Genomic Science Program
U.S. Department of Energy | Office of Science | Biological and Environmental Research Program

Encapsulin Nanocompartment Systems in Rhodococcus opacus for Compartmentalized Biosynthesis Applications


M.C. Yung M. C.1* (, T. M. Halvorsen1, D. F. Savage2, and T. S. Carpenter1


1Lawrence Livermore National Laboratory; and 2University of California–Berkeley


This project is focused on understanding how encapsulin nanocompartment systems can be used to enhance the biosynthesis of next-generation biomaterials in Rhodococcus species. The project seeks (1) to probe the mechanistic basis for how these compartments are regulated, biosynthesized, and maintained, and (2) to engineer these systems to achieve new biosynthetic functions (e.g., inorganic nanoparticle biosynthesis).


With recent innovations in synthetic biology, engineered microbes now have the potential to produce a wide variety of bioproducts from renewable sources (e.g., biomass) to support the U.S. bioeconomy. However, biosynthetic pathways leading to these products are often hindered by poor reaction efficiencies and toxicity, resulting in low yields.

Compartmentalization of these pathways could potentially overcome these challenges through co-localization, concentration, and sequestration. The goal of this Early Career research is to identify mechanisms for engineering compartmentalized biosynthesis in the emerging model bioproduction bacterium, Rhodococcus opacus PD630, using its native encapsulin nanocompartment system (herein called encapsulins). Toward this goal, the native regulation, biosynthesis, and maintenance of the encapsulin system will be investigated to uncover potential pathways for controlling encapsulin production. Gene-editing methods will be used to engineer encapsulins with novel structural properties for expanded bioproduction capabilities. As a case study, the R. opacus encapsulin system will be redirected to support and control the biosynthesis of cadmium sulfide (CdS) nanoparticle semiconducting materials used in optical and electronic applications (e.g., solar panels, light-emitting diodes). CdS nanoparticles have gained considerable interest as a bioproduction target because they can potentially be produced from upcycling cadmium-contaminated waste streams. Ultimately, this work will establish encapsulin compartmentalization systems as a means of improving yields and enabling new biosynthetic routes toward next generation bioproducts and biomaterials in support of DOE’s mission to build a strong bioeconomy and thus enhance U.S. energy security.

Funding Information

Work at LLNL is performed under the auspices of the U.S. Department of Energy at Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344 (LLNL-ABS-845214). This program is supported by the U.S. Department of Energy, Office of Science, through the Genomic Science Program, Office of Biological and Environmental Research, under FWP SCW1770 (Early Career Award).