Two Novel Targeting Peptide Degrading Proteases, PrePs, in Mitochondria and Chloroplasts, so Similar and Still Different

Ståhl, Anna; Nilsson, Stefan; Lundberg, Pontus; Bhushan, Shashi; Biverståhl, Henrik; Moberg, Per; Morisset, M.; Vener, Alexander V.; Mäler, Lena; Langel, Ülo; Glaser, Elzbieta

doi:10.1016/j.jmb.2005.04.023

Cited by 73 publications

(66 citation statements)

References 63 publications

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“…Interestingly, the main difference in subsite specificity between hPreP and IDE on A␤ proteins is that hPreP 1 Å (15). A, structural model of hPreP with A␤ (12)(13)(14)(15)(16)(17) bound to the active site. B, close-up of the active site with residues that differ in AtPreP shown in parentheses.…”

Section: Discussionmentioning

confidence: 99%

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Degradation of the Amyloid β-Protein by the Novel Mitochondrial Peptidasome, PreP

Falkevall

Alikhani

Bhushan

et al. 2006

Journal of Biological Chemistry

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181

177

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Recently we have identified the novel mitochondrial peptidase responsible for degrading presequences and other short unstructured peptides in mitochondria, the presequence peptidase, which we named PreP peptidasome. In the present study we have identified and characterized the human PreP homologue, hPreP, in brain mitochondria, and we show its capacity to degrade the amyloid ␤-protein (A␤). PreP belongs to the pitrilysin oligopeptidase family M16C containing an inverted zincbinding motif. We show that hPreP is localized to the mitochondrial matrix. In situ immuno-inactivation studies in human brain mitochondria using anti-hPreP antibodies showed complete inhibition of proteolytic activity against A␤. We have cloned, overexpressed, and purified recombinant hPreP and its mutant with catalytic base Glu 78 in the inverted zinc-binding motif replaced by Gln. In vitro studies using recombinant hPreP and liquid chromatography nanospray tandem mass spectrometry revealed novel cleavage specificities against A␤-(1-42), A␤-(1-40), and A␤ Arctic, a protein that causes increased protofibril formation an early onset familial variant of Alzheimer disease. In contrast to insulin degrading enzyme, which is a functional analogue of hPreP, hPreP does not degrade insulin but does degrade insulin B-chain. Molecular modeling of hPreP based on the crystal structure at 2.1 Å resolution of AtPreP allowed us to identify Cys 90 and Cys 527 that form disulfide bridges under oxidized conditions and might be involved in redox regulation of the enzyme. Degradation of the mitochondrial A␤ by hPreP may potentially be of importance in the pathology of Alzheimer disease.Several human disorders are associated with the deposition of aggregated peptides. One of them is Alzheimer disease (AD) 4 in which the polymerization of amyloid ␤-protein (A␤) into insoluble fibrils in brain seems to be a pathological event. An extracellular accumulation of A␤ has been the main focus of molecular studies associated with AD (1). However, increasing attention is directed toward intracellular events including the mitochondrial role in AD (2). There are many links between mitochondrial dysfunctions and AD (3, 4). Impairment of mitochondrial energy metabolism and altered cytochrome c oxidase activity are among the earliest detectable defects in AD (5, 6). It has been shown that Alzheimer amyloid precursor protein (APP) 695 is not only targeted to the plasma membrane but also to mitochondria (5). Accumulation of APP in the outer mitochondrial membrane caused dysfunctions and impaired energy metabolism. The active ␥-secretase complex including presenilin, nicastrin, APH-1, and PEN-2, which cleave APP to generate A␤, has been shown to be present in the mitochondrial outer membrane (7). Furthermore, the occurrence of A␤ in mitochondria of AD patients and its direct binding to ABAD (A␤-binding alcohol dehydrogenase, also called ERAB) induces apoptosis and free radical generation in neurons (8). A recent study demonstrated that A␤ is present in the mitochondrial matrix in A...

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Section: Discussionmentioning

confidence: 99%

“…AtPreP has been shown to degrade not only targeting peptides but also other unstructured peptides up to 70 amino acids residues in length but not small proteins (11,12). Furthermore, AtPreP is also present in chloroplasts, and it uses an ambiguous signal for targeting of the protein to both mitochondria and chloroplasts (13).…”

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confidence: 99%

Degradation of the Amyloid β-Protein by the Novel Mitochondrial Peptidasome, PreP

Falkevall

Alikhani

Bhushan

et al. 2006

Journal of Biological Chemistry

Self Cite

181

177

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“…Transit peptides are 26 to 146 amino acids long (Zybailov et al, 2008). Structural and biochemical studies have reported that PreP1 degrades various peptide substrates of 10 to 65 amino acids (Moberg et al, 2003;Ståhl et al, 2005), whereas OOP cleaves peptide fragments ranging from eight to 23 amino acids (Kmiec et al, 2013). Consequently, both proteases are able to function in transit peptide degradation, with OOP acting in parallel or downstream to PreP.…”

Section: Sequential Proteolytic Events For Preprotein Processing and mentioning

confidence: 99%

Chloroplast Proteases: Updates on Proteolysis within and across Suborganellar Compartments

2016

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ORCID IDs: 0000-0003-1718-9121 (Y.K.); 0000-0001-9747-5042 (W.S.).Chloroplasts originated from the endosymbiosis of ancestral cyanobacteria and maintain transcription and translation machineries for around 100 proteins. Most endosymbiont genes, however, have been transferred to the host nucleus, and the majority of the chloroplast proteome is composed of nucleus-encoded proteins that are biosynthesized in the cytosol and then imported into chloroplasts. How chloroplasts and the nucleus communicate to control the plastid proteome remains an important question. Protein-degrading machineries play key roles in chloroplast proteome biogenesis, remodeling, and maintenance. Research in the past few decades has revealed more than 20 chloroplast proteases, which are localized to specific suborganellar locations. In particular, two energy-dependent processive proteases of bacterial origin, Clp and FtsH, are central to protein homeostasis. Processing endopeptidases such as stromal processing peptidase and thylakoidal processing peptidase are involved in the maturation of precursor proteins imported into chloroplasts by cleaving off the amino-terminal transit peptides. Presequence peptidases and organellar oligopeptidase subsequently degrade the cleaved targeting peptides. Recent findings have indicated that not only intraplastidic but also extraplastidic processive protein-degrading systems participate in the regulation and quality control of protein translocation across the envelopes. In this review, we summarize current knowledge of the major chloroplast proteases in terms of type, suborganellar localization, and diversification. We present details of these degradation processes as case studies according to suborganellar compartment (envelope, stroma, and thylakoids). Key questions and future directions in this field are discussed.Over 1 billion years of plastid evolution since the endosymbiosis of ancestral cyanobacteria (Douzery et al., 2004), chloroplast biogenesis has gained complexity, with large sets of the endosymbiont genes being transferred to host nuclear genomes. While only 100 endosymbiont genes remain in the plastid genome, with the corresponding proteins biosynthesized there, the nuclear genes have often gained complexity by duplication and diversification of the original endosymbiotic genes. This complexity raises numerous questions regarding (1) at what level gene expression is coordinately controlled, (2) what molecules coordinate the cross talk between chloroplasts and the nucleus, (3) how proteins get across membranes and become imported into chloroplasts, and (4) how the stoichiometries of nucleus-and chloroplast-encoded subunits within individual chloroplast protein complexes such as photosystems and Rubisco are strictly maintained.Given these questions, chloroplast biogenesis has remained a central subject in plant physiology for the last few decades (Jarvis and López-Juez, 2013). In our view, the aforementioned questions point to the importance of protein homeostasis and posttranslational modificat...

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“…Stromal Zn 2+ -protease PreP1, stromal processing peptidase (SPP), and leucyl aminopeptidase2 (LAP2) were 2.4-to 5.5-fold upregulated (Table II). PreP1 was suggested to be involved in the degradation of cleaved chloroplast transit peptides Ståhl et al, 2005;Glaser et al, 2006), whereas stromal SPP is involved in the transit peptide removal of most nucleus-encoded, chloroplast-targeted proteins Lamppa, 1998, 1999). LAP2 belongs to the family of soluble aminopeptidases (Walling, 2006), and it was recently suggested that LAP2 also moonlights as a chaperone in the chloroplast (Scranton et al, 2012).…”

Section: Effects On Plastid Gene Expression and Protein Homeostasismentioning

confidence: 99%

Modified Clp Protease Complex in the ClpP3 Null Mutant and Consequences for Chloroplast Development and Function in Arabidopsis

Kim

Olinares

et al. 2013

Plant Physiology

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The plastid ClpPRT protease consists of two heptameric rings of ClpP1/ClpR1/ClpR2/ClpR3/ClpR4 (the R-ring) and ClpP3/ ClpP4/ClpP5/ClpP6 (the P-ring) and peripherally associated ClpT1/ClpT2 subunits. Here, we address the contributions of ClpP3 and ClpP4 to ClpPRT core organization and function in Arabidopsis (Arabidopsis thaliana). ClpP4 is strictly required for embryogenesis, similar to ClpP5. In contrast, loss of ClpP3 (clpp3-1) leads to arrest at the hypocotyl stage; this developmental arrest can be removed by supplementation with sucrose or glucose. Heterotrophically grown clpp3-1 can be transferred to soil and generate viable seed, which is surprising, since we previously showed that CLPR2 and CLPR4 null alleles are always sterile and die on soil. Based on native gels and mass spectrometry-based quantification, we show that despite the loss of ClpP3, modified ClpPR core(s) could be formed, albeit at strongly reduced levels. A large portion of ClpPR subunits accumulated in heptameric rings, with overaccumulation of ClpP1/ClpP5/ClpP6 and ClpR3. Remarkably, the association of ClpT1 to the modified Clp core was unchanged. Large-scale quantitative proteomics assays of clpp3-1 showed a 50% loss of photosynthetic capacity and the up-regulation of plastoglobules and all chloroplast stromal chaperone systems. Specific chloroplast proteases were significantly up-regulated, whereas the major thylakoid protease (FtsH1/FtsH2/FtsH5/FtsH8) was clearly unchanged, indicating a controlled protease network response. clpp3-1 showed a systematic decrease of chloroplast-encoded proteins that are part of the photosynthetic apparatus but not of chloroplast-encoded proteins with other functions. Candidate substrates and an explanation for the differential phenotypes between the CLPP3, CLPP4, and CLPP5 null mutants are discussed.

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Two Novel Targeting Peptide Degrading Proteases, PrePs, in Mitochondria and Chloroplasts, so Similar and Still Different

Cited by 73 publications

References 63 publications

Degradation of the Amyloid β-Protein by the Novel Mitochondrial Peptidasome, PreP

Degradation of the Amyloid β-Protein by the Novel Mitochondrial Peptidasome, PreP

Chloroplast Proteases: Updates on Proteolysis within and across Suborganellar Compartments

Modified Clp Protease Complex in the ClpP3 Null Mutant and Consequences for Chloroplast Development and Function in Arabidopsis

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