 METABOLIC NETWORK

Abstract

Microbial Fuel Cells (MFCs) are devices that generate electricity directly from organic compounds with microbes (electricigens) serving as anodic catalysts. As a novel environment-friendly energy source, MFCs have extensive practical value. Since the biological features and metabolic mechanism of electricigens have a great effect on the electricity production of MFCs, it is a big deal to screen strains with high electricity productivity for improving the power output of MFC. Reconstructions and simulations of metabolic networks are of significant help in studying the metabolism of microorganisms so as to guide gene engineering and metabolic engineering to improve their power-generating efficiency. Herein, we reconstructed a genome-scale constraint-based metabolic network model of Shewanella loihica PV-4, an important electricigen, based on its genomic functional annotations, reaction databases and published metabolic network models of seven microorganisms. The resulting network model iGX790 consists of 902 reactions (including 71 exchange reactions), 798 metabolites and 790 genes, covering the main pathways such as carbon metabolism, energy metabolism, amino acid metabolism, nucleic acid metabolism and lipid metabolism. Using the model, we simulated the growth rate, the maximal synthetic rate of ATP, the flux variability analysis of metabolic network, gene deletion and so on to examine the metabolism of S. loihica PV-4.

Reconstruction and analysis of thermodynamically-constrained models reveal metabolic responses of a deep-sea bacterium to temperature perturbations

“…WP2 has an optimal growth temperature of 10–15°C, a growth range of 0–20°C, and exhibits the hallmark metabolic versatility seen in the Shewanella genus (32, 33). WP2 belongs to the Group 1 Shewanella , a clade mainly consisting of deep-sea strains characterized by their tolerance and adaptation to low-temperature and high-pressure conditions (34, 35). WP2 represents a distinct clade that is distant from two other Group 1 Shewanella strains that have been represented using Genome-scale models (GEMs): Shewanella loihica PV-4 and S. piezotolerans WP3 (34, 36).…”

“…WP2 has an optimal growth temperature of 10-15°C, a growth range of 0-20°C, and exhibits the hallmark metabolic versatility seen in the Shewanella genus (32,33). WP2 belongs to the Group 1 Shewanella, a clade mainly consisting of deep-sea strains characterized by their tolerance and adaptation to low-temperature and high-pressure conditions (34,35).…”

Reconstruction and Analysis of Thermodynamically Constrained Models Reveal Metabolic Responses of a Deep-Sea Bacterium to Temperature Perturbations

“…WP2 has an optimal growth temperature of 10 to 15°C and a growth range of 0 to 20°C, and it exhibits the hallmark metabolic versatility seen in the Shewanella genus ( 31 , 32 ). WP2 belongs to group 1 Shewanella , a clade mainly consisting of deep-sea strains characterized by their tolerance and adaptation to low-temperature and high-pressure conditions ( 33 , 34 ). WP2 represents a distinct clade that is distant from two other group 1 Shewanella strains that have been represented using genome-scale models (GEMs), Shewanella loihica PV-4 and Shewanella piezotolerans WP3 ( 33 , 35 ).…”