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  1. Book ; Online ; Thesis: Investigation of the cellular structures containing the autophagy-related proteins GABARAP and LC3B by single molecule localization microscopy

    Abdollahzadeh, Iman [Verfasser]

    2020  

    Author's details Iman Abdollahzadeh
    Keywords Biowissenschaften, Biologie ; Life Science, Biology
    Subject code sg570
    Language English
    Publisher Universitäts- und Landesbibliothek der Heinrich-Heine-Universität Düsseldorf
    Publishing place Düsseldorf
    Document type Book ; Online ; Thesis
    Database Digital theses on the web

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  2. Article ; Online: Growth-rate dependency of ribosome abundance and translation elongation rate in Corynebacterium glutamicum differs from that in Escherichia coli.

    Matamouros, Susana / Gensch, Thomas / Cerff, Martin / Sachs, Christian C / Abdollahzadeh, Iman / Hendriks, Johnny / Horst, Lucas / Tenhaef, Niklas / Tenhaef, Julia / Noack, Stephan / Graf, Michaela / Takors, Ralf / Nöh, Katharina / Bott, Michael

    Nature communications

    2023  Volume 14, Issue 1, Page(s) 5611

    Abstract: Bacterial growth rate (µ) depends on the protein synthesis capacity of the cell and thus on the number of active ribosomes and their translation elongation rate. The relationship between these fundamental growth parameters have only been described for ... ...

    Abstract Bacterial growth rate (µ) depends on the protein synthesis capacity of the cell and thus on the number of active ribosomes and their translation elongation rate. The relationship between these fundamental growth parameters have only been described for few bacterial species, in particular Escherichia coli. Here, we analyse the growth-rate dependency of ribosome abundance and translation elongation rate for Corynebacterium glutamicum, a gram-positive model species differing from E. coli by a lower growth temperature optimum and a lower maximal growth rate. We show that, unlike in E. coli, there is little change in ribosome abundance for µ <0.4 h
    MeSH term(s) Corynebacterium glutamicum/genetics ; Escherichia coli/genetics ; Ribosomes/genetics ; Polyribosomes ; Temperature
    Language English
    Publishing date 2023-09-12
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-023-41176-y
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Heterologous expression of the Halothiobacillus neapolitanus carboxysomal gene cluster in Corynebacterium glutamicum.

    Baumgart, Meike / Huber, Isabel / Abdollahzadeh, Iman / Gensch, Thomas / Frunzke, Julia

    Journal of biotechnology

    2017  Volume 258, Page(s) 126–135

    Abstract: Compartmentalization represents a ubiquitous principle used by living organisms to optimize metabolic flux and to avoid detrimental interactions within the cytoplasm. Proteinaceous bacterial microcompartments (BMCs) have therefore created strong interest ...

    Abstract Compartmentalization represents a ubiquitous principle used by living organisms to optimize metabolic flux and to avoid detrimental interactions within the cytoplasm. Proteinaceous bacterial microcompartments (BMCs) have therefore created strong interest for the encapsulation of heterologous pathways in microbial model organisms. However, attempts were so far mostly restricted to Escherichia coli. Here, we introduced the carboxysomal gene cluster of Halothiobacillus neapolitanus into the biotechnological platform species Corynebacterium gluta-micum. Transmission electron microscopy, fluorescence microscopy and single molecule localization microscopy suggested the formation of BMC-like structures in cells expressing the complete carboxysome operon or only the shell proteins. Purified carboxysomes consisted of the expected protein components as verified by mass spectrometry. Enzymatic assays revealed the functional production of RuBisCO in C. glutamicum both in the presence and absence of carboxysomal shell proteins. Furthermore, we could show that eYFP is targeted to the carboxysomes by fusion to the large RuBisCO subunit. Overall, this study represents the first transfer of an α-carboxysomal gene cluster into a Gram-positive model species supporting the modularity and orthogonality of these microcompartments, but also identified important challenges which need to be addressed on the way towards biotechnological application.
    Language English
    Publishing date 2017-09-20
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 843647-2
    ISSN 1873-4863 ; 0168-1656 ; 1389-0352
    ISSN (online) 1873-4863
    ISSN 0168-1656 ; 1389-0352
    DOI 10.1016/j.jbiotec.2017.03.019
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 2299: Show issues Location:
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  4. Article ; Online: Autophagy-Related Proteins GABARAP and LC3B Label Structures of Similar Size but Different Shape in Super-Resolution Imaging.

    Abdollahzadeh, Iman / Hendriks, Johnny / Sanwald, Julia L / Simons, Indra M / Hoffmann, Silke / Weiergräber, Oliver H / Willbold, Dieter / Gensch, Thomas

    Molecules (Basel, Switzerland)

    2019  Volume 24, Issue 9

    Abstract: Subcellular structures containing autophagy-related proteins of the Atg8 protein family have been investigated with conventional wide-field fluorescence and single molecule localisation microscopy. Fusion proteins of GABARAP and LC3B, respectively, with ... ...

    Abstract Subcellular structures containing autophagy-related proteins of the Atg8 protein family have been investigated with conventional wide-field fluorescence and single molecule localisation microscopy. Fusion proteins of GABARAP and LC3B, respectively, with EYFP were overexpressed in HEK293 cells. While size distributions of structures labelled by the two proteins were found to be similar, shape distributions appeared quite disparate, with EYFP-GABARAP favouring circular structures and elliptical structures being dominant for EYFP-LC3B. The latter also featured a nearly doubled fraction of U-shape structures. The experimental results point towards highly differential localisation of the two proteins, which appear to label structures representing distinct stages or even specific channels of vesicular trafficking pathways. Our data also demonstrate that the application of super-resolution techniques expands the possibilities of fluorescence-based methods in autophagy studies and in some cases can rectify conclusions obtained from conventional fluorescence microscopy with diffraction-limited resolution.
    MeSH term(s) Adaptor Proteins, Signal Transducing/analysis ; HEK293 Cells ; Humans ; Microscopy/methods ; Microtubule-Associated Proteins/analysis
    Chemical Substances Adaptor Proteins, Signal Transducing ; GABARAP protein, human ; MAP1LC3B protein, human ; Microtubule-Associated Proteins
    Language English
    Publishing date 2019-05-13
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 1413402-0
    ISSN 1420-3049 ; 1431-5165 ; 1420-3049
    ISSN (online) 1420-3049
    ISSN 1431-5165 ; 1420-3049
    DOI 10.3390/molecules24091833
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    In stock of ZB MED Cologne/Königswinter

    Zs.MO 81: Show issues

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  5. Article: The Atg8 Family of Proteins-Modulating Shape and Functionality of Autophagic Membranes.

    Abdollahzadeh, Iman / Schwarten, Melanie / Gensch, Thomas / Willbold, Dieter / Weiergräber, Oliver H

    Frontiers in genetics

    2017  Volume 8, Page(s) 109

    Abstract: Aging is a multifactorial process involving an accumulation of alterations on various organizational levels, which finally compromises viability and limits the lifespan of organisms. It is now well-established that many aspects of aging can be positively ...

    Abstract Aging is a multifactorial process involving an accumulation of alterations on various organizational levels, which finally compromises viability and limits the lifespan of organisms. It is now well-established that many aspects of aging can be positively affected by (macro)autophagy, a mechanism of self-digestion found in virtually all eukaryotic cells. A comprehensive understanding of autophagy is thus expected to not only deepen our insight into the mechanisms of aging but to also open up new avenues toward increasing the healthy lifespan in humans. In this review, we focus on the Atg8 family of ubiquitin-like proteins, which play a crucial role in the autophagy process by virtue of their unique mode of reversible membrane association.
    Language English
    Publishing date 2017-08-28
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2606823-0
    ISSN 1664-8021
    ISSN 1664-8021
    DOI 10.3389/fgene.2017.00109
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Deficiency of GABARAP but not its Paralogs Causes Enhanced EGF-induced EGFR Degradation.

    Dobner, Jochen / Simons, Indra M / Rufinatscha, Kerstin / Hänsch, Sebastian / Schwarten, Melanie / Weiergräber, Oliver H / Abdollahzadeh, Iman / Gensch, Thomas / Bode, Johannes G / Hoffmann, Silke / Willbold, Dieter

    Cells

    2020  Volume 9, Issue 5

    Abstract: The γ-aminobutyric acid type A receptor-associated protein (GABARAP) and its close paralogs GABARAPL1 and GABARAPL2 constitute a subfamily of the autophagy-related 8 (Atg8) protein family. Being associated with a variety of dynamic membranous structures ... ...

    Abstract The γ-aminobutyric acid type A receptor-associated protein (GABARAP) and its close paralogs GABARAPL1 and GABARAPL2 constitute a subfamily of the autophagy-related 8 (Atg8) protein family. Being associated with a variety of dynamic membranous structures of autophagic and non-autophagic origin, Atg8 proteins functionalize membranes by either serving as docking sites for other proteins or by acting as membrane tethers or adhesion factors. In this study, we describe that deficiency for GABARAP alone, but not for its close paralogs, is sufficient for accelerated EGF receptor (EGFR) degradation in response to EGF, which is accompanied by the downregulation of EGFR-mediated MAPK signaling, altered target gene expression, EGF uptake, and EGF vesicle composition over time. We further show that GABARAP and EGFR converge in the same distinct compartments at endogenous GABARAP expression levels in response to EGF stimulation. Furthermore, GABARAP associates with EGFR in living cells and binds to synthetic peptides that are derived from the EGFR cytoplasmic tail in vitro. Thus, our data strongly indicate a unique and novel role for GABARAP during EGFR trafficking.
    MeSH term(s) Adaptor Proteins, Signal Transducing/metabolism ; Amino Acid Sequence ; Apoptosis Regulatory Proteins/deficiency ; Apoptosis Regulatory Proteins/metabolism ; Autophagy-Related Protein 8 Family/metabolism ; Cell Line, Tumor ; Endocytosis/drug effects ; Endosomes/drug effects ; Endosomes/metabolism ; Epidermal Growth Factor/metabolism ; ErbB Receptors/chemistry ; ErbB Receptors/metabolism ; Fluorescent Dyes/metabolism ; Gene Expression Regulation/drug effects ; HEK293 Cells ; Humans ; Lysosomes/drug effects ; Lysosomes/metabolism ; Microtubule-Associated Proteins/deficiency ; Microtubule-Associated Proteins/metabolism ; Models, Biological ; Phosphorylation/drug effects ; Proteasome Inhibitors/pharmacology ; Proteolysis/drug effects ; Sequence Homology, Amino Acid ; Signal Transduction/drug effects ; Transport Vesicles/drug effects ; Transport Vesicles/metabolism
    Chemical Substances Adaptor Proteins, Signal Transducing ; Apoptosis Regulatory Proteins ; Autophagy-Related Protein 8 Family ; Fluorescent Dyes ; GABARAP protein, human ; GABARAPL1 protein, human ; GABARAPL2 protein, human ; Microtubule-Associated Proteins ; Proteasome Inhibitors ; Epidermal Growth Factor (62229-50-9) ; EGFR protein, human (EC 2.7.10.1) ; ErbB Receptors (EC 2.7.10.1)
    Language English
    Publishing date 2020-05-22
    Publishing country Switzerland
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2661518-6
    ISSN 2073-4409 ; 2073-4409
    ISSN (online) 2073-4409
    ISSN 2073-4409
    DOI 10.3390/cells9051296
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