UC Berkeley

Cellular compartmentalization is a fundamental strategy through which complex tasks can be carried out, where each compartment carries out a specialized function. Compartmentalization strategies in the bacteria have (relatively) recently been discovered and are not present across the entire domain; they instead seem to be tied to niche specialization of the host species. For example, carboxysomes are necessary for all cyanobacteria to fix carbon dioxide in present-day atmospheric conditions. Carboxysomes are part of a larger family of bacterial organelles termed bacterial microcompartments (BMCs), which are all related by the proteinaceous shell that bounds the compartment.

Many different metabolic functions have been attributed to BMCs, such as carbon fixation, propanediol metabolism, and ethanolamine metabolism, and cursory genome gazing had hinted that there may be several more functional types of these organelles in a vast number of bacteria. In order to survey the functional and phylogenetic diversity of BMCs, a bioinformatic algorithm was developed to predict and categorize genetic loci that encode genes that can construct a complete organelle. Our analyses result in a taxonomy of BMCs that identifies several candidate loci and individual genes for further investigation.

We predicted many of these loci to encode for BMCs with novel functions, and examined one locus apparently isolated to the Planctomycetes and Verrucomicrobia phyla. By genetically manipulating Planctomyces limnophilus, we identified that this locus encodes a fully-functional organelle that is involved in degrading fucose and rhamnose, which is likely critical to the niche specialization of many Planctomycetes that associate with algae.

We also found the widespread usage of a novel phosphotransacetylase enzyme in the BMCs. By analyzing the primary, secondary, and quaternary structures of this novel protein, we identify well-conserved motifs within distinct domains of the protein and identify a peptide that is involved in modulating the quaternary structure.

One of the many uses of fundamental research is to provide the foundation for engineering synthetic constructs. Finally, we describe two bioengineering strategies geared towards the goal of improving the efficiency of the carbon fixation step of photosynthesis that are based on our knowledge of the cyanobacterial carbon concentrating mechanism, including the carboxysome. The first strategy focuses on the input for the carboxysome, where inorganic carbon must be transported into the cytosol. The second strategy utilizes a carboxysome assembly factor as a scaffolding mechanism.