Synthetic Biology Parts, Devices and Applications

14.3 ­roteinnBased Organelles 291

Encapsulins (also called nanocompartments) are a family of poorly charac­
terized proteins that have the defining feature of assembling into 20–30 nm
icosahedral complexes (Figure 14.5). The founding member, Linocin M18 from
Brevibacterium linens, was discovered as a secreted protein with bactericidal
activity, but recent results question this biological function [83, 86]. Since then,
the number of predicted encapsulins has increased dramatically, with the latest
bioinformatics study reporting over 900 putative encapsulins across 15 bacte­
rial and 2 archaeal phyla [87]. Encapsulins, like BMCs, also appear to be diverse,
with four families of capsids and seven classes of associated cargo [88]. Despite
the diversity, only a small number of encapsulins have been biochemically
characterized, including those from Thermotoga maritima, Pyrococcus furio-
sus, Mycobacterium tuberculosis, Myxococcus xanthus, and Rhodococcus jostii
RHA1.
The X‐ray crystal structures of three different encapsulins from P. furiosus,
T.  maritima, and most recently M. xanthus have been determined, clarifying
many open structural and functional questions [83, 89] (Figure 14.5b). The
structural shell is formed from a single protomeric protein that self‐assembles
into an icosahedral shell about 2 nm thick. In the Pyrococcus and Myxococcus
variants, 180 protomers assemble into a structure 30 nm in diameter, while in
the Thermotoga variant 60 protomers form a 20 nm structure, suggesting signifi­
cant structural heterogeneity can exist between encapsulins. Like in BMCs,
there are pores parallel to protomer symmetry axes. There are three distinct
classes of pores, each possessing a diameter of about 5 Å, located at the interface
between two adjacent protomers, sites of fivefold symmetry and sites of
threefold symmetry. While the first two classes show interspecies conservation
of the chemical property of the pore‐lining residues, the same is not true for the

(a) (b)

C-terminal signal

sequence

Signal sequence

Encapsulin

Ferritin-like

protein

T. maritima encapsulin operon

Encapsulin shell

60 protomers

Ferritin-like protein

10–60 copies

Lumen

Diameter ≈

25 nm

Figure 14.5 Model of an encapsulin. (a) Genomic organization in T. maritima highlight signal
sequence of cargo protein. (b) Structural model based on encapsulin X‐ray structure (PDB:
3DKT) and ferritin‐like protein (PDB: 3HL1).