Genome-Scale Metabolic Reconstruction and Analysis of Azoarcus Sp. Cib, a Model Bacterium in Anaerobic Degradation of Aromatic Compounds

Aromatic compounds are among the most widespread organic compounds in nature. Some of them are man-made environmental pollutants which after release into the environment become toxic to most organisms. Thus, there is a great interest in the research and development of biological strategies for removing these compounds from the ecosystems (bioremediation) and/or for their industrial conversion to high-added value products (bioconversions).  

Azoarcus sp. CIB is one of the few microorganisms able to degrade aromatic compounds both aerobically and anaerobically. Therefore, the stain CIB has become a model bacterium in bioremediation/bioconversion processes. However, the fundamental aspects of its metabolism remain poorly known hampering the true potential of Azoarcus sp. CIB in biotechnological processes. Constraint-based reconstruction and analysis (COBRA) approach offers the possibility to systematically analyze the metabolic capabilities of a target organism, at genome-scale, and has been successfully applied for addressing multiple biological topics (Lewis et al., 2012). However, the metabolism of aromatic compounds has received little attention to date. In this study, we apply COBRA approach for modeling and analyzing the metabolic features of strain CIB with special emphasis on those related to its remarkable ability to degrade aromatic compounds under changing environmental conditions.  

We have constructed a manually curated, full compartmentalized, and mass and charge balanced genome-scale metabolic reconstruction of Azoarcus sp. CIB based on well-known procedures (Nogales, 2014). The reconstruction of CIB, formally iLA938, accounts for 938 genes, 1164 reactions and 1063 metabolites distributed in 102 metabolic subsystems, including most of the metabolic capabilities of this bacterium. Noteworthy, iLA938 contains the most complete modeling of aromatic compounds catabolism to date, including pathways modeled in iLA938 by the first time. After conversion to computational format, the model was extensively validated based on quantitative and qualitative growth rate predictions on several carbon and final electron acceptor sources. This analysis allowed us to expand the known metabolic versatility in CIB by identifying new carbon sources supporting growth. Remarkably, iLA938 suggested the co-activation of the aerobic and anaerobic degradation pathways for optimal aromatic acid metabolism under microaerophilic conditions. This model-driven hypothesis was then validated by means of gene expression analysis during benzoate degradation, revealing that the aerobic and anaerobic pathways were highly expressed under these conditions, and suggesting that this behavior could provide an energetic advantage to bacteria living in fluctuating oxygen environments. Finally, the study of the accessory metabolism of aromatic compounds suggested a critical role of the electron-transferring flavoprotein systems (ETFs) as guarantor of redox state balancing. 

In summary, we presented here one of the more complete genome-scale metabolic models of environmental bacteria to date. iLA938 has shown to be highly accurate and has contributed to expand our knowledge about the metabolism of strain CIB at system level. Furthermore, iLA938 is expected to become a valuable computational tool driving biotechnological endeavors not only in Azoarcus sp. CIB, but also in other relevant environmental bacteria.

Lewis NE, et al (2012). Nat Rev Microbiol 10(4): 291–305

Nogales J (2014). Humana Press, New York, pp 1–25