Reconstruction of the Fatty Acid Biosynthetic Pathway of Exiguobacterium antarcticum B7 Based on Genomic and Bibliomic Data.
Exiguobacterium antarcticum B7 is extremophile Gram-positive bacteria able to survive in cold environments. A key factor to understanding cold adaptation processes is related to the modification of fatty acids composing the cell membranes of psychrotrophic bacteria. In our study we show the in silico reconstruction of the fatty acid biosynthesis pathway of E. antarcticum B7. To build the stoichiometric model, a semiautomatic procedure was applied, which integrates genome information using KEGG and RAST/SEED. Constraint-based methods, namely, Flux Balance Analysis (FBA) and elementary modes (EM), were applied. FBA was implemented in the sense of hexadecenoic acid production maximization. To evaluate the influence of the gene expression in the fluxome analysis, FBA was also calculated using the log2⁡FC values obtained in the transcriptome analysis at 0°C and 37°C. The fatty acid biosynthesis pathway showed a total of 13 elementary flux modes, four of which showed routes for the production of hexadecenoic acid. The reconstructed pathway demonstrated the capacity of E. antarcticum B7 to de novo produce fatty acid molecules. Under the influence of the transcriptome, the fluxome was altered, promoting the production of short-chain fatty acids. The calculated models contribute to better understanding of the bacterial adaptation at cold environments.
Genomics and Systems Biology Center, Institute of Biological Sciences, Federal University of Pará, 66075-110 Belém, PA, Brazil.
Regiane
R
Kawasaki
Genomics and Systems Biology Center, Institute of Biological Sciences, Federal University of Pará, 66075-110 Belém, PA, Brazil.
Rafael A
0000-0002-7837-7380
RA
Baraúna
Genomics and Systems Biology Center, Institute of Biological Sciences, Federal University of Pará, 66075-110 Belém, PA, Brazil.
Artur
0000-0002-4082-1132
A
Silva
Rede de Química e Tecnologia/Centro de Química Fina e Biológica, Chemistry Department, Universidade Nova de Lisboa, 2829-516 Costa da Caparica, Portugal.
Marta S P
MS
Carepo
Rede de Química e Tecnologia/Centro de Química Fina e Biológica, Chemistry Department, Universidade Nova de Lisboa, 2829-516 Costa da Caparica, Portugal.
Rui
R
Oliveira
Rede de Química e Tecnologia/Centro de Química Fina e Biológica, Chemistry Department, Universidade Nova de Lisboa, 2829-516 Costa da Caparica, Portugal.
Rodolfo
R
Marques
Genomics and Systems Biology Center, Institute of Biological Sciences, Federal University of Pará, 66075-110 Belém, PA, Brazil.
Rommel T J
RT
Ramos
Genomics and Systems Biology Center, Institute of Biological Sciences, Federal University of Pará, 66075-110 Belém, PA, Brazil.
Maria P C
MP
Schneider
D056449:Bacillales / Q000235:genetics* / Q000378:metabolism*; D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D005227:Fatty Acids / Q000096:biosynthesis* / Q000378:metabolism*; D016680:Genome, Bacterial; D053858:Metabolic Networks and Pathways / Q000235:genetics*
D005227:Fatty Acids