Isolation and Identification of a Novel Mitochondrial Metalloprotease (PreP) That Degrades Targeting Presequences in Plants

Ståhl, Anna; Moberg, Per; Ytterberg, A. Jimmy; Panfilov, Oleg; Löwenhielm, Helena Brockenhuus von; Nilsson, Fred; Glaser, Elzbieta

doi:10.1074/jbc.m205500200

Cited by 115 publications

(88 citation statements)

References 80 publications

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“…17). PreP initially was identified in plant mitochondria as the protease responsible for the degradation of the presequence of the ATPase beta subunit (pF 1 β) and the chloroplastic transit peptide of the small subunit of ribulose-1,5-bisphosphate carboxylase oxygenase (18,19). Consistent with this result, A. thaliana PreP (AtPreP) was shown to have a dual localization in mitochondrial matrix and chloroplastic stroma (18,20).…”

supporting

confidence: 66%

Organellar oligopeptidase (OOP) provides a complementary pathway for targeting peptide degradation in mitochondria and chloroplasts

Kmiec¹,

Teixeira²,

Berntsson³

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

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104

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Both mitochondria and chloroplasts contain distinct proteolytic systems for precursor protein processing catalyzed by the mitochondrial and stromal processing peptidases and for the degradation of targeting peptides catalyzed by presequence protease. Here, we have identified and characterized a component of the organellar proteolytic systems in Arabidopsis thaliana, the organellar oligopeptidase, OOP (At5g65620). OOP belongs to the M3A family of peptidedegrading metalloproteases. Using two independent in vivo methods, we show that the protease is dually localized to mitochondria and chloroplasts. Furthermore, we localized the OPP homolog At5g10540 to the cytosol. Analysis of peptide degradation by OOP revealed substrate size restriction from 8 to 23 aa residues. Short mitochondrial targeting peptides (presequence of the ribosomal protein L29 and presequence of 1-aminocyclopropane-1-carboxylic acid deaminase 1) and N-and C-terminal fragments derived from the presequence of the ATPase beta subunit ranging in size from 11 to 20 aa could be degraded. MS analysis showed that OOP does not exhibit a strict cleavage pattern but shows a weak preference for hydrophobic residues (F/L) at the P1 position. The crystal structures of OOP, at 1.8-1.9 Å, exhibit an ellipsoidal shape consisting of two major domains enclosing the catalytic cavity of 3,000 Å 3 . The structural and biochemical data suggest that the protein undergoes conformational changes to allow peptide binding and proteolysis. Our results demonstrate the complementary role of OOP in targeting-peptide degradation in mitochondria and chloroplasts.

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supporting

confidence: 66%

Organellar oligopeptidase (OOP) provides a complementary pathway for targeting peptide degradation in mitochondria and chloroplasts

Kmiec¹,

Teixeira²,

Berntsson³

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

104

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“…However, a complete proteolytic breakdown of mitochondrial proteins to amino acid residues has already been observed in early studies pointing to the presence of oligopeptidases in mitochondria (21). Until now only two ATP-independent mitochondrial oligopeptidases have been identified, a thimet oligopeptidase localized in the intermembrane space of yeast and human mitochondria (22,23) and the presequencedegrading metallopeptidase PreP in plant mitochondria (24). Other known peptidases act as processing enzymes cleaving off mitochondrial targeting sequences from newly imported preproteins (25).…”

mentioning

confidence: 99%

Oma1, a Novel Membrane-bound Metallopeptidase in Mitochondria with Activities Overlapping with the m-AAA Protease

Käser

Kambacheld

Kisters‐Woike

et al. 2003

Journal of Biological Chemistry

139

147

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The integrity of the inner membrane of mitochondria is maintained by a membrane-embedded quality control system that ensures the removal of misfolded membrane proteins. Two ATP-dependent AAA proteases with catalytic sites at opposite membrane surfaces are key components of this proteolytic system. Here we describe the identification of a novel conserved metallopeptidase that exerts activities overlapping with the m-AAA protease and was therefore termed Oma1. Both peptidases are integral parts of the inner membrane and mediate the proteolytic breakdown of a misfolded derivative of the polytopic inner membrane protein Oxa1. The m-AAA protease cleaves off the matrix-exposed C-terminal domain of Oxa1 and processively degrades its transmembrane domain. In the absence of the m-AAA protease, proteolysis of Oxa1 is mediated in an ATP-independent manner by Oma1 and a yet unknown peptidase resulting in the accumulation of N-and C-terminal proteolytic fragments. Oma1 exposes its proteolytic center to the matrix side; however, mapping of Oma1 cleavage sites reveals clipping of Oxa1 in loop regions at both membrane surfaces. These results identify Oma1 as a novel component of the quality control system in the inner membrane of mitochondria. Proteins homologous to Oma1 are present in higher eukaryotic cells, eubacteria and archaebacteria, suggesting that Oma1 is the founding member of a conserved family of membrane-embedded metallopeptidases.The majority of mitochondrial proteins is nuclear encoded and synthesized at cytosolic ribosomes. Import into mitochondria is mediated by various protein translocases in the outer and inner membrane that allow the passage of preproteins only in a largely unfolded conformation (1, 2). Folding and assembly of mitochondrial proteins must therefore occur inside mitochondria. Little is known about the efficiency of this process, but it is clear that mitochondria, as other organelles, harbor a quality control system that ensures the recognition and removal of non-native polypeptides, preventing their potentially harmful accumulation within the organelle (3). Notably, a functional impairment of components of this system leads to neurodegeneration in various forms of hereditary spastic paraplegia, illustrating the importance of protein quality control for mitochondrial function (4, 5).Molecular chaperone proteins and ATP-dependent proteases present in different subcompartments of mitochondria maintain protein quality control within the organelle (3). In line with the endosymbiotic origin of mitochondria, many of these components exhibit significant homology to bacterial proteins. ATP-dependent proteases homologous to Lon proteases (6 -8) and, at least in some organisms, Clp proteases (9, 10) have been identified in the mitochondrial matrix space, whereas the inner membrane harbors two AAA proteases homologous to bacterial FtsH proteases (11). These membrane-embedded peptidases were termed m-and i-AAA proteases to indicate their different topology in the inner membrane; the m-AAA protease is activ...

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“…The isolated targeting signal of a mitochondrial precursor remained stable in the presence of MPP (36). When a targeting signal was produced during processing in the mitochondrial matrix, however, its rapid hydrolysis by a novel peptidase occurred without detectable intermediates (37). However, in human ER membranes and E. coli inner membranes, proteolytic enzymes have been identified that internally cleave targeting signals after they have been removed from precursor proteins by signal peptidases (38,39).…”

Section: Discussionmentioning

confidence: 99%

Structural Properties of the Chloroplast Stromal Processing Peptidase Required for Its Function in Transit Peptide Removal

Richter

Lamppa

2003

Journal of Biological Chemistry

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The stromal processing peptidase (SPP) catalyzes removal of transit peptides from a diversity of precursor proteins imported into chloroplasts. SPP contains an HXXEH zinc-binding motif characteristic of members of the metallopeptidase family M16. We previously found that the three steps of precursor processing by SPP (i.e. transit peptide binding, removal, and conversion to a degradable subfragment) are mediated by features that reside in the C-terminal 10 -15 residues of the transit peptide. In this study, we performed a mutational analysis of SPP to identify structural elements that determine its function. SPP loses the ability to proteolytically remove the transit peptide when residues of the HXXEH motif, found in an N-terminal region, are mutated. Deletion of 240 amino acids from its C terminus also abolishes activity. Interestingly, however, SPP can still carry out the initial binding step, recognizing the Cterminal residues of the transit peptide. Hence, transit peptide binding and removal are two separable steps of the overall processing reaction. Transit peptide conversion to a subfragment also depends on the HXXEH motif. The precursor of SPP, containing an unusually long transit peptide itself, is not proteolytically active. Thus, the SPP precursor is synthesized as a latent form of the metallopeptidase.Chloroplast biogenesis and function depends on the import of a large diversity of proteins from the cytoplasm. These proteins are synthesized as precursors containing an N-terminal targeting signal, called the transit peptide, that mediates multiple steps in the import pathway (for reviews, see Refs. 1-4). Whereas the chloroplast is unique to the plant cell, the mitochondrion and the endoplasmic reticulum (ER) 1 are two other major eukaryotic organelles that depend on massive protein translocation mediated by N-terminal targeting signals. It has been predicted for Arabidopsis thaliana that up to 11,000 different precursor proteins may be targeted to these three organelles, ϳ3,500 to the chloroplast alone (5). Distinct properties of the targeting signals ensure organelle-specific sorting and translocation of the precursor proteins. Ultimately, highly specialized proteolytic enzymes that reside in each organelle remove the targeting signals (for a review, see Ref. 6).We have identified a general stromal processing peptidase (SPP) that removes transit peptides from an array of precursors involved in different biosynthetic pathways and destined for different chloroplast compartments (7). The activity of SPP, which is a soluble, monomeric enzyme, depends on metal ions (8). Analysis of a full-length SPP cDNA from pea revealed that the enzyme contains an HXXEH zinc-binding motif characteristic of members of the metallopeptidase family M16, such as pitrilysin, insulin-degrading enzyme, and the ␤-subunit of the mitochondrial processing peptidase (MPP) (9, 10). Conservation extends beyond the zinc-binding motif, where 25-30% identity is found in an N-terminal region of ϳ200 residues of SPP. The residues of the HXX...

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Isolation and Identification of a Novel Mitochondrial Metalloprotease (PreP) That Degrades Targeting Presequences in Plants

Cited by 115 publications

References 80 publications

Organellar oligopeptidase (OOP) provides a complementary pathway for targeting peptide degradation in mitochondria and chloroplasts

Organellar oligopeptidase (OOP) provides a complementary pathway for targeting peptide degradation in mitochondria and chloroplasts

Oma1, a Novel Membrane-bound Metallopeptidase in Mitochondria with Activities Overlapping with the m-AAA Protease

Structural Properties of the Chloroplast Stromal Processing Peptidase Required for Its Function in Transit Peptide Removal

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