1
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Wan L, Ke J, Zhu Y, Zhang W, Mu W. Recent advances in engineering synthetic biomolecular condensates. Biotechnol Adv 2024; 77:108452. [PMID: 39271032 DOI: 10.1016/j.biotechadv.2024.108452] [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: 04/12/2024] [Revised: 09/08/2024] [Accepted: 09/09/2024] [Indexed: 09/15/2024]
Abstract
Biomolecular condensates are intriguing entities found within living cells. These structures possess the ability to selectively concentrate specific components through phase separation, thereby playing a crucial role in the spatiotemporal regulation of a wide range of cellular processes and metabolic activities. To date, extensive studies have been dedicated to unraveling the intricate connections between molecular features, physical properties, and cellular functions of condensates. This collective effort has paved the way for deliberate engineering of tailor-made condensates with specific applications. In this review, we comprehensively examine the underpinnings governing condensate formation. Next, we summarize the material states of condensates and delve into the design of synthetic intrinsically disordered proteins with tunable phase behaviors and physical properties. Subsequently, we review the diverse biological functions demonstrated by synthetic biomolecular condensates, encompassing gene regulation, cellular behaviors, modulation of biochemical reactions, and manipulation of endogenous protein activities. Lastly, we discuss future challenges and opportunities in constructing synthetic condensates with tunable physical properties and customized cellular functions, which may shed light on the development of new types of sophisticated condensate systems with distinct functions applicable to various scenarios.
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Affiliation(s)
- Li Wan
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Juntao Ke
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Yingying Zhu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Wenli Zhang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Wanmeng Mu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China.
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2
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Bradley D, Hogrebe A, Dandage R, Dubé AK, Leutert M, Dionne U, Chang A, Villén J, Landry CR. The fitness cost of spurious phosphorylation. EMBO J 2024:10.1038/s44318-024-00200-7. [PMID: 39256561 DOI: 10.1038/s44318-024-00200-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 07/23/2024] [Accepted: 07/24/2024] [Indexed: 09/12/2024] Open
Abstract
The fidelity of signal transduction requires the binding of regulatory molecules to their cognate targets. However, the crowded cell interior risks off-target interactions between proteins that are functionally unrelated. How such off-target interactions impact fitness is not generally known. Here, we use Saccharomyces cerevisiae to inducibly express tyrosine kinases. Because yeast lacks bona fide tyrosine kinases, the resulting tyrosine phosphorylation is biologically spurious. We engineered 44 yeast strains each expressing a tyrosine kinase, and quantitatively analysed their phosphoproteomes. This analysis resulted in ~30,000 phosphosites mapping to ~3500 proteins. The number of spurious pY sites generated correlates strongly with decreased growth, and we predict over 1000 pY events to be deleterious. However, we also find that many of the spurious pY sites have a negligible effect on fitness, possibly because of their low stoichiometry. This result is consistent with our evolutionary analyses demonstrating a lack of phosphotyrosine counter-selection in species with tyrosine kinases. Our results suggest that, alongside the risk for toxicity, the cell can tolerate a large degree of non-functional crosstalk as interaction networks evolve.
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Affiliation(s)
- David Bradley
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Québec, QC, Canada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université du Québec à Montréal, Montréal, QC, Canada
- Université Laval Big Data Research Center (BDRC_UL), Québec, QC, Canada
- Department of Biology, Université Laval, Québec, QC, Canada
| | - Alexander Hogrebe
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Rohan Dandage
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Québec, QC, Canada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université du Québec à Montréal, Montréal, QC, Canada
- Université Laval Big Data Research Center (BDRC_UL), Québec, QC, Canada
- Department of Biology, Université Laval, Québec, QC, Canada
| | - Alexandre K Dubé
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Québec, QC, Canada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université du Québec à Montréal, Montréal, QC, Canada
- Université Laval Big Data Research Center (BDRC_UL), Québec, QC, Canada
- Department of Biology, Université Laval, Québec, QC, Canada
| | - Mario Leutert
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Ugo Dionne
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Québec, QC, Canada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université du Québec à Montréal, Montréal, QC, Canada
- Université Laval Big Data Research Center (BDRC_UL), Québec, QC, Canada
- Department of Biology, Université Laval, Québec, QC, Canada
| | - Alexis Chang
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Judit Villén
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
| | - Christian R Landry
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada.
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Québec, QC, Canada.
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université du Québec à Montréal, Montréal, QC, Canada.
- Université Laval Big Data Research Center (BDRC_UL), Québec, QC, Canada.
- Department of Biology, Université Laval, Québec, QC, Canada.
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3
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Pha K, Mirrashidi K, Sherry J, Tran CJ, Herrera CM, McMahon E, Elwell CA, Engel JN. The Chlamydia effector IncE employs two short linear motifs to reprogram host vesicle trafficking. Cell Rep 2024; 43:114624. [PMID: 39154341 DOI: 10.1016/j.celrep.2024.114624] [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: 04/24/2024] [Revised: 06/26/2024] [Accepted: 07/29/2024] [Indexed: 08/20/2024] Open
Abstract
Chlamydia trachomatis, a leading cause of bacterial sexually transmitted infections, creates a specialized intracellular replicative niche by translocation and insertion of a diverse array of effectors (Incs [inclusion membrane proteins]) into the inclusion membrane. Here, we characterize IncE, a multifunctional Inc that encodes two non-overlapping short linear motifs (SLiMs) within its short cytosolic C terminus. The proximal SLiM, by mimicking just a small portion of an R-N-ethylmaleimide-sensitive factor adaptor protein receptor (SNARE) motif, binds and recruits syntaxin (STX)7- and STX12-containing vesicles to the inclusion. The distal SLiM mimics the sorting nexin (SNX)5 and SNX6 cargo binding site to recruit SNX6-containing vesicles to the inclusion. By simultaneously binding two distinct vesicle classes, IncE brings these vesicles in close apposition with each other at the inclusion to facilitate C. trachomatis intracellular development. Our work suggests that Incs may have evolved SLiMs to enable rapid evolution in a limited protein space to disrupt host cell processes.
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Affiliation(s)
- Khavong Pha
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Kathleen Mirrashidi
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jessica Sherry
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Cuong Joseph Tran
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Clara M Herrera
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Eleanor McMahon
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Cherilyn A Elwell
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.
| | - Joanne N Engel
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA.
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4
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Gu Y, Oliferenko S. Mitosis: An expanded view of mitotic mechanisms that arose in evolution. Curr Biol 2024; 34:R741-R744. [PMID: 39106834 DOI: 10.1016/j.cub.2024.06.048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/09/2024]
Abstract
Mitosis exhibits astonishing evolutionary plasticity, with dividing eukaryotic cells differing in the organization of the mitotic spindle and the extent of nuclear envelope breakdown. A new study suggests that a multinucleated lifestyle may favor the evolution of closed nuclear division.
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Affiliation(s)
- Ying Gu
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London SE1 1UL, UK; The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Snezhana Oliferenko
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London SE1 1UL, UK; The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
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5
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László L, Kurilla A, Tilajka Á, Pancsa R, Takács T, Novák J, Buday L, Vas V. Unveiling epithelial plasticity regulation in lung cancer: Exploring the cross-talk among Tks4 scaffold protein partners. Mol Biol Cell 2024; 35:ar111. [PMID: 38985526 PMCID: PMC11321040 DOI: 10.1091/mbc.e24-03-0103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 06/24/2024] [Accepted: 07/01/2024] [Indexed: 07/12/2024] Open
Abstract
The epithelial-to-mesenchymal transition (EMT) represents a hallmark event in the evolution of lung cancer. This work aims to study a recently described EMT-regulating protein, Tks4, and to explore its potential as a prognostic biomarker in non-small cell lung cancer. In this study, we used CRISPR/Cas9 method to knockout (KO) Tks4 to study its functional roles in invadopodia formation, migration, and regulation of EMT marker expressions and we identified Tks4-interacting proteins. Tks4-KO A549 cells exhibited an EMT-like phenotype characterized by elongated morphology and increased expression of EMT markers. Furthermore, analyses of a large-scale lung cancer database and a patient-derived tissue array data revealed that the Tks4 mRNA level was decreased in more aggressive lung cancer stages. To understand the regulatory role of Tks4 in lung cancer, we performed a Tks4-interactome analysis via Tks4 immunoprecipitation-mass spectrometry on five different cell lines and identified CAPZA1 as a novel Tks4 partner protein. Thus, we propose that the absence of Tks4 leads to disruption of a connectome of multiple proteins and that the resulting undocking and likely mislocalization of signaling molecules impairs actin cytoskeleton rearrangement and activates EMT-like cell fate switches, both of which likely influence disease severity.
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Affiliation(s)
- Loretta László
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, 1117 Budapest, Hungary
- Doctoral School of Biology, Institute of Biology, ELTE Eötvös Loránd University, 1117 Budapest, Hungary
| | - Anita Kurilla
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, 1117 Budapest, Hungary
| | - Álmos Tilajka
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, 1117 Budapest, Hungary
- Doctoral School of Biology, Institute of Biology, ELTE Eötvös Loránd University, 1117 Budapest, Hungary
| | - Rita Pancsa
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, 1117 Budapest, Hungary
| | - Tamás Takács
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, 1117 Budapest, Hungary
- Doctoral School of Biology, Institute of Biology, ELTE Eötvös Loránd University, 1117 Budapest, Hungary
| | - Julianna Novák
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, 1117 Budapest, Hungary
| | - László Buday
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, 1117 Budapest, Hungary
- Department of Molecular Biology, Semmelweis University, 1094 Budapest, Hungary
| | - Virag Vas
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, 1117 Budapest, Hungary
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6
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Singer A, Ramos A, Keating AE. Elaboration of the Homer1 recognition landscape reveals incomplete divergence of paralogous EVH1 domains. Protein Sci 2024; 33:e5094. [PMID: 38989636 PMCID: PMC11237882 DOI: 10.1002/pro.5094] [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: 02/26/2024] [Revised: 06/11/2024] [Accepted: 06/16/2024] [Indexed: 07/12/2024]
Abstract
Short sequences that mediate interactions with modular binding domains are ubiquitous throughout eukaryotic proteomes. Networks of short linear motifs (SLiMs) and their corresponding binding domains orchestrate many cellular processes, and the low mutational barrier to evolving novel interactions provides a way for biological systems to rapidly sample selectable phenotypes. Mapping SLiM binding specificity and the rules that govern SLiM evolution is fundamental to uncovering the pathways regulated by these networks and developing the tools to manipulate them. We used high-throughput screening of the human proteome to identify sequences that bind to the Enabled/VASP homology 1 (EVH1) domain of the postsynaptic density scaffolding protein Homer1. This expanded our understanding of the determinants of Homer EVH1 binding preferences and defined a new motif that can facilitate the discovery of additional Homer-mediated interactions. Interestingly, the Homer1 EVH1 domain preferentially binds to sequences containing an N-terminally overlapping motif that is bound by the paralogous family of Ena/VASP actin polymerases, and many of these sequences can bind to EVH1 domains from both protein families. We provide evidence from orthologous EVH1 domains in pre-metazoan organisms that the overlap in human Ena/VASP and Homer binding preferences corresponds to an incomplete divergence from a common Ena/VASP ancestor. Given this overlap in binding profiles, promiscuous sequences that can be recognized by both families either achieve specificity through extrinsic regulatory strategies or may provide functional benefits via multi-specificity. This may explain why these paralogs incompletely diverged despite the accessibility of further diverged isoforms.
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Affiliation(s)
- Avinoam Singer
- Department of BiologyMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Alejandra Ramos
- Department of BiologyMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Amy E. Keating
- Department of BiologyMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
- Department of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
- Koch Institute for Integrative Cancer ResearchMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
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7
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Russell SL, Penunuri G, Condon C. Diverse genetic conflicts mediated by molecular mimicry and computational approaches to detect them. Semin Cell Dev Biol 2024; 165:1-12. [PMID: 39079455 DOI: 10.1016/j.semcdb.2024.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 07/03/2024] [Accepted: 07/14/2024] [Indexed: 09/07/2024]
Abstract
In genetic conflicts between intergenomic and selfish elements, driver and killer elements achieve biased survival, replication, or transmission over sensitive and targeted elements through a wide range of molecular mechanisms, including mimicry. Driving mechanisms manifest at all organismal levels, from the biased propagation of individual genes, as demonstrated by transposable elements, to the biased transmission of genomes, as illustrated by viruses, to the biased transmission of cell lineages, as in cancer. Targeted genomes are vulnerable to molecular mimicry through the conserved motifs they use for their own signaling and regulation. Mimicking these motifs enables an intergenomic or selfish element to control core target processes, and can occur at the sequence, structure, or functional level. Molecular mimicry was first appreciated as an important phenomenon more than twenty years ago. Modern genomics technologies, databases, and machine learning approaches offer tremendous potential to study the distribution of molecular mimicry across genetic conflicts in nature. Here, we explore the theoretical expectations for molecular mimicry between conflicting genomes, the trends in molecular mimicry mechanisms across known genetic conflicts, and outline how new examples can be gleaned from population genomic datasets. We discuss how mimics involving short sequence-based motifs or gene duplications can evolve convergently from new mutations. Whereas, processes that involve divergent domains or fully-folded structures occur among genomes by horizontal gene transfer. These trends are largely based on a small number of organisms and should be reevaluated in a general, phylogenetically independent framework. Currently, publicly available databases can be mined for genotypes driving non-Mendelian inheritance patterns, epistatic interactions, and convergent protein structures. A subset of these conflicting elements may be molecular mimics. We propose approaches for detecting genetic conflict and molecular mimicry from these datasets.
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Affiliation(s)
- Shelbi L Russell
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, United States; Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, United States.
| | - Gabriel Penunuri
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, United States; Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Christopher Condon
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, United States; Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, United States
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8
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Halpin JC, Keating AE. PairK: Pairwise k-mer alignment for quantifying protein motif conservation in disordered regions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.23.604860. [PMID: 39091826 PMCID: PMC11291154 DOI: 10.1101/2024.07.23.604860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Protein-protein interactions are often mediated by a modular peptide recognition domain binding to a short linear motif (SLiM) in the disordered region of another protein. The ability to predict domain-SLiM interactions would allow researchers to map protein interaction networks, predict the effects of perturbations to those networks, and develop biologically meaningful hypotheses. Unfortunately, sequence database searches for SLiMs generally yield mostly biologically irrelevant motif matches or false positives. To improve the prediction of novel SLiM interactions, researchers employ filters to discriminate between biologically relevant and improbable motif matches. One promising criterion for identifying biologically relevant SLiMs is the sequence conservation of the motif, exploiting the fact that functional motifs are more likely to be conserved than spurious motif matches. However, the difficulty of aligning disordered regions has significantly hampered the utility of this approach. We present PairK (pairwise k-mer alignment), an MSA-free method to quantify motif conservation in disordered regions. PairK outperforms both standard MSA-based conservation scores and a modern LLM-based conservation score predictor on the task of identifying biologically important motif instances. PairK can quantify conservation over wider phylogenetic distances than MSAs, indicating that SLiMs may be more conserved than is implied by MSA-based metrics. PairK is available as open-source code at https://github.com/jacksonh1/pairk.
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Affiliation(s)
- Jackson C. Halpin
- MIT Department of Biology, 77 Massachusetts Ave., Cambridge, MA 02139
| | - Amy E. Keating
- MIT Department of Biology, 77 Massachusetts Ave., Cambridge, MA 02139
- MIT Department of Biological Engineering, 77 Massachusetts Ave., Cambridge, MA 02139
- Koch Institute for Integrative Cancer Research, 77 Massachusetts Ave., Cambridge, MA 02139
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9
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Hao T, Zhang M, Song Z, Gou Y, Wang B, Sun J. Reconstruction of Eriocheir sinensis Protein-Protein Interaction Network Based on DGO-SVM Method. Curr Issues Mol Biol 2024; 46:7353-7372. [PMID: 39057077 PMCID: PMC11276262 DOI: 10.3390/cimb46070436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2024] [Revised: 06/25/2024] [Accepted: 07/10/2024] [Indexed: 07/28/2024] Open
Abstract
Eriocheir sinensis is an economically important aquatic animal. Its regulatory mechanisms underlying many biological processes are still vague due to the lack of systematic analysis tools. The protein-protein interaction network (PIN) is an important tool for the systematic analysis of regulatory mechanisms. In this work, a novel machine learning method, DGO-SVM, was applied to predict the protein-protein interaction (PPI) in E. sinensis, and its PIN was reconstructed. With the domain, biological process, molecular functions and subcellular locations of proteins as the features, DGO-SVM showed excellent performance in Bombyx mori, humans and five aquatic crustaceans, with 92-96% accuracy. With DGO-SVM, the PIN of E. sinensis was reconstructed, containing 14,703 proteins and 7,243,597 interactions, in which 35,604 interactions were associated with 566 novel proteins mainly involved in the response to exogenous stimuli, cellular macromolecular metabolism and regulation. The DGO-SVM demonstrated that the biological process, molecular functions and subcellular locations of proteins are significant factors for the precise prediction of PPIs. We reconstructed the largest PIN for E. sinensis, which provides a systematic tool for the regulatory mechanism analysis. Furthermore, the novel-protein-related PPIs in the PIN may provide important clues for the mechanism analysis of the underlying specific physiological processes in E. sinensis.
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Affiliation(s)
| | | | | | | | - Bin Wang
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin 300387, China; (T.H.); (M.Z.); (Z.S.); (Y.G.)
| | - Jinsheng Sun
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin 300387, China; (T.H.); (M.Z.); (Z.S.); (Y.G.)
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10
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Calia G, Porracciolo P, Chen Y, Kozlowski D, Schuler H, Cestaro A, Quentin M, Favery B, Danchin EGJ, Bottini S. Identification and characterization of specific motifs in effector proteins of plant parasites using MOnSTER. Commun Biol 2024; 7:850. [PMID: 38992096 PMCID: PMC11239862 DOI: 10.1038/s42003-024-06515-9] [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: 02/05/2024] [Accepted: 06/27/2024] [Indexed: 07/13/2024] Open
Abstract
Plant pathogens cause billions of dollars of crop loss every year and are a major threat to global food security. Identifying and characterizing pathogens effectors is crucial towards their improved control. Because of their poor sequence conservation, effector identification is challenging, and current methods generate too many candidates without indication for prioritizing experimental studies. In most phyla, effectors contain specific sequence motifs which influence their localization and targets in the plant. Therefore, there is an urgent need to develop bioinformatics tools tailored for pathogen effectors. To circumvent these limitations, we have developed MOnSTER a specific tool that identifies clusters of motifs of protein sequences (CLUMPs). MOnSTER can be fed with motifs identified by de novo tools or from databases such as Pfam and InterProScan. The advantage of MOnSTER is the reduction of motif redundancy by clustering them and associating a score. This score encompasses the physicochemical properties of AAs and the motif occurrences. We built up our method to identify discriminant CLUMPs in oomycetes effectors. Consequently, we applied MOnSTER on plant parasitic nematodes and identified six CLUMPs in about 60% of the known nematode candidate parasitism proteins. Furthermore, we found co-occurrences of CLUMPs with protein domains important for invasion and pathogenicity. The potentiality of this tool goes beyond the effector characterization and can be used to easily cluster motifs and calculate the CLUMP-score on any set of protein sequences.
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Affiliation(s)
- Giulia Calia
- Free University of Bolzano, Faculty of Agricultural Environmental and Food Science, Bolzano, Italy
- Fondazione Edmund Mach, Research and Innovation Centre, San Michele all'Adige, Italy
- INRAE, Université Côte d'Azur, CNRS, Institut Sophia Agrobiotech, Sophia-Antipolis, France
| | - Paola Porracciolo
- INRAE, Université Côte d'Azur, CNRS, Institut Sophia Agrobiotech, Sophia-Antipolis, France
- Université Côte d'Azur, Center of Modeling, Simulation and Interactions, Nice, France
| | - Yongpan Chen
- INRAE, Université Côte d'Azur, CNRS, Institut Sophia Agrobiotech, Sophia-Antipolis, France
- Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Djampa Kozlowski
- INRAE, Université Côte d'Azur, CNRS, Institut Sophia Agrobiotech, Sophia-Antipolis, France
- Université Côte d'Azur, Center of Modeling, Simulation and Interactions, Nice, France
| | - Hannes Schuler
- Free University of Bolzano, Faculty of Agricultural Environmental and Food Science, Bolzano, Italy
- Free University of Bolzano, Competence Centre for Plant Health, Bolzano, Italy
| | - Alessandro Cestaro
- Fondazione Edmund Mach, Research and Innovation Centre, San Michele all'Adige, Italy
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), National Research Council (CNR), Bari, Italy
| | - Michaël Quentin
- INRAE, Université Côte d'Azur, CNRS, Institut Sophia Agrobiotech, Sophia-Antipolis, France
| | - Bruno Favery
- INRAE, Université Côte d'Azur, CNRS, Institut Sophia Agrobiotech, Sophia-Antipolis, France
| | - Etienne G J Danchin
- INRAE, Université Côte d'Azur, CNRS, Institut Sophia Agrobiotech, Sophia-Antipolis, France
| | - Silvia Bottini
- INRAE, Université Côte d'Azur, CNRS, Institut Sophia Agrobiotech, Sophia-Antipolis, France.
- Université Côte d'Azur, Center of Modeling, Simulation and Interactions, Nice, France.
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11
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Nguyen A, Zhao H, Myagmarsuren D, Srinivasan S, Wu D, Chen J, Piszczek G, Schuck P. Modulation of biophysical properties of nucleocapsid protein in the mutant spectrum of SARS-CoV-2. eLife 2024; 13:RP94836. [PMID: 38941236 PMCID: PMC11213569 DOI: 10.7554/elife.94836] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2024] Open
Abstract
Genetic diversity is a hallmark of RNA viruses and the basis for their evolutionary success. Taking advantage of the uniquely large genomic database of SARS-CoV-2, we examine the impact of mutations across the spectrum of viable amino acid sequences on the biophysical phenotypes of the highly expressed and multifunctional nucleocapsid protein. We find variation in the physicochemical parameters of its extended intrinsically disordered regions (IDRs) sufficient to allow local plasticity, but also observe functional constraints that similarly occur in related coronaviruses. In biophysical experiments with several N-protein species carrying mutations associated with major variants, we find that point mutations in the IDRs can have nonlocal impact and modulate thermodynamic stability, secondary structure, protein oligomeric state, particle formation, and liquid-liquid phase separation. In the Omicron variant, distant mutations in different IDRs have compensatory effects in shifting a delicate balance of interactions controlling protein assembly properties, and include the creation of a new protein-protein interaction interface in the N-terminal IDR through the defining P13L mutation. A picture emerges where genetic diversity is accompanied by significant variation in biophysical characteristics of functional N-protein species, in particular in the IDRs.
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Affiliation(s)
- Ai Nguyen
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, United States
| | - Huaying Zhao
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, United States
| | - Dulguun Myagmarsuren
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, United States
| | - Sanjana Srinivasan
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, United States
| | - Di Wu
- Biophysics Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, United States
| | - Jiji Chen
- Advanced Imaging and Microscopy Resource, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, United States
| | - Grzegorz Piszczek
- Biophysics Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, United States
| | - Peter Schuck
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, United States
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12
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Pha K, Mirrashidi K, Sherry J, Tran CJ, Herrera CM, McMahon E, Elwell CA, Engel JN. The Chlamydia effector IncE employs two short linear motifs to reprogram host vesicle trafficking. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.23.590830. [PMID: 38712241 PMCID: PMC11071397 DOI: 10.1101/2024.04.23.590830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Chlamydia trachomatis, a leading cause of bacteria sexually transmitted infections, creates a specialized intracellular replicative niche by translocation and insertion of a diverse array of effectors (Incs) into the inclusion membrane. Here, we characterize IncE, a multi-functional Inc that encodes two non-overlapping short linear motifs (SLiMs) within its short cytosolic C-terminus. The proximal SLiM mimics an R-SNARE motif to recruit syntaxin (STX) 7 and 12-containing vesicles to the inclusion. The distal SLiM mimics the Sorting Nexin (SNX) 5 and 6 cargo binding site to recruit SNX6-containing vesicles to the inclusion. By simultaneously binding to two distinct vesicle classes, IncE reprograms host cell trafficking to promote the formation of a class of hybrid vesicles at the inclusion that are required for C. trachomatis intracellular development. Our work suggests that Incs may have evolved SLiMs to facilitate rapid evolution in a limited protein space to disrupt host cell processes.
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13
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Singer A, Ramos A, Keating AE. Elaboration of the Homer1 Recognition Landscape Reveals Incomplete Divergence of Paralogous EVH1 Domains. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.23.576863. [PMID: 38645240 PMCID: PMC11030225 DOI: 10.1101/2024.01.23.576863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Short sequences that mediate interactions with modular binding domains are ubiquitous throughout eukaryotic proteomes. Networks of Short Linear Motifs (SLiMs) and their corresponding binding domains orchestrate many cellular processes, and the low mutational barrier to evolving novel interactions provides a way for biological systems to rapidly sample selectable phenotypes. Mapping SLiM binding specificity and the rules that govern SLiM evolution is fundamental to uncovering the pathways regulated by these networks and developing the tools to manipulate them. We used high-throughput screening of the human proteome to identify sequences that bind to the Enabled/VASP homology 1 (EVH1) domain of the postsynaptic density scaffolding protein Homer1. In doing so, we expanded current understanding of the determinants of Homer EVH1 binding preferences and defined a new motif that can facilitate the discovery of additional Homer-mediated interactions. Interestingly, the Homer1 EVH1 domain preferentially binds to sequences containing an N-terminally overlapping motif that is bound by the paralogous family of Ena/VASP actin polymerases, and many of these sequences can bind to EVH1 domains from both protein families. We provide evidence from orthologous EVH1 domains in pre-metazoan organisms that the overlap in human Ena/VASP and Homer binding preferences corresponds to an incomplete divergence from a common Ena/VASP ancestor. Given this overlap in binding profiles, promiscuous sequences that can be recognized by both families either achieve specificity through extrinsic regulatory strategies or may provide functional benefits via multi-specificity. This may explain why these paralogs incompletely diverged despite the accessibility of further diverged isoforms.
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Affiliation(s)
- Avinoam Singer
- MIT Department of Biology, Cambridge, Massachusetts, USA
| | | | - Amy E. Keating
- MIT Department of Biology, Cambridge, Massachusetts, USA
- MIT Department of Biological Engineering, Cambridge, Massachusetts, USA
- Koch Institute for Integrative Cancer Research, Cambridge, Massachusetts, USA
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14
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Mac Donagh J, Marchesini A, Spiga A, Fallico MJ, Arrías PN, Monzon AM, Vagiona AC, Gonçalves-Kulik M, Mier P, Andrade-Navarro MA. Structured Tandem Repeats in Protein Interactions. Int J Mol Sci 2024; 25:2994. [PMID: 38474241 DOI: 10.3390/ijms25052994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 02/28/2024] [Accepted: 03/01/2024] [Indexed: 03/14/2024] Open
Abstract
Tandem repeats (TRs) in protein sequences are consecutive, highly similar sequence motifs. Some types of TRs fold into structural units that pack together in ensembles, forming either an (open) elongated domain or a (closed) propeller, where the last unit of the ensemble packs against the first one. Here, we examine TR proteins (TRPs) to see how their sequence, structure, and evolutionary properties favor them for a function as mediators of protein interactions. Our observations suggest that TRPs bind other proteins using large, structured surfaces like globular domains; in particular, open-structured TR ensembles are favored by flexible termini and the possibility to tightly coil against their targets. While, intuitively, open ensembles of TRs seem prone to evolve due to their potential to accommodate insertions and deletions of units, these evolutionary events are unexpectedly rare, suggesting that they are advantageous for the emergence of the ancestral sequence but are early fixed. We hypothesize that their flexibility makes it easier for further proteins to adapt to interact with them, which would explain their large number of protein interactions. We provide insight into the properties of open TR ensembles, which make them scaffolds for alternative protein complexes to organize genes, RNA and proteins.
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Affiliation(s)
- Juan Mac Donagh
- Science and Technology Department, National University of Quilmes, Bernal B1876, Argentina
- National Scientific and Technical Research Council (CONICET), Buenos Aires C1033AAJ, Argentina
| | - Abril Marchesini
- National Scientific and Technical Research Council (CONICET), Buenos Aires C1033AAJ, Argentina
- Biotechnology and Molecular Biology Institute (IBBM, UNLP-CONICET), Faculty of Exact Sciences, University of La Plata, La Plata 1900, Argentina
| | - Agostina Spiga
- Science and Technology Department, National University of Quilmes, Bernal B1876, Argentina
- National Scientific and Technical Research Council (CONICET), Buenos Aires C1033AAJ, Argentina
| | - Maximiliano José Fallico
- Laboratory of Bioactive Compound Research and Development, Faculty of Exact Sciences, University of La Plata, La Plata 1900, Argentina
| | - Paula Nazarena Arrías
- Department of Biomedical Sciences, University of Padova, Via U. Bassi 58/b, 35121 Padova, Italy
| | - Alexander Miguel Monzon
- Department of Information Engineering, University of Padova, Via Giovanni Gradenigo 6/B, 35131 Padova, Italy
| | - Aimilia-Christina Vagiona
- Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University, Hans-Dieter-Hüsch-Weg 15, 55128 Mainz, Germany
| | - Mariane Gonçalves-Kulik
- Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University, Hans-Dieter-Hüsch-Weg 15, 55128 Mainz, Germany
| | - Pablo Mier
- Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University, Hans-Dieter-Hüsch-Weg 15, 55128 Mainz, Germany
| | - Miguel A Andrade-Navarro
- Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University, Hans-Dieter-Hüsch-Weg 15, 55128 Mainz, Germany
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15
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Holehouse AS, Kragelund BB. The molecular basis for cellular function of intrinsically disordered protein regions. Nat Rev Mol Cell Biol 2024; 25:187-211. [PMID: 37957331 DOI: 10.1038/s41580-023-00673-0] [Citation(s) in RCA: 55] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2023] [Indexed: 11/15/2023]
Abstract
Intrinsically disordered protein regions exist in a collection of dynamic interconverting conformations that lack a stable 3D structure. These regions are structurally heterogeneous, ubiquitous and found across all kingdoms of life. Despite the absence of a defined 3D structure, disordered regions are essential for cellular processes ranging from transcriptional control and cell signalling to subcellular organization. Through their conformational malleability and adaptability, disordered regions extend the repertoire of macromolecular interactions and are readily tunable by their structural and chemical context, making them ideal responders to regulatory cues. Recent work has led to major advances in understanding the link between protein sequence and conformational behaviour in disordered regions, yet the link between sequence and molecular function is less well defined. Here we consider the biochemical and biophysical foundations that underlie how and why disordered regions can engage in productive cellular functions, provide examples of emerging concepts and discuss how protein disorder contributes to intracellular information processing and regulation of cellular function.
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Affiliation(s)
- Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO, USA.
- Center for Biomolecular Condensates, Washington University in St Louis, St Louis, MO, USA.
| | - Birthe B Kragelund
- REPIN, Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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16
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Suskiewicz MJ. The logic of protein post-translational modifications (PTMs): Chemistry, mechanisms and evolution of protein regulation through covalent attachments. Bioessays 2024; 46:e2300178. [PMID: 38247183 DOI: 10.1002/bies.202300178] [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: 09/19/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 01/23/2024]
Abstract
Protein post-translational modifications (PTMs) play a crucial role in all cellular functions by regulating protein activity, interactions and half-life. Despite the enormous diversity of modifications, various PTM systems show parallels in their chemical and catalytic underpinnings. Here, focussing on modifications that involve the addition of new elements to amino-acid sidechains, I describe historical milestones and fundamental concepts that support the current understanding of PTMs. The historical survey covers selected key research programmes, including the study of protein phosphorylation as a regulatory switch, protein ubiquitylation as a degradation signal and histone modifications as a functional code. The contribution of crucial techniques for studying PTMs is also discussed. The central part of the essay explores shared chemical principles and catalytic strategies observed across diverse PTM systems, together with mechanisms of substrate selection, the reversibility of PTMs by erasers and the recognition of PTMs by reader domains. Similarities in the basic chemical mechanism are highlighted and their implications are discussed. The final part is dedicated to the evolutionary trajectories of PTM systems, beginning with their possible emergence in the context of rivalry in the prokaryotic world. Together, the essay provides a unified perspective on the diverse world of major protein modifications.
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Affiliation(s)
- Marcin J Suskiewicz
- Centre de Biophysique Moléculaire, CNRS - Orléans, UPR 4301, affiliated with Université d'Orléans, Orléans, France
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17
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Zeke A, Gibson TJ, Dobson L. Linear motifs regulating protein secretion, sorting and autophagy in Leishmania parasites are diverged with respect to their host equivalents. PLoS Comput Biol 2024; 20:e1011902. [PMID: 38363808 PMCID: PMC10903960 DOI: 10.1371/journal.pcbi.1011902] [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: 08/02/2023] [Revised: 02/29/2024] [Accepted: 02/08/2024] [Indexed: 02/18/2024] Open
Abstract
The pathogenic, tropical Leishmania flagellates belong to an early-branching eukaryotic lineage (Kinetoplastida) with several unique features. Unfortunately, they are poorly understood from a molecular biology perspective, making development of mechanistically novel and selective drugs difficult. Here, we explore three functionally critical targeting short linear motif systems as well as their receptors in depth, using a combination of structural modeling, evolutionary sequence divergence and deep learning. Secretory signal peptides, endoplasmic reticulum (ER) retention motifs (KDEL motifs), and autophagy signals (motifs interacting with ATG8 family members) are ancient and essential components of cellular life. Although expected to be conserved amongst the kinetoplastids, we observe that all three systems show a varying degree of divergence from their better studied equivalents in animals, plants, or fungi. We not only describe their behaviour, but also build models that allow the prediction of localization and potential functions for several uncharacterized Leishmania proteins. The unusually Ala/Val-rich secretory signal peptides, endoplasmic reticulum resident proteins ending in Asp-Leu-COOH and atypical ATG8-like proteins are all unique molecular features of kinetoplastid parasites. Several of their critical protein-protein interactions could serve as targets of selective antimicrobial agents against Leishmaniasis due to their systematic divergence from the host.
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Affiliation(s)
- Andras Zeke
- Institute of Molecular Life Sciences, Research Centre for Natural Sciences, Budapest, Hungary
| | - Toby J. Gibson
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Laszlo Dobson
- Institute of Molecular Life Sciences, Research Centre for Natural Sciences, Budapest, Hungary
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Department of Bioinformatics, Semmelweis University, Budapest, Hungary
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18
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Garg A, González-Foutel NS, Gielnik MB, Kjaergaard M. Design of functional intrinsically disordered proteins. Protein Eng Des Sel 2024; 37:gzae004. [PMID: 38431892 DOI: 10.1093/protein/gzae004] [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: 10/02/2023] [Revised: 12/22/2023] [Indexed: 03/05/2024] Open
Abstract
Many proteins do not fold into a fixed three-dimensional structure, but rather function in a highly disordered state. These intrinsically disordered proteins pose a unique challenge to protein engineering and design: How can proteins be designed de novo if not by tailoring their structure? Here, we will review the nascent field of design of intrinsically disordered proteins with focus on applications in biotechnology and medicine. The design goals should not necessarily be the same as for de novo design of folded proteins as disordered proteins have unique functional strengths and limitations. We focus on functions where intrinsically disordered proteins are uniquely suited including disordered linkers, desiccation chaperones, sensors of the chemical environment, delivery of pharmaceuticals, and constituents of biomolecular condensates. Design of functional intrinsically disordered proteins relies on a combination of computational tools and heuristics gleaned from sequence-function studies. There are few cases where intrinsically disordered proteins have made it into industrial applications. However, we argue that disordered proteins can perform many roles currently performed by organic polymers, and that these proteins might be more designable due to their modularity.
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Affiliation(s)
- Ankush Garg
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
| | | | - Maciej B Gielnik
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
| | - Magnus Kjaergaard
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, 8000 Aarhus, Denmark
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19
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Wu CG, Balakrishnan VK, Merrill RA, Parihar PS, Konovolov K, Chen YC, Xu Z, Wei H, Sundaresan R, Cui Q, Wadzinski BE, Swingle MR, Musiyenko A, Chung WK, Honkanen RE, Suzuki A, Huang X, Strack S, Xing Y. B56δ long-disordered arms form a dynamic PP2A regulation interface coupled with global allostery and Jordan's syndrome mutations. Proc Natl Acad Sci U S A 2024; 121:e2310727120. [PMID: 38150499 PMCID: PMC10769853 DOI: 10.1073/pnas.2310727120] [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: 07/01/2023] [Accepted: 11/27/2023] [Indexed: 12/29/2023] Open
Abstract
Intrinsically disordered regions (IDR) and short linear motifs (SLiMs) play pivotal roles in the intricate signaling networks governed by phosphatases and kinases. B56δ (encoded by PPP2R5D) is a regulatory subunit of protein phosphatase 2A (PP2A) with long IDRs that harbor a substrate-mimicking SLiM and multiple phosphorylation sites. De novo missense mutations in PPP2R5D cause intellectual disabilities (ID), macrocephaly, Parkinsonism, and a broad range of neurological symptoms. Our single-particle cryo-EM structures of the PP2A-B56δ holoenzyme reveal that the long, disordered arms at the B56δ termini fold against each other and the holoenzyme core. This architecture suppresses both the phosphatase active site and the substrate-binding protein groove, thereby stabilizing the enzyme in a closed latent form with dual autoinhibition. The resulting interface spans over 190 Å and harbors unfavorable contacts, activation phosphorylation sites, and nearly all residues with ID-associated mutations. Our studies suggest that this dynamic interface is coupled to an allosteric network responsive to phosphorylation and altered globally by mutations. Furthermore, we found that ID mutations increase the holoenzyme activity and perturb the phosphorylation rates, and the severe variants significantly increase the mitotic duration and error rates compared to the normal variant.
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Affiliation(s)
- Cheng-Guo Wu
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin at Madison, School of Medicine and Public Health, Madison, WI53705
- Biophysics Program, University of Wisconsin at Madison, Madison, WI53706
| | - Vijaya K. Balakrishnan
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin at Madison, School of Medicine and Public Health, Madison, WI53705
| | - Ronald A. Merrill
- Department of Neuroscience and Pharmacology, University of Iowa, Iowa City, IA52242
| | - Pankaj S. Parihar
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin at Madison, School of Medicine and Public Health, Madison, WI53705
| | - Kirill Konovolov
- Chemistry Department, University of Wisconsin at Madison, Madison, WI53706
| | - Yu-Chia Chen
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin at Madison, School of Medicine and Public Health, Madison, WI53705
- Molecular and Cellular Pharmacology Program, University of Wisconsin at Madison, Madison, WI53706
| | - Zhen Xu
- Protein and Crystallography Facility, University of Iowa, Iowa City, IA52242
| | - Hui Wei
- The Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY10027
| | - Ramya Sundaresan
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin at Madison, School of Medicine and Public Health, Madison, WI53705
| | - Qiang Cui
- Department of Chemistry, Boston University, Boston, MA02215
| | | | - Mark R. Swingle
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, AL36688
| | - Alla Musiyenko
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, AL36688
| | - Wendy K. Chung
- Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, MA02215
| | - Richard E. Honkanen
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, AL36688
| | - Aussie Suzuki
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin at Madison, School of Medicine and Public Health, Madison, WI53705
- Biophysics Program, University of Wisconsin at Madison, Madison, WI53706
- Molecular and Cellular Pharmacology Program, University of Wisconsin at Madison, Madison, WI53706
| | - Xuhui Huang
- Biophysics Program, University of Wisconsin at Madison, Madison, WI53706
- Chemistry Department, University of Wisconsin at Madison, Madison, WI53706
| | - Stefan Strack
- Department of Neuroscience and Pharmacology, University of Iowa, Iowa City, IA52242
| | - Yongna Xing
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin at Madison, School of Medicine and Public Health, Madison, WI53705
- Biophysics Program, University of Wisconsin at Madison, Madison, WI53706
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20
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Schuck P, Zhao H. Diversity of short linear interaction motifs in SARS-CoV-2 nucleocapsid protein. mBio 2023; 14:e0238823. [PMID: 38018991 PMCID: PMC10746173 DOI: 10.1128/mbio.02388-23] [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: 09/01/2023] [Accepted: 10/16/2023] [Indexed: 11/30/2023] Open
Abstract
IMPORTANCE Short linear motifs (SLiMs) are 3-10 amino acid long binding motifs in intrinsically disordered protein regions (IDRs) that serve as ubiquitous protein-protein interaction modules in eukaryotic cells. Through molecular mimicry, viruses hijack these sequence motifs to control host cellular processes. It is thought that the small size of SLiMs and the high mutation frequencies of viral IDRs allow rapid host adaptation. However, a salient characteristic of RNA viruses, due to high replication errors, is their obligate existence as mutant swarms. Taking advantage of the uniquely large genomic database of SARS-CoV-2, here, we analyze the role of sequence diversity in the presentation of SLiMs, focusing on the highly abundant, multi-functional nucleocapsid protein. We find that motif mimicry is a highly dynamic process that produces an abundance of motifs transiently present in subsets of mutant species. This diversity allows the virus to efficiently explore eukaryotic motifs and evolve the host-virus interface.
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Affiliation(s)
- Peter Schuck
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, USA
| | - Huaying Zhao
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, USA
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21
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Tessier TM, King CR, Mymryk JS. Exploiting the endogenous yeast nuclear proteome to identify short linear motifs in vivo. CELL REPORTS METHODS 2023; 3:100637. [PMID: 37949066 PMCID: PMC10694487 DOI: 10.1016/j.crmeth.2023.100637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 09/01/2023] [Accepted: 10/17/2023] [Indexed: 11/12/2023]
Abstract
Peptide-domain interactions mediated by short linear motifs (SLiMs) play crucial roles in cellular biology. The simplicity of SLiMs poses challenges in their computational identification. Existing high-throughput methods for discovering SLiMs lack cellular context as they are typically performed in vitro. We developed a functional selection method using yeast to identify peptides that interact with the endogenous yeast nuclear proteome. Remarkably, peptides selected for in yeast also mediated nuclear import in human cells. Notably, the identified peptides did not resemble classical nuclear localization sequences. This platform has the potential to identify and investigate motifs that interact with the nuclear proteome of yeast and human and to aid in the identification and understanding of alternative protein nuclear import mechanisms.
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Affiliation(s)
- Tanner M Tessier
- Department of Microbiology and Immunology, Western University, London, ON, Canada
| | - Cason R King
- Department of Microbiology and Immunology, Western University, London, ON, Canada
| | - Joe S Mymryk
- Department of Microbiology and Immunology, Western University, London, ON, Canada; Department of Oncology, Western University, London, ON, Canada; Department of Otolaryngology, Western University, London, ON, Canada; London Regional Cancer Program, Lawson Health Research Institute, London, ON, Canada.
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22
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Bradley D, Hogrebe A, Dandage R, Dubé AK, Leutert M, Dionne U, Chang A, Villén J, Landry CR. The fitness cost of spurious phosphorylation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.08.561337. [PMID: 37873463 PMCID: PMC10592693 DOI: 10.1101/2023.10.08.561337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
The fidelity of signal transduction requires the binding of regulatory molecules to their cognate targets. However, the crowded cell interior risks off-target interactions between proteins that are functionally unrelated. How such off-target interactions impact fitness is not generally known, but quantifying this is required to understand the constraints faced by cell systems as they evolve. Here, we use the model organism S. cerevisiae to inducibly express tyrosine kinases. Because yeast lacks bona fide tyrosine kinases, most of the resulting tyrosine phosphorylation is spurious. This provides a suitable system to measure the impact of artificial protein interactions on fitness. We engineered 44 yeast strains each expressing a tyrosine kinase, and quantitatively analysed their phosphoproteomes. This analysis resulted in ~30,000 phosphosites mapping to ~3,500 proteins. Examination of the fitness costs in each strain revealed a strong correlation between the number of spurious pY sites and decreased growth. Moreover, the analysis of pY effects on protein structure and on protein function revealed over 1000 pY events that we predict to be deleterious. However, we also find that a large number of the spurious pY sites have a negligible effect on fitness, possibly because of their low stoichiometry. This result is consistent with our evolutionary analyses demonstrating a lack of phosphotyrosine counter-selection in species with bona fide tyrosine kinases. Taken together, our results suggest that, alongside the risk for toxicity, the cell can tolerate a large degree of non-functional crosstalk as interaction networks evolve.
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Affiliation(s)
- David Bradley
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Québec, QC, Canada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université du Québec à Montréal, Montréal, QC, Canada
- Université Laval Big Data Research Center (BDRC_UL), Québec, QC, Canada
- Department of Biology, Université Laval, Québec, QC, Canada
| | - Alexander Hogrebe
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Rohan Dandage
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Québec, QC, Canada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université du Québec à Montréal, Montréal, QC, Canada
- Université Laval Big Data Research Center (BDRC_UL), Québec, QC, Canada
- Department of Biology, Université Laval, Québec, QC, Canada
| | - Alexandre K Dubé
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Québec, QC, Canada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université du Québec à Montréal, Montréal, QC, Canada
- Université Laval Big Data Research Center (BDRC_UL), Québec, QC, Canada
- Department of Biology, Université Laval, Québec, QC, Canada
| | - Mario Leutert
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Ugo Dionne
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Québec, QC, Canada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université du Québec à Montréal, Montréal, QC, Canada
- Université Laval Big Data Research Center (BDRC_UL), Québec, QC, Canada
- Department of Biology, Université Laval, Québec, QC, Canada
| | - Alexis Chang
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Judit Villén
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Christian R Landry
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Québec, QC, Canada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université du Québec à Montréal, Montréal, QC, Canada
- Université Laval Big Data Research Center (BDRC_UL), Québec, QC, Canada
- Department of Biology, Université Laval, Québec, QC, Canada
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23
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Pei J, Cong Q. Computational analysis of regulatory regions in human protein kinases. Protein Sci 2023; 32:e4764. [PMID: 37632170 PMCID: PMC10503413 DOI: 10.1002/pro.4764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 08/08/2023] [Accepted: 08/22/2023] [Indexed: 08/27/2023]
Abstract
Eukaryotic proteins often feature modular domain structures comprising globular domains that are connected by linker regions and intrinsically disordered regions that may contain important functional motifs. The intramolecular interactions of globular domains and nonglobular regions can play critical roles in different aspects of protein function. However, studying these interactions and their regulatory roles can be challenging due to the flexibility of nonglobular regions, the long insertions separating interacting modules, and the transient nature of some interactions. Obtaining the experimental structures of multiple domains and functional regions is more difficult than determining the structures of individual globular domains. High-quality structural models generated by AlphaFold offer a unique opportunity to study intramolecular interactions in eukaryotic proteins. In this study, we systematically explored intramolecular interactions between human protein kinase domains (KDs) and potential regulatory regions, including globular domains, N- and C-terminal tails, long insertions, and distal nonglobular regions. Our analysis identified intramolecular interactions between human KDs and 35 different types of globular domains, exhibiting a variety of interaction modes that could contribute to orthosteric or allosteric regulation of kinase activity. We also identified prevalent interactions between human KDs and their flanking regions (N- and C-terminal tails). These interactions exhibit group-specific characteristics and can vary within each specific kinase group. Although long-range interactions between KDs and nonglobular regions are relatively rare, structural details of these interactions offer new insights into the regulation mechanisms of several kinases, such as HASPIN, MAPK7, MAPK15, and SIK1B.
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Affiliation(s)
- Jimin Pei
- Eugene McDermott Center for Human Growth and DevelopmentUniversity of Texas Southwestern Medical CenterDallasTexasUSA
- Department of BiophysicsUniversity of Texas Southwestern Medical CenterDallasTexasUSA
- Harold C. Simmons Comprehensive Cancer CenterUniversity of Texas Southwestern Medical CenterDallasTexasUSA
| | - Qian Cong
- Eugene McDermott Center for Human Growth and DevelopmentUniversity of Texas Southwestern Medical CenterDallasTexasUSA
- Department of BiophysicsUniversity of Texas Southwestern Medical CenterDallasTexasUSA
- Harold C. Simmons Comprehensive Cancer CenterUniversity of Texas Southwestern Medical CenterDallasTexasUSA
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24
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Byerly CD, Patterson LL, Pittner NA, Solomon RN, Patel JG, Rogan MR, McBride JW. Ehrlichia Wnt SLiM ligand mimic deactivates the Hippo pathway to engage the anti-apoptotic Yap-GLUT1-BCL-xL axis. Infect Immun 2023; 91:e0008523. [PMID: 37530530 PMCID: PMC10501218 DOI: 10.1128/iai.00085-23] [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: 03/02/2023] [Accepted: 06/03/2023] [Indexed: 08/03/2023] Open
Abstract
Ehrlichia chaffeensis TRP120 effector has evolved short linear motif (SLiM) ligand mimicry to repurpose multiple evolutionarily conserved cellular signaling pathways, including Wnt, Notch, and Hedgehog. In this investigation, we demonstrate that E. chaffeensis and recombinant TRP120 deactivate Hippo signaling, resulting in the activation of Hippo transcription coactivator Yes-associated protein (Yap). Moreover, a homologous 6 amino acid (QDVASH) SLiM shared by TRP120 and Wnt3a/5a ligands phenocopied Yap and β-catenin activation induced by E. chaffeensis, rTRP120, and Wnt5a. Similar Hippo gene expression profiles were also stimulated by E. chaffeensis, rTRP120, SLiM, and Wnt5a. Single siRNA knockdown of Hippo transcription co-activator/factors, Yap, and transcriptional enhanced associate domain (TEAD) significantly decreased E. chaffeensis infection. Yap activation was abolished in THP-1 Wnt Frizzled-5 (Fzd5) receptor knockout cells (KO), demonstrating Fzd5 receptor dependence. In addition, the TRP120-Wnt-SLiM antibody blocked Hippo deactivation (Yap activation). Expression of anti-apoptotic Hippo target gene SLC2A1 (encodes glucose transporter 1; GLUT1) was upregulated by E. chaffeensis and corresponded to increased levels of GLUT1. Conversely, siRNA knockdown of SLC2A1 significantly inhibited infection. Higher GLUT1 levels correlated with increased B cell lymphoma-extra large (BCL-xL) and decreased BCL2-associated X, apoptosis regulator (Bax) levels. Moreover, blocking Yap activation with the inhibitor Verteporfin induced apoptosis that corresponded to significant reductions in GLUT1 and BCL-xL levels and activation of Bax and Caspase-3 and -9. This study identifies a novel shared Wnt/Hippo SLiM ligand mimic and demonstrates that E. chaffeensis deactivates the Hippo pathway to engage the anti-apoptotic Yap-GLUT1-BCL-xL axis.
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Affiliation(s)
- Caitlan D. Byerly
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, USA
| | - LaNisha L. Patterson
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Nicholas A. Pittner
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Regina N. Solomon
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Jignesh G. Patel
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Madison R. Rogan
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Jere W. McBride
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, Texas, USA
- Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, Texas, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, Texas, USA
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25
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Jacobsen NL, Bloch M, Millard PS, Ruidiaz SF, Elsborg JD, Boomsma W, Hendus‐Altenburger R, Hartmann‐Petersen R, Kragelund BB. Phosphorylation of Schizosaccharomyces pombe Dss1 mediates direct binding to the ubiquitin-ligase Dma1 in vitro. Protein Sci 2023; 32:e4733. [PMID: 37463013 PMCID: PMC10443397 DOI: 10.1002/pro.4733] [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: 03/28/2023] [Revised: 07/12/2023] [Accepted: 07/14/2023] [Indexed: 08/25/2023]
Abstract
Intrinsically disordered proteins (IDPs) are often multifunctional and frequently posttranslationally modified. Deleted in split hand/split foot 1 (Dss1-Sem1 in budding yeast) is a highly multifunctional IDP associated with a range of protein complexes. However, it remains unknown if the different functions relate to different modified states. In this work, we show that Schizosaccharomyces pombe Dss1 is a substrate for casein kinase 2 in vitro, and we identify three phosphorylated threonines in its linker region separating two known disordered ubiquitin-binding motifs. Phosphorylations of the threonines had no effect on ubiquitin-binding but caused a slight destabilization of the C-terminal α-helix and mediated a direct interaction with the forkhead-associated (FHA) domain of the RING-FHA E3-ubiquitin ligase defective in mitosis 1 (Dma1). The phosphorylation sites are not conserved and are absent in human Dss1. Sequence analyses revealed that the Txx(E/D) motif, which is important for phosphorylation and Dma1 binding, is not linked to certain branches of the evolutionary tree. Instead, we find that the motif appears randomly, supporting the mechanism of ex nihilo evolution of novel motifs. In support of this, other threonine-based motifs, although frequent, are nonconserved in the linker, pointing to additional functions connected to this region. We suggest that Dss1 acts as an adaptor protein that docks to Dma1 via the phosphorylated FHA-binding motifs, while the C-terminal α-helix is free to bind mitotic septins, thereby stabilizing the complex. The presence of Txx(D/E) motifs in the disordered regions of certain septin subunits may be of further relevance to the formation and stabilization of these complexes.
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Affiliation(s)
- Nina L. Jacobsen
- Structural Biology and NMR LaboratoryUniversity of CopenhagenCopenhagen NDenmark
- REPINUniversity of CopenhagenCopenhagen NDenmark
- The Linderstrøm Lang Centre for Protein Science, Department of BiologyUniversity of CopenhagenCopenhagen NDenmark
| | - Magnus Bloch
- Structural Biology and NMR LaboratoryUniversity of CopenhagenCopenhagen NDenmark
| | - Peter S. Millard
- REPINUniversity of CopenhagenCopenhagen NDenmark
- The Linderstrøm Lang Centre for Protein Science, Department of BiologyUniversity of CopenhagenCopenhagen NDenmark
| | - Sarah F. Ruidiaz
- Structural Biology and NMR LaboratoryUniversity of CopenhagenCopenhagen NDenmark
- REPINUniversity of CopenhagenCopenhagen NDenmark
| | - Jonas D. Elsborg
- Structural Biology and NMR LaboratoryUniversity of CopenhagenCopenhagen NDenmark
| | - Wouter Boomsma
- Department of Computer ScienceUniversity of CopenhagenCopenhagen ØDenmark
| | | | - Rasmus Hartmann‐Petersen
- REPINUniversity of CopenhagenCopenhagen NDenmark
- The Linderstrøm Lang Centre for Protein Science, Department of BiologyUniversity of CopenhagenCopenhagen NDenmark
| | - Birthe B. Kragelund
- Structural Biology and NMR LaboratoryUniversity of CopenhagenCopenhagen NDenmark
- REPINUniversity of CopenhagenCopenhagen NDenmark
- The Linderstrøm Lang Centre for Protein Science, Department of BiologyUniversity of CopenhagenCopenhagen NDenmark
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26
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Suskiewicz MJ, Munnur D, Strømland Ø, Yang JC, Easton L, Chatrin C, Zhu K, Baretić D, Goffinont S, Schuller M, Wu WF, Elkins J, Ahel D, Sanyal S, Neuhaus D, Ahel I. Updated protein domain annotation of the PARP protein family sheds new light on biological function. Nucleic Acids Res 2023; 51:8217-8236. [PMID: 37326024 PMCID: PMC10450202 DOI: 10.1093/nar/gkad514] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 05/09/2023] [Accepted: 06/03/2023] [Indexed: 06/17/2023] Open
Abstract
AlphaFold2 and related computational tools have greatly aided studies of structural biology through their ability to accurately predict protein structures. In the present work, we explored AF2 structural models of the 17 canonical members of the human PARP protein family and supplemented this analysis with new experiments and an overview of recent published data. PARP proteins are typically involved in the modification of proteins and nucleic acids through mono or poly(ADP-ribosyl)ation, but this function can be modulated by the presence of various auxiliary protein domains. Our analysis provides a comprehensive view of the structured domains and long intrinsically disordered regions within human PARPs, offering a revised basis for understanding the function of these proteins. Among other functional insights, the study provides a model of PARP1 domain dynamics in the DNA-free and DNA-bound states and enhances the connection between ADP-ribosylation and RNA biology and between ADP-ribosylation and ubiquitin-like modifications by predicting putative RNA-binding domains and E2-related RWD domains in certain PARPs. In line with the bioinformatic analysis, we demonstrate for the first time PARP14's RNA-binding capability and RNA ADP-ribosylation activity in vitro. While our insights align with existing experimental data and are probably accurate, they need further validation through experiments.
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Affiliation(s)
| | - Deeksha Munnur
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Øyvind Strømland
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Ji-Chun Yang
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Laura E Easton
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Chatrin Chatrin
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Kang Zhu
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Domagoj Baretić
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | | | - Marion Schuller
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Wing-Fung Wu
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Jonathan M Elkins
- Centre for Medicines Discovery, University of Oxford, Oxford OX3 7DQ, UK
| | - Dragana Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Sumana Sanyal
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - David Neuhaus
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
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27
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Nguyen H, Kettenbach AN. Substrate and phosphorylation site selection by phosphoprotein phosphatases. Trends Biochem Sci 2023; 48:713-725. [PMID: 37173206 PMCID: PMC10523993 DOI: 10.1016/j.tibs.2023.04.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 04/11/2023] [Accepted: 04/13/2023] [Indexed: 05/15/2023]
Abstract
Dynamic protein phosphorylation and dephosphorylation are essential regulatory mechanisms that ensure proper cellular signaling and biological functions. Deregulation of either reaction has been implicated in several human diseases. Here, we focus on the mechanisms that govern the specificity of the dephosphorylation reaction. Most cellular serine/threonine dephosphorylation is catalyzed by 13 highly conserved phosphoprotein phosphatase (PPP) catalytic subunits, which form hundreds of holoenzymes by binding to regulatory and scaffolding subunits. PPP holoenzymes recognize phosphorylation site consensus motifs and interact with short linear motifs (SLiMs) or structural elements distal to the phosphorylation site. We review recent advances in understanding the mechanisms of PPP site-specific dephosphorylation preference and substrate recruitment and highlight examples of their interplay in the regulation of cell division.
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Affiliation(s)
- Hieu Nguyen
- Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth College, Hanover, NH 03755, USA
| | - Arminja N Kettenbach
- Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth College, Hanover, NH 03755, USA; Dartmouth Cancer Center, Lebanon, NH 03756, USA.
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28
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Heidari B, Nemie-Feyissa D, Lillo C. Distinct Clades of Protein Phosphatase 2A Regulatory B'/B56 Subunits Engage in Different Physiological Processes. Int J Mol Sci 2023; 24:12255. [PMID: 37569631 PMCID: PMC10418862 DOI: 10.3390/ijms241512255] [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: 06/30/2023] [Revised: 07/27/2023] [Accepted: 07/28/2023] [Indexed: 08/13/2023] Open
Abstract
Protein phosphatase 2A (PP2A) is a strongly conserved and major protein phosphatase in all eukaryotes. The canonical PP2A complex consists of a catalytic (C), scaffolding (A), and regulatory (B) subunit. Plants have three groups of evolutionary distinct B subunits: B55, B' (B56), and B''. Here, the Arabidopsis B' group is reviewed and compared with other eukaryotes. Members of the B'α/B'β clade are especially important for chromatid cohesion, and dephosphorylation of transcription factors that mediate brassinosteroid (BR) signaling in the nucleus. Other B' subunits interact with proteins at the cell membrane to dampen BR signaling or harness immune responses. The transition from vegetative to reproductive phase is influenced differentially by distinct B' subunits; B'α and B'β being of little importance, whereas others (B'γ, B'ζ, B'η, B'θ, B'κ) promote transition to flowering. Interestingly, the latter B' subunits have three motifs in a conserved manner, i.e., two docking sites for protein phosphatase 1 (PP1), and a POLO consensus phosphorylation site between these motifs. This supports the view that a conserved PP1-PP2A dephosphorelay is important in a variety of signaling contexts throughout eukaryotes. A profound understanding of these regulators may help in designing future crops and understand environmental issues.
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Affiliation(s)
| | | | - Cathrine Lillo
- IKBM, Department of Chemistry, Bioscience and Environmental Engineering, University of Stavanger, 4036 Stavanger, Norway; (B.H.); (D.N.-F.)
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29
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Gunnarsson PA, Babu MM. Predicting evolutionary outcomes through the probability of accessing sequence variants. SCIENCE ADVANCES 2023; 9:eade2903. [PMID: 37506212 PMCID: PMC10381947 DOI: 10.1126/sciadv.ade2903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 06/27/2023] [Indexed: 07/30/2023]
Abstract
Natural selection can only operate on available genetic variation. Thus, determining the probability of accessing different sequence variants from a starting sequence can help predict evolutionary trajectories and outcomes. We define the concept of "variant accessibility" as the probability that a set of genotypes encoding a particular protein function will arise through mutations before subject to natural selection. This probability is shaped by the mutational biases of nucleotides and the structure of the genetic code. Using the influenza A virus as a model, we discuss how a more accessible but less fit variant can emerge as an adaptation rather than a more fit variant. We describe a genotype-accessibility landscape, complementary to the genotype-fitness landscape, that informs the likelihood of a starting sequence reaching different parts of genotype space. The proposed framework lays the foundation for predicting the emergence of adaptive genotypes in evolving systems such as viruses and tumors.
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Affiliation(s)
- P. Alexander Gunnarsson
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
- Department of Structural Biology and Center of Excellence for Data-Driven Discovery, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - M. Madan Babu
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
- Department of Structural Biology and Center of Excellence for Data-Driven Discovery, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
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30
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He S, Valkov E, Cheloufi S, Murn J. The nexus between RNA-binding proteins and their effectors. Nat Rev Genet 2023; 24:276-294. [PMID: 36418462 DOI: 10.1038/s41576-022-00550-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/24/2022] [Indexed: 11/25/2022]
Abstract
RNA-binding proteins (RBPs) regulate essentially every event in the lifetime of an RNA molecule, from its production to its destruction. Whereas much has been learned about RNA sequence specificity and general functions of individual RBPs, the ways in which numerous RBPs instruct a much smaller number of effector molecules, that is, the core engines of RNA processing, as to where, when and how to act remain largely speculative. Here, we survey the known modes of communication between RBPs and their effectors with a particular focus on converging RBP-effector interactions and their roles in reducing the complexity of RNA networks. We discern the emerging unifying principles and discuss their utility in our understanding of RBP function, regulation of biological processes and contribution to human disease.
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Affiliation(s)
- Shiyang He
- Department of Biochemistry, University of California, Riverside, CA, USA
- Center for RNA Biology and Medicine, Riverside, CA, USA
| | - Eugene Valkov
- RNA Biology Laboratory & Center for Structural Biology, Center for Cancer Research, National Cancer Institute (NCI), Frederick, MD, USA
| | - Sihem Cheloufi
- Department of Biochemistry, University of California, Riverside, CA, USA.
- Center for RNA Biology and Medicine, Riverside, CA, USA.
- Stem Cell Center, University of California, Riverside, CA, USA.
| | - Jernej Murn
- Department of Biochemistry, University of California, Riverside, CA, USA.
- Center for RNA Biology and Medicine, Riverside, CA, USA.
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31
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Simonetti L, Nilsson J, McInerney G, Ivarsson Y, Davey NE. SLiM-binding pockets: an attractive target for broad-spectrum antivirals. Trends Biochem Sci 2023; 48:420-427. [PMID: 36623987 DOI: 10.1016/j.tibs.2022.12.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 12/09/2022] [Accepted: 12/15/2022] [Indexed: 01/08/2023]
Abstract
Short linear motif (SLiM)-mediated interactions offer a unique strategy for viral intervention due to their compact interfaces, ease of convergent evolution, and key functional roles. Consequently, many viruses extensively mimic host SLiMs to hijack or deregulate cellular pathways and the same motif-binding pocket is often targeted by numerous unrelated viruses. A toolkit of therapeutics targeting commonly mimicked SLiMs could provide prophylactic and therapeutic broad-spectrum antivirals and vastly improve our ability to treat ongoing and future viral outbreaks. In this opinion article, we discuss the therapeutic relevance of SLiMs, advocating their suitability as targets for broad-spectrum antiviral inhibitors.
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Affiliation(s)
| | - Jakob Nilsson
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Faculty of Health and Medical Sciences, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Gerald McInerney
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Ylva Ivarsson
- Department of Chemistry - BMC, Husargatan 3, 751 23 Uppsala, Sweden
| | - Norman E Davey
- Division of Cancer Biology, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK.
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32
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Wu CG, Balakrishnan VK, Parihar PS, Konovolov K, Chen YC, Merrill RA, Wei H, Carragher B, Sundaresan R, Cui Q, Wadzinski BE, Swingle MR, Musiyenko A, Honkanen R, Chung WK, Suzuki A, Strack S, Huang X, Xing Y. Extended regulation interface coupled to the allosteric network and disease mutations in the PP2A-B56δ holoenzyme. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.09.530109. [PMID: 37066309 PMCID: PMC10103954 DOI: 10.1101/2023.03.09.530109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
An increasing number of mutations associated with devastating human diseases are diagnosed by whole-genome/exon sequencing. Recurrent de novo missense mutations have been discovered in B56δ (encoded by PPP2R5D), a regulatory subunit of protein phosphatase 2A (PP2A), that cause intellectual disabilities (ID), macrocephaly, Parkinsonism, and a broad range of neurological symptoms. Single-particle cryo-EM structures show that the PP2A-B56δ holoenzyme possesses closed latent and open active forms. In the closed form, the long, disordered arms of B56δ termini fold against each other and the holoenzyme core, establishing dual autoinhibition of the phosphatase active site and the substrate-binding protein groove. The resulting interface spans over 190 Å and harbors unfavorable contacts, activation phosphorylation sites, and nearly all residues with ID-associated mutations. Our studies suggest that this dynamic interface is close to an allosteric network responsive to activation phosphorylation and altered globally by mutations. Furthermore, we found that ID mutations perturb the activation phosphorylation rates, and the severe variants significantly increase the mitotic duration and error rates compared to the wild variant.
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Affiliation(s)
- Cheng-Guo Wu
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin at Madison, School of Medicine and Public Health, Madison, Wisconsin 53705, USA
- Biophysics program, University of Wisconsin at Madison, Wisconsin 53706, USA
| | - Vijaya K. Balakrishnan
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin at Madison, School of Medicine and Public Health, Madison, Wisconsin 53705, USA
| | - Pankaj S. Parihar
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin at Madison, School of Medicine and Public Health, Madison, Wisconsin 53705, USA
| | - Kirill Konovolov
- Chemistry Department, University of Wisconsin at Madison, Wisconsin 53706, USA
| | - Yu-Chia Chen
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin at Madison, School of Medicine and Public Health, Madison, Wisconsin 53705, USA
- Molecular and Cellular Pharmacology program, University of Wisconsin at Madison, Wisconsin 53706, USA
| | - Ronald A Merrill
- Department of Neuroscience and Pharmacology, University of Iowa, Iowa City, IA 52242, USA
| | - Hui Wei
- New York Structural biology Center, New York, NY 10027, USA
| | | | - Ramya Sundaresan
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin at Madison, School of Medicine and Public Health, Madison, Wisconsin 53705, USA
| | - Qiang Cui
- Department of Chemistry, Metcalf Center for Science & Engineering, Boston University, Boston, MA 02215, USA
| | - Brian E. Wadzinski
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA
| | - Mark R. Swingle
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Alla Musiyenko
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Richard Honkanen
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Wendy K. Chung
- Departments of Pediatrics and Medicine, Columbia University, New York, NY 10032, USA
| | - Aussie Suzuki
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin at Madison, School of Medicine and Public Health, Madison, Wisconsin 53705, USA
- Biophysics program, University of Wisconsin at Madison, Wisconsin 53706, USA
- Department of Neuroscience and Pharmacology, University of Iowa, Iowa City, IA 52242, USA
| | - Stefan Strack
- Department of Neuroscience and Pharmacology, University of Iowa, Iowa City, IA 52242, USA
| | - Xuhui Huang
- Biophysics program, University of Wisconsin at Madison, Wisconsin 53706, USA
- Chemistry Department, University of Wisconsin at Madison, Wisconsin 53706, USA
| | - Yongna Xing
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin at Madison, School of Medicine and Public Health, Madison, Wisconsin 53705, USA
- Biophysics program, University of Wisconsin at Madison, Wisconsin 53706, USA
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33
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Byerly CD, Patterson LL, Pittner NA, Solomon RN, Patel JG, Rogan MR, McBride JW. Ehrlichia Wnt short linear motif ligand mimetic deactivates the Hippo pathway to engage the anti-apoptotic Yap-GLUT1-BCL-xL axis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.06.531456. [PMID: 36945589 PMCID: PMC10028901 DOI: 10.1101/2023.03.06.531456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Abstract
Ehrlichia chaffeensis TRP120 effector has evolved short linear motif (SLiM) ligand mimicry to repurpose multiple evolutionarily conserved cellular signaling pathways including Wnt, Notch and Hedgehog. In this investigation, we demonstrate that E. chaffeensis and recombinant TRP120 deactivate Hippo signaling resulting in activation of Hippo transcription coactivator Yap and target gene expression. Moreover, a homologous 6 amino acid (QDVASH) SLiM shared by TRP120 and Wnt3a/5a ligands phenocopied Yap and β-catenin activation induced by E. chaffeensis, rTRP120 and Wnt5a. Similar Hippo gene expression profiles were also stimulated by E. chaffeensis, rTRP120, SLiM and Wnt5a. Single siRNA knockdown of Hippo transcription co-activator/factors (Yap and TEAD) significantly decreased E. chaffeensis infection. Yap activation was abolished in THP-1 Wnt Frizzled-5 (Fzd5) receptor knockout cells (KO), demonstrating Fzd5 receptor dependence. In addition, TRP120 Wnt-SLiM antibody blocked Hippo deactivation (Yap activation). Expression of anti-apoptotic Hippo target gene SLC2A1 (encodes glucose transporter 1; GLUT1) was upregulated by E. chaffeensis and corresponded to increased levels of GLUT1. Conversely, siRNA knockdown of SLC2A1 significantly inhibited infection. Higher GLUT1 levels correlated with increased BCL-xL and decreased Bax levels. Moreover, blocking Yap activation with the inhibitor Verteporfin induced apoptosis that corresponded to significant reductions in levels of GLUT1 and BCL-xL, and activation of Bax and Caspase-3 and -9. This study identifies a novel shared Wnt/Hippo SLiM ligand mimetic and demonstrates that E. chaffeensis deactivates the Hippo pathway to engage the anti-apoptotic Yap-GLUT1-BCL-xL axis.
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Affiliation(s)
- Caitlan D. Byerly
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, USA
| | - LaNisha L. Patterson
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Nicholas A. Pittner
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Regina N. Solomon
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Jignesh G. Patel
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Madison R. Rogan
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Jere W. McBride
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, USA
- Department Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, Texas, USA
- Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, Texas, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, Texas, USA
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Evolutionary Conserved Short Linear Motifs Provide Insights into the Cellular Response to Stress. Antioxidants (Basel) 2022; 12:antiox12010096. [PMID: 36670957 PMCID: PMC9854524 DOI: 10.3390/antiox12010096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 11/22/2022] [Accepted: 12/22/2022] [Indexed: 01/03/2023] Open
Abstract
Short linear motifs (SLiMs) are evolutionarily conserved functional modules of proteins composed of 3 to 10 residues and involved in multiple cellular functions. Here, we performed a search for SLiMs that exert sequence similarity to two segments of alpha-fetoprotein (AFP), a major mammalian embryonic and cancer-associated protein. Biological activities of the peptides, LDSYQCT (AFP14-20) and EMTPVNPGV (GIP-9), have been previously confirmed under in vitro and in vivo conditions. In our study, we retrieved a vast array of proteins that contain SLiMs of interest from both prokaryotic and eukaryotic species, including viruses, bacteria, archaea, invertebrates, and vertebrates. Comprehensive Gene Ontology enrichment analysis showed that proteins from multiple functional classes, including enzymes, transcription factors, as well as those involved in signaling, cell cycle, and quality control, and ribosomal proteins were implicated in cellular adaptation to environmental stress conditions. These include response to oxidative and metabolic stress, hypoxia, DNA and RNA damage, protein degradation, as well as antimicrobial, antiviral, and immune response. Thus, our data enabled insights into the common functions of SLiMs evolutionary conserved across all taxonomic categories. These SLiMs can serve as important players in cellular adaptation to stress, which is crucial for cell functioning.
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Evolution of SLiM-mediated hijack functions in intrinsically disordered viral proteins. Essays Biochem 2022; 66:945-958. [DOI: 10.1042/ebc20220059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 12/07/2022]
Abstract
Abstract
Viruses and their hosts are involved in an ‘arms race’ where they continually evolve mechanisms to overcome each other. It has long been proposed that intrinsic disorder provides a substrate for the evolution of viral hijack functions and that short linear motifs (SLiMs) are important players in this process. Here, we review evidence in support of this tenet from two model systems: the papillomavirus E7 protein and the adenovirus E1A protein. Phylogenetic reconstructions reveal that SLiMs appear and disappear multiple times across evolution, providing evidence of convergent evolution within individual viral phylogenies. Multiple functionally related SLiMs show strong coevolution signals that persist across long distances in the primary sequence and occur in unrelated viral proteins. Moreover, changes in SLiMs are associated with changes in phenotypic traits such as host range and tropism. Tracking viral evolutionary events reveals that host switch events are associated with the loss of several SLiMs, suggesting that SLiMs are under functional selection and that changes in SLiMs support viral adaptation. Fine-tuning of viral SLiM sequences can improve affinity, allowing them to outcompete host counterparts. However, viral SLiMs are not always competitive by themselves, and tethering of two suboptimal SLiMs by a disordered linker may instead enable viral hijack. Coevolution between the SLiMs and the linker indicates that the evolution of disordered regions may be more constrained than previously thought. In summary, experimental and computational studies support a role for SLiMs and intrinsic disorder in viral hijack functions and in viral adaptive evolution.
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Sowa ST, Bosetti C, Galera-Prat A, Johnson MS, Lehtiö L. An Evolutionary Perspective on the Origin, Conservation and Binding Partner Acquisition of Tankyrases. Biomolecules 2022; 12:1688. [PMID: 36421702 PMCID: PMC9688111 DOI: 10.3390/biom12111688] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 11/08/2022] [Accepted: 11/08/2022] [Indexed: 01/04/2024] Open
Abstract
Tankyrases are poly-ADP-ribosyltransferases that regulate many crucial and diverse cellular processes in humans such as Wnt signaling, telomere homeostasis, mitotic spindle formation and glucose metabolism. While tankyrases are present in most animals, functional differences across species may exist. In this work, we confirm the widespread distribution of tankyrases throughout the branches of multicellular animal life and identify the single-celled choanoflagellates as earliest origin of tankyrases. We further show that the sequences and structural aspects of TNKSs are well-conserved even between distantly related species. We also experimentally characterized an anciently diverged tankyrase homolog from the sponge Amphimedon queenslandica and show that the basic functional aspects, such as poly-ADP-ribosylation activity and interaction with the canonical tankyrase binding peptide motif, are conserved. Conversely, the presence of tankyrase binding motifs in orthologs of confirmed interaction partners varies greatly between species, indicating that tankyrases may have different sets of interaction partners depending on the animal lineage. Overall, our analysis suggests a remarkable degree of conservation for tankyrases, and that their regulatory functions in cells have likely changed considerably throughout evolution.
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Affiliation(s)
- Sven T. Sowa
- Faculty for Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, 90220 Oulu, Finland
| | - Chiara Bosetti
- Faculty for Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, 90220 Oulu, Finland
| | - Albert Galera-Prat
- Faculty for Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, 90220 Oulu, Finland
| | - Mark S. Johnson
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering and InFLAMES Research Flagship Center, Åbo Akademi University, 20520 Turku, Finland
| | - Lari Lehtiö
- Faculty for Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, 90220 Oulu, Finland
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Halpin JC, Whitney D, Rigoldi F, Sivaraman V, Singer A, Keating AE. Molecular determinants of TRAF6 binding specificity suggest that native interaction partners are not optimized for affinity. Protein Sci 2022; 31:e4429. [PMID: 36305766 PMCID: PMC9597381 DOI: 10.1002/pro.4429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 08/14/2022] [Accepted: 08/19/2022] [Indexed: 11/25/2022]
Abstract
TRAF6 is an adaptor protein involved in signaling pathways that are essential for development and the immune system. It participates in many protein-protein interactions, some of which are mediated by the C-terminal MATH domain, which binds to short peptide segments containing the motif PxExx[FYWHDE], where x is any amino acid. Blocking MATH domain interactions is associated with favorable effects in various disease models. To better define TRAF6 MATH domain binding preferences, we screened a combinatorial library using bacterial cell-surface peptide display. We identified 236 of the best TRAF6-interacting peptides and a set of 1,200 peptides that match the sequence PxE but do not bind TRAF6 MATH. The peptides that were most enriched in the screen bound TRAF6 tighter than previously measured native peptides. To better understand the structural basis for TRAF6 interaction preferences, we built all-atom structural models of the MATH domain in complex with high-affinity binders and nonbinders identified in the screen. We identified favorable interactions for motif features in binders as well as negative design elements distributed across the motif that can disfavor or preclude binding. Searching the human proteome revealed that the most biologically relevant TRAF6 motif matches occupy a different sequence space from the best hits discovered in combinatorial library screening, suggesting that native interactions are not optimized for affinity. Our experimentally determined binding preferences and structural models support the design of peptide-based interaction inhibitors with higher affinities than endogenous TRAF6 ligands.
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Affiliation(s)
| | | | | | | | | | - Amy E. Keating
- MIT Department of BiologyCambridgeMassachusettsUSA
- MIT Department of Biological EngineeringCambridgeMassachusettsUSA
- Koch Institute for Integrative Cancer ResearchCambridgeMassachusettsUSA
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Meszaros A, Ahmed J, Russo G, Tompa P, Lazar T. The evolution and polymorphism of mono-amino acid repeats in androgen receptor and their regulatory role in health and disease. Front Med (Lausanne) 2022; 9:1019803. [PMID: 36388907 PMCID: PMC9642029 DOI: 10.3389/fmed.2022.1019803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 09/30/2022] [Indexed: 12/24/2022] Open
Abstract
Androgen receptor (AR) is a key member of nuclear hormone receptors with the longest intrinsically disordered N-terminal domain (NTD) in its protein family. There are four mono-amino acid repeats (polyQ1, polyQ2, polyG, and polyP) located within its NTD, of which two are polymorphic (polyQ1 and polyG). The length of both polymorphic repeats shows clinically important correlations with disease, especially with cancer and neurodegenerative diseases, as shorter and longer alleles exhibit significant differences in expression, activity and solubility. Importantly, AR has also been shown to undergo condensation in the nucleus by liquid-liquid phase separation, a process highly sensitive to protein solubility and concentration. Nonetheless, in prostate cancer cells, AR variants also partition into transcriptional condensates, which have been shown to alter the expression of target gene products. In this review, we summarize current knowledge on the link between AR repeat polymorphisms and cancer types, including mechanistic explanations and models comprising the relationship between condensate formation, polyQ1 length and transcriptional activity. Moreover, we outline the evolutionary paths of these recently evolved amino acid repeats across mammalian species, and discuss new research directions with potential breakthroughs and controversies in the literature.
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Affiliation(s)
- Attila Meszaros
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie (VIB), Brussels, Belgium
- Structural Biology Brussels (SBB), Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Junaid Ahmed
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie (VIB), Brussels, Belgium
- Structural Biology Brussels (SBB), Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Giorgio Russo
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie (VIB), Brussels, Belgium
- Structural Biology Brussels (SBB), Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Peter Tompa
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie (VIB), Brussels, Belgium
- Structural Biology Brussels (SBB), Vrije Universiteit Brussel (VUB), Brussels, Belgium
- Research Centre for Natural Sciences (RCNS), ELKH, Budapest, Hungary
| | - Tamas Lazar
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie (VIB), Brussels, Belgium
- Structural Biology Brussels (SBB), Vrije Universiteit Brussel (VUB), Brussels, Belgium
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39
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Kastano K, Mier P, Dosztányi Z, Promponas VJ, Andrade-Navarro MA. Functional Tuning of Intrinsically Disordered Regions in Human Proteins by Composition Bias. Biomolecules 2022; 12:biom12101486. [PMID: 36291695 PMCID: PMC9599065 DOI: 10.3390/biom12101486] [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: 08/19/2022] [Revised: 09/30/2022] [Accepted: 10/11/2022] [Indexed: 11/16/2022] Open
Abstract
Intrinsically disordered regions (IDRs) in protein sequences are flexible, have low structural constraints and as a result have faster rates of evolution. This lack of evolutionary conservation greatly limits the use of sequence homology for the classification and functional assessment of IDRs, as opposed to globular domains. The study of IDRs requires other properties for their classification and functional prediction. While composition bias is not a necessary property of IDRs, compositionally biased regions (CBRs) have been noted as frequent part of IDRs. We hypothesized that to characterize IDRs, it could be helpful to study their overlap with particular types of CBRs. Here, we evaluate this overlap in the human proteome. A total of 2/3 of residues in IDRs overlap CBRs. Considering CBRs enriched in one type of amino acid, we can distinguish CBRs that tend to be fully included within long IDRs (R, H, N, D, P, G), from those that partially overlap shorter IDRs (S, E, K, T), and others that tend to overlap IDR terminals (Q, A). CBRs overlap more often IDRs in nuclear proteins and in proteins involved in liquid-liquid phase separation (LLPS). Study of protein interaction networks reveals the enrichment of CBRs in IDRs by tandem repetition of short linear motifs (rich in S or P), and the existence of E-rich polar regions that could support specific protein interactions with non-specific interactions. Our results open ways to pin down the function of IDRs from their partial compositional biases.
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Affiliation(s)
- Kristina Kastano
- Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University, Biozentrum I, Hans-Dieter-Hüsch-Weg 15, 55128 Mainz, Germany
| | - Pablo Mier
- Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University, Biozentrum I, Hans-Dieter-Hüsch-Weg 15, 55128 Mainz, Germany
| | - Zsuzsanna Dosztányi
- Department of Biochemistry, ELTE Eötvös Loránd University, Pázmány Péter stny 1/c, H-1117 Budapest, Hungary
| | - Vasilis J. Promponas
- Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus, 1678 Nicosia, Cyprus
| | - Miguel A. Andrade-Navarro
- Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University, Biozentrum I, Hans-Dieter-Hüsch-Weg 15, 55128 Mainz, Germany
- Correspondence:
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40
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Calvi I, Schwager F, Gotta M. PP1 phosphatases control PAR-2 localization and polarity establishment in C. elegans embryos. J Cell Biol 2022; 221:213453. [PMID: 36083688 PMCID: PMC9467853 DOI: 10.1083/jcb.202201048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 06/28/2022] [Accepted: 08/08/2022] [Indexed: 01/12/2023] Open
Abstract
Cell polarity relies on the asymmetric distribution of the conserved PAR proteins, which is regulated by phosphorylation/dephosphorylation reactions. While the kinases involved have been well studied, the role of phosphatases remains poorly understood. In Caenorhabditis elegans zygotes, phosphorylation of the posterior PAR-2 protein by the atypical protein kinase PKC-3 inhibits PAR-2 cortical localization. Polarity establishment depends on loading of PAR-2 at the posterior cortex. We show that the PP1 phosphatases GSP-1 and GSP-2 are required for polarity establishment in embryos. We find that codepletion of GSP-1 and GSP-2 abrogates the cortical localization of PAR-2 and that GSP-1 and GSP-2 interact with PAR-2 via a PP1 docking motif in PAR-2. Mutating this motif in vivo, to prevent binding of PAR-2 to PP1, abolishes cortical localization of PAR-2, while optimizing this motif extends PAR-2 cortical localization. Our data suggest a model in which GSP-1/-2 counteracts PKC-3 phosphorylation of PAR-2, allowing its cortical localization at the posterior and polarization of the one-cell embryo.
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Affiliation(s)
- Ida Calvi
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Françoise Schwager
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Monica Gotta
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland
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41
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Handa T, Kundu D, Dubey VK. Perspectives on evolutionary and functional importance of intrinsically disordered proteins. Int J Biol Macromol 2022; 224:243-255. [DOI: 10.1016/j.ijbiomac.2022.10.120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 10/08/2022] [Accepted: 10/10/2022] [Indexed: 11/05/2022]
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42
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Ripamonti M, Lamarca A, Davey NE, Tonoli D, Surini S, de Curtis I. A functional interaction between liprin-α1 and B56γ regulatory subunit of protein phosphatase 2A supports tumor cell motility. Commun Biol 2022; 5:1025. [PMID: 36171301 PMCID: PMC9519923 DOI: 10.1038/s42003-022-03989-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 09/13/2022] [Indexed: 11/25/2022] Open
Abstract
Scaffold liprin-α1 is required to assemble dynamic plasma membrane-associated platforms (PMAPs) at the front of migrating breast cancer cells, to promote protrusion and invasion. We show that the N-terminal region of liprin-α1 contains an LxxIxE motif interacting with B56 regulatory subunits of serine/threonine protein phosphatase 2A (PP2A). The specific interaction of B56γ with liprin-α1 requires an intact motif, since two point mutations strongly reduce the interaction. B56γ mediates the interaction of liprin-α1 with the heterotrimeric PP2A holoenzyme. Most B56γ protein is recovered in the cytosolic fraction of invasive MDA-MB-231 breast cancer cells, where B56γ is complexed with liprin-α1. While mutation of the short linear motif (SLiM) does not affect localization of liprin-α1 to PMAPs, localization of B56γ at these sites specifically requires liprin-α1. Silencing of B56γ or liprin-α1 inhibits to similar extent cell spreading on extracellular matrix, invasion, motility and lamellipodia dynamics in migrating MDA-MB-231 cells, suggesting that B56γ/PP2A is a novel component of the PMAPs machinery regulating tumor cell motility. In this direction, inhibition of cell spreading by silencing liprin-α1 is not rescued by expression of B56γ binding-defective liprin-α1 mutant. We propose that liprin-α1-mediated recruitment of PP2A via B56γ regulates cell motility by controlling protrusion in migrating MDA-MB-231 cells.
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Affiliation(s)
- Marta Ripamonti
- San Raffaele Scientific Institute and Università Vita-Salute San Raffaele, Milano, Italy
| | - Andrea Lamarca
- San Raffaele Scientific Institute and Università Vita-Salute San Raffaele, Milano, Italy
| | - Norman E Davey
- Division of Cancer Biology, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
| | - Diletta Tonoli
- San Raffaele Scientific Institute and Università Vita-Salute San Raffaele, Milano, Italy
| | - Sara Surini
- San Raffaele Scientific Institute and Università Vita-Salute San Raffaele, Milano, Italy
| | - Ivan de Curtis
- San Raffaele Scientific Institute and Università Vita-Salute San Raffaele, Milano, Italy.
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43
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Putta S, Alvarez L, Lüdtke S, Sehr P, Müller GA, Fernandez SM, Tripathi S, Lewis J, Gibson TJ, Chemes LB, Rubin SM. Structural basis for tunable affinity and specificity of LxCxE-dependent protein interactions with the retinoblastoma protein family. Structure 2022; 30:1340-1353.e3. [PMID: 35716663 PMCID: PMC9444907 DOI: 10.1016/j.str.2022.05.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 04/25/2022] [Accepted: 05/25/2022] [Indexed: 11/25/2022]
Abstract
The retinoblastoma protein (Rb) and its homologs p107 and p130 are critical regulators of gene expression during the cell cycle and are commonly inactivated in cancer. Rb proteins use their "pocket domain" to bind an LxCxE sequence motif in other proteins, many of which function with Rb proteins to co-regulate transcription. Here, we present binding data and crystal structures of the p107 pocket domain in complex with LxCxE peptides from the transcriptional co-repressor proteins HDAC1, ARID4A, and EID1. Our results explain why Rb and p107 have weaker affinity for cellular LxCxE proteins compared with the E7 protein from human papillomavirus, which has been used as the primary model for understanding LxCxE motif interactions. Our structural and mutagenesis data also identify and explain differences in Rb and p107 affinities for some LxCxE-containing sequences. Our study provides new insights into how Rb proteins bind their cell partners with varying affinity and specificity.
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Affiliation(s)
- Sivasankar Putta
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | - Lucia Alvarez
- Instituto de Investigaciones Biotecnológicas (IIBiO-CONICET), Escuela de Bio y Nanotecnologías (EByN), Universidad Nacional de San Martín, Av. 25 de Mayo y Francia, Buenos Aires CP1650, Argentina
| | - Stephan Lüdtke
- Belyntic GmbH, Richard-Willstätter-Str. 11, 12489 Berlin, Germany
| | - Peter Sehr
- Chemical Biology Core Facility, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Gerd A Müller
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | - Samantha M Fernandez
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | - Sarvind Tripathi
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | - Joe Lewis
- Chemical Biology Core Facility, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Toby J Gibson
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Lucia B Chemes
- Instituto de Investigaciones Biotecnológicas (IIBiO-CONICET), Escuela de Bio y Nanotecnologías (EByN), Universidad Nacional de San Martín, Av. 25 de Mayo y Francia, Buenos Aires CP1650, Argentina.
| | - Seth M Rubin
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA.
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Dreier JE, Prestel A, Martins JM, Brøndum SS, Nielsen O, Garbers AE, Suga H, Boomsma W, Rogers JM, Hartmann-Petersen R, Kragelund BB. A context-dependent and disordered ubiquitin-binding motif. Cell Mol Life Sci 2022; 79:484. [PMID: 35974206 PMCID: PMC9381478 DOI: 10.1007/s00018-022-04486-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 07/06/2022] [Accepted: 07/14/2022] [Indexed: 02/07/2023]
Abstract
Ubiquitin is a small, globular protein that is conjugated to other proteins as a posttranslational event. A palette of small, folded domains recognizes and binds ubiquitin to translate and effectuate this posttranslational signal. Recent computational studies have suggested that protein regions can recognize ubiquitin via a process of folding upon binding. Using peptide binding arrays, bioinformatics, and NMR spectroscopy, we have uncovered a disordered ubiquitin-binding motif that likely remains disordered when bound and thus expands the palette of ubiquitin-binding proteins. We term this motif Disordered Ubiquitin-Binding Motif (DisUBM) and find it to be present in many proteins with known or predicted functions in degradation and transcription. We decompose the determinants of the motif showing it to rely on features of aromatic and negatively charged residues, and less so on distinct sequence positions in line with its disordered nature. We show that the affinity of the motif is low and moldable by the surrounding disordered chain, allowing for an enhanced interaction surface with ubiquitin, whereby the affinity increases ~ tenfold. Further affinity optimization using peptide arrays pushed the affinity into the low micromolar range, but compromised context dependence. Finally, we find that DisUBMs can emerge from unbiased screening of randomized peptide libraries, featuring in de novo cyclic peptides selected to bind ubiquitin chains. We suggest that naturally occurring DisUBMs can recognize ubiquitin as a posttranslational signal to act as affinity enhancers in IDPs that bind to folded and ubiquitylated binding partners.
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Affiliation(s)
- Jesper E Dreier
- Structural Biology and NMR Laboratory, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark.,REPIN, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
| | - Andreas Prestel
- Structural Biology and NMR Laboratory, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
| | - João M Martins
- Department of Computer Science, University of Copenhagen, Universitetsparken 1, 2100, Copenhagen Ø, Denmark
| | - Sebastian S Brøndum
- Structural Biology and NMR Laboratory, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
| | - Olaf Nielsen
- Functional Genomics, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
| | - Anna E Garbers
- Structural Biology and NMR Laboratory, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark.,REPIN, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Wouter Boomsma
- Department of Computer Science, University of Copenhagen, Universitetsparken 1, 2100, Copenhagen Ø, Denmark
| | - Joseph M Rogers
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 160, 2100, Copenhagen Ø, Denmark
| | - Rasmus Hartmann-Petersen
- REPIN, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark. .,The Linderstrøm Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark.
| | - Birthe B Kragelund
- Structural Biology and NMR Laboratory, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark. .,REPIN, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark. .,The Linderstrøm Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark.
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45
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Sangster AG, Zarin T, Moses AM. Evolution of short linear motifs and disordered proteins Topic: yeast as model system to study evolution. Curr Opin Genet Dev 2022; 76:101964. [PMID: 35939968 DOI: 10.1016/j.gde.2022.101964] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 06/29/2022] [Accepted: 07/08/2022] [Indexed: 11/26/2022]
Abstract
Evolutionary preservation of protein structure had a major influence on the field of molecular evolution: changes in individual amino acids that did not disrupt protein folding would either have no effect or subtly change the 'lock' so that it could fit a new 'key'. Homology of individual amino acids could be confidently assigned through sequence alignments, and models of evolution could be tested. This view of molecular evolution excluded large regions of proteins that could not be confidently aligned, such as intrinsically disordered regions (IDRs) that do not fold into stable structures. In the last decade, major progress has been made in understanding the evolution of IDRs, much of it facilitated by new experimental and computational approaches in yeast. Here, we review this progress as well as several still outstanding questions.
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Affiliation(s)
- Ami G Sangster
- Cell & Systems Biology, University of Toronto, 25 Harbord St., Toronto, ON M5S 3G5, Canada
| | - Taraneh Zarin
- Cell & Systems Biology, University of Toronto, 25 Harbord St., Toronto, ON M5S 3G5, Canada. https://twitter.com/@taraneh_z
| | - Alan M Moses
- Cell & Systems Biology, University of Toronto, 25 Harbord St., Toronto, ON M5S 3G5, Canada.
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Li Y, Balakrishnan VK, Rowse M, Wu CG, Bravos AP, Yadav VK, Ivarsson YI, Strack S, Novikova IV, Xing Y. Coupling to short linear motifs creates versatile PME-1 activities in PP2A holoenzyme demethylation and inhibition. eLife 2022; 11:79736. [PMID: 35924897 PMCID: PMC9398451 DOI: 10.7554/elife.79736] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 08/03/2022] [Indexed: 11/30/2022] Open
Abstract
Protein phosphatase 2A (PP2A) holoenzymes target broad substrates by recognizing short motifs via regulatory subunits. PP2A methylesterase 1 (PME-1) is a cancer-promoting enzyme and undergoes methylesterase activation upon binding to the PP2A core enzyme. Here, we showed that PME-1 readily demethylates different families of PP2A holoenzymes and blocks substrate recognition in vitro. The high-resolution cryoelectron microscopy structure of a PP2A-B56 holoenzyme–PME-1 complex reveals that PME-1 disordered regions, including a substrate-mimicking motif, tether to the B56 regulatory subunit at remote sites. They occupy the holoenzyme substrate-binding groove and allow large structural shifts in both holoenzyme and PME-1 to enable multipartite contacts at structured cores to activate the methylesterase. B56 interface mutations selectively block PME-1 activity toward PP2A-B56 holoenzymes and affect the methylation of a fraction of total cellular PP2A. The B56 interface mutations allow us to uncover B56-specific PME-1 functions in p53 signaling. Our studies reveal multiple mechanisms of PME-1 in suppressing holoenzyme functions and versatile PME-1 activities derived from coupling substrate-mimicking motifs to dynamic structured cores.
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Affiliation(s)
- Yitong Li
- Department of Oncology, University of Wisconsin-Madison, Madison, United States
| | | | - Michael Rowse
- Indiana University - Purdue University Columbus, Columbus, United States
| | - Cheng-Guo Wu
- Department of Oncology, University of Wisconsin-Madison, Madison, United States
| | | | - Vikash K Yadav
- 5Department of Chemistry, Uppsala University, Uppsala, Sweden
| | - YIva Ivarsson
- 5Department of Chemistry, Uppsala University, Uppsala, Sweden
| | - Stefan Strack
- Department of Neuroscience and Pharmacology, University of Iowa, Iowa City, United States
| | - Irina V Novikova
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, United States
| | - Yongna Xing
- Department of Oncology, University of Wisconsin-Madison, Madison, United States
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Elkhaligy H, Balbin CA, Siltberg-Liberles J. Comparative Analysis of Structural Features in SLiMs from Eukaryotes, Bacteria, and Viruses with Importance for Host-Pathogen Interactions. Pathogens 2022; 11:pathogens11050583. [PMID: 35631103 PMCID: PMC9147284 DOI: 10.3390/pathogens11050583] [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: 03/18/2022] [Revised: 05/06/2022] [Accepted: 05/11/2022] [Indexed: 11/19/2022] Open
Abstract
Protein-protein interactions drive functions in eukaryotes that can be described by short linear motifs (SLiMs). Conservation of SLiMs help illuminate functional SLiMs in eukaryotic protein families. However, the simplicity of eukaryotic SLiMs makes them appear by chance due to mutational processes not only in eukaryotes but also in pathogenic bacteria and viruses. Further, functional eukaryotic SLiMs are often found in disordered regions. Although proteomes from pathogenic bacteria and viruses have less disorder than eukaryotic proteomes, their proteins can successfully mimic eukaryotic SLiMs and disrupt host cellular function. Identifying important SLiMs in pathogens is difficult but essential for understanding potential host-pathogen interactions. We performed a comparative analysis of structural features for experimentally verified SLiMs from the Eukaryotic Linear Motif (ELM) database across viruses, bacteria, and eukaryotes. Our results revealed that many viral SLiMs and specific motifs found across viruses and eukaryotes, such as some glycosylation motifs, have less disorder. Analyzing the disorder and coil properties of equivalent SLiMs from pathogens and eukaryotes revealed that some motifs are more structured in pathogens than their eukaryotic counterparts and vice versa. These results support a varying mechanism of interaction between pathogens and their eukaryotic hosts for some of the same motifs.
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48
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Wadie B, Kleshchevnikov V, Sandaltzopoulou E, Benz C, Petsalaki E. Use of viral motif mimicry improves the proteome-wide discovery of human linear motifs. Cell Rep 2022; 39:110764. [PMID: 35508127 DOI: 10.1016/j.celrep.2022.110764] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 02/09/2022] [Accepted: 04/08/2022] [Indexed: 12/16/2022] Open
Abstract
Linear motifs have an integral role in dynamic cell functions, including cell signaling. However, due to their small size, low complexity, and frequent mutations, identifying novel functional motifs poses a challenge. Viruses rely extensively on the molecular mimicry of cellular linear motifs. In this study, we apply systematic motif prediction combined with functional filters to identify human linear motifs convergently evolved also in viral proteins. We observe an increase in the sensitivity of motif prediction and improved enrichment in known instances. We identify >7,300 non-redundant motif instances at various confidence levels, 99 of which are supported by all functional and structural filters. Overall, we provide a pipeline to improve the identification of functional linear motifs from interactomics datasets and a comprehensive catalog of putative human motifs that can contribute to our understanding of the human domain-linear motif code and the associated mechanisms of viral interference.
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Affiliation(s)
- Bishoy Wadie
- European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Vitalii Kleshchevnikov
- European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Elissavet Sandaltzopoulou
- European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Caroline Benz
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | - Evangelia Petsalaki
- European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK.
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49
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Byerly CD, Mitra S, Patterson LL, Pittner NA, Velayutham TS, Paessler S, Veljkovic V, McBride JW. Ehrlichia SLiM ligand mimetic activates Hedgehog signaling to engage a BCL-2 anti-apoptotic cellular program. PLoS Pathog 2022; 18:e1010345. [PMID: 35576232 PMCID: PMC9135340 DOI: 10.1371/journal.ppat.1010345] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 05/26/2022] [Accepted: 04/21/2022] [Indexed: 11/19/2022] Open
Abstract
Ehrlichia chaffeensis (E. chaffeensis) has evolved eukaryotic ligand mimicry to repurpose multiple cellular signaling pathways for immune evasion. In this investigation, we demonstrate that TRP120 has a novel repetitive short linear motif (SLiM) that activates the evolutionarily conserved Hedgehog (Hh) signaling pathway to inhibit apoptosis. In silico analysis revealed that TRP120 has sequence and functional similarity with Hh ligands and a candidate Hh ligand SLiM was identified. siRNA knockdown of Hh signaling and transcriptional components significantly reduced infection. Co-immunoprecipitation and surface plasmon resonance demonstrated that rTRP120-TR interacted directly with Hh receptor Patched-2 (PTCH2). E. chaffeensis infection resulted in early upregulation of Hh transcription factor GLI-1 and regulation of Hh target genes. Moreover, soluble recombinant TRP120 (rTRP120) activated Hh and induced gene expression consistent with the eukaryotic Hh ligand. The TRP120-Hh-SLiM (NPEVLIKD) induced nuclear translocation of GLI-1 in THP-1 cells and primary human monocytes and induced a rapid and expansive activation of Hh pathway target genes. Furthermore, Hh activation was blocked by an α-TRP120-Hh-SLiM antibody. TRP120-Hh-SLiM significantly increased levels of Hh target, anti-apoptotic protein B-cell lymphoma 2 (BCL-2), and siRNA knockdown of BCL-2 dramatically inhibited infection. Blocking Hh signaling with the inhibitor Vismodegib, induced a pro-apoptotic cellular program defined by decreased mitochondria membrane potential, significant reductions in BCL-2, activation of caspase 3 and 9, and increased apoptotic cells. This study reveals a novel E. chaffeensis SLiM ligand mimetic that activates Hh signaling to maintain E. chaffeensis infection by engaging a BCL-2 anti-apoptotic cellular program.
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Affiliation(s)
- Caitlan D. Byerly
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Shubhajit Mitra
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - LaNisha L. Patterson
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Nicholas A. Pittner
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Thangam S. Velayutham
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Slobodan Paessler
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Biomed Protection, LLC, Galveston, Texas, United States of America
| | - Veljko Veljkovic
- Biomed Protection, LLC, Galveston, Texas, United States of America
| | - Jere W. McBride
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, Texas, United States of America
- Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, Texas, United States of America
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, Texas, United States of America
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Pierros V, Kontopodis E, Stravopodis DJ, Tsangaris GT. Unique peptide signatures of SARS-CοV-2 virus against human proteome reveal variants’ immune escape and infectiveness. Heliyon 2022; 8:e09222. [PMID: 35399374 PMCID: PMC8979629 DOI: 10.1016/j.heliyon.2022.e09222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/19/2021] [Accepted: 03/21/2022] [Indexed: 10/29/2022] Open
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