Bacterial rhomboid proteases mediate quality control of orphan membrane proteins.

Guangyu Liu,Rachel M Exley,Stephen E Beaton,Kvido Strisovsky,Rhiannon Evans,Fraser A Armstrong,Adam G Grieve,Matthew Freeman,Miranda Rogers,Christoph M Tang

doi:10.15252/embj.2019102922

Abstract

Although multiprotein membrane complexes play crucial roles in bacterial physiology and virulence, the mechanisms governing their quality control remain incompletely understood. In particular, it is not known how unincorporated, orphan components of protein complexes are recognised and eliminated from membranes. Rhomboids, the most widespread and largest superfamily of intramembrane proteases, are known to play key roles in eukaryotes. In contrast, the function of prokaryotic rhomboids has remained enigmatic. Here, we show that the Shigella sonnei rhomboid proteases GlpG and the newly identified Rhom7 are involved in membrane protein quality control by specifically targeting components of respiratory complexes, with the metastable transmembrane domains (TMDs) of rhomboid substrates protected when they are incorporated into a functional complex. Initial cleavage by GlpG or Rhom7 allows subsequent degradation of the orphan substrate. Given the occurrence of this strategy in an evolutionary ancient organism and the presence of rhomboids in all domains of life, it is likely that this form of quality control also mediates critical events in eukaryotes and protects cells from the damaging effects of orphan proteins.

Highlights

Multiprotein membrane complexes in bacteria mediate fundamental processes such as respiration, secretion of virulence factors and nutrient acquisition (Unden et al, 2014; Costa et al, 2015; Sheldon et al, 2016)
Our findings reveal that rhomboids contribute to the quality control of multiprotein membrane complexes and membrane proteostasis, with rhomboid-mediated proteolysis serving as the critical licensing step that allows downstream proteolytic degradation of orphan substrates, so preventing their aggregation
We characterised two rhomboids in Shigella sonnei (Ss). sonnei, GlpG and Rhom7, which share sequence homology with E. coli GlpG and P. stuartii AarA, respectively. We found that both GlpG and Rhom7 are active enzymes that selectively target orphan components of respiratory complexes

Summary

Introduction

Multiprotein membrane complexes in bacteria mediate fundamental processes such as respiration, secretion of virulence factors and nutrient acquisition (Unden et al, 2014; Costa et al, 2015; Sheldon et al, 2016). Aberrant assembly or disassembly of complexes results in orphan proteins, which usually require prompt degradation to maintain cellular proteostasis (Harper & Bennett, 2016; Juszkiewicz & Hegde, 2018). Little is known how unincorporated, orphan components of bacterial protein complexes are sensed and eliminated from membranes. Rhomboids are the largest family of intramembrane proteases (IMPs) and are found in all kingdoms of life. These enzymes rapidly scan membranes for their substrates (Kreutzberger et al, 2019) and have their active sites embedded in the lipid bilayer where they cleave their substrates in or adjacent to transmembrane domains (TMDs). A wide range of functions has been ascribed to eukaryotic rhomboids including growth factor signalling (Urban et al, 2001), lipid metabolism (Saita et al, 2018), energy production (Spinazzi et al, 2019), chloroplast development (Thompson et al, 2012), apoptosis regulation (Saita et al, 2017), endoplasmic reticulum (ER) protein trafficking (Fleig et al, 2012) and surface antigen shedding in the apicomplexan parasites (Shen et al, 2014)

Methods

Results

Conclusion