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Mitra R, Usher ET, Dedeoğlu S, Crotteau MJ, Fraser OA, Yennawar NH, Gadkari VV, Ruotolo BT, Holehouse AS, Salmon L, Showalter SA, Bardwell JCA. Molecular insights into the interaction between a disordered protein and a folded RNA. Proc Natl Acad Sci U S A 2024; 121:e2409139121. [PMID: 39589885 PMCID: PMC11626198 DOI: 10.1073/pnas.2409139121] [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: 05/07/2024] [Accepted: 10/16/2024] [Indexed: 11/28/2024] Open
Abstract
Intrinsically disordered protein regions (IDRs) are well established as contributors to intermolecular interactions and the formation of biomolecular condensates. In particular, RNA-binding proteins (RBPs) often harbor IDRs in addition to folded RNA-binding domains that contribute to RBP function. To understand the dynamic interactions of an IDR-RNA complex, we characterized the RNA-binding features of a small (68 residues), positively charged IDR-containing protein, Small ERDK-Rich Factor (SERF). At high concentrations, SERF and RNA undergo charge-driven associative phase separation to form a protein- and RNA-rich dense phase. A key advantage of this model system is that this threshold for demixing is sufficiently high that we could use solution-state biophysical methods to interrogate the stoichiometric complexes of SERF with RNA in the one-phase regime. Herein, we describe our comprehensive characterization of SERF alone and in complex with a small fragment of the HIV-1 Trans-Activation Response (TAR) RNA with complementary biophysical methods and molecular simulations. We find that this binding event is not accompanied by the acquisition of structure by either molecule; however, we see evidence for a modest global compaction of the SERF ensemble when bound to RNA. This behavior likely reflects attenuated charge repulsion within SERF via binding to the polyanionic RNA and provides a rationale for the higher-order assembly of SERF in the context of RNA. We envision that the SERF-RNA system will lower the barrier to accessing the details that support IDR-RNA interactions and likewise deepen our understanding of the role of IDR-RNA contacts in complex formation and liquid-liquid phase separation.
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Affiliation(s)
- Rishav Mitra
- HHMI, University of Michigan, Ann Arbor, MI48109
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI48109
| | - Emery T. Usher
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO63110
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO63110
| | - Selin Dedeoğlu
- Centre de Résonance Magnétique Nucléaire à Très Hauts Champs, UMR 5082, CNRS, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, Université de Lyon, Villeurbanne69100, France
| | - Matthew J. Crotteau
- HHMI, University of Michigan, Ann Arbor, MI48109
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI48109
| | - Olivia A. Fraser
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA16802
| | - Neela H. Yennawar
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA16802
| | - Varun V. Gadkari
- Department of Chemistry, University of Michigan, Ann Arbor, MI48109
| | | | - Alex S. Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO63110
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO63110
| | - Loïc Salmon
- Centre de Résonance Magnétique Nucléaire à Très Hauts Champs, UMR 5082, CNRS, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, Université de Lyon, Villeurbanne69100, France
| | - Scott A. Showalter
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA16802
- Department of Chemistry, The Pennsylvania State University, University Park, PA16802
| | - James C. A. Bardwell
- HHMI, University of Michigan, Ann Arbor, MI48109
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI48109
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Sahoo BR, Subramanian V, Bardwell JC. Backbone 1H, 13C, and 15N chemical shift assignments for human SERF2. BIOMOLECULAR NMR ASSIGNMENTS 2024; 18:51-57. [PMID: 38466543 PMCID: PMC12022958 DOI: 10.1007/s12104-024-10167-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 02/28/2024] [Indexed: 03/13/2024]
Abstract
Human small EDRK-rich factor protein SERF2 is a cellular driver of protein amyloid formation, a process that has been linked to neurodegenerative diseases including Alzheimer's and Parkinson's disease. SERF2 is a 59 amino acid protein, highly charged, and well conserved whose structure and physiological function is unclear. SERF family proteins including human SERF2 have shown a tendency to form fuzzy complexes with misfolded proteins such as α-Synuclein which has been linked to Parkinson's disease. SERF family proteins have been recently identified to bind nucleic acids, but the binding mechanism(s) remain enigmatic. Here, using multidimensional solution NMR, we report the 1H, 15N, and 13C chemical shift assignments (~ 86% of backbone resonance assignments) for human SERF2. TALOS-N predicted secondary structure of SERF2 showed three very short helices (3-4 residues long) in the N-terminal region of the protein and a long helix in the C-terminal region spanning residues 37-46 which is consistent with the helical content indicated by circular dichroism spectroscopy. Paramagnetic relaxation enhancement NMR analysis revealed that a short C-terminal region E53-K55 is in the proximity of the N-terminus. Having the backbone assignment of SERF2 allowed us to probe its interaction with α-Synuclein and to identify the residues in SERF2 binding interfaces that likely promote α-Synuclein aggregation.
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Affiliation(s)
- Bikash R. Sahoo
- Howard Hughes Medical Institute, Chevy Chase MD-20815, USA
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor MI-48109, USA
| | | | - James C.A. Bardwell
- Howard Hughes Medical Institute, Chevy Chase MD-20815, USA
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor MI-48109, USA
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Zhou H, Fu N, Tian Y, Zhang N, Fan Q, Zeng F, Wang Y, Bai G, Chen B. Transcriptome Sequencing of Gingival Tissues from Impacted Third Molars Patients Reveals the Alterations of Gene Expression. Comb Chem High Throughput Screen 2024; 27:2350-2365. [PMID: 38178683 DOI: 10.2174/0113862073256803231114095626] [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: 06/21/2023] [Revised: 09/25/2023] [Accepted: 10/02/2023] [Indexed: 01/06/2024]
Abstract
OBJECTIVE The removal of impacted third molars by surgery may occur with a series of complications, whereas limited information about the postoperative pathogenesis is available. The objective of this study is to identify changes in gene expression after flap surgical removal of impacted third molars and provide potential information to reduce postoperative complications. METHODS The gingival tissues of twenty patients with flap surgical removal of impacted third molars and twenty healthy volunteers were collected for gene expression testing. The collected gingival tissues were used RNA sequencing technology and quantitative real-time PCR validation was performed. DEG was mapped to protein databases such as GO and KEGG for functional annotation and, based on annotation information, for mining of differential expression genes in patients with mpacted third molars. RESULTS A total of 555 genes were differentially expressed. Among the top up-regulated genes, HLA-DRB4, CCL20, and CXCL8 were strongly associated with immune response and signal transduction. Among the top down-regulated genes, SPRR2B, CLDN17, LCE3D and LCE3E were related to keratinocyte differentiation, IFITM5, and BGLAP were related to bone mineralization, UGT2B17 is associated with susceptibility to osteoporosis. KEGG results showed that the DEGs were related to multiple disease-related pathways. CONCLUSION This first transcriptome analysis of gingival tissues from patients with surgical removal of impacted third molars provides new insights into postoperative genetic changes. The results may establish a basis for future research on minimizing the incidence of complications after flap-treated third molars.
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Affiliation(s)
- Haolin Zhou
- Oral Disease Research Key Laboratory of Guizhou Tertiary Institution, Institute of Life Sciences, Zunyi Medical University, Zunyi, Guizhou, 563000, China
- Hospital of Stomatology, Zunyi Medical University, Zunyi, Guizhou, 563000, China
| | - Nanqing Fu
- Oral Disease Research Key Laboratory of Guizhou Tertiary Institution, Institute of Life Sciences, Zunyi Medical University, Zunyi, Guizhou, 563000, China
| | - Yuan Tian
- Oral Disease Research Key Laboratory of Guizhou Tertiary Institution, Institute of Life Sciences, Zunyi Medical University, Zunyi, Guizhou, 563000, China
- Hospital of Stomatology, Zunyi Medical University, Zunyi, Guizhou, 563000, China
| | - Nini Zhang
- Hospital of Stomatology, Zunyi Medical University, Zunyi, Guizhou, 563000, China
| | - Qin Fan
- Oral Disease Research Key Laboratory of Guizhou Tertiary Institution, Institute of Life Sciences, Zunyi Medical University, Zunyi, Guizhou, 563000, China
- Hospital of Stomatology, Zunyi Medical University, Zunyi, Guizhou, 563000, China
| | - Fengjiao Zeng
- Oral Disease Research Key Laboratory of Guizhou Tertiary Institution, Institute of Life Sciences, Zunyi Medical University, Zunyi, Guizhou, 563000, China
- Hospital of Stomatology, Zunyi Medical University, Zunyi, Guizhou, 563000, China
| | - Yueyue Wang
- Oral Disease Research Key Laboratory of Guizhou Tertiary Institution, Institute of Life Sciences, Zunyi Medical University, Zunyi, Guizhou, 563000, China
- Hospital of Stomatology, Zunyi Medical University, Zunyi, Guizhou 563000, China
| | - Guohui Bai
- Oral Disease Research Key Laboratory of Guizhou Tertiary Institution, Institute of Life Sciences, Zunyi Medical University, Zunyi, Guizhou, 563000, China
- Hospital of Stomatology, Zunyi Medical University, Zunyi, Guizhou, 563000, China
| | - Bin Chen
- Oral Disease Research Key Laboratory of Guizhou Tertiary Institution, Institute of Life Sciences, Zunyi Medical University, Zunyi, Guizhou, 563000, China
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