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  1. Article: Role of amino acid metabolism in mitochondrial homeostasis.

    Li, Qiaochu / Hoppe, Thorsten

    Frontiers in cell and developmental biology

    2023  Volume 11, Page(s) 1127618

    Abstract: Mitochondria are central hubs for energy production, metabolism and cellular signal transduction in eukaryotic cells. Maintenance of mitochondrial homeostasis is important for cellular function and survival. In particular, cellular metabolic state is in ... ...

    Abstract Mitochondria are central hubs for energy production, metabolism and cellular signal transduction in eukaryotic cells. Maintenance of mitochondrial homeostasis is important for cellular function and survival. In particular, cellular metabolic state is in constant communication with mitochondrial homeostasis. One of the most important metabolic processes that provide energy in the cell is amino acid metabolism. Almost all of the 20 amino acids that serve as the building blocks of proteins are produced or degraded in the mitochondria. The synthesis of the amino acids aspartate and arginine depends on the activity of the respiratory chain, which is essential for cell proliferation. The degradation of branched-chain amino acids mainly occurs in the mitochondrial matrix, contributing to energy metabolism, mitochondrial biogenesis, as well as protein quality control in both mitochondria and cytosol. Dietary supplementation or restriction of amino acids in worms, flies and mice modulates lifespan and health, which has been associated with changes in mitochondrial biogenesis, antioxidant response, as well as the activity of tricarboxylic acid cycle and respiratory chain. Consequently, impaired amino acid metabolism has been associated with both primary mitochondrial diseases and diseases with mitochondrial dysfunction such as cancer. Here, we present recent observations on the crosstalk between amino acid metabolism and mitochondrial homeostasis, summarise the underlying molecular mechanisms to date, and discuss their role in cellular functions and organismal physiology.
    Language English
    Publishing date 2023-02-27
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2737824-X
    ISSN 2296-634X
    ISSN 2296-634X
    DOI 10.3389/fcell.2023.1127618
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Chemical cross-linking to study protein self-assembly in cellulo.

    Müller, Leonie / Salman, Sirin / Hoppe, Thorsten

    STAR protocols

    2024  Volume 5, Issue 2, Page(s) 103032

    Abstract: Many proteins self-assemble into dimers and higher-order oligomers. Therefore, the goal of this protocol is to characterize the conformational states of an endogenous protein of interest. Here, we present a protocol for assessing protein self-assembly in ...

    Abstract Many proteins self-assemble into dimers and higher-order oligomers. Therefore, the goal of this protocol is to characterize the conformational states of an endogenous protein of interest. Here, we present a protocol for assessing protein self-assembly in cell lysates using chemical cross-linking. We describe steps for chemical cross-linking with recombinant proteins as well as steps for cell culture and cell lysate preparation, chemical cross-linking, SDS-PAGE, and western blotting for the detection of endogenous proteins. For complete details on the use and execution of this protocol, please refer to Balaji et al.
    Language English
    Publishing date 2024-04-22
    Publishing country United States
    Document type Journal Article
    ISSN 2666-1667
    ISSN (online) 2666-1667
    DOI 10.1016/j.xpro.2024.103032
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Temperature-Dependent Regulation of Proteostasis and Longevity.

    Vakkayil, Kavya Leo / Hoppe, Thorsten

    Frontiers in aging

    2022  Volume 3, Page(s) 853588

    Abstract: Temperature is an important environmental condition that determines the physiology and behavior of all organisms. Animals use different response strategies to adapt and survive fluctuations in ambient temperature. The ... ...

    Abstract Temperature is an important environmental condition that determines the physiology and behavior of all organisms. Animals use different response strategies to adapt and survive fluctuations in ambient temperature. The hermaphrodite
    Language English
    Publishing date 2022-03-24
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 3076785-4
    ISSN 2673-6217 ; 2673-6217
    ISSN (online) 2673-6217
    ISSN 2673-6217
    DOI 10.3389/fragi.2022.853588
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: A ubiquitin fusion reporter to monitor muscle proteostasis in

    Kutzner, Carl Elias / Bauer, Karen Carolyn / Hoppe, Thorsten

    microPublication biology

    2023  Volume 2023

    Abstract: Muscle is a highly dynamic tissue in which a variety of folding and degradation processes are active to maintain protein homeostasis (proteostasis) and functionality. The muscle-specific chaperone UNC-45 folds the motor protein myosin and assembles it ... ...

    Abstract Muscle is a highly dynamic tissue in which a variety of folding and degradation processes are active to maintain protein homeostasis (proteostasis) and functionality. The muscle-specific chaperone UNC-45 folds the motor protein myosin and assembles it into myofilaments. Malfunction of this chaperone leads to misfolding of myosin, disorganization of myofilaments, and degradation of misfolded myosin molecules by the proteasome. Here, we present a new muscle-specific ubiquitin fusion degradation (UFD) model substrate in
    Language English
    Publishing date 2023-04-21
    Publishing country United States
    Document type Journal Article
    ISSN 2578-9430
    ISSN (online) 2578-9430
    DOI 10.17912/micropub.biology.000824
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Cutting through the stress: RNA decay pathways at the endoplasmic reticulum.

    Ottens, Franziska / Efstathiou, Sotirios / Hoppe, Thorsten

    Trends in cell biology

    2023  

    Abstract: The endoplasmic reticulum (ER) is central to the processing of luminal, transmembrane, and secretory proteins, and maintaining a functional ER is essential for organismal physiology and health. Increased protein-folding load on the ER causes ER stress, ... ...

    Abstract The endoplasmic reticulum (ER) is central to the processing of luminal, transmembrane, and secretory proteins, and maintaining a functional ER is essential for organismal physiology and health. Increased protein-folding load on the ER causes ER stress, which activates quality control mechanisms to restore ER function and protein homeostasis. Beyond protein quality control, mRNA decay pathways have emerged as potent ER fidelity regulators, but their mechanistic roles in ER quality control and their interrelationships remain incompletely understood. Herein, we review ER-associated RNA decay pathways - including regulated inositol-requiring enzyme 1α (IRE1α)-dependent mRNA decay (RIDD), nonsense-mediated mRNA decay (NMD), and Argonaute-dependent RNA silencing - in ER homeostasis, and highlight the intricate coordination of ER-targeted RNA and protein decay mechanisms and their association with antiviral defense.
    Language English
    Publishing date 2023-11-25
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 30122-x
    ISSN 1879-3088 ; 0962-8924
    ISSN (online) 1879-3088
    ISSN 0962-8924
    DOI 10.1016/j.tcb.2023.11.003
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Organismal Protein Homeostasis Mechanisms.

    Hoppe, Thorsten / Cohen, Ehud

    Genetics

    2021  Volume 215, Issue 4, Page(s) 889–901

    Abstract: Sustaining a healthy proteome is a lifelong challenge for each individual cell of an organism. However, protein homeostasis or proteostasis is constantly jeopardized since damaged proteins accumulate under proteotoxic stress that originates from ever- ... ...

    Abstract Sustaining a healthy proteome is a lifelong challenge for each individual cell of an organism. However, protein homeostasis or proteostasis is constantly jeopardized since damaged proteins accumulate under proteotoxic stress that originates from ever-changing metabolic, environmental, and pathological conditions. Proteostasis is achieved via a conserved network of quality control pathways that orchestrate the biogenesis of correctly folded proteins, prevent proteins from misfolding, and remove potentially harmful proteins by selective degradation. Nevertheless, the proteostasis network has a limited capacity and its collapse deteriorates cellular functionality and organismal viability, causing metabolic, oncological, or neurodegenerative disorders. While cell-autonomous quality control mechanisms have been described intensely, recent work on
    MeSH term(s) Animals ; Caenorhabditis elegans/physiology ; HSP70 Heat-Shock Proteins/metabolism ; Homeostasis ; Humans ; Protein Folding ; Proteome/metabolism ; Proteostasis ; Proteostasis Deficiencies/physiopathology ; Signal Transduction ; Stress, Physiological
    Chemical Substances HSP70 Heat-Shock Proteins ; Proteome
    Language English
    Publishing date 2021-07-06
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 2167-2
    ISSN 1943-2631 ; 0016-6731
    ISSN (online) 1943-2631
    ISSN 0016-6731
    DOI 10.1534/genetics.120.301283
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Book ; Online ; Thesis: Metabolic Regulation of the Ubiquitin-Proteasome System

    Ravanelli, Sonia [Verfasser] / Hoppe, Thorsten [Gutachter]

    2022  

    Author's details Sonia Ravanelli ; Gutachter: Thorsten Hoppe
    Keywords Naturwissenschaften ; Science
    Subject code sg500
    Language English
    Publisher Universitäts- und Stadtbibliothek Köln
    Publishing place Köln
    Document type Book ; Online ; Thesis
    Database Digital theses on the web

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  8. Article ; Online: Regulation of E3 ubiquitin ligases by homotypic and heterotypic assembly.

    Balaji, Vishnu / Hoppe, Thorsten

    F1000Research

    2020  Volume 9

    Abstract: Protein ubiquitylation is essential for the maintenance of cellular homeostasis. E3 ubiquitin ligases are key components of the enzymatic machinery catalyzing the attachment of ubiquitin to substrate proteins. Consequently, enzymatic dysfunction has been ...

    Abstract Protein ubiquitylation is essential for the maintenance of cellular homeostasis. E3 ubiquitin ligases are key components of the enzymatic machinery catalyzing the attachment of ubiquitin to substrate proteins. Consequently, enzymatic dysfunction has been associated with medical conditions including cancer, diabetes, and cardiovascular and neurodegenerative disorders. To safeguard substrate selection and ubiquitylation, the activity of E3 ligases is tightly regulated by post-translational modifications including phosphorylation, sumoylation, and ubiquitylation, as well as binding of alternative adaptor molecules and cofactors. Recent structural studies identified homotypic and heterotypic interactions between E3 ligases, adding another layer of control for rapid adaptation to changing environmental and physiological conditions. Here, we discuss the regulation of E3 ligase activity by combinatorial oligomerization and summarize examples of associated ubiquitylation pathways and mechanisms.
    MeSH term(s) Humans ; Protein Processing, Post-Translational ; Ubiquitin/metabolism ; Ubiquitin-Protein Ligases/genetics ; Ubiquitin-Protein Ligases/metabolism ; Ubiquitination
    Chemical Substances Ubiquitin ; Ubiquitin-Protein Ligases (EC 2.3.2.27)
    Language English
    Publishing date 2020-02-06
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 2699932-8
    ISSN 2046-1402 ; 2046-1402
    ISSN (online) 2046-1402
    ISSN 2046-1402
    DOI 10.12688/f1000research.21253.1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Limited proteolysis: DisRUPting proteasomal inhibition.

    Hoppe, Thorsten

    Current biology : CB

    2014  Volume 24, Issue 15, Page(s) R693–5

    Abstract: The 26S proteasome is a protease complex that completely degrades substrate proteins marked with a chain of ubiquitins, but is also able to perform endoproteolytic cleavage. A new study now demonstrates that regulated ubiquitin-proteasome-dependent ... ...

    Abstract The 26S proteasome is a protease complex that completely degrades substrate proteins marked with a chain of ubiquitins, but is also able to perform endoproteolytic cleavage. A new study now demonstrates that regulated ubiquitin-proteasome-dependent processing ameliorates proteasomal inhibition.
    MeSH term(s) Endoplasmic Reticulum/metabolism ; Humans ; Nuclear Respiratory Factor 1/metabolism ; Proteasome Endopeptidase Complex/metabolism ; Proteasome Inhibitors/pharmacology
    Chemical Substances Nuclear Respiratory Factor 1 ; Proteasome Inhibitors ; Proteasome Endopeptidase Complex (EC 3.4.25.1)
    Language English
    Publishing date 2014-08-04
    Publishing country England
    Document type Comment ; Journal Article
    ZDB-ID 1071731-6
    ISSN 1879-0445 ; 0960-9822
    ISSN (online) 1879-0445
    ISSN 0960-9822
    DOI 10.1016/j.cub.2014.06.056
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Membrane localization of LGG-1/GABARAP is dispensable for autophagy in

    Leboutet, Romane / Largeau, Céline / Culetto, Emmanuel / Lefebvre, Christophe / Hoppe, Thorsten / Legouis, Renaud

    Autophagy

    2023  Volume 19, Issue 12, Page(s) 3254–3255

    Abstract: Most of the functions of LC3/GABARAP in macroautophagy/autophagy are considered to depend on their association with the phagophore membrane through a conjugation to a lipid. Using site-directed mutagenesis, we inhibited the conjugation of LGG-1, the ... ...

    Abstract Most of the functions of LC3/GABARAP in macroautophagy/autophagy are considered to depend on their association with the phagophore membrane through a conjugation to a lipid. Using site-directed mutagenesis, we inhibited the conjugation of LGG-1, the single homolog of GABARAP in
    MeSH term(s) Animals ; Caenorhabditis elegans ; Autophagy ; Microtubule-Associated Proteins ; Autophagosomes ; Caenorhabditis elegans Proteins
    Chemical Substances Microtubule-Associated Proteins ; Caenorhabditis elegans Proteins ; LGG-1 protein, C elegans
    Language English
    Publishing date 2023-08-23
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2454135-7
    ISSN 1554-8635 ; 1554-8627
    ISSN (online) 1554-8635
    ISSN 1554-8627
    DOI 10.1080/15548627.2023.2249393
    Database MEDical Literature Analysis and Retrieval System OnLINE

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