Advances in encapsulin nanocompartment biology and engineering

Abstract

Compartmentalization is an essential feature of all cells. It allows cells to segregate and coordinate physiological functions in a controlled and ordered manner. Different mechanisms of compartmentalization exist, with the most relevant to prokaryotes being encapsulation via self-assembling protein-based compartments. One widespread example of such is that of encapsulins-cage-like protein nanocompartments able to compartmentalize specific reactions, pathways, and processes in bacteria and archaea. While still relatively nascent bioengineering tools, encapsulins exhibit many promising characteristics, including a number of defined compartment sizes ranging from 24 to 42 nm, straightforward expression, the ability to self-assemble via the Hong Kong 97-like fold, marked physical robustness, and internal and external handles primed for rational genetic and molecular manipulation. Moreover, encapsulins allow for facile and specific encapsulation of native or heterologous cargo proteins via naturally or rationally fused targeting peptide sequences. Taken together, the attributes of encapsulins promise substantial customizability and broad usability. This review discusses recent advances in employing engineered encapsulins across various fields, from their use as bionanoreactors to targeted delivery systems and beyond. A special focus will be provided on the rational engineering of encapsulin systems and their potential promise as biomolecular research tools.

Triggered reversible disassembly of an engineered protein nanocage

“…18 The E-loop is also located away from the N-terminal helix important for cargo loading. 25 Therefore, the E-loop was selected as the insertion site for the disassembly trigger.…”

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

“…4 One of the most widespread and diverse classes of protein-based compartments are encapsulin nanocompartments, or simply encapsulins. [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.…”

Nanotechnological Applications Based on Bacterial Encapsulins

“…Enabled mainly by advances in imaging techniques, recent decades have witnessed a steady increase in our understanding of the complexity of the subcellular architecture of some bacterial and archaeal species [2][3][4]. Subcellular compartments delimited by semipermeable protein shells [5,6], lipid bilayers [7,8], lipid monolayers [1], or phase-separated membraneless condensates [9] are now being described with increased detail.…”

“…Among the prokaryotic protein-bounded compartments are the bacterial microcompartments (BMC) [10,11] and the encapsulins [5,12,13]; these micro-and nanometer-sized semi-permeable protein cages encase an enzymatic core. BMC are complex polyhedral structures,~40 to 200 nm in diameter, built of many thousands of protein subunits of 10-20 distinct types [14].…”