Prokaryotic nanocompartments, also known as encapsulins, are a recently discovered proteinaceous organelle-like compartments in prokaryotes that compartmentalize cargo enzymes. While initial studies have begun to elucidate the structure and physiological roles of encapsulins, bioinformatic evidence suggests that a great diversity of encapsulin nanocompartments remains unexplored. Here, we describe a novel encapsulin in the freshwater cyanobacterium Synechococcus elongatus PCC 7942. This nanocompartment is upregulated upon sulfate starvation and encapsulates a cysteine desulfurase enzyme via an N-terminal targeting sequence. Using cryo-electron microscopy, we have determined the structure of the nanocompartment complex to 2.2 Å resolution. Lastly, biochemical characterization of the complex demonstrated that the activity of the cysteine desulfurase is enhanced upon encapsulation. Taken together, our discovery, structural analysis, and enzymatic characterization of this prokaryotic nanocompartment provide a foundation for future studies seeking to understand the physiological role of this encapsulin in various bacteria.

Studying the genetic differences between related microorganisms from different environment types can indicate factors associated with their movement among habitats. This is particularly interesting for bacteria from the Candidate Phyla Radiation because their minimal metabolic capabilities require associations with microbial hosts.

18Prokaryotic nanocompartments, also known as encapsulins, are a recently discovered 19 proteinaceous organelle in prokaryotes that compartmentalize cargo enzymes. While initial 20 studies have begun to elucidate the structure and physiological roles of encapsulins, bioinformatic 21 evidence suggests that a great diversity of encapsulin nanocompartments remains unexplored. 22Here, we describe a novel encapsulin in the freshwater cyanobacterium Synechococcus 23 elongatus PCC 7942. This nanocompartment is upregulated upon sulfate starvation and 24 encapsulates a cysteine desulfurase enzyme via an N-terminal targeting sequence. Using cryo-25 electron microscopy, we have determined the structure of the nanocompartment complex to 2.2 26 Å resolution. Lastly, biochemical characterization of the complex demonstrated that the activity of 27 the cysteine desulfurase is enhanced upon encapsulation. Taken together, our discovery, 28 structural analysis, and enzymatic characterization of this prokaryotic nanocompartment provide 29 a foundation for future studies seeking to understand the physiological role of this encapsulin in 30 various bacteria. 31 2

Despite very low concentrations of cobalt in marine waters, cyanobacteria in the genusProchlorococcusretain the genetic machinery for the synthesis and use of cobalt-bearing cofactors (cobalamins) in their genomes. We explore cobalt metabolism in aProchlorococcusisolate from the equatorial Pacific Ocean (strain MIT9215) through a series of growth experiments under iron- and cobalt-limiting conditions. Metal uptake rates, quantitative proteomic measurements of cobalamin-dependent enzymes, and theoretical calculations all indicate thatProchlorococcusMIT9215 can sustain growth with less than 50 cobalt atoms per cell, ∼100-fold lower than minimum iron requirements for these cells (∼5,100 atoms per cell). Quantitative descriptions ofProchlorococcuscobalt limitation are used to interpret the cobalt distribution in the equatorial Pacific Ocean, where surface concentrations are among the lowest measured globally butProchlorococcusbiomass is high. A low minimum cobalt quota ensures that other nutrients, notably iron, will be exhausted before cobalt can be fully depleted, helping to explain the persistence of cobalt-dependent metabolism in marine cyanobacteria.