1
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Linhartova K, Falginella FL, Matl M, Sebesta M, Vácha R, Stefl R. Sequence and structural determinants of RNAPII CTD phase-separation and phosphorylation by CDK7. Nat Commun 2024; 15:9163. [PMID: 39448580 PMCID: PMC11502803 DOI: 10.1038/s41467-024-53305-2] [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: 03/05/2024] [Accepted: 10/09/2024] [Indexed: 10/26/2024] Open
Abstract
The intrinsically disordered carboxy-terminal domain (CTD) of the largest subunit of RNA Polymerase II (RNAPII) consists of multiple tandem repeats of the consensus heptapeptide Y1-S2-P3-T4-S5-P6-S7. The CTD promotes liquid-liquid phase-separation (LLPS) of RNAPII in vivo. However, understanding the role of the conserved heptad residues in LLPS is hampered by the lack of direct biochemical characterization of the CTD. Here, we generated a systematic array of CTD variants to unravel the sequence-encoded molecular grammar underlying the LLPS of the human CTD. Using in vitro experiments and molecular dynamics simulations, we report that the aromaticity of tyrosine and cis-trans isomerization of prolines govern CTD phase-separation. The cis conformation of prolines and β-turns in the SPXX motif contribute to a more compact CTD ensemble, enhancing interactions among CTD residues. We further demonstrate that prolines and tyrosine in the CTD consensus sequence are required for phosphorylation by Cyclin-dependent kinase 7 (CDK7). Under phase-separation conditions, CDK7 associates with the surface of the CTD droplets, drastically accelerating phosphorylation and promoting the release of hyperphosphorylated CTD from the droplets. Our results highlight the importance of conformationally restricted local structures within spacer regions, separating uniformly spaced tyrosine stickers of the CTD heptads, which are required for CTD phase-separation.
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Affiliation(s)
- Katerina Linhartova
- CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czechia
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia
| | | | - Martin Matl
- CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czechia
| | - Marek Sebesta
- CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czechia.
| | - Robert Vácha
- CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czechia.
| | - Richard Stefl
- CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czechia.
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia.
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2
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Amith W, Chen VT, Dutagaci B. Clustering of RNA Polymerase II C-Terminal Domain Models upon Phosphorylation. J Phys Chem B 2024; 128:10385-10396. [PMID: 39395159 PMCID: PMC11514005 DOI: 10.1021/acs.jpcb.4c04457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Revised: 09/23/2024] [Accepted: 10/01/2024] [Indexed: 10/14/2024]
Abstract
RNA polymerase II (Pol II) C-terminal domain (CTD) is known to have crucial roles in regulating transcription. CTD has also been highly recognized for undergoing phase separation, which is further associated with its regulatory functions. However, the molecular interactions that the CTD forms to induce clustering to drive phase separations and how the phosphorylation of the CTD affects clustering are not entirely known. In this work, we studied the concentrated solutions of two heptapeptide repeat (2CTD) models at different phosphorylation patterns and protein and ion concentrations using all-atom molecular dynamics simulations to investigate clustering behavior and molecular interactions driving the cluster formation. Our results show that salt concentration and phosphorylation patterns play an important role in determining the clustering pattern, specifically at low protein concentrations. The balance between inter- and intrapeptide interactions and counterion coordination together impact the clustering behavior upon phosphorylation.
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Affiliation(s)
- Weththasinghage
D. Amith
- Department
of Molecular and Cell Biology, University
of California, Merced, California 95343, United States
| | - Vincent T. Chen
- Department
of Molecular and Cell Biology, University
of California, Merced, California 95343, United States
| | - Bercem Dutagaci
- Department
of Molecular and Cell Biology, University
of California, Merced, California 95343, United States
- Health
Sciences Research Institute, University
of California, Merced, California 95343, United States
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3
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Kawasaki K, Fukaya T. Regulatory landscape of enhancer-mediated transcriptional activation. Trends Cell Biol 2024; 34:826-837. [PMID: 38355349 DOI: 10.1016/j.tcb.2024.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/21/2023] [Accepted: 01/22/2024] [Indexed: 02/16/2024]
Abstract
Enhancers are noncoding regulatory elements that instruct spatial and temporal specificity of gene transcription in response to a variety of intrinsic and extrinsic signals during development. Although it has long been postulated that enhancers physically interact with target promoters through the formation of stable loops, recent studies have changed this static view: sequence-specific transcription factors (TFs) and coactivators are dynamically recruited to enhancers and assemble so-called transcription hubs. Dynamic assembly of transcription hubs appears to serve as a key scaffold to integrate regulatory information encoded by surrounding genome and biophysical properties of transcription machineries. In this review, we outline emerging new models of transcriptional regulation by enhancers and discuss future perspectives.
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Affiliation(s)
- Koji Kawasaki
- Laboratory of Transcription Dynamics, Research Center for Biological Visualization, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Takashi Fukaya
- Laboratory of Transcription Dynamics, Research Center for Biological Visualization, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan; Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan.
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4
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Changiarath A, Arya A, Xenidis VA, Padeken J, Stelzl LS. Sequence determinants of protein phase separation and recognition by protein phase-separated condensates through molecular dynamics and active learning. Faraday Discuss 2024. [PMID: 39319382 DOI: 10.1039/d4fd00099d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/26/2024]
Abstract
Elucidating how protein sequence determines the properties of disordered proteins and their phase-separated condensates is a great challenge in computational chemistry, biology, and biophysics. Quantitative molecular dynamics simulations and derived free energy values can in principle capture how a sequence encodes the chemical and biological properties of a protein. These calculations are, however, computationally demanding, even after reducing the representation by coarse-graining; exploring the large spaces of potentially relevant sequences remains a formidable task. We employ an "active learning" scheme introduced by Yang et al. (bioRxiv, 2022, https://doi.org/10.1101/2022.08.05.502972) to reduce the number of labelled examples needed from simulations, where a neural network-based model suggests the most useful examples for the next training cycle. Applying this Bayesian optimisation framework, we determine properties of protein sequences with coarse-grained molecular dynamics, which enables the network to establish sequence-property relationships for disordered proteins and their self-interactions and their interactions in phase-separated condensates. We show how iterative training with second virial coefficients derived from the simulations of disordered protein sequences leads to a rapid improvement in predicting peptide self-interactions. We employ this Bayesian approach to efficiently search for new sequences that bind to condensates of the disordered C-terminal domain (CTD) of RNA Polymerase II, by simulating molecular recognition of peptides to phase-separated condensates in coarse-grained molecular dynamics. By searching for protein sequences which prefer to self-interact rather than interact with another protein sequence we are able to shape the morphology of protein condensates and design multiphasic protein condensates.
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Affiliation(s)
- Arya Changiarath
- Institute of Physics, Johannes Gutenberg University (JGU) Mainz, Germany
| | - Aayush Arya
- Institute of Physics, Johannes Gutenberg University (JGU) Mainz, Germany
| | | | - Jan Padeken
- Institute of Molecular Biology (IMB) Mainz, Germany
| | - Lukas S Stelzl
- Institute of Molecular Biology (IMB) Mainz, Germany
- Institute of Molecular Physiology, Johannes Gutenberg University (JGU) Mainz, Germany.
- KOMET1, Institute of Physics, Johannes Gutenberg University (JGU) Mainz, Germany
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5
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De La Cruz N, Pradhan P, Veettil RT, Conti BA, Oppikofer M, Sabari BR. Disorder-mediated interactions target proteins to specific condensates. Mol Cell 2024; 84:3497-3512.e9. [PMID: 39232584 DOI: 10.1016/j.molcel.2024.08.017] [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: 12/15/2023] [Revised: 05/03/2024] [Accepted: 08/10/2024] [Indexed: 09/06/2024]
Abstract
Selective compartmentalization of cellular contents is fundamental to the regulation of biochemistry. Although membrane-bound organelles control composition by using a semi-permeable barrier, biomolecular condensates rely on interactions among constituents to determine composition. Condensates are formed by dynamic multivalent interactions, often involving intrinsically disordered regions (IDRs) of proteins, yet whether distinct compositions can arise from these dynamic interactions is not known. Here, by comparative analysis of proteins differentially partitioned by two different condensates, we find that distinct compositions arise through specific IDR-mediated interactions. The IDRs of differentially partitioned proteins are necessary and sufficient for selective partitioning. Distinct sequence features are required for IDRs to partition, and swapping these sequence features changes the specificity of partitioning. Swapping whole IDRs retargets proteins and their biochemical activity to different condensates. Our results demonstrate that IDR-mediated interactions can target proteins to specific condensates, enabling the spatial regulation of biochemistry within the cell.
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Affiliation(s)
- Nancy De La Cruz
- Laboratory of Nuclear Organization, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Research, Department of Obstetrics and Gynecology, Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Prashant Pradhan
- Laboratory of Nuclear Organization, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Research, Department of Obstetrics and Gynecology, Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Reshma T Veettil
- Laboratory of Nuclear Organization, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Research, Department of Obstetrics and Gynecology, Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Brooke A Conti
- Pfizer Centers for Therapeutic Innovation, Pfizer Inc., New York, NY 10016, USA
| | - Mariano Oppikofer
- Pfizer Centers for Therapeutic Innovation, Pfizer Inc., New York, NY 10016, USA
| | - Benjamin R Sabari
- Laboratory of Nuclear Organization, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Research, Department of Obstetrics and Gynecology, Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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6
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Zhang Q, Kim W, Panina SB, Mayfield JE, Portz B, Zhang YJ. Variation of C-terminal domain governs RNA polymerase II genomic locations and alternative splicing in eukaryotic transcription. Nat Commun 2024; 15:7985. [PMID: 39266551 PMCID: PMC11393077 DOI: 10.1038/s41467-024-52391-6] [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: 01/11/2024] [Accepted: 09/04/2024] [Indexed: 09/14/2024] Open
Abstract
The C-terminal domain of RPB1 (CTD) orchestrates transcription by recruiting regulators to RNA Pol II upon phosphorylation. With CTD driving condensate formation on gene loci, the molecular mechanism behind how CTD-mediated recruitment of transcriptional regulators influences condensates formation remains unclear. Our study unveils that phosphorylation reversibly dissolves phase separation induced by the unphosphorylated CTD. Phosphorylated CTD, upon specific association with transcription regulators, forms distinct condensates from unphosphorylated CTD. Functional studies demonstrate CTD variants with diverse condensation properties exhibit differences in promoter binding and mRNA co-processing in cells. Notably, varying CTD lengths influence the assembly of RNA processing machinery and alternative splicing outcomes, which in turn affects cellular growth, linking the evolution of CTD variation/length with the complexity of splicing from yeast to human. These findings provide compelling evidence for a model wherein post-translational modification enables the transition of functionally specialized condensates, highlighting a co-evolution link between CTD condensation and splicing.
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Affiliation(s)
- Qian Zhang
- Department of Molecular Biosciences, University of Texas, Austin, TX, USA
| | - Wantae Kim
- McKetta Department of Chemical Engineering, University of Texas, Austin, TX, USA
| | - Svetlana B Panina
- Department of Molecular Biosciences, University of Texas, Austin, TX, USA
| | - Joshua E Mayfield
- Department of Pharmacology, Pathology, Chemistry, and Biochemistry, and Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | | | - Y Jessie Zhang
- Department of Molecular Biosciences, University of Texas, Austin, TX, USA.
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7
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Wilson CB, Lee M, Yau WM, Tycko R. Conformations of a Low-Complexity Protein in Homogeneous and Phase-Separated Frozen Solutions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.25.605144. [PMID: 39372747 PMCID: PMC11451737 DOI: 10.1101/2024.07.25.605144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/08/2024]
Abstract
Solutions of the intrinsically disordered, low-complexity domain of the FUS protein (FUS-LC) undergo liquid-liquid phase separation (LLPS) below temperatures TLLPS in the 20-40° C range. To investigate whether local conformational distributions are detectably different in the homogeneous and phase-separated states of FUS-LC, we performed solid state nuclear magnetic resonance (ssNMR) measurements on solutions that were frozen on sub-millisecond time scales after equilibration at temperatures well above (50° C) or well below (4° C) TLLPS. Measurements were performed at 25 K with signal enhancements from dynamic nuclear polarization. Crosspeak patterns in two-dimensional (2D) ssNMR spectra of rapidly frozen solutions in which FUS-LC was uniformly 15N,13C-labeled were found to be nearly identical for the two states. Similar results were obtained for solutions in which FUS-LC was labeled only at Thr, Tyr, and Gly residues, as well as solutions of a FUS construct in which five specific residues were labeled by ligation of synthetic and recombinant fragments. These experiments show that local conformational distributions are nearly the same in the homogeneous and phase-separated solutions, despite the much greater protein concentrations and more abundant intermolecular interactions within phase-separated, protein-rich "droplets". Comparison of the experimental results with simulations of the sensitivity of 2D crosspeak patterns to an enhanced population of β-strand-like conformations suggests that changes in conformational distributions are no larger than 5-10%. Statement of Significance Liquid-liquid phase separation (LLPS) in solutions of proteins with intrinsically disordered domains has attracted recent attention because of its relevance to multiple biological processes and its inherent interest from the standpoint of protein biophysics. The high protein concentrations and abundant intermolecular interactions within protein-rich, phase-separated "droplets" suggests that conformational distributions of intrinsically disordered proteins may differ in homogeneous and phase-separated solutions. To investigate whether detectable differences exist, we performed experiments on the low-complexity domain of the FUS protein (FUS-LC) in which FUS-LC solutions were first equilibrated at temperatures well above or well below their LLPS transition temperatures, then rapidly frozen and examined at very low temperatures by solid state nuclear magnetic resonance (ssNMR) spectroscopy. The ssNMR data for homogeneous and phase-separated frozen solutions of FUS-LC were found to be nearly identical, showing that LLPS is not accompanied by substantial changes in the local conformational distributions of this intrinsically disordered protein.
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Affiliation(s)
- C. Blake Wilson
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892
| | - Myungwoon Lee
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892
- current address: Department of Chemistry, Drexel University, Philadelphia, PA 19104
| | - Wai-Ming Yau
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892
| | - Robert Tycko
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892
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8
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Keown J, Baazaoui A, Šebesta M, Štefl R, Carrique L, Fodor E, Grimes JM. Structural and functional characterization of the interaction between the influenza A virus RNA polymerase and the CTD of host RNA polymerase II. J Virol 2024; 98:e0013824. [PMID: 38563748 PMCID: PMC11092357 DOI: 10.1128/jvi.00138-24] [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: 01/19/2024] [Accepted: 03/10/2024] [Indexed: 04/04/2024] Open
Abstract
Influenza A viruses, causing seasonal epidemics and occasional pandemics, rely on interactions with host proteins for their RNA genome transcription and replication. The viral RNA polymerase utilizes host RNA polymerase II (Pol II) and interacts with the serine 5 phosphorylated (pS5) C-terminal domain (CTD) of Pol II to initiate transcription. Our study, using single-particle electron cryomicroscopy (cryo-EM), reveals the structure of the 1918 pandemic influenza A virus polymerase bound to a synthetic pS5 CTD peptide composed of four heptad repeats mimicking the 52 heptad repeat mammalian Pol II CTD. The structure shows that the CTD peptide binds at the C-terminal domain of the PA viral polymerase subunit (PA-C) and reveals a previously unobserved position of the 627 domain of the PB2 subunit near the CTD. We identify crucial residues of the CTD peptide that mediate interactions with positively charged cavities on PA-C, explaining the preference of the viral polymerase for pS5 CTD. Functional analysis of mutants targeting the CTD-binding site within PA-C reveals reduced transcriptional function or defects in replication, highlighting the multifunctional role of PA-C in viral RNA synthesis. Our study provides insights into the structural and functional aspects of the influenza virus polymerase-host Pol II interaction and identifies a target for antiviral development.IMPORTANCEUnderstanding the intricate interactions between influenza A viruses and host proteins is crucial for developing targeted antiviral strategies. This study employs advanced imaging techniques to uncover the structural nuances of the 1918 pandemic influenza A virus polymerase bound to a specific host protein, shedding light on the vital process of viral RNA synthesis. The study identifies key amino acid residues in the influenza polymerase involved in binding host polymerase II (Pol II) and highlights their role in both viral transcription and genome replication. These findings not only deepen our understanding of the influenza virus life cycle but also pinpoint a potential target for antiviral development. By elucidating the structural and functional aspects of the influenza virus polymerase-host Pol II interaction, this research provides a foundation for designing interventions to disrupt viral replication and transcription, offering promising avenues for future antiviral therapies.
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Affiliation(s)
- Jeremy Keown
- Division of Structural Biology, Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Alaa Baazaoui
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Marek Šebesta
- CEITEC–Central European Institute of Technology, Masaryk University, Brno, Czechia
| | - Richard Štefl
- CEITEC–Central European Institute of Technology, Masaryk University, Brno, Czechia
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia
| | - Loïc Carrique
- Division of Structural Biology, Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Ervin Fodor
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Jonathan M. Grimes
- Division of Structural Biology, Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
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9
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Valyaeva AA, Sheval EV. Nonspecific Interactions in Transcription Regulation and Organization of Transcriptional Condensates. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:688-700. [PMID: 38831505 DOI: 10.1134/s0006297924040084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/19/2023] [Accepted: 11/20/2023] [Indexed: 06/05/2024]
Abstract
Eukaryotic cells are characterized by a high degree of compartmentalization of their internal contents, which ensures precise and controlled regulation of intracellular processes. During many processes, including different stages of transcription, dynamic membraneless compartments termed biomolecular condensates are formed. Transcription condensates contain various transcription factors and RNA polymerase and are formed by high- and low-specificity interactions between the proteins, DNA, and nearby RNA. This review discusses recent data demonstrating important role of nonspecific multivalent protein-protein and RNA-protein interactions in organization and regulation of transcription.
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Affiliation(s)
- Anna A Valyaeva
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119991, Russia.
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
- Department of Cell Biology and Histology, Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Eugene V Sheval
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
- Department of Cell Biology and Histology, Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
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10
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Wake N, Weng SL, Zheng T, Wang SH, Kirilenko V, Mittal J, Fawzi NL. Expanding the molecular grammar of polar residues and arginine in FUS prion-like domain phase separation and aggregation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.15.580391. [PMID: 38405719 PMCID: PMC10888811 DOI: 10.1101/2024.02.15.580391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
A molecular grammar governing low-complexity prion-like domains phase separation (PS) has been proposed based on mutagenesis experiments that identified tyrosine and arginine as primary drivers of phase separation via aromatic-aromatic and aromatic-arginine interactions. Here we show that additional residues make direct favorable contacts that contribute to phase separation, highlighting the need to account for these contributions in PS theories and models. We find that tyrosine and arginine make important contacts beyond only tyrosine-tyrosine and tyrosine-arginine, including arginine-arginine contacts. Among polar residues, glutamine in particular contributes to phase separation with sequence/position-specificity, making contacts with both tyrosine and arginine as well as other residues, both before phase separation and in condensed phases. For glycine, its flexibility, not its small solvation volume, favors phase separation by allowing favorable contacts between other residues and inhibits the liquid-to-solid (LST) transition. Polar residue types also make sequence-specific contributions to aggregation that go beyond simple rules, which for serine positions is linked to formation of an amyloid-core structure by the FUS low-complexity domain. Hence, here we propose a revised molecular grammar expanding the role of arginine and polar residues in prion-like domain protein phase separation and aggregation.
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Affiliation(s)
- Noah Wake
- Therapeutic Sciences Graduate Program, Brown University, Providence, RI 02912
| | - Shuo-Lin Weng
- Department of Chemistry, Texas A&M University, College Station, TX 77843
| | - Tongyin Zheng
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912
| | - Szu-Huan Wang
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912
| | - Valentin Kirilenko
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912
| | - Jeetain Mittal
- Department of Chemistry, Texas A&M University, College Station, TX 77843
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843
- Interdisciplinary Graduate Program in Genetics and Genomics, Texas A&M University, College Station, TX 77843
| | - Nicolas L Fawzi
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912
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11
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Davis RB, Supakar A, Ranganath AK, Moosa MM, Banerjee PR. Heterotypic interactions can drive selective co-condensation of prion-like low-complexity domains of FET proteins and mammalian SWI/SNF complex. Nat Commun 2024; 15:1168. [PMID: 38326345 PMCID: PMC10850361 DOI: 10.1038/s41467-024-44945-5] [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: 04/12/2023] [Accepted: 01/08/2024] [Indexed: 02/09/2024] Open
Abstract
Prion-like domains (PLDs) are low-complexity protein sequences enriched within nucleic acid-binding proteins including those involved in transcription and RNA processing. PLDs of FUS and EWSR1 play key roles in recruiting chromatin remodeler mammalian SWI/SNF (mSWI/SNF) complex to oncogenic FET fusion protein condensates. Here, we show that disordered low-complexity domains of multiple SWI/SNF subunits are prion-like with a strong propensity to undergo intracellular phase separation. These PLDs engage in sequence-specific heterotypic interactions with the PLD of FUS in the dilute phase at sub-saturation conditions, leading to the formation of PLD co-condensates. In the dense phase, homotypic and heterotypic PLD interactions are highly cooperative, resulting in the co-mixing of individual PLD phases and forming spatially homogeneous condensates. Heterotypic PLD-mediated positive cooperativity in protein-protein interaction networks is likely to play key roles in the co-phase separation of mSWI/SNF complex with transcription factors containing homologous low-complexity domains.
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Affiliation(s)
- Richoo B Davis
- Department of Physics, University at Buffalo, Buffalo, NY, 14260, USA
| | - Anushka Supakar
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, 14260, USA
| | | | | | - Priya R Banerjee
- Department of Physics, University at Buffalo, Buffalo, NY, 14260, USA.
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, 14260, USA.
- Department of Chemical and Biological Engineering, University at Buffalo, Buffalo, NY, 14260, USA.
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12
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Zhang Q, Kim W, Panina S, Mayfield JE, Portz B, Zhang YJ. Variation of C-terminal domain governs RNA polymerase II genomic locations and alternative splicing in eukaryotic transcription. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.01.573828. [PMID: 38260389 PMCID: PMC10802280 DOI: 10.1101/2024.01.01.573828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The C-terminal domain of RPB1 (CTD) orchestrates transcription by recruiting regulators to RNA Pol II upon phosphorylation. Recent insights highlight the pivotal role of CTD in driving condensate formation on gene loci. Yet, the molecular mechanism behind how CTD-mediated recruitment of transcriptional regulators influences condensates formation remains unclear. Our study unveils that phosphorylation reversibly dissolves phase separation induced by the unphosphorylated CTD. Phosphorylated CTD, upon specific association with transcription regulatory proteins, forms distinct condensates from unphosphorylated CTD. Function studies demonstrate CTD variants with diverse condensation properties in vitro exhibit difference in promoter binding and mRNA co-processing in cells. Notably, varying CTD lengths lead to alternative splicing outcomes impacting cellular growth, linking the evolution of CTD variation/length with the complexity of splicing from yeast to human. These findings provide compelling evidence for a model wherein post-translational modification enables the transition of functionally specialized condensates, highlighting a co-evolution link between CTD condensation and splicing.
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Affiliation(s)
- Qian Zhang
- Department of Molecular Biosciences, University of Texas, Austin, Texas, 78712
| | - Wantae Kim
- McKetta Department of Chemical Engineering, University of Texas, Austin, Texas, 78712
| | - Svetlana Panina
- Department of Molecular Biosciences, University of Texas, Austin, Texas, 78712
| | - Joshua E. Mayfield
- Department of Pharmacology, Chemistry, and Biochemistry, and Cellular and Molecular Medicine, University of California San Diego, La Jolla, California 92093
| | - Bede Portz
- Dewpoint Therapeutics, 451 D Street, Boston, Massachusetts 02210
| | - Y. Jessie Zhang
- Department of Molecular Biosciences, University of Texas, Austin, Texas, 78712
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13
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Heimhalt M, Ladurner AG. Disordered protein regions partner up the cBAF remodeler for a chromatin dance. Mol Cell 2023; 83:3763-3765. [PMID: 37922870 DOI: 10.1016/j.molcel.2023.10.002] [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: 10/04/2023] [Revised: 10/04/2023] [Accepted: 10/04/2023] [Indexed: 11/07/2023]
Abstract
Intrinsically disordered protein regions form condensates and mediate interactions with factors that regulate gene activity. Patil et al.1 decode how such regions within the chromatin remodeler cBAF choreograph self-condensation and non-self interactions with transcriptional regulators, potentially impacting disease.
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Affiliation(s)
- Maren Heimhalt
- Biomedical Center Munich, Faculty of Medicine, LMU Munich, Planegg, Martinsried, Germany
| | - Andreas G Ladurner
- Biomedical Center Munich, Faculty of Medicine, LMU Munich, Planegg, Martinsried, Germany; Eisbach Bio GmbH, Planegg, Martinsried, Germany; International Max Planck Research School (IMPRS) for Molecules of Life, Planegg, Martinsried, Germany.
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