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Article ; Online: Approches nouvelles pour l’étude des interactions protéine-protéine.

Béganton, Benoît / Coyaud, Etienne / Mangé, Alain / Solassol, Jérôme

2019 Volume 35, Issue 3, Page(s) 223–231

Abstract: The proteome is a dynamic system in which protein-protein interactions play a crucial role to model together the cellular phenotype. However, given the inherent limitation of the available technologies to depict the dynamic nature of these interactions, ... ...

Title translation	New approaches for protein-protein interaction study.
Abstract	The proteome is a dynamic system in which protein-protein interactions play a crucial role to model together the cellular phenotype. However, given the inherent limitation of the available technologies to depict the dynamic nature of these interactions, identify protein-protein interaction has for a long time represented an important challenge in proteomic. The recent development of BioID and APEX, two proximity-dependent labeling technologies, opens today new perspectives and yet start changing our vision of protein-protein interaction, and more globally our vision of the proteome. In this review, we describe the recent and conventional tools available to study protein-protein interactions, compare the advantages and limitations of these technics, and discuss the recent progress brought by the proximity-dependent labelling to complete our vision of the proteome, and thus better understand cellular mechanisms.
MeSH term(s)	Animals ; Biotinylation/methods ; Humans ; Protein Binding ; Protein Interaction Domains and Motifs ; Protein Interaction Maps ; Proteome/analysis ; Proteomics/methods ; Staining and Labeling/methods
Chemical Substances	Proteome
Language	French
Publishing date	2019-04-01
Publishing country	France
Document type	Journal Article ; Review
ZDB-ID	632733-3
ISSN	1958-5381 ; 0767-0974
ISSN (online)	1958-5381
ISSN	0767-0974
DOI	10.1051/medsci/2019035
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Article ; Online: DPCD is a regulator of R2TP in ciliogenesis initiation through Akt signaling.

Mao, Yu-Qian / Seraphim, Thiago V / Wan, Yimei / Wu, Ruikai / Coyaud, Etienne / Bin Munim, Muhammad / Mollica, Antonio / Laurent, Estelle / Babu, Mohan / Mennella, Vito / Raught, Brian / Houry, Walid A

Cell reports

2024 Volume 43, Issue 2, Page(s) 113713

Abstract: R2TP is a chaperone complex consisting of the AAA+ ATPases RUVBL1 and RUVBL2, as well as RPAP3 and PIH1D1 proteins. R2TP is responsible for the assembly of macromolecular complexes mainly acting through different adaptors. Using proximity-labeling mass ... ...

Abstract	R2TP is a chaperone complex consisting of the AAA+ ATPases RUVBL1 and RUVBL2, as well as RPAP3 and PIH1D1 proteins. R2TP is responsible for the assembly of macromolecular complexes mainly acting through different adaptors. Using proximity-labeling mass spectrometry, we identified deleted in primary ciliary dyskinesia (DPCD) as an adaptor of R2TP. Here, we demonstrate that R2TP-DPCD influences ciliogenesis initiation through a unique mechanism by interaction with Akt kinase to regulate its phosphorylation levels rather than its stability. We further show that DPCD is a heart-shaped monomeric protein with two domains. A highly conserved region in the cysteine- and histidine-rich domains-containing proteins and SGT1 (CS) domain of DPCD interacts with the RUVBL2 DII domain with high affinity to form a stable R2TP-DPCD complex both in cellulo and in vitro. Considering that DPCD is one among several CS-domain-containing proteins found to associate with RUVBL1/2, we propose that RUVBL1/2 are CS-domain-binding proteins that regulate complex assembly and downstream signaling.
MeSH term(s)	Proto-Oncogene Proteins c-akt ; Signal Transduction ; Phosphorylation ; ATPases Associated with Diverse Cellular Activities ; Cognition
Chemical Substances	Proto-Oncogene Proteins c-akt (EC 2.7.11.1) ; ATPases Associated with Diverse Cellular Activities (EC 3.6.4.-)
Language	English
Publishing date	2024-02-01
Publishing country	United States
Document type	Journal Article
ZDB-ID	2649101-1
ISSN	2211-1247 ; 2211-1247
ISSN (online)	2211-1247
ISSN	2211-1247
DOI	10.1016/j.celrep.2024.113713
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Article ; Online: Tankyrase regulates epithelial lumen formation via suppression of Rab11 GEFs.

Chandrakumar, Arun A / Coyaud, Étienne / Marshall, Christopher B / Ikura, Mitsuhiko / Raught, Brian / Rottapel, Robert

The Journal of cell biology

2021 Volume 220, Issue 7

Abstract: Rab11 GTPase proteins are required for cytokinesis, ciliogenesis, and lumenogenesis. Rab11a is critical for apical delivery of podocalyxin (PODXL) during lumen formation in epithelial cells. SH3BP5 and SH3BP5L are guanine nucleotide exchange factors ( ... ...

Abstract	Rab11 GTPase proteins are required for cytokinesis, ciliogenesis, and lumenogenesis. Rab11a is critical for apical delivery of podocalyxin (PODXL) during lumen formation in epithelial cells. SH3BP5 and SH3BP5L are guanine nucleotide exchange factors (GEFs) for Rab11. We show that SH3BP5 and SH3BP5L are required for activation of Rab11a and cyst lumen formation. Using proximity-dependent biotin identification (BioID) interaction proteomics, we have identified SH3BP5 and its paralogue SH3BP5L as new substrates of the poly-ADP-ribose polymerase Tankyrase and the E3 ligase RNF146. We provide data demonstrating that epithelial polarity via cyst lumen formation is governed by Tankyrase, which inhibits Rab11a activation through the suppression of SH3BP5 and SH3BP5L. RNF146 reduces Tankyrase protein abundance and restores Rab11a activation and lumen formation. Thus, Rab11a activation is controlled by a signaling pathway composed of the sequential inhibition of SH3BP5 paralogues by Tankyrase, which is itself suppressed by RNF146.
MeSH term(s)	Adaptor Proteins, Signal Transducing/genetics ; Guanine Nucleotide Exchange Factors ; Humans ; Protein Binding ; Sialoglycoproteins/genetics ; Signal Transduction/genetics ; Tankyrases/genetics ; Ubiquitin-Protein Ligases/genetics ; rab GTP-Binding Proteins/genetics
Chemical Substances	Adaptor Proteins, Signal Transducing ; Guanine Nucleotide Exchange Factors ; SH3BP5 protein, human ; SH3D19 protein, human ; Sialoglycoproteins ; podocalyxin ; RNF146 protein, human (EC 2.3.2.27) ; Ubiquitin-Protein Ligases (EC 2.3.2.27) ; Tankyrases (EC 2.4.2.30) ; rab11 protein (EC 3.6.1.-) ; rab GTP-Binding Proteins (EC 3.6.5.2)
Language	English
Publishing date	2021-06-15
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.202008037
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Article ; Online: The in vivo Interaction Landscape of Histones H3.1 and H3.3.

Siddaway, Robert / Milos, Scott / Coyaud, Étienne / Yun, Hwa Young / Morcos, Shahir M / Pajovic, Sanja / Campos, Eric I / Raught, Brian / Hawkins, Cynthia

Molecular & cellular proteomics : MCP

2022 Volume 21, Issue 10, Page(s) 100411

Abstract: Chromatin structure, transcription, DNA replication, and repair are regulated via locus-specific incorporation of histone variants and posttranslational modifications that guide effector chromatin-binding proteins. Here we report unbiased, quantitative ... ...

Abstract	Chromatin structure, transcription, DNA replication, and repair are regulated via locus-specific incorporation of histone variants and posttranslational modifications that guide effector chromatin-binding proteins. Here we report unbiased, quantitative interactomes for the replication-coupled (H3.1) and replication-independent (H3.3) histone H3 variants based on BioID proximity labeling, which allows interactions in intact, living cells to be detected. Along with a significant proportion of previously reported interactions detected by affinity purification followed by mass spectrometry, three quarters of the 608 histone-associated proteins that we identified are new, uncharacterized histone associations. The data reveal important biological nuances not captured by traditional biochemical means. For example, we found that the chromatin assembly factor-1 histone chaperone not only deposits the replication-coupled H3.1 histone variant during S-phase but also associates with H3.3 throughout the cell cycle in vivo. We also identified other variant-specific associations, such as with transcription factors, chromatin regulators, and with the mitotic machinery. Our proximity-based analysis is thus a rich resource that extends the H3 interactome and reveals new sets of variant-specific associations.
MeSH term(s)	Histones/metabolism ; Histone Chaperones/genetics ; Histone Chaperones/metabolism ; Chromatin ; Chromatin Assembly Factor-1/genetics ; Chromatin Assembly Factor-1/metabolism ; Transcription Factors/metabolism ; Nucleosomes
Chemical Substances	Histones ; Histone Chaperones ; Chromatin ; Chromatin Assembly Factor-1 ; Transcription Factors ; Nucleosomes
Language	English
Publishing date	2022-09-09
Publishing country	United States
Document type	Journal Article
ZDB-ID	2075924-1
ISSN	1535-9484 ; 1535-9476
ISSN (online)	1535-9484
ISSN	1535-9476
DOI	10.1016/j.mcpro.2022.100411
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Article ; Online: Salmonella exploits membrane reservoirs for invasion of host cells.

Zhu, Hongxian / Sydor, Andrew M / Boddy, Kirsten C / Coyaud, Etienne / Laurent, Estelle M N / Au, Aaron / Tan, Joel M J / Yan, Bing-Ru / Moffat, Jason / Muise, Aleixo M / Yip, Christopher M / Grinstein, Sergio / Raught, Brian / Brumell, John H

Nature communications

2024 Volume 15, Issue 1, Page(s) 3120

Abstract: Salmonella utilizes a type 3 secretion system to translocate virulence proteins (effectors) into host cells during ... ...

Abstract	Salmonella utilizes a type 3 secretion system to translocate virulence proteins (effectors) into host cells during infection
MeSH term(s)	Humans ; Salmonella typhimurium/metabolism ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Salmonella Infections/microbiology ; Cell Membrane/metabolism ; Membranes/metabolism ; HeLa Cells
Chemical Substances	Bacterial Proteins
Language	English
Publishing date	2024-04-10
Publishing country	England
Document type	Journal Article
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-024-47183-x
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Article ; Online: LUZP1 and the tumor suppressor EPLIN modulate actin stability to restrict primary cilia formation.

Gonçalves, João / Sharma, Amit / Coyaud, Étienne / Laurent, Estelle M N / Raught, Brian / Pelletier, Laurence

The Journal of cell biology

2020 Volume 219, Issue 7

Abstract: Cilia and flagella are microtubule-based cellular projections with important sensory and motility functions. Their absence or malfunction is associated with a growing number of human diseases collectively referred to as ciliopathies. However, the ... ...

Abstract	Cilia and flagella are microtubule-based cellular projections with important sensory and motility functions. Their absence or malfunction is associated with a growing number of human diseases collectively referred to as ciliopathies. However, the fundamental mechanisms underpinning cilia biogenesis and functions remain only partly understood. Here, we show that depleting LUZP1 or its interacting protein, EPLIN, increases the levels of MyosinVa at the centrosome and primary cilia formation. We further show that LUZP1 localizes to both actin filaments and the centrosome/basal body. Like EPLIN, LUZP1 is an actin-stabilizing protein that regulates actin dynamics, at least in part, by mobilizing ARP2 to the centrosomes. Both LUZP1 and EPLIN interact with known ciliogenesis and cilia-length regulators and as such represent novel players in actin-dependent centrosome to basal body conversion. Ciliogenesis deregulation caused by LUZP1 or EPLIN loss may thus contribute to the pathology of their associated disease states.
MeSH term(s)	Actin Cytoskeleton/metabolism ; Actin Cytoskeleton/ultrastructure ; Actin-Related Protein 2/chemistry ; Actin-Related Protein 2/genetics ; Actin-Related Protein 2/metabolism ; Actins/chemistry ; Actins/genetics ; Actins/metabolism ; Animals ; Basal Bodies/metabolism ; Basal Bodies/ultrastructure ; Cell Line, Tumor ; Centrosome/metabolism ; Centrosome/ultrastructure ; Cilia/metabolism ; Cilia/ultrastructure ; Ciliopathies/genetics ; Ciliopathies/metabolism ; Ciliopathies/pathology ; Cytoskeletal Proteins/chemistry ; Cytoskeletal Proteins/genetics ; Cytoskeletal Proteins/metabolism ; Epithelial Cells/metabolism ; Epithelial Cells/ultrastructure ; Fibroblasts/metabolism ; Fibroblasts/ultrastructure ; Flagella/metabolism ; Flagella/ultrastructure ; Gene Expression ; HEK293 Cells ; HeLa Cells ; Humans ; MCF-7 Cells ; Microtubules/metabolism ; Microtubules/ultrastructure ; Myosin Heavy Chains/chemistry ; Myosin Heavy Chains/genetics ; Myosin Heavy Chains/metabolism ; Myosin Type V/chemistry ; Myosin Type V/genetics ; Myosin Type V/metabolism ; Protein Stability ; Recombinant Proteins/chemistry ; Recombinant Proteins/genetics ; Recombinant Proteins/metabolism
Chemical Substances	ACTR2 protein, human ; Actin-Related Protein 2 ; Actins ; Cytoskeletal Proteins ; LIMA1 protein, human ; LUZP1 protein, human ; Recombinant Proteins ; MYO5A protein, human (148971-15-7) ; Myosin Type V (EC 3.6.1.-) ; Myosin Heavy Chains (EC 3.6.4.1)
Language	English
Publishing date	2020-06-04
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.201908132
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Article ; Online: MAPL loss dysregulates bile and liver metabolism in mice.

Goyon, Vanessa / Besse-Patin, Aurèle / Zunino, Rodolfo / Ignatenko, Olesia / Nguyen, Mai / Coyaud, Étienne / Lee, Jonathan M / Nguyen, Bich N / Raught, Brian / McBride, Heidi M

EMBO reports

2023 Volume 24, Issue 12, Page(s) e57972

Abstract: Mitochondrial and peroxisomal anchored protein ligase (MAPL) is a dual ubiquitin and small ubiquitin-like modifier (SUMO) ligase with roles in mitochondrial quality control, cell death and inflammation in cultured cells. Here, we show that MAPL function ... ...

Abstract	Mitochondrial and peroxisomal anchored protein ligase (MAPL) is a dual ubiquitin and small ubiquitin-like modifier (SUMO) ligase with roles in mitochondrial quality control, cell death and inflammation in cultured cells. Here, we show that MAPL function in the organismal context converges on metabolic control, as knockout mice are viable, insulin-sensitive, and protected from diet-induced obesity. MAPL loss leads to liver-specific activation of the integrated stress response, inducing secretion of stress hormone FGF21. MAPL knockout mice develop fully penetrant spontaneous hepatocellular carcinoma. Mechanistically, the peroxisomal bile acid transporter ABCD3 is a primary MAPL interacting partner and SUMOylated in a MAPL-dependent manner. MAPL knockout leads to increased bile acid production coupled with defective regulatory feedback in liver in vivo and in isolated primary hepatocytes, suggesting cell-autonomous function. Together, our findings establish MAPL function as a regulator of bile acid synthesis whose loss leads to the disruption of bile acid feedback mechanisms. The consequences of MAPL loss in liver, along with evidence of tumor suppression through regulation of cell survival pathways, ultimately lead to hepatocellular carcinogenesis.
MeSH term(s)	Animals ; Mice ; Bile/metabolism ; Bile Acids and Salts ; Liver/metabolism ; Mice, Knockout ; Mitochondrial Proteins/genetics ; Mitochondrial Proteins/metabolism ; Ubiquitin-Protein Ligases/genetics ; Ubiquitin-Protein Ligases/metabolism ; Ubiquitins
Chemical Substances	Bile Acids and Salts ; Mitochondrial Proteins ; Ubiquitin-Protein Ligases (EC 2.3.2.27) ; Ubiquitins ; MUL1 protein, mouse (EC 2.3.2.27)
Language	English
Publishing date	2023-11-14
Publishing country	England
Document type	Journal Article
ZDB-ID	2020896-0
ISSN	1469-3178 ; 1469-221X
ISSN (online)	1469-3178
ISSN	1469-221X
DOI	10.15252/embr.202357972
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Article ; Online: Enhancer of Zeste Homolog 2 Inhibition Induces HLA Class I Re-Expression in Merkel Cell Carcinoma.

Durand, Marie-Alice / Drouin, Aurélie / Bachiri, Kamel / Durand, Laurine / Berthon, Patricia / Houben, Roland / Schrama, David / Coyaud, Etienne / Samimi, Mahtab / Touzé, Antoine / Kervarrec, Thibault

The Journal of investigative dermatology

2023

Language	English
Publishing date	2023-12-03
Publishing country	United States
Document type	Journal Article
ZDB-ID	80136-7
ISSN	1523-1747 ; 0022-202X
ISSN (online)	1523-1747
ISSN	0022-202X
DOI	10.1016/j.jid.2023.10.036
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Article ; Online: The SUMO-specific isopeptidase SENP2 is targeted to intracellular membranes via a predicted N-terminal amphipathic α-helix.

Odeh, Hana M / Coyaud, Etienne / Raught, Brian / Matunis, Michael J

Molecular biology of the cell

2018 Volume 29, Issue 15, Page(s) 1878–1890

Abstract: Sumoylation regulates a wide range of essential cellular functions, many of which are associated with activities in the nucleus. Although there is also emerging evidence for the involvement of the small ubiquitin-related modifier (SUMO) at intracellular ... ...

Abstract	Sumoylation regulates a wide range of essential cellular functions, many of which are associated with activities in the nucleus. Although there is also emerging evidence for the involvement of the small ubiquitin-related modifier (SUMO) at intracellular membranes, the mechanisms by which sumoylation is regulated at membranes is largely unexplored. In this study, we report that the SUMO-specific isopeptidase, SENP2, uniquely associates with intracellular membranes. Using in vivo analyses and in vitro binding assays, we show that SENP2 is targeted to intracellular membranes via a predicted N-terminal amphipathic α-helix that promotes direct membrane binding. Furthermore, we demonstrate that SENP2 binding to intracellular membranes is regulated by interactions with the nuclear import receptor karyopherin-α. Consistent with membrane association, biotin identification (BioID) revealed interactions between SENP2 and endoplasmic reticulum, Golgi, and inner nuclear membrane-associated proteins. Collectively, our findings indicate that SENP2 binds to intracellular membranes where it interacts with membrane-associated proteins and has the potential to regulate their sumoylation and membrane-associated functions.
MeSH term(s)	Amino Acid Sequence ; Cell Nucleus/metabolism ; Cysteine Endopeptidases/chemistry ; Cysteine Endopeptidases/metabolism ; Endoplasmic Reticulum/metabolism ; Golgi Apparatus/metabolism ; HeLa Cells ; Humans ; Intracellular Membranes/metabolism ; Membrane Proteins/metabolism ; Models, Biological ; Nuclear Localization Signals ; Nuclear Pore Complex Proteins/metabolism ; Protein Binding ; Protein Isoforms/metabolism ; Protein Structure, Secondary ; Small Ubiquitin-Related Modifier Proteins/metabolism ; Structure-Activity Relationship ; alpha Karyopherins/metabolism
Chemical Substances	Membrane Proteins ; Nuclear Localization Signals ; Nuclear Pore Complex Proteins ; Protein Isoforms ; Small Ubiquitin-Related Modifier Proteins ; alpha Karyopherins ; Cysteine Endopeptidases (EC 3.4.22.-) ; SENP2 protein, human (EC 3.4.22.-)
Language	English
Publishing date	2018-06-06
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; 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.E17-07-0445
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Article ; Online: Interfaces with Structure Dynamics of the Workhorses from Cells Revealed through Cross-Linking Mass Spectrometry (CLMS).

Kalathiya, Umesh / Padariya, Monikaben / Faktor, Jakub / Coyaud, Etienne / Alfaro, Javier A / Fahraeus, Robin / Hupp, Ted R / Goodlett, David R

Biomolecules

2021 Volume 11, Issue 3

Abstract: The fundamentals of how protein-protein/RNA/DNA interactions influence the structures and functions of the workhorses from the cells have been well documented in the 20th century. A diverse set of methods exist to determine such interactions between ... ...

Abstract	The fundamentals of how protein-protein/RNA/DNA interactions influence the structures and functions of the workhorses from the cells have been well documented in the 20th century. A diverse set of methods exist to determine such interactions between different components, particularly, the mass spectrometry (MS) methods, with its advanced instrumentation, has become a significant approach to analyze a diverse range of biomolecules, as well as bring insights to their biomolecular processes. This review highlights the principal role of chemistry in MS-based structural proteomics approaches, with a particular focus on the chemical cross-linking of protein-protein/DNA/RNA complexes. In addition, we discuss different methods to prepare the cross-linked samples for MS analysis and tools to identify cross-linked peptides. Cross-linking mass spectrometry (CLMS) holds promise to identify interaction sites in larger and more complex biological systems. The typical CLMS workflow allows for the measurement of the proximity in three-dimensional space of amino acids, identifying proteins in direct contact with DNA or RNA, and it provides information on the folds of proteins as well as their topology in the complexes. Principal CLMS applications, its notable successes, as well as common pipelines that bridge proteomics, molecular biology, structural systems biology, and interactomics are outlined.
MeSH term(s)	Animals ; DNA/chemistry ; DNA/metabolism ; Humans ; Mass Spectrometry/methods ; Protein Binding ; Protein Conformation ; Proteins/chemistry ; Proteins/metabolism
Chemical Substances	Proteins ; DNA (9007-49-2)
Language	English
Publishing date	2021-03-04
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2701262-1
ISSN	2218-273X ; 2218-273X
ISSN (online)	2218-273X
ISSN	2218-273X
DOI	10.3390/biom11030382
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