Rhomboid proteins: conserved membrane proteases with divergent biological functions

Abstract

The rhomboid gene was discovered in Drosophila, where it encodes a seven transmembrane protein that is the signal-generating component of epidermal growth factor (EGF) receptor signaling during development. Although metazoan developmental regulators are rarely conserved outside the animal kingdom, rhomboid proteins are conserved in all kingdoms of life, but the significance of this remains unclear. Recent biochemical reconstitution and high-resolution crystal structures have provided proof that rhomboid proteins function as novel intramembrane proteases, with a serine proteaselike catalytic apparatus embedded within the membrane bilayer, buried in a hydrophilic cavity formed by a protein ring. A thorough consideration of all known examples of rhomboid function suggests that, despite biochemical similarity in mechanism and specificity, rhomboid proteins function in diverse processes including quorum sensing in bacteria, mitochondrial membrane fusion, apoptosis, and stem cell differentiation in eukaryotes; rhomboid proteins are also now starting to be linked to human disease, including early-onset blindness, diabetes, and parasitic diseases. Regulating cell signaling is at the heart of rhomboid protein function in many, but not all, of these processes. Further study of these novel enzymes promises to reveal the evolutionary path of rhomboid protein function, which could provide insights into the forces that drive the molecular evolution of regulatory mechanisms.Developmental biology has progressed from descriptive observation to mechanistic analysis in the latter half of the 20th century (Wolpert 1998). Powerful genetic tools applied to model organisms have led to an intricate and beautiful picture of how genes build complex organisms. Parallel analyses in diverse animals and sequencing of their genomes revealed that a relatively small number of master genes and core regulatory pathways are used repeatedly in different contexts to build complex patterns, and these factors are conserved among animals.In addition to revealing some of the underlying logic of how organisms are constructed, these approaches were powerful in identifying the factors that mediate this intricate level of organization. But little is still known about how these key regulators exert their functions biochemically, which is central to understanding core biological processes that drive development at the molecular level.Most developmental regulators are conserved in the animal kingdom but are not found in other kingdoms, including plants, perhaps because plants and animals evolved multicellular development after splitting from a common ancestor (Meyerowitz 2002). But in recent years a small number of factors have been discovered that are conserved across kingdoms, raising the exciting possibility that they are key regulators that evolved very early. One such class of regulatory proteins are intramembrane proteases.Intramembrane proteolysis, the cleavage of membrane proteins within their membrane spanning segments, has recently been discovered to...

Enzymatic analysis of a rhomboid intramembrane protease implicates transmembrane helix 5 as the lateral substrate gate

“…cell signaling ͉ presenilin ͉ signal peptide peptidase ͉ site-2 protease S cission of peptide bonds within the membrane bilayer is an unexpected biochemical reaction that serves as a regulatory point of multiple cellular processes (1)(2)(3). The membraneembedded proteases that catalyze these reactions are conserved in all branches of life, implying that they are ancient enzymes that assumed key roles early in the evolution of modern cells.…”

A cut short to death: Parl and Opa1 in the regulation of mitochondrial morphology and apoptosis

“…66 In D. melanogaster they activate the epidermal growth factor (EGF) signalling pathway, by proteolytically cleaving the EGF receptor ligands Spitz, Gurken and Keren. 67 A serine protease catalytic dyad is conserved in all rhomboids, 66 suggesting that they can cleave TM domains of integral membrane proteins. Therefore, they have been functionally assigned to a class of highly hydrophobic proteases involved in regulated intramembrane proteolysis (RIP).…”

“…Therefore, they have been functionally assigned to a class of highly hydrophobic proteases involved in regulated intramembrane proteolysis (RIP). 67 The Rhomboids RIP is a new paradigm of signal transduction, which appears to be prominent in all forms of life. 67 Under RIP, membranebound proteins undergo site-specific proteolysis within one of Figure 1 Fate of Opa1 oligomers during apoptosis.…”

“…67 The Rhomboids RIP is a new paradigm of signal transduction, which appears to be prominent in all forms of life. 67 Under RIP, membranebound proteins undergo site-specific proteolysis within one of Figure 1 Fate of Opa1 oligomers during apoptosis. A sequence of cartoons depicting the changes occurring during cristae remodelling is presented.…”

“…70,71 This family also includes the signal peptide peptidase, which catalyses intramembrane proteolysis of signal sequence remnants and possibly also membrane proteins in the ER membrane. 72 The third and most recently discovered I-Clip family are the rhomboids, 67 which are the most evolutionary conserved one and, by implication, the first to emerge in life. 66 In spite of the presence of rhomboids in the majority of modern life forms from all three primary superkingdoms, phylogenetic analysis suggests that this family has not been inherited from the last universal common ancestor.…”