- Email: [email protected]
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Clan MA(E) M41 | 146. The i-AAA Protease
Chapter 146
The i-AAA Protease DATABANKS MEROPS name: i-AAA peptidase MEROPS classification: clan MA, subclan MA(E), family M41, peptidase M41.004 Species distribution: superkingdom Eukaryota Reference sequence from: Saccharomyces cerevisiae (UniProt: P32795)
Name and History The mitochondrial i-AAA protease was identified as the result of genetics screens performed in the budding yeast Saccharomyces cervisiae that were aimed at characterizing the genetic basis of the escape of mitochondrial DNA (mtDNA) from within the organelle. Of the six complementation groups first described [1], one gene, termed YME1 (for yeast mitochondrial escape), was predicted to yield a 747 amino acid residue product of 82 kDa. YME1 null cells exhibit additional phenotypes, which include slowed growth on non-fermentable carbon sources at 37 C, cold-sensitive growth retardation on glucose media, and severely retarded growth in the absence of mtDNA; the latter distinguishing Δyme1 as a petite-negative mutant. Since the primary amino acid sequence of Yme1 displays significant sequence identity to the bacterial ATP-dependent protease FtsH as well as other members of the FtsH-Sec18-Pas-CDC48 family of AAA ATPase encoding genes, an involvement of Yme1 in mitochondrial fission and/or fusion was proposed [1]. YME1 was also independently identified in a genomic PCR-based screen for yeast Tat-binding protein analogs (YTAs), putatively coding for a novel family of ATPases [2]. Notable among these 12 analogs are YTA10 (AFG3), YTA11 (YME1), and YTA12 (RCA1), all of which would later be characterized as members of the AAA family, so termed for ATPases associated with a variety of cellular activities [3]. The homologs of YME1, YTA10 and YTA12, encode subunits of the m-AAA protease, a paralogous enzyme active in the mitochondrial matrix [4]. Deficiencies in respiratory chain enzyme biogenesis led researchers to the independent identification of the OSD1 gene [3]. The corresponding gene product, later
revealed to be Yme1, was shown to be responsible for degrading cytochrome c oxidase subunit II (Cox2) unable to assemble into the multi-subunit respiratory chain complex cytochrome c oxidase due to the creation of a downstream block in assembly caused by the absence of Cox4 (Δcox4) [5] or, alternatively, cytochrome c (Δcyc1Δcyc7) [6]. The accelerated degradation of all three mtDNAencoded subunits of cytochrome c oxidase in the latter mutant was only partially reversed upon the additional deletion of YME1, suggesting that turnover of these unassembled subunits is mediated, at least in the context of these [6] and other [7] mutant yeast strains, by an additional protease. Homologs of Yme1 have been identified in all eukaryotic cells. In Neurospora crassa, IAP-1 (for intermembrane space AAA protease) [7] encodes a polypeptide of 738 amino acid residues with a predicted molecular mass of 80 kDa and shares B46% sequence identity with Yme1 of S. cervisiae. In humans, YME1L1 (for YME1-like) encodes a gene product of 716 amino acid residues exhibiting 50% sequence identity with the yeast homolog [8]. In mice, the homolog of YME1 (YME1L1) is responsible for the constitutive processing of the mitochondrial fusion protein OPA1 [9]. Genome sequencing efforts have identified homologs of YME1 in Drosophila and Caenorhabditis elegans [10] and mutagenesis screens in Arabidopsis thaliana helped uncover the existence of two orthologs, designated AtFtsH4 and AtFtsH11, both of which localize to mitochondria [11]. Indeed, both the conservation of this ubiquitous metallopeptidase throughout evolution and the recapitulation of severe cellular consequences that result in its absence reflect the importance of the many roles the i-AAA protease plays in mitochondrial and cellular homeostasis. Yet despite this functional conservation, attempts at expressing either Neurospora IAP-1 [12], Human YME1L1 [13], or AtFtsH4 and AtFtsH11 [11] in Δyme1 yeast cells result only in partial complementation, perhaps reflecting species-specific differences in substrate specificity.
Activity and Specificity The i-AAA protease is an ATP-dependent metalloprotease. The requirement of ATP for the activity of the
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i-AAA protease CH HExxH WB
PD
SRH AAA
WA NH TM
IMS IM
ND
M
MTS FIGURE 146.1 Yme1 spans the inner mitochondrial membrane (IM) with the amino-terminal (ND) exposed to the matrix (M) and the AAA and proteolytic (PD) domains of the carboxy-terminal exposed to the intermembrane space (IMS). MTS, mitochondrial targeting sequence; TM, transmembrane domain (TMHMM Server v2.0); NH, N-terminal helices region; WA, Walker-A motif (GPPGTGKT, residues 321328); WB, Walker-B motif (IIFIDELD, residues 376383); SRH, second region of homology (TNFPEALDKALTRPGRF, residues 423439); HExxH (residues 540544), protease catalytic site; CH, C-terminal helices region.
i-AAA proteases is shown by the abolished proteolytic activity resulting from mutations generated in the conserved A and B boxes of the ATPase domain (so-called Walker A and B motifs) of Yme1 (Figure 146.1) or the removal or substitution of ATP by a non-hydrolyzable form of ATP within the intermembrane space. Interestingly, the AAA domain is not only required for ATP hydrolysis but also participates in substrate binding. Truncated Yme1 harboring either the entire IMS portion or simply the AAA domain of Yme1 alone binds unfolded model substrates provided in vitro [14]. All three enzymes also require metal binding for activity and this is mediated by the proteolytic core characterized by a consensus HExxH sequence found at the carboxy terminal end of the protein. Mutation (Glu541Gln) of this conserved metal binding motif of Yme1 inhibits the proteolytic activity of the i-AAA protease as do the addition of mitochondrial chelating agents like EDTA or 1,10phenanthroline [13]. Zinc is the most likely candidate to bind to the i-AAA proteases, but direct experimental proof is still awaited. Zinc is likely coordinated by the two histidine residues in the consensus metal binding motif as well as a more distal aspartic acid residue that has been identified as the third ligand in studies on bacterial FtsH [15,16]. The i-AAA protease mediates the turnover of misfolded or damaged proteins to peptides but can also act as a processing enzyme regulating the activity of proteins in the intermembrane space (IMS). It regulates the stability of inner mitochondrial membrane (IM) proteins exposed to the IMS as well as peripheral IMS proteins. The
i-AAA protease and m-AAA protease have been shown to exhibit overlapping quality control activities from the synthetic lethality [14,17,18] that results upon deletion of the genes encoding both the i- and m-AAA proteases and their capacity to degrade the same polytopic model substrates [13]. The membrane topology of substrate proteins appears to determine the involvement of one or both AAA proteases in proteolytic degradation [14]. At least 1015 amino acid residues of the substrate protein need to be exposed to allow the proteolytic attack of the AAA protease on the same side of the membrane and once exposed, proteolysis can be initiated from both the N- and C-terminal end of the substrate protein as well as from internal peptide bonds.
Turnover of IM and IMS Proteins The i-AAA protease has been demonstrated to mediate the degradation of a number of non-assembled IM proteins. The identification of Cox2 as the first substrate of the i-AAA protease began with the analysis of respiratory mutants Δcox4 [5] and Δcyc1Δcyc7 [6] that block the integration of Cox2 into the S1 assembly intermediate of the multi-subunit cytochrome c oxidase complex resulting in the subsequent degradation of the mtDNA-encoded polytopic subunits of the complex [19]. Deletion of Yme1 in these mutants greatly reduces the degradation of these polytopic integral inner membrane proteins. A misfolded model substrate containing the first 74 amino acids of Cox2 fused to murine dihydrofolate reductase was the first substrate demonstrated to be cleaved by both the i- and m-AAA proteases [4]. Proteolysis of this model substrate yielded four proteolytic fragments; two were generated in Yme1-dependent fashion and the other two were dependent upon the m-AAA protease. Under normal conditions, the aforementioned subunits of cytochrome c oxidase do not appear to be subjected to turnover by the m-AAA protease. However, when the posttranslational translocation of Cox2 into the membrane is blocked, as in Δcox18 mutants, the degradation of unassembled Cox2 is performed by the m-AAA protease [7]. Similarly, both AAA proteases were shown to specifically and concomitantly degrade Yme2, a large inner membrane-spanning protein harboring solvent-exposed domains in both the matrix and IMS, further illustrating the overlapping activities of these paralagous proteolytic enzymes [13]. The i-AAA protease was also shown to degrade unassembled Phb1 [20], which, along with Phb2 assembles into a large multimeric prohibitin complex that negatively regulates the proteolytic activity of the m-AAA protease [21]. Mutational analyses of the CH region of the peptidase domain of Yme1 has revealed its importance for both binding and subsequent proteolysis
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of Phb1 [22] yet somehow this region appears to be dispensable for the proteolysis of Cox2. Hence, it is fair to propose that substrates may enter the proteolytic chamber along different pathways. The i-AAA protease has been shown to degrade mutant variants of Taz1, a factor that participates in regulation the mitochondrial phospholipid cardiolipin, which is exclusive to the inner mitochondrial membrane and essential for mitochondrial energy metabolism. In humans, mutations in the TAZ gene are responsible for a congenital disorder characterized by dilated or hypertrophic cardiomyopathy [23]. Similar mutations created in the yeast TAZ1 gene yield unstable polypeptides that are rapidly degraded by Yme1 [24]. While these proteins are degraded by the i-AAA protease acting as a quality control enzyme, a study in yeast identified the conserved IMS proteins Ups1 and Ups2 as intrinsically unstable proteins whose proteolysis is mediated by the i-AAA protease [25]. Ups1 and Ups2 regulate the accumulation of cardiolipin and phosphatidylethnaolamine, respectively, in mitochondrial membranes. Both Ups proteins are constitutively degraded by the i-AAA protease and Ups1 is also subject to proteolysis by Atp23 (Chapter 383), another ATP-dependent IMS protease. A fine balance of both proteins within mitochondria appears to be required for phospholipid homeostasis, as shown by the alteration of phospholipid levels upon deletion of either UPS1, UPS2, and, to a lesser extent, YME1 [26]. Importantly, the regulated turnover of these native substrates brings to light a novel regulatory activity of the i-AAA protease that is categorically distinct from quality control activities previously discovered, illustrating the central role of the i-AAA protease for mitochondrial homeostasis.
Substrate Processing In addition to the degradation of misfolded substrates and the regulated turnover of intrinsically unstable proteins, the i-AAA protease also serves in the proteolytic cleavage and maturation of mitochondrial polypeptides. The mammalian i-AAA protease YME1L has been linked to the processing of the dynamin-like GTPase of the dynaminlike GTPase OPA1, generating long and short protein isoforms, both of which are required for mitochondrial fusion [27]. The dynamic equilibrium between mitochondrial fusion and fission is vital for quality control at the organellar level as functional impairment of mutant mitochondria (e.g. carrying a mutation in mtDNA) can be alleviated upon fusion and content mixing with neighboring mitochondria carrying a normal complement of the defective proteins [26]. Both OPA1 and its yeast ortholog Mgm1 undergo proteolytic processing. In yeast, Mgm1 is first cleaved by MPP to yield a long form (l-Mgm1), which can be further processed by the ATP-independent
Clan MA(E) M41 | 146. The i-AAA Protease
protease Pcp1/Rbd1 to generate a short form (s-Mgm1) [29]. In mice, eight splice variants of OPA1 are expressed and each variant is capable of producing a long form as well as one or more short forms. In contrast to Mgm1, the mammalian homolog of Pcp1/Rbd1, known as PARL, is not responsible for the processing of OPA1 isoforms [30]. Rather, cleavage is induced at specific proteolytic sites (designated S1 and S2) by the metallopeptidases OMA1 and YME1L1, respectively [3133]. Notably, while the evidence that OMA1 and YME1L1 cleave OPA1 is compelling, a direct physical interaction has not yet been demonstrated.
Non-Proteolytic Function Independent of its proteolytic function, the i-AAA protease has been proposed to be involved in the import and membrane translocation of PNPase, a mitochondrial polynucleotide phosphorylase that regulates the splicing and maturation of mitochondrial transcripts in mammals [34]. A heterologous yeast assay was used to demonstrate that the functional assembly of human PNPase in yeast mitochondria requires the presence of the i-AAA protease. Mitochondria from Δyme1 yeast complemented with either wild-type Yme1 or the proteolytically-inactive yme1 Glu541Gln variant were both capable of ensuring import of PNPase into the intermembrane space, suggesting that the proteolytic activity of Yme1 is, at least in this particular context, dispensable.
Structural Chemistry Yme1 and its homologs belong to a subfamily of the AAA family of proteins. The predicted molecular mass of S. cerevisiae Yme1, as deduced from the DNA sequence, is 81 768 Da with a pI of 6.89. The 747 amino acid precursor protein is encoded in the nucleus and contains a canonical mitochondrial targeting sequence at the aminoterminal that is cleaved by the mitochondrial processing peptidase (MPP). A single hydrophobic transmembrane helix anchors it to the inner mitochondrial membrane thereby exposing the bulk of the protein to the intermembrane space. Following the transmembrane domain is a conserved P-loop ATPase domain of approximately 230 amino acids, which is characteristic of the AAA1 superfamily of ATPases [35]. An M41 metallopeptidase domain follows, characterized by a canonical HExxH metal binding motif found in all metallopeptidases in the clan MA. In the case of FtsH, the two histidine residues with the aforementioned motif and a structurally proximate aspartate residue coordinate metal ion binding. The AAA domain and protease domains exhibit different symmetries and this has led researchers to propose that such molecular architecture serves to facilitate translocation of
Clan MA(E) M41 | 146. The i-AAA Protease
substrates into the proteolytic chamber of the complex [16]. The crystal structure of the i-AAA protease has yet to be solved, but detailed molecular characterization of the bacterial homolog FtsH catalytic domain [16] and more recently the yeast m-AAA protease [36] all point to a hexameric ring-like assembly of Yme1. In vivo, Yme1 exists as part of an B850 kDa complex [4] whose assembly is Tim54-dependent [37]. Adapter proteins Mgr1 and Mgr3 [17] are present in this complex and ensure maximal proteolytic activity of the i-AAA protease, presumably by facilitating the interaction and subsequent translocation of cognate substrates and the i-AAA protease. Mitochondria from yeast lacking either Mgr1 and/or Mgr3 partially stabilize imported model substrates usually degraded by the i-AAA protease, but not to the extent that is observed in Δyme1 mitochondria [38]. Indeed, the conspicuous absence of metazoan orthologs points to functional divergence in substrate specificity. In plants, the mitochondrial i-AAA protease complexes composed of either AtFtsH4 and AtFtsH11 gene products migrate at approximately 1500 kDa on BNPAGE, although additional constituents remain to be identified [11].
Preparation No purification scheme for Yme1 or any of its orthologs has been reported.
Biological Aspects Mitochondria play central roles in the generation of cellular energy by oxidative phosphorylation, calcium regulation, signaling, and cell death. Defects in the synthesis, import, and modification of mitochondrial polypeptides as well as the impaired assembly of multi-subunit enzyme complexes figure prominently in the pathophysiology of neurodegenerative and congenital cardiovascular disorders, infertility, and aging [39]. Fortunately, mitochondria have evolved several cyto-protective countermeasures designed to maintain organellar integrity. Among these safeguards are ATP-dependent proteases, which regulate mitochondrial biogenesis and degrade misfolded proteins that might otherwise accumulate to toxic levels [28]. Interestingly, impaired quality control (QC) in the cytoplasm is particularly destructive to neurons, as shown by the accumulation of insoluble aggregates in both agingassociated diseases (e.g. idiopathic Alzheimer’s disease and Parkinson’s disease) and neurodegenerative disorders (e.g. Huntington’s disease and amyotrophic lateral sclerosis) [40]. It is no surprise to find that primary neurological defects are manifested in the face of abrogated function
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of mitochondrial AAA proteases. Mutations in paraplegin, a subunit of the matrix AAA (m-AAA) protease, cause a recessive form of hereditary spastic paraplegia [41] while mutations in AFG3L2, another m-AAA protease subunit, cause a form of spinocerebellar ataxia [42]. Just as the m-AAA protease attends to QC in the matrix, so too does the i-AAA protease complex turnover misfolded proteins in the IMS. In addition to its role in quality control, the i-AAA protease is charged with the tasks of the constitutive, regulatory turnover of native IMS factors (e.g. Ups1, Ups2) and proteolytic processing and activation of the mitochondrial fusion protein OPA1, the latter of which causes a dominant form of optic atrophy when mutated in humans [43]. The murine i-AAA protease constitutively cleaves OPA1 to maintain the requisite balance of long and short OPA1 isoforms presumed necessary for inner membrane fusion. Similar to the genetic inactivation of OPA1, the depletion of the i-AAA protease in both yeast and mammals disrupts mitochondrial morphology [9]. Studies have indicated that mitochondrial fragmentation in culture human cells facilitates the ensuing apoptotic events such as the release of cytochrome c and are reminiscent of a role of Yme1 in yeast programmed cell death [44]. In yeast, the pleiotropic phenotypes that stem from the loss of the i-AAA protease and the inability to identify suppressors able to complement all of these phenotypes simultaneously [45], underscores the diverse physiological roles substrates that are regulated by this metalloprotease play in their own right. The identification of additional substrates and interactors has the potential to illuminate the entirety of the biological processes orchestrated by i-AAA protease and reconcile the pleiotropic phenotypes that accompany the loss of YME1 in yeast. In humans, the discovery that the genetic basis for two clinically distinct inherited forms of peripheral neuropathies stems from the mutational inactivation of the m-AAA protease isozymes paraplegin [41] and AFG3L2 [42] has made YME1L1 an attractive candidate gene. Yet, sequencing efforts of YME1L1 have failed to uncover mutations in patients with inborn errors of energy metabolism [46], although the ubiquitous tissue distribution and paucity of identified substrates in humans makes the prediction of a clinical manifestation and, in turn, definition of the appropriate patient cohort all the more challenging. At the moment, we have only a rudimentary understanding of the relevance of the mammalian i-AAA protease at the cellular and organellar levels.
Related Peptidases Please consult the following chapters for more information regarding the paralogous eukaryotic m-AAA protease (Chapter 145) and homologous prokaryotic FtsH protease (Chapter 144).
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Further Reading Further research on i-AAA protease can be found in Tatsuta & Langer [26].
References [1] Thorsness, P.E., White, K.H., Fox, T.D. (1993). Inactivation of YME1, a member of the ftsH-SEC18-PAS1-CDC48 family of putative ATPase-encoding genes, causes increased escape of DNA from mitochondria in Saccharomyces cerevisiae. Mol. Cell. Biol. 13(9), 54185426. [2] Schnall, R., Mannhaupt, G., Stucka, R., Tauer, R., Ehnle, S., Schwarzlose, C., Vetter, I., Feldmann, H. (1994). Identification of a set of yeast genes coding for a novel family of putative ATPases with high similarity to constituents of the 26S protease complex. Yeast 10(9), 11411155. [3] Nakai, T., Yasuhara, T., Fujiki, Y., Ohashi, A. (1995). Multiple genes, including a member of the AAA family, are essential for the degradation of unassembled subunit 2 of cytochrome c oxidase in yeast mitochondria. Mol. Cell. Biol. 15, 44414452. [4] Leonhard, K., Herrmann, J.M., Stuart, R.A., Mannhaupt, G., Neupert, W., Langer, T. (1996). AAA proteases with catalytic sites on opposite membrane surfaces comprise a proteolytic system for the ATP-dependent degradation of inner membrane proteins in mitochondria. EMBO J. 15, 42184229. [5] Nakai, T., Mera, Y., Yasuhara, T., Ohashi, A. (1994). Divalent metal ion-dependent mitochondrial degradation of unassembled subunits 2 and 3 of cytochrome c oxidase. J. Biochem. (Tokyo) 116 (4), 752758. [6] Pearce, D.A., Sherman, F. (1995). Diminished degradation of yeast cytochrome c by interactions with its physiological partners. Proc. Natl. Acad. Sci. USA 92, 37353739. [7] Fiumera, H.L., Dunham, M.J., Saracco, S.A., Butler, C.A., Kelly, J.A., Fox, T.D. (2009). Translocation and assembly of mitochondrially coded Saccharomyces cerevisiae cytochrome c oxidase subunit Cox2 by Oxa1 and Yme1 in the absence of Cox18. Genetics 182(2), 519528. [8] Coppola, M., Pizzigoni, A., Banfi, S., Casari, G., Bassi, M.T., Incerti, B. (2000). Identification and characterization of YME1L1, a novel paraplegin related gene. Genomics 66, 4854. [9] Song, Z., Chen, H., Fiket, M., Alexander, C., Chan, D.C. (2007). OPA1 processing controls mitochondrial fusion and is regulated by mRNA splicing, membrane potential, and Yme1L. J. Cell Biol. 178(5), 749755. [10] Juhola, M.K., Shah, Z.H., Grivell, L.A., Jacobs, H.T. (2000). The mitochondrial inner membrane AAA metalloprotease family in metazoans. FEBS Lett. 481, 9195. [11] Urantowka, A., Knorpp, C., Olczak, T., Kolodziejczak, M., Janska, H. (2005). Plant mitochondria contain at least two i-AAAlike complexes. Plant. Mol. Biol. 59(2), 239252. [12] Shah, Z.H., Hakkaart, G.A.J., Arku, B., DeJong, L., Van der Speck, H., Grivell, L., Jacobs, H.T. (2000). The human homologue of the yeast mitochondrial AAA metalloprotease Yme1p complements a yeast yme1 disruptant. FEBS Lett. 478, 267270. [13] Leonhard, K., Stiegler, A., Neupert, W., Langer, T. (1999). Chaperone-like activity of the AAA domain of the yeast Yme1 AAA protease. Nature 398, 348351.
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[14] Leonhard, K., Guiard, B., Pellechia, G., Tzagoloff, A., Neupert, W., Langer, T. (2000). Membrane protein degradation by AAA proteases in mitochondria: extraction of substrates from either membrane surface. Mol. Cell 5, 629638. [15] Langklotz, S., Baumann, U., Narberhaus, F. (2011). Structure and function of the bacterial AAA protease FtsH. Biochim. Biophys. Acta 1823, 4048. [16] Bieniossek, C., Schalch, T., Bumann, M., Meister, M., Meier, R., Baumann, U. (2006). The molecular architecture of the metalloprotease FtsH. Proc. Natl. Acad. Sci. USA 103, 30663071. [17] Dunn, C.D., Lee, M.S., Spencer, F.A., Jensen, R.E. (2006). A genomewide screen for petite-negative yeast strains yields a new subunit of the i-AAA protease complex. Mol. Biol. Cell 17, 213226. [18] Lemaire, C., Hamel, P., Velours, J., Dujardin, G. (2000). Absence of the mitochondrial AAA protease Yme1p restores FO-ATPase subunit accumulation in an oxa1 deletion mutant of Saccharomyces cerevisiae. J. Biol. Chem. 275, 2347123475. [19] Pearce, D.A., Sherman, F. (1995). Degradation of cytochrome oxidase subunits in mutants of yeast lacking cytochrome c and suppression of the degradation by mutation of yme1. J. Biol. Chem. 270(35), 14. [20] Kambacheld, M., Augustin, S., Tatsuta, T., Muller, S., Langer, T. (2005). Role of the novel metallopeptidase Mop112 and saccharolysin for the complete degradation of proteins residing in different subcompartments of mitochondria. J. Biol. Chem. 280(20), 2013220139. [21] Steglich, G., Neupert, W., Langer, T. (1999). Prohibitins regulate membrane protein degradation by the m-AAA protease in mitochondria. Mol. Cell. Biol. 19, 34353442. [22] Graef, M., Seewald, G., Langer, T. (2007). Substrate recognition by AAA1 ATPases: Distinct substrate binding modes in the ATPdependent protease Yme1 of the mitochondrial intermembrane space. Mol. Cell. Biol. 27(2), 24762485. [23] Bione, S., D’Adamo, P., Maestrini, E., Gedeon, A.K., Bolhuis, P.A., Toniolo, D. (1996). A novel X-linked gene, G4.5, is responsible for Barth syndrome. Nat. Genet. 12(4), 385389. [24] Claypool, S.M., McCaffery, J.M., Koehler, C.M. (2006). Mitochondrial mislocalization and altered assembly of a cluster of Barth syndrome mutant tafazzins. J. Cell. Biol. 174(3), 379390. [25] Potting, C., Wilmes, C., Engmann, T., Osman, C., Langer, T. (2010). Regulation of mitochondrial phospholipids by Ups1/ PRELI-like proteins depends on proteolysis and Mdm35. EMBO J. 29(17), 28882898. [26] Nebauer, R., Schuiki, I., Kulterer, B., Trajanoski, Z., Daum, G. (2007). The phosphatidylethanolamine level of yeast mitochondria is affected by the mitochondrial components Oxa1p and Yme1p. FEBS J. 274, 61806190. [27] Ehses, S., Raschke, I., Mancuso, G., Bernacchia, A., Geimer, S., Tondera, D., Martinou, J.C., Westermann, B., Rugarli, E.I., Langer, T. (2009). Regulation of OPA1 processing and mitochondrial fusion by m-AAA protease isoenzymes and OMA1. J. Cell. Biol. 187(7), 10231036. [28] Tatsuta, T., Langer, T. (2008). Quality control of mitochondria: protection against neurodegeneration and ageing. EMBO J. 27(2), 306314. [29] McQuibban, G.A., Saurya, S., Freeman, M. (2003). Mitochondrial membrane remodelling regulated by a conserved rhomboid protease. Nature 423(6939), 537541.
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[30] Griparic, L., Kanazawa, T., van der Bliek, A.M. (2007). Regulation of the mitochondrial dynamin-like protein Opa1 by proteolytic cleavage. J. Cell. Biol. 178(5), 757764. [31] Ishihara, N., Fujita, Y., Oka, T., Mihara, K. (2006). Regulation of mitochondrial morphology through proteolytic cleavage of OPA1. EMBO J. 25, 29662977. [32] Duvezin-Caubet, S., Jagasia, R., Wagener, J., Hofmann, S., Trifunovic, A., Hansson, A., Chomyn, A., Bauer, M.F., Attardi, G., Larsson, N.G., Neupert, W., Reichert, A.S. (2006). Proteolytic processing of OPA1 links mitochondrial dysfunction to alterations in mitochondrial morphology. J. Biol. Chem. 281(49), 3797237979. [33] Head, B., Griparic, L., Amiri, M., Gandre-Babbe, S., van der Bliek, A.M. (2009). Inducible proteolytic inactivation of OPA1 mediated by the OMA1 protease in mammalian cells. J. Cell. Biol. 187(7), 959966. [34] Rainey, R.N., Glavin, J.D., Chen, H.W., French, S.W., Teitell, M.A., Koehler, C.M. (2006). A new function in translocation for the mitochondrial i-AAA Protease Yme1: Import of polynucleotide phosphorylase into the intermembrane Space. Mol. Cell. Biol. 26(22), 84888497. [35] Neuwald, A.F., Aravind, L., Spouge, J.L., Koonin, E.V. (1999). AAA1 : A class of chaperone-like ATPases associated with the assembly, operation, and disassembly of protein complexes. Genome Res. 9, 2743. [36] Lee, S., Augustin, S., Tatsuta, T., Gerdes, F., Langer, T., Tsai, F.T. (2011). Electron cryomicroscopy structure of a membrane-anchored mitochondrial AAA protease. J. Biol. Chem. 286(6), 44044411. [37] Hwang, D.K., Claypool, S.M., Leuenberger, D., Tienson, H.L., Koehler, C.M. (2007). Tim54p connects inner membrane assembly and proteolytic pathways in the mitochondrion. J. Cell. Biol. 178, 11611175. [38] Dunn, C.D., Tamura, Y., Sesaki, H., Jensen, R.E. (2008). Mgr3p and Mgr1p are adaptors for the mitochondrial i-AAA protease complex. Mol. Biol. Cell 19(12), 53875397.
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[39] Taylor, R.W., Turnbull, D.M. (2005). Mitochondrial DNA mutations in human disease. Nat. Rev. Genet. 6(5), 389402. [40] Soto, C. (2003). Unfolding the role of protein misfolding in neurodegenerative diseases. Nat. Rev. Neurosci. 4(1), 4960. [41] Casari, G., De-Fusco, M., Ciarmatori, S., Zeviani, M., Mora, M., Fernandez, P., DeMichele, G., Filla, A., Cocozza, S., Marconi, R., Durr, A., Fontaine, B., Ballabio, A. (1998). Spastic paraplegia and OXPHOS impairment caused by mutations in paraplegin, a nuclear-encoded mitochondrial metalloprotease. Cell 93, 973983. [42] Di Bella, D., Lazzaro, F., Brusco, A., Plumari, M., Battaglia, G., Pastore, A., Finardi, A., Cagnoli, C., Tempia, F., Frontali, M., Veneziano, L., Sacco, T., Boda, E., Brussino, A., Bonn, F., Castellotti, B., Baratta, S., Mariotti, C., Gellera, C., Fracasso, V., Magri, S., Langer, T., Plevani, P., Di Donato, S., MuziFalconi, M., Taroni, F. (2010). Mutations in the mitochondrial protease gene AFG3L2 cause dominant hereditary ataxia SCA28. Nat. Genet. 42(4), 313321. [43] Alexander, C., Votruba, M., Pesch, U.E., Thiselton, D.L., Mayer, S., Moore, A., Rodriguez, M., Kellner, U., Leo-Kottler, B., Auburger, G., Bhattacharya, S.S., Wissinger, B. (2000). OPA1, encoding a dynaminrelated GTPase, is mutated in autosomal dominant optic atrophy linked to chromosome 3q28. Nat. Genet. 26, 211215. [44] Manon, S., Priault, M., Camougrand, N. (2001). Mitochondrial AAA-type protease Yme1p is involved in Bax effects on cytochrome c oxidase. Biochem. Biophys. Res. Commun. 289(5), 13141319. [45] Hanekamp, T., Thorsness, P.E. (1999). YNT20, a bypass suppressor of yme1 yme2, encodes a putative 30 50 -exonuclease localized in mitochondria of Saccharomyces cerevisiae. Curr. Genet. 34, 438448. [46] Coenen, M.J., Smeitink, J.A., Smeets, R., Trijbels, F.J., van den Heuvel, L.P. (2005). Mutation detection in four candidate genes (OXA1L, MRS2L, YME1L and MIPEP) for combined deficiencies in the oxidative phosphorylation system. J. Inherit. Metab. Dis. 28 (6), 10911097.
Timothy Wai Institute for Genetics, Center for Molecular Medicine (CMMC), Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Zuelpicher Str. 47a, 50674 Cologne, Germany; Max-Planck-Institute for Biology of Aging, 50931 Cologne, Germany. Email: [email protected]
Thomas Langer Institute for Genetics, Center for Molecular Medicine (CMMC), Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Zuelpicher Str. 47a, 50674 Cologne, Germany; Max-Planck-Institute for Biology of Aging, 50931 Cologne, Germany. Email: [email protected] Handbook of Proteolytic Enzymes, 3rd Edn ISBN: 978-0-12-382219-2
© 2013 Elsevier Ltd. All rights reserved. DOI: http://dx.doi.org/10.1016/B978-0-12-382219-2.00146-0
Clan MA(E) M41 | 146. The i-AAA Protease
Chapter 146
The i-AAA Protease DATABANKS MEROPS name: i-AAA peptidase MEROPS classification: clan MA, subclan MA(E), family M41, peptidase M41.004 Species distribution: superkingdom Eukaryota Reference sequence from: Saccharomyces cerevisiae (UniProt: P32795)
Name and History The mitochondrial i-AAA protease was identified as the result of genetics screens performed in the budding yeast Saccharomyces cervisiae that were aimed at characterizing the genetic basis of the escape of mitochondrial DNA (mtDNA) from within the organelle. Of the six complementation groups first described [1], one gene, termed YME1 (for yeast mitochondrial escape), was predicted to yield a 747 amino acid residue product of 82 kDa. YME1 null cells exhibit additional phenotypes, which include slowed growth on non-fermentable carbon sources at 37 C, cold-sensitive growth retardation on glucose media, and severely retarded growth in the absence of mtDNA; the latter distinguishing Δyme1 as a petite-negative mutant. Since the primary amino acid sequence of Yme1 displays significant sequence identity to the bacterial ATP-dependent protease FtsH as well as other members of the FtsH-Sec18-Pas-CDC48 family of AAA ATPase encoding genes, an involvement of Yme1 in mitochondrial fission and/or fusion was proposed [1]. YME1 was also independently identified in a genomic PCR-based screen for yeast Tat-binding protein analogs (YTAs), putatively coding for a novel family of ATPases [2]. Notable among these 12 analogs are YTA10 (AFG3), YTA11 (YME1), and YTA12 (RCA1), all of which would later be characterized as members of the AAA family, so termed for ATPases associated with a variety of cellular activities [3]. The homologs of YME1, YTA10 and YTA12, encode subunits of the m-AAA protease, a paralogous enzyme active in the mitochondrial matrix [4]. Deficiencies in respiratory chain enzyme biogenesis led researchers to the independent identification of the OSD1 gene [3]. The corresponding gene product, later
revealed to be Yme1, was shown to be responsible for degrading cytochrome c oxidase subunit II (Cox2) unable to assemble into the multi-subunit respiratory chain complex cytochrome c oxidase due to the creation of a downstream block in assembly caused by the absence of Cox4 (Δcox4) [5] or, alternatively, cytochrome c (Δcyc1Δcyc7) [6]. The accelerated degradation of all three mtDNAencoded subunits of cytochrome c oxidase in the latter mutant was only partially reversed upon the additional deletion of YME1, suggesting that turnover of these unassembled subunits is mediated, at least in the context of these [6] and other [7] mutant yeast strains, by an additional protease. Homologs of Yme1 have been identified in all eukaryotic cells. In Neurospora crassa, IAP-1 (for intermembrane space AAA protease) [7] encodes a polypeptide of 738 amino acid residues with a predicted molecular mass of 80 kDa and shares B46% sequence identity with Yme1 of S. cervisiae. In humans, YME1L1 (for YME1-like) encodes a gene product of 716 amino acid residues exhibiting 50% sequence identity with the yeast homolog [8]. In mice, the homolog of YME1 (YME1L1) is responsible for the constitutive processing of the mitochondrial fusion protein OPA1 [9]. Genome sequencing efforts have identified homologs of YME1 in Drosophila and Caenorhabditis elegans [10] and mutagenesis screens in Arabidopsis thaliana helped uncover the existence of two orthologs, designated AtFtsH4 and AtFtsH11, both of which localize to mitochondria [11]. Indeed, both the conservation of this ubiquitous metallopeptidase throughout evolution and the recapitulation of severe cellular consequences that result in its absence reflect the importance of the many roles the i-AAA protease plays in mitochondrial and cellular homeostasis. Yet despite this functional conservation, attempts at expressing either Neurospora IAP-1 [12], Human YME1L1 [13], or AtFtsH4 and AtFtsH11 [11] in Δyme1 yeast cells result only in partial complementation, perhaps reflecting species-specific differences in substrate specificity.
Activity and Specificity The i-AAA protease is an ATP-dependent metalloprotease. The requirement of ATP for the activity of the
Clan MA(E) M41 | 146. The i-AAA Protease
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i-AAA protease CH HExxH WB
PD
SRH AAA
WA NH TM
IMS IM
ND
M
MTS FIGURE 146.1 Yme1 spans the inner mitochondrial membrane (IM) with the amino-terminal (ND) exposed to the matrix (M) and the AAA and proteolytic (PD) domains of the carboxy-terminal exposed to the intermembrane space (IMS). MTS, mitochondrial targeting sequence; TM, transmembrane domain (TMHMM Server v2.0); NH, N-terminal helices region; WA, Walker-A motif (GPPGTGKT, residues 321328); WB, Walker-B motif (IIFIDELD, residues 376383); SRH, second region of homology (TNFPEALDKALTRPGRF, residues 423439); HExxH (residues 540544), protease catalytic site; CH, C-terminal helices region.
i-AAA proteases is shown by the abolished proteolytic activity resulting from mutations generated in the conserved A and B boxes of the ATPase domain (so-called Walker A and B motifs) of Yme1 (Figure 146.1) or the removal or substitution of ATP by a non-hydrolyzable form of ATP within the intermembrane space. Interestingly, the AAA domain is not only required for ATP hydrolysis but also participates in substrate binding. Truncated Yme1 harboring either the entire IMS portion or simply the AAA domain of Yme1 alone binds unfolded model substrates provided in vitro [14]. All three enzymes also require metal binding for activity and this is mediated by the proteolytic core characterized by a consensus HExxH sequence found at the carboxy terminal end of the protein. Mutation (Glu541Gln) of this conserved metal binding motif of Yme1 inhibits the proteolytic activity of the i-AAA protease as do the addition of mitochondrial chelating agents like EDTA or 1,10phenanthroline [13]. Zinc is the most likely candidate to bind to the i-AAA proteases, but direct experimental proof is still awaited. Zinc is likely coordinated by the two histidine residues in the consensus metal binding motif as well as a more distal aspartic acid residue that has been identified as the third ligand in studies on bacterial FtsH [15,16]. The i-AAA protease mediates the turnover of misfolded or damaged proteins to peptides but can also act as a processing enzyme regulating the activity of proteins in the intermembrane space (IMS). It regulates the stability of inner mitochondrial membrane (IM) proteins exposed to the IMS as well as peripheral IMS proteins. The
i-AAA protease and m-AAA protease have been shown to exhibit overlapping quality control activities from the synthetic lethality [14,17,18] that results upon deletion of the genes encoding both the i- and m-AAA proteases and their capacity to degrade the same polytopic model substrates [13]. The membrane topology of substrate proteins appears to determine the involvement of one or both AAA proteases in proteolytic degradation [14]. At least 1015 amino acid residues of the substrate protein need to be exposed to allow the proteolytic attack of the AAA protease on the same side of the membrane and once exposed, proteolysis can be initiated from both the N- and C-terminal end of the substrate protein as well as from internal peptide bonds.
Turnover of IM and IMS Proteins The i-AAA protease has been demonstrated to mediate the degradation of a number of non-assembled IM proteins. The identification of Cox2 as the first substrate of the i-AAA protease began with the analysis of respiratory mutants Δcox4 [5] and Δcyc1Δcyc7 [6] that block the integration of Cox2 into the S1 assembly intermediate of the multi-subunit cytochrome c oxidase complex resulting in the subsequent degradation of the mtDNA-encoded polytopic subunits of the complex [19]. Deletion of Yme1 in these mutants greatly reduces the degradation of these polytopic integral inner membrane proteins. A misfolded model substrate containing the first 74 amino acids of Cox2 fused to murine dihydrofolate reductase was the first substrate demonstrated to be cleaved by both the i- and m-AAA proteases [4]. Proteolysis of this model substrate yielded four proteolytic fragments; two were generated in Yme1-dependent fashion and the other two were dependent upon the m-AAA protease. Under normal conditions, the aforementioned subunits of cytochrome c oxidase do not appear to be subjected to turnover by the m-AAA protease. However, when the posttranslational translocation of Cox2 into the membrane is blocked, as in Δcox18 mutants, the degradation of unassembled Cox2 is performed by the m-AAA protease [7]. Similarly, both AAA proteases were shown to specifically and concomitantly degrade Yme2, a large inner membrane-spanning protein harboring solvent-exposed domains in both the matrix and IMS, further illustrating the overlapping activities of these paralagous proteolytic enzymes [13]. The i-AAA protease was also shown to degrade unassembled Phb1 [20], which, along with Phb2 assembles into a large multimeric prohibitin complex that negatively regulates the proteolytic activity of the m-AAA protease [21]. Mutational analyses of the CH region of the peptidase domain of Yme1 has revealed its importance for both binding and subsequent proteolysis
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of Phb1 [22] yet somehow this region appears to be dispensable for the proteolysis of Cox2. Hence, it is fair to propose that substrates may enter the proteolytic chamber along different pathways. The i-AAA protease has been shown to degrade mutant variants of Taz1, a factor that participates in regulation the mitochondrial phospholipid cardiolipin, which is exclusive to the inner mitochondrial membrane and essential for mitochondrial energy metabolism. In humans, mutations in the TAZ gene are responsible for a congenital disorder characterized by dilated or hypertrophic cardiomyopathy [23]. Similar mutations created in the yeast TAZ1 gene yield unstable polypeptides that are rapidly degraded by Yme1 [24]. While these proteins are degraded by the i-AAA protease acting as a quality control enzyme, a study in yeast identified the conserved IMS proteins Ups1 and Ups2 as intrinsically unstable proteins whose proteolysis is mediated by the i-AAA protease [25]. Ups1 and Ups2 regulate the accumulation of cardiolipin and phosphatidylethnaolamine, respectively, in mitochondrial membranes. Both Ups proteins are constitutively degraded by the i-AAA protease and Ups1 is also subject to proteolysis by Atp23 (Chapter 383), another ATP-dependent IMS protease. A fine balance of both proteins within mitochondria appears to be required for phospholipid homeostasis, as shown by the alteration of phospholipid levels upon deletion of either UPS1, UPS2, and, to a lesser extent, YME1 [26]. Importantly, the regulated turnover of these native substrates brings to light a novel regulatory activity of the i-AAA protease that is categorically distinct from quality control activities previously discovered, illustrating the central role of the i-AAA protease for mitochondrial homeostasis.
Substrate Processing In addition to the degradation of misfolded substrates and the regulated turnover of intrinsically unstable proteins, the i-AAA protease also serves in the proteolytic cleavage and maturation of mitochondrial polypeptides. The mammalian i-AAA protease YME1L has been linked to the processing of the dynamin-like GTPase of the dynaminlike GTPase OPA1, generating long and short protein isoforms, both of which are required for mitochondrial fusion [27]. The dynamic equilibrium between mitochondrial fusion and fission is vital for quality control at the organellar level as functional impairment of mutant mitochondria (e.g. carrying a mutation in mtDNA) can be alleviated upon fusion and content mixing with neighboring mitochondria carrying a normal complement of the defective proteins [26]. Both OPA1 and its yeast ortholog Mgm1 undergo proteolytic processing. In yeast, Mgm1 is first cleaved by MPP to yield a long form (l-Mgm1), which can be further processed by the ATP-independent
Clan MA(E) M41 | 146. The i-AAA Protease
protease Pcp1/Rbd1 to generate a short form (s-Mgm1) [29]. In mice, eight splice variants of OPA1 are expressed and each variant is capable of producing a long form as well as one or more short forms. In contrast to Mgm1, the mammalian homolog of Pcp1/Rbd1, known as PARL, is not responsible for the processing of OPA1 isoforms [30]. Rather, cleavage is induced at specific proteolytic sites (designated S1 and S2) by the metallopeptidases OMA1 and YME1L1, respectively [3133]. Notably, while the evidence that OMA1 and YME1L1 cleave OPA1 is compelling, a direct physical interaction has not yet been demonstrated.
Non-Proteolytic Function Independent of its proteolytic function, the i-AAA protease has been proposed to be involved in the import and membrane translocation of PNPase, a mitochondrial polynucleotide phosphorylase that regulates the splicing and maturation of mitochondrial transcripts in mammals [34]. A heterologous yeast assay was used to demonstrate that the functional assembly of human PNPase in yeast mitochondria requires the presence of the i-AAA protease. Mitochondria from Δyme1 yeast complemented with either wild-type Yme1 or the proteolytically-inactive yme1 Glu541Gln variant were both capable of ensuring import of PNPase into the intermembrane space, suggesting that the proteolytic activity of Yme1 is, at least in this particular context, dispensable.
Structural Chemistry Yme1 and its homologs belong to a subfamily of the AAA family of proteins. The predicted molecular mass of S. cerevisiae Yme1, as deduced from the DNA sequence, is 81 768 Da with a pI of 6.89. The 747 amino acid precursor protein is encoded in the nucleus and contains a canonical mitochondrial targeting sequence at the aminoterminal that is cleaved by the mitochondrial processing peptidase (MPP). A single hydrophobic transmembrane helix anchors it to the inner mitochondrial membrane thereby exposing the bulk of the protein to the intermembrane space. Following the transmembrane domain is a conserved P-loop ATPase domain of approximately 230 amino acids, which is characteristic of the AAA1 superfamily of ATPases [35]. An M41 metallopeptidase domain follows, characterized by a canonical HExxH metal binding motif found in all metallopeptidases in the clan MA. In the case of FtsH, the two histidine residues with the aforementioned motif and a structurally proximate aspartate residue coordinate metal ion binding. The AAA domain and protease domains exhibit different symmetries and this has led researchers to propose that such molecular architecture serves to facilitate translocation of
Clan MA(E) M41 | 146. The i-AAA Protease
substrates into the proteolytic chamber of the complex [16]. The crystal structure of the i-AAA protease has yet to be solved, but detailed molecular characterization of the bacterial homolog FtsH catalytic domain [16] and more recently the yeast m-AAA protease [36] all point to a hexameric ring-like assembly of Yme1. In vivo, Yme1 exists as part of an B850 kDa complex [4] whose assembly is Tim54-dependent [37]. Adapter proteins Mgr1 and Mgr3 [17] are present in this complex and ensure maximal proteolytic activity of the i-AAA protease, presumably by facilitating the interaction and subsequent translocation of cognate substrates and the i-AAA protease. Mitochondria from yeast lacking either Mgr1 and/or Mgr3 partially stabilize imported model substrates usually degraded by the i-AAA protease, but not to the extent that is observed in Δyme1 mitochondria [38]. Indeed, the conspicuous absence of metazoan orthologs points to functional divergence in substrate specificity. In plants, the mitochondrial i-AAA protease complexes composed of either AtFtsH4 and AtFtsH11 gene products migrate at approximately 1500 kDa on BNPAGE, although additional constituents remain to be identified [11].
Preparation No purification scheme for Yme1 or any of its orthologs has been reported.
Biological Aspects Mitochondria play central roles in the generation of cellular energy by oxidative phosphorylation, calcium regulation, signaling, and cell death. Defects in the synthesis, import, and modification of mitochondrial polypeptides as well as the impaired assembly of multi-subunit enzyme complexes figure prominently in the pathophysiology of neurodegenerative and congenital cardiovascular disorders, infertility, and aging [39]. Fortunately, mitochondria have evolved several cyto-protective countermeasures designed to maintain organellar integrity. Among these safeguards are ATP-dependent proteases, which regulate mitochondrial biogenesis and degrade misfolded proteins that might otherwise accumulate to toxic levels [28]. Interestingly, impaired quality control (QC) in the cytoplasm is particularly destructive to neurons, as shown by the accumulation of insoluble aggregates in both agingassociated diseases (e.g. idiopathic Alzheimer’s disease and Parkinson’s disease) and neurodegenerative disorders (e.g. Huntington’s disease and amyotrophic lateral sclerosis) [40]. It is no surprise to find that primary neurological defects are manifested in the face of abrogated function
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of mitochondrial AAA proteases. Mutations in paraplegin, a subunit of the matrix AAA (m-AAA) protease, cause a recessive form of hereditary spastic paraplegia [41] while mutations in AFG3L2, another m-AAA protease subunit, cause a form of spinocerebellar ataxia [42]. Just as the m-AAA protease attends to QC in the matrix, so too does the i-AAA protease complex turnover misfolded proteins in the IMS. In addition to its role in quality control, the i-AAA protease is charged with the tasks of the constitutive, regulatory turnover of native IMS factors (e.g. Ups1, Ups2) and proteolytic processing and activation of the mitochondrial fusion protein OPA1, the latter of which causes a dominant form of optic atrophy when mutated in humans [43]. The murine i-AAA protease constitutively cleaves OPA1 to maintain the requisite balance of long and short OPA1 isoforms presumed necessary for inner membrane fusion. Similar to the genetic inactivation of OPA1, the depletion of the i-AAA protease in both yeast and mammals disrupts mitochondrial morphology [9]. Studies have indicated that mitochondrial fragmentation in culture human cells facilitates the ensuing apoptotic events such as the release of cytochrome c and are reminiscent of a role of Yme1 in yeast programmed cell death [44]. In yeast, the pleiotropic phenotypes that stem from the loss of the i-AAA protease and the inability to identify suppressors able to complement all of these phenotypes simultaneously [45], underscores the diverse physiological roles substrates that are regulated by this metalloprotease play in their own right. The identification of additional substrates and interactors has the potential to illuminate the entirety of the biological processes orchestrated by i-AAA protease and reconcile the pleiotropic phenotypes that accompany the loss of YME1 in yeast. In humans, the discovery that the genetic basis for two clinically distinct inherited forms of peripheral neuropathies stems from the mutational inactivation of the m-AAA protease isozymes paraplegin [41] and AFG3L2 [42] has made YME1L1 an attractive candidate gene. Yet, sequencing efforts of YME1L1 have failed to uncover mutations in patients with inborn errors of energy metabolism [46], although the ubiquitous tissue distribution and paucity of identified substrates in humans makes the prediction of a clinical manifestation and, in turn, definition of the appropriate patient cohort all the more challenging. At the moment, we have only a rudimentary understanding of the relevance of the mammalian i-AAA protease at the cellular and organellar levels.
Related Peptidases Please consult the following chapters for more information regarding the paralogous eukaryotic m-AAA protease (Chapter 145) and homologous prokaryotic FtsH protease (Chapter 144).
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Further Reading Further research on i-AAA protease can be found in Tatsuta & Langer [26].
References [1] Thorsness, P.E., White, K.H., Fox, T.D. (1993). Inactivation of YME1, a member of the ftsH-SEC18-PAS1-CDC48 family of putative ATPase-encoding genes, causes increased escape of DNA from mitochondria in Saccharomyces cerevisiae. Mol. Cell. Biol. 13(9), 54185426. [2] Schnall, R., Mannhaupt, G., Stucka, R., Tauer, R., Ehnle, S., Schwarzlose, C., Vetter, I., Feldmann, H. (1994). Identification of a set of yeast genes coding for a novel family of putative ATPases with high similarity to constituents of the 26S protease complex. Yeast 10(9), 11411155. [3] Nakai, T., Yasuhara, T., Fujiki, Y., Ohashi, A. (1995). Multiple genes, including a member of the AAA family, are essential for the degradation of unassembled subunit 2 of cytochrome c oxidase in yeast mitochondria. Mol. Cell. Biol. 15, 44414452. [4] Leonhard, K., Herrmann, J.M., Stuart, R.A., Mannhaupt, G., Neupert, W., Langer, T. (1996). AAA proteases with catalytic sites on opposite membrane surfaces comprise a proteolytic system for the ATP-dependent degradation of inner membrane proteins in mitochondria. EMBO J. 15, 42184229. [5] Nakai, T., Mera, Y., Yasuhara, T., Ohashi, A. (1994). Divalent metal ion-dependent mitochondrial degradation of unassembled subunits 2 and 3 of cytochrome c oxidase. J. Biochem. (Tokyo) 116 (4), 752758. [6] Pearce, D.A., Sherman, F. (1995). Diminished degradation of yeast cytochrome c by interactions with its physiological partners. Proc. Natl. Acad. Sci. USA 92, 37353739. [7] Fiumera, H.L., Dunham, M.J., Saracco, S.A., Butler, C.A., Kelly, J.A., Fox, T.D. (2009). Translocation and assembly of mitochondrially coded Saccharomyces cerevisiae cytochrome c oxidase subunit Cox2 by Oxa1 and Yme1 in the absence of Cox18. Genetics 182(2), 519528. [8] Coppola, M., Pizzigoni, A., Banfi, S., Casari, G., Bassi, M.T., Incerti, B. (2000). Identification and characterization of YME1L1, a novel paraplegin related gene. Genomics 66, 4854. [9] Song, Z., Chen, H., Fiket, M., Alexander, C., Chan, D.C. (2007). OPA1 processing controls mitochondrial fusion and is regulated by mRNA splicing, membrane potential, and Yme1L. J. Cell Biol. 178(5), 749755. [10] Juhola, M.K., Shah, Z.H., Grivell, L.A., Jacobs, H.T. (2000). The mitochondrial inner membrane AAA metalloprotease family in metazoans. FEBS Lett. 481, 9195. [11] Urantowka, A., Knorpp, C., Olczak, T., Kolodziejczak, M., Janska, H. (2005). Plant mitochondria contain at least two i-AAAlike complexes. Plant. Mol. Biol. 59(2), 239252. [12] Shah, Z.H., Hakkaart, G.A.J., Arku, B., DeJong, L., Van der Speck, H., Grivell, L., Jacobs, H.T. (2000). The human homologue of the yeast mitochondrial AAA metalloprotease Yme1p complements a yeast yme1 disruptant. FEBS Lett. 478, 267270. [13] Leonhard, K., Stiegler, A., Neupert, W., Langer, T. (1999). Chaperone-like activity of the AAA domain of the yeast Yme1 AAA protease. Nature 398, 348351.
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[14] Leonhard, K., Guiard, B., Pellechia, G., Tzagoloff, A., Neupert, W., Langer, T. (2000). Membrane protein degradation by AAA proteases in mitochondria: extraction of substrates from either membrane surface. Mol. Cell 5, 629638. [15] Langklotz, S., Baumann, U., Narberhaus, F. (2011). Structure and function of the bacterial AAA protease FtsH. Biochim. Biophys. Acta 1823, 4048. [16] Bieniossek, C., Schalch, T., Bumann, M., Meister, M., Meier, R., Baumann, U. (2006). The molecular architecture of the metalloprotease FtsH. Proc. Natl. Acad. Sci. USA 103, 30663071. [17] Dunn, C.D., Lee, M.S., Spencer, F.A., Jensen, R.E. (2006). A genomewide screen for petite-negative yeast strains yields a new subunit of the i-AAA protease complex. Mol. Biol. Cell 17, 213226. [18] Lemaire, C., Hamel, P., Velours, J., Dujardin, G. (2000). Absence of the mitochondrial AAA protease Yme1p restores FO-ATPase subunit accumulation in an oxa1 deletion mutant of Saccharomyces cerevisiae. J. Biol. Chem. 275, 2347123475. [19] Pearce, D.A., Sherman, F. (1995). Degradation of cytochrome oxidase subunits in mutants of yeast lacking cytochrome c and suppression of the degradation by mutation of yme1. J. Biol. Chem. 270(35), 14. [20] Kambacheld, M., Augustin, S., Tatsuta, T., Muller, S., Langer, T. (2005). Role of the novel metallopeptidase Mop112 and saccharolysin for the complete degradation of proteins residing in different subcompartments of mitochondria. J. Biol. Chem. 280(20), 2013220139. [21] Steglich, G., Neupert, W., Langer, T. (1999). Prohibitins regulate membrane protein degradation by the m-AAA protease in mitochondria. Mol. Cell. Biol. 19, 34353442. [22] Graef, M., Seewald, G., Langer, T. (2007). Substrate recognition by AAA1 ATPases: Distinct substrate binding modes in the ATPdependent protease Yme1 of the mitochondrial intermembrane space. Mol. Cell. Biol. 27(2), 24762485. [23] Bione, S., D’Adamo, P., Maestrini, E., Gedeon, A.K., Bolhuis, P.A., Toniolo, D. (1996). A novel X-linked gene, G4.5, is responsible for Barth syndrome. Nat. Genet. 12(4), 385389. [24] Claypool, S.M., McCaffery, J.M., Koehler, C.M. (2006). Mitochondrial mislocalization and altered assembly of a cluster of Barth syndrome mutant tafazzins. J. Cell. Biol. 174(3), 379390. [25] Potting, C., Wilmes, C., Engmann, T., Osman, C., Langer, T. (2010). Regulation of mitochondrial phospholipids by Ups1/ PRELI-like proteins depends on proteolysis and Mdm35. EMBO J. 29(17), 28882898. [26] Nebauer, R., Schuiki, I., Kulterer, B., Trajanoski, Z., Daum, G. (2007). The phosphatidylethanolamine level of yeast mitochondria is affected by the mitochondrial components Oxa1p and Yme1p. FEBS J. 274, 61806190. [27] Ehses, S., Raschke, I., Mancuso, G., Bernacchia, A., Geimer, S., Tondera, D., Martinou, J.C., Westermann, B., Rugarli, E.I., Langer, T. (2009). Regulation of OPA1 processing and mitochondrial fusion by m-AAA protease isoenzymes and OMA1. J. Cell. Biol. 187(7), 10231036. [28] Tatsuta, T., Langer, T. (2008). Quality control of mitochondria: protection against neurodegeneration and ageing. EMBO J. 27(2), 306314. [29] McQuibban, G.A., Saurya, S., Freeman, M. (2003). Mitochondrial membrane remodelling regulated by a conserved rhomboid protease. Nature 423(6939), 537541.
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[30] Griparic, L., Kanazawa, T., van der Bliek, A.M. (2007). Regulation of the mitochondrial dynamin-like protein Opa1 by proteolytic cleavage. J. Cell. Biol. 178(5), 757764. [31] Ishihara, N., Fujita, Y., Oka, T., Mihara, K. (2006). Regulation of mitochondrial morphology through proteolytic cleavage of OPA1. EMBO J. 25, 29662977. [32] Duvezin-Caubet, S., Jagasia, R., Wagener, J., Hofmann, S., Trifunovic, A., Hansson, A., Chomyn, A., Bauer, M.F., Attardi, G., Larsson, N.G., Neupert, W., Reichert, A.S. (2006). Proteolytic processing of OPA1 links mitochondrial dysfunction to alterations in mitochondrial morphology. J. Biol. Chem. 281(49), 3797237979. [33] Head, B., Griparic, L., Amiri, M., Gandre-Babbe, S., van der Bliek, A.M. (2009). Inducible proteolytic inactivation of OPA1 mediated by the OMA1 protease in mammalian cells. J. Cell. Biol. 187(7), 959966. [34] Rainey, R.N., Glavin, J.D., Chen, H.W., French, S.W., Teitell, M.A., Koehler, C.M. (2006). A new function in translocation for the mitochondrial i-AAA Protease Yme1: Import of polynucleotide phosphorylase into the intermembrane Space. Mol. Cell. Biol. 26(22), 84888497. [35] Neuwald, A.F., Aravind, L., Spouge, J.L., Koonin, E.V. (1999). AAA1 : A class of chaperone-like ATPases associated with the assembly, operation, and disassembly of protein complexes. Genome Res. 9, 2743. [36] Lee, S., Augustin, S., Tatsuta, T., Gerdes, F., Langer, T., Tsai, F.T. (2011). Electron cryomicroscopy structure of a membrane-anchored mitochondrial AAA protease. J. Biol. Chem. 286(6), 44044411. [37] Hwang, D.K., Claypool, S.M., Leuenberger, D., Tienson, H.L., Koehler, C.M. (2007). Tim54p connects inner membrane assembly and proteolytic pathways in the mitochondrion. J. Cell. Biol. 178, 11611175. [38] Dunn, C.D., Tamura, Y., Sesaki, H., Jensen, R.E. (2008). Mgr3p and Mgr1p are adaptors for the mitochondrial i-AAA protease complex. Mol. Biol. Cell 19(12), 53875397.
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[39] Taylor, R.W., Turnbull, D.M. (2005). Mitochondrial DNA mutations in human disease. Nat. Rev. Genet. 6(5), 389402. [40] Soto, C. (2003). Unfolding the role of protein misfolding in neurodegenerative diseases. Nat. Rev. Neurosci. 4(1), 4960. [41] Casari, G., De-Fusco, M., Ciarmatori, S., Zeviani, M., Mora, M., Fernandez, P., DeMichele, G., Filla, A., Cocozza, S., Marconi, R., Durr, A., Fontaine, B., Ballabio, A. (1998). Spastic paraplegia and OXPHOS impairment caused by mutations in paraplegin, a nuclear-encoded mitochondrial metalloprotease. Cell 93, 973983. [42] Di Bella, D., Lazzaro, F., Brusco, A., Plumari, M., Battaglia, G., Pastore, A., Finardi, A., Cagnoli, C., Tempia, F., Frontali, M., Veneziano, L., Sacco, T., Boda, E., Brussino, A., Bonn, F., Castellotti, B., Baratta, S., Mariotti, C., Gellera, C., Fracasso, V., Magri, S., Langer, T., Plevani, P., Di Donato, S., MuziFalconi, M., Taroni, F. (2010). Mutations in the mitochondrial protease gene AFG3L2 cause dominant hereditary ataxia SCA28. Nat. Genet. 42(4), 313321. [43] Alexander, C., Votruba, M., Pesch, U.E., Thiselton, D.L., Mayer, S., Moore, A., Rodriguez, M., Kellner, U., Leo-Kottler, B., Auburger, G., Bhattacharya, S.S., Wissinger, B. (2000). OPA1, encoding a dynaminrelated GTPase, is mutated in autosomal dominant optic atrophy linked to chromosome 3q28. Nat. Genet. 26, 211215. [44] Manon, S., Priault, M., Camougrand, N. (2001). Mitochondrial AAA-type protease Yme1p is involved in Bax effects on cytochrome c oxidase. Biochem. Biophys. Res. Commun. 289(5), 13141319. [45] Hanekamp, T., Thorsness, P.E. (1999). YNT20, a bypass suppressor of yme1 yme2, encodes a putative 30 50 -exonuclease localized in mitochondria of Saccharomyces cerevisiae. Curr. Genet. 34, 438448. [46] Coenen, M.J., Smeitink, J.A., Smeets, R., Trijbels, F.J., van den Heuvel, L.P. (2005). Mutation detection in four candidate genes (OXA1L, MRS2L, YME1L and MIPEP) for combined deficiencies in the oxidative phosphorylation system. J. Inherit. Metab. Dis. 28 (6), 10911097.
Timothy Wai Institute for Genetics, Center for Molecular Medicine (CMMC), Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Zuelpicher Str. 47a, 50674 Cologne, Germany; Max-Planck-Institute for Biology of Aging, 50931 Cologne, Germany. Email: [email protected]
Thomas Langer Institute for Genetics, Center for Molecular Medicine (CMMC), Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Zuelpicher Str. 47a, 50674 Cologne, Germany; Max-Planck-Institute for Biology of Aging, 50931 Cologne, Germany. Email: [email protected] Handbook of Proteolytic Enzymes, 3rd Edn ISBN: 978-0-12-382219-2
© 2013 Elsevier Ltd. All rights reserved. DOI: http://dx.doi.org/10.1016/B978-0-12-382219-2.00146-0