In Silico Metabolic Model of Gordonia Alkanivorans to Study Its Desulfurization Characteristics

In silico Metabolic Model of Gordonia alkanivorans to Study its Desulfurization Characteristics

Shilpi Aggarwal¹, I A Karimi¹, Gregorius Reinaldi Ivan¹

¹Dept of Chemical & Biomolecular Engineering, National University of Singapore, Singapore 117576

In absence of any competitive and economical renewable fuel, fossil fuels continue to be the major source of energy worldwide. However, fossil fuels contain various heteroatom based compounds that on combustion lead to the release of various pollutants such as oxides of carbon, nitrogen, and sulfur. Of these, oxides of sulfur (SO_x) have attracted major attention owing to the harmful effects that they exert on both environment and human health. As such, the governments have laid stringent regulations to limit the sulfur content in fuels [1] thereby, making desulfurization an important step in their pre-processing. However, the prevalent method for desulfurization, namely hydrodesulfurization is energy-intensive, expensive, and requires extreme conditions of temperature and pressure to desulfurize certain recalcitrant sulfur compounds such as benzothiophene (BT), dibenzothiophene (DBT), and their derivatives present in fossil fuels. Clearly there is a need to improve the existing desulfurization methods and develop more efficient and economical ones. The researchers have identified biodesulfurization as a potential alternative.

Biodesulfurization is a process in which either microbial whole cells or enzymes catalyze the removal of sulfur atom from the compounds present in fossil fuels. Compared to hydrodesulfurization, biodesulfurization is less energy intensive, more specific in action, and is relatively economical [1]. Several bacterial strains belonging to Rhodococcus, Gordonia, Mycobacterium, etc. have been isolated for their ability to desulfurize BT, DBT, and their derivatives. Of these G. alkanivorans is of high interest as it exhibits higher desulfurization activity for several recalcitrant compounds [2]. However, the desulfurization rates obtained with the wild type G. alkanivorans are too low for any commercial application [3]. Even the genetically engineered strains are incapable of giving the desired level of activity. This is mainly because most genetic manipulations normally target the elements of desulfurization pathway, while the other host functions affecting the desulfurization activity in G. alkanivorans are unknown. A cellular phenotype such as desulfurization activity depends on the complex interactions among the various metabolic pathways and biochemical reactions [4] occurring within the cell. Therefore, it is critical to study desulfurization by G. alkanivorans as an integral part of its metabolism in a holistic manner.

In this work, we reconstruct a genome scale metabolic model of G. alkanivorans for a holistic study of its metabolism. The model consists of main metabolic pathways such as central, amino acids, nucleotide, nitrogen, and sulfur metabolism. It can aid in understanding the metabolic architecture of G. alkanivorans, and its host functions related to desulfurization. The model depicts the dependence of the desulfurization pathway on the various intracellular activities. We validate the model using the experimental data available in literature. The model is found to predict the biomass growth closely using the experimental DBT uptake rates [5] as inputs. Also, it shows that G. alkanivorans prefers BT over DBT as reported in literature [2]. The analysis of our model suggests that ethanol is the best carbon source for obtaining higher desulfurization activity and growth rates with G. alkanivorans. In addition, in silico experiments using our model shows the effect of various amino acids and vitamins on the desulfurization activity of G. alkanivorans. The flux variability and flux sum analyses with the model show the importance of various pathways and metabolites in determining the extent of desulfurization and growth of G. alkanivorans. Finally, the model provides several useful insights into the interactions between the desulfurization activity and the other parts of the metabolism in G. alkanivorans.

References

1.         Soleimani, M., A. Bassi, and A. Margaritis, Biodesulfurization of refractory organic sulfur compounds in fossil fuels. Biotechnology Advances, 2007. 25(6): p. 570-596.

2.         Alves, L., et al., Desulfurization of dibenzothiophene, benzothiophene, and other thiophene analogs by a newly isolated bacterium, Gordonia alkanivorans strain 1B. Applied Biochemistry and Biotechnology - Part A Enzyme Engineering and Biotechnology, 2005. 120(3): p. 199-208.

3.         Kilbane Ii, J.J., Microbial biocatalyst developments to upgrade fossil fuels. Current Opinion in Biotechnology, 2006. 17(3): p. 305-314.

4.         Raman, K. and N. Chandra, Flux balance analysis of biological systems: Applications and challenges. Briefings in Bioinformatics, 2009. 10(4): p. 435-449.

5.         Rhee, S.K., et al., Desulfurization of dibenzothiophene and diesel oils by a newly isolated Gordona strain, CYKS1. Applied and Environmental Microbiology, 1998. 64(6): p. 2327-2331.