Rhomboid intramembrane protease YqgP licenses bacterial membrane protein quality control as adaptor of FtsH AAA protease

Abstract

Magnesium homeostasis is essential for life and depends on magnesium transporters, whose activity and ion selectivity need to be tightly controlled. Rhomboid intramembrane proteases pervade the prokaryotic kingdom, but their functions are largely elusive. Using proteomics, we find that Bacillus subtilis rhomboid protease YqgP interacts with the membrane-bound ATP-dependent processive metalloprotease FtsH and cleaves MgtE, the major highaffinity magnesium transporter in B. subtilis. MgtE cleavage by YqgP is potentiated in conditions of low magnesium and high manganese or zinc, thereby protecting B. subtilis from Mn 2+ /Zn 2+ toxicity. The N-terminal cytosolic domain of YqgP binds Mn 2+ and Zn 2+ ions and facilitates MgtE cleavage. Independently of its intrinsic protease activity, YqgP acts as a substrate adaptor for FtsH, a function that is necessary for degradation of MgtE. YqgP thus unites protease and pseudoprotease function, hinting at the evolutionary origin of rhomboid pseudoproteases such as Derlins that are intimately involved in eukaryotic ER-associated degradation (ERAD). Conceptually, the YqgP-FtsH system we describe here is analogous to a primordial form of "ERAD" in bacteria and exemplifies an ancestral function of rhomboid-superfamily proteins.

Derlins with scissors: primordial ERAD in bacteria

“…This has led to the question of what the conserved, primordial role of rhomboids is. In light of the studies by Began et al () and Liu et al (), protein degradation now emerges as the conserved function (Fig ). Showing high similarity to bacterial rhomboids, the mitochondrial rhomboid protease PARL has been demonstrated to assemble with the AAA protease YME1L to regulate processing and turnover of the protein kinase PINK1 and the phosphatase PGAM5 (Wai et al , ).…”

“…Another intriguing observation by Began et al () is that B. subtilis rhomboid YqgP also functions as a substrate adaptor for the AAA protease FtsH. This is independent of its rhomboid intramembrane protease activity, but requires the enzyme active site, and resembles the function of eukaryotic rhomboid pseudoproteases.…”

“…Intramembrane proteolysis is an unusual, yet crucial reaction involved in diverse cellular processes. Began et al () report a previously uncharacterized function for the Bacillus subtilis rhomboid protease YqgP in the degradation of the magnesium transporter MgtE, both by direct cleavage and by acting as a substrate adaptor for the AAA protease FtsH. Liu et al (), studying the Shigella sonnei rhomboid proteases GlpG and Rhom7 (a new rhomboid that had not been characterized before), identified subunits of respiratory complexes as rhomboid substrates.…”

“…YqgP seems not to require such a distinct substrate feature. Instead, MgtE cleavage by YqgP is triggered by toxic manganese that spuriously enters the cell via MgtE during magnesium starvation, a stress condition sensed by a cytoplasmic metal‐binding domain in YqgP (Began et al , ). These two roles, degradation of orphaned proteins and regulated abundance control, parallel the functions of endoplasmic reticulum (ER)‐associated protein degradation (ERAD) in eukaryotic cells (as reviewed in Wu & Rapoport, ).…”

“…Likewise, derlins act as rhomboid pseudoproteases in eukaryotic ERAD of both soluble and integral membrane proteins (Greenblatt et al , ; Neal et al , ). The observation that the B. subtilis YqgP.S288A active site mutant mimics a pseudoprotease function implies that the protease mechanism and rhomboid‐assisted recognition of a membrane protein for processing by the AAA protease FtsH follow shared principles (Began et al , ). In eukaryotes, however, rhomboids may act in even more complex processes.…”