Microbial Protein Compartments

Microbial compartmentalization strategies

Biological cells employ compartmentalization to overcome many difficult metabolic and physiological challenges. Eukaryotes mainly use membrane-bound organelles to sequester and control the flow of metabolites, store genetic information and segregate protein processing and export. In contrast, the majority of prokaryotes do not possess intracytoplasmic membrane systems and instead rely on protein-based approaches to achieve spatial control. However, certain specialized membrane compartments have been identified in specific bacterial strains, including polyphosphate-storing acidocalcisomes, photosynthetic thylakoids in cyanobacteria, magnetosomes in magnetotactic bacteria and pirellulosomes and anammoxosomes in morphologically complex Planctomycetes (Figure 1). Important examples for protein-based organelles include bacterial microcompartments (BMCs) like the CO2-fixing carboxysome, ferritins involved in iron homeostasis and maintaining redox balance and functionally diverse encapsulin nanocompartments (Figure 1). Encapsulating enzymes or biosynthetic pathways in semi-permeable protein organelles can increase the local concentrations of metabolites and enzymes, prevent the loss of toxic or volatile intermediates and create unique microenvironments necessary for the proper functioning of specialized enzymes. In addition, encapsulation allows for incompatible reactions and processes to take place in a single cell at the same time.

Figure 1: Overview of protein- and membrane-based microbial compartments.

Encapsulins
We have characterized new encapsulins and used them as a modular cell engineering platform. We discovered a potential role for encapsulins in the critical annamox process in bacteria key to the global nitrogen cycle. We have engineered encapsulins to form new inorganic nanoparticles and centers of carbon fixation. Encapsulins are found only in prokaryotes but can be assembled in eukaryotes such as yeast where they can efficiently sequester chemical reactions and increase the overall efficiency of production.