User:Eliane Küttler/rhomboid

Rhomboid (Enzyme)

Rhomboids are intramembrane serine proteases. They are located in the lipid-bilayer and have their active side located within their transmembrane domain (TMD) [5]. Their substrates are transmembrane proteins and have their cleavage site either directly in or immediately adjacent to their transmembrane domain. Upon cleavage, the soluble domains of the substrates are released either to the inside or the outside of the cell and can then fulﬁll their functions.

Classification

Four classes of intramembrane proteases have been described: The site-2 protease family, which are metalloproteases, gamma secretases and the signal peptide peptidase-like family, which are both aspartyl proteases, and ﬁnally the rhomboid-like family, which are serine proteases [36, 9, 48, 56]. The rhomboid-like family can be further divided into three major groups: Active proteases, inactive rhomboid-like proteins (termed iRhoms), which lack catalytic residues, and a number of other rhomboid-like proteins that are predicted to be inactive but do not cluster with themselves or with the iRhoms. The eukaryotic active rhomboids can be further divided into two major subfamilies: Secretase rhomboids, like Drosophila Rhomboid-1, which reside in the secretory pathway, and PARL-type rhomboids, which are mitochondrial [21].

Structure

The crystal structure of the E.coli rhomboid GlpG has been solved, thus leading to some understanding on the topology of the enzyme: Instead of using a triad consisting of serine, histidine, and aspartate, like other serine proteases, rhomboids rely on a serine-histidine dyad, without need for a third residue [22]. The dyad of a serine and a histidine lies at the bottom of a cavity which opens towards the aqueous environment outside of the membrane. The serine sits on top of a short TMD and is shielded by longer TMDs that span the whole bilayer. The histidine is oriented in a way so that it can act as a base and abstract a proton from the serine, thus rendering the latter a reactive nucleophile. The whole catalytic site is situated several Å beneath the surface of the bilayer [3, 24, 55, 58].

Biological function

Rhomboid genes have been conserved throughout evolution and are common in all kingdoms of life, making them some of the most widely spread transmembrane proteins yet identiﬁed [21]. Consequently they seem to have various functions within the different organisms: The ﬁrst rhomboid was discovered in Drosophila and has been named Rhomboid-1 [28, 48]. It participates in the epidermal growth factor receptor (EGFR) pathway [10, 45]. The EGFR is a receptor tyrosine kinase. Its pathway mediates intercellular growth factor signaling which in turn controls many aspects of Drosophila development [40]. Rhomboid-1 catalyzes the release of the active EGF-like growth factor Spitz from the membrane [48]. Besides their involvement in the EGF-signaling pathway, rhomboids are involved in many more processes: The rhomboid AarA from Providencia stuartii has been shown to be involved in quorum sensing, the intercellular signaling coordinating certain behaviors based on the local density of the bacterial population [12, 35]. AarA from P. stuartii and Rhomboid-1 from Drosophila can functionally replace each other in vivo [12, 50]. The substrate of AarA has been discovered to be TatA, a major subunit of the twin arginine protein translocase that exports fully folded and modiﬁed proteins across the bacterial membrane into the periplasm [20]. TatA has a single transmembrane domain but multimerizes to form the translocation channel [13]. Through alignments of various TatA sequences it was found that the P. stuartii TatA has a short N-terminal extension of eight amino acids, MESTIATA, that is missing in other species. This extension elongates the TMD. AarA cleaves the TatA TMD to remove the N-terminal extension, thereby activating the TatA channel [42]. It remains unclear why the uncleaved TatA is not functional. Nevertheless it seems clear that TatA inactivity blocks export of quorum sensing signal factors or involved factors from the cell, that way inhibiting quorum sensing. In apicomplexan parasites rhomboids have been shown to be involved in the cleavage of adhesins, which are important in the infection mechanism [47].

Medical relevance

The yeast Saccharomyces cerevisiae has only two rhomboids, one of them located in the mitochondrion, where it cleaves the cytochrome c peroxidase (Ccp1) and Mgm1, a dynamin-like GTPase [8, 39]. Both substrates are important for maintenance of the mitochondrion morphology through membrane ﬁssion and fusion. Mgm1 functions speciﬁcally in membrane fusion and its cleavage releases a soluble GTPase domain into the intermembrane space [57]. In cells it is found in both the full-length and processed forms, and both are required for efﬁcient fusion [39]. Mgm1 is the yeast homologue of the mammalian protein OPA1. Loss of one copy of the human OPA1 gene causes dominant optic atrophy, the most common inherited form of childhood-onset blindness [7]. This proves by analogy to yeast that rhomboids might be involved in more than only the TGF-pathway in humans. Although it has been shown that rhomboids participate in the cleavage of adhesins during the life cycle of apicomplexan parasites, regulate aspects of mitochondrial morphology and function, and have a role in quorum sensing in Providencia, the regulation of the multifunctional EGFR pathway in Drosophila might be the most interesting one [49]. The latter raises the question whether rhomboids control EGFR signaling in other species, especially in humans, where excess EGFR activity is a major factor in disease, in particularly cancer [29].

Regulation of rhomboid activity

Only little has been discovered about how rhomboid activity is controlled. It has been shown that the lipid composition of the mem- brane can inﬂuence rhomboid activity [51]. Also compartmentalization seems to play a role; the precision of membrane trafﬁcking controls access of substrates to the enzymes [19]. Moreover, the extramembrane domains of the rhomboids show a high diversity throughout the species. These domains could include motifs for posttranslational modiﬁcation or ligand binding. It is also possible that interactions between the rhomboid and its substrate outside of the TMD is necessary for cleavage, as it has been shown for the mammalian rhomboid RHBDL2 substrate thrombomodulin [27]. The extramembrane domains can contain many modiﬁcations thereby increasing the options for speciﬁcity and control. Finally, auxiliary proteins, such as Hax-1 in the case of HtrA2-cleavage through the mitochondrial rhomboid PARL, could present possible regulatory elements [6].