Rhomboid protease

The rhomboid proteases are a family of

• Later, Drosophilas' Rhomboid-1 was shown to regulate sleep, through a new function of an already-discovered mechanism.^{[6]: 201–2}
• Although less well established than in Drosophila, there is some evidence that rhomboids may participate in growth factor signalling in mammals, including humans.^{[14][8]: 240, Mammalian Rhomboid Proteases} They have also been implicated in ephrin signalling,^[15] the cleavage of the anticoagulant protein thrombomodulin^[16] and wound healing.^[17]
• All
  cristae,^[21] is implicated in cell death^[21] and metabolism,^[22] and there is increasing evidence of an important role in Parkinson's disease;^[23][24][25]
• Toxoplasma specifically, some serpins inhibit rhomboids.^[27]
  ^: 519
• A rhomboid in the
  Gram-negative bacterium Providencia stuartii is required for the function of the twin-arginine protein translocation (TAT) machinery.^[35]
• Rhomboids control EGF receptor signaling in Caenorhabditis elegans as in Drosophila.^[6]: 201

Structure

Rhomboids were the first intramembrane proteases for which a high resolution crystal structure was solved.^{[36][37][38][39][40]} These structures confirmed predictions that rhomboids have a core of six transmembrane domains, and that the catalytic site depends on a serine and histidine catalytic dyad. The structures also explained how a proteolytic reaction, which requires water molecules, can occur in the hydrophobic environment of a lipid bilayer: one of the central mysteries of intramembrane proteases.^[41] The active site of rhomboid protease is in a hydrophilic indentation, in principle accessible to water from the bulk solution.^{[36][37][38][39][40]} However, it has been proposed that there might be an auxiliary mechanism to facilitate access of water molecules to the catalytic dyad at the bottom of the active site to ensure catalytic efficiency.^[42]

The active site of rhomboid protease is protected laterally from the lipid bilayer by its six constituent transmembrane helices, suggesting that substrate access to rhomboid active site is regulated. One area of uncertainty has been the route of

Rhomboids do not cleave all transmembrane domains. In fact, they are highly specific, with a limited number of substrates. Most natural Rhomboid substrates known so far are type 1 single transmembrane domain proteins, with their amino termini in the luminal/extracellular compartment. However, recent studies suggested that type 2 membrane protein (i.e. with opposite topology: the amino terminus is cytoplasmic),[50] or even multipass membrane proteins could act as rhomboid substrates.^[51] The specificity of rhomboids underlies their ability to control functions in a wide range of biological processes and, in turn, understanding what makes a particular transmembrane domain into a rhomboid substrate can shed light on rhomboid function in different contexts.

Initial work indicated that rhomboids recognise instability of the transmembrane alpha-helix at the site of cleavage as the main substrate determinant.^[52] More recently, it has been found that rhomboid substrates are defined by two separable elements: the transmembrane domain and a primary sequence motif in or immediately adjacent to it.^[48] This recognition motif directs where the substrate is cleaved, which can occur either within, or just outside, the transmembrane domain, in the juxtamembrane region.^[48] In the former case helix destabilising residues downstream in substrate TMS are also necessary for efficient cleavage.^[48] A detailed enzyme kinetics analysis has in fact shown that the recognition motif interactions with rhomboid active site determine the k_cat of substrate cleavage.^[53] The principles of substrate TMS recognition by rhomboid remain poorly understood, but numerous lines of evidence indicate that rhomboids (and perhaps also other intramembrane proteases) somehow recognise the structural flexibility or dynamics of transmembrane domain of their substrates.^[42][54] Full appreciation of the biophysical and structural principles involved will require structural characterisation of the complex of rhomboid with the full transmembrane substrate.^[55] As a first step towards this goal, a recent co-crystal structure of the enzyme in complex with a substrate-derived peptide containing mechanism-based inhibitor explains the observed recognition motif sequence preferences in rhomboid substrates structurally, and provides a significant advance in the current understanding of rhomboid specificity and mechanism of rhomboid-family proteins.^[46]

In some

The diversity of biological functions already known to depend on rhomboids is reflected in evidence that rhomboids play a role in a variety of diseases including cancer,^{[citation needed]} parasite infection,^[13] and diabetes.^{[citation needed]} It is important to note, however, that there is no case yet established where a precise medical significance is fully validated.^[6]

No drugs that modulate rhomboid activity have yet been reported, although a recent study has identified small molecule, mechanism-based inhibitors that could provide a basis for future drug development.^[57]

The rhomboid-like family

Rhomboid proteases appear to be conserved in all

Phylogenetic analysis indicates that rhomboids are in fact members of a larger rhomboid-like superfamily or clan, which includes the derlin proteins, also involved in ERAD.^[64]

Kinetoplastids have an unusually small rhomboid family repertoire, in Trypanosoma brucei XP 001561764 and XP 001561544, and in T. cruzi XP 805971, XP 802860, and XP 821055.^[65]

Various rhomboid family proteins are vital to Toxoplasma gondii virulence and motility, including TgMIC2, TgMIC6, various AMA1 variants including TgAMA1, TgROM1, TgROM4, and TgROM5.^[66]

iRhoms are rhomboid-like proteins, but are not proteases. As with rhomboids they were first discovered in Drosophilae. To the contrary of rhomboids, however, iRhoms inhibit EGFr signaling. Knockout mice for iRhom2 have severe immune compromise.[8]^{: 243, iRhoms}

References