1
|
Garadi Suresh H, Bonneil E, Albert B, Dominique C, Costanzo M, Pons C, Masinas MPD, Shuteriqi E, Shore D, Henras AK, Thibault P, Boone C, Andrews BJ. K29-linked free polyubiquitin chains affect ribosome biogenesis and direct ribosomal proteins to the intranuclear quality control compartment. Mol Cell 2024; 84:2337-2352.e9. [PMID: 38870935 PMCID: PMC11193623 DOI: 10.1016/j.molcel.2024.05.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 01/25/2024] [Accepted: 05/17/2024] [Indexed: 06/15/2024]
Abstract
Ribosome assembly requires precise coordination between the production and assembly of ribosomal components. Mutations in ribosomal proteins that inhibit the assembly process or ribosome function are often associated with ribosomopathies, some of which are linked to defects in proteostasis. In this study, we examine the interplay between several yeast proteostasis enzymes, including deubiquitylases (DUBs) Ubp2 and Ubp14, and E3 ligases Ufd4 and Hul5, and we explore their roles in the regulation of the cellular levels of K29-linked unanchored polyubiquitin (polyUb) chains. Accumulating K29-linked unanchored polyUb chains associate with maturing ribosomes to disrupt their assembly, activate the ribosome assembly stress response (RASTR), and lead to the sequestration of ribosomal proteins at the intranuclear quality control compartment (INQ). These findings reveal the physiological relevance of INQ and provide insights into mechanisms of cellular toxicity associated with ribosomopathies.
Collapse
Affiliation(s)
- Harsha Garadi Suresh
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada.
| | - Eric Bonneil
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Benjamin Albert
- Department of Molecular Biology, Institute of Genetics and Genomics of Geneva (iGE3), Geneva, Switzerland; Molecular, Cellular and Developmental Biology Unit (MCD), Centre for Integrative Biology (CBI), University of Toulouse, CNRS, UPS, Toulouse, France
| | - Carine Dominique
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre for Integrative Biology (CBI), University of Toulouse, CNRS, UPS, Toulouse, France
| | - Michael Costanzo
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Carles Pons
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute for Science and Technology, Barcelona, Catalonia, Spain
| | - Myra Paz David Masinas
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Ermira Shuteriqi
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - David Shore
- Department of Molecular Biology, Institute of Genetics and Genomics of Geneva (iGE3), Geneva, Switzerland
| | - Anthony K Henras
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre for Integrative Biology (CBI), University of Toulouse, CNRS, UPS, Toulouse, France
| | - Pierre Thibault
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montréal, QC H3C 3J7, Canada; Department of Chemistry, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Charles Boone
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada.
| | - Brenda J Andrews
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada.
| |
Collapse
|
2
|
Subhadarshini S, Tandon H, Srinivasan N, Sowdhamini R. Normal Mode Analysis Elicits Conformational Shifts in Proteins at Both Proximal and Distal Regions to the Phosphosite Stemming from Single-Site Phosphorylation. ACS OMEGA 2024; 9:24520-24537. [PMID: 38882086 PMCID: PMC11170700 DOI: 10.1021/acsomega.4c00523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 04/29/2024] [Accepted: 05/13/2024] [Indexed: 06/18/2024]
Abstract
Phosphorylation, a fundamental biochemical switch, intricately regulates protein function and signaling pathways. Our study employs extensive computational structural analyses on a curated data set of phosphorylated and unphosphorylated protein pairs to explore the multifaceted impact of phosphorylation on protein conformation. Using normal mode analysis (NMA), we investigated changes in protein flexibility post-phosphorylation, highlighting an enhanced level of structural dynamism. Our findings reveal that phosphorylation induces not only local changes at the phosphorylation site but also extensive alterations in distant regions, showcasing its far-reaching influence on protein structure-dynamics. Through in-depth case studies on polyubiquitin B and glycogen synthase kinase-3 beta, we elucidate how phosphorylation at distinct sites leads to variable structural and dynamic modifications, potentially dictating functional outcomes. While phosphorylation largely preserves the residue motion correlation, it significantly disrupts low-frequency global modes, presenting a dualistic impact on protein dynamics. We also explored alterations in the total accessible surface area (ASA), emphasizing region-specific changes around phosphorylation sites. This study sheds light on phosphorylation-induced conformational changes, dynamic modulation, and surface accessibility alterations, leveraging an integrated computational approach with RMSD, NMA, and ASA, thereby contributing to a comprehensive understanding of cellular regulation and suggesting promising avenues for therapeutic interventions.
Collapse
Affiliation(s)
| | - Himani Tandon
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | | | - Ramanathan Sowdhamini
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
- Computational Approaches to Protein Science, National Centre for Biological Sciences, Bangalore 560065, India
- Computational Biology, Institute of Bioinformatics and Applied Biotechnology, Bangalore 560100, India
| |
Collapse
|
3
|
Grain B, Desmet R, Snella B, Melnyk O, Agouridas V. Incorporation of a Highly Reactive Oxalyl Thioester-Based Interacting Handle into Proteins. Org Lett 2023; 25:5117-5122. [PMID: 37384828 PMCID: PMC10353032 DOI: 10.1021/acs.orglett.3c01846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Indexed: 07/01/2023]
Abstract
Providing biomolecules with extended physicochemical, biochemical, or biological properties is a contemporary challenge motivated by impactful benefits in life or materials sciences. In this study, we show that a latent and highly reactive oxalyl thioester precursor can be efficiently introduced as a pending functionality into a fully synthetic protein domain following a protection/late-stage deprotection strategy and can serve as an on-demand reactive handle. The approach is illustrated with the production of a 10 kDa ubiquitin Lys48 conjugate.
Collapse
Affiliation(s)
- Benjamin Grain
- Univ.
Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 -
UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Rémi Desmet
- Univ.
Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 -
UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Benoît Snella
- Univ.
Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 -
UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Oleg Melnyk
- Univ.
Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 -
UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Vangelis Agouridas
- Univ.
Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 -
UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
- Centrale
Lille, F-59000 Lille, France
| |
Collapse
|
4
|
Suresh HG, Bonneil E, Albert B, Dominique C, Costanzo M, Pons C, David Masinas MP, Shuteriqi E, Shore D, Henras AK, Thibault P, Boone C, Andrews BJ. K29-linked unanchored polyubiquitin chains disrupt ribosome biogenesis and direct ribosomal proteins to the Intranuclear Quality control compartment (INQ). BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.03.539259. [PMID: 37205480 PMCID: PMC10187189 DOI: 10.1101/2023.05.03.539259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Ribosome assembly requires precise coordination between the production and assembly of ribosomal components. Mutations in ribosomal proteins that inhibit the assembly process or ribosome function are often associated with Ribosomopathies, some of which are linked to defects in proteostasis. In this study, we examine the interplay between several yeast proteostasis enzymes, including deubiquitylases (DUBs), Ubp2 and Ubp14, and E3 ligases, Ufd4 and Hul5, and we explore their roles in the regulation of the cellular levels of K29-linked unanchored polyubiquitin (polyUb) chains. Accumulating K29-linked unanchored polyUb chains associate with maturing ribosomes to disrupt their assembly, activate the Ribosome assembly stress response (RASTR), and lead to the sequestration of ribosomal proteins at the Intranuclear Quality control compartment (INQ). These findings reveal the physiological relevance of INQ and provide insights into mechanisms of cellular toxicity associated with Ribosomopathies.
Collapse
|
5
|
Blake LI, Cann MJ. Carbon Dioxide and the Carbamate Post-Translational Modification. Front Mol Biosci 2022; 9:825706. [PMID: 35300111 PMCID: PMC8920986 DOI: 10.3389/fmolb.2022.825706] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 02/03/2022] [Indexed: 01/10/2023] Open
Abstract
Carbon dioxide is essential for life. It is at the beginning of every life process as a substrate of photosynthesis. It is at the end of every life process as the product of post-mortem decay. Therefore, it is not surprising that this gas regulates such diverse processes as cellular chemical reactions, transport, maintenance of the cellular environment, and behaviour. Carbon dioxide is a strategically important research target relevant to crop responses to environmental change, insect vector-borne disease and public health. However, we know little of carbon dioxide’s direct interactions with the cell. The carbamate post-translational modification, mediated by the nucleophilic attack by carbon dioxide on N-terminal α-amino groups or the lysine ɛ-amino groups, is one mechanism by which carbon dioxide might alter protein function to form part of a sensing and signalling mechanism. We detail known protein carbamates, including the history of their discovery. Further, we describe recent studies on new techniques to isolate this problematic post-translational modification.
Collapse
|
6
|
Hafez N, Modather El-Awadly Z, Arafa RK. UCH-L3 structure and function: Insights about a promising drug target. Eur J Med Chem 2022; 227:113970. [PMID: 34752952 DOI: 10.1016/j.ejmech.2021.113970] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/29/2021] [Accepted: 10/30/2021] [Indexed: 11/04/2022]
Abstract
In the past few years, researchers have shed light on the immense importance of ubiquitin in numerous regulatory pathways. The post-translational addition of mono or poly-ubiquitin molecules namely "ubiquitinoylation" is therefore pivotal to maintain the cell's vitality, maturation, differentiation, and division. Part of conserving homeostasis stems from maintaining the ubiquitin pool in the vicinity of the cell's intracellular environment; this crucial role is played by deubiquitylating enzymes (DUBs) that cleave ubiquitin molecules from target molecules. To date, they are categorized into 7 families with ubiquitin carboxyl c-terminal de-hydrolase family (UCH) as the most common and well-studied. Ubiquitin C-terminal hydrolase L (UCH-L3) is a significant protein in this family as it has been implicated in many molecular and cellular processes with its mRNA identified in a range of body tissues including the brain. It goes without saying that it manifests in maintaining health and when abnormally regulated in disease. As it is an attractive small molecule drug target, scientists have used high throughput screening (HTS) and other drug discovery methods to discover inhibitors for this enzyme for the treatment of cancer and neurodegenerative diseases. In this review we present an overview of UCH-L3 catalytic mechanism, structure, its role in DNA repair and cancer along with the inhibitors discovered so far to halt its activity.
Collapse
Affiliation(s)
- Noha Hafez
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Cairo, 12578, Egypt
| | - Zahraa Modather El-Awadly
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Cairo, 12578, Egypt
| | - Reem K Arafa
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Cairo, 12578, Egypt; Drug Design and Discovery Laboratory, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Cairo, 12578, Egypt.
| |
Collapse
|
7
|
Morimoto D, Nishizawa R, Walinda E, Takashima S, Sugase K, Shirakawa M. Hydrogen-Deuterium Exchange Profiles of Polyubiquitin Fibrils. Polymers (Basel) 2018; 10:E240. [PMID: 30966275 PMCID: PMC6414897 DOI: 10.3390/polym10030240] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 02/23/2018] [Accepted: 02/24/2018] [Indexed: 11/16/2022] Open
Abstract
Ubiquitin and its polymeric forms are conjugated to intracellular proteins to regulate diverse intracellular processes. Intriguingly, polyubiquitin has also been identified as a component of pathological protein aggregates associated with Alzheimer's disease and other neurodegenerative disorders. We recently found that polyubiquitin can form amyloid-like fibrils, and that these fibrillar aggregates can be degraded by macroautophagy. Although the structural properties appear to function in recognition of the fibrils, no structural information on polyubiquitin fibrils has been reported so far. Here, we identify the core of M1-linked diubiquitin fibrils from hydrogen-deuterium exchange experiments using solution nuclear magnetic resonance (NMR) spectroscopy. Intriguingly, intrinsically flexible regions became highly solvent-protected in the fibril structure. These results indicate that polyubiquitin fibrils are formed by inter-molecular interactions between relatively flexible structural components, including the loops and edges of secondary structure elements.
Collapse
Affiliation(s)
- Daichi Morimoto
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-Ku, Kyoto 615-8510, Japan.
| | - Ryo Nishizawa
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-Ku, Kyoto 615-8510, Japan.
| | - Erik Walinda
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, Kyoto University, Yoshida Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.
| | - Shingo Takashima
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-Ku, Kyoto 615-8510, Japan.
| | - Kenji Sugase
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-Ku, Kyoto 615-8510, Japan.
| | - Masahiro Shirakawa
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-Ku, Kyoto 615-8510, Japan.
| |
Collapse
|
8
|
Bacchi M, Fould B, Jullian M, Kreiter A, Maurras A, Nosjean O, Coursindel T, Puget K, Ferry G, Boutin JA. Screening ubiquitin specific protease activities using chemically synthesized ubiquitin and ubiquitinated peptides. Anal Biochem 2017; 519:57-70. [PMID: 27993553 DOI: 10.1016/j.ab.2016.12.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 12/13/2016] [Accepted: 12/15/2016] [Indexed: 12/12/2022]
Abstract
Ubiquitin, a 76 amino acid protein, is a key component that contributes to cellular protein homeostasis. The specificity of this modification is due to a series of enzymes: ligases, attaching the ubiquitin to a lysine, and deubiquitinases, which remove it. More than a hundred of such proteins are implicated in the regulation of protein turnover. Their specificities are only partially understood. We chemically synthesized ubiquitin, attached it to lysines belonging to the protein sequences known to be ubiquitinated. We chose the model protein "murine double minute 2" (mdm2), a ubiquitin ligase, itself ubiquitinated and deubiquitinated. We folded the ubiquitinated peptides and checked their tridimensional conformation. We assessed the use of these substrates with a series of fifteen deubiquitinases to show the potentiality of such an enzymological technique. By manipulating the sequence of the peptide on which ubiquitin is attached, we were able to detect differences in the enzyme/substrate recognition, and to determine that these differences are deubiquitinase-dependent. This approach could be used to understand the substrate/protein relationship between the protagonists of this reaction. The methodology could be customized for a given substrate and used to advance our understanding of the key amino acids responsible for the deubiquitinase specificities.
Collapse
Affiliation(s)
- Marine Bacchi
- Pôle d'Expertise Biotechnologie, Chimie & Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, 78290 Croissy-sur-Seine, France
| | - Benjamin Fould
- Pôle d'Expertise Biotechnologie, Chimie & Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, 78290 Croissy-sur-Seine, France
| | - Magali Jullian
- Genepep S.A., 12 Rue du Fer à Cheval, 34430 Saint-Jean-de-Védas, France
| | - Aude Kreiter
- Genepep S.A., 12 Rue du Fer à Cheval, 34430 Saint-Jean-de-Védas, France
| | - Amélie Maurras
- Genepep S.A., 12 Rue du Fer à Cheval, 34430 Saint-Jean-de-Védas, France
| | - Olivier Nosjean
- Pôle d'Expertise Biotechnologie, Chimie & Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, 78290 Croissy-sur-Seine, France
| | | | - Karine Puget
- Genepep S.A., 12 Rue du Fer à Cheval, 34430 Saint-Jean-de-Védas, France
| | - Gilles Ferry
- Pôle d'Expertise Biotechnologie, Chimie & Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, 78290 Croissy-sur-Seine, France
| | - Jean A Boutin
- Pôle d'Expertise Biotechnologie, Chimie & Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, 78290 Croissy-sur-Seine, France.
| |
Collapse
|