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  1. Article ; Online: Assays to Monitor Autophagy in Saccharomyces cerevisiae

    Raffaela Torggler / Daniel Papinski / Claudine Kraft

    Cells, Vol 6, Iss 3, p

    2017  Volume 23

    Abstract: Autophagy is an intracellular process responsible for the degradation and recycling of cytoplasmic components. It selectively removes harmful cellular material and enables the cell to survive starvation by mobilizing nutrients via the bulk degradation of ...

    Abstract Autophagy is an intracellular process responsible for the degradation and recycling of cytoplasmic components. It selectively removes harmful cellular material and enables the cell to survive starvation by mobilizing nutrients via the bulk degradation of cytoplasmic components. While research over the last decades has led to the discovery of the key factors involved in autophagy, the pathway is not yet completely understood. The first studies of autophagy on a molecular level were conducted in the yeast Saccharomyces cerevisiae. Building up on these studies, many homologs have been found in higher eukaryotes. Yeast remains a highly relevant model organism for studying autophagy, with a wide range of established methods to elucidate the molecular details of the autophagy pathway. In this review, we provide an overview of methods to study both selective and bulk autophagy, including intermediate steps in the yeast Saccharomyces cerevisiae. We compare different assays, discuss their advantages and limitations and list potential applications.
    Keywords yeast ; bulk autophagy ; Cvt pathway ; selective autophagy ; PAS ; autophagosome ; autophagic body ; iPass ; M-Track ; Biology (General) ; QH301-705.5
    Subject code 571
    Language English
    Publishing date 2017-07-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Spatial control of avidity regulates initiation and progression of selective autophagy

    David M. Hollenstein / Mariya Licheva / Nicole Konradi / David Schweida / Hector Mancilla / Muriel Mari / Fulvio Reggiori / Claudine Kraft

    Nature Communications, Vol 12, Iss 1, Pp 1-

    2021  Volume 18

    Abstract: The molecular principles governing the initiation of autophagosome formation are not clearly understood. Here we show that the vacuolar protein Vac8 coordinates this process by promoting an avidity-driven assembly of several autophagy factors. ...

    Abstract The molecular principles governing the initiation of autophagosome formation are not clearly understood. Here we show that the vacuolar protein Vac8 coordinates this process by promoting an avidity-driven assembly of several autophagy factors.
    Keywords Science ; Q
    Language English
    Publishing date 2021-12-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Dual role of Mic10 in mitochondrial cristae organization and ATP synthase-linked metabolic adaptation and respiratory growth

    Heike Rampelt / Florian Wollweber / Mariya Licheva / Rinse de Boer / Inge Perschil / Liesa Steidle / Thomas Becker / Maria Bohnert / Ida van der Klei / Claudine Kraft / Martin van der Laan / Nikolaus Pfanner

    Cell Reports, Vol 38, Iss 4, Pp 110290- (2022)

    2022  

    Abstract: Summary: Invaginations of the mitochondrial inner membrane, termed cristae, are hubs for oxidative phosphorylation. The mitochondrial contact site and cristae organizing system (MICOS) and the dimeric F1Fo-ATP synthase play important roles in controlling ...

    Abstract Summary: Invaginations of the mitochondrial inner membrane, termed cristae, are hubs for oxidative phosphorylation. The mitochondrial contact site and cristae organizing system (MICOS) and the dimeric F1Fo-ATP synthase play important roles in controlling cristae architecture. A fraction of the MICOS core subunit Mic10 is found in association with the ATP synthase, yet it is unknown whether this interaction is of relevance for mitochondrial or cellular functions. Here, we established conditions to selectively study the role of Mic10 at the ATP synthase. Mic10 variants impaired in MICOS functions stimulate ATP synthase oligomerization like wild-type Mic10 and promote efficient inner membrane energization, adaptation to non-fermentable carbon sources, and respiratory growth. Mic10's functions in respiratory growth largely depend on Mic10ATPsynthase, not on Mic10MICOS. We conclude that Mic10 plays a dual role as core subunit of MICOS and as partner of the F1Fo-ATP synthase, serving distinct functions in cristae shaping and respiratory adaptation and growth.
    Keywords mitochondria ; inner membrane ; membrane architecture ; MICOS ; ATP synthase ; cristae organization ; Biology (General) ; QH301-705.5
    Subject code 570
    Language English
    Publishing date 2022-01-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Reticulophagy and Ribophagy

    Eduardo Cebollero / Fulvio Reggiori / Claudine Kraft

    International Journal of Cell Biology, Vol

    Regulated Degradation of Protein Production Factories

    2012  Volume 2012

    Keywords Cytology ; QH573-671 ; Biology (General) ; QH301-705.5 ; Science ; Q ; DOAJ:Cytology ; DOAJ:Biology ; DOAJ:Biology and Life Sciences
    Language English
    Publishing date 2012-01-01T00:00:00Z
    Publisher Hindawi Publishing Corporation
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: Posttranslational insertion of small membrane proteins by the bacterial signal recognition particle.

    Ruth Steinberg / Andrea Origi / Ana Natriashvili / Pinku Sarmah / Mariya Licheva / Princess M Walker / Claudine Kraft / Stephen High / Joen Luirink / Wei Q Shi / Martin Helmstädter / Maximilian H Ulbrich / Hans-Georg Koch

    PLoS Biology, Vol 18, Iss 9, p e

    2020  Volume 3000874

    Abstract: Small membrane proteins represent a largely unexplored yet abundant class of proteins in pro- and eukaryotes. They essentially consist of a single transmembrane domain and are associated with stress response mechanisms in bacteria. How these proteins are ...

    Abstract Small membrane proteins represent a largely unexplored yet abundant class of proteins in pro- and eukaryotes. They essentially consist of a single transmembrane domain and are associated with stress response mechanisms in bacteria. How these proteins are inserted into the bacterial membrane is unknown. Our study revealed that in Escherichia coli, the 27-amino-acid-long model protein YohP is recognized by the signal recognition particle (SRP), as indicated by in vivo and in vitro site-directed cross-linking. Cross-links to SRP were also observed for a second small membrane protein, the 33-amino-acid-long YkgR. However, in contrast to the canonical cotranslational recognition by SRP, SRP was found to bind to YohP posttranslationally. In vitro protein transport assays in the presence of a SecY inhibitor and proteoliposome studies demonstrated that SRP and its receptor FtsY are essential for the posttranslational membrane insertion of YohP by either the SecYEG translocon or by the YidC insertase. Furthermore, our data showed that the yohP mRNA localized preferentially and translation-independently to the bacterial membrane in vivo. In summary, our data revealed that YohP engages an unique SRP-dependent posttranslational insertion pathway that is likely preceded by an mRNA targeting step. This further highlights the enormous plasticity of bacterial protein transport machineries.
    Keywords Biology (General) ; QH301-705.5
    Subject code 570
    Language English
    Publishing date 2020-09-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: Global kinome profiling reveals DYRK1A as critical activator of the human mitochondrial import machinery

    Corvin Walter / Adinarayana Marada / Tamara Suhm / Ralf Ernsberger / Vera Muders / Cansu Kücükköse / Pablo Sánchez-Martín / Zehan Hu / Abhishek Aich / Stefan Loroch / Fiorella Andrea Solari / Daniel Poveda-Huertes / Alexandra Schwierzok / Henrike Pommerening / Stanka Matic / Jan Brix / Albert Sickmann / Claudine Kraft / Jörn Dengjel /
    Sven Dennerlein / Tilman Brummer / F.-Nora Vögtle / Chris Meisinger

    Nature Communications, Vol 12, Iss 1, Pp 1-

    2021  Volume 12

    Abstract: Mitochondrial protein import is mediated by the translocase of the outer membrane (TOM), through which nearly all precursors traverse. Here, the authors perform global in vitro kinome profiling and by this identify that DYRK1A phosphorylates TOM70 and ... ...

    Abstract Mitochondrial protein import is mediated by the translocase of the outer membrane (TOM), through which nearly all precursors traverse. Here, the authors perform global in vitro kinome profiling and by this identify that DYRK1A phosphorylates TOM70 and promotes import.
    Keywords Science ; Q
    Language English
    Publishing date 2021-07-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: Atg4 proteolytic activity can be inhibited by Atg1 phosphorylation

    Jana Sánchez-Wandelmer / Franziska Kriegenburg / Sabrina Rohringer / Martina Schuschnig / Rubén Gómez-Sánchez / Bettina Zens / Susana Abreu / Ralph Hardenberg / David Hollenstein / Jieqiong Gao / Christian Ungermann / Sascha Martens / Claudine Kraft / Fulvio Reggiori

    Nature Communications, Vol 8, Iss 1, Pp 1-

    2017  Volume 10

    Abstract: The protease Atg4 mediates Atg8 lipidation, required for autophagosome biogenesis, but also triggers Atg8 release from the membranes, however is unclear how these steps are coordinated. Here the authors show that phosphorylation by Atg1 inhibits Atg4 at ... ...

    Abstract The protease Atg4 mediates Atg8 lipidation, required for autophagosome biogenesis, but also triggers Atg8 release from the membranes, however is unclear how these steps are coordinated. Here the authors show that phosphorylation by Atg1 inhibits Atg4 at autophagosome formation sites.
    Keywords Science ; Q
    Language English
    Publishing date 2017-08-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article: Two Independent Pathways within Selective Autophagy Converge to Activate Atg1 Kinase at the Vacuole

    Torggler, Raffaela / Andrea Brezovich / Claudine Kraft / Daniel Papinski / David Schweida / Levent Bas / Martina Schuschnig / Sabrina Rohringer / Tamara Matzhold / Thaddäus Pfaffenwimmer / Thorsten Brach

    Molecular cell. 2016 Oct. 20, v. 64, no. 2

    2016  

    Abstract: Autophagy is a potent cellular degradation pathway, and its activation needs to be tightly controlled. Cargo receptors mediate selectivity during autophagy by bringing cargo to the scaffold protein Atg11 and, in turn, to the autophagic machinery, ... ...

    Abstract Autophagy is a potent cellular degradation pathway, and its activation needs to be tightly controlled. Cargo receptors mediate selectivity during autophagy by bringing cargo to the scaffold protein Atg11 and, in turn, to the autophagic machinery, including the central autophagy kinase Atg1. Here we show how selective autophagy is tightly regulated in space and time to prevent aberrant Atg1 kinase activation and autophagy induction. We established an induced bypass approach (iPass) that combines genetic deletion with chemically induced dimerization to evaluate the roles of Atg13 and cargo receptors in Atg1 kinase activation and selective autophagy progression. We show that Atg1 activation does not require cargo receptors, cargo-bound Atg11, or Atg13 per se. Rather, these proteins function in two independent pathways that converge to activate Atg1 at the vacuole. This pathway architecture underlies the spatiotemporal control of Atg1 kinase activity, thereby preventing inappropriate autophagosome formation.
    Keywords autophagy ; dimerization ; receptors ; scaffolding proteins ; space and time ; vacuoles
    Language English
    Dates of publication 2016-1020
    Size p. 221-235.
    Publishing place Elsevier Inc.
    Document type Article
    ZDB-ID 1415236-8
    ISSN 1097-4164 ; 1097-2765
    ISSN (online) 1097-4164
    ISSN 1097-2765
    DOI 10.1016/j.molcel.2016.09.008
    Database NAL-Catalogue (AGRICOLA)

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  9. Article ; Online: Mechanism of cargo-directed Atg8 conjugation during selective autophagy

    Dorotea Fracchiolla / Justyna Sawa-Makarska / Bettina Zens / Anita de Ruiter / Gabriele Zaffagnini / Andrea Brezovich / Julia Romanov / Kathrin Runggatscher / Claudine Kraft / Bojan Zagrovic / Sascha Martens

    eLife, Vol

    2016  Volume 5

    Abstract: Selective autophagy is mediated by cargo receptors that link the cargo to the isolation membrane via interactions with Atg8 proteins. Atg8 proteins are localized to the membrane in an ubiquitin-like conjugation reaction, but how this conjugation is ... ...

    Abstract Selective autophagy is mediated by cargo receptors that link the cargo to the isolation membrane via interactions with Atg8 proteins. Atg8 proteins are localized to the membrane in an ubiquitin-like conjugation reaction, but how this conjugation is coupled to the presence of the cargo is unclear. Here we show that the S. cerevisiae Atg19, Atg34 and the human p62, Optineurin and NDP52 cargo receptors interact with the E3-like enzyme Atg12~Atg5-Atg16, which stimulates Atg8 conjugation. The interaction of Atg19 with the Atg12~Atg5-Atg16 complex is mediated by its Atg8-interacting motifs (AIMs). We identify the AIM-binding sites in the Atg5 subunit and mutation of these sites impairs selective autophagy. In a reconstituted system the recruitment of the E3 to the prApe1 cargo is sufficient to drive accumulation of conjugated Atg8 at the cargo. The interaction of the Atg12~Atg5-Atg16 complex and Atg8 with Atg19 is mutually exclusive, which may confer directionality to the system.
    Keywords selective autophagy ; protein conjugation ; cargo receptor ; biochemical reconstitution ; membrane biology ; Medicine ; R ; Science ; Q ; Biology (General) ; QH301-705.5
    Subject code 571
    Language English
    Publishing date 2016-11-01T00:00:00Z
    Publisher eLife Sciences Publications Ltd
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article ; Online: The coordinated action of the MVB pathway and autophagy ensures cell survival during starvation

    Martin Müller / Oliver Schmidt / Mihaela Angelova / Klaus Faserl / Sabine Weys / Leopold Kremser / Thaddäus Pfaffenwimmer / Thomas Dalik / Claudine Kraft / Zlatko Trajanoski / Herbert Lindner / David Teis

    eLife, Vol

    2015  Volume 4

    Abstract: The degradation and recycling of cellular components is essential for cell growth and survival. Here we show how selective and non-selective lysosomal protein degradation pathways cooperate to ensure cell survival upon nutrient limitation. A quantitative ...

    Abstract The degradation and recycling of cellular components is essential for cell growth and survival. Here we show how selective and non-selective lysosomal protein degradation pathways cooperate to ensure cell survival upon nutrient limitation. A quantitative analysis of starvation-induced proteome remodeling in yeast reveals comprehensive changes already in the first three hours. In this period, many different integral plasma membrane proteins undergo endocytosis and degradation in vacuoles via the multivesicular body (MVB) pathway. Their degradation becomes essential to maintain critical amino acids levels that uphold protein synthesis early during starvation. This promotes cellular adaptation, including the de novo synthesis of vacuolar hydrolases to boost the vacuolar catabolic activity. This order of events primes vacuoles for the efficient degradation of bulk cytoplasm via autophagy. Hence, a catabolic cascade including the coordinated action of the MVB pathway and autophagy is essential to enter quiescence to survive extended periods of nutrient limitation.
    Keywords endocytosis ; MVB pathway ; autophagy ; Medicine ; R ; Science ; Q ; Biology (General) ; QH301-705.5
    Subject code 570
    Language English
    Publishing date 2015-04-01T00:00:00Z
    Publisher eLife Sciences Publications Ltd
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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