Mechanism of the oxidative stress‐mediated increase in lipid accumulation by the bacterium, R. opacus PD630: Experimental analysis and genome‐scale metabolic modeling

Abstract

Appropriate species of oleaginous bacteria, with their high growth rates and lipid accumulation capabilities, can be good contenders for industrial triacylglycerol (TAG) production, compared to microalgae. Further, oxidative stress (OS) can be used to significantly increase TAG yields in oleaginous microbes, but the mechanism is unexplored. In a first, this study explored the mechanism behind OS‐mediated increase in TAG accumulation by the bacterium, Rhodococccus opacus PD630, through experimental analysis and metabolic modelling. Two mechanisms that could increase acetyl‐CoA (TAG‐precursor) levels were hypothesized based on literature information. One was OS‐mediated inactivation of the aconitase (TCA cycle), and another was the inactivation of the triosephosphate isomerase (TPI; glycolysis). The results negated the involvement of aconitase in increased acetyl‐CoA levels. Analysis of the metabolic model showed that inactivation of TPI, re‐routed the flux through the pentose phosphate pathway (PPP), supplying both NADPH and acetyl‐CoA for TAG synthesis. Additionally, inactivation of TPI increased TAG flux by 143%, whereas, inactivating both TPI and aconitase, increased it by 152%. We present experimental evidence for OS‐mediated decrease in TPI activity and increase in activity of glucose‐6‐phosphate dehydrogenase (PPP enzyme). The findings indicate that increased flux through PPP can be explored to improve TAG accumulation on a large‐scale.

Shear stress and microRNAs for better metastatic cancer management

“…Shear stress was reported to induce apoptosis in breast cancer cells in circulation by enhancing the mitochondrial production of superoxide 22 . Moreover, it is now clear that reactive species (RS), especially the reactive oxygen species (ROS), are the molecular mediators of the effects of many stresses on cells 23,24 . Thus, we studied the effects of shear stress on si‐RS in HCT116 cancer cells.…”

“…22 Moreover, it is now clear that reactive species (RS), especially the reactive oxygen species (ROS), are the molecular mediators of the effects of many stresses on cells. 23,24 Thus, we studied the effects of shear stress on si-RS in HCT116 cancer cells.…”

A High-Quality Genome-Scale Model for Rhodococcus opacus Metabolism

“…iGR1773 consists of 3025 reactions and 1956 metabolites obtained from annotating its completed genome, adding the corresponding metabolic reactions, and testing the predictions derived by it. Although previous publications have reported a GSM for R. opacus PD630, , this model did not use an annotation of the R. opacus PD630 genome. This model repurposed the Rhodococcus jostii GSM by doing some minor modifications including setting fluxes to polyhydroxyalkanoates (PHA), polyhydroxyvalerates (PHV), glycogen, and acetate to zero and adjusting the TAG reaction to reflect the fatty acid composition of R. opacus PD630 .…”

“…Although previous publications have reported a GSM for R. opacus PD630, , this model did not use an annotation of the R. opacus PD630 genome. This model repurposed the Rhodococcus jostii GSM by doing some minor modifications including setting fluxes to polyhydroxyalkanoates (PHA), polyhydroxyvalerates (PHV), glycogen, and acetate to zero and adjusting the TAG reaction to reflect the fatty acid composition of R. opacus PD630 . Notably, iGR1773 was validated in three different ways: via the Metabolic Model Test (MEMOTE) suite, by checking growth rate predictions, and by comparing flux predictions to 13 C-metabolic flux analysis ( 13 C-MFA) results.…”

Modeling the effect of oxidative stress on Bordetella pertussis fermentations

“…16 Several studies on bacteria have reported that the inhibition of glycolysis allows cells to divert flux into the pentose phosphate pathway to promote NADPH synthesis and enhance the protection against oxidative stress. [17][18][19] On the other hand, B. pertussis does not have an active glycolysis pathway and instead uses gluconeogenesis to process the product of the TCA cycle that is driven by glutamate as the main nutrient. In fact, it has been shown that B. pertussis can synthesize most amino acids and grow in media containing mostly glutamate and proline which is also converted to glutamate.…”