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Author: Zahedi, René P. × DDC: 570 × Version: publishedVersion × WGL Institute: ISAS ×

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Now showing 1 - 4 of 4
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    Identification of cleavage sites and substrate proteins for two mitochondrial intermediate peptidases in Arabidopsis thaliana
    (Oxford : Oxford University Press, 2015) Carrie, Chris; Venne, A. Saskia; Zahedi, René P.; Soll, Jürgen
    Most mitochondrial proteins contain an N-terminal targeting signal that is removed by specific proteases following import. In plant mitochondria, only mitochondrial processing peptidase (MPP) has been characterized to date. Therefore, we sought to determine the substrates and cleavage sites of the Arabidopsis thaliana homologues to the yeast Icp55 and Oct1 proteins, using the newly developed ChaFRADIC method for N-terminal protein sequencing. We identified 88 and seven putative substrates for Arabidopsis ICP55 and OCT1, respectively. It was determined that the Arabidopsis ICP55 contains an almost identical cleavage site to that of Icp55 from yeast. However, it can also remove a far greater range of amino acids. The OCT1 substrates from Arabidopsis displayed no consensus cleavage motif, and do not contain the classical –10R motif identified in other eukaryotes. Arabidopsis OCT1 can also cleave presequences independently, without the prior cleavage of MPP. It was concluded that while both OCT1 and ICP55 were probably acquired early on in the evolution of mitochondria, their substrate profiles and cleavage sites have either remained very similar or diverged completely.
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    Current strategies and findings in clinically relevant post-translational modification-specific proteomics
    (Milton Park : Taylor & Francis, 2015) Pagel, Oliver; Loroch, Stefan; Sickmann, Albert; Zahedi, René P.
    Mass spectrometry-based proteomics has considerably extended our knowledge about the occurrence and dynamics of protein post-translational modifications (PTMs). So far, quantitative proteomics has been mainly used to study PTM regulation in cell culture models, providing new insights into the role of aberrant PTM patterns in human disease. However, continuous technological and methodical developments have paved the way for an increasing number of PTM-specific proteomic studies using clinical samples, often limited in sample amount. Thus, quantitative proteomics holds a great potential to discover, validate and accurately quantify biomarkers in body fluids and primary tissues. A major effort will be to improve the complete integration of robust but sensitive proteomics technology to clinical environments. Here, we discuss PTMs that are relevant for clinical research, with a focus on phosphorylation, glycosylation and proteolytic cleavage; furthermore, we give an overview on the current developments and novel findings in mass spectrometry-based PTM research.
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    FYCO1 Increase and Effect of Arimoclomol–Treatment in Human VCP–Pathology
    (Basel : MDPI, 2022) Guettsches, Anne-Katrin; Meyer, Nancy; Zahedi, René P.; Evangelista, Teresinha; Muentefering, Thomas; Ruck, Tobias; Lacene, Emmanuelle; Heute, Christoph; Gonczarowska-Jorge, Humberto; Schoser, Benedikt; Krause, Sabine; Hentschel, Andreas; Vorgerd, Matthias; Roos, Andreas
    Dominant VCP–mutations cause a variety of neurological manifestations including inclusion body myopathy with early–onset Paget disease and frontotemporal dementia 1 (IBMPFD). VCP encodes a ubiquitously expressed multifunctional protein that is a member of the AAA+ protein family, implicated in multiple cellular functions ranging from organelle biogenesis to ubiquitin–dependent protein degradation. The latter function accords with the presence of protein aggregates in muscle biopsy specimens derived from VCP–patients. Studying the proteomic signature of VCP–mutant fibroblasts, we identified a (pathophysiological) increase of FYCO1, a protein involved in autophagosome transport. We confirmed this finding applying immunostaining also in muscle biopsies derived from VCP–patients. Treatment of fibroblasts with arimoclomol, an orphan drug thought to restore physiologic cellular protein repair pathways, ameliorated cellular cytotoxicity in VCP–patient derived cells. This finding was accompanied by increased abundance of proteins involved in immune response with a direct impact on protein clearaqnce as well as by elevation of pro–survival proteins as unravelled by untargeted proteomic profiling. Hence, the combined results of our study reveal a dysregulation of FYCO1 in the context of VCP–etiopathology, highlight arimoclomol as a potential drug and introduce proteins targeted by the pre–clinical testing of this drug in fibroblasts.
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    The Caveolin-3 G56S sequence variant of unknown significance: Muscle biopsy findings and functional cell biological analysis
    (Hoboken, NJ : Wiley, 2016) Brauers, Eva; Roos, Andreas; Kollipara, Laxmikanth; Zahedi, René P.; Beckmann, Alf; Mohanadas, Nilane; Bauer, Hartmut; Häusler, Martin; Thoma, Stéphanie; Kress, Wolfram; Senderek, Jan; Weis, Joachim
    Purpose: In the era of next-generation sequencing, we are increasingly confronted with se- quence variants of unknown significance. This phenomenon is also known for variations in Caveolin-3 and can complicate the molecular diagnosis of the disease. Here, we aimed to study the ambiguous character of the G56S Caveolin-3 variant. Experimental design: A comprehensive approach combining genetic and morphological stud- ies of muscle derived from carriers of the G56S Caveolin-3 variant were carried out and linked to biochemical assays (including phosphoblot studies and proteome profiling) and morphological investigations of cultured myoblasts. Results: Muscles showed moderate chronic myopathic changes in all carriers of the variant. Myogenic RCMH cells expressing the G56S Caveolin-3 protein presented irregular Caveolin-3 deposits within the Golgi in addition to a regular localization of the protein to the plasma mem- brane. This result was associated with abnormal findings on the ultra-structural level. Phos- phoblot studies revealed that G56S affects EGFR-signaling. Proteomic profiling demonstrated alterations in levels of physiologically relevant proteins which are indicative for antagonization of G56S Caveolin-3 expression. Remarkably, some proteomic alterations were enhanced by osmotic/mechanical stress. Conclusions and clinical relevance: Our studies suggest that G56S might influence the mani- festation of myopathic changes upon the presence of additional cellular stress burden. Results of our studies moreover improve the current understanding of (genetic) causes of myopathic disorders classified as caveolinopathies.