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Article ; Online: Mechanistic Insights into the Role of Atg11 in Selective Autophagy.

Zientara-Rytter, Katarzyna / Subramani, Suresh

2019 Volume 432, Issue 1, Page(s) 104–122

Abstract: Macroautophagy (referred to hereafter as autophagy) is an intracellular degradation pathway in which the formation of a double-membrane vesicle called the autophagosome is a key event in the transport of multiple cytoplasmic cargo (e.g., proteins, ... ...

Abstract	Macroautophagy (referred to hereafter as autophagy) is an intracellular degradation pathway in which the formation of a double-membrane vesicle called the autophagosome is a key event in the transport of multiple cytoplasmic cargo (e.g., proteins, protein aggregates, lipid droplets or organelles) to the vacuole (lysosome in mammals) for degradation and recycling. During this process, autophagosomes are formed de novo by membrane fusion events leading to phagophore formation initiated at the phagophore assembly site. In yeast, Atg11 and Atg17 function as protein scaffolds, essential for selective and non-selective types of autophagy, respectively. While Atg17 functions in non-selective autophagy are well-defined in the literature, less attention is concentrated on recent findings regarding the roles of Atg11 in selective autophagy. Here, we summarize current knowledge about the Atg11 scaffold protein and review recent findings in the context of its role in selective autophagy initiation and autophagosome formation.
MeSH term(s)	Animals ; Autophagosomes/metabolism ; Autophagy ; Autophagy-Related Proteins/metabolism ; Humans ; Macroautophagy ; Protein Interaction Maps ; Saccharomyces cerevisiae/cytology ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/metabolism ; Vesicular Transport Proteins/metabolism
Chemical Substances	Atg11 protein, S cerevisiae ; Atg17 protein, S cerevisiae ; Autophagy-Related Proteins ; Saccharomyces cerevisiae Proteins ; Vesicular Transport Proteins
Language	English
Publishing date	2019-06-22
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	80229-3
ISSN	1089-8638 ; 0022-2836
ISSN (online)	1089-8638
ISSN	0022-2836
DOI	10.1016/j.jmb.2019.06.017
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Article: The Roles of Ubiquitin-Binding Protein Shuttles in the Degradative Fate of Ubiquitinated Proteins in the Ubiquitin-Proteasome System and Autophagy.

Zientara-Rytter, Katarzyna / Subramani, Suresh

Cells

2019 Volume 8, Issue 1

Abstract: The ubiquitin-proteasome system (UPS) and autophagy are the two major intracellular protein quality control (PQC) pathways that are responsible for cellular proteostasis (homeostasis of the proteome) by ensuring the timely degradation of misfolded, ... ...

Abstract	The ubiquitin-proteasome system (UPS) and autophagy are the two major intracellular protein quality control (PQC) pathways that are responsible for cellular proteostasis (homeostasis of the proteome) by ensuring the timely degradation of misfolded, damaged, and unwanted proteins. Ubiquitination serves as the degradation signal in both these systems, but substrates are precisely targeted to one or the other pathway. Determining how and when cells target specific proteins to these two alternative PQC pathways and control the crosstalk between them are topics of considerable interest. The ubiquitin (Ub) recognition code based on the type of Ub-linked chains on substrate proteins was believed to play a pivotal role in this process, but an increasing body of evidence indicates that the PQC pathway choice is also made based on other criteria. These include the oligomeric state of the Ub-binding protein shuttles, their conformation, protein modifications, and the presence of motifs that interact with ATG8/LC3/GABARAP (autophagy-related protein 8/microtubule-associated protein 1A/1B-light chain 3/GABA type A receptor-associated protein) protein family members. In this review, we summarize the current knowledge regarding the Ub recognition code that is bound by Ub-binding proteasomal and autophagic receptors. We also discuss how cells can modify substrate fate by modulating the structure, conformation, and physical properties of these receptors to affect their shuttling between both degradation pathways.
MeSH term(s)	Animals ; Autophagy ; Humans ; Plants/metabolism ; Proteasome Endopeptidase Complex/metabolism ; Proteolysis ; Ubiquitin/metabolism ; Ubiquitin-Protein Ligase Complexes/metabolism ; Ubiquitinated Proteins/metabolism ; Ubiquitination ; Yeasts/metabolism
Chemical Substances	Ubiquitin ; Ubiquitinated Proteins ; Ubiquitin-Protein Ligase Complexes (EC 2.3.2.23) ; Proteasome Endopeptidase Complex (EC 3.4.25.1)
Language	English
Publishing date	2019-01-10
Publishing country	Switzerland
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2661518-6
ISSN	2073-4409
ISSN	2073-4409
DOI	10.3390/cells8010040
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: AIM/LIR-based fluorescent sensors-new tools to monitor mAtg8 functions.

Zientara-Rytter, Katarzyna / Subramani, Suresh

Autophagy

2018 Volume 14, Issue 6, Page(s) 1074–1078

Abstract: Macroautophagy/autophagy, a catabolic process by which cytoplasmic materials are degraded and recycled in lysosomes/vacuoles, remains a rapidly expanding research topic with the need for constantly improved methodologies to study each step of this ... ...

Abstract	Macroautophagy/autophagy, a catabolic process by which cytoplasmic materials are degraded and recycled in lysosomes/vacuoles, remains a rapidly expanding research topic with the need for constantly improved methodologies to study each step of this pathway. Recently Lee and colleagues, as well as Stolz et al., independently reported the development of new AIM/LIR-based fluorescent sensors, which mark individual endogenous mammalian Atg8-family (mAtg8) proteins without affecting the autophagic flux. When expressed in cells, each sensor selectively recognizes individual mAtg8 isoforms and distinguishes mammalian MAP1LC3/LC3 proteins from the related GABARAPs. Such selectivity was achieved by using various LC3-interacting regions with high binding affinity to either a subgroup, or a specific, mAtg8 isoform as part of the sensor. Here we discuss the utility of these sensors in autophagy research and highlight their strengths, weaknesses and future directions.
MeSH term(s)	Amino Acid Motifs ; Animals ; Autophagy-Related Protein 8 Family/metabolism ; Fluorescence ; Fluorescent Dyes/metabolism ; Humans ; Mammals/metabolism ; Microtubule-Associated Proteins/metabolism ; Protein Binding
Chemical Substances	Autophagy-Related Protein 8 Family ; Fluorescent Dyes ; Microtubule-Associated Proteins
Language	English
Publishing date	2018-05-11
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2454135-7
ISSN	1554-8635 ; 1554-8627
ISSN (online)	1554-8635
ISSN	1554-8627
DOI	10.1080/15548627.2018.1454238
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Article: Mechanistic Insights into the Role of Atg11 in Selective Autophagy

Zientara-Rytter, Katarzyna / Subramani, Suresh

Journal of molecular biology. 2020 Jan. 03, v. 432, no. 1

2020

Abstract	Macroautophagy (referred to hereafter as autophagy) is an intracellular degradation pathway in which the formation of a double-membrane vesicle called the autophagosome is a key event in the transport of multiple cytoplasmic cargo (e.g., proteins, protein aggregates, lipid droplets or organelles) to the vacuole (lysosome in mammals) for degradation and recycling. During this process, autophagosomes are formed de novo by membrane fusion events leading to phagophore formation initiated at the phagophore assembly site. In yeast, Atg11 and Atg17 function as protein scaffolds, essential for selective and non-selective types of autophagy, respectively. While Atg17 functions in non-selective autophagy are well-defined in the literature, less attention is concentrated on recent findings regarding the roles of Atg11 in selective autophagy. Here, we summarize current knowledge about the Atg11 scaffold protein and review recent findings in the context of its role in selective autophagy initiation and autophagosome formation.
Keywords	autophagy ; droplets ; lipids ; lysosomes ; mammals ; membrane fusion ; protein aggregates ; scaffolding proteins ; vacuoles ; yeasts
Language	English
Dates of publication	2020-0103
Size	p. 104-122.
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.2019.06.017
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Recognition and Chaperoning by Pex19, Followed by Trafficking and Membrane Insertion of the Peroxisome Proliferation Protein, Pex11.

Zientara-Rytter, Katarzyna M / Mahalingam, Shanmuga S / Farré, Jean-Claude / Carolino, Krypton / Subramani, Suresh

Cells

2022 Volume 11, Issue 1

Abstract: Pex11, an abundant peroxisomal membrane protein (PMP), is required for division of peroxisomes and is robustly imported to peroxisomal membranes. We present a comprehensive analysis of how ... ...

Abstract	Pex11, an abundant peroxisomal membrane protein (PMP), is required for division of peroxisomes and is robustly imported to peroxisomal membranes. We present a comprehensive analysis of how the
MeSH term(s)	Amino Acid Sequence ; Cell Proliferation ; Humans ; Membrane Proteins/metabolism ; Molecular Chaperones/metabolism
Chemical Substances	Membrane Proteins ; Molecular Chaperones ; PEX11A protein, human ; PEX19 protein, human (157153-79-2)
Language	English
Publishing date	2022-01-04
Publishing country	Switzerland
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2661518-6
ISSN	2073-4409 ; 2073-4409
ISSN (online)	2073-4409
ISSN	2073-4409
DOI	10.3390/cells11010157
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Balancing the Opposing Principles That Govern Peroxisome Homeostasis

Mahalingam, Shanmuga S / Shukla, Nandini / Farré, Jean-Claude / Zientara-Rytter, Katarzyna / Subramani, Suresh

Trends in biochemical sciences. 2021 Mar., v. 46, no. 3

2021

Abstract: Despite major advances in our understanding of players and mechanisms involved in peroxisome biogenesis and peroxisome degradation, very few studies have focused on unraveling the multi-layered connections between, and the coordination of, these two ... ...

Abstract	Despite major advances in our understanding of players and mechanisms involved in peroxisome biogenesis and peroxisome degradation, very few studies have focused on unraveling the multi-layered connections between, and the coordination of, these two opposing processes that regulate peroxisome homeostasis. The intersection between these processes also provides exciting avenues for future research. This review highlights the links between peroxisome biogenesis and degradation, incorporating an integrative approach that is critical not only for a mechanistic understanding, but also for manipulating the balance between these processes in relevant disease models.
Keywords	biogenesis ; disease models ; homeostasis
Language	English
Dates of publication	2021-03
Size	p. 200-212.
Publishing place	Elsevier Ltd
Document type	Article
Note	NALT-AP-4-rerunAP2-fuzzy
ZDB-ID	194220-7
ISSN	0968-0004 ; 0376-5067
ISSN	0968-0004 ; 0376-5067
DOI	10.1016/j.tibs.2020.09.006
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Fluorescent Reporters for Ubiquitin-Dependent Proteolysis in Plants.

Zientara-Rytter, Katarzyna / Sirko, Agnieszka

Methods in molecular biology (Clifton, N.J.)

2016 Volume 1450, Page(s) 45–54

Abstract: Ubiquitin is a small protein commonly used as a signal molecule which upon attachment to the proteins affects their function and their fate in the cells. For example, it can be used as a degradation marker by the cell. Ubiquitin plays a significant role ... ...

Abstract	Ubiquitin is a small protein commonly used as a signal molecule which upon attachment to the proteins affects their function and their fate in the cells. For example, it can be used as a degradation marker by the cell. Ubiquitin plays a significant role in regulation of numerous cellular processes. Therefore, monitoring of ubiquitin-dependent proteolysis can provide important information. Here, we describe construction of YFP-based proteasome substrates containing modified ubiquitin and the protocol for their transient expression in plant cells for functional analysis of the ubiquitin/proteasome system. To facilitate further subcloning all plasmids generated by us are based on the Gateway(®) Cloning Technology and are compatible with the Gateway(®) destination vectors.
Language	English
Publishing date	2016
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-4939-3759-2_5
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Autophagic degradation of peroxisomes in mammals.

Zientara-Rytter, Katarzyna / Subramani, Suresh

Biochemical Society transactions

2016 Volume 44, Issue 2, Page(s) 431–440

Abstract: Peroxisomes are essential organelles required for proper cell function in all eukaryotic organisms. They participate in a wide range of cellular processes including the metabolism of lipids and generation, as well as detoxification, of hydrogen peroxide ( ...

Abstract	Peroxisomes are essential organelles required for proper cell function in all eukaryotic organisms. They participate in a wide range of cellular processes including the metabolism of lipids and generation, as well as detoxification, of hydrogen peroxide (H2O2). Therefore, peroxisome homoeostasis, manifested by the precise and efficient control of peroxisome number and functionality, must be tightly regulated in response to environmental changes. Due to the existence of many physiological disorders and diseases associated with peroxisome homoeostasis imbalance, the dynamics of peroxisomes have been widely examined. The increasing volume of reports demonstrating significant involvement of the autophagy machinery in peroxisome removal leads us to summarize current knowledge of peroxisome degradation in mammalian cells. In this review we present current models of peroxisome degradation. We particularly focus on pexophagy-the selective clearance of peroxisomes through autophagy. We also critically discuss concepts of peroxisome recognition for pexophagy, including signalling and selectivity factors. Finally, we present examples of the pathological effects of pexophagy dysfunction and suggest promising future directions.
MeSH term(s)	Animals ; Autophagy ; Humans ; Mammals ; Models, Biological ; Peroxisomes/metabolism
Language	English
Publishing date	2016--15
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Review
ZDB-ID	184237-7
ISSN	1470-8752 ; 0300-5127
ISSN (online)	1470-8752
ISSN	0300-5127
DOI	10.1042/BST20150268
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Article ; Online: Role of actin in shaping autophagosomes.

Zientara-Rytter, Katarzyna / Subramani, Suresh

Autophagy

2016 Volume 12, Issue 12, Page(s) 2512–2515

Abstract: One of the main unanswered questions regarding the early steps of macroautophagy/autophagy is the mechanism of membrane-modeling events required for autophagosome formation. Three independent studies have recently revealed an actin cytoskeleton ... ...

Abstract	One of the main unanswered questions regarding the early steps of macroautophagy/autophagy is the mechanism of membrane-modeling events required for autophagosome formation. Three independent studies have recently revealed an actin cytoskeleton involvement in this process, providing significant details regarding the role of actin in nucleation events both inside and outside the phagophore membrane during its expansion and assembly.
MeSH term(s)	Actins/metabolism ; Animals ; Autophagosomes/metabolism ; Cell Membrane/metabolism ; Humans ; Microtubule-Associated Proteins/metabolism ; Models, Biological
Chemical Substances	Actins ; Microtubule-Associated Proteins
Language	English
Publishing date	2016-10-10
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	2454135-7
ISSN	1554-8635 ; 1554-8627
ISSN (online)	1554-8635
ISSN	1554-8627
DOI	10.1080/15548627.2016.1236877
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Article ; Online: To deliver or to degrade - an interplay of the ubiquitin-proteasome system, autophagy and vesicular transport in plants.

Zientara-Rytter, Katarzyna / Sirko, Agnieszka

The FEBS journal

2016 Volume 283, Issue 19, Page(s) 3534–3555

Abstract: The efficient utilization and subsequent reuse of cell components is a key factor in determining the proper growth and functioning of all cells under both optimum and stress conditions. The process of intracellular and intercellular recycling is ... ...

Abstract	The efficient utilization and subsequent reuse of cell components is a key factor in determining the proper growth and functioning of all cells under both optimum and stress conditions. The process of intracellular and intercellular recycling is especially important for the appropriate control of cellular metabolism and nutrient management in immobile organisms, such as plants. Therefore, the accurate recycling of amino acids, lipids, carbohydrates or micro- and macronutrients available in the plant cell becomes a critical factor that ensures plant survival and growth. Plant cells possess two main degradation mechanisms: a ubiquitin-proteasome system and autophagy, which, as a part of an intracellular trafficking system, is based on vesicle transport. This review summarizes knowledge of both the ubiquitin-proteasome system and autophagy pathways, describes the cross-talk between the two and discusses the relationships between autophagy and the vesicular transport systems.
MeSH term(s)	Autophagy ; Biological Transport ; Plants/metabolism ; Proteasome Endopeptidase Complex/metabolism ; Transport Vesicles/metabolism ; Ubiquitin/metabolism ; Ubiquitination
Chemical Substances	Ubiquitin ; Proteasome Endopeptidase Complex (EC 3.4.25.1)
Language	English
Publishing date	2016-10
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	2173655-8
ISSN	1742-4658 ; 1742-464X
ISSN (online)	1742-4658
ISSN	1742-464X
DOI	10.1111/febs.13712
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