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Article ; Online: The DEAD-Box RNA Helicase Ded1 Is Associated with Translating Ribosomes

Yeter-Alat, Hilal / Belgareh-Touzé, Naïma / Huvelle, Emmeline / Banroques, Josette / Tanner, N. Kyle

Genes (Basel). 2023 July 31, v. 14, no. 8

2023

Abstract: DEAD-box RNA helicases are ATP-dependent RNA binding proteins and RNA-dependent ATPases that possess weak, nonprocessive unwinding activity in vitro, but they can form long-lived complexes on RNAs when the ATPase activity is inhibited. Ded1 is a yeast ... ...

Abstract	DEAD-box RNA helicases are ATP-dependent RNA binding proteins and RNA-dependent ATPases that possess weak, nonprocessive unwinding activity in vitro, but they can form long-lived complexes on RNAs when the ATPase activity is inhibited. Ded1 is a yeast DEAD-box protein, the functional ortholog of mammalian DDX3, that is considered important for the scanning efficiency of the 48S pre-initiation complex ribosomes to the AUG start codon. We used a modified PAR-CLIP technique, which we call quicktime PAR-CLIP (qtPAR-CLIP), to crosslink Ded1 to 4-thiouridine-incorporated RNAs in vivo using UV light centered at 365 nm. The irradiation conditions are largely benign to the yeast cells and to Ded1, and we are able to obtain a high efficiency of crosslinking under physiological conditions. We find that Ded1 forms crosslinks on the open reading frames of many different mRNAs, but it forms the most extensive interactions on relatively few mRNAs, and particularly on mRNAs encoding certain ribosomal proteins and translation factors. Under glucose-depletion conditions, the crosslinking pattern shifts to mRNAs encoding metabolic and stress-related proteins, which reflects the altered translation. These data are consistent with Ded1 functioning in the regulation of translation elongation, perhaps by pausing or stabilizing the ribosomes through its ATP-dependent binding.
Keywords	DEAD-box RNA helicases ; RNA ; adenosinetriphosphatase ; crosslinking ; irradiation ; mammals ; ribosomes ; start codon ; ultraviolet radiation ; yeasts
Language	English
Dates of publication	2023-0731
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article ; Online
ZDB-ID	2527218-4
ISSN	2073-4425
ISSN	2073-4425
DOI	10.3390/genes14081566
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: The DEAD-Box RNA Helicase Ded1 Is Associated with Translating Ribosomes.

Yeter-Alat, Hilal / Belgareh-Touzé, Naïma / Huvelle, Emmeline / Banroques, Josette / Tanner, N Kyle

Genes

2023 Volume 14, Issue 8

Abstract	DEAD-box RNA helicases are ATP-dependent RNA binding proteins and RNA-dependent ATPases that possess weak, nonprocessive unwinding activity in vitro, but they can form long-lived complexes on RNAs when the ATPase activity is inhibited. Ded1 is a yeast DEAD-box protein, the functional ortholog of mammalian DDX3, that is considered important for the scanning efficiency of the 48S pre-initiation complex ribosomes to the AUG start codon. We used a modified PAR-CLIP technique, which we call quicktime PAR-CLIP (qtPAR-CLIP), to crosslink Ded1 to 4-thiouridine-incorporated RNAs in vivo using UV light centered at 365 nm. The irradiation conditions are largely benign to the yeast cells and to Ded1, and we are able to obtain a high efficiency of crosslinking under physiological conditions. We find that Ded1 forms crosslinks on the open reading frames of many different mRNAs, but it forms the most extensive interactions on relatively few mRNAs, and particularly on mRNAs encoding certain ribosomal proteins and translation factors. Under glucose-depletion conditions, the crosslinking pattern shifts to mRNAs encoding metabolic and stress-related proteins, which reflects the altered translation. These data are consistent with Ded1 functioning in the regulation of translation elongation, perhaps by pausing or stabilizing the ribosomes through its ATP-dependent binding.
MeSH term(s)	Animals ; Saccharomyces cerevisiae/genetics ; Ribosomes/genetics ; Ribosomal Proteins ; RNA ; RNA, Messenger ; Fungal Proteins ; Heat-Shock Proteins ; DEAD-box RNA Helicases/genetics ; Adenosine Triphosphate/genetics ; Mammals
Chemical Substances	Ribosomal Proteins ; RNA (63231-63-0) ; RNA, Messenger ; Fungal Proteins ; Heat-Shock Proteins ; DEAD-box RNA Helicases (EC 3.6.4.13) ; Adenosine Triphosphate (8L70Q75FXE)
Language	English
Publishing date	2023-07-31
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2527218-4
ISSN	2073-4425 ; 2073-4425
ISSN (online)	2073-4425
ISSN	2073-4425
DOI	10.3390/genes14081566
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Article ; Online: Mitofusin-mediated contacts between mitochondria and peroxisomes regulate mitochondrial fusion.

Alsayyah, Cynthia / Singh, Manish K / Morcillo-Parra, Maria Angeles / Cavellini, Laetitia / Shai, Nadav / Schmitt, Christine / Schuldiner, Maya / Zalckvar, Einat / Mallet, Adeline / Belgareh-Touzé, Naïma / Zimmer, Christophe / Cohen, Mickaël M

PLoS biology

2024 Volume 22, Issue 4, Page(s) e3002602

Abstract: Mitofusins are large GTPases that trigger fusion of mitochondrial outer membranes. Similarly to the human mitofusin Mfn2, which also tethers mitochondria to the endoplasmic reticulum (ER), the yeast mitofusin Fzo1 stimulates contacts between Peroxisomes ... ...

Abstract	Mitofusins are large GTPases that trigger fusion of mitochondrial outer membranes. Similarly to the human mitofusin Mfn2, which also tethers mitochondria to the endoplasmic reticulum (ER), the yeast mitofusin Fzo1 stimulates contacts between Peroxisomes and Mitochondria when overexpressed. Yet, the physiological significance and function of these "PerMit" contacts remain unknown. Here, we demonstrate that Fzo1 naturally localizes to peroxisomes and promotes PerMit contacts in physiological conditions. These contacts are regulated through co-modulation of Fzo1 levels by the ubiquitin-proteasome system (UPS) and by the desaturation status of fatty acids (FAs). Contacts decrease under low FA desaturation but reach a maximum during high FA desaturation. High-throughput genetic screening combined with high-resolution cellular imaging reveal that Fzo1-mediated PerMit contacts favor the transit of peroxisomal citrate into mitochondria. In turn, citrate enters the TCA cycle to stimulate the mitochondrial membrane potential and maintain efficient mitochondrial fusion upon high FA desaturation. These findings thus unravel a mechanism by which inter-organelle contacts safeguard mitochondrial fusion.
Language	English
Publishing date	2024-04-26
Publishing country	United States
Document type	Journal Article
ZDB-ID	2126776-5
ISSN	1545-7885 ; 1544-9173
ISSN (online)	1545-7885
ISSN	1544-9173
DOI	10.1371/journal.pbio.3002602
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Article ; Online: Exploring selective autophagy events in multiple biologic models using LC3-interacting regions (LIR)-based molecular traps.

Quinet, Grégoire / Génin, Pierre / Ozturk, Oznur / Belgareh-Touzé, Naima / Courtot, Lilas / Legouis, Renaud / Weil, Robert / Cohen, Mickael M / Rodriguez, Manuel S

Scientific reports

2022 Volume 12, Issue 1, Page(s) 7652

Abstract: Autophagy is an essential cellular pathway that ensures degradation of a wide range of substrates including damaged organelles or large protein aggregates. Understanding how this proteolytic pathway is regulated would increase our comprehension on its ... ...

Abstract	Autophagy is an essential cellular pathway that ensures degradation of a wide range of substrates including damaged organelles or large protein aggregates. Understanding how this proteolytic pathway is regulated would increase our comprehension on its role in cellular physiology and contribute to identify biomarkers or potential drug targets to develop more specific treatments for disease in which autophagy is dysregulated. Here, we report the development of molecular traps based in the tandem disposition of LC3-interacting regions (LIR). The estimated affinity of LC3-traps for distinct recombinant LC3/GABARAP proteins is in the low nanomolar range and allows the capture of these proteins from distinct mammalian cell lines, S. cerevisiae and C. elegans. LC3-traps show preferences for GABARAP/LGG1 or LC3/LGG2 and pull-down substrates targeted to proteaphagy and mitophagy. Therefore, LC3-traps are versatile tools that can be adapted to multiple applications to monitor selective autophagy events in distinct physiologic and pathologic circumstances.
MeSH term(s)	Animals ; Autophagy ; Caenorhabditis elegans/metabolism ; Macroautophagy ; Mammals/metabolism ; Microtubule-Associated Proteins/metabolism ; Models, Biological ; Protein Binding ; Saccharomyces cerevisiae/metabolism
Chemical Substances	Microtubule-Associated Proteins
Language	English
Publishing date	2022-05-10
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-022-11417-z
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Article ; Online: Analysis of ATG8 Family Members Using LC3-Interacting Regions (LIR)-Based Molecular Traps.

Quinet, Grégoire / Génin, Pierre / Belgareh-Touzé, Naima / Ozturk, Oznur / Weil, Robert / Cohen, Mickael M / Legouis, Renaud / Rodriguez, Manuel S

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

2022 Volume 2602, Page(s) 191–204

Abstract: The ATG8 family of proteins regulates the autophagy process from the autophagosome maturation and cargo recruitment up to degradation. Autophagy dysfunction is involved in the development of multiple diseases. The LC3 interacting region (LIR)-based ... ...

Abstract	The ATG8 family of proteins regulates the autophagy process from the autophagosome maturation and cargo recruitment up to degradation. Autophagy dysfunction is involved in the development of multiple diseases. The LC3 interacting region (LIR)-based molecular traps have been designed to isolate endogenous ATG8 proteins and their interactors in order to facilitate the study of selective autophagy events. Here, we summarize protocols describing LC3 traps and sample preparation as well as adaptations for the analysis of ATG8 proteins in different biological models. This protocol was optimized to prepare affinity columns, reduce background, and improve the protein recovery to be analyzed by immunodetection with antibodies recognizing proteins of interest.
MeSH term(s)	Autophagy-Related Protein 8 Family/genetics ; Macroautophagy ; Acclimatization ; Antibodies ; Autophagy
Chemical Substances	Autophagy-Related Protein 8 Family ; Antibodies
Language	English
Publishing date	2022-11-29
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-2859-1_14
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Article: The regulation of mitochondrial homeostasis by the ubiquitin proteasome system

Alsayyah, Cynthia / Ozturk, Oznur / Cavellini, Laetitia / Belgareh-Touzé, Naïma / Cohen, Mickael M

Biochimica et biophysica acta. 2020 Dec. 01, v. 1861, no. 12

2020

Abstract: From mitochondrial quality control pathways to the regulation of specific functions, the Ubiquitin Proteasome System (UPS) could be compared to a Swiss knife without which mitochondria could not maintain its integrity in the cell. Here, we review the ... ...

Abstract	From mitochondrial quality control pathways to the regulation of specific functions, the Ubiquitin Proteasome System (UPS) could be compared to a Swiss knife without which mitochondria could not maintain its integrity in the cell. Here, we review the mechanisms that the UPS employs to regulate mitochondrial function and efficiency. For this purpose, we depict how Ubiquitin and the Proteasome participate in diverse quality control pathways that safeguard entry into the mitochondrial compartment. A focus is then achieved on the UPS-mediated control of the yeast mitofusin Fzo1 which provides insights into the complex regulation of this particular protein in mitochondrial fusion. We ultimately dissect the mechanisms by which the UPS controls the degradation of mitochondria by autophagy in both mammalian and yeast systems. This organization should offer a useful overview of this abundant but fascinating literature on the crosstalks between mitochondria and the UPS.
Keywords	autophagy ; homeostasis ; mammals ; mitochondria ; proteasome endopeptidase complex ; quality control ; ubiquitin ; yeasts
Language	English
Dates of publication	2020-1201
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	282711-6
ISSN	0005-2728 ; 0304-4173
ISSN	0005-2728 ; 0304-4173
DOI	10.1016/j.bbabio.2020.148302
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Article ; Online: The regulation of mitochondrial homeostasis by the ubiquitin proteasome system.

Alsayyah, Cynthia / Ozturk, Oznur / Cavellini, Laetitia / Belgareh-Touzé, Naïma / Cohen, Mickael M

Biochimica et biophysica acta. Bioenergetics

2020 Volume 1861, Issue 12, Page(s) 148302

Abstract	From mitochondrial quality control pathways to the regulation of specific functions, the Ubiquitin Proteasome System (UPS) could be compared to a Swiss knife without which mitochondria could not maintain its integrity in the cell. Here, we review the mechanisms that the UPS employs to regulate mitochondrial function and efficiency. For this purpose, we depict how Ubiquitin and the Proteasome participate in diverse quality control pathways that safeguard entry into the mitochondrial compartment. A focus is then achieved on the UPS-mediated control of the yeast mitofusin Fzo1 which provides insights into the complex regulation of this particular protein in mitochondrial fusion. We ultimately dissect the mechanisms by which the UPS controls the degradation of mitochondria by autophagy in both mammalian and yeast systems. This organization should offer a useful overview of this abundant but fascinating literature on the crosstalks between mitochondria and the UPS.
MeSH term(s)	Animals ; Homeostasis ; Humans ; Mitochondria/metabolism ; Mitophagy ; Proteasome Endopeptidase Complex/metabolism ; Ubiquitin/metabolism ; Ubiquitination
Chemical Substances	Ubiquitin ; Proteasome Endopeptidase Complex (EC 3.4.25.1)
Language	English
Publishing date	2020-08-27
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	60-7
ISSN	1879-2650 ; 1879-2596 ; 1879-260X ; 1872-8006 ; 1879-2642 ; 1879-2618 ; 0006-3002 ; 0005-2728 ; 0005-2736 ; 0304-4165 ; 0167-4838 ; 1388-1981 ; 0167-4889 ; 0167-4781 ; 0304-419X ; 1570-9639 ; 0925-4439 ; 1874-9399
ISSN (online)	1879-2650 ; 1879-2596 ; 1879-260X ; 1872-8006 ; 1879-2642 ; 1879-2618
ISSN	0006-3002 ; 0005-2728 ; 0005-2736 ; 0304-4165 ; 0167-4838 ; 1388-1981 ; 0167-4889 ; 0167-4781 ; 0304-419X ; 1570-9639 ; 0925-4439 ; 1874-9399
DOI	10.1016/j.bbabio.2020.148302
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Article ; Online: Ubiquitination of ERMES components by the E3 ligase Rsp5 is involved in mitophagy.

Belgareh-Touzé, Naïma / Cavellini, Laetitia / Cohen, Mickael M

Autophagy

2017 Volume 13, Issue 1, Page(s) 114–132

Abstract: Mitochondria are dynamic organelles that undergo permanent fission and fusion events. These processes play an essential role in maintaining normal cellular function. In the yeast Saccharomyces cerevisiae, the endoplasmic reticulum-mitochondrial encounter ...

Abstract	Mitochondria are dynamic organelles that undergo permanent fission and fusion events. These processes play an essential role in maintaining normal cellular function. In the yeast Saccharomyces cerevisiae, the endoplasmic reticulum-mitochondrial encounter structure (ERMES) is a marker of sites of mitochondrial division, but it is also involved in a plethora of other mitochondrial functions. However, it remains unclear how these different functions are regulated. We show here that Mdm34 and Mdm12, 2 components of ERMES, are ubiquitinated by the E3 ligase Rsp5. This ubiquitination is not involved in mitochondrial dynamics or in the distribution and turnover of ERMES. Nevertheless, the ubiquitination of Mdm34 and Mdm12 was required for efficient mitophagy. We thus report here the first identification of ubiquitinated substrates participating in yeast mitophagy.
Language	English
Publishing date	2017-01-02
Publishing country	United States
Document type	Journal Article
ZDB-ID	2454135-7
ISSN	1554-8635 ; 1554-8627
ISSN (online)	1554-8635
ISSN	1554-8627
DOI	10.1080/15548627.2016.1252889
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Zs.A 6741: Show issues

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Article ; Online: An ubiquitin-dependent balance between mitofusin turnover and fatty acids desaturation regulates mitochondrial fusion.

Cavellini, Laetitia / Meurisse, Julie / Findinier, Justin / Erpapazoglou, Zoi / Belgareh-Touzé, Naïma / Weissman, Allan M / Cohen, Mickael M

Nature communications

2017 Volume 8, Page(s) 15832

Abstract: Mitochondrial integrity relies on homotypic fusion between adjacent outer membranes, which is mediated by large GTPases called mitofusins. The regulation of this process remains nonetheless elusive. Here, we report a crosstalk between the ubiquitin ... ...

Abstract	Mitochondrial integrity relies on homotypic fusion between adjacent outer membranes, which is mediated by large GTPases called mitofusins. The regulation of this process remains nonetheless elusive. Here, we report a crosstalk between the ubiquitin protease Ubp2 and the ubiquitin ligases Mdm30 and Rsp5 that modulates mitochondrial fusion. Ubp2 is an antagonist of Rsp5, which promotes synthesis of the fatty acids desaturase Ole1. We show that Ubp2 also counteracts Mdm30-mediated turnover of the yeast mitofusin Fzo1 and that Mdm30 targets Ubp2 for degradation thereby inducing Rsp5-mediated desaturation of fatty acids. Exogenous desaturated fatty acids inhibit Ubp2 degradation resulting in higher levels of Fzo1 and maintenance of efficient mitochondrial fusion. Our results demonstrate that the Mdm30-Ubp2-Rsp5 crosstalk regulates mitochondrial fusion by coordinating an intricate balance between Fzo1 turnover and the status of fatty acids saturation. This pathway may link outer membrane fusion to lipids homeostasis.
MeSH term(s)	Endopeptidases/genetics ; Endopeptidases/metabolism ; Endosomal Sorting Complexes Required for Transport/genetics ; Endosomal Sorting Complexes Required for Transport/metabolism ; F-Box Proteins/genetics ; F-Box Proteins/metabolism ; Fatty Acids/metabolism ; GTP Phosphohydrolases/genetics ; GTP Phosphohydrolases/metabolism ; Membrane Proteins/genetics ; Membrane Proteins/metabolism ; Mitochondria/genetics ; Mitochondria/metabolism ; Mitochondrial Dynamics ; Mitochondrial Proteins/genetics ; Mitochondrial Proteins/metabolism ; Saccharomyces cerevisiae/enzymology ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism ; Ubiquitin/metabolism ; Ubiquitin-Protein Ligase Complexes/genetics ; Ubiquitin-Protein Ligase Complexes/metabolism
Chemical Substances	Endosomal Sorting Complexes Required for Transport ; F-Box Proteins ; Fatty Acids ; Mdm30 protein, S cerevisiae ; Membrane Proteins ; Mitochondrial Proteins ; Saccharomyces cerevisiae Proteins ; Ubiquitin ; Ubiquitin-Protein Ligase Complexes (EC 2.3.2.23) ; Endopeptidases (EC 3.4.-) ; ubiquitin-Nalpha-protein hydrolase (EC 3.4.99.-) ; FZO1 protein, S cerevisiae (EC 3.6.1.-) ; GTP Phosphohydrolases (EC 3.6.1.-) ; RSP5 protein, S cerevisiae (EC 6.3.2.-)
Language	English
Publishing date	2017-06-13
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2041-1723
ISSN (online)	2041-1723
DOI	10.1038/ncomms15832
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Article: Expressing the Erwinia amylovora type III effector DspA/E in the yeast Saccharomyces cerevisiae strongly alters cellular trafficking.

Siamer, Sabrina / Patrit, Oriane / Fagard, Mathilde / Belgareh-Touzé, Naïma / Barny, Marie-Anne

FEBS open bio

2011 Volume 1, Page(s) 23–28

Abstract: Erwinia amylovora is responsible for fire blight, a necrotic disease of apples and pears. E. amylovora relies on a type III secretion system (T3SS) to induce disease on host plants. DspA/E belongs to the AvrE family of type III effector. Effectors of the ...

Abstract	Erwinia amylovora is responsible for fire blight, a necrotic disease of apples and pears. E. amylovora relies on a type III secretion system (T3SS) to induce disease on host plants. DspA/E belongs to the AvrE family of type III effector. Effectors of the AvrE family are injected via the T3SS in plant cell and are important to promote bacterial growth following infection and to suppress plant defense responses. Their mode of action in the plant cells is unknown. Here we study the physiological effects induced by dspA/E expression in the yeast Saccharomyces cerevisiae. Expression of dspA/E in the yeast inhibits cell growth. This growth inhibition is associated with perturbations of the actin cytoskeleton and endocytosis.
Language	English
Publishing date	2011-11-11
Publishing country	England
Document type	Journal Article
ZDB-ID	2651702-4
ISSN	2211-5463
ISSN	2211-5463
DOI	10.1016/j.fob.2011.11.001
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