(582cj) 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.