1
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Sood A, Zhang B. Preserving condensate structure and composition by lowering sequence complexity. Biophys J 2024; 123:1815-1826. [PMID: 38824391 DOI: 10.1016/j.bpj.2024.05.026] [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: 01/26/2024] [Revised: 04/25/2024] [Accepted: 05/28/2024] [Indexed: 06/03/2024] Open
Abstract
Biomolecular condensates play a vital role in organizing cellular chemistry. They selectively partition biomolecules, preventing unwanted cross talk and buffering against chemical noise. Intrinsically disordered proteins (IDPs) serve as primary components of these condensates due to their flexibility and ability to engage in multivalent interactions, leading to spontaneous aggregation. Theoretical advancements are critical at connecting IDP sequences with condensate emergent properties to establish the so-called molecular grammar. We proposed an extension to the stickers and spacers model, incorporating heterogeneous, nonspecific pairwise interactions between spacers alongside specific interactions among stickers. Our investigation revealed that although spacer interactions contribute to phase separation and co-condensation, their nonspecific nature leads to disorganized condensates. Specific sticker-sticker interactions drive the formation of condensates with well-defined networked structures and molecular composition. We discussed how evolutionary pressures might emerge to affect these interactions, leading to the prevalence of low-complexity domains in IDP sequences. These domains suppress spurious interactions and facilitate the formation of biologically meaningful condensates.
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Affiliation(s)
- Amogh Sood
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts.
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2
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Gebauer F. RNA glues it all. Nat Cell Biol 2024; 26:1021-1022. [PMID: 38992140 DOI: 10.1038/s41556-024-01454-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2024]
Affiliation(s)
- Fátima Gebauer
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain.
- Universitat Pompeu Fabra, Barcelona, Spain.
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3
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Modic M, Adamek M, Ule J. The impact of IDR phosphorylation on the RNA binding profiles of proteins. Trends Genet 2024; 40:580-586. [PMID: 38705823 DOI: 10.1016/j.tig.2024.04.004] [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: 01/30/2024] [Revised: 04/08/2024] [Accepted: 04/10/2024] [Indexed: 05/07/2024]
Abstract
Due to their capacity to mediate repetitive protein interactions, intrinsically disordered regions (IDRs) are crucial for the formation of various types of protein-RNA complexes. The functions of IDRs are strongly modulated by post-translational modifications (PTMs). Phosphorylation is the most common and well-studied modification of IDRs, which can alter homomeric or heteromeric interactions of proteins and impact their ability to phase separate. Moreover, phosphorylation can influence the RNA-binding properties of proteins, and recent studies demonstrated its selective impact on the global profiles of protein-RNA binding and regulation. These findings highlight the need for further integrative approaches to understand how signalling remodels protein-RNA networks in cells.
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Affiliation(s)
- Miha Modic
- National Institute of Chemistry, Ljubljana, Slovenia; The Francis Crick Institute, London, UK; UK Dementia Research Institute at King's College London, London, UK.
| | - Maksimiljan Adamek
- National Institute of Chemistry, Ljubljana, Slovenia; PhD Program 'Biosciences', Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Jernej Ule
- National Institute of Chemistry, Ljubljana, Slovenia; The Francis Crick Institute, London, UK; UK Dementia Research Institute at King's College London, London, UK.
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4
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Eibauer M, Weber MS, Kronenberg-Tenga R, Beales CT, Boujemaa-Paterski R, Turgay Y, Sivagurunathan S, Kraxner J, Köster S, Goldman RD, Medalia O. Vimentin filaments integrate low-complexity domains in a complex helical structure. Nat Struct Mol Biol 2024; 31:939-949. [PMID: 38632361 PMCID: PMC11189308 DOI: 10.1038/s41594-024-01261-2] [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: 05/08/2023] [Accepted: 03/01/2024] [Indexed: 04/19/2024]
Abstract
Intermediate filaments (IFs) are integral components of the cytoskeleton. They provide cells with tissue-specific mechanical properties and are involved in numerous cellular processes. Due to their intricate architecture, a 3D structure of IFs has remained elusive. Here we use cryo-focused ion-beam milling, cryo-electron microscopy and tomography to obtain a 3D structure of vimentin IFs (VIFs). VIFs assemble into a modular, intertwined and flexible helical structure of 40 α-helices in cross-section, organized into five protofibrils. Surprisingly, the intrinsically disordered head domains form a fiber in the lumen of VIFs, while the intrinsically disordered tails form lateral connections between the protofibrils. Our findings demonstrate how protein domains of low sequence complexity can complement well-folded protein domains to construct a biopolymer with striking mechanical strength and stretchability.
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Affiliation(s)
- Matthias Eibauer
- Department of Biochemistry, University of Zurich, Zurich, Switzerland.
| | - Miriam S Weber
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | | | - Charlie T Beales
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | | | - Yagmur Turgay
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
- Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Suganya Sivagurunathan
- Department of Cell and Developmental Biology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Julia Kraxner
- Institute for X-Ray Physics, University of Göttingen, Göttingen, Germany
- MDC Berlin-Buch, Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany
| | - Sarah Köster
- Institute for X-Ray Physics, University of Göttingen, Göttingen, Germany
| | - Robert D Goldman
- Department of Cell and Developmental Biology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Ohad Medalia
- Department of Biochemistry, University of Zurich, Zurich, Switzerland.
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5
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Zhan ML, Zhao X, Li XD, Tan ZZ, Xu QZ, Zhou M, Zhao KH. Photoreversible Aggregation of the Biliprotein Containing the First and Second GAF Domains of a Cyanobacteriochrome All2699 in Nostoc sp. PCC7120. Biochemistry 2024; 63:1225-1233. [PMID: 38682295 DOI: 10.1021/acs.biochem.4c00058] [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: 05/01/2024]
Abstract
As plant photoreceptors, phytochromes are capable of detecting red light and far-red light, thereby governing plant growth. All2699 is a photoreceptor found in Nostoc sp. PCC7120 that specifically responds to red light and far-red light. All2699g1g2 is a truncated protein carrying the first and second GAF (cGMP phosphodiesterase/adenylyl cyclase/FhlA) domains of All2699. In this study, we found that, upon exposure to red light, the protein underwent aggregation, resulting in the formation of protein aggregates. Conversely, under far-red light irradiation, these protein aggregates dissociated. We delved into the factors that impact the aggregation of All2699g1g2, focusing on the protein structure. Our findings showed that the GAF2 domain contains a low-complexity (LC) loop region, which plays a crucial role in mediating protein aggregation. Specifically, phenylalanine at position 239 within the LC loop region was identified as a key site for the aggregation process. Furthermore, our research revealed that various factors, including irradiation time, temperature, concentration, NaCl concentration, and pH value, can impact the aggregation of All2699g1g2. The aggregation led to variations in Pfr concentration depending on temperature, NaCl concentration, and pH value. In contrast, ΔLC did not aggregate and therefore lacked responses to these factors. Consequently, the LC loop region of All2699g1g2 extended and enhanced sensory properties.
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Affiliation(s)
- Min-Li Zhan
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Xi Zhao
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Xiao-Dan Li
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Zi-Zhu Tan
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Qian-Zhao Xu
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Ming Zhou
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Kai-Hong Zhao
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, P. R. China
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6
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Zheng H, Sun H, Cai Q, Tai HC. The Enigma of Tau Protein Aggregation: Mechanistic Insights and Future Challenges. Int J Mol Sci 2024; 25:4969. [PMID: 38732197 PMCID: PMC11084794 DOI: 10.3390/ijms25094969] [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: 03/30/2024] [Revised: 04/20/2024] [Accepted: 04/23/2024] [Indexed: 05/13/2024] Open
Abstract
Tau protein misfolding and aggregation are pathological hallmarks of Alzheimer's disease and over twenty neurodegenerative disorders. However, the molecular mechanisms of tau aggregation in vivo remain incompletely understood. There are two types of tau aggregates in the brain: soluble aggregates (oligomers and protofibrils) and insoluble filaments (fibrils). Compared to filamentous aggregates, soluble aggregates are more toxic and exhibit prion-like transmission, providing seeds for templated misfolding. Curiously, in its native state, tau is a highly soluble, heat-stable protein that does not form fibrils by itself, not even when hyperphosphorylated. In vitro studies have found that negatively charged molecules such as heparin, RNA, or arachidonic acid are generally required to induce tau aggregation. Two recent breakthroughs have provided new insights into tau aggregation mechanisms. First, as an intrinsically disordered protein, tau is found to undergo liquid-liquid phase separation (LLPS) both in vitro and inside cells. Second, cryo-electron microscopy has revealed diverse fibrillar tau conformations associated with different neurodegenerative disorders. Nonetheless, only the fibrillar core is structurally resolved, and the remainder of the protein appears as a "fuzzy coat". From this review, it appears that further studies are required (1) to clarify the role of LLPS in tau aggregation; (2) to unveil the structural features of soluble tau aggregates; (3) to understand the involvement of fuzzy coat regions in oligomer and fibril formation.
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Affiliation(s)
| | | | | | - Hwan-Ching Tai
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University, Xiamen 361102, China
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7
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McKnight SL. Protein domains of low sequence complexity-dark matter of the proteome. Genes Dev 2024; 38:205-212. [PMID: 38503517 PMCID: PMC11065162 DOI: 10.1101/gad.351465.123] [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] [Indexed: 03/21/2024]
Abstract
This perspective begins with a speculative consideration of the properties of the earliest proteins to appear during evolution. What did these primitive proteins look like, and how were they of benefit to early forms of life? I proceed to hypothesize that primitive proteins have been preserved through evolution and now serve diverse functions important to the dynamics of cell morphology and biological regulation. The primitive nature of these modern proteins is easy to spot. They are composed of a limited subset of the 20 amino acids used by traditionally evolved proteins and thus are of low sequence complexity. This chemical simplicity limits protein domains of low sequence complexity to forming only a crude and labile type of protein structure currently hidden from the computational powers of machine learning. I conclude by hypothesizing that this structural weakness represents the underlying virtue of proteins that, at least for the moment, constitute the dark matter of the proteome.
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Affiliation(s)
- Steven L McKnight
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas 75390-9152, USA
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8
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Thirumalai D, Kumar A, Chakraborty D, Straub JE, Mugnai ML. Conformational fluctuations and phases in fused in sarcoma (FUS) low-complexity domain. Biopolymers 2024; 115:e23558. [PMID: 37399327 PMCID: PMC10831756 DOI: 10.1002/bip.23558] [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] [Revised: 05/30/2023] [Accepted: 06/15/2023] [Indexed: 07/05/2023]
Abstract
The well-known phenomenon of phase separation in synthetic polymers and proteins has become a major topic in biophysics because it has been invoked as a mechanism of compartment formation in cells, without the need for membranes. Most of the coacervates (or condensates) are composed of Intrinsically Disordered Proteins (IDPs) or regions that are structureless, often in interaction with RNA and DNA. One of the more intriguing IDPs is the 526-residue RNA-binding protein, Fused in Sarcoma (FUS), whose monomer conformations and condensates exhibit unusual behavior that are sensitive to solution conditions. By focussing principally on the N-terminus low-complexity domain (FUS-LC comprising residues 1-214) and other truncations, we rationalize the findings of solid-state NMR experiments, which show that FUS-LC adopts a non-polymorphic fibril structure (core-1) involving residues 39-95, flanked by fuzzy coats on both the N- and C-terminal ends. An alternate structure (core-2), whose free energy is comparable to core-1, emerges only in the truncated construct (residues 110-214). Both core-1 and core-2 fibrils are stabilized by a Tyrosine ladder as well as hydrophilic interactions. The morphologies (gels, fibrils, and glass-like) adopted by FUS seem to vary greatly, depending on the experimental conditions. The effect of phosphorylation is site-specific. Simulations show that phosphorylation of residues within the fibril has a greater destabilization effect than residues that are outside the fibril region, which accords well with experiments. Many of the peculiarities associated with FUS may also be shared by other IDPs, such as TDP43 and hnRNPA2. We outline a number of problems for which there is no clear molecular explanation.
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Affiliation(s)
- D Thirumalai
- Department of Chemistry, The University of Texas at Austin, Austin, Texas, USA
- Department of Physics, The University of Texas at Austin, Austin, Texas, USA
| | - Abhinaw Kumar
- Department of Chemistry, The University of Texas at Austin, Austin, Texas, USA
| | - Debayan Chakraborty
- Department of Chemistry, The University of Texas at Austin, Austin, Texas, USA
| | - John E Straub
- Department of Chemistry, Boston University, Boston, Massachusetts, USA
| | - Mauro L Mugnai
- Institute for Soft Matter Synthesis and Metrology, Georgetown University, Washington, DC, USA
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9
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Zolotarev N, Wang Y, Du M, Bayer M, Grosschedl A, Cisse I, Grosschedl R. Regularly spaced tyrosines in EBF1 mediate BRG1 recruitment and formation of nuclear subdiffractive clusters. Genes Dev 2024; 38:4-10. [PMID: 38233109 PMCID: PMC10903943 DOI: 10.1101/gad.350828.123] [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: 05/26/2023] [Accepted: 12/21/2023] [Indexed: 01/19/2024]
Abstract
B lineage priming by pioneer transcription factor EBF1 requires the function of an intrinsically disordered region (IDR). Here, we examine the role of regularly spaced tyrosines in the IDR as potential determinants of IDR function and activity of EBF1. We found that four Y > A mutations in EBF1 reduced the formation of condensates in vitro and subdiffractive clusters in vivo. Notably, Y > A mutant EBF1 was inefficient in promoting B cell differentiation and showed impaired chromatin binding, recruitment of BRG1, and activation of specific target genes. Thus, regularly spaced tyrosines in the IDR contribute to the biophysical and functional properties of EBF1.
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Affiliation(s)
- Nikolay Zolotarev
- Laboratory of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
- Department of Biological Physics, Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | - Yuanting Wang
- Laboratory of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | - Manyu Du
- Department of Biological Physics, Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | - Marc Bayer
- Laboratory of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | - Anna Grosschedl
- Department of Biological Physics, Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | - Ibrahim Cisse
- Department of Biological Physics, Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | - Rudolf Grosschedl
- Laboratory of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany;
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10
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Wesp V, Theißen G, Schuster S. Statistical analysis of synonymous and stop codons in pseudo-random and real sequences as a function of GC content. Sci Rep 2023; 13:22996. [PMID: 38151539 PMCID: PMC10752896 DOI: 10.1038/s41598-023-49626-9] [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: 06/13/2023] [Accepted: 12/10/2023] [Indexed: 12/29/2023] Open
Abstract
Knowledge of the frequencies of synonymous triplets in protein-coding and non-coding DNA stretches can be used in gene finding. These frequencies depend on the GC content of the genome or parts of it. An example of interest is provided by stop codons. This is relevant for the definition of Open Reading Frames. A generic case is provided by pseudo-random sequences, especially when they code for complex proteins or when they are non-coding and not subject to selection pressure. Here, we calculate, for such sequences and for all 25 known genetic codes, the frequency of each amino acid and stop codon based on their set of codons and as a function of GC content. The amino acids can be classified into five groups according to the GC content where their expected frequency reaches its maximum. We determine the overall Shannon information based on groups of synonymous codons and show that it becomes maximum at a percent GC of 43.3% (for the standard code). This is in line with the observation that in most fungi, plants, and animals, this genomic parameter is in the range from 35 to 50%. By analysing natural sequences, we show that there is a clear bias for triplets corresponding to stop codons near the 5'- and 3'-splice sites in the introns of various clades.
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Affiliation(s)
- Valentin Wesp
- Department of Bioinformatics, Matthias Schleiden Institute, Friedrich Schiller University Jena, Ernst-Abbe-Platz 2, 07743, Jena, Germany
| | - Günter Theißen
- Department of Genetics, Matthias Schleiden Institute, Friedrich Schiller University Jena, Philosophenweg 12, 07743, Jena, Germany
| | - Stefan Schuster
- Department of Bioinformatics, Matthias Schleiden Institute, Friedrich Schiller University Jena, Ernst-Abbe-Platz 2, 07743, Jena, Germany.
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11
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Zhou X, Kato M, McKnight SL. How do disordered head domains assist in the assembly of intermediate filaments? Curr Opin Cell Biol 2023; 85:102262. [PMID: 37871501 PMCID: PMC11009871 DOI: 10.1016/j.ceb.2023.102262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 08/23/2023] [Accepted: 09/24/2023] [Indexed: 10/25/2023]
Abstract
The dominant structural feature of intermediate filament (IF) proteins is a centrally located α-helix. These long α-helical segments become paired in a parallel orientation to form coiled-coil dimers. Pairs of dimers further coalesce in an anti-parallel orientation to form tetramers. These early stages of intermediate filament assembly can be accomplished solely by the central α-helices. By contrast, the assembly of tetramers into mature intermediate filaments is reliant upon an N-terminal head domain. IF head domains measure roughly 100 amino acids in length and have long been understood to exist in a state of structural disorder. Here, we describe experiments favoring the unexpected idea that head domains self-associate to form transient structural order in the form of labile cross-β interactions. We propose that this weak form of protein structure allows for dynamic regulation of IF assembly and disassembly. We further offer that what we have learned from studies of IF head domains may represent a simple, unifying template for understanding how thousands of other intrinsically disordered proteins help to establish dynamic morphological order within eukaryotic cells.
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Affiliation(s)
- Xiaoming Zhou
- Department of Biochemistry, UT Southwestern Medical Center, 5323 Harry Hines Blvd. Dallas, Texas 75390-9152, USA
| | - Masato Kato
- Department of Biochemistry, UT Southwestern Medical Center, 5323 Harry Hines Blvd. Dallas, Texas 75390-9152, USA; Institute for Quantum Life Science, National Institutes for Quantum Science and Technology (QST), 4-9-1, Anagawa, Inage-ku, Chiba, 263-8555, Japan
| | - Steven L McKnight
- Department of Biochemistry, UT Southwestern Medical Center, 5323 Harry Hines Blvd. Dallas, Texas 75390-9152, USA.
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12
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Gao G, Sumrall ES, Pitchiaya S, Bitzer M, Alberti S, Walter NG. Biomolecular condensates in kidney physiology and disease. Nat Rev Nephrol 2023; 19:756-770. [PMID: 37752323 DOI: 10.1038/s41581-023-00767-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/27/2023] [Indexed: 09/28/2023]
Abstract
The regulation and preservation of distinct intracellular and extracellular solute microenvironments is crucial for the maintenance of cellular homeostasis. In mammals, the kidneys control bodily salt and water homeostasis. Specifically, the urine-concentrating mechanism within the renal medulla causes fluctuations in extracellular osmolarity, which enables cells of the kidney to either conserve or eliminate water and electrolytes, depending on the balance between intake and loss. However, relatively little is known about the subcellular and molecular changes caused by such osmotic stresses. Advances have shown that many cells, including those of the kidney, rapidly (within seconds) and reversibly (within minutes) assemble membraneless, nano-to-microscale subcellular assemblies termed biomolecular condensates via the biophysical process of hyperosmotic phase separation (HOPS). Mechanistically, osmotic cell compression mediates changes in intracellular hydration, concentration and molecular crowding, rendering HOPS one of many related phase-separation phenomena. Osmotic stress causes numerous homo-multimeric proteins to condense, thereby affecting gene expression and cell survival. HOPS rapidly regulates specific cellular biochemical processes before appropriate protective or corrective action by broader stress response mechanisms can be initiated. Here, we broadly survey emerging evidence for, and the impact of, biomolecular condensates in nephrology, where initial concentration buffering by HOPS and its subsequent cellular escalation mechanisms are expected to have important implications for kidney physiology and disease.
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Affiliation(s)
- Guoming Gao
- Biophysics Graduate Program, University of Michigan, Ann Arbor, MI, USA
- Department of Chemistry and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI, USA
| | - Emily S Sumrall
- Biophysics Graduate Program, University of Michigan, Ann Arbor, MI, USA
- Department of Chemistry and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI, USA
| | | | - Markus Bitzer
- Department of Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Simon Alberti
- Technische Universität Dresden, Biotechnology Center (BIOTEC) and Center for Molecular and Cellular Engineering (CMCB), Dresden, Germany
| | - Nils G Walter
- Department of Chemistry and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI, USA.
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13
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Phillips CL, Faridounnia M, Armao D, Snider NT. Stability dynamics of neurofilament and GFAP networks and protein fragments. Curr Opin Cell Biol 2023; 85:102266. [PMID: 37866019 DOI: 10.1016/j.ceb.2023.102266] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 09/21/2023] [Accepted: 09/24/2023] [Indexed: 10/24/2023]
Abstract
Neurofilaments (NFs) and GFAP are cytoskeletal intermediate filaments (IFs) that support cellular processes unfolding within the uniquely complex environments of neurons and astrocytes, respectively. This review highlights emerging concepts on the transitions between stable and destabilized IF networks in the nervous system. While self-association between transiently structured low-complexity IF domains promotes filament assembly, the opposing destabilizing actions of phosphorylation-mediated filament severing facilitate faster intracellular transport. Cellular proteases, including caspases and calpains, produce a variety of IF fragments, which may interact with N-degron and C-degron pathways of the protein degradation machinery. The rapid adoption of NF and GFAP-based clinical biomarker tests is contrasted with the lagging understanding of the dynamics between the native IF proteins and their fragments.
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Affiliation(s)
- Cassandra L Phillips
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, USA
| | - Maryam Faridounnia
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, USA
| | - Diane Armao
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, USA; Department of Radiology, University of North Carolina at Chapel Hill, USA
| | - Natasha T Snider
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, USA.
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14
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Sood A, Zhang B. Preserving condensate structure and composition by lowering sequence complexity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.29.569249. [PMID: 38076908 PMCID: PMC10705451 DOI: 10.1101/2023.11.29.569249] [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: 12/22/2023]
Abstract
Biological condensates play a vital role in organizing cellular chemistry. They selectively partition biomolecules, preventing unwanted cross-talk and buffering against chemical noise. Intrinsically disordered proteins (IDPs) serve as primary components of these condensates due to their flexibility and ability to engage in multivalent, non-specific interactions, leading to spontaneous aggregation. Theoretical advancements are critical at connecting IDP sequences with condensate emergent properties to establish the so-called molecular grammar. We proposed an extension to the stickers and spacers model, incorporating non-specific pairwise interactions between spacers alongside specific interactions among stickers. Our investigation revealed that while spacer interactions contribute to phase separation and co-condensation, their non-specific nature leads to disorganized condensates. Specific sticker-sticker interactions drive the formation of condensates with well-defined structures and molecular composition. We discussed how evolutionary pressures might emerge to affect these interactions, leading to the prevalence of low complexity domains in IDP sequences. These domains suppress spurious interactions and facilitate the formation of biologically meaningful condensates.
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Affiliation(s)
- Amogh Sood
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
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15
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Jackson-Jones KA, McKnight Á, Sloan RD. The innate immune factor RPRD2/REAF and its role in the Lv2 restriction of HIV. mBio 2023; 14:e0257221. [PMID: 37882563 PMCID: PMC10746242 DOI: 10.1128/mbio.02572-21] [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] [Indexed: 10/27/2023] Open
Abstract
Intracellular innate immunity involves co-evolved antiviral restriction factors that specifically inhibit infecting viruses. Studying these restrictions has increased our understanding of viral replication, host-pathogen interactions, and pathogenesis, and represent potential targets for novel antiviral therapies. Lentiviral restriction 2 (Lv2) was identified as an unmapped early-phase restriction of HIV-2 and later shown to also restrict HIV-1 and simian immunodeficiency virus. The viral determinants of Lv2 susceptibility have been mapped to the envelope and capsid proteins in both HIV-1 and HIV-2, and also viral protein R (Vpr) in HIV-1, and appears dependent on cellular entry mechanism. A genome-wide screen identified several likely contributing host factors including members of the polymerase-associated factor 1 (PAF1) and human silencing hub (HUSH) complexes, and the newly characterized regulation of nuclear pre-mRNA domain containing 2 (RPRD2). Subsequently, RPRD2 (or RNA-associated early-stage antiviral factor) has been shown to be upregulated upon T cell activation, is highly expressed in myeloid cells, binds viral reverse transcripts, and potently restricts HIV-1 infection. RPRD2 is also bound by HIV-1 Vpr and targeted for degradation by the proteasome upon reverse transcription, suggesting RPRD2 impedes reverse transcription and Vpr targeting overcomes this block. RPRD2 is mainly localized to the nucleus and binds RNA, DNA, and DNA:RNA hybrids. More recently, RPRD2 has been shown to negatively regulate genome-wide transcription and interact with the HUSH and PAF1 complexes which repress HIV transcription and are implicated in maintenance of HIV latency. In this review, we examine Lv2 restriction and the antiviral role of RPRD2 and consider potential mechanism(s) of action.
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Affiliation(s)
- Kathryn A. Jackson-Jones
- Centre for Inflammation Research, Institute of Regeneration and Repair, The University of Edinburgh, Edinburgh, United Kingdom
- Division of Infectious Diseases & Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Áine McKnight
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Richard D. Sloan
- Centre for Inflammation Research, Institute of Regeneration and Repair, The University of Edinburgh, Edinburgh, United Kingdom
- ZJU-UoE Institute, Zhejiang University, Haining, China
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16
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Oh C, Buckley PM, Choi J, Hierro A, DiMaio D. Sequence-independent activity of a predicted long disordered segment of the human papillomavirus type 16 L2 capsid protein during virus entry. Proc Natl Acad Sci U S A 2023; 120:e2307721120. [PMID: 37819982 PMCID: PMC10589650 DOI: 10.1073/pnas.2307721120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Accepted: 08/28/2023] [Indexed: 10/13/2023] Open
Abstract
The activity of proteins is thought to be invariably determined by their amino acid sequence or composition, but we show that a long segment of a viral protein can support infection independent of its sequence or composition. During virus entry, the papillomavirus L2 capsid protein protrudes through the endosome membrane into the cytoplasm to bind cellular factors such as retromer required for intracellular virus trafficking. Here, we show that an ~110 amino acid segment of L2 is predicted to be disordered and that large deletions in this segment abolish infectivity of HPV16 pseudoviruses by inhibiting cytoplasmic protrusion of L2, association with retromer, and proper virus trafficking. The activity of these mutants can be restored by insertion of protein segments with diverse sequences, compositions, and chemical properties, including scrambled amino acid sequences, a tandem array of a short sequence, and the intrinsically disordered region of an unrelated cellular protein. The infectivity of mutants with small in-frame deletions in this segment directly correlates with the size of the segment. These results indicate that the length of the disordered segment, not its sequence or composition, determines its activity during HPV16 pseudovirus infection. We propose that a minimal length of L2 is required for it to protrude far enough into the cytoplasm to bind cytoplasmic trafficking factors, but the sequence of this segment is largely irrelevant. Thus, protein segments can carry out complex biological functions such as Human papillomavirus pseudovirus infection in a sequence-independent manner. This finding has important implications for protein function and evolution.
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Affiliation(s)
- Changin Oh
- Department of Genetics, Yale School of Medicine, New Haven, CT06520-8005
| | - Patrick M. Buckley
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT06536-0812
| | - Jeongjoon Choi
- Department of Genetics, Yale School of Medicine, New Haven, CT06520-8005
| | - Aitor Hierro
- Center for Cooperative Research in Biosciences, Bilbao, Derio48160, Spain
- Basque Foundation for Science, Bilbao48009, Spain
| | - Daniel DiMaio
- Department of Genetics, Yale School of Medicine, New Haven, CT06520-8005
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT06520-8040
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT06520-8024
- Yale Cancer Center, New Haven, CT06520-8028
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17
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Gu J, Zhou X, Sutherland L, Kato M, Jaczynska K, Rizo J, McKnight SL. Oxidative regulation of TDP-43 self-association by a β-to-α conformational switch. Proc Natl Acad Sci U S A 2023; 120:e2311416120. [PMID: 37782781 PMCID: PMC10576115 DOI: 10.1073/pnas.2311416120] [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: 07/10/2023] [Accepted: 09/04/2023] [Indexed: 10/04/2023] Open
Abstract
An evolutionarily conserved region of the TDP-43 low-complexity domain (LCD) twenty residues in length can adopt either an α-helical or β-strand conformation. When in the latter conformation, TDP-43 self-associates via the formation of a labile, cross-β structure. Self-association can be monitored via the formation of phase-separated protein droplets. Exposure of droplets to hydrogen peroxide leads to oxidation of conserved methionine residues distributed throughout the LCD. Oxidation disassembles the cross-β structure, thus eliminating both self-association and phase separation. Here, we demonstrate that this process reciprocally enables formation of α-helical structure in precisely the same region formerly functioning to facilitate β-strand-mediated self-association. We further observe that the α-helical conformation allows interaction with a lipid-like detergent and that exposure to lipids enhances the β-to-α conformational switch. We hypothesize that regulation of this oxidative switch will prove to be important to the control of localized translation within vertebrate cells. The experimental observations reported herein were heavily reliant on studies of 1,6-hexanediol, a chemical agent that selectively dissolves labile structures formed via the self-association of protein domains of low sequence complexity. This aliphatic alcohol is shown to exert its dissociative activity primarily via hydrogen-bonding interactions with carbonyl oxygen atoms of the polypeptide backbone. Such observations underscore the central importance of backbone-mediated protein:protein interactions that facilitate the self-association and phase separation of LCDs.
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Affiliation(s)
- Jinge Gu
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX75235
| | - Xiaoming Zhou
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX75235
| | - Lillian Sutherland
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX75235
| | - Masato Kato
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX75235
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, Inage-ku, Chiba263-8555, Japan
| | - Klaudia Jaczynska
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX75235
| | - Josep Rizo
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX75235
| | - Steven L. McKnight
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX75235
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18
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Schibler U. How the circadian nuclear orphan receptor REV-ERBα represses transcription: Temporal and spatial phase separation combined. Mol Cell 2023; 83:3399-3401. [PMID: 37802021 DOI: 10.1016/j.molcel.2023.09.017] [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: 09/12/2023] [Revised: 09/12/2023] [Accepted: 09/12/2023] [Indexed: 10/08/2023]
Abstract
In this issue of Molecular Cell, Zhu et al.1 demonstrate that REV-ERBα and its co-repressor NCOR1 are assembled into daytime-dependent liquid droplets that constitute hubs in which the transcription of multiple REV-ERBα target genes is simultaneously repressed.
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Affiliation(s)
- Ueli Schibler
- Department of Molecular and Cellular Biology, Faculty of Sciences, University of Geneva, Geneva, Switzerland.
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19
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Zhu K, Celwyn IJ, Guan D, Xiao Y, Wang X, Hu W, Jiang C, Cheng L, Casellas R, Lazar MA. An intrinsically disordered region controlling condensation of a circadian clock component and rhythmic transcription in the liver. Mol Cell 2023; 83:3457-3469.e7. [PMID: 37802023 PMCID: PMC10575687 DOI: 10.1016/j.molcel.2023.09.010] [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: 06/05/2023] [Revised: 08/09/2023] [Accepted: 09/08/2023] [Indexed: 10/08/2023]
Abstract
Circadian gene transcription is fundamental to metabolic physiology. Here we report that the nuclear receptor REV-ERBα, a repressive component of the molecular clock, forms circadian condensates in the nuclei of mouse liver. These condensates are dictated by an intrinsically disordered region (IDR) located in the protein's hinge region which specifically concentrates nuclear receptor corepressor 1 (NCOR1) at the genome. IDR deletion diminishes the recruitment of NCOR1 and disrupts rhythmic gene transcription in vivo. REV-ERBα condensates are located at high-order transcriptional repressive hubs in the liver genome that are highly correlated with circadian gene repression. Deletion of the IDR disrupts transcriptional repressive hubs and diminishes silencing of target genes by REV-ERBα. This work demonstrates physiological circadian protein condensates containing REV-ERBα whose IDR is required for hub formation and the control of rhythmic gene expression.
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Affiliation(s)
- Kun Zhu
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Isaac J Celwyn
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Dongyin Guan
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Medicine, Division of Diabetes, Endocrinology and Metabolism, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yang Xiao
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Xiang Wang
- Laboratory of Lymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD 20892, USA
| | - Wenxiang Hu
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Basic Research, Guangzhou Laboratory, Guangdong 510005, China
| | - Chunjie Jiang
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Lan Cheng
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Rafael Casellas
- Laboratory of Lymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD 20892, USA
| | - Mitchell A Lazar
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
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20
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Gu J, Zhou X, Sutherland L, Kato M, Jaczynska K, Rizo J, McKnight SL. Oxidative regulation of TDP-43 self-association by a β-to-α conformational switch. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.29.555361. [PMID: 37693418 PMCID: PMC10491227 DOI: 10.1101/2023.08.29.555361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
An evolutionarily conserved region of the TDP-43 low complexity domain twenty residues in length can adopt either an α-helical or β-strand conformation. When in the latter conformation, TDP-43 self-associates via the formation of a labile, cross-β structure. Self-association can be monitored via the formation of phase separated protein droplets. Exposure of droplets to hydrogen peroxide leads to oxidation of conserved methionine residues distributed throughout the low complexity domain. Oxidation disassembles the cross-β structure, thus eliminating both self-association and phase separation. Here we demonstrate that this process reciprocally enables formation of α-helical structure in precisely the same region formerly functioning to facilitate β-strand mediated self-association. We further observe that the α-helical conformation allows interaction with a lipid-like detergent, and that exposure to lipids enhances the β-to-α conformational switch. We hypothesize that regulation of this oxidative switch will prove to be important to the control of localized translation within vertebrate cells. The experimental observations reported herein were heavily reliant on studies of 1,6-hexanediol, a chemical agent that selectively dissolves labile structures formed via the self-association of protein domains of low sequence complexity. This aliphatic alcohol is shown to exert its dissociative activity primarily via hydrogen bonding interactions with carbonyl oxygen atoms of the polypeptide backbone. Such observations underscore the central importance of backbone-mediated protein:protein interactions that facilitate the self-association and phase separation of low complexity domains. Significance Statement The TDP-43 protein is a constituent of RNA granules involved in regulated translation. TDP-43 contains a C-terminal domain of 150 amino acids of low sequence complexity conspicuously decorated with ten methionine residues. An evolutionarily conserved region (ECR) of 20 residues within this domain can adopt either of two forms of labile secondary structure. Under normal conditions wherein methionine residues are reduced, the ECR forms a labile cross-β structure that enables RNA granule condensation. Upon methionine oxidation, the ECR undergoes a conformational switch to become an α-helix incompatible with self-association and granule integrity. Oxidation of the TDP-43 low complexity domain is hypothesized to occur proximal to mitochondria, thus facilitating dissolution of RNA granules and activation of localized translation.
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Affiliation(s)
- Jinge Gu
- Department of Biochemistry, UT Southwestern Medical Center 5323 Harry Hines Blvd., Dallas, Texas 75235
| | - Xiaoming Zhou
- Department of Biochemistry, UT Southwestern Medical Center 5323 Harry Hines Blvd., Dallas, Texas 75235
| | - Lillian Sutherland
- Department of Biochemistry, UT Southwestern Medical Center 5323 Harry Hines Blvd., Dallas, Texas 75235
| | - Masato Kato
- Department of Biochemistry, UT Southwestern Medical Center 5323 Harry Hines Blvd., Dallas, Texas 75235
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology (QST) 4-9-1, Anagawa, Inage-ku, Chiba, JAPAN 263-8555
| | - Klaudia Jaczynska
- Department of Biophysics, UT Southwestern Medical Center 5323 Harry Hines Blvd., Dallas, Texas 75235
| | - Josep Rizo
- Department of Biophysics, UT Southwestern Medical Center 5323 Harry Hines Blvd., Dallas, Texas 75235
| | - Steven L. McKnight
- Department of Biochemistry, UT Southwestern Medical Center 5323 Harry Hines Blvd., Dallas, Texas 75235
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21
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Arakawa K, Hirose T, Inada T, Ito T, Kai T, Oyama M, Tomari Y, Yoda T, Nakagawa S. Nondomain biopolymers: Flexible molecular strategies to acquire biological functions. Genes Cells 2023; 28:539-552. [PMID: 37249032 DOI: 10.1111/gtc.13050] [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: 04/30/2023] [Revised: 05/15/2023] [Accepted: 05/16/2023] [Indexed: 05/31/2023]
Abstract
A long-standing assumption in molecular biology posits that the conservation of protein and nucleic acid sequences emphasizes the functional significance of biomolecules. These conserved sequences fold into distinct secondary and tertiary structures, enable highly specific molecular interactions, and regulate complex yet organized molecular processes within living cells. However, recent evidence suggests that biomolecules can also function through primary sequence regions that lack conservation across species or gene families. These regions typically do not form rigid structures, and their inherent flexibility is critical for their functional roles. This review examines the emerging roles and molecular mechanisms of "nondomain biomolecules," whose functions are not easily predicted due to the absence of conserved functional domains. We propose the hypothesis that both domain- and nondomain-type molecules work together to enable flexible and efficient molecular processes within the highly crowded intracellular environment.
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Grants
- 21H05273 Ministry of Education, Culture, Sports, Science and Technology
- 21H05274 Ministry of Education, Culture, Sports, Science and Technology
- 21H05275 Ministry of Education, Culture, Sports, Science and Technology
- 21H05276 Ministry of Education, Culture, Sports, Science and Technology
- 21H05277 Ministry of Education, Culture, Sports, Science and Technology
- 21H05278 Ministry of Education, Culture, Sports, Science and Technology
- 21H05279 Ministry of Education, Culture, Sports, Science and Technology
- 21H05280 Ministry of Education, Culture, Sports, Science and Technology
- 21H05281 Ministry of Education, Culture, Sports, Science and Technology
- 21H05282 Ministry of Education, Culture, Sports, Science and Technology
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Affiliation(s)
- Kazuharu Arakawa
- Institute for Advanced Biosciences, Keio University, Tokyo, Japan
| | - Tetsuro Hirose
- RNA Biofunction Laboratory, Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Toshifumi Inada
- Division of RNA and Gene Regulation, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Takuhiro Ito
- Laboratory for Translation Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Japan
| | - Toshie Kai
- Germline Biology Laboratory, Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Masaaki Oyama
- Medical Proteomics Laboratory, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yukihide Tomari
- Laboratory of RNA Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Takao Yoda
- Nagahama Institute of Bio-Science and Technology, Nagahama, Japan
| | - Shinichi Nakagawa
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
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22
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Alghoul E, Basbous J, Constantinou A. Compartmentalization of the DNA damage response: Mechanisms and functions. DNA Repair (Amst) 2023; 128:103524. [PMID: 37320957 DOI: 10.1016/j.dnarep.2023.103524] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 05/31/2023] [Accepted: 06/02/2023] [Indexed: 06/17/2023]
Abstract
Cells have evolved an arsenal of molecular mechanisms to respond to continuous alterations in the primary structure of DNA. At the cellular level, DNA damage response proteins accumulate at sites of DNA damage and organize into nuclear foci. As recounted by Errol Friedberg, pioneering work on DNA repair in the 1930 s was stimulated by collaborations between physicists and geneticists. In recent years, the introduction of ideas from physics on self-organizing compartments has taken the field of cell biology by storm. Percolation and phase separation theories are increasingly used to model the self-assembly of compartments, called biomolecular condensates, that selectively concentrate molecules without a surrounding membrane. In this review, we discuss these concepts in the context of the DNA damage response. We discuss how studies of DNA repair foci as condensates can link molecular mechanisms with cell physiological functions, provide new insights into regulatory mechanisms, and open new perspectives for targeting DNA damage responses for therapeutic purposes.
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Affiliation(s)
- Emile Alghoul
- Institut de Génétique Humaine, Université de Montpellier, CNRS, Montpellier, France
| | - Jihane Basbous
- Institut de Génétique Humaine, Université de Montpellier, CNRS, Montpellier, France
| | - Angelos Constantinou
- Institut de Génétique Humaine, Université de Montpellier, CNRS, Montpellier, France.
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23
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Thirumalai D, Kumar A, Chakraborty D, Straub JE, Mugnai ML. Conformational Fluctuations and Phases in Fused in Sarcoma (FUS) Low-Complexity Domain. ARXIV 2023:arXiv:2303.04215v2. [PMID: 36945688 PMCID: PMC10029050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
The well known phenomenon of phase separation in synthetic polymers and proteins has become a major topic in biophysics because it has been invoked as a mechanism of compartment formation in cells, without the need for membranes. Most of the coacervates (or condensates) are composed of Intrinsically Disordered Proteins (IDPs) or regions that are structureless, often in interaction with RNA and DNA. One of the more intriguing IDPs is the 526-residue RNA binding protein, Fused In Sarcoma (FUS), whose monomer conformations and condensates exhibit unusual behavior that are sensitive to solution conditions. By focussing principally on the N-terminus low complexity domain (FUS-LC comprising residues 1-214) and other truncations, we rationalize the findings of solid state NMR experiments, which show that FUS-LC adopts a non-polymorphic fibril (core-1) involving residues 39-95, flanked by fuzzy coats on both the N- and C- terminal ends. An alternate structure (core-2), whose free energy is comparable to core-1, emerges only in the truncated construct (residues 110-214). Both core-1 and core-2 fibrils are stabilized by a Tyrosine ladder as well as hydrophilic interactions. The morphologies (gels, fibrils, and glass-like behavior) adopted by FUS seem to vary greatly, depending on the experimental conditions. The effect of phosphorylation is site specific and affects the stability of the fibril depending on the sites that are phosphorylated. Many of the peculiarities associated with FUS may also be shared by other IDPs, such as TDP43 and hnRNPA2. We outline a number of problems for which there is no clear molecular understanding.
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Affiliation(s)
- D Thirumalai
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712
- Department of Physics, The University of Texas at Austin, Austin, TX 78712
| | - Abhinaw Kumar
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712
| | - Debayan Chakraborty
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712
| | - John E Straub
- Department of Chemistry, Boston University, Boston, MA 78712
| | - Mauro L Mugnai
- Institute of Soft Matter Synthesis and Metrology, Georgetown University, Washington, DC 20057
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24
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Tayeb-Fligelman E, Bowler JT, Tai CE, Sawaya MR, Jiang YX, Garcia G, Griner SL, Cheng X, Salwinski L, Lutter L, Seidler PM, Lu J, Rosenberg GM, Hou K, Abskharon R, Pan H, Zee CT, Boyer DR, Li Y, Anderson DH, Murray KA, Falcon G, Cascio D, Saelices L, Damoiseaux R, Arumugaswami V, Guo F, Eisenberg DS. Low complexity domains of the nucleocapsid protein of SARS-CoV-2 form amyloid fibrils. Nat Commun 2023; 14:2379. [PMID: 37185252 PMCID: PMC10127185 DOI: 10.1038/s41467-023-37865-3] [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: 07/29/2022] [Accepted: 04/03/2023] [Indexed: 05/17/2023] Open
Abstract
The self-assembly of the Nucleocapsid protein (NCAP) of SARS-CoV-2 is crucial for its function. Computational analysis of the amino acid sequence of NCAP reveals low-complexity domains (LCDs) akin to LCDs in other proteins known to self-assemble as phase separation droplets and amyloid fibrils. Previous reports have described NCAP's propensity to phase-separate. Here we show that the central LCD of NCAP is capable of both, phase separation and amyloid formation. Within this central LCD we identified three adhesive segments and determined the atomic structure of the fibrils formed by each. Those structures guided the design of G12, a peptide that interferes with the self-assembly of NCAP and demonstrates antiviral activity in SARS-CoV-2 infected cells. Our work, therefore, demonstrates the amyloid form of the central LCD of NCAP and suggests that amyloidogenic segments of NCAP could be targeted for drug development.
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Affiliation(s)
- Einav Tayeb-Fligelman
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
- Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA
| | - Jeannette T Bowler
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
- Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA
| | - Christen E Tai
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
| | - Michael R Sawaya
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
- Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA
- UCLA-DOE Institute of Genomics and Proteomics, UCLA, Los Angeles, CA, 90095, USA
| | - Yi Xiao Jiang
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
- Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA
| | - Gustavo Garcia
- Department of Molecular and Medical Pharmacology, UCLA, Los Angeles, CA, 90095, USA
| | - Sarah L Griner
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
- Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA
| | - Xinyi Cheng
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
- Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA
| | - Lukasz Salwinski
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- UCLA-DOE Institute of Genomics and Proteomics, UCLA, Los Angeles, CA, 90095, USA
| | - Liisa Lutter
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
- Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA
| | - Paul M Seidler
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California School of Pharmacy, Los Angeles, CA, 90089-9121, USA
| | - Jiahui Lu
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
- Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA
| | - Gregory M Rosenberg
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
- Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA
| | - Ke Hou
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
- Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA
| | - Romany Abskharon
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
- Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA
| | - Hope Pan
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
- Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA
| | - Chih-Te Zee
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
| | - David R Boyer
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
- Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA
| | - Yan Li
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
| | - Daniel H Anderson
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
- Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA
| | - Kevin A Murray
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
- Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA
| | - Genesis Falcon
- UCLA-DOE Institute of Genomics and Proteomics, UCLA, Los Angeles, CA, 90095, USA
| | - Duilio Cascio
- UCLA-DOE Institute of Genomics and Proteomics, UCLA, Los Angeles, CA, 90095, USA
| | - Lorena Saelices
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- Center for Alzheimer's and Neurodegenerative Diseases, Department of Biophysics, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Robert Damoiseaux
- Department of Molecular and Medical Pharmacology, UCLA, Los Angeles, CA, 90095, USA
- Department of Bioengineering, UCLA, Los Angeles, CA, 90095, USA
- California NanoSystems Institute, UCLA, Los Angeles, CA, 90095, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, CA, 90095, USA
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA, 90095, USA
| | - Vaithilingaraja Arumugaswami
- Department of Molecular and Medical Pharmacology, UCLA, Los Angeles, CA, 90095, USA
- California NanoSystems Institute, UCLA, Los Angeles, CA, 90095, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, CA, 90095, USA
| | - Feng Guo
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA, 90095, USA
| | - David S Eisenberg
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA.
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA.
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA.
- Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA.
- UCLA-DOE Institute of Genomics and Proteomics, UCLA, Los Angeles, CA, 90095, USA.
- California NanoSystems Institute, UCLA, Los Angeles, CA, 90095, USA.
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25
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Oh C, Buckley PM, Choi J, Hierro A, DiMaio D. Sequence independent activity of a predicted long disordered segment of the human papillomavirus L2 capsid protein during virus entry. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.21.533711. [PMID: 36993745 PMCID: PMC10055320 DOI: 10.1101/2023.03.21.533711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
The papillomavirus L2 capsid protein protrudes through the endosome membrane into the cytoplasm during virus entry to bind cellular factors required for intracellular virus trafficking. Cytoplasmic protrusion of HPV16 L2, virus trafficking, and infectivity are inhibited by large deletions in an ∼110 amino acid segment of L2 that is predicted to be disordered. The activity of these mutants can be restored by inserting protein segments with diverse compositions and chemical properties into this region, including scrambled sequences, a tandem array of a short sequence, and the intrinsically disordered region of a cellular protein. The infectivity of mutants with small in-frame insertions and deletions in this segment directly correlates with the size of the segment. These results indicate that the length of the disordered segment, not its sequence or its composition, determines its activity during virus entry. Sequence independent but length dependent activity has important implications for protein function and evolution.
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26
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Staples MI, Frazer C, Fawzi NL, Bennett RJ. Phase separation in fungi. Nat Microbiol 2023; 8:375-386. [PMID: 36782025 PMCID: PMC10081517 DOI: 10.1038/s41564-022-01314-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 12/16/2022] [Indexed: 02/15/2023]
Abstract
Phase separation, in which macromolecules partition into a concentrated phase that is immiscible with a dilute phase, is involved with fundamental cellular processes across the tree of life. We review the principles of phase separation and highlight how it impacts diverse processes in the fungal kingdom. These include the regulation of autophagy, cell signalling pathways, transcriptional circuits and the establishment of asymmetry in fungal cells. We describe examples of stable, phase-separated assemblies including membraneless organelles such as the nucleolus as well as transient condensates that also arise through phase separation and enable cells to rapidly and reversibly respond to important environmental cues. We showcase how research into phase separation in model yeasts, such as Saccharomyces cerevisiae and Schizosaccharomyces pombe, in conjunction with that in plant and human fungal pathogens, such as Ashbya gossypii and Candida albicans, is continuing to enrich our understanding of fundamental molecular processes.
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Affiliation(s)
- Mae I Staples
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, USA
| | - Corey Frazer
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, USA
| | - Nicolas L Fawzi
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA
| | - Richard J Bennett
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, USA.
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27
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Ng SC, Biswas A, Huyton T, Schünemann J, Reber S, Görlich D. Barrier properties of Nup98 FG phases ruled by FG motif identity and inter-FG spacer length. Nat Commun 2023; 14:747. [PMID: 36765044 PMCID: PMC9918544 DOI: 10.1038/s41467-023-36331-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 01/24/2023] [Indexed: 02/12/2023] Open
Abstract
Nup98 FG repeat domains comprise hydrophobic FG motifs linked through uncharged spacers. FG motifs capture nuclear transport receptors (NTRs) during nuclear pore complex (NPC) passage, confer inter-repeat cohesion, and condense the domains into a selective phase with NPC-typical barrier properties. We show that shortening inter-FG spacers enhances cohesion, increases phase density, and tightens such barrier - all consistent with a sieve-like phase. Phase separation tolerates mutating the Nup98-typical GLFG motifs, provided domain-hydrophobicity remains preserved. NTR-entry, however, is sensitive to (certain) deviations from canonical FG motifs, suggesting co-evolutionary adaptation. Unexpectedly, we observed that arginines promote FG-phase-entry apparently also by hydrophobic interactions/ hydrogen-bonding and not just through cation-π interactions. Although incompatible with NTR·cargo complexes, a YG phase displays remarkable transport selectivity, particularly for engineered GFPNTR-variants. GLFG to FSFG mutations make the FG phase hypercohesive, precluding NTR-entry. Extending spacers relaxes this hypercohesion. Thus, antagonism between cohesion and NTR·FG interactions is key to transport selectivity.
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Affiliation(s)
- Sheung Chun Ng
- Department of Cellular Logistics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Abin Biswas
- Quantitative Biology, IRI Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany.,Department of Biological Optomechanics, Max Planck Institute for the Science of Light, Erlangen, Germany
| | - Trevor Huyton
- Department of Cellular Logistics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Jürgen Schünemann
- Department of Cellular Logistics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Simone Reber
- Quantitative Biology, IRI Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Dirk Görlich
- Department of Cellular Logistics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
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28
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RG/RGG repeats in the C. elegans homologs of Nucleolin and GAR1 contribute to sub-nucleolar phase separation. Nat Commun 2022; 13:6585. [PMID: 36329008 PMCID: PMC9633708 DOI: 10.1038/s41467-022-34225-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 10/13/2022] [Indexed: 11/06/2022] Open
Abstract
The intrinsically disordered RG/RGG repeat domain is found in several nucleolar and P-granule proteins, but how it influences their phase separation into biomolecular condensates is unclear. We survey all RG/RGG repeats in C. elegans and uncover nucleolar and P-granule-specific RG/RGG motifs. An uncharacterized protein, K07H8.10, contains the longest nucleolar-like RG/RGG domain in C. elegans. Domain and sequence similarity, as well as nucleolar localization, reveals K07H8.10 (NUCL-1) to be the homolog of Nucleolin, a protein conserved across animals, plants, and fungi, but previously thought to be absent in nematodes. Deleting the RG/RGG repeats within endogenous NUCL-1 and a second nucleolar protein, GARR-1 (GAR1), demonstrates these domains are dispensable for nucleolar accumulation. Instead, their RG/RGG repeats contribute to the phase separation of proteins into nucleolar sub-compartments. Despite this common RG/RGG repeat function, only removal of the GARR-1 RG/RGG domain affects worm fertility and development, decoupling precise sub-nucleolar structure from nucleolar function.
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29
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Lee J, Cho H, Kwon I. Phase separation of low-complexity domains in cellular function and disease. EXPERIMENTAL & MOLECULAR MEDICINE 2022; 54:1412-1422. [PMID: 36175485 PMCID: PMC9534829 DOI: 10.1038/s12276-022-00857-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/15/2022] [Accepted: 07/19/2022] [Indexed: 11/09/2022]
Abstract
In this review, we discuss the ways in which recent studies of low-complexity (LC) domains have challenged our understanding of the mechanisms underlying cellular organization. LC sequences, long believed to function in the absence of a molecular structure, are abundant in the proteomes of all eukaryotic organisms. Over the past decade, the phase separation of LC domains has emerged as a fundamental mechanism driving dynamic multivalent interactions of many cellular processes. We review the key evidence showing the role of phase separation of individual proteins in organizing cellular assemblies and facilitating biological function while implicating the dynamics of phase separation as a key to biological validity and functional utility. We also highlight the evidence showing that pathogenic LC proteins alter various phase separation-dependent interactions to elicit debilitating human diseases, including cancer and neurodegenerative diseases. Progress in understanding the biology of phase separation may offer useful hints toward possible therapeutic interventions to combat the toxicity of pathogenic proteins.
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Affiliation(s)
- Jiwon Lee
- Department of Anatomy and Cell Biology, Sungkyunkwan University School of Medicine, Suwon, 16419, Korea
| | - Hana Cho
- Department of Physiology, Sungkyunkwan University School of Medicine, Suwon, 16419, Korea.
| | - Ilmin Kwon
- Department of Anatomy and Cell Biology, Sungkyunkwan University School of Medicine, Suwon, 16419, Korea.
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30
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Petsko GA, Small SA. Elucidating the causes of neurodegeneration. Science 2022; 377:31-32. [PMID: 35771902 DOI: 10.1126/science.adc9969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Investigating phase separation in neurodegeneration highlights evidence needed for causation.
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Affiliation(s)
- Gregory A Petsko
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham & Women's Hospital and Harvard Medical School, Boson, MA, USA
| | - Scott A Small
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Department of Neurology, Columbia University, New York, NY, USA
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31
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Aledo JC. A Census of Human Methionine-Rich Prion-like Domain-Containing Proteins. Antioxidants (Basel) 2022; 11:antiox11071289. [PMID: 35883780 PMCID: PMC9312190 DOI: 10.3390/antiox11071289] [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: 05/29/2022] [Revised: 06/24/2022] [Accepted: 06/27/2022] [Indexed: 11/16/2022] Open
Abstract
Methionine-rich prion-like proteins can regulate liquid–liquid phase separation processes in response to stresses. To date, however, very few proteins have been identified as methionine-rich prion-like. Herein, we have performed a computational survey of the human proteome to search for methionine-rich prion-like domains. We present a census of 51 manually curated methionine-rich prion-like proteins. Our results show that these proteins tend to be modular in nature, with molecular sizes significantly greater than those we would expect due to random sampling effects. These proteins also exhibit a remarkably high degree of spatial compaction when compared to average human proteins, even when protein size is accounted for. Computational evidence suggests that such a high degree of compactness might be due to the aggregation of methionine residues, pointing to a potential redox regulation of compactness. Gene ontology and network analyses, performed to shed light on the biological processes in which these proteins might participate, indicate that methionine-rich and non-methionine-rich prion-like proteins share gene ontology terms related to the regulation of transcription and translation but, more interestingly, these analyses also reveal that proteins from the methionine-rich group tend to share more gene ontology terms among them than they do with their non-methionine-rich prion-like counterparts.
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Affiliation(s)
- Juan Carlos Aledo
- Department of Molecular Biology and Biochemistry, University of Malaga, 29071 Malaga, Spain
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32
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Rosenberg GM, Murray KA, Salwinski L, Hughes MP, Abskharon R, Eisenberg DS. Bioinformatic identification of previously unrecognized amyloidogenic proteins. J Biol Chem 2022; 298:101920. [PMID: 35405097 PMCID: PMC9108986 DOI: 10.1016/j.jbc.2022.101920] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 04/05/2022] [Accepted: 04/06/2022] [Indexed: 12/04/2022] Open
Abstract
Low-complexity domains (LCDs) of proteins have been shown to self-associate, and pathogenic mutations within these domains often drive the proteins into amyloid aggregation associated with disease. These domains may be especially susceptible to amyloidogenic mutations because they are commonly intrinsically disordered and function in self-association. The question therefore arises whether a search for pathogenic mutations in LCDs of the human proteome can lead to identification of other proteins associated with amyloid disease. Here, we take a computational approach to identify documented pathogenic mutations within LCDs that may favor amyloid formation. Using this approach, we identify numerous known amyloidogenic mutations, including several such mutations within proteins previously unidentified as amyloidogenic. Among the latter group, we focus on two mutations within the TRK-fused gene protein (TFG), known to play roles in protein secretion and innate immunity, which are associated with two different peripheral neuropathies. We show that both mutations increase the propensity of TFG to form amyloid fibrils. We therefore conclude that TFG is a novel amyloid protein and propose that the diseases associated with its mutant forms may be amyloidoses.
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Affiliation(s)
- Gregory M Rosenberg
- Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA-DOE Institute, Molecular Biology Institute, and Howard Hughes Medical Institute, UCLA, Los Angeles, California, USA
| | - Kevin A Murray
- Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA-DOE Institute, Molecular Biology Institute, and Howard Hughes Medical Institute, UCLA, Los Angeles, California, USA
| | - Lukasz Salwinski
- Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA-DOE Institute, Molecular Biology Institute, and Howard Hughes Medical Institute, UCLA, Los Angeles, California, USA
| | - Michael P Hughes
- Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA-DOE Institute, Molecular Biology Institute, and Howard Hughes Medical Institute, UCLA, Los Angeles, California, USA; Department of Cell and Molecular Biology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Romany Abskharon
- Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA-DOE Institute, Molecular Biology Institute, and Howard Hughes Medical Institute, UCLA, Los Angeles, California, USA
| | - David S Eisenberg
- Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA-DOE Institute, Molecular Biology Institute, and Howard Hughes Medical Institute, UCLA, Los Angeles, California, USA.
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