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Bondos SE, Dunker AK, Uversky VN. Intrinsically disordered proteins play diverse roles in cell signaling. Cell Commun Signal 2022; 20:20. [PMID: 35177069 PMCID: PMC8851865 DOI: 10.1186/s12964-022-00821-7] [Citation(s) in RCA: 67] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 12/11/2021] [Indexed: 11/29/2022] Open
Abstract
Signaling pathways allow cells to detect and respond to a wide variety of chemical (e.g. Ca2+ or chemokine proteins) and physical stimuli (e.g., sheer stress, light). Together, these pathways form an extensive communication network that regulates basic cell activities and coordinates the function of multiple cells or tissues. The process of cell signaling imposes many demands on the proteins that comprise these pathways, including the abilities to form active and inactive states, and to engage in multiple protein interactions. Furthermore, successful signaling often requires amplifying the signal, regulating or tuning the response to the signal, combining information sourced from multiple pathways, all while ensuring fidelity of the process. This sensitivity, adaptability, and tunability are possible, in part, due to the inclusion of intrinsically disordered regions in many proteins involved in cell signaling. The goal of this collection is to highlight the many roles of intrinsic disorder in cell signaling. Following an overview of resources that can be used to study intrinsically disordered proteins, this review highlights the critical role of intrinsically disordered proteins for signaling in widely diverse organisms (animals, plants, bacteria, fungi), in every category of cell signaling pathway (autocrine, juxtacrine, intracrine, paracrine, and endocrine) and at each stage (ligand, receptor, transducer, effector, terminator) in the cell signaling process. Thus, a cell signaling pathway cannot be fully described without understanding how intrinsically disordered protein regions contribute to its function. The ubiquitous presence of intrinsic disorder in different stages of diverse cell signaling pathways suggest that more mechanisms by which disorder modulates intra- and inter-cell signals remain to be discovered.
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Affiliation(s)
- Sarah E. Bondos
- Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, TX 77843 USA
| | - A. Keith Dunker
- Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202 USA
| | - Vladimir N. Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612 USA
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Pushchino, Moscow Region, Russia 142290
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Grape ASR-Silencing Sways Nuclear Proteome, Histone Marks and Interplay of Intrinsically Disordered Proteins. Int J Mol Sci 2022; 23:ijms23031537. [PMID: 35163458 PMCID: PMC8835812 DOI: 10.3390/ijms23031537] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/25/2022] [Accepted: 01/26/2022] [Indexed: 01/27/2023] Open
Abstract
In order to unravel the functions of ASR (Abscisic acid, Stress, Ripening-induced) proteins in the nucleus, we created a new model of genetically transformed grape embryogenic cells by RNAi-knockdown of grape ASR (VvMSA). Nuclear proteomes of wild-type and VvMSA-RNAi grape cell lines were analyzed by quantitative isobaric tagging (iTRAQ 8-plex). The most significantly up- or down-regulated nuclear proteins were involved in epigenetic regulation, DNA replication/repair, transcription, mRNA splicing/stability/editing, rRNA processing/biogenesis, metabolism, cell division/differentiation and stress responses. The spectacular up-regulation in VvMSA-silenced cells was that of the stress response protein VvLEA D-29 (Late Embryogenesis Abundant). Both VvMSA and VvLEA D-29 genes displayed strong and contrasted responsiveness to auxin depletion, repression of VvMSA and induction of VvLEA D-29. In silico analysis of VvMSA and VvLEA D-29 proteins highlighted their intrinsically disordered nature and possible compensatory relationship. Semi-quantitative evaluation by medium-throughput immunoblotting of eighteen post-translational modifications of histones H3 and H4 in VvMSA-knockdown cells showed significant enrichment/depletion of the histone marks H3K4me1, H3K4me3, H3K9me1, H3K9me2, H3K36me2, H3K36me3 and H4K16ac. We demonstrate that grape ASR repression differentially affects members of complex nucleoprotein structures and may not only act as molecular chaperone/transcription factor, but also participates in plant responses to developmental and environmental cues through epigenetic mechanisms.
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Carugo O. Uses and Abuses of the Atomic Displacement Parameters in Structural Biology. Methods Mol Biol 2022; 2449:281-298. [PMID: 35507268 DOI: 10.1007/978-1-0716-2095-3_12] [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] [Indexed: 06/14/2023]
Abstract
B-factors determined with X-ray crystallographic analyses are commonly used to estimate the flexibility degree of atoms, residues, and molecular moieties in biological macromolecules. In this chapter, the most recent studies and applications of B-factors in protein engineering and structural biology are briefly summarized. Particular emphasis is given to the limitations in using B-factors, in order to prevent inappropriate applications. It is eventually predicted that future applications will involve anisotropically refined B-factors, deep learning, and data produced by cryo-EM.
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Tamburrini KC, Terrapon N, Lombard V, Bissaro B, Longhi S, Berrin JG. Bioinformatic Analysis of Lytic Polysaccharide Monooxygenases Reveals the Pan-Families Occurrence of Intrinsically Disordered C-Terminal Extensions. Biomolecules 2021; 11:1632. [PMID: 34827630 PMCID: PMC8615602 DOI: 10.3390/biom11111632] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/26/2021] [Accepted: 10/30/2021] [Indexed: 01/17/2023] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are monocopper enzymes secreted by many organisms and viruses. LPMOs catalyze the oxidative cleavage of different types of polysaccharides and are today divided into eight families (AA9-11, AA13-17) within the Auxiliary Activity enzyme class of the CAZy database. LPMOs minimal architecture encompasses a catalytic domain, to which can be appended a carbohydrate-binding module. Intriguingly, we observed that some LPMO sequences also display a C-terminal extension of varying length not associated with any known function or fold. Here, we analyzed 27,060 sequences from different LPMO families and show that 60% have a C-terminal extension predicted to be intrinsically disordered. Our analysis shows that these disordered C-terminal regions (dCTRs) are widespread in all LPMO families (except AA13) and differ in terms of sequence length and amino-acid composition. Noteworthily, these dCTRs have so far only been observed in LPMOs. LPMO-dCTRs share a common polyampholytic nature and an enrichment in serine and threonine residues, suggesting that they undergo post-translational modifications. Interestingly, dCTRs from AA11 and AA15 are enriched in redox-sensitive, conditionally disordered regions. The widespread occurrence of dCTRs in LPMOs from evolutionarily very divergent organisms, hints at a possible functional role and opens new prospects in the field of LPMOs.
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Affiliation(s)
- Ketty C. Tamburrini
- Architecture et Fonction des Macromolécules Biologiques (AFMB), Centre National de la Recherche Scientifique (CNRS), Aix-Marseille Université (AMU), UMR 7257, 13288 Marseille, France; (K.C.T.); (N.T.); (V.L.)
- Biodiversité et Biotechnologie Fongiques (BBF), French National Institute for Agriculture, Food, and Environment (INRAE), Aix-Marseille Université (AMU), UMR 1163, 13288 Marseille, France;
| | - Nicolas Terrapon
- Architecture et Fonction des Macromolécules Biologiques (AFMB), Centre National de la Recherche Scientifique (CNRS), Aix-Marseille Université (AMU), UMR 7257, 13288 Marseille, France; (K.C.T.); (N.T.); (V.L.)
- Architecture et Fonction des Macromolécules Biologiques (AFMB), French National Institute for Agriculture, Food, and Environment (INRAE), USC 1408, 13288 Marseille, France
| | - Vincent Lombard
- Architecture et Fonction des Macromolécules Biologiques (AFMB), Centre National de la Recherche Scientifique (CNRS), Aix-Marseille Université (AMU), UMR 7257, 13288 Marseille, France; (K.C.T.); (N.T.); (V.L.)
- Architecture et Fonction des Macromolécules Biologiques (AFMB), French National Institute for Agriculture, Food, and Environment (INRAE), USC 1408, 13288 Marseille, France
| | - Bastien Bissaro
- Biodiversité et Biotechnologie Fongiques (BBF), French National Institute for Agriculture, Food, and Environment (INRAE), Aix-Marseille Université (AMU), UMR 1163, 13288 Marseille, France;
| | - Sonia Longhi
- Architecture et Fonction des Macromolécules Biologiques (AFMB), Centre National de la Recherche Scientifique (CNRS), Aix-Marseille Université (AMU), UMR 7257, 13288 Marseille, France; (K.C.T.); (N.T.); (V.L.)
| | - Jean-Guy Berrin
- Biodiversité et Biotechnologie Fongiques (BBF), French National Institute for Agriculture, Food, and Environment (INRAE), Aix-Marseille Université (AMU), UMR 1163, 13288 Marseille, France;
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Brocca S, Grandori R, Longhi S, Uversky V. Liquid-Liquid Phase Separation by Intrinsically Disordered Protein Regions of Viruses: Roles in Viral Life Cycle and Control of Virus-Host Interactions. Int J Mol Sci 2020; 21:E9045. [PMID: 33260713 PMCID: PMC7730420 DOI: 10.3390/ijms21239045] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 11/23/2020] [Accepted: 11/24/2020] [Indexed: 12/13/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) are unable to adopt a unique 3D structure under physiological conditions and thus exist as highly dynamic conformational ensembles. IDPs are ubiquitous and widely spread in the protein realm. In the last decade, compelling experimental evidence has been gathered, pointing to the ability of IDPs and intrinsically disordered regions (IDRs) to undergo liquid-liquid phase separation (LLPS), a phenomenon driving the formation of membrane-less organelles (MLOs). These biological condensates play a critical role in the spatio-temporal organization of the cell, where they exert a multitude of key biological functions, ranging from transcriptional regulation and silencing to control of signal transduction networks. After introducing IDPs and LLPS, we herein survey available data on LLPS by IDPs/IDRs of viral origin and discuss their functional implications. We distinguish LLPS associated with viral replication and trafficking of viral components, from the LLPS-mediated interference of viruses with host cell functions. We discuss emerging evidence on the ability of plant virus proteins to interfere with the regulation of MLOs of the host and propose that bacteriophages can interfere with bacterial LLPS, as well. We conclude by discussing how LLPS could be targeted to treat phase separation-associated diseases, including viral infections.
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Affiliation(s)
- Stefania Brocca
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milano, Italy
| | - Rita Grandori
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milano, Italy
| | - Sonia Longhi
- Laboratoire Architecture et Fonction des Macromolécules Biologiques (AFMB), Aix-Marseille University and CNRS, 13288 Marseille, France
| | - Vladimir Uversky
- Department of Molecular Medicine, Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33601, USA
- Laboratory of New Methods in Biology, Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, 142290 Pushchino, Russia
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Carugo O. Atomic displacement parameters in structural biology. Amino Acids 2018; 50:775-786. [DOI: 10.1007/s00726-018-2574-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 04/19/2018] [Indexed: 01/14/2023]
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Takahashi M, Takahashi E, Joudeh LI, Marini M, Das G, Elshenawy MM, Akal A, Sakashita K, Alam I, Tehseen M, Sobhy MA, Stingl U, Merzaban JS, Di Fabrizio E, Hamdan SM. Dynamic structure mediates halophilic adaptation of a DNA polymerase from the deep-sea brines of the Red Sea. FASEB J 2018; 32:3346-3360. [PMID: 29401622 PMCID: PMC6051491 DOI: 10.1096/fj.201700862rr] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The deep-sea brines of the Red Sea are remote and unexplored environments characterized by high temperatures, anoxic water, and elevated concentrations of salt and heavy metals. This environment provides a rare system to study the interplay between halophilic and thermophilic adaptation in biologic macromolecules. The present article reports the first DNA polymerase with halophilic and thermophilic features. Biochemical and structural analysis by Raman and circular dichroism spectroscopy showed that the charge distribution on the protein’s surface mediates the structural balance between stability for thermal adaptation and flexibility for counteracting the salt-induced rigid and nonfunctional hydrophobic packing. Salt bridge interactions via increased negative and positive charges contribute to structural stability. Salt tolerance, conversely, is mediated by a dynamic structure that becomes more fixed and functional with increasing salt concentration. We propose that repulsive forces among excess negative charges, in addition to a high percentage of negatively charged random coils, mediate this structural dynamism. This knowledge enabled us to engineer a halophilic version of Thermococcus kodakarensis DNA polymerase.—Takahashi, M., Takahashi, E., Joudeh, L. I., Marini, M., Das, G., Elshenawy, M. M., Akal, A., Sakashita, K., Alam, I., Tehseen, M., Sobhy, M. A., Stingl, U., Merzaban, J. S., Di Fabrizio, E., Hamdan, S. M. Dynamic structure mediates halophilic adaptation of a DNA polymerase from the deep-sea brines of the Red Sea.
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Affiliation(s)
- Masateru Takahashi
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Jeddah, Saudi Arabia
| | - Etsuko Takahashi
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Jeddah, Saudi Arabia
| | - Luay I Joudeh
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Jeddah, Saudi Arabia
| | - Monica Marini
- Physical Science and Engineering Division, King Abdullah University of Science and Technology, Jeddah, Saudi Arabia
| | - Gobind Das
- Physical Science and Engineering Division, King Abdullah University of Science and Technology, Jeddah, Saudi Arabia
| | - Mohamed M Elshenawy
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Jeddah, Saudi Arabia
| | - Anastassja Akal
- Physical Science and Engineering Division, King Abdullah University of Science and Technology, Jeddah, Saudi Arabia.,KAUST Catalysis Center, King Abdullah University of Science and Technology, Jeddah, Saudi Arabia
| | - Kosuke Sakashita
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Jeddah, Saudi Arabia
| | - Intikhab Alam
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Jeddah, Saudi Arabia; and
| | - Muhammad Tehseen
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Jeddah, Saudi Arabia
| | - Mohamed A Sobhy
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Jeddah, Saudi Arabia
| | - Ulrich Stingl
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Jeddah, Saudi Arabia.,Fort Lauderdale Research and Education Center, University of Florida, Davie, Florida, USA
| | - Jasmeen S Merzaban
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Jeddah, Saudi Arabia
| | - Enzo Di Fabrizio
- Physical Science and Engineering Division, King Abdullah University of Science and Technology, Jeddah, Saudi Arabia
| | - Samir M Hamdan
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Jeddah, Saudi Arabia
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Carugo O. Hydrophobicity diversity in globular and nonglobular proteins measured with the Gini index. Protein Eng Des Sel 2017; 30:781-784. [DOI: 10.1093/protein/gzx060] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 11/14/2017] [Indexed: 01/23/2023] Open
Affiliation(s)
- Oliviero Carugo
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, 1030 Vienna, Austria, and Department of Chemistry, University of Pavia, viale Taramelli 12, 27100 Pavia, Italy
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Structural disorder and induced folding within two cereal, ABA stress and ripening (ASR) proteins. Sci Rep 2017; 7:15544. [PMID: 29138428 PMCID: PMC5686140 DOI: 10.1038/s41598-017-15299-4] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 10/04/2017] [Indexed: 11/13/2022] Open
Abstract
Abscisic acid (ABA), stress and ripening (ASR) proteins are plant-specific proteins involved in plant response to multiple abiotic stresses. We previously isolated the ASR genes and cDNAs from durum wheat (TtASR1) and barley (HvASR1). Here, we show that HvASR1 and TtASR1 are consistently predicted to be disordered and further confirm this experimentally. Addition of glycerol, which mimics dehydration, triggers a gain of structure in both proteins. Limited proteolysis showed that they are highly sensitive to protease degradation. Addition of 2,2,2-trifluoroethanol (TFE) however, results in a decreased susceptibility to proteolysis that is paralleled by a gain of structure. Mass spectrometry analyses (MS) led to the identification of a protein fragment resistant to proteolysis. Addition of zinc also induces a gain of structure and Hydrogen/Deuterium eXchange-Mass Spectrometry (HDX-MS) allowed identification of the region involved in the disorder-to-order transition. This study is the first reported experimental characterization of HvASR1 and TtASR1 proteins, and paves the way for future studies aimed at unveiling the functional impact of the structural transitions that these proteins undergo in the presence of zinc and at achieving atomic-resolution conformational ensemble description of these two plant intrinsically disordered proteins (IDPs).
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