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9.B.104 The Rhomboid Protease Family

Structures of the prokaryotic homologue of rhomboid proteases reveal a core of six transmembrane helices, with the active-site residues residing in a hydrophilic cavity. The native environment of rhomboid protease is a lipid bilayer. Akiyama and Maegawa 2007 characterized sequence features in LY2 that allow efficient cleavage by GlpG and identified two elements, a hydrophilic region encompassing the cleavage site and helix-destabilizing residues in the downstream hydrophobic region. GlpG prefers residues with a small side chain and a negative charge at the P1 and P1' sites, respectively.

  Crystals of GlpG, an E. coli rhomboid protease in a lipid environment were obtained at 1.7Å resolution (Vinothkumar, 2011). The structure revealed well-ordered and partly ordered lipid molecules forming an annulus around the protein. Lipid molecules adapt to the surface features of the protein and arrange such that they match the hydrophobic thickness of GlpG. 

The primary function of rhomboids is to cleave integral membrane proteins to release signalling molecules. These signals, when disrupted, can contribute to various diseases. The Ser-His catalytic dyad is buried within the membrane. The substrate entry gate is composed of helix 5 and loop 5 (Lazareno-Saez et al., 2011). Lazareno-Saez et al. (2011) compared the open and closed conformations of GlpG. Possibly loop 4 acts as an anchor for the substrate gate. Membrane immersion bestows rhomboid proteases with the ability to identify substrates primarily based on reading their intrinsic transmembrane dynamics (Moin and Urban 2012).

The ER-associated degradation (ERAD) pathway serves as an important cellular safeguard by directing incorrectly folded and unassembled proteins from the ER of eukaryotes to the proteasome. Fleig et al. (2012) showed that the evolutionarily conserved rhomboid family protein RHBDL4 is a ubiquitin-dependent ER-resident intramembrane protease that is upregulated upon ER stress. RHBDL4 cleaves single-spanning and polytopic membrane proteins with unstable transmembrane helices, leading to their degradation by the canonical ERAD machinery. RHBDL4 specifically binds the AAA -ATPase p97, suggesting that proteolytic processing and dislocation into the cytosol are functionally linked. The phylogenetic relationship between rhomboids and the ERAD factor derlin suggests that substrates for intramembrane proteolysis and protein dislocation are recruited by a shared mechanism.

The BAG6 complex is an upstream loading factor for tail-anchored membrane proteins entering the TRC40-dependent pathway for posttranslational delivery to the endoplasmic reticulum.  BAG6 also enhances proteasomal degradation of mislocalized proteins by selectively promoting their ubiquitination. BAG6-dependent ubiquitination of mislocalized proteins is reversible, and the glutamine-rich tetratricopeptide repeat-containing protein α, (SGTA) antagonizes this process. Promoting the deubiquitination of mislocalized proteins that are already covalently modified reverses the actions of BAG6, inhibiting its capacity to promote substrate-specific degradation (Leznicki and High 2012). 

From proteases that cleave peptide bonds in the plane of the membrane, rhomboids have evolved into a heterogeneous superfamily with a wide range of different mechanistic properties (Bergbold and Lemberg 2013). In mammals, 14 family members have been annotated based on a shared conserved membrane-integral rhomboid core domain.  Homologues include intramembrane serine proteases and diverse proteolytically inactive proteins. While the function of rhomboid proteases is the proteolytic release of membrane-tethered factors, rhomboid pseudoproteases, including iRhoms and derlins, interact with their clients without cleaving them. It has become evident that specific recognition of membrane protein substrates by the rhomboid fold reflects a spectrum of cellular functions ranging from growth factor activationand trafficking control to membrane protein degradation (Bergbold and Lemberg 2013).

This family belongs to the: MFS Superfamily.

References associated with 9.B.104 family:

Akiyama, Y. and S. Maegawa. (2007). Sequence features of substrates required for cleavage by GlpG, an Escherichia coli rhomboid protease. Mol. Microbiol. 64: 1028-1037. 17501925
Bergbold, N. and M.K. Lemberg. (2013). Emerging role of rhomboid family proteins in mammalian biology and disease. Biochim. Biophys. Acta. 1828: 2840-2848. 23562403
Fleig, L., N. Bergbold, P. Sahasrabudhe, B. Geiger, L. Kaltak, and M.K. Lemberg. (2012). Ubiquitin-dependent intramembrane rhomboid protease promotes ERAD of membrane proteins. Mol. Cell 47: 558-569. 22795130
Lazareno-Saez, C., C.L. Brooks, and M.J. Lemieux. (2011). Structural comparison of substrate entry gate for rhomboid intramembrane peptidases. Biochem. Cell Biol. 89: 216-223. 21455272
Lemieux, M.J., S.J. Fischer, M.M. Cherney, K.S. Bateman, and M.N. James. (2007). The crystal structure of the rhomboid peptidase from Haemophilus influenzae provides insight into intramembrane proteolysis. Proc. Natl. Acad. Sci. USA 104: 750-754. 17210913
Leznicki, P. and S. High. (2012). SGTA antagonizes BAG6-mediated protein triage. Proc. Natl. Acad. Sci. USA 109: 19214-19219. 23129660
Meissner C., Lorenz H., Hehn B. and Lemberg MK. (201). Intramembrane protease PARL defines a negative regulator of PINK1- and PARK2/Parkin-dependent mitophagy. Autophagy. 11(9):1484-98. 26101826
Moin, S.M. and S. Urban. (2012). Membrane immersion allows rhomboid proteases to achieve specificity by reading transmembrane segment dynamics. Elife 1: e00173. 23150798
Vinothkumar, K.R. (2011). Structure of rhomboid protease in a lipid environment. J. Mol. Biol. 407: 232-247. 21256137
Wu, Z., N. Yan, L. Feng, A. Oberstein, H. Yan, R.P. Baker, L. Gu, P.D. Jeffrey, S. Urban, and Y. Shi. (2006). Structural analysis of a rhomboid family intramembrane protease reveals a gating mechanism for substrate entry. Nat Struct Mol Biol 13: 1084-1091. 17099694