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Article ; Online: Regulation of Autophagy By Signaling Through the Atg1/ULK1 Complex.

Papinski, Daniel / Kraft, Claudine

2016 Volume 428, Issue 9 Pt A, Page(s) 1725–1741

Abstract: Autophagy is an intracellular degradation pathway highly conserved in eukaryotic species. It is characterized by selective or bulk trafficking of cytosolic structures-ranging from single proteins to cell organelles-to the vacuole or a lysosome, in which ... ...

Abstract	Autophagy is an intracellular degradation pathway highly conserved in eukaryotic species. It is characterized by selective or bulk trafficking of cytosolic structures-ranging from single proteins to cell organelles-to the vacuole or a lysosome, in which the autophagic cargo is degraded. Autophagy fulfils a large set of roles, including nutrient mobilization in starvation conditions, clearance of protein aggregates and host defence against intracellular pathogens. Not surprisingly, autophagy has been linked to several human diseases, among them neurodegenerative disorders and cancer. Autophagy is coordinated by the action of the Atg1/ULK1 kinase, which is the target of several important stress signaling cascades. In this review, we will discuss the available information on both upstream regulation and downstream effectors of Atg1/ULK1, with special focus on reported and proposed kinase substrates.
MeSH term(s)	Autophagosomes/metabolism ; Autophagy ; Autophagy-Related Protein-1 Homolog/metabolism ; Eukaryota ; Gene Expression Regulation ; Signal Transduction
Chemical Substances	Autophagy-Related Protein-1 Homolog (EC 2.7.11.1)
Language	English
Publishing date	2016-04-06
Publishing country	England
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	80229-3
ISSN	1089-8638 ; 0022-2836
ISSN (online)	1089-8638
ISSN	0022-2836
DOI	10.1016/j.jmb.2016.03.030
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Article: Regulation of Autophagy By Signaling Through the Atg1/ULK1 Complex

Papinski, Daniel / Kraft, Claudine

Journal of Molecular Biology. 2016 May 08, v. 428

2016

Abstract: Autophagy is an intracellular degradation pathway highly conserved in eukaryotic species. It is characterized by selective or bulk trafficking of cytosolic structures—ranging from single proteins to cell organelles—to the vacuole or a lysosome, in which ... ...

Abstract	Autophagy is an intracellular degradation pathway highly conserved in eukaryotic species. It is characterized by selective or bulk trafficking of cytosolic structures—ranging from single proteins to cell organelles—to the vacuole or a lysosome, in which the autophagic cargo is degraded. Autophagy fulfils a large set of roles, including nutrient mobilization in starvation conditions, clearance of protein aggregates and host defence against intracellular pathogens. Not surprisingly, autophagy has been linked to several human diseases, among them neurodegenerative disorders and cancer. Autophagy is coordinated by the action of the Atg1/ULK1 kinase, which is the target of several important stress signaling cascades. In this review, we will discuss the available information on both upstream regulation and downstream effectors of Atg1/ULK1, with special focus on reported and proposed kinase substrates.
Keywords	autophagy ; human diseases ; lysosomes ; neoplasms ; neurodegenerative diseases ; pathogens ; protein aggregates ; vacuoles
Language	English
Dates of publication	2016-0508
Size	p. 1725-1741.
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	80229-3
ISSN	1089-8638 ; 0022-2836
ISSN (online)	1089-8638
ISSN	0022-2836
DOI	10.1016/j.jmb.2016.03.030
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Article: Ykt6 mediates autophagosome-vacuole fusion.

Bas, Levent / Papinski, Daniel / Kraft, Claudine

Molecular & cellular oncology

2018 Volume 5, Issue 6, Page(s) e1526006

Abstract: Studying the mechanism of autophagosome-vacuole fusion has proven difficult in live yeast cells. Developing a ... ...

Abstract	Studying the mechanism of autophagosome-vacuole fusion has proven difficult in live yeast cells. Developing a novel
Language	English
Publishing date	2018-10-04
Publishing country	United States
Document type	Journal Article
ISSN	2372-3556
ISSN	2372-3556
DOI	10.1080/23723556.2018.1526006
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Article: Assays to Monitor Autophagy in Saccharomyces cerevisiae.

Torggler, Raffaela / Papinski, Daniel / Kraft, Claudine

Cells

2017 Volume 6, Issue 3

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
Language	English
Publishing date	2017-07-13
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2661518-6
ISSN	2073-4409
ISSN	2073-4409
DOI	10.3390/cells6030023
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Article ; Online: Atg1 kinase organizes autophagosome formation by phosphorylating Atg9.

Papinski, Daniel / Kraft, Claudine

Autophagy

2014 Volume 10, Issue 7, Page(s) 1338–1340

Abstract: The conserved Ser/Thr kinase Atg1/ULK1 plays a crucial role in the regulation of autophagy. However, only very few Atg1 targets have been identified, impeding elucidation of the mechanisms by which Atg1 regulates autophagy. In our study, we determined ... ...

Abstract	The conserved Ser/Thr kinase Atg1/ULK1 plays a crucial role in the regulation of autophagy. However, only very few Atg1 targets have been identified, impeding elucidation of the mechanisms by which Atg1 regulates autophagy. In our study, we determined the Saccharomyces cerevisiae Atg1 consensus phosphorylation sequence using a peptide array-based approach. Among proteins containing this sequence we identified Atg9, another essential component of the autophagic machinery. We showed that phosphorylation of Atg9 by Atg1 is required for phagophore elongation, shedding light on the mechanism by which Atg1 regulates early steps of autophagy.
MeSH term(s)	Autophagy ; Autophagy-Related Proteins ; Membrane Proteins/metabolism ; Models, Biological ; Phagosomes/metabolism ; Phosphorylation ; Protein Kinases/metabolism ; Saccharomyces cerevisiae/cytology ; Saccharomyces cerevisiae/enzymology ; Saccharomyces cerevisiae Proteins/metabolism
Chemical Substances	ATG9 protein, S cerevisiae ; Autophagy-Related Proteins ; Membrane Proteins ; Saccharomyces cerevisiae Proteins ; Protein Kinases (EC 2.7.-) ; ATG1 protein, S cerevisiae (EC 2.7.1.-)
Language	English
Publishing date	2014-04-28
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	10.4161/auto.28971
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Article ; Online: Reconstitution reveals Ykt6 as the autophagosomal SNARE in autophagosome-vacuole fusion.

Bas, Levent / Papinski, Daniel / Licheva, Mariya / Torggler, Raffaela / Rohringer, Sabrina / Schuschnig, Martina / Kraft, Claudine

The Journal of cell biology

2018 Volume 217, Issue 10, Page(s) 3656–3669

Abstract: Autophagy mediates the bulk degradation of cytoplasmic material, particularly during starvation. Upon the induction of autophagy, autophagosomes form a sealed membrane around cargo, fuse with a lytic compartment, and release the cargo for degradation. ... ...

Abstract	Autophagy mediates the bulk degradation of cytoplasmic material, particularly during starvation. Upon the induction of autophagy, autophagosomes form a sealed membrane around cargo, fuse with a lytic compartment, and release the cargo for degradation. The mechanism of autophagosome-vacuole fusion is poorly understood, although factors that mediate other cellular fusion events have been implicated. In this study, we developed an in vitro reconstitution assay that enables systematic discovery and dissection of the players involved in autophagosome-vacuole fusion. We found that this process requires the Atg14-Vps34 complex to generate PI3P and thus recruit the Ypt7 module to autophagosomes. The HOPS-tethering complex, recruited by Ypt7, is required to prepare SNARE proteins for fusion. Furthermore, we discovered that fusion requires the R-SNARE Ykt6 on the autophagosome, together with the Q-SNAREs Vam3, Vam7, and Vti1 on the vacuole. These findings shed new light on the mechanism of autophagosome-vacuole fusion and reveal that the R-SNARE Ykt6 is required for this process.
MeSH term(s)	Autophagosomes/metabolism ; Class III Phosphatidylinositol 3-Kinases/genetics ; Class III Phosphatidylinositol 3-Kinases/metabolism ; Membrane Fusion ; Qa-SNARE Proteins/genetics ; Qa-SNARE Proteins/metabolism ; Qb-SNARE Proteins/genetics ; Qb-SNARE Proteins/metabolism ; R-SNARE Proteins/genetics ; R-SNARE Proteins/metabolism ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism ; Synaptosomal-Associated Protein 25/genetics ; Synaptosomal-Associated Protein 25/metabolism ; Vacuoles/genetics ; Vacuoles/metabolism ; rab GTP-Binding Proteins/genetics ; rab GTP-Binding Proteins/metabolism
Chemical Substances	Qa-SNARE Proteins ; Qb-SNARE Proteins ; R-SNARE Proteins ; Saccharomyces cerevisiae Proteins ; Synaptosomal-Associated Protein 25 ; VAM3 protein, S cerevisiae ; VAM7 protein, S cerevisiae ; VTI1 protein, S cerevisiae ; YKT6 protein, S cerevisiae ; Class III Phosphatidylinositol 3-Kinases (EC 2.7.1.137) ; YPT7 protein, S cerevisiae (EC 3.6.1.-) ; rab GTP-Binding Proteins (EC 3.6.5.2)
Language	English
Publishing date	2018-08-10
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	218154-x
ISSN	1540-8140 ; 0021-9525
ISSN (online)	1540-8140
ISSN	0021-9525
DOI	10.1083/jcb.201804028
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Article ; Online: Atg9 establishes Atg2-dependent contact sites between the endoplasmic reticulum and phagophores.

Gómez-Sánchez, Rubén / Rose, Jaqueline / Guimarães, Rodrigo / Mari, Muriel / Papinski, Daniel / Rieter, Ester / Geerts, Willie J / Hardenberg, Ralph / Kraft, Claudine / Ungermann, Christian / Reggiori, Fulvio

The Journal of cell biology

2018 Volume 217, Issue 8, Page(s) 2743–2763

Abstract: The autophagy-related (Atg) proteins play a key role in the formation of autophagosomes, the hallmark of autophagy. The function of the cluster composed by Atg2, Atg18, and transmembrane Atg9 is completely unknown despite their importance in autophagy. ... ...

Abstract	The autophagy-related (Atg) proteins play a key role in the formation of autophagosomes, the hallmark of autophagy. The function of the cluster composed by Atg2, Atg18, and transmembrane Atg9 is completely unknown despite their importance in autophagy. In this study, we provide insights into the molecular role of these proteins by identifying and characterizing Atg2 point mutants impaired in Atg9 binding. We show that Atg2 associates to autophagosomal membranes through lipid binding and independently from Atg9. Its interaction with Atg9, however, is key for Atg2 confinement to the growing phagophore extremities and subsequent association of Atg18. Assembly of the Atg9-Atg2-Atg18 complex is important to establish phagophore-endoplasmic reticulum (ER) contact sites. In turn, disruption of the Atg2-Atg9 interaction leads to an aberrant topological distribution of both Atg2 and ER contact sites on forming phagophores, which severely impairs autophagy. Altogether, our data shed light in the interrelationship between Atg9, Atg2, and Atg18 and highlight the possible functional relevance of the phagophore-ER contact sites in phagophore expansion.
MeSH term(s)	Autophagy/physiology ; Autophagy-Related Proteins/genetics ; Autophagy-Related Proteins/metabolism ; Autophagy-Related Proteins/physiology ; Endoplasmic Reticulum/metabolism ; Lipid Metabolism ; Membrane Proteins/genetics ; Membrane Proteins/metabolism ; Membrane Proteins/physiology ; Phosphatidylinositol Phosphates/metabolism ; Phosphatidylinositol Phosphates/physiology ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism ; Saccharomyces cerevisiae Proteins/physiology
Chemical Substances	ATG18 protein, S cerevisiae ; ATG2 protein, S cerevisiae ; ATG9 protein, S cerevisiae ; Autophagy-Related Proteins ; Membrane Proteins ; Phosphatidylinositol Phosphates ; Saccharomyces cerevisiae Proteins ; phosphatidylinositol 3-phosphate
Language	English
Publishing date	2018-05-30
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	218154-x
ISSN	1540-8140 ; 0021-9525
ISSN (online)	1540-8140
ISSN	0021-9525
DOI	10.1083/jcb.201710116
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Article ; Online: An Early mtUPR: Redistribution of the Nuclear Transcription Factor Rox1 to Mitochondria Protects against Intramitochondrial Proteotoxic Aggregates.

Poveda-Huertes, Daniel / Matic, Stanka / Marada, Adinarayana / Habernig, Lukas / Licheva, Mariya / Myketin, Lisa / Gilsbach, Ralf / Tosal-Castano, Sergi / Papinski, Daniel / Mulica, Patrycja / Kretz, Oliver / Kücükköse, Cansu / Taskin, Asli Aras / Hein, Lutz / Kraft, Claudine / Büttner, Sabrina / Meisinger, Chris / Vögtle, F-Nora

Molecular cell

2019 Volume 77, Issue 1, Page(s) 180–188.e9

Abstract: The mitochondrial proteome is built mainly by import of nuclear-encoded precursors, which are targeted mostly by cleavable presequences. Presequence processing upon import is essential for proteostasis and survival, but the consequences of dysfunctional ... ...

Abstract	The mitochondrial proteome is built mainly by import of nuclear-encoded precursors, which are targeted mostly by cleavable presequences. Presequence processing upon import is essential for proteostasis and survival, but the consequences of dysfunctional protein maturation are unknown. We find that impaired presequence processing causes accumulation of precursors inside mitochondria that form aggregates, which escape degradation and unexpectedly do not cause cell death. Instead, cells survive via activation of a mitochondrial unfolded protein response (mtUPR)-like pathway that is triggered very early after precursor accumulation. In contrast to classical stress pathways, this immediate response maintains mitochondrial protein import, membrane potential, and translation through translocation of the nuclear HMG-box transcription factor Rox1 to mitochondria. Rox1 binds mtDNA and performs a TFAM-like function pivotal for transcription and translation. Induction of early mtUPR provides a reversible stress model to mechanistically dissect the initial steps in mtUPR pathways with the stressTFAM Rox1 as the first line of defense.
MeSH term(s)	Cell Death/physiology ; Cell Nucleus/metabolism ; DNA, Mitochondrial/metabolism ; Membrane Potentials/physiology ; Mitochondria/metabolism ; Protein Biosynthesis/physiology ; Repressor Proteins/metabolism ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/metabolism ; Transcription Factors/metabolism ; Transcription, Genetic/physiology ; Unfolded Protein Response/physiology
Chemical Substances	DNA, Mitochondrial ; ROX1 protein, S cerevisiae ; Repressor Proteins ; Saccharomyces cerevisiae Proteins ; Transcription Factors
Language	English
Publishing date	2019-10-17
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1415236-8
ISSN	1097-4164 ; 1097-2765
ISSN (online)	1097-4164
ISSN	1097-2765
DOI	10.1016/j.molcel.2019.09.026
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Zs.A 5055: Show issues

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Article ; Online: Hrr25 kinase promotes selective autophagy by phosphorylating the cargo receptor Atg19.

Pfaffenwimmer, Thaddaeus / Reiter, Wolfgang / Brach, Thorsten / Nogellova, Veronika / Papinski, Daniel / Schuschnig, Martina / Abert, Christine / Ammerer, Gustav / Martens, Sascha / Kraft, Claudine

EMBO reports

2014 Volume 15, Issue 8, Page(s) 862–870

Abstract: Autophagy is the major pathway for the delivery of cytoplasmic material to the vacuole or lysosome. Selective autophagy is mediated by cargo receptors, which link the cargo to the scaffold protein Atg11 and to Atg8 family proteins on the forming ... ...

Abstract	Autophagy is the major pathway for the delivery of cytoplasmic material to the vacuole or lysosome. Selective autophagy is mediated by cargo receptors, which link the cargo to the scaffold protein Atg11 and to Atg8 family proteins on the forming autophagosomal membrane. We show that the essential kinase Hrr25 activates the cargo receptor Atg19 by phosphorylation, which is required to link cargo to the Atg11 scaffold, allowing selective autophagy to proceed. We also find that the Atg34 cargo receptor is regulated in a similar manner, suggesting a conserved mechanism.
MeSH term(s)	Amino Acid Sequence ; Autophagy ; Autophagy-Related Proteins ; Casein Kinase I/physiology ; Molecular Sequence Data ; Phosphorylation ; Protein Binding ; Protein Interaction Domains and Motifs ; Protein Processing, Post-Translational ; Protein Transport ; Receptors, Cell Surface/chemistry ; Receptors, Cell Surface/metabolism ; Receptors, Cytoplasmic and Nuclear/metabolism ; Saccharomyces cerevisiae/enzymology ; Saccharomyces cerevisiae Proteins/chemistry ; Saccharomyces cerevisiae Proteins/metabolism ; Saccharomyces cerevisiae Proteins/physiology ; Vesicular Transport Proteins/chemistry ; Vesicular Transport Proteins/metabolism
Chemical Substances	ATG19 protein, S cerevisiae ; Atg11 protein, S cerevisiae ; Atg34 protein, S cerevisiae ; Autophagy-Related Proteins ; Receptors, Cell Surface ; Receptors, Cytoplasmic and Nuclear ; Saccharomyces cerevisiae Proteins ; Vesicular Transport Proteins ; Casein Kinase I (EC 2.7.11.1) ; HRR25 protein, S cerevisiae (EC 2.7.11.1)
Language	English
Publishing date	2014-06-26
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2020896-0
ISSN	1469-3178 ; 1469-221X
ISSN (online)	1469-3178
ISSN	1469-221X
DOI	10.15252/embr.201438932
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Zs.A 5433: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: The bacterial translocon SecYEG opens upon ribosome binding.

Knyazev, Denis G / Lents, Alexander / Krause, Eberhard / Ollinger, Nicole / Siligan, Christine / Papinski, Daniel / Winter, Lukas / Horner, Andreas / Pohl, Peter

The Journal of biological chemistry

2013 Volume 288, Issue 25, Page(s) 17941–17946

Abstract: In co-translational translocation, the ribosome funnel and the channel of the protein translocation complex SecYEG are aligned. For the nascent chain to enter the channel immediately after synthesis, a yet unidentified signal triggers displacement of the ...

Abstract	In co-translational translocation, the ribosome funnel and the channel of the protein translocation complex SecYEG are aligned. For the nascent chain to enter the channel immediately after synthesis, a yet unidentified signal triggers displacement of the SecYEG sealing plug from the pore. Here, we show that ribosome binding to the resting SecYEG channel triggers this conformational transition. The purified and reconstituted SecYEG channel opens to form a large ion-conducting channel, which has the conductivity of the plug deletion mutant. The number of ion-conducting channels inserted into the planar bilayer per fusion event roughly equals the number of SecYEG channels counted by fluorescence correlation spectroscopy in a single proteoliposome. Thus, the open probability of the channel must be close to unity. To prevent the otherwise lethal proton leak, a closed post-translational conformation of the SecYEG complex bound to a ribosome must exist.
MeSH term(s)	Escherichia coli Proteins/genetics ; Escherichia coli Proteins/metabolism ; Ion Channel Gating ; Ion Channels/genetics ; Ion Channels/metabolism ; Lipid Bilayers/metabolism ; Membrane Lipids/metabolism ; Membrane Proteins/genetics ; Membrane Proteins/metabolism ; Microscopy, Confocal ; Multiprotein Complexes/genetics ; Multiprotein Complexes/metabolism ; Mutation ; Protein Binding ; Protein Transport ; Ribosomes/metabolism ; SEC Translocation Channels ; Spectrometry, Fluorescence
Chemical Substances	Escherichia coli Proteins ; Ion Channels ; Lipid Bilayers ; Membrane Lipids ; Membrane Proteins ; Multiprotein Complexes ; SEC Translocation Channels ; SecE protein, E coli ; SecG protein, E coli ; SecY protein, E coli
Language	English
Publishing date	2013-05-03
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1074/jbc.M113.477893
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