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Article: Switching on regeneration.

van der Vaart, Aniek / van den Heuvel, Sander

2016 Volume 3, Page(s) 41

Language	English
Publishing date	2016-08-19
Publishing country	China
Document type	Comment ; Journal Article
ZDB-ID	2884645-X
ISSN	2313-0792 ; 2306-9759
ISSN (online)	2313-0792
ISSN	2306-9759
DOI	10.21037/sci.2016.08.05
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Article ; Online: Dose-dependent functions of SWI/SNF BAF in permitting and inhibiting cell proliferation in vivo.

van der Vaart, Aniek / Godfrey, Molly / Portegijs, Vincent / van den Heuvel, Sander

Science advances

2020 Volume 6, Issue 21, Page(s) eaay3823

Abstract: SWI/SNF (switch/sucrose nonfermenting) complexes regulate transcription through chromatin remodeling and opposing gene silencing by Polycomb group (PcG) proteins. Genes encoding SWI/SNF components are critical for normal development and frequently ... ...

Abstract	SWI/SNF (switch/sucrose nonfermenting) complexes regulate transcription through chromatin remodeling and opposing gene silencing by Polycomb group (PcG) proteins. Genes encoding SWI/SNF components are critical for normal development and frequently mutated in human cancer. We characterized the in vivo contributions of SWI/SNF and PcG complexes to proliferation-differentiation decisions, making use of the reproducible development of the nematode
Language	English
Publishing date	2020-05-20
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2810933-8
ISSN	2375-2548 ; 2375-2548
ISSN (online)	2375-2548
ISSN	2375-2548
DOI	10.1126/sciadv.aay3823
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Article ; Online: DLK-1/p38 MAP Kinase Signaling Controls Cilium Length by Regulating RAB-5 Mediated Endocytosis in Caenorhabditis elegans.

van der Vaart, Aniek / Rademakers, Suzanne / Jansen, Gert

PLoS genetics

2015 Volume 11, Issue 12, Page(s) e1005733

Abstract: Cilia are sensory organelles present on almost all vertebrate cells. Cilium length is constant, but varies between cell types, indicating that cilium length is regulated. How this is achieved is unclear, but protein transport in cilia (intraflagellar ... ...

Abstract	Cilia are sensory organelles present on almost all vertebrate cells. Cilium length is constant, but varies between cell types, indicating that cilium length is regulated. How this is achieved is unclear, but protein transport in cilia (intraflagellar transport, IFT) plays an important role. Several studies indicate that cilium length and function can be modulated by environmental cues. As a model, we study a C. elegans mutant that carries a dominant active G protein α subunit (gpa-3QL), resulting in altered IFT and short cilia. In a screen for suppressors of the gpa-3QL short cilium phenotype, we identified uev-3, which encodes an E2 ubiquitin-conjugating enzyme variant that acts in a MAP kinase pathway. Mutation of two other components of this pathway, dual leucine zipper-bearing MAPKKK DLK-1 and p38 MAPK PMK-3, also suppress the gpa-3QL short cilium phenotype. However, this suppression seems not to be caused by changes in IFT. The DLK-1/p38 pathway regulates several processes, including microtubule stability and endocytosis. We found that reducing endocytosis by mutating rabx-5 or rme-6, RAB-5 GEFs, or the clathrin heavy chain, suppresses gpa-3QL. In addition, gpa-3QL animals showed reduced levels of two GFP-tagged proteins involved in endocytosis, RAB-5 and DPY-23, whereas pmk-3 mutant animals showed accumulation of GFP-tagged RAB-5. Together our results reveal a new role for the DLK-1/p38 MAPK pathway in control of cilium length by regulating RAB-5 mediated endocytosis.
MeSH term(s)	Animals ; Caenorhabditis elegans/cytology ; Caenorhabditis elegans/genetics ; Caenorhabditis elegans/metabolism ; Caenorhabditis elegans Proteins/genetics ; Caenorhabditis elegans Proteins/metabolism ; Cilia/metabolism ; Endocytosis ; GTP-Binding Protein alpha Subunits, Gi-Go/genetics ; GTP-Binding Protein alpha Subunits, Gi-Go/metabolism ; Guanine Nucleotide Exchange Factors/genetics ; Guanine Nucleotide Exchange Factors/metabolism ; MAP Kinase Kinase Kinases/genetics ; MAP Kinase Kinase Kinases/metabolism ; MAP Kinase Signaling System ; Mitogen-Activated Protein Kinases/genetics ; Mitogen-Activated Protein Kinases/metabolism
Chemical Substances	Caenorhabditis elegans Proteins ; Guanine Nucleotide Exchange Factors ; RABX-5 protein, C elegans ; RME-6 protein, C elegans ; gpa-3 protein, C elegans ; Mitogen-Activated Protein Kinases (EC 2.7.11.24) ; pmk-3 protein, C elegans (EC 2.7.11.24) ; DLK-1 protein, C elegans (EC 2.7.11.25) ; MAP Kinase Kinase Kinases (EC 2.7.11.25) ; GTP-Binding Protein alpha Subunits, Gi-Go (EC 3.6.5.1)
Language	English
Publishing date	2015-12
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2186725-2
ISSN	1553-7404 ; 1553-7390
ISSN (online)	1553-7404
ISSN	1553-7390
DOI	10.1371/journal.pgen.1005733
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Article ; Online: Understanding phosphatidylinositol-3-phosphate dynamics during autophagosome biogenesis.

Cebollero, Eduardo / van der Vaart, Aniek / Reggiori, Fulvio

Autophagy

2012 Volume 8, Issue 12, Page(s) 1868–1870

Abstract: Autophagosomes, the hallmark of autophagy, are double-membrane vesicles sequestering cytoplasmic components. They are generated at the phagophore assembly site (PAS), the phagophore being the precursor structure of these carriers. According to the ... ...

Abstract	Autophagosomes, the hallmark of autophagy, are double-membrane vesicles sequestering cytoplasmic components. They are generated at the phagophore assembly site (PAS), the phagophore being the precursor structure of these carriers. According to the current model, autophagosomes result from the elongation and reorganization of membranes at the PAS/phagophore driven by the concerted action of the autophagy-related (Atg) proteins. Once an autophagosome is completed, the Atg proteins that were associated with the expanding phagophore are released in the cytoplasm and reused for the biogenesis of new vesicles. One molecular event required for autophagosome formation is the generation of phosphatidylinositol 3-phosphate (PtdIns3P) at the PAS. Our data indicate that in addition to the synthesis of this lipid, the dephosphorylation of PtdIns3P is also crucial for autophagy progression. In the absence of Ymr1, a specific PtdIns3P phosphatase and the only yeast member of the myotubularin protein family, Atg proteins remain associated with complete autophagosomes, which are thus unable to fuse with the vacuole.
MeSH term(s)	Animals ; Autophagy ; Endosomes/metabolism ; Humans ; Models, Biological ; Multivesicular Bodies/metabolism ; Phagosomes/metabolism ; Phosphatidylinositol Phosphates/metabolism ; Saccharomyces cerevisiae/cytology ; Saccharomyces cerevisiae/metabolism
Chemical Substances	Phosphatidylinositol Phosphates ; phosphatidylinositol 3-phosphate
Language	English
Publishing date	2012-09-19
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.22162
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Article ; Online: The Golgi complex as a source for yeast autophagosomal membranes.

van der Vaart, Aniek / Reggiori, Fulvio

Autophagy

2010 Volume 6, Issue 6, Page(s) 800–801

Abstract: Today, more than 50 years after the discovery of autophagy, the origin of the autophagosomal membranes remains for the most part elusive. Many sources for the lipid bilayers have been proposed, but no conclusive evidence has been found to support one ... ...

Abstract	Today, more than 50 years after the discovery of autophagy, the origin of the autophagosomal membranes remains for the most part elusive. Many sources for the lipid bilayers have been proposed, but no conclusive evidence has been found to support one particular origin. The lipids do not appear to be generated at the site of autophagosome formation, the phagophore assembly site (PAS), since so far no lipid synthesizing enzyme has been found at this location. The current consensus is also that the autophagosomes do not directly bud off from a pre-existing compartment, and recent evidence in mammalian cells has revealed that the nascent autophagosome could expand through a lipid transfer mechanism from an adjacent organelle. In yeast, such an event has never been observed and data from our and other laboratories suggest that the Golgi complex could be a key player in mediating the expansion of the phagophore.
MeSH term(s)	Animals ; Autophagy ; Golgi Apparatus/metabolism ; Intracellular Membranes/metabolism ; Models, Biological ; Phagosomes/metabolism ; Protein Transport ; Saccharomyces cerevisiae/cytology ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/metabolism
Chemical Substances	Saccharomyces cerevisiae Proteins
Language	English
Publishing date	2010-08
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	10.1091/mbc.E09-04-0345
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Article ; Online: Exit from the Golgi is required for the expansion of the autophagosomal phagophore in yeast Saccharomyces cerevisiae.

van der Vaart, Aniek / Griffith, Janice / Reggiori, Fulvio

Molecular biology of the cell

2010 Volume 21, Issue 13, Page(s) 2270–2284

Abstract: The delivery of proteins and organelles to the vacuole by autophagy involves membrane rearrangements that result in the formation of large vesicles called autophagosomes. The mechanism underlying autophagosome biogenesis and the origin of the membranes ... ...

Abstract	The delivery of proteins and organelles to the vacuole by autophagy involves membrane rearrangements that result in the formation of large vesicles called autophagosomes. The mechanism underlying autophagosome biogenesis and the origin of the membranes composing these vesicles remains largely unclear. We have investigated the role of the Golgi complex in autophagy and have determined that in yeast, activation of ADP-ribosylation factor (Arf)1 and Arf2 GTPases by Sec7, Gea1, and Gea2 is essential for this catabolic process. The two main events catalyzed by these components, the biogenesis of COPI- and clathrin-coated vesicles, do not play a critical role in autophagy. Analysis of the sec7 strain under starvation conditions revealed that the autophagy machinery is correctly assembled and the precursor membrane cisterna of autophagosomes, the phagophore, is normally formed. However, the expansion of the phagophore into an autophagosome is severely impaired. Our data show that the Golgi complex plays a crucial role in supplying the lipid bilayers necessary for the biogenesis of double-membrane vesicles possibly through a new class of transport carriers or a new mechanism.
MeSH term(s)	ADP-Ribosylation Factor 1/genetics ; ADP-Ribosylation Factor 1/metabolism ; ADP-Ribosylation Factors/genetics ; ADP-Ribosylation Factors/metabolism ; Antifungal Agents/pharmacology ; Autophagy/physiology ; Autophagy-Related Protein 8 Family ; Golgi Apparatus/metabolism ; Golgi Apparatus/ultrastructure ; Guanine Nucleotide Exchange Factors/genetics ; Guanine Nucleotide Exchange Factors/metabolism ; Intracellular Membranes/metabolism ; Intracellular Membranes/ultrastructure ; Microtubule-Associated Proteins/genetics ; Microtubule-Associated Proteins/metabolism ; Phagosomes/metabolism ; Phagosomes/ultrastructure ; Recombinant Fusion Proteins/genetics ; Recombinant Fusion Proteins/metabolism ; Saccharomyces cerevisiae/cytology ; Saccharomyces cerevisiae/drug effects ; Saccharomyces cerevisiae/physiology ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism ; Sirolimus/pharmacology ; Vacuoles/metabolism
Chemical Substances	ATG8 protein, S cerevisiae ; Antifungal Agents ; Autophagy-Related Protein 8 Family ; GEA1 protein, S cerevisiae ; GEA2 protein, S cerevisiae ; Guanine Nucleotide Exchange Factors ; Microtubule-Associated Proteins ; Recombinant Fusion Proteins ; Saccharomyces cerevisiae Proteins ; Sec7 guanine nucleotide exchange factors ; ARF2 protein, S cerevisiae (EC 3.6.1.-) ; ADP-Ribosylation Factor 1 (EC 3.6.5.2) ; ADP-Ribosylation Factors (EC 3.6.5.2) ; Sirolimus (W36ZG6FT64)
Language	English
Publishing date	2010-05-05
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1098979-1
ISSN	1939-4586 ; 1059-1524
ISSN (online)	1939-4586
ISSN	1059-1524
DOI	10.1091/mbc.E09-04-0345
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Zs.A 2853: 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: A picky eater: exploring the mechanisms of selective autophagy in human pathologies.

van der Vaart, Aniek / Mari, Muriel / Reggiori, Fulvio

Traffic (Copenhagen, Denmark)

2008 Volume 9, Issue 3, Page(s) 281–289

Abstract: Autophagy is a catabolic process conserved among all eukaryotes essential for the cellular and organismal homeostasis. One of the principal roles of this pathway is to maintain an accurate balance between synthesis, degradation and subsequent recycling ... ...

Abstract	Autophagy is a catabolic process conserved among all eukaryotes essential for the cellular and organismal homeostasis. One of the principal roles of this pathway is to maintain an accurate balance between synthesis, degradation and subsequent recycling of cellular components. Under certain conditions, however, cells are also able to modulate autophagy and specifically remove a number of structures that are potentially harmful. Aberrant protein aggregates, damaged organelles or pathogens can be selectively incorporated into large double-membrane vesicles called autophagosomes to be delivered into lysosomes for destruction. This ability to eliminate specific structures is exploited by the cells in several physiological processes as well as in multiple pathological situations, making autophagy a precious multitask cellular degradative pathway. In this review, we will first examine what is known about the basic mechanisms of autophagy and then discuss in a second part the nature of the cargoes that are selectively sequestered into autophagosomes, what provides the specificity and the possible implications of selective types of autophagy in human pathologies.
MeSH term(s)	Aging/pathology ; Aging/physiology ; Autophagy/genetics ; Autophagy/physiology ; Endoplasmic Reticulum/metabolism ; Genes, Fungal ; Humans ; Infection/pathology ; Infection/physiopathology ; Models, Biological ; Multiprotein Complexes ; Oxidative Stress ; Phagosomes/physiology ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/physiology ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/physiology
Chemical Substances	Multiprotein Complexes ; Saccharomyces cerevisiae Proteins
Language	English
Publishing date	2008-03
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	1483852-7
ISSN	1600-0854 ; 1398-9219
ISSN (online)	1600-0854
ISSN	1398-9219
DOI	10.1111/j.1600-0854.2007.00674.x
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Article ; Online: Phosphatidylinositol-3-phosphate clearance plays a key role in autophagosome completion.

Cebollero, Eduardo / van der Vaart, Aniek / Zhao, Mantong / Rieter, Ester / Klionsky, Daniel J / Helms, J Bernd / Reggiori, Fulvio

Current biology : CB

2012 Volume 22, Issue 17, Page(s) 1545–1553

Abstract: Background: The biogenesis of autophagosomes, the hallmark of autophagy, depends on the function of the autophagy-related (Atg) proteins and the generation of phosphatidylinositol-3-phosphate (PtdIns3P) at the phagophore assembly site (PAS), the ... ...

Abstract	Background: The biogenesis of autophagosomes, the hallmark of autophagy, depends on the function of the autophagy-related (Atg) proteins and the generation of phosphatidylinositol-3-phosphate (PtdIns3P) at the phagophore assembly site (PAS), the location where autophagosomes arise. The current model is that PtdIns3P is involved primarily in the recruitment of Atg proteins to the PAS and that once an autophagosome is complete, the Atg machinery is released from its surface back into the cytoplasm and reused for the formation of new vesicles. Results: We have identified a PtdIns3P phosphatase, Ymr1, that is essential for the normal progression of both bulk and selective types of autophagy. This protein is recruited to the PAS at an early stage of formation of this structure through a process that requires both its GRAM domain and its catalytic activity. In the absence of Ymr1, Atg proteins fail to dissociate from the limiting membrane of autophagosomes, and these vesicles accumulate in the cytoplasm. Conclusions: Our data thus reveal a key role for PtdIns3P turnover in the regulation of the late steps of autophagosome biogenesis and indicate that the disassembly of the Atg machinery from the surface of autophagosomes is a requisite for their fusion with the vacuole.
MeSH term(s)	Autophagy/physiology ; Fungal Proteins/analysis ; Fungal Proteins/genetics ; Fungal Proteins/physiology ; Phosphatidylinositol Phosphates/metabolism ; Yeasts/cytology ; Yeasts/genetics ; Yeasts/metabolism
Chemical Substances	Fungal Proteins ; Phosphatidylinositol Phosphates ; phosphatidylinositol 3-phosphate
Language	English
Publishing date	2012-07-05
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1071731-6
ISSN	1879-0445 ; 0960-9822
ISSN (online)	1879-0445
ISSN	0960-9822
DOI	10.1016/j.cub.2012.06.029
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Article: A Picky Eater: Exploring the Mechanisms of Selective Autophagy in Human Pathologies

van der Vaart, Aniek / Mari, Muriel / Reggiori, Fulvio

Traffic. 2008 Mar., v. 9, no. 3

2008

Abstract	Autophagy is a catabolic process conserved among all eukaryotes essential for the cellular and organismal homeostasis. One of the principal roles of this pathway is to maintain an accurate balance between synthesis, degradation and subsequent recycling of cellular components. Under certain conditions, however, cells are also able to modulate autophagy and specifically remove a number of structures that are potentially harmful. Aberrant protein aggregates, damaged organelles or pathogens can be selectively incorporated into large double-membrane vesicles called autophagosomes to be delivered into lysosomes for destruction. This ability to eliminate specific structures is exploited by the cells in several physiological processes as well as in multiple pathological situations, making autophagy a precious multitask cellular degradative pathway. In this review, we will first examine what is known about the basic mechanisms of autophagy and then discuss in a second part the nature of the cargoes that are selectively sequestered into autophagosomes, what provides the specificity and the possible implications of selective types of autophagy in human pathologies.
Keywords	degradation ; immunity ; vacuoles
Language	English
Dates of publication	2008-03
Size	p. 281-289.
Publisher	Blackwell Publishing Ltd
Publishing place	Oxford, UK
Document type	Article
ZDB-ID	1483852-7
ISSN	1600-0854 ; 1398-9219
ISSN (online)	1600-0854
ISSN	1398-9219
DOI	10.1111/j.1600-0854.2007.00674.x
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Article ; Online: Autophagy competes for a common phosphatidylethanolamine pool with major cellular PE-consuming pathways in Saccharomyces cerevisiae.

Wilson-Zbinden, Caroline / dos Santos, Aline Xavier da Silveira / Stoffel-Studer, Ingrid / van der Vaart, Aniek / Hofmann, Kay / Reggiori, Fulvio / Riezman, Howard / Kraft, Claudine / Peter, Matthias

Genetics

2014 Volume 199, Issue 2, Page(s) 475–485

Abstract: Autophagy is a highly regulated pathway that selectively degrades cellular constituents such as protein aggregates and excessive or damaged organelles. This transport route is characterized by engulfment of the targeted cargo by autophagosomes. The ... ...

Abstract	Autophagy is a highly regulated pathway that selectively degrades cellular constituents such as protein aggregates and excessive or damaged organelles. This transport route is characterized by engulfment of the targeted cargo by autophagosomes. The formation of these double-membrane vesicles requires the covalent conjugation of the ubiquitin-like protein Atg8 to phosphatidylethanolamine (PE). However, the origin of PE and the regulation of lipid flux required for autophagy remain poorly understood. Using a genetic screen, we found that the temperature-sensitive growth and intracellular membrane organization defects of mcd4-174 and mcd4-P301L mutants are suppressed by deletion of essential autophagy genes such as ATG1 or ATG7. MCD4 encodes an ethanolamine phosphate transferase that uses PE as a precursor for an essential step in the synthesis of the glycosylphosphatidylinositol (GPI) anchor used to link a subset of plasma membrane proteins to lipid bilayers. Similar to the deletion of CHO2, a gene encoding the enzyme converting PE to phosphatidylcholine (PC), deletion of ATG7 was able to restore lipidation and plasma membrane localization of the GPI-anchored protein Gas1 and normal organization of intracellular membranes. Conversely, overexpression of Cho2 was lethal in mcd4-174 cells grown at restrictive temperature. Quantitative lipid analysis revealed that PE levels are substantially reduced in the mcd4-174 mutant but can be restored by deletion of ATG7 or CHO2. Taken together, these data suggest that autophagy competes for a common PE pool with major cellular PE-consuming pathways such as the GPI anchor and PC synthesis, highlighting the possible interplay between these pathways and the existence of signals that may coordinate PE flux.
MeSH term(s)	Autophagy/genetics ; Ethanolamines/metabolism ; Gene Deletion ; Gene Expression ; Gene Expression Profiling ; Genes, Essential ; Metabolic Networks and Pathways ; Mutation ; Phosphatidylethanolamines/metabolism ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/genetics ; Signal Transduction
Chemical Substances	Ethanolamines ; Phosphatidylethanolamines ; Saccharomyces cerevisiae Proteins ; phosphatidylethanolamine (39382-08-6)
Language	English
Publishing date	2014-12-17
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2167-2
ISSN	1943-2631 ; 0016-6731
ISSN (online)	1943-2631
ISSN	0016-6731
DOI	10.1534/genetics.114.169797
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