A New Proteomics Approach Reveals How Nitrogen Starvation Rewires Metabolism in Oil-Producing Yeast Rhodotorula toruloides

The Science                                  

Recent research at Pacific Northwest National Laboratory (PNNL) demonstrated that nitrogen limitation causes major shifts in metabolic pathways, underscoring the emerging significance of post-translational modifications (PTM) in synthetic biology research and setting the stage for optimizing stress response and lipid production in Rhodotorula toruloides.

It is known that yeast cells with limited nitrogen show a higher percentage of lipid content—an essential component in bioproduction—while cells rich in nitrogen have a lower percentage of lipids. But until now, scientists did not know that lipid accumulation is largely a consequence of carbon rerouting and cellular recycling governed by changes to PTMs and not increases in the abundance of enzymes involved in central carbon metabolism and fatty acid biosynthesis.

The Impact

PNNL is poised to help the nation grow its bioeconomy. To do this, though, we need to understand the molecular functions of complex biological systems to successfully re-engineer them, which will facilitate the synthesis of bioproducts that are critical to the bioeconomy. Oleaginous yeasts such as R. toruloides prove to be an excellent and alternative source of oleochemicals, which find applications in the food industry, skincare, biofuels, and bioplastics. And yet, the role PTMs play in these yeast remains understudied. 

With this research, scientists at PNNL now have a better understanding how environmental factors influence the molecular function of R. toruloides, which centers on modifications of the PTMs. This information can be used to engineer organisms to channel their energy into what we want the cells to make.

Summary

Scientists investigated R. toruloides under nitrogen-rich and starved conditions over time and sought to link the yeast oleaginous phenotype to protein function by integrating lipidomics, redox proteomics, and phosphoproteomics. Their lipidomics results unearthed interactions that underscore the significant role PTMs play in cellular function, including metabolic pathways.

With the help of a newly developed proteomics approach, scientists concluded that lipid accumulation is driven by cellular recycling processes that balance carbon and nitrogen to maintain anabolic requirements for cell survival, stress response, and lipid accumulation. These results reveal novel PTM-based regulatory mechanisms and known redox switches with potential for expanding synthetic biology tools to improve fitness and lipid production of oleaginous yeasts.

The research is part of PNNL’s Predictive Phenomics Initiative, an internal investment aimed at understanding the molecular basis of function so that scientists can re-engineer high-value phenotypes that impact bioproduction, human health, and national security. 

Contact

Tong Zhang, Chemist, Pacific Northwest National Laboratory, Tong.Zhang@pnnl.gov

Funding

The research described here is part of the Predictive Phenomics Initiative at Pacific Northwest National Laboratory (PNNL) and conducted under the Laboratory Directed Research and Development Program. PNNL is a multiprogram national laboratory operated by Battelle for the U.S. Department of Energy under Contract No. DE-AC05-76RL01830.