The encapsulin from Thermotoga maritima is a flavoprotein with a symmetry matched ferritin-like cargo protein

Benjamin J Lafrance,Eva Nogales,Robert J Nichols,Luke M Oltrogge,Caleb Cassidy-Amstutz,David F Savage

doi:10.1038/s41598-021-01932-w

Abstract

Bacterial nanocompartments, also known as encapsulins, are an emerging class of protein-based ‘organelles’ found in bacteria and archaea. Encapsulins are virus-like icosahedral particles comprising a ~ 25–50 nm shell surrounding a specific cargo enzyme. Compartmentalization is thought to create a unique chemical environment to facilitate catalysis and isolate toxic intermediates. Many questions regarding nanocompartment structure–function remain unanswered, including how shell symmetry dictates cargo loading and to what extent the shell facilitates enzymatic activity. Here, we explore these questions using the model Thermotoga maritima nanocompartment known to encapsulate a redox-active ferritin-like protein. Biochemical analysis revealed the encapsulin shell to possess a flavin binding site located at the interface between capsomere subunits, suggesting the shell may play a direct and active role in the function of the encapsulated cargo. Furthermore, we used cryo-EM to show that cargo proteins use a form of symmetry-matching to facilitate encapsulation and define stoichiometry. In the case of the Thermotoga maritima encapsulin, the decameric cargo protein with fivefold symmetry preferentially binds to the pentameric-axis of the icosahedral shell. Taken together, these observations suggest the shell is not simply a passive barrier—it also plays a significant role in the structure and function of the cargo enzyme.

Highlights

Bacterial nanocompartments, known as encapsulins, are an emerging class of protein-based ‘organelles’ found in bacteria and archaea
One example of the redox role within encapsulins is found in the hyperthermophilic bacterium Thermotoga maritima, where the cargo is a ferritin-like protein (FLP)
Mineralization prevents soluble iron from spontaneously reacting with reactive oxygen species, as occurs in the Fenton reaction, which can damage the cell. This was shown to be the case for Myxococcus xanthus, which contains an encapsulin with FLP cargo

Summary

Introduction

Known as encapsulins, are an emerging class of protein-based ‘organelles’ found in bacteria and archaea. One example of the redox role within encapsulins is found in the hyperthermophilic bacterium Thermotoga maritima, where the cargo is a ferritin-like protein (FLP). The work presented here accurately resolves an FLP cargo in relation to the encapsulin shell and reveals that the T. maritima encapsulin is a flavoprotein.

Results

Conclusion