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Szulc NA, Stefaniak F, Piechota M, Soszyńska A, Piórkowska G, Cappannini A, Bujnicki J, Maniaci C, Pokrzywa W. DEGRONOPEDIA: a web server for proteome-wide inspection of degrons. Nucleic Acids Res 2024; 52:W221-W232. [PMID: 38567734 PMCID: PMC11223883 DOI: 10.1093/nar/gkae238] [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: 02/02/2024] [Revised: 03/12/2024] [Accepted: 03/20/2024] [Indexed: 07/06/2024] Open
Abstract
E3 ubiquitin ligases recognize substrates through their short linear motifs termed degrons. While degron-signaling has been a subject of extensive study, resources for its systematic screening are limited. To bridge this gap, we developed DEGRONOPEDIA, a web server that searches for degrons and maps them to nearby residues that can undergo ubiquitination and disordered regions, which may act as protein unfolding seeds. Along with an evolutionary assessment of degron conservation, the server also reports on post-translational modifications and mutations that may modulate degron availability. Acknowledging the prevalence of degrons at protein termini, DEGRONOPEDIA incorporates machine learning to assess N-/C-terminal stability, supplemented by simulations of proteolysis to identify degrons in newly formed termini. An experimental validation of a predicted C-terminal destabilizing motif, coupled with the confirmation of a post-proteolytic degron in another case, exemplifies its practical application. DEGRONOPEDIA can be freely accessed at degronopedia.com.
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Affiliation(s)
- Natalia A Szulc
- Laboratory of Protein Metabolism, International Institute of Molecular and Cell Biology in Warsaw, 4 Ks. Trojdena Str., 02-109 Warsaw, Poland
| | - Filip Stefaniak
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, 4 Ks. Trojdena Str., 02-109 Warsaw, Poland
| | - Małgorzata Piechota
- Laboratory of Protein Metabolism, International Institute of Molecular and Cell Biology in Warsaw, 4 Ks. Trojdena Str., 02-109 Warsaw, Poland
| | - Anna Soszyńska
- Laboratory of Protein Metabolism, International Institute of Molecular and Cell Biology in Warsaw, 4 Ks. Trojdena Str., 02-109 Warsaw, Poland
| | - Gabriela Piórkowska
- Laboratory of Protein Metabolism, International Institute of Molecular and Cell Biology in Warsaw, 4 Ks. Trojdena Str., 02-109 Warsaw, Poland
| | - Andrea Cappannini
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, 4 Ks. Trojdena Str., 02-109 Warsaw, Poland
| | - Janusz M Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, 4 Ks. Trojdena Str., 02-109 Warsaw, Poland
| | - Chiara Maniaci
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Wojciech Pokrzywa
- Laboratory of Protein Metabolism, International Institute of Molecular and Cell Biology in Warsaw, 4 Ks. Trojdena Str., 02-109 Warsaw, Poland
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2
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Grønbæk-Thygesen M, Voutsinos V, Johansson KE, Schulze TK, Cagiada M, Pedersen L, Clausen L, Nariya S, Powell RL, Stein A, Fowler DM, Lindorff-Larsen K, Hartmann-Petersen R. Deep mutational scanning reveals a correlation between degradation and toxicity of thousands of aspartoacylase variants. Nat Commun 2024; 15:4026. [PMID: 38740822 DOI: 10.1038/s41467-024-48481-0] [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: 10/18/2023] [Accepted: 05/02/2024] [Indexed: 05/16/2024] Open
Abstract
Unstable proteins are prone to form non-native interactions with other proteins and thereby may become toxic. To mitigate this, destabilized proteins are targeted by the protein quality control network. Here we present systematic studies of the cytosolic aspartoacylase, ASPA, where variants are linked to Canavan disease, a lethal neurological disorder. We determine the abundance of 6152 of the 6260 ( ~ 98%) possible single amino acid substitutions and nonsense ASPA variants in human cells. Most low abundance variants are degraded through the ubiquitin-proteasome pathway and become toxic upon prolonged expression. The data correlates with predicted changes in thermodynamic stability, evolutionary conservation, and separate disease-linked variants from benign variants. Mapping of degradation signals (degrons) shows that these are often buried and the C-terminal region functions as a degron. The data can be used to interpret Canavan disease variants and provide insight into the relationship between protein stability, degradation and cell fitness.
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Affiliation(s)
- Martin Grønbæk-Thygesen
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Vasileios Voutsinos
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Kristoffer E Johansson
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Thea K Schulze
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Matteo Cagiada
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Line Pedersen
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Lene Clausen
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Snehal Nariya
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Rachel L Powell
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Amelie Stein
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Douglas M Fowler
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Department of Bioengineering, University of Washington, Seattle, WA, USA.
| | - Kresten Lindorff-Larsen
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Rasmus Hartmann-Petersen
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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3
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Yu Q, Wang Z, Tu Y, Cao Y, Zhu H, Shao J, Zhuang R, Zhou Y, Zhang J. Proteasome activation: A novel strategy for targeting undruggable intrinsically disordered proteins. Bioorg Chem 2024; 145:107217. [PMID: 38368657 DOI: 10.1016/j.bioorg.2024.107217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 01/23/2024] [Accepted: 02/14/2024] [Indexed: 02/20/2024]
Abstract
Intrinsically disordered proteins (IDPs) are characterized by their inability to adopt well-defined tertiary structures under physiological conditions. Nonetheless, they often play pivotal roles in the progression of various diseases, including cancer, neurodegenerative disorders, and cardiovascular ailments. Owing to their inherent dynamism, conventional drug design approaches based on structural considerations encounter substantial challenges when applied to IDPs. Consequently, the pursuit of therapeutic interventions directed towards IDPs presents a complex endeavor. While there are indeed existing methodologies for targeting IDPs, they are encumbered by noteworthy constrains. Hence, there exists an imminent imperative to investigate more efficacious and universally applicable strategies for modulating IDPs. Here, we present an overview of the latest advancements in the research pertaining to IDPs, along with the indirect regulation approach involving the modulation of IDP degradation through proteasome. By comprehending these advancements in research, novel insights can be generated to facilitate the development of new drugs targeted at addressing the accumulation of IDPs in diverse pathological conditions.
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Affiliation(s)
- Qian Yu
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, 310015, Zhejiang Province, China; College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang Province, China
| | - Zheng Wang
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, 310015, Zhejiang Province, China; College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang Province, China
| | - Yutong Tu
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Yu Cao
- Department of Pharmaceutical Preparation, Hangzhou Xixi Hospital, Hangzhou, 310023, Zhejiang Province, China
| | - Huajian Zhu
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, 310015, Zhejiang Province, China; College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang Province, China
| | - Jiaan Shao
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, 310015, Zhejiang Province, China; College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang Province, China
| | - Rangxiao Zhuang
- Department of Pharmaceutical Preparation, Hangzhou Xixi Hospital, Hangzhou, 310023, Zhejiang Province, China.
| | - Yubo Zhou
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
| | - Jiankang Zhang
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, 310015, Zhejiang Province, China; College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang Province, China.
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4
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Lemaitre T, Cornu M, Schwalen F, Since M, Kieffer C, Voisin-Chiret AS. Molecular glue degraders: exciting opportunities for novel drug discovery. Expert Opin Drug Discov 2024; 19:433-449. [PMID: 38240114 DOI: 10.1080/17460441.2024.2306845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 01/15/2024] [Indexed: 01/25/2024]
Abstract
INTRODUCTION Molecular Glue Degraders (MGDs) is a concept that refers to a class of compounds that facilitate the interaction between two proteins or molecules within a cell. These compounds act as bridge that enhances specific Protein-Protein Interactions (PPIs). Over the past decade, this technology has gained attention as a potential strategy to target proteins that were traditionally considered undruggable using small molecules. AREAS COVERED This review presents the concept of cellular homeostasis and the balance between protein synthesis and protein degradation. The concept of protein degradation is concerned with molecular glues, which form part of the broader field of Targeted Protein Degradation (TPD). Next, pharmacochemical strategies for the rational design of MGDs are detailed and illustrated by examples of Ligand-Based (LBDD), Structure-Based (SBDD) and Fragment-Based Drug Design (FBDD). EXPERT OPINION Expanding the scope of what can be effectively targeted in the development of treatments for diseases that are incurable or resistant to conventional therapies offers new therapeutic options. The treatment of microbial infections and neurodegenerative diseases is a major societal challenge, and the discovery of MGDs appears to be a promising avenue. Combining different approaches to discover and exploit a variety of innovative therapeutic agents will create opportunities to treat diseases that are still incurable.
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Affiliation(s)
| | - Marie Cornu
- Normandie University, UNICAEN, CERMN, Caen, France
| | - Florian Schwalen
- Normandie University, UNICAEN, CERMN, Caen, France
- Department of Pharmacy, Caen University Hospital, Caen, France
| | - Marc Since
- Normandie University, UNICAEN, CERMN, Caen, France
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Vankova P, Pacheco-Garcia JL, Loginov DS, Gómez-Mulas A, Kádek A, Martín-Garcia JM, Salido E, Man P, Pey AL. Insights into the pathogenesis of primary hyperoxaluria type I from the structural dynamics of alanine:glyoxylate aminotransferase variants. FEBS Lett 2024; 598:485-499. [PMID: 38243391 DOI: 10.1002/1873-3468.14800] [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: 10/13/2023] [Revised: 12/06/2023] [Accepted: 12/20/2023] [Indexed: 01/21/2024]
Abstract
Primary hyperoxaluria type I (PH1) is caused by deficient alanine:glyoxylate aminotransferase (AGT) activity. PH1-causing mutations in AGT lead to protein mistargeting and aggregation. Here, we use hydrogen-deuterium exchange (HDX) to characterize the wild-type (WT), the LM (a polymorphism frequent in PH1 patients) and the LM G170R (the most common mutation in PH1) variants of AGT. We provide the first experimental analysis of AGT structural dynamics, showing that stability is heterogeneous in the native state and providing a blueprint for frustrated regions with potentially functional relevance. The LM and LM G170R variants only show local destabilization. Enzymatic transamination of the pyridoxal 5-phosphate cofactor bound to AGT hardly affects stability. Our study, thus, supports that AGT misfolding is not caused by dramatic effects on structural dynamics.
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Affiliation(s)
- Pavla Vankova
- Institute of Biotechnology - BioCeV, Academy of Sciences of the Czech Republic, Vestec, Czech Republic
| | | | - Dmitry S Loginov
- Institute of Microbiology - BioCeV, Academy of Sciences of the Czech Republic, Vestec, Czech Republic
| | | | - Alan Kádek
- Institute of Microbiology - BioCeV, Academy of Sciences of the Czech Republic, Vestec, Czech Republic
| | - José Manuel Martín-Garcia
- Department of Crystallography & Structural Biology, Institute of Physical Chemistry Blas Cabrera, Spanish National Research Council (CSIC), Madrid, Spain
| | - Eduardo Salido
- Center for Rare Diseases (CIBERER), Hospital Universitario de Canarias, Universidad de la Laguna, Tenerife, Spain
| | - Petr Man
- Institute of Microbiology - BioCeV, Academy of Sciences of the Czech Republic, Vestec, Czech Republic
| | - Angel L Pey
- Departamento de Química Física, Unidad de Excelencia en Química Aplicada a Biomedicina y Medioambiente e Instituto de Biotecnología, Universidad de Granada, Spain
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Pereira GP, Jiménez-García B, Pellarin R, Launay G, Wu S, Martin J, Souza PCT. Rational Prediction of PROTAC-Compatible Protein-Protein Interfaces by Molecular Docking. J Chem Inf Model 2023; 63:6823-6833. [PMID: 37877240 DOI: 10.1021/acs.jcim.3c01154] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2023]
Abstract
Proteolysis targeting chimeras (PROTACs) are heterobifunctional ligands that mediate the interaction between a protein target and an E3 ligase, resulting in a ternary complex, whose interaction with the ubiquitination machinery leads to target degradation. This technology is emerging as an exciting new avenue for therapeutic development, with several PROTACs currently undergoing clinical trials targeting cancer. Here, we describe a general and computationally efficient methodology combining restraint-based docking, energy-based rescoring, and a filter based on the minimal solvent-accessible surface distance to produce PROTAC-compatible PPIs suitable for when there is no a priori known PROTAC ligand. In a benchmark employing a manually curated data set of 13 ternary complex crystals, we achieved an accuracy of 92% when starting from bound structures and 77% when starting from unbound structures, respectively. Our method only requires that the ligand-bound structures of the monomeric forms of the E3 ligase and target proteins be given to run, making it general, accurate, and highly efficient, with the ability to impact early-stage PROTAC-based drug design campaigns where no structural information about the ternary complex structure is available.
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Affiliation(s)
- Gilberto P Pereira
- Molecular Microbiology and Structural Biochemistry, CNRS UMR 5086 and Université Claude Bernard Lyon 1, 7 Passage du Vercors, 69007 Lyon, France
- Laboratory of Biology and Modeling of the Cell, École Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5239 and Inserm U1293, 46 Allée d'Italie, 69007 Lyon, France
| | | | - Riccardo Pellarin
- Molecular Microbiology and Structural Biochemistry, CNRS UMR 5086 and Université Claude Bernard Lyon 1, 7 Passage du Vercors, 69007 Lyon, France
- Laboratory of Biology and Modeling of the Cell, École Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5239 and Inserm U1293, 46 Allée d'Italie, 69007 Lyon, France
| | - Guillaume Launay
- Molecular Microbiology and Structural Biochemistry, CNRS UMR 5086 and Université Claude Bernard Lyon 1, 7 Passage du Vercors, 69007 Lyon, France
- Laboratory of Biology and Modeling of the Cell, École Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5239 and Inserm U1293, 46 Allée d'Italie, 69007 Lyon, France
| | - Sangwook Wu
- PharmCADD, Busan 48792, Republic of Korea
- Department of Physics, Pukyong National University, Busan 48513, Republic of Korea
| | - Juliette Martin
- Molecular Microbiology and Structural Biochemistry, CNRS UMR 5086 and Université Claude Bernard Lyon 1, 7 Passage du Vercors, 69007 Lyon, France
- Laboratory of Biology and Modeling of the Cell, École Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5239 and Inserm U1293, 46 Allée d'Italie, 69007 Lyon, France
| | - Paulo C T Souza
- Molecular Microbiology and Structural Biochemistry, CNRS UMR 5086 and Université Claude Bernard Lyon 1, 7 Passage du Vercors, 69007 Lyon, France
- Laboratory of Biology and Modeling of the Cell, École Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5239 and Inserm U1293, 46 Allée d'Italie, 69007 Lyon, France
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7
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Brunner A, Li Q, Fisicaro S, Kourtesakis A, Viiliäinen J, Johansson HJ, Pandey V, Mayank AK, Lehtiö J, Wohlschlegel JA, Spruck C, Rantala JK, Orre LM, Sangfelt O. FBXL12 degrades FANCD2 to regulate replication recovery and promote cancer cell survival under conditions of replication stress. Mol Cell 2023; 83:3720-3739.e8. [PMID: 37591242 PMCID: PMC10592106 DOI: 10.1016/j.molcel.2023.07.026] [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: 06/16/2022] [Revised: 05/14/2023] [Accepted: 07/26/2023] [Indexed: 08/19/2023]
Abstract
Fanconi anemia (FA) signaling, a key genomic maintenance pathway, is activated in response to replication stress. Here, we report that phosphorylation of the pivotal pathway protein FANCD2 by CHK1 triggers its FBXL12-dependent proteasomal degradation, facilitating FANCD2 clearance at stalled replication forks. This promotes efficient DNA replication under conditions of CYCLIN E- and drug-induced replication stress. Reconstituting FANCD2-deficient fibroblasts with phosphodegron mutants failed to re-establish fork progression. In the absence of FBXL12, FANCD2 becomes trapped on chromatin, leading to replication stress and excessive DNA damage. In human cancers, FBXL12, CYCLIN E, and FA signaling are positively correlated, and FBXL12 upregulation is linked to reduced survival in patients with high CYCLIN E-expressing breast tumors. Finally, depletion of FBXL12 exacerbated oncogene-induced replication stress and sensitized cancer cells to drug-induced replication stress by WEE1 inhibition. Collectively, our results indicate that FBXL12 constitutes a vulnerability and a potential therapeutic target in CYCLIN E-overexpressing cancers.
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Affiliation(s)
- Andrä Brunner
- Department of Cell and Molecular Biology, Karolinska Institutet, Solna 17165, Stockholms län, Sweden.
| | - Qiuzhen Li
- Department of Cell and Molecular Biology, Karolinska Institutet, Solna 17165, Stockholms län, Sweden
| | - Samuele Fisicaro
- Department of Cell and Molecular Biology, Karolinska Institutet, Solna 17165, Stockholms län, Sweden
| | - Alexandros Kourtesakis
- Department of Cell and Molecular Biology, Karolinska Institutet, Solna 17165, Stockholms län, Sweden
| | - Johanna Viiliäinen
- Department of Cell and Molecular Biology, Karolinska Institutet, Solna 17165, Stockholms län, Sweden
| | - Henrik J Johansson
- Department of Oncology and Pathology, Karolinska Institutet, Science for Life Laboratory, Solna 17165, Stockholms län, Sweden
| | - Vijaya Pandey
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles 90095, CA, USA
| | - Adarsh K Mayank
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles 90095, CA, USA
| | - Janne Lehtiö
- Department of Oncology and Pathology, Karolinska Institutet, Science for Life Laboratory, Solna 17165, Stockholms län, Sweden
| | - James A Wohlschlegel
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles 90095, CA, USA
| | - Charles Spruck
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla 92037, CA, USA
| | - Juha K Rantala
- Department of Oncology and Metabolism, University of Sheffield, Sheffield S10 2RX, South Yorkshire, UK; Misvik Biology, Turku 20520, Finland
| | - Lukas M Orre
- Department of Oncology and Pathology, Karolinska Institutet, Science for Life Laboratory, Solna 17165, Stockholms län, Sweden
| | - Olle Sangfelt
- Department of Cell and Molecular Biology, Karolinska Institutet, Solna 17165, Stockholms län, Sweden.
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Oliveira AS, Aredes-Riguetti LM, Pereira BAS, Alves CR, Souza-Silva F. Degron Pathways and Leishmaniasis: Debating Potential Roles of Leishmania spp. Proteases Activity on Guiding Hosts Immune Response and Their Relevance to the Development of Vaccines. Vaccines (Basel) 2023; 11:1015. [PMID: 37376405 DOI: 10.3390/vaccines11061015] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 03/08/2023] [Accepted: 03/09/2023] [Indexed: 06/29/2023] Open
Abstract
Degrons are short peptide sequences that signalize target sites for protein degradation by proteases. Herein, we bring forth the discussion on degrons present in proteins related to the immune system of Mus musculus that are potential targets for cysteine and serine proteases of Leishmania spp. and their possible roles on host immune regulation by parasites. The Merops database was used to identify protease substrates and proteases sequence motifs, while MAST/MEME Suite was applied to find degron motifs in murine cytokines (IFN-y, IL-4, IL-5, IL-13, IL-17) and transcription factors (NF-kappaB, STAT-1, AP-1, CREB, and BACH2). STRING tool was used to construct an interaction network for the immune factors and SWISS-MODEL server to generate three-dimensional models of proteins. In silico assays confirm the occurrence of degrons in the selected immune response factors. Further analyses were conducted only in those with resolved three-dimensional structures. The predicted interaction network of degron-containing M. musculus proteins shows the possibility that the specific activity of parasite proteases could interfere with the trend of Th1/Th2 immune responses. Data suggest that degrons may play a role in the immune responses in leishmaniases as targets for parasite proteases activity, directing the degradation of specific immune-related factors.
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Affiliation(s)
- Adriane Silva Oliveira
- Laboratório de Biologia Molecular e Doenças Endêmicas, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Manguinhos, Rio de Janeiro 21040-360, RJ, Brazil
| | - Lara Mata Aredes-Riguetti
- Laboratório de Biologia Molecular e Doenças Endêmicas, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Manguinhos, Rio de Janeiro 21040-360, RJ, Brazil
| | | | - Carlos Roberto Alves
- Laboratório de Biologia Molecular e Doenças Endêmicas, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Manguinhos, Rio de Janeiro 21040-360, RJ, Brazil
| | - Franklin Souza-Silva
- Centro de Desenvolvimento Tecnológico em Saúde, Fundação Oswaldo Cruz, Manguinhos, Rio de Janeiro 21040-360, RJ, Brazil
- Faculdade de Ciências Biológicas e da Saúde, Universidade Iguaçu, Avenida Abílio Augusto Távora, 2134, Dom Rodrigo, Nova Iguaçu 26260-100, RJ, Brazil
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9
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Paul AA, Szulc NA, Kobiela A, Brown SJ, Pokrzywa W, Gutowska-Owsiak D. In silico analysis of the profilaggrin sequence indicates alterations in the stability, degradation route, and intracellular protein fate in filaggrin null mutation carriers. Front Mol Biosci 2023; 10:1105678. [PMID: 37200867 PMCID: PMC10185843 DOI: 10.3389/fmolb.2023.1105678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 04/19/2023] [Indexed: 05/20/2023] Open
Abstract
Background: Loss of function mutation in FLG is the major genetic risk factor for atopic dermatitis (AD) and other allergic manifestations. Presently, little is known about the cellular turnover and stability of profilaggrin, the protein encoded by FLG. Since ubiquitination directly regulates the cellular fate of numerous proteins, their degradation and trafficking, this process could influence the concentration of filaggrin in the skin. Objective: To determine the elements mediating the interaction of profilaggrin with the ubiquitin-proteasome system (i.e., degron motifs and ubiquitination sites), the features responsible for its stability, and the effect of nonsense and frameshift mutations on profilaggrin turnover. Methods: The effect of inhibition of proteasome and deubiquitinases on the level and modifications of profilaggrin and processed products was assessed by immunoblotting. Wild-type profilaggrin sequence and its mutated variants were analysed in silico using the DEGRONOPEDIA and Clustal Omega tool. Results: Inhibition of proteasome and deubiquitinases stabilizes profilaggrin and its high molecular weight of presumably ubiquitinated derivatives. In silico analysis of the sequence determined that profilaggrin contains 18 known degron motifs as well as multiple canonical and non-canonical ubiquitination-prone residues. FLG mutations generate products with increased stability scores, altered usage of the ubiquitination marks, and the frequent appearance of novel degrons, including those promoting C-terminus-mediated degradation routes. Conclusion: The proteasome is involved in the turnover of profilaggrin, which contains multiple degrons and ubiquitination-prone residues. FLG mutations alter those key elements, affecting the degradation routes and the mutated products' stability.
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Affiliation(s)
- Argho Aninda Paul
- Experimental and Translational Immunology Group, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, Gdansk, Poland
| | - Natalia A. Szulc
- Laboratory of Protein Metabolism, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Adrian Kobiela
- Experimental and Translational Immunology Group, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, Gdansk, Poland
| | - Sara J. Brown
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Wojciech Pokrzywa
- Laboratory of Protein Metabolism, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Danuta Gutowska-Owsiak
- Experimental and Translational Immunology Group, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, Gdansk, Poland
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10
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Xiaoling X, Xinmei L, Shuhua F, Qian Z, Fu G, Qifang J, Lin X, Xiong Y. TRIM40 ameliorates diabetic retinopathy through suppressing inflammation via Reelin/DAB1 signaling disruption: A mechanism by proteasomal degradation of DAB1. Biochem Biophys Res Commun 2023; 664:117-127. [PMID: 37146559 DOI: 10.1016/j.bbrc.2023.04.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 04/08/2023] [Indexed: 05/07/2023]
Abstract
Diabetic retinopathy (DR) is a common microvascular complication of diabetes mellitus. Reelin, an extracellular matrix protein, and its effector protein Disabled1 (DAB1) have been linked to cellular events and retinal development. However, whether and how Reelin/DAB1 signaling causes DR remains to be investigated. In our study, significantly increased expression of Reelin, very low density lipoprotein receptor (VLDLR), ApoE receptor 2 (ApoER2) and phosphorylated DAB1 in retinas of streptozotocin (STZ)-induced DR mouse model was observed, along with enhanced expression of proinflammatory factors. Similar results are confirmed in high glucose (HG)-treated human retinal pigment epithelium cell line ARPE-19. Surprisingly, dysregulated tripartite motif-containing 40 (TRIM40), an E3 ubiquitin ligase, is found to be involved in DR progression by bioinformatic analysis. We observe a negative correlation between TRIM40 and p-DAB1 protein expression levels under HG conditions. Importantly, we find that TRIM40 over-expression markedly ameliorates HG-induced p-DAB1, PI3K, p-protein B kinase (AKT) and inflammatory response in HG-treated cells, but dose not affect Reelin expression. Of note, Co-IP and double immunofluorescence identify an interaction between TRIM40 and DAB1. Furthermore, we show that TRIM40 enhances K48-linked polyubiquitination of DAB1, thereby promoting DAB1 degradation. Finally, promoting TRIM40 expression by intravenous injection of the constructed adeno-associated virus (AAV-TRIM40) markedly ameliorates DR phenotypes in STZ-treated mice, as indicated by the decreased blood glucose and glycosylated hemoglobin (HbAlc) levels, and increased hemoglobin contents. Additionally, diabetes-related elevation of acellular capillaries was also meliorated in mice over-expressing TRIM40. The electroretinogram (ERG) deficits were strongly rescued in mice receiving AAV-TRIM40 injection. Moreover, AAV-TRIM40 attenuates the inflammation and p-DAB1 expression in retinal tissues of STZ-treated mice. Collectively, our findings disclose a mechanism through which TRIM40 limits DAB1 stability under physiological conditions and reveals TRIM40 as a potential therapeutic target for the intervention of Reelin/DAB1 signaling, contributing to DR treatment.
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Affiliation(s)
- Xu Xiaoling
- Department of Ophthalmology, The Second Affiliated Hospital of Nanchang University, Nanchang, 330006, China
| | - Lan Xinmei
- Department of Ophthalmology, The Second Affiliated Hospital of Nanchang University, Nanchang, 330006, China
| | - Fu Shuhua
- Department of Ophthalmology, The Second Affiliated Hospital of Nanchang University, Nanchang, 330006, China
| | - Zhang Qian
- Department of Ophthalmology, The Second Affiliated Hospital of Nanchang University, Nanchang, 330006, China
| | - Gui Fu
- Department of Ophthalmology, The Second Affiliated Hospital of Nanchang University, Nanchang, 330006, China
| | - Jin Qifang
- Department of Ophthalmology, The Second Affiliated Hospital of Nanchang University, Nanchang, 330006, China
| | - Xie Lin
- Department of Ophthalmology, The Second Affiliated Hospital of Nanchang University, Nanchang, 330006, China
| | - Yu Xiong
- Department of Ophthalmology, The Second Affiliated Hospital of Nanchang University, Nanchang, 330006, China.
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11
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Peng Y, Liu J, Inuzuka H, Wei W. Targeted protein posttranslational modifications by chemically induced proximity for cancer therapy. J Biol Chem 2023; 299:104572. [PMID: 36870680 PMCID: PMC10050664 DOI: 10.1016/j.jbc.2023.104572] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/17/2023] [Accepted: 02/22/2023] [Indexed: 03/06/2023] Open
Abstract
Post-translational modifications (PTMs) regulate all aspects of protein function. Therefore, upstream regulators of PTMs, such as kinases, acetyltransferases, or methyltransferases, are potential therapeutic targets for human diseases, including cancer. To date, multiple inhibitors and/or agonists of these PTM upstream regulators are in clinical use, while others are still in development. However, these upstream regulators control not only the PTMs of disease-related target proteins but also other disease-irrelevant substrate proteins. Thus, nontargeted perturbing activities may introduce unwanted off-target toxicity issues that limit the use of these drugs in successful clinical applications. Therefore, alternative drugs that solely regulate a specific PTM of the disease-relevant protein target may provide a more precise effect in treating disease with relatively low side effects. To this end, chemically induced proximity has recently emerged as a powerful research tool, and several chemical inducers of proximity (CIPs) have been used to target and regulate protein ubiquitination, phosphorylation, acetylation, and glycosylation. These CIPs have a high potential to be translated into clinical drugs and several examples such as PROTACs and MGDs are now in clinical trials. Hence, more CIPs need to be developed to cover all types of PTMs, such as methylation and palmitoylation, thus providing a full spectrum of tools to regulate protein PTM in basic research and also in clinical application for effective cancer treatment.
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Affiliation(s)
- Yunhua Peng
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA; The Key Laboratory of Biomedical Information Engineering of Ministry of Education, Center for Mitochondrial Biology and Medicine, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Jing Liu
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Hiroyuki Inuzuka
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Wenyi Wei
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA.
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12
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Apte S, Bhutda S, Ghosh S, Sharma K, Barton TE, Dibyachintan S, Sahay O, Roy S, Sinha AR, Adicherla H, Rakshit J, Tang S, Datey A, Santra S, Joseph J, Sasidharan S, Hammerschmidt S, Chakravortty D, Oggioni MR, Santra MK, Neill DR, Banerjee A. An innate pathogen sensing strategy involving ubiquitination of bacterial surface proteins. SCIENCE ADVANCES 2023; 9:eade1851. [PMID: 36947610 PMCID: PMC10032600 DOI: 10.1126/sciadv.ade1851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 02/17/2023] [Indexed: 06/18/2023]
Abstract
Sensing of pathogens by ubiquitination is a critical arm of cellular immunity. However, universal ubiquitination targets on microbes remain unidentified. Here, using in vitro, ex vivo, and in vivo studies, we identify the first protein-based ubiquitination substrates on phylogenetically diverse bacteria by unveiling a strategy that uses recognition of degron-like motifs. Such motifs form a new class of intra-cytosolic pathogen-associated molecular patterns (PAMPs). Their incorporation enabled recognition of nonubiquitin targets by host ubiquitin ligases. We find that SCFFBW7 E3 ligase, supported by the regulatory kinase, glycogen synthase kinase 3β, is crucial for effective pathogen detection and clearance. This provides a mechanistic explanation for enhanced risk of infections in patients with chronic lymphocytic leukemia bearing mutations in F-box and WD repeat domain containing 7 protein. We conclude that exploitation of this generic pathogen sensing strategy allows conservation of host resources and boosts antimicrobial immunity.
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Affiliation(s)
- Shruti Apte
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, Maharashtra, India
| | - Smita Bhutda
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, Maharashtra, India
| | - Sourav Ghosh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, Maharashtra, India
| | - Kuldeep Sharma
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, Maharashtra, India
| | - Thomas E. Barton
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, L69 7BE Liverpool, UK
| | - Soham Dibyachintan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, Maharashtra, India
| | - Osheen Sahay
- Cancer Biology and Epigenetics Laboratory, National Centre for Cell Science, Ganeshkhind Road, Pune 411007, Maharashtra, India
| | - Suvapriya Roy
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, Maharashtra, India
| | - Akash Raj Sinha
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, Maharashtra, India
| | - Harikrishna Adicherla
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Habsiguda, Hyderabad 500007 Telangana, India
| | - Jyotirmoy Rakshit
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, Maharashtra, India
| | - Shiying Tang
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Akshay Datey
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru 560012, Karnataka, India
| | - Shweta Santra
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, Maharashtra, India
| | - Jincy Joseph
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, Maharashtra, India
| | - Sreeja Sasidharan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, Maharashtra, India
| | - Sven Hammerschmidt
- Department of Molecular Genetics and Infection Biology, Interfaculty Institute of Genetics and Functional Genomics, Center for Functional Genomics of Microbes, University of Greifswald, D-17487 Greifswald, Germany
| | - Dipshikha Chakravortty
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru 560012, Karnataka, India
| | - Marco R. Oggioni
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Manas Kumar Santra
- Cancer Biology and Epigenetics Laboratory, National Centre for Cell Science, Ganeshkhind Road, Pune 411007, Maharashtra, India
| | - Daniel R. Neill
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, L69 7BE Liverpool, UK
| | - Anirban Banerjee
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, Maharashtra, India
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13
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Reciprocal regulatory balance within the CLEC16A-RNF41 mitophagy complex depends on an intrinsically disordered protein region. J Biol Chem 2023; 299:103057. [PMID: 36822331 PMCID: PMC10066562 DOI: 10.1016/j.jbc.2023.103057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 01/26/2023] [Indexed: 02/23/2023] Open
Abstract
CLEC16A is an E3 ubiquitin ligase that regulates mitochondrial quality control through mitophagy and is associated with over 20 human diseases. CLEC16A forms a complex with another E3 ligase, RNF41, and a ubiquitin-specific peptidase, USP8; however, regions that regulate CLEC16A activity or the assembly of the tripartite mitophagy regulatory complex are unknown. Here, we report that CLEC16A contains an internal intrinsically disordered protein region (IDPR) that is crucial for CLEC16A function and turnover. IDPRs lack a fixed secondary structure and possess emerging, yet still equivocal roles in protein stability, interactions, and enzymatic activity. We find that the internal IDPR of CLEC16A is crucial for its degradation. CLEC16A turnover was promoted by RNF41, which binds and acts upon the internal IDPR to destabilize CLEC16A. Loss of this internal IDPR also destabilized the ubiquitin-dependent tripartite CLEC16A-RNF41-USP8 complex. Finally, the presence of an internal IDPR within CLEC16A was confirmed using NMR and circular dichroism spectroscopy. Together, our studies reveal that an IDPR is essential to control the reciprocal regulatory balance between CLEC16A and RNF41, which could be targeted to improve mitochondrial health in disease.
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14
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Sun H, Yang K, Zhang X, Fu Y, Yarbro J, Wu Z, Chen PC, Chen T, Peng J. Evaluation of a Pooling Chemoproteomics Strategy with an FDA-Approved Drug Library. Biochemistry 2023; 62:624-632. [PMID: 35969671 PMCID: PMC9905291 DOI: 10.1021/acs.biochem.2c00256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Chemoproteomics is a key platform for characterizing the mode of action for compounds, especially for targeted protein degraders such as proteolysis targeting chimeras (PROTACs) and molecular glues. With deep proteome coverage, multiplexed tandem mass tag-mass spectrometry (TMT-MS) can tackle up to 18 samples in a single experiment. Here, we present a pooling strategy for further enhancing the throughput and apply the strategy to an FDA-approved drug library (95 best-in-class compounds). The TMT-MS-based pooling strategy was evaluated in the following steps. First, we demonstrated the capability of TMT-MS by analyzing more than 15 000 unique proteins (> 12 000 gene products) in HEK293 cells treated with five PROTACs (two BRD/BET degraders and three degraders for FAK, ALK, and BTK kinases). We then introduced a rationalized pooling strategy to separate structurally similar compounds in different pools and identified the proteomic response to 14 pools from the drug library. Finally, we validated the proteomic response from one pool by reprofiling the cells via treatment with individual drugs with sufficient replicates. Interestingly, numerous proteins were found to change upon drug treatment, including AMD1, ODC1, PRKX, PRKY, EXO1, AEN, and LRRC58 with 7-hydroxystaurosporine; C6orf64, HMGCR, and RRM2 with Sorafenib; SYS1 and ALAS1 with Venetoclax; and ATF3, CLK1, and CLK4 with Palbocilib. Thus, pooling chemoproteomics screening provides an efficient method for dissecting the molecular targets of compound libraries.
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Affiliation(s)
- Huan Sun
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA, Equal Contribution
| | - Ka Yang
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA, Equal Contribution
| | - Xue Zhang
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Yingxue Fu
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Jay Yarbro
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Zhiping Wu
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Ping-Chung Chen
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Taosheng Chen
- Chemical Biology & Therapeutics Department, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Junmin Peng
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA, Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA,Correspondence:
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15
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Shu Y, Hai Y, Cao L, Wu J. Deep-learning based approach to identify substrates of human E3 ubiquitin ligases and deubiquitinases. Comput Struct Biotechnol J 2023; 21:1014-1021. [PMID: 36733699 PMCID: PMC9883182 DOI: 10.1016/j.csbj.2023.01.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 01/16/2023] [Accepted: 01/16/2023] [Indexed: 01/19/2023] Open
Abstract
E3 ubiquitin ligases (E3s) and deubiquitinating enzymes (DUBs) play key roles in protein degradation. However, a large number of E3 substrate interactions (ESIs) and DUB substrate interactions (DSIs) remain elusive. Here, we present DeepUSI, a deep learning-based framework to identify ESIs and DSIs using the rich information present in protein sequences. Utilizing the collected golden standard dataset, key hyperparameters in the process of model training, including the ones relevant to data sampling and number of epochs, have been systematically assessed. The performance of DeepUSI was thoroughly evaluated by multiple metrics, based on internal and external validation. Application of DeepUSI to cancer-associated E3 and DUB genes identified a list of druggable substrates with functional implications, warranting further investigation. Together, DeepUSI presents a new framework for predicting substrates of E3 ubiquitin ligases and deubiquitinates.
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Key Words
- AUPRC, area under the PR curve
- AUROC, area under the ROC curve
- CNN, convolutional neutral network
- DSI, DUB-substrate interaction
- DUB, deubiquitinating enzymes
- DUB-substrate interactions
- Deep learning
- E1, ubiquitin-activating enzymes
- E2, ubiquitin-conjugating enzymes
- E3, ubiquitin ligases
- E3-substrate interactions
- ESI, E3-substrate interaction
- GSP, gold standard positive dataset
- PR, precision recall
- Pan-cancer analysis
- ROC, receiver operating characteristic
- TCGA, The Cancer Genome Atlas
- UPS, ubiquitin-proteasome system
- Ubiquitin proteasome system
- Ubiquitination
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Affiliation(s)
- Yixuan Shu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Center for Cancer Bioinformatics, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Yanru Hai
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Center for Cancer Bioinformatics, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Lihua Cao
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Center for Cancer Bioinformatics, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Jianmin Wu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Center for Cancer Bioinformatics, Peking University Cancer Hospital & Institute, Beijing 100142, China,Peking University International Cancer Institute, Peking University, Beijing 100191, China,Correspondence to: Center for Cancer Bioinformatics, Peking University Cancer Hospital & Institute, 52 Fu-Cheng Road, Hai-Dian District, Beijing 100142, China.
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16
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Control of protein stability by post-translational modifications. Nat Commun 2023; 14:201. [PMID: 36639369 PMCID: PMC9839724 DOI: 10.1038/s41467-023-35795-8] [Citation(s) in RCA: 85] [Impact Index Per Article: 85.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 01/02/2023] [Indexed: 01/15/2023] Open
Abstract
Post-translational modifications (PTMs) can occur on specific amino acids localized within regulatory domains of target proteins, which control a protein's stability. These regions, called degrons, are often controlled by PTMs, which act as signals to expedite protein degradation (PTM-activated degrons) or to forestall degradation and stabilize a protein (PTM-inactivated degrons). We summarize current knowledge of the regulation of protein stability by various PTMs. We aim to display the variety and breadth of known mechanisms of regulation as well as highlight common themes in PTM-regulated degrons to enhance potential for identifying novel drug targets where druggable targets are currently lacking.
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17
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Abildgaard AB, Voutsinos V, Petersen SD, Larsen FB, Kampmeyer C, Johansson KE, Stein A, Ravid T, Andréasson C, Jensen MK, Lindorff-Larsen K, Hartmann-Petersen R. HSP70-binding motifs function as protein quality control degrons. Cell Mol Life Sci 2023; 80:32. [PMID: 36609589 PMCID: PMC11072582 DOI: 10.1007/s00018-022-04679-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 12/21/2022] [Accepted: 12/21/2022] [Indexed: 01/09/2023]
Abstract
Protein quality control (PQC) degrons are short protein segments that target misfolded proteins for proteasomal degradation, and thus protect cells against the accumulation of potentially toxic non-native proteins. Studies have shown that PQC degrons are hydrophobic and rarely contain negatively charged residues, features which are shared with chaperone-binding regions. Here we explore the notion that chaperone-binding regions may function as PQC degrons. When directly tested, we found that a canonical Hsp70-binding motif (the APPY peptide) functioned as a dose-dependent PQC degron both in yeast and in human cells. In yeast, Hsp70, Hsp110, Fes1, and the E3 Ubr1 target the APPY degron. Screening revealed that the sequence space within the chaperone-binding region of APPY that is compatible with degron function is vast. We find that the number of exposed Hsp70-binding sites in the yeast proteome correlates with a reduced protein abundance and half-life. Our results suggest that when protein folding fails, chaperone-binding sites may operate as PQC degrons, and that the sequence properties leading to PQC-linked degradation therefore overlap with those of chaperone binding.
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Affiliation(s)
- Amanda B Abildgaard
- Department of Biology, The Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Copenhagen, Denmark
| | - Vasileios Voutsinos
- Department of Biology, The Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Copenhagen, Denmark
| | - Søren D Petersen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Fia B Larsen
- Department of Biology, The Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Copenhagen, Denmark
| | - Caroline Kampmeyer
- Department of Biology, The Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Copenhagen, Denmark
| | - Kristoffer E Johansson
- Department of Biology, The Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Copenhagen, Denmark
| | - Amelie Stein
- Department of Biology, The Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Copenhagen, Denmark
| | - Tommer Ravid
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Claes Andréasson
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Michael K Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Kresten Lindorff-Larsen
- Department of Biology, The Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Copenhagen, Denmark.
| | - Rasmus Hartmann-Petersen
- Department of Biology, The Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Copenhagen, Denmark.
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18
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Phosphorylation of Thr9 Affects the Folding Landscape of the N-Terminal Segment of Human AGT Enhancing Protein Aggregation of Disease-Causing Mutants. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27248762. [PMID: 36557898 PMCID: PMC9786777 DOI: 10.3390/molecules27248762] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/07/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022]
Abstract
The mutations G170R and I244T are the most common disease cause in primary hyperoxaluria type I (PH1). These mutations cause the misfolding of the AGT protein in the minor allele AGT-LM that contains the P11L polymorphism, which may affect the folding of the N-terminal segment (NTT-AGT). The NTT-AGT is phosphorylated at T9, although the role of this event in PH1 is unknown. In this work, phosphorylation of T9 was mimicked by introducing the T9E mutation in the NTT-AGT peptide and the full-length protein. The NTT-AGT conformational landscape was studied by circular dichroism, NMR, and statistical mechanical methods. Functional and stability effects on the full-length AGT protein were characterized by spectroscopic methods. The T9E and P11L mutations together reshaped the conformational landscape of the isolated NTT-AGT peptide by stabilizing ordered conformations. In the context of the full-length AGT protein, the T9E mutation had no effect on the overall AGT function or conformation, but enhanced aggregation of the minor allele (LM) protein and synergized with the mutations G170R and I244T. Our findings indicate that phosphorylation of T9 may affect the conformation of the NTT-AGT and synergize with PH1-causing mutations to promote aggregation in a genotype-specific manner. Phosphorylation should be considered a novel regulatory mechanism in PH1 pathogenesis.
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19
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Mashahreh B, Armony S, Johansson KE, Chappleboim A, Friedman N, Gardner RG, Hartmann-Petersen R, Lindorff-Larsen K, Ravid T. Conserved degronome features governing quality control associated proteolysis. Nat Commun 2022; 13:7588. [PMID: 36481666 PMCID: PMC9732359 DOI: 10.1038/s41467-022-35298-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 11/24/2022] [Indexed: 12/13/2022] Open
Abstract
The eukaryotic proteome undergoes constant surveillance by quality control systems that either sequester, refold, or eliminate aberrant proteins by ubiquitin-dependent mechanisms. Ubiquitin-conjugation necessitates the recognition of degradation determinants, termed degrons, by their cognate E3 ubiquitin-protein ligases. To learn about the distinctive properties of quality control degrons, we performed an unbiased peptidome stability screen in yeast. The search identify a large cohort of proteome-derived degrons, some of which exhibited broad E3 ligase specificity. Consequent application of a machine-learning algorithm establishes constraints governing degron potency, including the amino acid composition and secondary structure propensities. According to the set criteria, degrons with transmembrane domain-like characteristics are the most probable sequences to act as degrons. Similar quality control degrons are present in viral and human proteins, suggesting conserved degradation mechanisms. Altogether, the emerging data indicate that transmembrane domain-like degron features have been preserved in evolution as key quality control determinants of protein half-life.
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Affiliation(s)
- Bayan Mashahreh
- grid.9619.70000 0004 1937 0538Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Shir Armony
- grid.9619.70000 0004 1937 0538Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Kristoffer Enøe Johansson
- grid.5254.60000 0001 0674 042XThe Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Alon Chappleboim
- grid.9619.70000 0004 1937 0538Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Nir Friedman
- grid.9619.70000 0004 1937 0538Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Richard G. Gardner
- grid.34477.330000000122986657Department of Pharmacology, University of Washington, Seattle, WA 98195 USA
| | - Rasmus Hartmann-Petersen
- grid.5254.60000 0001 0674 042XThe Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Kresten Lindorff-Larsen
- grid.5254.60000 0001 0674 042XThe Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Tommer Ravid
- grid.9619.70000 0004 1937 0538Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
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20
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VanDyke D, Taylor JD, Kaeo KJ, Hunt J, Spangler JB. Biologics-based degraders - an expanding toolkit for targeted-protein degradation. Curr Opin Biotechnol 2022; 78:102807. [PMID: 36179405 PMCID: PMC9742328 DOI: 10.1016/j.copbio.2022.102807] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 08/26/2022] [Accepted: 08/27/2022] [Indexed: 12/14/2022]
Abstract
Targeted protein degradation (TPD) is a broadly useful proteome editing tool for biological research and therapeutic development. TPD offers several advantages over functional inhibition alone, including the ability to target previously undruggable proteins and the substantial and sustained knockout of protein activity. A variety of small molecule approaches hijack endogenous protein degradation machinery, but are limited to proteins with a cytosolic domain and suitable binding pocket. Recently, biologics-based methods have expanded the TPD toolbox by allowing access to extracellular and surface-exposed proteins and increasing target specificity. Here, we summarize recent advances in the use of biologics to deplete proteins through either the ubiquitin-proteasome system or the lysosomal degradation pathway, and discuss routes to their effective delivery as potential therapeutic interventions.
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Affiliation(s)
- Derek VanDyke
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA; Translational Tissue Engineering Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Biologics Engineering, R&D, AstraZeneca, Gaithersburg, MD, USA
| | | | - Kyle J Kaeo
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA; Translational Tissue Engineering Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - James Hunt
- Biologics Engineering, R&D, AstraZeneca, Cambridge, UK
| | - Jamie B Spangler
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA; Translational Tissue Engineering Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Bloomberg∼Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University, Baltimore, MD, USA; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA; Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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21
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How phosphorylation impacts intrinsically disordered proteins and their function. Essays Biochem 2022; 66:901-913. [PMID: 36350035 PMCID: PMC9760426 DOI: 10.1042/ebc20220060] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 10/14/2022] [Accepted: 10/17/2022] [Indexed: 11/10/2022]
Abstract
Phosphorylation is the most common post-translational modification (PTM) in eukaryotes, occurring particularly frequently in intrinsically disordered proteins (IDPs). These proteins are highly flexible and dynamic by nature. Thus, it is intriguing that the addition of a single phosphoryl group to a disordered chain can impact its function so dramatically. Furthermore, as many IDPs carry multiple phosphorylation sites, the number of possible states increases, enabling larger complexities and novel mechanisms. Although a chemically simple and well-understood process, the impact of phosphorylation on the conformational ensemble and molecular function of IDPs, not to mention biological output, is highly complex and diverse. Since the discovery of the first phosphorylation site in proteins 75 years ago, we have come to a much better understanding of how this PTM works, but with the diversity of IDPs and their capacity for carrying multiple phosphoryl groups, the complexity grows. In this Essay, we highlight some of the basic effects of IDP phosphorylation, allowing it to serve as starting point when embarking on studies into this topic. We further describe how recent complex cases of multisite phosphorylation of IDPs have been instrumental in widening our view on the effect of protein phosphorylation. Finally, we put forward perspectives on the phosphorylation of IDPs, both in relation to disease and in context of other PTMs; areas where deep insight remains to be uncovered.
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22
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Piersimoni L, Abd El Malek M, Bhatia T, Bender J, Brankatschk C, Calvo Sánchez J, Dayhoff GW, Di Ianni A, Figueroa Parra JO, Garcia-Martinez D, Hesselbarth J, Köppen J, Lauth LM, Lippik L, Machner L, Sachan S, Schmidt L, Selle R, Skalidis I, Sorokin O, Ubbiali D, Voigt B, Wedler A, Wei AAJ, Zorn P, Dunker AK, Köhn M, Sinz A, Uversky VN. Lighting up Nobel Prize-winning studies with protein intrinsic disorder. Cell Mol Life Sci 2022; 79:449. [PMID: 35882686 PMCID: PMC11072364 DOI: 10.1007/s00018-022-04468-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/18/2022] [Accepted: 07/04/2022] [Indexed: 11/03/2022]
Abstract
Intrinsically disordered proteins and regions (IDPs and IDRs) and their importance in biology are becoming increasingly recognized in biology, biochemistry, molecular biology and chemistry textbooks, as well as in current protein science and structural biology curricula. We argue that the sequence → dynamic conformational ensemble → function principle is of equal importance as the classical sequence → structure → function paradigm. To highlight this point, we describe the IDPs and/or IDRs behind the discoveries associated with 17 Nobel Prizes, 11 in Physiology or Medicine and 6 in Chemistry. The Nobel Laureates themselves did not always mention that the proteins underlying the phenomena investigated in their award-winning studies are in fact IDPs or contain IDRs. In several cases, IDP- or IDR-based molecular functions have been elucidated, while in other instances, it is recognized that the respective protein(s) contain IDRs, but the specific IDR-based molecular functions have yet to be determined. To highlight the importance of IDPs and IDRs as general principle in biology, we present here illustrative examples of IDPs/IDRs in Nobel Prize-winning mechanisms and processes.
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Affiliation(s)
- Lolita Piersimoni
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Marina Abd El Malek
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Twinkle Bhatia
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Julian Bender
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Christin Brankatschk
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Jaime Calvo Sánchez
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Guy W Dayhoff
- Department of Chemistry, College of Art and Sciences, University of South Florida, Tampa, FL, 33620, USA
| | - Alessio Di Ianni
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | | | - Dailen Garcia-Martinez
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Julia Hesselbarth
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Janett Köppen
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Luca M Lauth
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Laurin Lippik
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Lisa Machner
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Shubhra Sachan
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Lisa Schmidt
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Robin Selle
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Ioannis Skalidis
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Oleksandr Sorokin
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Daniele Ubbiali
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Bruno Voigt
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Alice Wedler
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Alan An Jung Wei
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Peter Zorn
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Alan Keith Dunker
- Department of Biochemistry and Molecular Biology, Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Marcel Köhn
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany.
| | - Andrea Sinz
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany.
| | - Vladimir N Uversky
- Department of Molecular Medicine, USF Health Byrd Alzheimer's Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA.
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23
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Sasso J, Tenchov R, Wang D, Johnson LS, Wang X, Zhou QA. Molecular Glues: The Adhesive Connecting Targeted Protein Degradation to the Clinic. Biochemistry 2022; 62:601-623. [PMID: 35856839 PMCID: PMC9910052 DOI: 10.1021/acs.biochem.2c00245] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Targeted protein degradation is a rapidly exploding drug discovery strategy that uses small molecules to recruit disease-causing proteins for rapid destruction mainly via the ubiquitin-proteasome pathway. It shows great potential for treating diseases such as cancer and infectious, inflammatory, and neurodegenerative diseases, especially for those with "undruggable" pathogenic protein targets. With the recent rise of the "molecular glue" type of protein degraders, which tighten and simplify the connection of an E3 ligase with a disease-causing protein for ubiquitination and subsequent degradation, new therapies for unmet medical needs are being designed and developed. Here we use data from the CAS Content Collection and the publication landscape of recent research on targeted protein degraders to provide insights into these molecules, with a special focus on molecular glues. We also outline the advantages of the molecular glues and summarize the advances in drug discovery practices for molecular glue degraders. We further provide a thorough review of drug candidates in targeted protein degradation through E3 ligase recruitment. Finally, we highlight the progression of molecular glues in drug discovery pipelines and their targeted diseases. Overall, our paper provides a comprehensive reference to support the future development of molecular glues in medicine.
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24
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Hou C, Li Y, Wang M, Wu H, Li T. Systematic prediction of degrons and E3 ubiquitin ligase binding via deep learning. BMC Biol 2022; 20:162. [PMID: 35836176 PMCID: PMC9281121 DOI: 10.1186/s12915-022-01364-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 06/29/2022] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Degrons are short linear motifs, bound by E3 ubiquitin ligase to target protein substrates to be degraded by the ubiquitin-proteasome system. Mutations leading to deregulation of degron functionality disrupt control of protein abundance due to mistargeting of proteins destined for degradation and often result in pathologies. Targeting degrons by small molecules also emerges as an exciting drug design strategy to upregulate the expression of specific proteins. Despite their essential function and disease targetability, reliable identification of degrons remains a conundrum. Here, we developed a deep learning-based model named Degpred that predicts general degrons directly from protein sequences. RESULTS We showed that the BERT-based model performed well in predicting degrons singly from protein sequences. Then, we used the deep learning model Degpred to predict degrons proteome-widely. Degpred successfully captured typical degron-related sequence properties and predicted degrons beyond those from motif-based methods which use a handful of E3 motifs to match possible degrons. Furthermore, we calculated E3 motifs using predicted degrons on the substrates in our collected E3-substrate interaction dataset and constructed a regulatory network of protein degradation by assigning predicted degrons to specific E3s with calculated motifs. Critically, we experimentally verified that a predicted SPOP binding degron on CBX6 prompts CBX6 degradation and mediates the interaction with SPOP. We also showed that the protein degradation regulatory system is important in tumorigenesis by surveying degron-related mutations in TCGA. CONCLUSIONS Degpred provides an efficient tool to proteome-wide prediction of degrons and binding E3s singly from protein sequences. Degpred successfully captures typical degron-related sequence properties and predicts degrons beyond those from previously used motif-based methods, thus greatly expanding the degron landscape, which should advance the understanding of protein degradation, and allow exploration of uncharacterized alterations of proteins in diseases. To make it easier for readers to access collected and predicted datasets, we integrated these data into the website http://degron.phasep.pro/ .
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Affiliation(s)
- Chao Hou
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191 China
- Key Laboratory for Neuroscience, Ministry of Education/National Health Commission of China, Peking University, Beijing, 100191 China
| | - Yuxuan Li
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191 China
- Key Laboratory for Neuroscience, Ministry of Education/National Health Commission of China, Peking University, Beijing, 100191 China
| | - Mengyao Wang
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, 100871 China
- Peking-Tsinghua Center for Life Sciences, Beijing, China
| | - Hong Wu
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, 100871 China
- Peking-Tsinghua Center for Life Sciences, Beijing, China
- Institute for Cancer Research, Shenzhen Bay Laboratory, Shenzhen, China
| | - Tingting Li
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191 China
- Key Laboratory for Neuroscience, Ministry of Education/National Health Commission of China, Peking University, Beijing, 100191 China
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25
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Okoye CN, Rowling PJE, Itzhaki LS, Lindon C. Counting Degrons: Lessons From Multivalent Substrates for Targeted Protein Degradation. Front Physiol 2022; 13:913063. [PMID: 35860655 PMCID: PMC9289945 DOI: 10.3389/fphys.2022.913063] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 06/08/2022] [Indexed: 11/18/2022] Open
Abstract
E3s comprise a structurally diverse group of at least 800 members, most of which target multiple substrates through specific and regulated protein-protein interactions. These interactions typically rely on short linear motifs (SLiMs), called "degrons", in an intrinsically disordered region (IDR) of the substrate, with variable rules of engagement governing different E3-docking events. These rules of engagement are of importance to the field of targeted protein degradation (TPD), where substrate ubiquitination and destruction require tools to effectively harness ubiquitin ligases (E3s). Substrates are often found to contain multiple degrons, or multiple copies of a degron, contributing to the affinity and selectivity of the substrate for its E3. One important paradigm for E3-substrate docking is presented by the Anaphase-Promoting Complex/Cyclosome (APC/C), a multi-subunit E3 ligase that targets hundreds of proteins for destruction during mitotic exit. APC/C substrate targeting takes place in an ordered manner thought to depend on tightly regulated interactions of substrates, with docking sites provided by the substoichiometric APC/C substrate adaptors and coactivators, Cdc20 or Cdh1/FZR1. Both structural and functional studies of individual APC/C substrates indicate that productive ubiquitination usually requires more than one degron, and that degrons are of different types docking to distinct sites on the coactivators. However, the dynamic nature of APC/C substrate recruitment, and the influence of multiple degrons, remains poorly understood. Here we review the significance of multiple degrons in a number of E3-substrate interactions that have been studied in detail, illustrating distinct kinetic effects of multivalency and allovalency, before addressing the role of multiple degrons in APC/C substrates, key to understanding ordered substrate destruction by APC/C. Lastly, we consider how lessons learnt from these studies can be applied in the design of TPD tools.
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Affiliation(s)
| | | | | | - Catherine Lindon
- Department of Pharmacology, University of Cambridge, Cambridge, United Kingdom
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26
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Vasconcelos-Cardoso M, Batista-Almeida D, Rios-Barros LV, Castro-Gomes T, Girao H. Cellular and molecular mechanisms underlying plasma membrane functionality and integrity. J Cell Sci 2022; 135:275922. [PMID: 35801807 DOI: 10.1242/jcs.259806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The plasma membrane not only protects the cell from the extracellular environment, acting as a selective barrier, but also regulates cellular events that originate at the cell surface, playing a key role in various biological processes that are essential for the preservation of cell homeostasis. Therefore, elucidation of the mechanisms involved in the maintenance of plasma membrane integrity and functionality is of utmost importance. Cells have developed mechanisms to ensure the quality of proteins that inhabit the cell surface, as well as strategies to cope with injuries inflicted to the plasma membrane. Defects in these mechanisms can lead to the development or onset of several diseases. Despite the importance of these processes, a comprehensive and holistic perspective of plasma membrane quality control is still lacking. To tackle this gap, in this Review, we provide a thorough overview of the mechanisms underlying the identification and targeting of membrane proteins that are to be removed from the cell surface, as well as the membrane repair mechanisms triggered in both physiological and pathological conditions. A better understanding of the mechanisms underlying protein quality control at the plasma membrane can reveal promising and unanticipated targets for the development of innovative therapeutic approaches.
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Affiliation(s)
- Maria Vasconcelos-Cardoso
- University of Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, 3000-548 Coimbra, Portugal.,University of Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB), 3000-548 Coimbra, Portugal.,Clinical Academic Centre of Coimbra (CACC), 3000-548 Coimbra, Portugal
| | - Daniela Batista-Almeida
- University of Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, 3000-548 Coimbra, Portugal.,University of Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB), 3000-548 Coimbra, Portugal.,Clinical Academic Centre of Coimbra (CACC), 3000-548 Coimbra, Portugal
| | - Laura Valeria Rios-Barros
- Department of Parasitology, Federal University of Minas Gerais, Belo Horizonte, CEP 31270-901, Brazil
| | - Thiago Castro-Gomes
- Department of Parasitology, Federal University of Minas Gerais, Belo Horizonte, CEP 31270-901, Brazil
| | - Henrique Girao
- University of Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, 3000-548 Coimbra, Portugal.,University of Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB), 3000-548 Coimbra, Portugal.,Clinical Academic Centre of Coimbra (CACC), 3000-548 Coimbra, Portugal
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27
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Guharoy M, Lazar T, Macossay-Castillo M, Tompa P. Degron masking outlines degronons, co-degrading functional modules in the proteome. Commun Biol 2022; 5:445. [PMID: 35545699 PMCID: PMC9095673 DOI: 10.1038/s42003-022-03391-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 04/22/2022] [Indexed: 11/28/2022] Open
Abstract
Effective organization of proteins into functional modules (networks, pathways) requires systems-level coordination between transcription, translation and degradation. Whereas the cooperation between transcription and translation was extensively studied, the cooperative degradation regulation of protein complexes and pathways has not been systematically assessed. Here we comprehensively analyzed degron masking, a major mechanism by which cellular systems coordinate degron recognition and protein degradation. For over 200 substrates with characterized degrons (E3 ligase targeting motifs, ubiquitination sites and disordered proteasomal entry sequences), we demonstrate that degrons extensively overlap with protein-protein interaction sites. Analysis of binding site information and protein abundance comparisons show that regulatory partners effectively outcompete E3 ligases, masking degrons from the ubiquitination machinery. Protein abundance variations between normal and cancer cells highlight the dynamics of degron masking components. Finally, integrative analysis of gene co-expression, half-life correlations and functional relationships between interacting proteins point towards higher-order, co-regulated degradation modules (‘degronons’) in the proteome. Systematic bioinformatics analysis of cooperative degradation of protein complexes indicates that degrons extensively overlap with protein-protein interaction sites, hiding degrons from ubiquitination machinery and suggesting the existence of co-degrading functional modules in the proteome.
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Affiliation(s)
- Mainak Guharoy
- VIB-VUB Center for Structural Biology, Pleinlaan 2, 1050, Brussels, Belgium. .,Structural Biology Brussels, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium. .,VIB Bioinformatics Core, Technologiepark-Zwijnaarde 75, 9052, Ghent, Belgium.
| | - Tamas Lazar
- VIB-VUB Center for Structural Biology, Pleinlaan 2, 1050, Brussels, Belgium.,Structural Biology Brussels, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Mauricio Macossay-Castillo
- VIB-VUB Center for Structural Biology, Pleinlaan 2, 1050, Brussels, Belgium.,Structural Biology Brussels, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Peter Tompa
- VIB-VUB Center for Structural Biology, Pleinlaan 2, 1050, Brussels, Belgium. .,Structural Biology Brussels, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium. .,Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, 1117, Budapest, Hungary.
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28
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Dindo M, Pascarelli S, Chiasserini D, Grottelli S, Costantini C, Uechi G, Giardina G, Laurino P, Cellini B. Structural dynamics shape the fitness window of alanine:glyoxylate aminotransferase. Protein Sci 2022; 31:e4303. [PMID: 35481644 PMCID: PMC8996469 DOI: 10.1002/pro.4303] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 03/02/2022] [Accepted: 03/17/2022] [Indexed: 01/24/2023]
Abstract
The conformational landscape of a protein is constantly expanded by genetic variations that have a minimal impact on the function(s) while causing subtle effects on protein structure. The wider the conformational space sampled by these variants, the higher the probabilities to adapt to changes in environmental conditions. However, the probability that a single mutation may result in a pathogenic phenotype also increases. Here we present a paradigmatic example of how protein evolution balances structural stability and dynamics to maximize protein adaptability and preserve protein fitness. We took advantage of known genetic variations of human alanine:glyoxylate aminotransferase (AGT1), which is present as a common major allelic form (AGT-Ma) and a minor polymorphic form (AGT-Mi) expressed in 20% of Caucasian population. By integrating crystallographic studies and molecular dynamics simulations, we show that AGT-Ma is endowed with structurally unstable (frustrated) regions, which become disordered in AGT-Mi. An in-depth biochemical characterization of variants from an anticonsensus library, encompassing the frustrated regions, correlates this plasticity to a fitness window defined by AGT-Ma and AGT-Mi. Finally, co-immunoprecipitation analysis suggests that structural frustration in AGT1 could favor additional functions related to protein-protein interactions. These results expand our understanding of protein structural evolution by establishing that naturally occurring genetic variations tip the balance between stability and frustration to maximize the ensemble of conformations falling within a well-defined fitness window, thus expanding the adaptability potential of the protein.
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Affiliation(s)
- Mirco Dindo
- Protein Engineering and Evolution UnitOkinawa Institute of Science and Technology Graduate UniversityOkinawaJapan
| | - Stefano Pascarelli
- Protein Engineering and Evolution UnitOkinawa Institute of Science and Technology Graduate UniversityOkinawaJapan
| | | | - Silvia Grottelli
- Department of Medicine and SurgeryUniversity of PerugiaPerugiaItaly
| | | | - Gen‐Ichiro Uechi
- Protein Engineering and Evolution UnitOkinawa Institute of Science and Technology Graduate UniversityOkinawaJapan
| | - Giorgio Giardina
- Department of Biochemical Sciences “A. Rossi Fanelli”Sapienza University of RomeRomeItaly
| | - Paola Laurino
- Protein Engineering and Evolution UnitOkinawa Institute of Science and Technology Graduate UniversityOkinawaJapan
| | - Barbara Cellini
- Department of Medicine and SurgeryUniversity of PerugiaPerugiaItaly
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29
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Abstract
Targeted protein degradation (TPD) is an emerging therapeutic modality with the potential to tackle disease-causing proteins that have historically been highly challenging to target with conventional small molecules. In the 20 years since the concept of a proteolysis-targeting chimera (PROTAC) molecule harnessing the ubiquitin-proteasome system to degrade a target protein was reported, TPD has moved from academia to industry, where numerous companies have disclosed programmes in preclinical and early clinical development. With clinical proof-of-concept for PROTAC molecules against two well-established cancer targets provided in 2020, the field is poised to pursue targets that were previously considered 'undruggable'. In this Review, we summarize the first two decades of PROTAC discovery and assess the current landscape, with a focus on industry activity. We then discuss key areas for the future of TPD, including establishing the target classes for which TPD is most suitable, expanding the use of ubiquitin ligases to enable precision medicine and extending the modality beyond oncology.
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Affiliation(s)
| | | | - Craig M Crews
- Department of Molecular, Cellular & Developmental Biology, Yale University, New Haven, CT, USA.
- Department of Pharmacology, Yale University, New Haven, CT, USA.
- Department of Chemistry, Yale University, New Haven, CT, USA.
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30
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Wang C, Tan X, Tang D, Gou Y, Han C, Ning W, Lin S, Zhang W, Chen M, Peng D, Xue Y. GPS-Uber: a hybrid-learning framework for prediction of general and E3-specific lysine ubiquitination sites. Brief Bioinform 2022; 23:6509047. [PMID: 35037020 DOI: 10.1093/bib/bbab574] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 12/11/2021] [Accepted: 12/14/2021] [Indexed: 12/13/2022] Open
Abstract
As an important post-translational modification, lysine ubiquitination participates in numerous biological processes and is involved in human diseases, whereas the site specificity of ubiquitination is mainly decided by ubiquitin-protein ligases (E3s). Although numerous ubiquitination predictors have been developed, computational prediction of E3-specific ubiquitination sites is still a great challenge. Here, we carefully reviewed the existing tools for the prediction of general ubiquitination sites. Also, we developed a tool named GPS-Uber for the prediction of general and E3-specific ubiquitination sites. From the literature, we manually collected 1311 experimentally identified site-specific E3-substrate relations, which were classified into different clusters based on corresponding E3s at different levels. To predict general ubiquitination sites, we integrated 10 types of sequence and structure features, as well as three types of algorithms including penalized logistic regression, deep neural network and convolutional neural network. Compared with other existing tools, the general model in GPS-Uber exhibited a highly competitive accuracy, with an area under curve values of 0.7649. Then, transfer learning was adopted for each E3 cluster to construct E3-specific models, and in total 112 individual E3-specific predictors were implemented. Using GPS-Uber, we conducted a systematic prediction of human cancer-associated ubiquitination events, which could be helpful for further experimental consideration. GPS-Uber will be regularly updated, and its online service is free for academic research at http://gpsuber.biocuckoo.cn/.
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Affiliation(s)
- Chenwei Wang
- Department of Bioinformatics and Systems Biology, MOE Key Laboratory of Molecular Biophysics, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Xiaodan Tan
- Department of Bioinformatics and Systems Biology, MOE Key Laboratory of Molecular Biophysics, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Dachao Tang
- Department of Bioinformatics and Systems Biology, MOE Key Laboratory of Molecular Biophysics, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Yujie Gou
- Department of Bioinformatics and Systems Biology, MOE Key Laboratory of Molecular Biophysics, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Cheng Han
- Department of Bioinformatics and Systems Biology, MOE Key Laboratory of Molecular Biophysics, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Wanshan Ning
- Department of Bioinformatics and Systems Biology, MOE Key Laboratory of Molecular Biophysics, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Shaofeng Lin
- Department of Bioinformatics and Systems Biology, MOE Key Laboratory of Molecular Biophysics, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Weizhi Zhang
- Department of Bioinformatics and Systems Biology, MOE Key Laboratory of Molecular Biophysics, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Miaomiao Chen
- Department of Bioinformatics and Systems Biology, MOE Key Laboratory of Molecular Biophysics, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Di Peng
- Department of Bioinformatics and Systems Biology, MOE Key Laboratory of Molecular Biophysics, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Yu Xue
- Department of Bioinformatics and Systems Biology, MOE Key Laboratory of Molecular Biophysics, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
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31
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Lv D, Pal P, Liu X, Jia Y, Thummuri D, Zhang P, Hu W, Pei J, Zhang Q, Zhou S, Khan S, Zhang X, Hua N, Yang Q, Arango S, Zhang W, Nayak D, Olsen SK, Weintraub ST, Hromas R, Konopleva M, Yuan Y, Zheng G, Zhou D. Development of a BCL-xL and BCL-2 dual degrader with improved anti-leukemic activity. Nat Commun 2021; 12:6896. [PMID: 34824248 PMCID: PMC8617031 DOI: 10.1038/s41467-021-27210-x] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 11/05/2021] [Indexed: 02/04/2023] Open
Abstract
PROteolysis-TArgeting Chimeras (PROTACs) have emerged as an innovative drug development platform. However, most PROTACs have been generated empirically because many determinants of PROTAC specificity and activity remain elusive. Through computational modelling of the entire NEDD8-VHL Cullin RING E3 ubiquitin ligase (CRLVHL)/PROTAC/BCL-xL/UbcH5B(E2)-Ub/RBX1 complex, we find that this complex can only ubiquitinate the lysines in a defined band region on BCL-xL. Using this approach to guide our development of a series of ABT263-derived and VHL-recruiting PROTACs, we generate a potent BCL-xL and BCL-2 (BCL-xL/2) dual degrader with significantly improved antitumor activity against BCL-xL/2-dependent leukemia cells. Our results provide experimental evidence that the accessibility of lysines on a target protein plays an important role in determining the selectivity and potency of a PROTAC in inducing protein degradation, which may serve as a conceptual framework to guide the future development of PROTACs.
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Affiliation(s)
- Dongwen Lv
- grid.15276.370000 0004 1936 8091Department of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, FL USA
| | - Pratik Pal
- grid.15276.370000 0004 1936 8091Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL USA
| | - Xingui Liu
- grid.15276.370000 0004 1936 8091Department of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, FL USA
| | - Yannan Jia
- grid.240145.60000 0001 2291 4776Department of Leukemia, University of Texas M.D. Anderson Cancer Center, Houston, TX USA
| | - Dinesh Thummuri
- grid.15276.370000 0004 1936 8091Department of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, FL USA
| | - Peiyi Zhang
- grid.15276.370000 0004 1936 8091Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL USA
| | - Wanyi Hu
- grid.15276.370000 0004 1936 8091Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL USA
| | - Jing Pei
- grid.15276.370000 0004 1936 8091Department of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, FL USA
| | - Qi Zhang
- grid.240145.60000 0001 2291 4776Department of Leukemia, University of Texas M.D. Anderson Cancer Center, Houston, TX USA
| | - Shuo Zhou
- grid.15276.370000 0004 1936 8091Department of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, FL USA
| | - Sajid Khan
- grid.15276.370000 0004 1936 8091Department of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, FL USA
| | - Xuan Zhang
- grid.15276.370000 0004 1936 8091Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL USA
| | - Nan Hua
- grid.15276.370000 0004 1936 8091Department of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, FL USA
| | - Qingping Yang
- grid.15276.370000 0004 1936 8091Department of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, FL USA
| | - Sebastian Arango
- grid.15276.370000 0004 1936 8091Department of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, FL USA
| | - Weizhou Zhang
- grid.15276.370000 0004 1936 8091Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL USA
| | - Digant Nayak
- grid.267309.90000 0001 0629 5880Department of Biochemistry & Structure Biology, Long School of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX USA ,grid.267309.90000 0001 0629 5880Mays Cancer Center, the Long School of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX USA
| | - Shaun K. Olsen
- grid.267309.90000 0001 0629 5880Department of Biochemistry & Structure Biology, Long School of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX USA ,grid.267309.90000 0001 0629 5880Mays Cancer Center, the Long School of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX USA
| | - Susan T. Weintraub
- grid.267309.90000 0001 0629 5880Department of Biochemistry & Structure Biology, Long School of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX USA
| | - Robert Hromas
- grid.267309.90000 0001 0629 5880Mays Cancer Center, the Long School of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX USA
| | - Marina Konopleva
- grid.240145.60000 0001 2291 4776Department of Leukemia, University of Texas M.D. Anderson Cancer Center, Houston, TX USA
| | - Yaxia Yuan
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, FL, USA.
| | - Guangrong Zheng
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL, USA.
| | - Daohong Zhou
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, FL, USA.
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32
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Arinze NV, Yin W, Lotfollahzadeh S, Napoleon MA, Richards S, Walker JA, Belghasem M, Ravid JD, Hassan Kamel M, Whelan SA, Lee N, Siracuse JJ, Anderson S, Farber A, Sherr D, Francis J, Hamburg NM, Rahimi N, Chitalia VC. Tryptophan metabolites suppress Wnt pathway and promote adverse limb events in CKD patients. J Clin Invest 2021; 132:142260. [PMID: 34752422 PMCID: PMC8718145 DOI: 10.1172/jci142260] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 11/02/2021] [Indexed: 11/30/2022] Open
Abstract
Chronic kidney disease (CKD) imposes a strong and independent risk for peripheral artery disease (PAD). While solutes retained in CKD patients (uremic solutes) inflict vascular damage, their role in PAD remains elusive. Here, we show that the dietary tryptophan-derived uremic solutes including indoxyl sulfate (IS) and kynurenine (Kyn) at concentrations corresponding to those in CKD patients suppress β-catenin in several cell types, including microvascular endothelial cells (ECs), inhibiting Wnt activity and proangiogenic Wnt targets in ECs. Mechanistic probing revealed that these uremic solutes downregulated β-catenin in a manner dependent on serine 33 in its degron motif and through the aryl hydrocarbon receptor (AHR). Hindlimb ischemia in adenine-induced CKD and IS solute–specific mouse models showed diminished β-catenin and VEGF-A in the capillaries and reduced capillary density, which correlated inversely with blood levels of IS and Kyn and AHR activity in ECs. An AHR inhibitor treatment normalized postischemic angiogenic response in CKD mice to a non-CKD level. In a prospective cohort of PAD patients, plasma levels of tryptophan metabolites and plasma’s AHR-inducing activity in ECs significantly increased the risk of future adverse limb events. This work uncovers the tryptophan metabolite/AHR/β-catenin axis as a mediator of microvascular rarefaction in CKD patients and demonstrates its targetability for PAD in CKD models.
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Affiliation(s)
- Nkiruka V Arinze
- Department of Surgery, Boston University School of Medicine, Boston, United States of America
| | - Wenqing Yin
- Department of Medicine, Boston University School of Medicine, Boston, United States of America
| | - Saran Lotfollahzadeh
- Department of Medicine, Boston University School of Medicine, Boston, United States of America
| | - Marc Arthur Napoleon
- Department of Medicine, Boston University School of Medicine, Boston, United States of America
| | - Sean Richards
- Department of Medicine, Boston University School of Medicine, Boston, United States of America
| | - Joshua A Walker
- Department of Medicine, Boston University School of Medicine, Boston, United States of America
| | - Mostafa Belghasem
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, United States of America
| | - Jonathan D Ravid
- School of Medicine, Boston University School of Medicine, Boston, United States of America
| | - Mohamed Hassan Kamel
- Department of Medicine, Boston University School of Medicine, Boston, United States of America
| | - Stephen A Whelan
- Department of Chemistry, Boston University, Boston, United States of America
| | - Norman Lee
- Department of Chemistry, Boston University, Boston, United States of America
| | - Jeffrey J Siracuse
- Department of Surgery, Boston University School of Medicine, Boston, United States of America
| | - Stephan Anderson
- Department of Radiology, Boston University School of Medicine, Boston, United States of America
| | - Alik Farber
- Department of Surgery, Boston University School of Medicine, Boston, United States of America
| | - David Sherr
- Boston University, Boston, United States of America
| | - Jean Francis
- Department of Medicine, Boston University School of Medicine, Boston, United States of America
| | - Naomi M Hamburg
- Whitaker Cardiovascular Institute, Boston University School of Medicine, Boston, United States of America
| | - Nader Rahimi
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, United States of America
| | - Vipul C Chitalia
- Department of Medicine, Boston University School of Medicine, Boston, United States of America
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33
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Kim HK, Seol JE, Ahn SW, Jeon S, Park CS, Han J. Cereblon: promise and challenges for combating human diseases. Pflugers Arch 2021; 473:1695-1711. [PMID: 34553266 DOI: 10.1007/s00424-021-02624-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/12/2021] [Accepted: 09/14/2021] [Indexed: 12/18/2022]
Abstract
Cereblon (CRBN) is a substrate recognition protein in the E3-ligase ubiquitin complex. The binding target of CRBN varies according to tissues and cells, and the protein regulates various biological functions by regulating tissue-specific targets. As new endogenous targets of CRBN have been identified over the past decade, the physiological and pathological functions of CRBN and its potential as a therapeutic target in various diseases have greatly expanded. For this purpose, in this review article, we introduce the basic principle of the ubiquitin-proteasome system, the regulation of physiological/pathological functions related to the endogenous substrate of CRBN, and the discovery of immunomodulatory imide drug-mediated neo-substrates of CRBN. In addition, the development of CRBN-based proteolysis-targeting chimeras, which has been actively researched recently, and strategies for developing therapeutic agents using them are introduced. These recent updates on CRBN will be useful in the establishment of strategies for disease treatment and utilization of CRBNs in biomedical engineering and clinical medicine.
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Affiliation(s)
- Hyoung Kyu Kim
- Department of Physiology, College of Medicine, Cardiovascular and Metabolic Disease Center, Smart Marine Therapeutic Center, Department of Health Sciences and Technology, Graduate School, Inje University, 47392, Busan, Korea
| | - Jung Eun Seol
- Department of Physiology, College of Medicine, Cardiovascular and Metabolic Disease Center, Smart Marine Therapeutic Center, Department of Health Sciences and Technology, Graduate School, Inje University, 47392, Busan, Korea
- Department of Dermatology, Inje University Busan Paik Hospital, Inje University, 47392, Busan, Korea
| | - Sang Woo Ahn
- Department of Dermatology, Inje University Busan Paik Hospital, Inje University, 47392, Busan, Korea
| | - Seungje Jeon
- Department of Physiology, College of Medicine, Cardiovascular and Metabolic Disease Center, Smart Marine Therapeutic Center, Department of Health Sciences and Technology, Graduate School, Inje University, 47392, Busan, Korea
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Korea
| | - Chul-Seung Park
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Korea
| | - Jin Han
- Department of Physiology, College of Medicine, Cardiovascular and Metabolic Disease Center, Smart Marine Therapeutic Center, Department of Health Sciences and Technology, Graduate School, Inje University, 47392, Busan, Korea.
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34
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Cascarina SM, Kaplan JP, Elder MR, Brookbank L, Ross ED. Generalizable Compositional Features Influencing the Proteostatic Fates of Polar Low-Complexity Domains. Int J Mol Sci 2021; 22:ijms22168944. [PMID: 34445649 PMCID: PMC8396281 DOI: 10.3390/ijms22168944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/11/2021] [Accepted: 08/16/2021] [Indexed: 11/25/2022] Open
Abstract
Protein aggregation is associated with a growing list of human diseases. A substantial fraction of proteins in eukaryotic proteomes constitutes a proteostasis network—a collection of proteins that work together to maintain properly folded proteins. One of the overarching functions of the proteostasis network is the prevention or reversal of protein aggregation. How proteins aggregate in spite of the anti-aggregation activity of the proteostasis machinery is incompletely understood. Exposed hydrophobic patches can trigger degradation by the ubiquitin-proteasome system, a key branch of the proteostasis network. However, in a recent study, we found that model glycine (G)-rich or glutamine/asparagine (Q/N)-rich prion-like domains differ in their susceptibility to detection and degradation by this system. Here, we expand upon this work by examining whether the features controlling the degradation of our model prion-like domains generalize broadly to G-rich and Q/N-rich domains. Experimentally, native yeast G-rich domains in isolation are sensitive to the degradation-promoting effects of hydrophobic residues, whereas native Q/N-rich domains completely resist these effects and tend to aggregate instead. Bioinformatic analyses indicate that native G-rich domains from yeast and humans tend to avoid degradation-promoting features, suggesting that the proteostasis network may act as a form of selection at the molecular level that constrains the sequence space accessible to G-rich domains. However, the sensitivity or resistance of G-rich and Q/N-rich domains, respectively, was not always preserved in their native protein contexts, highlighting that proteins can evolve other sequence features to overcome the intrinsic sensitivity of some LCDs to degradation.
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35
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Nagati JS, Kobeissy PH, Nguyen MQ, Xu M, Garcia T, Comerford SA, Hammer RE, Garcia JA. Mammalian acetate-dependent acetyl CoA synthetase 2 contains multiple protein destabilization and masking elements. J Biol Chem 2021; 297:101037. [PMID: 34343565 PMCID: PMC8405932 DOI: 10.1016/j.jbc.2021.101037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 07/13/2021] [Accepted: 07/30/2021] [Indexed: 11/05/2022] Open
Abstract
Besides contributing to anabolism, cellular metabolites serve as substrates or cofactors for enzymes and may also have signaling functions. Given these roles, multiple control mechanisms likely ensure fidelity of metabolite-generating enzymes. Acetate-dependent acetyl CoA synthetases (ACS) are de novo sources of acetyl CoA, a building block for fatty acids and a substrate for acetyltransferases. Eukaryotic acetate-dependent acetyl CoA synthetase 2 (Acss2) is predominantly cytosolic, but is also found in the nucleus following oxygen or glucose deprivation, or upon acetate exposure. Acss2-generated acetyl CoA is used in acetylation of Hypoxia-Inducible Factor 2 (HIF-2), a stress-responsive transcription factor. Mutation of a putative nuclear localization signal in endogenous Acss2 abrogates HIF-2 acetylation and signaling, but surprisingly also results in reduced Acss2 protein levels due to unmasking of two protein destabilization elements (PDE) in the Acss2 hinge region. In the current study, we identify up to four additional PDE in the Acss2 hinge region and determine that a previously identified PDE, the ABC domain, consists of two functional PDE. We show that the ABC domain and other PDE are likely masked by intramolecular interactions with other domains in the Acss2 hinge region. We also characterize mice with a prematurely truncated Acss2 that exposes a putative ABC domain PDE, which exhibits reduced Acss2 protein stability and impaired HIF-2 signaling. Finally, using primary mouse embryonic fibroblasts, we demonstrate that the reduced stability of select Acss2 mutant proteins is due to a shortened half-life, which is a result of enhanced degradation via a nonproteasome, nonautophagy pathway.
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Affiliation(s)
- Jason S Nagati
- Department of Medicine, Columbia University Medical Center, New York, New York, USA
| | - Philippe H Kobeissy
- Department of Medicine, Columbia University Medical Center, New York, New York, USA
| | - Minh Q Nguyen
- Department of Medicine, Columbia University Medical Center, New York, New York, USA
| | - Min Xu
- Department of Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Trent Garcia
- Department of Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Sarah A Comerford
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Robert E Hammer
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Joseph A Garcia
- Department of Medicine, Columbia University Medical Center, New York, New York, USA; Department of Research, James J. Peters VA Medical Center, New York, New York, USA.
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36
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Yousefi R, Jevdokimenko K, Kluever V, Pacheu-Grau D, Fornasiero EF. Influence of Subcellular Localization and Functional State on Protein Turnover. Cells 2021; 10:cells10071747. [PMID: 34359917 PMCID: PMC8306977 DOI: 10.3390/cells10071747] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 07/02/2021] [Accepted: 07/07/2021] [Indexed: 12/14/2022] Open
Abstract
Protein homeostasis is an equilibrium of paramount importance that maintains cellular performance by preserving an efficient proteome. This equilibrium avoids the accumulation of potentially toxic proteins, which could lead to cellular stress and death. While the regulators of proteostasis are the machineries controlling protein production, folding and degradation, several other factors can influence this process. Here, we have considered two factors influencing protein turnover: the subcellular localization of a protein and its functional state. For this purpose, we used an imaging approach based on the pulse-labeling of 17 representative SNAP-tag constructs for measuring protein lifetimes. With this approach, we obtained precise measurements of protein turnover rates in several subcellular compartments. We also tested a selection of mutants modulating the function of three extensively studied proteins, the Ca2+ sensor calmodulin, the small GTPase Rab5a and the brain creatine kinase (CKB). Finally, we followed up on the increased lifetime observed for the constitutively active Rab5a (Q79L), and we found that its stabilization correlates with enlarged endosomes and increased interaction with membranes. Overall, our data reveal that both changes in protein localization and functional state are key modulators of protein turnover, and protein lifetime fluctuations can be considered to infer changes in cellular behavior.
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Affiliation(s)
- Roya Yousefi
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073 Göttingen, Germany; (R.Y.); (K.J.); (V.K.)
- Department of Cellular Biochemistry, University Medical Center Göttingen, 37073 Göttingen, Germany;
| | - Kristina Jevdokimenko
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073 Göttingen, Germany; (R.Y.); (K.J.); (V.K.)
| | - Verena Kluever
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073 Göttingen, Germany; (R.Y.); (K.J.); (V.K.)
| | - David Pacheu-Grau
- Department of Cellular Biochemistry, University Medical Center Göttingen, 37073 Göttingen, Germany;
| | - Eugenio F. Fornasiero
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073 Göttingen, Germany; (R.Y.); (K.J.); (V.K.)
- Correspondence:
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37
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Characterization of the structural determinants of the ubiquitin-dependent proteasomal degradation of human hepatic tryptophan 2,3-dioxygenase. Biochem J 2021; 478:1999-2017. [PMID: 33960368 DOI: 10.1042/bcj20210213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 11/17/2022]
Abstract
Human hepatic tryptophan 2,3-dioxygenase (hTDO) is a homotetrameric hemoprotein. It is one of the most rapidly degraded liver proteins with a half-life (t1/2) of ∼2.3 h, relative to an average t1/2 of ∼2-3 days for total liver protein. The molecular mechanism underlying the poor longevity of hTDO remains elusive. Previously, we showed that hTDO could be recognized and ubiquitinated by two E3 ubiquitin (Ub) ligases, gp78/AMFR and CHIP, and subsequently degraded via Ub-dependent proteasomal degradation pathway. Additionally, we identified 15 ubiquitination K-sites and demonstrated that Trp-binding to an exosite impeded its proteolytic degradation. Here, we further established autophagic-lysosomal degradation as an alternative back-up pathway for cellular hTDO degradation. In addition, with protein kinases A and C, we identified 13 phosphorylated Ser/Thr (pS/pT) sites. Mapping these pS/pT sites on the hTDO surface revealed their propinquity to acidic Asp/Glu (D/E) residues engendering negatively charged DEpSpT clusters vicinal to the ubiquitination K-sites over the entire protein surface. Through site-directed mutagenesis of positively charged patches of gp78, previously documented to interact with the DEpSpT clusters in other target proteins, we uncovered the likely role of the DEpSpT clusters in the molecular recognition of hTDO by gp78 and plausibly other E3 Ub-ligases. Furthermore, cycloheximide-chase analyses revealed the critical structural relevance of the disordered N- and C-termini not only in the Ub-ligase recognition, but also in the proteasome engagement. Together, the surface DEpSpT clusters and the N- and C-termini constitute an intrinsic bipartite degron for hTDO physiological turnover.
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38
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Renneville A, Gasser JA, Grinshpun DE, Jean Beltran PM, Udeshi ND, Matyskiela ME, Clayton T, McConkey M, Viswanathan K, Tepper A, Guirguis AA, Sellar RS, Cotteret S, Marzac C, Saada V, De Botton S, Kiladjian JJ, Cayuela JM, Rolfe M, Chamberlain PP, Carr SA, Ebert BL. Avadomide induces degradation of ZMYM2 fusion oncoproteins in hematologic malignancies. Blood Cancer Discov 2021; 2:250-265. [PMID: 34027417 DOI: 10.1158/2643-3230.bcd-20-0105] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Thalidomide analogs exert their therapeutic effects by binding to the CRL4CRBN E3 ubiquitin ligase, promoting ubiquitination and subsequent proteasomal degradation of specific protein substrates. Drug-induced degradation of IKZF1 and IKZF3 in B-cell malignancies demonstrates the clinical utility of targeting disease-relevant transcription factors for degradation. Here, we found that avadomide (CC-122) induces CRBN-dependent ubiquitination and proteasomal degradation of ZMYM2 (ZNF198), a transcription factor involved in balanced chromosomal rearrangements with FGFR1 and FLT3 in aggressive forms of hematologic malignancies. The minimal drug-responsive element of ZMYM2 is a zinc-chelating MYM domain and is contained in the N-terminal portion of ZMYM2 that is universally included in the derived fusion proteins. We demonstrate that avadomide has the ability to induce proteasomal degradation of ZMYM2-FGFR1 and ZMYM2-FLT3 chimeric oncoproteins, both in vitro and in vivo. Our findings suggest that patients with hematologic malignancies harboring these ZMYM2 fusion proteins may benefit from avadomide treatment.
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Affiliation(s)
- Aline Renneville
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,INSERM U1287, Gustave Roussy Cancer Campus, Villejuif, France
| | - Jessica A Gasser
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Daniel E Grinshpun
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | | | - Namrata D Udeshi
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Mary E Matyskiela
- Celgene/Bristol-Myers Squibb corporation, San Diego, California, USA
| | - Thomas Clayton
- Celgene/Bristol-Myers Squibb corporation, San Diego, California, USA
| | - Marie McConkey
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Kaushik Viswanathan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Alexander Tepper
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Andrew A Guirguis
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Rob S Sellar
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Department of Haematology, UCL Cancer Institute, London, United Kingdom
| | - Sophie Cotteret
- Département de Biologie et Pathologie, Gustave Roussy Cancer Campus, Villejuif, France
| | - Christophe Marzac
- Département de Biologie et Pathologie, Gustave Roussy Cancer Campus, Villejuif, France
| | - Véronique Saada
- Département de Biologie et Pathologie, Gustave Roussy Cancer Campus, Villejuif, France
| | - Stéphane De Botton
- Département d'Hématologie, Gustave Roussy Cancer Campus, Villejuif, France
| | - Jean-Jacques Kiladjian
- Université de Paris, AP-HP, Hôpital Saint-Louis, Centre d'Investigations Cliniques CIC 1427, INSERM, Paris, France
| | - Jean-Michel Cayuela
- Hematology Laboratory and EA3518, University Hospital Saint-Louis, Université de Paris, Paris, France
| | - Mark Rolfe
- Celgene/Bristol-Myers Squibb corporation, San Diego, California, USA
| | | | - Steven A Carr
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Benjamin L Ebert
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Howard Hughes Medical Institute, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
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Lim S, Khoo R, Juang YC, Gopal P, Zhang H, Yeo C, Peh KM, Teo J, Ng S, Henry B, Partridge AW. Exquisitely Specific anti-KRAS Biodegraders Inform on the Cellular Prevalence of Nucleotide-Loaded States. ACS CENTRAL SCIENCE 2021; 7:274-291. [PMID: 33655066 PMCID: PMC7908030 DOI: 10.1021/acscentsci.0c01337] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Indexed: 05/05/2023]
Abstract
Mutations to RAS proteins (H-, N-, and K-RAS) are among the most common oncogenic drivers, and tumors harboring these lesions are some of the most difficult to treat. Although covalent small molecules against KRASG12C have shown promising efficacy against lung cancers, traditional barriers remain for drugging the more prevalent KRASG12D and KRASG12V mutants. Targeted degradation has emerged as an attractive alternative approach, but for KRAS, identification of the required high-affinity ligands continues to be a challenge. Another significant hurdle is the discovery of a hybrid molecule that appends an E3 ligase-recruiting moiety in a manner that satisfies the precise geometries required for productive polyubiquitin transfer while maintaining favorable druglike properties. To gain insights into the advantages and feasibility of KRAS targeted degradation, we applied a protein-based degrader (biodegrader) approach. This workflow centers on the intracellular expression of a chimeric protein consisting of a high-affinity target-binding domain fused to an engineered E3 ligase adapter. A series of anti-RAS biodegraders spanning different RAS isoform/nucleotide-state specificities and leveraging different E3 ligases provided definitive evidence for RAS degradability. Further, these established that the functional consequences of KRAS degradation are context dependent. Of broader significance, using the exquisite degradation specificity that biodegraders can possess, we demonstrated how this technology can be applied to answer questions that other approaches cannot. Specifically, application of the GDP-state specific degrader uncovered the relative prevalence of the "off-state" of WT and various KRAS mutants in the cellular context. Finally, if delivery challenges can be addressed, anti-RAS biodegraders will be exciting candidates for clinical development.
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Kaiho-Soma A, Akizuki Y, Igarashi K, Endo A, Shoda T, Kawase Y, Demizu Y, Naito M, Saeki Y, Tanaka K, Ohtake F. TRIP12 promotes small-molecule-induced degradation through K29/K48-branched ubiquitin chains. Mol Cell 2021; 81:1411-1424.e7. [PMID: 33567268 DOI: 10.1016/j.molcel.2021.01.023] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 12/13/2020] [Accepted: 01/20/2021] [Indexed: 12/19/2022]
Abstract
Targeted protein degradation is an emerging therapeutic paradigm. Small-molecule degraders such as proteolysis-targeting chimeras (PROTACs) induce the degradation of neo-substrates by hijacking E3 ubiquitin ligases. Although ubiquitylation of endogenous substrates has been extensively studied, the mechanism underlying forced degradation of neo-substrates is less well understood. We found that the ubiquitin ligase TRIP12 promotes PROTAC-induced and CRL2VHL-mediated degradation of BRD4 but is dispensable for the degradation of the endogenous CRL2VHL substrate HIF-1α. TRIP12 associates with BRD4 via CRL2VHL and specifically assembles K29-linked ubiquitin chains, facilitating the formation of K29/K48-branched ubiquitin chains and accelerating the assembly of K48 linkage by CRL2VHL. Consequently, TRIP12 promotes the PROTAC-induced apoptotic response. TRIP12 also supports the efficiency of other degraders that target CRABP2 or TRIM24 or recruit CRBN. These observations define TRIP12 and K29/K48-branched ubiquitin chains as accelerators of PROTAC-directed targeted protein degradation, revealing a cooperative mechanism of branched ubiquitin chain assembly unique to the degradation of neo-substrates.
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Affiliation(s)
- Ai Kaiho-Soma
- Institute for Advanced Life Sciences, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo 142-8501, Japan
| | - Yoshino Akizuki
- School of Pharmacy and Pharmaceutical Sciences, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo 142-8501, Japan
| | - Katsuhide Igarashi
- Institute for Advanced Life Sciences, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo 142-8501, Japan; School of Pharmacy and Pharmaceutical Sciences, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo 142-8501, Japan
| | - Akinori Endo
- Protein Metabolism Project, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan
| | - Takuji Shoda
- Division of Organic Chemistry, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki city, Kanagawa 210-9501, Japan
| | - Yasuko Kawase
- Protein Metabolism Project, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan
| | - Yosuke Demizu
- Division of Organic Chemistry, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki city, Kanagawa 210-9501, Japan
| | - Mikihiko Naito
- Division of Organic Chemistry, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki city, Kanagawa 210-9501, Japan; Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki city, Kanagawa 210-9501, Japan
| | - Yasushi Saeki
- Protein Metabolism Project, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan
| | - Keiji Tanaka
- Protein Metabolism Project, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan
| | - Fumiaki Ohtake
- Institute for Advanced Life Sciences, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo 142-8501, Japan; School of Pharmacy and Pharmaceutical Sciences, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo 142-8501, Japan; Protein Metabolism Project, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan.
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Banford S, McCorvie TJ, Pey AL, Timson DJ. Galactosemia: Towards Pharmacological Chaperones. J Pers Med 2021; 11:jpm11020106. [PMID: 33562227 PMCID: PMC7914515 DOI: 10.3390/jpm11020106] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 02/02/2021] [Accepted: 02/04/2021] [Indexed: 02/07/2023] Open
Abstract
Galactosemia is a rare inherited metabolic disease resulting from mutations in the four genes which encode enzymes involved in the metabolism of galactose. The current therapy, the removal of galactose from the diet, is inadequate. Consequently, many patients suffer lifelong physical and cognitive disability. The phenotype varies from almost asymptomatic to life-threatening disability. The fundamental biochemical cause of the disease is a decrease in enzymatic activity due to failure of the affected protein to fold and/or function correctly. Many novel therapies have been proposed for the treatment of galactosemia. Often, these are designed to treat the symptoms and not the fundamental cause. Pharmacological chaperones (PC) (small molecules which correct the folding of misfolded proteins) represent an exciting potential therapy for galactosemia. In theory, they would restore enzyme function, thus preventing downstream pathological consequences. In practice, no PCs have been identified for potential application in galactosemia. Here, we review the biochemical basis of the disease, identify opportunities for the application of PCs and describe how these might be discovered. We will conclude by considering some of the clinical issues which will affect the future use of PCs in the treatment of galactosemia.
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Affiliation(s)
- Samantha Banford
- South Eastern Health and Social Care Trust, Downpatrick BT30 6RL, UK;
| | - Thomas J. McCorvie
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK;
| | - Angel L. Pey
- Departamento de Química Física, Unidad de Excelencia de Química aplicada a Biomedicina y Medioambiente e Instituto de Biotecnología, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain;
| | - David J. Timson
- School of Pharmacy and Biomolecular Sciences, The University of Brighton, Brighton BN2 4GJ, UK
- Correspondence:
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Feng Y, Ariosa AR, Yang Y, Hu Z, Dengjel J, Klionsky DJ. Downregulation of autophagy by Met30-mediated Atg9 ubiquitination. Proc Natl Acad Sci U S A 2021; 118:e2005539118. [PMID: 33443148 PMCID: PMC7817162 DOI: 10.1073/pnas.2005539118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Macroautophagy/autophagy is a highly conserved eukaryotic molecular process that facilitates the recycling of superfluous cytoplasmic materials, damaged organelles, and invading pathogens, resulting in proper cellular homeostasis and survival during stress conditions. Autophagy is stringently regulated at multiple stages, including control at transcriptional, translational, and posttranslational levels. In this work, we identified a mechanism by which regulation of autophagy is achieved through the posttranslational modification of Atg9. Here, we show that, in order to limit autophagy to a low, basal level during normal conditions, Atg9 is ubiquitinated and subsequently targeted for degradation in a proteasome-dependent manner through the action of the E3 ligase Met30. When cells require increased autophagy flux to respond to nutrient deprivation, the proteolysis of Atg9 is significantly reduced. Overall, this work reveals an additional layer of mechanistic regulation that allows cells to further maintain appropriate levels of autophagy and to rapidly induce this process in response to stress.
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Affiliation(s)
- Yuchen Feng
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109
| | - Aileen R Ariosa
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109
| | - Ying Yang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109
| | - Zehan Hu
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
| | - Jörn Dengjel
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
| | - Daniel J Klionsky
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109;
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109
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43
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Salladini E, Jørgensen MLM, Theisen FF, Skriver K. Intrinsic Disorder in Plant Transcription Factor Systems: Functional Implications. Int J Mol Sci 2020; 21:E9755. [PMID: 33371315 PMCID: PMC7767404 DOI: 10.3390/ijms21249755] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/17/2020] [Accepted: 12/18/2020] [Indexed: 01/07/2023] Open
Abstract
Eukaryotic cells are complex biological systems that depend on highly connected molecular interaction networks with intrinsically disordered proteins as essential components. Through specific examples, we relate the conformational ensemble nature of intrinsic disorder (ID) in transcription factors to functions in plants. Transcription factors contain large regulatory ID-regions with numerous orphan sequence motifs, representing potential important interaction sites. ID-regions may affect DNA-binding through electrostatic interactions or allosterically as for the bZIP transcription factors, in which the DNA-binding domains also populate ensembles of dynamic transient structures. The flexibility of ID is well-suited for interaction networks requiring efficient molecular adjustments. For example, Radical Induced Cell Death1 depends on ID in transcription factors for its numerous, structurally heterogeneous interactions, and the JAZ:MYC:MED15 regulatory unit depends on protein dynamics, including binding-associated unfolding, for regulation of jasmonate-signaling. Flexibility makes ID-regions excellent targets of posttranslational modifications. For example, the extent of phosphorylation of the NAC transcription factor SOG1 regulates target gene expression and the DNA-damage response, and phosphorylation of the AP2/ERF transcription factor DREB2A acts as a switch enabling heat-regulated degradation. ID-related phase separation is emerging as being important to transcriptional regulation with condensates functioning in storage and inactivation of transcription factors. The applicative potential of ID-regions is apparent, as removal of an ID-region of the AP2/ERF transcription factor WRI1 affects its stability and consequently oil biosynthesis. The highlighted examples show that ID plays essential functional roles in plant biology and has a promising potential in engineering.
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Affiliation(s)
| | | | | | - Karen Skriver
- REPIN and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark; (E.S.); (M.L.M.J.); (F.F.T.)
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Sciarrillo R, Wojtuszkiewicz A, Assaraf YG, Jansen G, Kaspers GJL, Giovannetti E, Cloos J. The role of alternative splicing in cancer: From oncogenesis to drug resistance. Drug Resist Updat 2020; 53:100728. [PMID: 33070093 DOI: 10.1016/j.drup.2020.100728] [Citation(s) in RCA: 127] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 09/17/2020] [Accepted: 09/21/2020] [Indexed: 12/15/2022]
Abstract
Alternative splicing is a tightly regulated process whereby non-coding sequences of pre-mRNA are removed and protein-coding segments are assembled in diverse combinations, ultimately giving rise to proteins with distinct or even opposing functions. In the past decade, whole genome/transcriptome sequencing studies revealed the high complexity of splicing regulation, which occurs co-transcriptionally and is influenced by chromatin status and mRNA modifications. Consequently, splicing profiles of both healthy and malignant cells display high diversity and alternative splicing was shown to be widely deregulated in multiple cancer types. In particular, mutations in pre-mRNA regulatory sequences, splicing regulators and chromatin modifiers, as well as differential expression of splicing factors are important contributors to cancer pathogenesis. It has become clear that these aberrations contribute to many facets of cancer, including oncogenic transformation, cancer progression, response to anticancer drug treatment as well as resistance to therapy. In this respect, alternative splicing was shown to perturb the expression a broad spectrum of relevant genes involved in drug uptake/metabolism (i.e. SLC29A1, dCK, FPGS, and TP), activation of nuclear receptor pathways (i.e. GR, AR), regulation of apoptosis (i.e. MCL1, BCL-X, and FAS) and modulation of response to immunotherapy (CD19). Furthermore, aberrant splicing constitutes an important source of novel cancer biomarkers and the spliceosome machinery represents an attractive target for a novel and rapidly expanding class of therapeutic agents. Small molecule inhibitors targeting SF3B1 or splice factor kinases were highly cytotoxic against a wide range of cancer models, including drug-resistant cells. Importantly, these effects are enhanced in specific cancer subsets, such as splicing factor-mutated and c-MYC-driven tumors. Furthermore, pre-clinical studies report synergistic effects of spliceosome modulators in combination with conventional antitumor agents. These strategies based on the use of low dose splicing modulators could shift the therapeutic window towards decreased toxicity in healthy tissues. Here we provide an extensive overview of the latest findings in the field of regulation of splicing in cancer, including molecular mechanisms by which cancer cells harness alternative splicing to drive oncogenesis and evade anticancer drug treatment as well as splicing-based vulnerabilities that can provide novel treatment opportunities. Furthermore, we discuss current challenges arising from genome-wide detection and prediction methods of aberrant splicing, as well as unravelling functional relevance of the plethora of cancer-related splicing alterations.
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Affiliation(s)
- Rocco Sciarrillo
- Department of Hematology, Amsterdam UMC, VU University Medical Center, Cancer Center Amsterdam, Amsterdam, Netherlands; Department of Pediatric Oncology, Emma's Children's Hospital, Amsterdam UMC, VU University Medical Center, Cancer Center Amsterdam, Amsterdam, Netherlands; Department of Medical Oncology, Amsterdam UMC, VU University Medical Center, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Anna Wojtuszkiewicz
- Department of Hematology, Amsterdam UMC, VU University Medical Center, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Yehuda G Assaraf
- The Fred Wyszkowski Cancer Research Laboratory, Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Gerrit Jansen
- Amsterdam Immunology and Rheumatology Center, Amsterdam UMC, VU University Medical Center, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Gertjan J L Kaspers
- Department of Pediatric Oncology, Emma's Children's Hospital, Amsterdam UMC, VU University Medical Center, Cancer Center Amsterdam, Amsterdam, Netherlands; Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Elisa Giovannetti
- Department of Medical Oncology, Amsterdam UMC, VU University Medical Center, Cancer Center Amsterdam, Amsterdam, Netherlands; Fondazione Pisana per la Scienza, Pisa, Italy
| | - Jacqueline Cloos
- Department of Hematology, Amsterdam UMC, VU University Medical Center, Cancer Center Amsterdam, Amsterdam, Netherlands.
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Ting TC, Goralski M, Klein K, Wang B, Kim J, Xie Y, Nijhawan D. Aryl Sulfonamides Degrade RBM39 and RBM23 by Recruitment to CRL4-DCAF15. Cell Rep 2020; 29:1499-1510.e6. [PMID: 31693891 DOI: 10.1016/j.celrep.2019.09.079] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 09/09/2019] [Accepted: 09/26/2019] [Indexed: 12/12/2022] Open
Abstract
Indisulam and related sulfonamides recruit the splicing factor RBM39 to the CRL4-DCAF15 E3 ubiquitin ligase, resulting in RBM39 ubiquitination and degradation. Here, we used a combination of domain mapping and random mutagenesis to identify domains or residues that are necessary for indisulam-dependent RBM39 ubiquitination. DCAF15 mutations at Q232 or D475 prevent RBM39 recruitment by indisulam. RBM39 is recruited to DCAF15 by its RRM2 (RNA recognition motif 2) and is ubiquitinated on its N terminus. RBM23, which is an RBM39 paralog, is also recruited to the CRL4-DCAF15 ligase through its RRM2 domain and undergoes sulfonamide-dependent degradation. Indisulam alters the expression of more than 3,000 genes and causes widespread intron retention and exon skipping. All of these changes can be attributed to RBM39, and none are the consequence of RBM23 degradation. Our findings demonstrate that indisulam selectively degrades RBM23 and RBM39, the latter of which is critically important for splicing and gene expression.
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Affiliation(s)
- Tabitha C Ting
- Medical Scientist Training Program, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Maria Goralski
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Katherine Klein
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Baiyun Wang
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jiwoong Kim
- Quantitative Biomedical Research Center, Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yang Xie
- Quantitative Biomedical Research Center, Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Deepak Nijhawan
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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Blount JR, Johnson SL, Libohova K, Todi SV, Tsou WL. Degron capability of the hydrophobic C-terminus of the polyglutamine disease protein, ataxin-3. J Neurosci Res 2020; 98:2096-2108. [PMID: 32643791 DOI: 10.1002/jnr.24684] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 05/27/2020] [Accepted: 06/08/2020] [Indexed: 11/12/2022]
Abstract
Ataxin-3 is a deubiquitinase and polyglutamine disease protein whose cellular properties and functions are not entirely understood. Mutations in ataxin-3 cause spinocerebellar ataxia type 3 (SCA3), a neurodegenerative disorder that is a member of the polyglutamine family of diseases. Two major isoforms arise from alternative splicing of ATXN3 and are differently toxic in vivo as a result of faster proteasomal degradation of one isoform compared to the other. The isoforms vary only at their C-termini, suggesting that the hydrophobic C-terminus of the more quickly degraded form of ataxin-3 (here referred to as isoform 2) functions as a degron-that is, a peptide sequence that expedites the degradation of its host protein. We explored this notion in this study and present evidence that: (a) the C-terminus of ataxin-3 isoform 2 signals its degradation in a proteasome-dependent manner, (b) this effect from the C-terminus of isoform 2 does not require the ubiquitination of ataxin-3, and (c) the isolated C-terminus of isoform 2 can enhance the degradation of an unrelated protein. According to our data, the C-terminus of ataxin-3 isoform 2 is a degron, increasing overall understanding of the cellular properties of the SCA3 protein.
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Affiliation(s)
- Jessica R Blount
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Sean L Johnson
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Kozeta Libohova
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Sokol V Todi
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI, USA.,Department of Neurology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Wei-Ling Tsou
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI, USA
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Niemeyer M, Moreno Castillo E, Ihling CH, Iacobucci C, Wilde V, Hellmuth A, Hoehenwarter W, Samodelov SL, Zurbriggen MD, Kastritis PL, Sinz A, Calderón Villalobos LIA. Flexibility of intrinsically disordered degrons in AUX/IAA proteins reinforces auxin co-receptor assemblies. Nat Commun 2020; 11:2277. [PMID: 32385295 PMCID: PMC7210949 DOI: 10.1038/s41467-020-16147-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 04/17/2020] [Indexed: 12/31/2022] Open
Abstract
Cullin RING-type E3 ubiquitin ligases SCFTIR1/AFB1-5 and their AUX/IAA targets perceive the phytohormone auxin. The F-box protein TIR1 binds a surface-exposed degron in AUX/IAAs promoting their ubiquitylation and rapid auxin-regulated proteasomal degradation. Here, by adopting biochemical, structural proteomics and in vivo approaches we unveil how flexibility in AUX/IAAs and regions in TIR1 affect their conformational ensemble allowing surface accessibility of degrons. We resolve TIR1·auxin·IAA7 and TIR1·auxin·IAA12 complex topology, and show that flexible intrinsically disordered regions (IDRs) in the degron’s vicinity, cooperatively position AUX/IAAs on TIR1. We identify essential residues at the TIR1 N- and C-termini, which provide non-native interaction interfaces with IDRs and the folded PB1 domain of AUX/IAAs. We thereby establish a role for IDRs in modulating auxin receptor assemblies. By securing AUX/IAAs on two opposite surfaces of TIR1, IDR diversity supports locally tailored positioning for targeted ubiquitylation, and might provide conformational flexibility for a multiplicity of functional states. Auxin-mediated recruitment of AUX/IAAs by the F-box protein TIR1 prompts rapid AUX/IAA ubiquitylation and degradation. By resolving auxin receptor topology, the authors show that intrinsically disordered regions near the degrons of two Aux/IAA proteins reinforce complex assembly and position Aux/IAAs for ubiquitylation.
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Affiliation(s)
- Michael Niemeyer
- Molecular Signal Processing Department, Leibniz Institute of Plant Biochemistry (IPB), Weinberg 3, 06120, Halle (Saale), Germany
| | - Elena Moreno Castillo
- Molecular Signal Processing Department, Leibniz Institute of Plant Biochemistry (IPB), Weinberg 3, 06120, Halle (Saale), Germany
| | - Christian H Ihling
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Charles Tanford Protein Center, Kurt-Mothes-Straße 3a, 06120, Halle (Saale), Germany
| | - Claudio Iacobucci
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Charles Tanford Protein Center, Kurt-Mothes-Straße 3a, 06120, Halle (Saale), Germany
| | - Verona Wilde
- Molecular Signal Processing Department, Leibniz Institute of Plant Biochemistry (IPB), Weinberg 3, 06120, Halle (Saale), Germany
| | - Antje Hellmuth
- Molecular Signal Processing Department, Leibniz Institute of Plant Biochemistry (IPB), Weinberg 3, 06120, Halle (Saale), Germany
| | - Wolfgang Hoehenwarter
- Proteome Analytics, Leibniz Institute of Plant Biochemistry (IPB), Weinberg 3, 06120, Halle (Saale), Germany
| | - Sophia L Samodelov
- Institute of Synthetic Biology & Cluster of Excellence on Plant Science (CEPLAS), Heinrich-Heine University of Düsseldorf, Universitätsstrasse 1, 40225, Düsseldorf, Germany
| | - Matias D Zurbriggen
- Institute of Synthetic Biology & Cluster of Excellence on Plant Science (CEPLAS), Heinrich-Heine University of Düsseldorf, Universitätsstrasse 1, 40225, Düsseldorf, Germany
| | - Panagiotis L Kastritis
- ZIK HALOMEM & Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Biozentrum, Weinbergweg 22, 06120, Halle (Saale), Germany
| | - Andrea Sinz
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Charles Tanford Protein Center, Kurt-Mothes-Straße 3a, 06120, Halle (Saale), Germany
| | - Luz Irina A Calderón Villalobos
- Molecular Signal Processing Department, Leibniz Institute of Plant Biochemistry (IPB), Weinberg 3, 06120, Halle (Saale), Germany.
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bioPROTACs as versatile modulators of intracellular therapeutic targets including proliferating cell nuclear antigen (PCNA). Proc Natl Acad Sci U S A 2020; 117:5791-5800. [PMID: 32123106 DOI: 10.1073/pnas.1920251117] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Targeted degradation approaches such as proteolysis targeting chimeras (PROTACs) offer new ways to address disease through tackling challenging targets and with greater potency, efficacy, and specificity over traditional approaches. However, identification of high-affinity ligands to serve as PROTAC starting points remains challenging. As a complementary approach, we describe a class of molecules termed biological PROTACs (bioPROTACs)-engineered intracellular proteins consisting of a target-binding domain directly fused to an E3 ubiquitin ligase. Using GFP-tagged proteins as model substrates, we show that there is considerable flexibility in both the choice of substrate binders (binding positions, scaffold-class) and the E3 ligases. We then identified a highly effective bioPROTAC against an oncology target, proliferating cell nuclear antigen (PCNA) to elicit rapid and robust PCNA degradation and associated effects on DNA synthesis and cell cycle progression. Overall, bioPROTACs are powerful tools for interrogating degradation approaches, target biology, and potentially for making therapeutic impacts.
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Yang Y, Zhou H, Hou L, Xing K, Shu H. Transcriptional profiling of skeletal muscle reveals starvation response and compensatory growth in Spinibarbus hollandi. BMC Genomics 2019; 20:938. [PMID: 31805873 PMCID: PMC6896686 DOI: 10.1186/s12864-019-6345-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Accepted: 11/27/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Spinibarbus hollandi is an economically important fish species in southern China. This fish is known to have nutritional and medicinal properties; however, its farming is limited by its slow growth rate. In the present study, we observed that a compensatory growth phenomenon could be induced by adequate refeeding following 7 days of fasting in S. hollandi. To understand the starvation response and compensatory growth mechanisms in this fish, the muscle transcriptomes of S. hollandi under control, fasting, and refeeding conditions were profiled using next-generation sequencing (NGS) techniques. RESULTS More than 4.45 × 108 quality-filtered 150-base-pair Illumina reads were obtained from all nine muscle samples. De novo assemblies yielded a total of 156,735 unigenes, among which 142,918 (91.18%) could be annotated in at least one available database. After 7 days of fasting, 2422 differentially expressed genes were detected, including 1510 up-regulated genes and 912 down-regulated genes. Genes involved in fat, protein, and carbohydrate metabolism were significantly up-regulated, and genes associated with the cell cycle, DNA replication, and immune and cellular structures were inhibited during fasting. After refeeding, 84 up-regulated genes and 16 down-regulated genes were identified. Many genes encoding the components of myofibers were significantly up-regulated. Histological analysis of muscle verified the important role of muscle hypertrophy in compensatory growth. CONCLUSION In the present work, we reported the transcriptome profiles of S. hollandi muscle under different conditions. During fasting, the genes involved in the mobilization of stored energy were up-regulated, while the genes associated with growth were down-regulated. After refeeding, muscle hypertrophy contributed to the recovery of growth. The results of this study may help to elucidate the mechanisms underlying the starvation response and compensatory growth.
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Affiliation(s)
- Yang Yang
- School of Life Science, Guangzhou University, Guangzhou, 510006 China
| | - Huiqiang Zhou
- School of Life Science, Guangzhou University, Guangzhou, 510006 China
| | - Liping Hou
- School of Life Science, Guangzhou University, Guangzhou, 510006 China
| | - Ke Xing
- School of Life Science, Guangzhou University, Guangzhou, 510006 China
| | - Hu Shu
- School of Life Science, Guangzhou University, Guangzhou, 510006 China
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Systematic analysis of alterations in the ubiquitin proteolysis system reveals its contribution to driver mutations in cancer. ACTA ACUST UNITED AC 2019; 1:122-135. [DOI: 10.1038/s43018-019-0001-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 10/11/2019] [Indexed: 12/21/2022]
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