Publications by authors named "Tim König"

13 Publications

  • Page 1 of 1

Phosphoproteomics of the developing heart identifies PERM1 - An outer mitochondrial membrane protein.

J Mol Cell Cardiol 2021 05 5;154:41-59. Epub 2021 Feb 5.

CECAD Research Center, Institute for Genetics, University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany; Center for Molecular Medicine (CMMC), University of Cologne, 50931 Cologne, Germany. Electronic address:

Heart development relies on PTMs that control cardiomyocyte proliferation, differentiation and cardiac morphogenesis. We generated a map of phosphorylation sites during the early stages of cardiac postnatal development in mice; we quantified over 10,000 phosphorylation sites and 5000 proteins that were assigned to different pathways. Analysis of mitochondrial proteins led to the identification of PGC-1- and ERR-induced regulator in muscle 1 (PERM1), which is specifically expressed in skeletal muscle and heart tissue and associates with the outer mitochondrial membrane. We demonstrate PERM1 is subject to rapid changes mediated by the UPS through phosphorylation of its PEST motif by casein kinase 2. Ablation of Perm1 in mice results in reduced protein expression of lipin-1 accompanied by accumulation of specific phospholipid species. Isolation of Perm1-deficient mitochondria revealed significant downregulation of mitochondrial transport proteins for amino acids and carnitines, including SLC25A12/13/29/34 and CPT2. Consistently, we observed altered levels of various lipid species, amino acids, and acylcarnitines in Perm1 mitochondria. We conclude that the outer mitochondrial membrane protein PERM1 regulates homeostasis of lipid and amino acid metabolites in mitochondria.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.yjmcc.2021.01.010DOI Listing
May 2021

Loss of the mitochondrial -AAA protease YME1L leads to ocular dysfunction and spinal axonopathy.

EMBO Mol Med 2019 01;11(1)

Max-Planck-Institute for Biology of Ageing, Cologne, Germany

Disturbances in the morphology and function of mitochondria cause neurological diseases, which can affect the central and peripheral nervous system. The -AAA protease YME1L ensures mitochondrial proteostasis and regulates mitochondrial dynamics by processing of the dynamin-like GTPase OPA1. Mutations in cause a multi-systemic mitochondriopathy associated with neurological dysfunction and mitochondrial fragmentation but pathogenic mechanisms remained enigmatic. Here, we report on striking cell-type-specific defects in mice lacking YME1L in the nervous system. YME1L-deficient mice manifest ocular dysfunction with microphthalmia and cataracts and develop deficiencies in locomotor activity due to specific degeneration of spinal cord axons, which relay proprioceptive signals from the hind limbs to the cerebellum. Mitochondrial fragmentation occurs throughout the nervous system and does not correlate with the degenerative phenotype. Deletion of restores tubular mitochondria but deteriorates axonal degeneration in the absence of YME1L, demonstrating that impaired mitochondrial proteostasis rather than mitochondrial fragmentation causes the observed neurological defects.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.15252/emmm.201809288DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6328943PMC
January 2019

PARL partitions the lipid transfer protein STARD7 between the cytosol and mitochondria.

EMBO J 2018 02 4;37(4). Epub 2018 Jan 4.

Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany

Intramembrane-cleaving peptidases of the rhomboid family regulate diverse cellular processes that are critical for development and cell survival. The function of the rhomboid protease PARL in the mitochondrial inner membrane has been linked to mitophagy and apoptosis, but other regulatory functions are likely to exist. Here, we identify the START domain-containing protein STARD7 as an intramitochondrial lipid transfer protein for phosphatidylcholine. We demonstrate that PARL-mediated cleavage during mitochondrial import partitions STARD7 to the cytosol and the mitochondrial intermembrane space. Negatively charged amino acids in STARD7 serve as a sorting signal allowing mitochondrial release of mature STARD7 upon cleavage by PARL On the other hand, membrane insertion of STARD7 mediated by the TIM23 complex promotes mitochondrial localization of mature STARD7. Mitochondrial STARD7 is necessary and sufficient for the accumulation of phosphatidylcholine in the inner membrane and for the maintenance of respiration and cristae morphogenesis. Thus, PARL preserves mitochondrial membrane homeostasis via STARD7 processing and is emerging as a critical regulator of protein localization between mitochondria and the cytosol.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.15252/embj.201797909DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5813258PMC
February 2018

Acylglycerol Kinase Mutated in Sengers Syndrome Is a Subunit of the TIM22 Protein Translocase in Mitochondria.

Mol Cell 2017 Aug 14;67(3):471-483.e7. Epub 2017 Jul 14.

Institute for Genetics, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine (CMMC), University of Cologne, Cologne, Germany. Electronic address:

Mutations in mitochondrial acylglycerol kinase (AGK) cause Sengers syndrome, which is characterized by cataracts, hypertrophic cardiomyopathy, and skeletal myopathy. AGK generates phosphatidic acid and lysophosphatidic acid, bioactive phospholipids involved in lipid signaling and the regulation of tumor progression. However, the molecular mechanisms of the mitochondrial pathology remain enigmatic. Determining its mitochondrial interactome, we have identified AGK as a constituent of the TIM22 complex in the mitochondrial inner membrane. AGK assembles with TIMM22 and TIMM29 and supports the import of a subset of multi-spanning membrane proteins. The function of AGK as a subunit of the TIM22 complex does not depend on its kinase activity. However, enzymatically active AGK is required to maintain mitochondrial cristae morphogenesis and the apoptotic resistance of cells. The dual function of AGK as lipid kinase and constituent of the TIM22 complex reveals that disturbances in both phospholipid metabolism and mitochondrial protein biogenesis contribute to the pathogenesis of Sengers syndrome.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.molcel.2017.06.013DOI Listing
August 2017

Joint deformable liver registration and bias field correction for MR-guided HDR brachytherapy.

Int J Comput Assist Radiol Surg 2017 Dec 6;12(12):2169-2180. Epub 2017 Jul 6.

Department of Radiology, University Hospital Cologne, Kerpener Straße 62, 50937, Cologne, Germany.

Purpose: In interstitial high-dose rate brachytherapy, liver cancer is treated by internal radiation, requiring percutaneous placement of applicators within or close to the tumor. To maximize utility, the optimal applicator configuration is pre-planned on magnetic resonance images. The pre-planned configuration is then implemented via a magnetic resonance-guided intervention. Mapping the pre-planning information onto interventional data would reduce the radiologist's cognitive load during the intervention and could possibly minimize discrepancies between optimally pre-planned and actually placed applicators.

Methods: We propose a fast and robust two-step registration framework suitable for interventional settings: first, we utilize a multi-resolution rigid registration to correct for differences in patient positioning (rotation and translation). Second, we employ a novel iterative approach alternating between bias field correction and Markov random field deformable registration in a multi-resolution framework to compensate for non-rigid movements of the liver, the tumors and the organs at risk. In contrast to existing pre-correction methods, our multi-resolution scheme can recover bias field artifacts of different extents at marginal computational costs.

Results: We compared our approach to deformable registration via B-splines, demons and the SyN method on 22 registration tasks from eleven patients. Results showed that our approach is more accurate than the contenders for liver as well as for tumor tissues. We yield average liver volume overlaps of 94.0 ± 2.7% and average surface-to-surface distances of 2.02 ± 0.87 mm and 3.55 ± 2.19 mm for liver and tumor tissue, respectively. The reported distances are close to (or even below) the slice spacing (2.5 - 3.0 mm) of our data. Our approach is also the fastest, taking 35.8 ± 12.8 s per task.

Conclusion: The presented approach is sufficiently accurate to map information available from brachytherapy pre-planning onto interventional data. It is also reasonably fast, providing a starting point for computer-aidance during intervention.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s11548-017-1633-2DOI Listing
December 2017

Somatic increase of CCT8 mimics proteostasis of human pluripotent stem cells and extends C. elegans lifespan.

Nat Commun 2016 11 28;7:13649. Epub 2016 Nov 28.

Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph Stelzmann Strasse 26, Cologne 50931, Germany.

Human embryonic stem cells can replicate indefinitely while maintaining their undifferentiated state and, therefore, are immortal in culture. This capacity may demand avoidance of any imbalance in protein homeostasis (proteostasis) that would otherwise compromise stem cell identity. Here we show that human pluripotent stem cells exhibit enhanced assembly of the TRiC/CCT complex, a chaperonin that facilitates the folding of 10% of the proteome. We find that ectopic expression of a single subunit (CCT8) is sufficient to increase TRiC/CCT assembly. Moreover, increased TRiC/CCT complex is required to avoid aggregation of mutant Huntingtin protein. We further show that increased expression of CCT8 in somatic tissues extends Caenorhabditis elegans lifespan in a TRiC/CCT-dependent manner. Ectopic expression of CCT8 also ameliorates the age-associated demise of proteostasis and corrects proteostatic deficiencies in worm models of Huntington's disease. Our results suggest proteostasis is a common principle that links organismal longevity with hESC immortality.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/ncomms13649DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5133698PMC
November 2016

The membrane scaffold SLP2 anchors a proteolytic hub in mitochondria containing PARL and the i-AAA protease YME1L.

EMBO Rep 2016 12 13;17(12):1844-1856. Epub 2016 Oct 13.

Institute for Genetics Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), and University of Cologne, Cologne, Germany

The SPFH (stomatin, prohibitin, flotillin, HflC/K) superfamily is composed of scaffold proteins that form ring-like structures and locally specify the protein-lipid composition in a variety of cellular membranes. Stomatin-like protein 2 (SLP2) is a member of this superfamily that localizes to the mitochondrial inner membrane (IM) where it acts as a membrane organizer. Here, we report that SLP2 anchors a large protease complex composed of the rhomboid protease PARL and the i-AAA protease YME1L, which we term the SPY complex (for SLP2-PARL-YME1L). Association with SLP2 in the SPY complex regulates PARL-mediated processing of PTEN-induced kinase PINK1 and the phosphatase PGAM5 in mitochondria. Moreover, SLP2 inhibits the stress-activated peptidase OMA1, which can bind to SLP2 and cleaves PGAM5 in depolarized mitochondria. SLP2 restricts OMA1-mediated processing of the dynamin-like GTPase OPA1 allowing stress-induced mitochondrial hyperfusion under starvation conditions. Together, our results reveal an important role of SLP2 membrane scaffolds for the spatial organization of IM proteases regulating mitochondrial dynamics, quality control, and cell survival.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.15252/embr.201642698DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5283581PMC
December 2016

The m-AAA Protease Associated with Neurodegeneration Limits MCU Activity in Mitochondria.

Mol Cell 2016 10 15;64(1):148-162. Epub 2016 Sep 15.

Institute for Genetics, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine (CMMC), University of Cologne, 50931 Cologne, Germany; Max Planck Institute for Biology of Aging, 50931 Cologne, Germany. Electronic address:

Mutations in subunits of mitochondrial m-AAA proteases in the inner membrane cause neurodegeneration in spinocerebellar ataxia (SCA28) and hereditary spastic paraplegia (HSP7). m-AAA proteases preserve mitochondrial proteostasis, mitochondrial morphology, and efficient OXPHOS activity, but the cause for neuronal loss in disease is unknown. We have determined the neuronal interactome of m-AAA proteases in mice and identified a complex with C2ORF47 (termed MAIP1), which counteracts cell death by regulating the assembly of the mitochondrial Ca uniporter MCU. While MAIP1 assists biogenesis of the MCU subunit EMRE, the m-AAA protease degrades non-assembled EMRE and ensures efficient assembly of gatekeeper subunits with MCU. Loss of the m-AAA protease results in accumulation of constitutively active MCU-EMRE channels lacking gatekeeper subunits in neuronal mitochondria and facilitates mitochondrial Ca overload, mitochondrial permeability transition pore opening, and neuronal death. Together, our results explain neuronal loss in m-AAA protease deficiency by deregulated mitochondrial Ca homeostasis.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.molcel.2016.08.020DOI Listing
October 2016

Loss of CLPP alleviates mitochondrial cardiomyopathy without affecting the mammalian UPRmt.

EMBO Rep 2016 07 6;17(7):953-64. Epub 2016 May 6.

Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD) and Institute for Mitochondrial Diseases and Aging, Medical Faculty, University of Cologne, Cologne, Germany

The mitochondrial matrix protease CLPP plays a central role in the activation of the mitochondrial unfolded protein response (UPR(mt)) in Caenorhabditis elegans Far less is known about mammalian UPR(mt) signaling, although similar roles were assumed for central players, including CLPP To better understand the mammalian UPR(mt) signaling, we deleted CLPP in hearts of DARS2-deficient animals that show robust induction of UPR(mt) due to strong dysregulation of mitochondrial translation. Remarkably, our results clearly show that mammalian CLPP is neither required for, nor it regulates the UPR(mt) in mammals. Surprisingly, we demonstrate that a strong mitochondrial cardiomyopathy and diminished respiration due to DARS2 deficiency can be alleviated by the loss of CLPP, leading to an increased de novo synthesis of individual OXPHOS subunits. These results question our current understanding of the UPR(mt) signaling in mammals, while introducing CLPP as a possible novel target for therapeutic intervention in mitochondrial diseases.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.15252/embr.201642077DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4931557PMC
July 2016

Stomatin-like protein 2 is required for in vivo mitochondrial respiratory chain supercomplex formation and optimal cell function.

Mol Cell Biol 2015 May 16;35(10):1838-47. Epub 2015 Mar 16.

Microbiome and Disease Tolerance Centre, Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada

Stomatin-like protein 2 (SLP-2) is a mainly mitochondrial protein that is widely expressed and is highly conserved across evolution. We have previously shown that SLP-2 binds the mitochondrial lipid cardiolipin and interacts with prohibitin-1 and -2 to form specialized membrane microdomains in the mitochondrial inner membrane, which are associated with optimal mitochondrial respiration. To determine how SLP-2 functions, we performed bioenergetic analysis of primary T cells from T cell-selective Slp-2 knockout mice under conditions that forced energy production to come almost exclusively from oxidative phosphorylation. These cells had a phenotype characterized by increased uncoupled mitochondrial respiration and decreased mitochondrial membrane potential. Since formation of mitochondrial respiratory chain supercomplexes (RCS) may correlate with more efficient electron transfer during oxidative phosphorylation, we hypothesized that the defect in mitochondrial respiration in SLP-2-deficient T cells was due to deficient RCS formation. We found that in the absence of SLP-2, T cells had decreased levels and activities of complex I-III2 and I-III2-IV(1-3) RCS but no defects in assembly of individual respiratory complexes. Impaired RCS formation in SLP-2-deficient T cells correlated with significantly delayed T cell proliferation in response to activation under conditions of limiting glycolysis. Altogether, our findings identify SLP-2 as a key regulator of the formation of RCS in vivo and show that these supercomplexes are required for optimal cell function.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1128/MCB.00047-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4405640PMC
May 2015

Ultrasound texture-based CAD system for detecting neuromuscular diseases.

Int J Comput Assist Radiol Surg 2015 Sep 2;10(9):1493-503. Epub 2014 Dec 2.

Department of Simulation and Graphics, Otto von Guericke University, Universitätsplatz 2, 39106, Magdeburg, Germany,

Purpose: Diagnosis of neuromuscular diseases in ultrasonography is a challenging task since experts are often unable to discriminate between healthy and pathological cases. A computer-aided diagnosis (CAD) system for skeletal muscle ultrasonography was developed and tested for myositis detection in ultrasound images of biceps brachii.

Methods: Several types of features were extracted from rectangular and polygonal image regions-of-interest (ROIs), including first-order statistics, wavelet-based features, and Haralick's features. Features were chosen that are sensitive to the change in contrast and structure for pathological ultrasound images of neuromuscular diseases. The number of features was reduced by applying different sequential feature selection strategies followed by a supervised principal component analysis. For classification, two linear approaches were investigated: Fisher's classifier and the linear support vector machine (SVM) as well as the nonlinear [Formula: see text]-nearest neighbor approach. The CAD system was benchmarked on datasets of 18 subjects, seven of which were healthy, while 11 were affected by myositis. Three expert radiologists provided pre-classification and testing interpretations.

Results: Leave-one-out cross-validation on the training data revealed that the linear SVM was best suited for discriminating healthy and pathological muscle tissue, achieving 85/87 % accuracy, 90 % sensitivity, and 83/85 % specificity, depending on the radiologist.

Conclusion: A muscle ultrasonography CAD system was developed, allowing a classification of an ultrasound image by one-click positioning of rectangular ROIs with minimal user effort. The applicability of the system was demonstrated with the challenging example of myositis detection, showing highly accurate results that were robust to imprecise user input.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s11548-014-1133-6DOI Listing
September 2015

Phosphoproteomic analysis reveals regulatory mechanisms at the kidney filtration barrier.

J Am Soc Nephrol 2014 Jul 7;25(7):1509-22. Epub 2014 Feb 7.

Department of Internal Medicine II, Center for Molecular Medicine, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, Systems Biology of Ageing Cologne,

Diseases of the kidney filtration barrier are a leading cause of ESRD. Most disorders affect the podocytes, polarized cells with a limited capacity for self-renewal that require tightly controlled signaling to maintain their integrity, viability, and function. Here, we provide an atlas of in vivo phosphorylated, glomerulus-expressed proteins, including podocyte-specific gene products, identified in an unbiased tandem mass spectrometry-based approach. We discovered 2449 phosphorylated proteins corresponding to 4079 identified high-confidence phosphorylated residues and performed a systematic bioinformatics analysis of this dataset. We discovered 146 phosphorylation sites on proteins abundantly expressed in podocytes. The prohibitin homology domain of the slit diaphragm protein podocin contained one such site, threonine 234 (T234), located within a phosphorylation motif that is mutated in human genetic forms of proteinuria. The T234 site resides at the interface of podocin dimers. Free energy calculation through molecular dynamic simulations revealed a role for T234 in regulating podocin dimerization. We show that phosphorylation critically regulates formation of high molecular weight complexes and that this may represent a general principle for the assembly of proteins containing prohibitin homology domains.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1681/ASN.2013070760DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4073431PMC
July 2014

TRIAP1/PRELI complexes prevent apoptosis by mediating intramitochondrial transport of phosphatidic acid.

Cell Metab 2013 Aug;18(2):287-95

Institute for Genetics, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, Center for Molecular Medicine, University of Cologne, Germany.

Cardiolipin (CL), a mitochondria-specific glycerophospholipid, is required for diverse mitochondrial processes and orchestrates the function of various death-inducing proteins during apoptosis. Here, we identify a complex of the p53-regulated protein TRIAP1 (p53CSV) and PRELI in the mitochondrial intermembrane space (IMS), which ensures the accumulation of CL in mitochondria. TRIAP1/PRELI complexes exert lipid transfer activity in vitro and supply phosphatidic acid (PA) for CL synthesis in the inner membrane. Loss of TRIAP1 or PRELI impairs the accumulation of CL, facilitates the release of cytochrome c, and renders cells vulnerable to apoptosis upon intrinsic and extrinsic stimulation. Survival of TRIAP1- and PRELI-deficient cells is conferred by an excess of exogenously provided phosphatidylglycerol. Our results reveal a p53-dependent cell-survival pathway and highlight the importance of the CL content of mitochondrial membranes in apoptosis.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.cmet.2013.07.008DOI Listing
August 2013