Discovery and characterization of a novel family of prokaryotic nanocompartments involved in sulfur metabolism

Abstract

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

Advances in encapsulin nanocompartment biology and engineering

“…These encapsulins discussed thus far represent classical, or family 1, encapsulins. A recent study described a second family of encapsulins widespread in prokaryotes (Nichols et al, 2020) distinctly different than the classical encapsulins, but due to the fact that only family 1 encapsulins have been used in engineering applications so far, we will limit our discussion to them and refer to them simply as encapsulins.…”

“…Even though recent discoveries have broadened our general understanding of encapsulin biology, the field is still in its infancy with many novel systems and functions to be discovered and characterized, highlighted by the recent discovery of the family 2 encapsulins mentioned above (Nichols et al, 2020). Nevertheless, encapsulins have already been used in various engineering and synthetic biology applications.…”

Large-scale computational discovery and analysis of virus-derived microbial nanocompartments

“…[5][6][7] So far, two families of encapsulins have been reported in a variety of bacterial and archaeal phyla. [8][9][10] They are proposed to be involved in oxidative stress resistance, 9,[11][12][13] iron mineralization and storage, 14,15 anaerobic ammonium oxidation, 16 and sulfur metabolism. 8 All known encapsulins self-assemble from a single capsid protein into compartments between 24 and 42 nm in diameter with either T=1, T=3 or T=4 icosahedral symmetry.…”

“…[8][9][10] They are proposed to be involved in oxidative stress resistance, 9,[11][12][13] iron mineralization and storage, 14,15 anaerobic ammonium oxidation, 16 and sulfur metabolism. 8 All known encapsulins self-assemble from a single capsid protein into compartments between 24 and 42 nm in diameter with either T=1, T=3 or T=4 icosahedral symmetry. 10,12,15 Their defining feature is the ability to selectively encapsulate cargo proteins which include ferritin-like proteins, hemerythrins, peroxidases and desulfurases.…”

A nanocompartment containing the peroxidase DypB contributes to defense against oxidative stress inM. tuberculosis

“…This shell surrounds ("encapsulates") an enzymatic cargo protein 1 . Although putative encapsulin systems have been identified in >900 bacterial and archaeal genomes 2,7 , very little is known about their physiological function. Based on genomic organization, encapsulin systems are often predicted to compartmentalize enzymes involved in oxidative stress defense, iron storage, and anaerobic ammonium oxidation 2 .…”