1
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Patel CK, Mukherjee TK. Biomolecular Condensation of Trypsin Prevents Autolysis and Promotes Ca 2+-Mediated Activation of Esterase Activity. Biomacromolecules 2024; 25:6082-6092. [PMID: 39116325 DOI: 10.1021/acs.biomac.4c00736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2024]
Abstract
The presence of Ca2+ ions is known to facilitate the activity of trypsin-like serine proteases via structural stabilization against thermal denaturation and autolysis. Herein, we report a new and hidden regulatory role of Ca2+ in the catalytic pathways of trypsin and α-chymotrypsin under physiological conditions. We discovered that macromolecular crowding promotes spontaneous homotypic condensation of trypsin via liquid-liquid phase separation to yield membraneless condensates over a broad range of concentrations, pH, and temperature, which are stabilized by multivalent hydrophobic interactions. Interestingly, we found that Ca2+ binding in the calcium binding loop reversibly regulates the condensation of trypsin and α-chymotrypsin. Spontaneous condensation effectively prevents autolysis of trypsin and preserves its native-like esterase activity for a prolonged period of time. It has also been found that phase-separated trypsin responds to Ca2+-dependent activation of its esterase activity even after 14 days of storage while free trypsin failed to do so. The present study highlights an important physiological aspect by which cells can spatiotemporally regulate the biocatalytic efficacy of trypsin-like serine proteases via Ca2+-signaling.
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Affiliation(s)
- Chinmaya Kumar Patel
- Department of Chemistry, Indian Institute of Technology (IIT) Indore, Simrol, Indore 453552, Madhya Pradesh, India
| | - Tushar Kanti Mukherjee
- Department of Chemistry, Indian Institute of Technology (IIT) Indore, Simrol, Indore 453552, Madhya Pradesh, India
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2
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Kettel P, Marosits L, Spinetti E, Rechberger M, Giannini C, Radler P, Niedermoser I, Fischer I, Versteeg GA, Loose M, Covino R, Karagöz GE. Disordered regions in the IRE1α ER lumenal domain mediate its stress-induced clustering. EMBO J 2024:10.1038/s44318-024-00207-0. [PMID: 39232130 DOI: 10.1038/s44318-024-00207-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 07/02/2024] [Accepted: 07/23/2024] [Indexed: 09/06/2024] Open
Abstract
Conserved signaling cascades monitor protein-folding homeostasis to ensure proper cellular function. One of the evolutionary conserved key players is IRE1, which maintains endoplasmic reticulum (ER) homeostasis through the unfolded protein response (UPR). Upon accumulation of misfolded proteins in the ER, IRE1 forms clusters on the ER membrane to initiate UPR signaling. What regulates IRE1 cluster formation is not fully understood. Here, we show that the ER lumenal domain (LD) of human IRE1α forms biomolecular condensates in vitro. IRE1α LD condensates were stabilized both by binding to unfolded polypeptides as well as by tethering to model membranes, suggesting their role in assembling IRE1α into signaling-competent stable clusters. Molecular dynamics simulations indicated that weak multivalent interactions drive IRE1α LD clustering. Mutagenesis experiments identified disordered regions in IRE1α LD to control its clustering in vitro and in cells. Importantly, dysregulated clustering of IRE1α mutants led to defects in IRE1α signaling. Our results revealed that disordered regions in IRE1α LD control its clustering and suggest their role as a common strategy in regulating protein assembly on membranes.
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Affiliation(s)
- Paulina Kettel
- Max Perutz Laboratories Vienna, Vienna BioCenter, Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Laura Marosits
- Max Perutz Laboratories Vienna, Vienna BioCenter, Vienna, Austria
- Medical University of Vienna, Vienna, Austria
| | - Elena Spinetti
- Frankfurt Institute for Advanced Studies, Frankfurt, Germany
- Institute of Biophysics, Goethe University, Frankfurt, Germany
| | | | - Caterina Giannini
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Philipp Radler
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Isabell Niedermoser
- Max Perutz Laboratories Vienna, Vienna BioCenter, Vienna, Austria
- Medical University of Vienna, Vienna, Austria
| | - Irmgard Fischer
- Max Perutz Laboratories Vienna, Vienna BioCenter, Vienna, Austria
| | - Gijs A Versteeg
- Max Perutz Laboratories Vienna, Vienna BioCenter, Vienna, Austria
- Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna, Austria
| | - Martin Loose
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Roberto Covino
- Frankfurt Institute for Advanced Studies, Frankfurt, Germany
- IMPRS on Cellular Biophysics, Frankfurt, Germany
| | - G Elif Karagöz
- Max Perutz Laboratories Vienna, Vienna BioCenter, Vienna, Austria.
- Medical University of Vienna, Vienna, Austria.
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3
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Wu C, Wang X, Li Y, Zhen W, Wang C, Wang X, Xie Z, Xu X, Guo S, Botella JR, Zheng B, Wang W, Song CP, Hu Z. Sequestration of DBR1 to stress granules promotes lariat intronic RNAs accumulation for heat-stress tolerance. Nat Commun 2024; 15:7696. [PMID: 39227617 PMCID: PMC11371829 DOI: 10.1038/s41467-024-52034-w] [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: 11/25/2023] [Accepted: 08/22/2024] [Indexed: 09/05/2024] Open
Abstract
Heat stress (HS) poses a significant challenge to plant survival, necessitating sophisticated molecular mechanisms to maintain cellular homeostasis. Here, we identify SICKLE (SIC) as a key modulator of HS responses in Arabidopsis (Arabidopsis thaliana). SIC is required for the sequestration of RNA DEBRANCHING ENZYME 1 (DBR1), a rate-limiting enzyme of lariat intronic RNA (lariRNA) decay, into stress granules (SGs). The sequestration of DBR1 by SIC enhances the accumulation of lariRNAs, branched circular RNAs derived from excised introns during pre-mRNA splicing, which in turn promote the transcription of their parental genes. Our findings further demonstrate that SIC-mediated DBR1 sequestration in SGs is crucial for plant HS tolerance, as deletion of the N-terminus of SIC (SIC1-244) impairs DBR1 sequestration and compromises plant response to HS. Overall, our study unveils a mechanism of transcriptional regulation in the HS response, where lariRNAs are enriched through DBR1 sequestration, ultimately promoting the transcription of heat stress tolerance genes.
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Affiliation(s)
- Chengyun Wu
- The Zhongzhou Laboratory for Integrative Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
- Sanya Institute, Henan University, Sanya, 572025, China
- The National Engineering Lab of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Xingsong Wang
- The Zhongzhou Laboratory for Integrative Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Yan Li
- The Zhongzhou Laboratory for Integrative Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Weibo Zhen
- The Zhongzhou Laboratory for Integrative Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Chunfei Wang
- The Zhongzhou Laboratory for Integrative Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Xiaoqing Wang
- The Zhongzhou Laboratory for Integrative Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Zhouli Xie
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Xiumei Xu
- The Zhongzhou Laboratory for Integrative Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
- Sanya Institute, Henan University, Sanya, 572025, China
| | - Siyi Guo
- The Zhongzhou Laboratory for Integrative Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
- Sanya Institute, Henan University, Sanya, 572025, China
| | - José Ramón Botella
- Plant Genetic Engineering Laboratory, School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Binglian Zheng
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Wei Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
- Center for Life Sciences, Beijing, 100871, China
| | - Chun-Peng Song
- The Zhongzhou Laboratory for Integrative Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China.
- Sanya Institute, Henan University, Sanya, 572025, China.
| | - Zhubing Hu
- The Zhongzhou Laboratory for Integrative Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China.
- Sanya Institute, Henan University, Sanya, 572025, China.
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4
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Lima CR, Antunes D, Caffarena E, Carels N. Structural Characterization of Heat Shock Protein 90β and Molecular Interactions with Geldanamycin and Ritonavir: A Computational Study. Int J Mol Sci 2024; 25:8782. [PMID: 39201468 PMCID: PMC11354266 DOI: 10.3390/ijms25168782] [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: 06/20/2024] [Revised: 08/07/2024] [Accepted: 08/09/2024] [Indexed: 09/02/2024] Open
Abstract
Drug repositioning is an important therapeutic strategy for treating breast cancer. Hsp90β chaperone is an attractive target for inhibiting cell progression. Its structure has a disordered and flexible linker region between the N-terminal and central domains. Geldanamycin was the first Hsp90β inhibitor to interact specifically at the N-terminal site. Owing to the toxicity of geldanamycin, we investigated the repositioning of ritonavir as an Hsp90β inhibitor, taking advantage of its proven efficacy against cancer. In this study, we used molecular modeling techniques to analyze the contribution of the Hsp90β linker region to the flexibility and interaction between the ligands geldanamycin, ritonavir, and Hsp90β. Our findings indicate that the linker region is responsible for the fluctuation and overall protein motion without disturbing the interaction between the inhibitors and the N-terminus. We also found that ritonavir established similar interactions with the substrate ATP triphosphate, filling the same pharmacophore zone.
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Affiliation(s)
- Carlyle Ribeiro Lima
- Laboratory of Biological System Modeling, Centro de Desenvolvimento Tecnológico em Saúde (CDTS), Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 21040-900, Brazil
| | - Deborah Antunes
- Laboratório de Genômica Aplicada e Bioinovações, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 21040-900, Brazil;
| | - Ernesto Caffarena
- Grupo de Biofísica Computacional e Modelagem Molecular, Programa de Computação Científica (PROCC), Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 21040-900, Brazil;
| | - Nicolas Carels
- Laboratory of Biological System Modeling, Centro de Desenvolvimento Tecnológico em Saúde (CDTS), Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 21040-900, Brazil
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5
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Martínez-Valencia D, Bañuelos C, García-Rivera G, Talamás-Lara D, Orozco E. The Entamoeba histolytica Vps26 (EhVps26) retromeric protein is involved in phagocytosis: Bioinformatic and experimental approaches. PLoS One 2024; 19:e0304842. [PMID: 39116045 PMCID: PMC11309391 DOI: 10.1371/journal.pone.0304842] [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: 01/29/2024] [Accepted: 05/21/2024] [Indexed: 08/10/2024] Open
Abstract
The retromer is a cellular structure that recruits and recycles proteins inside the cell. In mammalian and yeast, the retromer components have been widely studied, but very little in parasites. In yeast, it is formed by a SNX-BAR membrane remodeling heterodimer and the cargo selecting complex (CSC), composed by three proteins. One of them, the Vps26 protein, possesses a flexible and intrinsically disordered region (IDR), that facilitates interactions with other proteins and contributes to the retromer binding to the endosomal membrane. In Entamoeba histolytica, the protozoan parasite responsible for human amoebiasis, the retromer actively participates during the high mobility and phagocytosis of trophozoites, but the molecular details in these events, are almost unknown. Here, we studied the EhVps26 role in phagocytosis. Bioinformatic analyses of EhVps26 revealed a typical arrestin folding structure of the protein, and a long and charged IDR, as described in other systems. EhVps26 molecular dynamics simulations (MDS) allowed us to predict binding pockets for EhVps35, EhSNX3, and a PX domain-containing protein; these pockets were disorganized in a EhVps26 truncated version lacking the IDR. The AlphaFold2 software predicted the interaction of EhVps26 with EhVps35, EhVps29 and EhSNX3, in a model similar to the reported mammalian crystals. By confocal and transmission electron microscopy, EhVps26 was found in the trophozoites plasma membrane, cytosol, endosomes, and Golgi-like apparatus. During phagocytosis, it followed the erythrocytes pathway, probably participating in cargoes selection and recycling. Ehvps26 gene knocking down evidenced that the EhVps26 protein is necessary for efficient phagocytosis.
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Affiliation(s)
- Diana Martínez-Valencia
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Ciudad de México, México
| | - Cecilia Bañuelos
- Doctorado Transdisciplinario en Desarrollo Científico y Tecnológico para la Sociedad, Cinvestav, Ciudad de México, México
| | - Guillermina García-Rivera
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Ciudad de México, México
| | - Daniel Talamás-Lara
- Laboratorios Nacionales de Servicios Experimentales (LaNSE), Cinvestav, Unidad de Microscopía Electrónica, Ciudad de México, México
| | - Esther Orozco
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Ciudad de México, México
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6
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Xiao YX, Lee SY, Aguilera-Uribe M, Samson R, Au A, Khanna Y, Liu Z, Cheng R, Aulakh K, Wei J, Farias AG, Reilly T, Birkadze S, Habsid A, Brown KR, Chan K, Mero P, Huang JQ, Billmann M, Rahman M, Myers C, Andrews BJ, Youn JY, Yip CM, Rotin D, Derry WB, Forman-Kay JD, Moses AM, Pritišanac I, Gingras AC, Moffat J. The TSC22D, WNK, and NRBP gene families exhibit functional buffering and evolved with Metazoa for cell volume regulation. Cell Rep 2024; 43:114417. [PMID: 38980795 DOI: 10.1016/j.celrep.2024.114417] [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: 02/22/2024] [Revised: 05/08/2024] [Accepted: 06/13/2024] [Indexed: 07/11/2024] Open
Abstract
The ability to sense and respond to osmotic fluctuations is critical for the maintenance of cellular integrity. We used gene co-essentiality analysis to identify an unappreciated relationship between TSC22D2, WNK1, and NRBP1 in regulating cell volume homeostasis. All of these genes have paralogs and are functionally buffered for osmo-sensing and cell volume control. Within seconds of hyperosmotic stress, TSC22D, WNK, and NRBP family members physically associate into biomolecular condensates, a process that is dependent on intrinsically disordered regions (IDRs). A close examination of these protein families across metazoans revealed that TSC22D genes evolved alongside a domain in NRBPs that specifically binds to TSC22D proteins, which we have termed NbrT (NRBP binding region with TSC22D), and this co-evolution is accompanied by rapid IDR length expansion in WNK-family kinases. Our study reveals that TSC22D, WNK, and NRBP genes evolved in metazoans to co-regulate rapid cell volume changes in response to osmolarity.
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Affiliation(s)
- Yu-Xi Xiao
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Seon Yong Lee
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Magali Aguilera-Uribe
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Reuben Samson
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health, Toronto, ON, Canada
| | - Aaron Au
- Institute for Biomedical Engineering, University of Toronto, Toronto, ON, Canada; Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada; Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Yukti Khanna
- Otto-Loewi Research Center, Division of Medicinal Chemistry, Medical University of Graz, Neue Stiftingtalstrabe 6, 8010, Graz, Austria
| | - Zetao Liu
- Program in Cell Biology, The Hospital for Sick Children, Toronto, ON, Canada; Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Ran Cheng
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Kamaldeep Aulakh
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Jiarun Wei
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Adrian Granda Farias
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Taylor Reilly
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Saba Birkadze
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Andrea Habsid
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Kevin R Brown
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Katherine Chan
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Patricia Mero
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Jie Qi Huang
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON, Canada
| | - Maximilian Billmann
- Institute of Human Genetics, School of Medicine and University Hospital Bonn, University of Bonn, 53127 Bonn, Germany
| | - Mahfuzur Rahman
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Chad Myers
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Brenda J Andrews
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Ji-Young Youn
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON, Canada
| | - Christopher M Yip
- Institute for Biomedical Engineering, University of Toronto, Toronto, ON, Canada; Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Daniela Rotin
- Program in Cell Biology, The Hospital for Sick Children, Toronto, ON, Canada; Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - W Brent Derry
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Julie D Forman-Kay
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada; Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON, Canada
| | - Alan M Moses
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Iva Pritišanac
- Otto-Loewi Research Center, Division of Medicinal Chemistry, Medical University of Graz, Neue Stiftingtalstrabe 6, 8010, Graz, Austria
| | - Anne-Claude Gingras
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health, Toronto, ON, Canada
| | - Jason Moffat
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; Institute for Biomedical Engineering, University of Toronto, Toronto, ON, Canada.
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7
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Naudi-Fabra S, Elena-Real CA, Vedel IM, Tengo M, Motzny K, Jiang PL, Schmieder P, Liu F, Milles S. An extended interaction site determines binding between AP180 and AP2 in clathrin mediated endocytosis. Nat Commun 2024; 15:5884. [PMID: 39003270 PMCID: PMC11246429 DOI: 10.1038/s41467-024-50212-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 07/03/2024] [Indexed: 07/15/2024] Open
Abstract
The early phases of clathrin mediated endocytosis are organized through a highly complex interaction network mediated by clathrin associated sorting proteins (CLASPs) that comprise long intrinsically disordered regions (IDRs). AP180 is a CLASP exclusively expressed in neurons and comprises a long IDR of around 600 residues, whose function remains partially elusive. Using NMR spectroscopy, we discovered an extended and strong interaction site within AP180 with the major adaptor protein AP2, and describe its binding dynamics at atomic resolution. We find that the 70 residue-long site determines the overall interaction between AP180 and AP2 in a dynamic equilibrium between its bound and unbound states, while weaker binding sites contribute to the overall affinity at much higher concentrations of AP2. Our data suggest that this particular interaction site might play a central role in recruitment of adaptors to the clathrin coated pit, whereas more transient and promiscuous interactions allow reshaping of the interaction network until cargo uptake inside a coated vesicle.
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Affiliation(s)
- Samuel Naudi-Fabra
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125, Berlin, Germany
- Université Grenoble Alpes, CNRS, CEA, IBS, F-38000, Grenoble, France
| | - Carlos A Elena-Real
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Ida Marie Vedel
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Maud Tengo
- Université Grenoble Alpes, CNRS, CEA, IBS, F-38000, Grenoble, France
| | - Kathrin Motzny
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Pin-Lian Jiang
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Peter Schmieder
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Fan Liu
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Sigrid Milles
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125, Berlin, Germany.
- Université Grenoble Alpes, CNRS, CEA, IBS, F-38000, Grenoble, France.
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8
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Reys V, Pons JL, Labesse G. SLiMAn 2.0: meaningful navigation through peptide-protein interaction networks. Nucleic Acids Res 2024; 52:W313-W317. [PMID: 38783158 PMCID: PMC11223867 DOI: 10.1093/nar/gkae398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/17/2024] [Accepted: 04/30/2024] [Indexed: 05/25/2024] Open
Abstract
Among the myriad of protein-protein interactions occurring in living organisms, a substantial amount involves small linear motifs (SLiMs) recognized by structured domains. However, predictions of SLiM-based networks are tedious, due to the abundance of such motifs and a high portion of false positive hits. For this reason, a webserver SLiMAn (Short Linear Motif Analysis) was developed to focus the search on the most relevant SLiMs. Using SLiMAn, one can navigate into a given (meta-)interactome and tune a variety of parameters associated to each type of SLiMs in attempt to identify functional ELM motifs and their recognition domains. The IntAct and BioGRID databases bring experimental information, while IUPred and AlphaFold provide boundaries of folded and disordered regions. Post-translational modifications listed in PhosphoSite+ are highlighted. Links to PubMed accelerate scrutiny into the literature, to support (or not) putative pairings. Dedicated visualization features are also incorporated, such as Cytoscape for macromolecular networks and BINANA for intermolecular contacts within structural models generated by SCWRL 3.0. The use of SLiMAn 2.0 is illustrated on a simple example. It is freely available at https://sliman2.cbs.cnrs.fr.
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Affiliation(s)
- Victor Reys
- Centre de Biologie Structurale, CNRS, INSERM, Univ. Montpellier, Montpellier, France
| | - Jean-Luc Pons
- Centre de Biologie Structurale, CNRS, INSERM, Univ. Montpellier, Montpellier, France
| | - Gilles Labesse
- Centre de Biologie Structurale, CNRS, INSERM, Univ. Montpellier, Montpellier, France
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9
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Alici H, Uversky VN, Kang DE, Woo JA, Coskuner-Weber O. The impacts of the mitochondrial myopathy-associated G58R mutation on the dynamic structural properties of CHCHD10. J Biomol Struct Dyn 2024; 42:5607-5616. [PMID: 37349880 DOI: 10.1080/07391102.2023.2227713] [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: 12/16/2022] [Accepted: 06/14/2023] [Indexed: 06/24/2023]
Abstract
The mitochondria are responsible for producing energy within the cell, and in mitochondrial myopathy, there is a defect in the energy production process. The CHCHD10 gene codes for a protein called coiled-coil-helix-coiled-coil-helix domain-containing protein 10 (CHCHD10), which is found in the mitochondria and is involved in the regulation of mitochondrial function. G58R mutation has been shown to disrupt the normal function of CHCHD10, leading to mitochondrial dysfunction and ultimately to the development of mitochondrial myopathy. The structures of G58R mutant CHCHD10 and how G58R mutation impacts the wild-type CHCHD10 protein at the monomeric level are unknown. To address this problem, we conducted homology modeling, multiple run molecular dynamics simulations and bioinformatics calculations. We represent herein the structural ensemble properties of the G58R mutant CHCHD10 (CHCHD10G58R) in aqueous solution. Moreover, we describe the impacts of G58R mutation on the structural ensembles of wild-type CHCHD10 (CHCHD10WT) in aqueous solution. The dynamics properties as well as structural properties of CHCHD10WT are impacted by the mitochondrial myopathy-related G58R mutation. Specifically, the secondary and tertiary structure properties, root mean square fluctuations, Ramachandran diagrams and results from principal component analysis demonstrate that the CHCHD10WT and CHCHD10G58R proteins possess different structural ensemble characteristics and describe the impacts of G58R mutation on CHCHD10WT. These findings may be helpful for designing new treatments for mitochondrial myopathy.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Hakan Alici
- Faculty of Sciences, Department of Physics, Zonguldak Bulent Ecevit University, Zonguldak, Turkey
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - David E Kang
- School of Medicine, Department of Pathology, Case Western Reserve University, Cleveland, USA
- Louis Stokes Cleveland VA Medical Center, Cleveland, USA
| | - Junga Alexa Woo
- School of Medicine, Department of Pathology, Case Western Reserve University, Cleveland, USA
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10
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Khachatryan H, Matevosyan M, Harutyunyan V, Gevorgyan S, Shavina A, Tirosyan I, Gabrielyan Y, Ayvazyan M, Bozdaganyan M, Fakhar Z, Gharaghani S, Zakaryan H. Computational evaluation and benchmark study of 342 crystallographic holo-structures of SARS-CoV-2 Mpro enzyme. Sci Rep 2024; 14:14255. [PMID: 38902397 PMCID: PMC11189913 DOI: 10.1038/s41598-024-65228-5] [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: 03/07/2024] [Accepted: 06/18/2024] [Indexed: 06/22/2024] Open
Abstract
The coronavirus disease 19 pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has led to a global health crisis with millions of confirmed cases and related deaths. The main protease (Mpro) of SARS-CoV-2 is crucial for viral replication and presents an attractive target for drug development. Despite the approval of some drugs, the search for effective treatments continues. In this study, we systematically evaluated 342 holo-crystal structures of Mpro to identify optimal conformations for structure-based virtual screening (SBVS). Our analysis revealed limited structural flexibility among the structures. Three docking programs, AutoDock Vina, rDock, and Glide were employed to assess the efficiency of virtual screening, revealing diverse performances across selected Mpro structures. We found that the structures 5RHE, 7DDC, and 7DPU (PDB Ids) consistently displayed the lowest EF, AUC, and BEDROCK scores. Furthermore, these structures demonstrated the worst pose prediction results in all docking programs. Two structural differences contribute to variations in docking performance: the absence of the S1 subsite in 7DDC and 7DPU, and the presence of a subpocket in the S2 subsite of 7DDC, 7DPU, and 5RHE. These findings underscore the importance of selecting appropriate Mpro conformations for SBVS, providing valuable insights for advancing drug discovery efforts.
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Affiliation(s)
- Hamlet Khachatryan
- Denovo Sciences Inc, 0060, Yerevan, Armenia.
- Laboratory of Antiviral Drug Discovery, Institute of Molecular Biology of NAS, Hasratyan 7, 0014, Yerevan, Armenia.
| | - Mher Matevosyan
- Laboratory of Antiviral Drug Discovery, Institute of Molecular Biology of NAS, Hasratyan 7, 0014, Yerevan, Armenia
| | - Vardan Harutyunyan
- Laboratory of Antiviral Drug Discovery, Institute of Molecular Biology of NAS, Hasratyan 7, 0014, Yerevan, Armenia
| | - Smbat Gevorgyan
- Denovo Sciences Inc, 0060, Yerevan, Armenia
- Laboratory of Antiviral Drug Discovery, Institute of Molecular Biology of NAS, Hasratyan 7, 0014, Yerevan, Armenia
| | - Anastasiya Shavina
- Denovo Sciences Inc, 0060, Yerevan, Armenia
- Laboratory of Antiviral Drug Discovery, Institute of Molecular Biology of NAS, Hasratyan 7, 0014, Yerevan, Armenia
| | - Irina Tirosyan
- Laboratory of Antiviral Drug Discovery, Institute of Molecular Biology of NAS, Hasratyan 7, 0014, Yerevan, Armenia
| | - Yeva Gabrielyan
- Laboratory of Antiviral Drug Discovery, Institute of Molecular Biology of NAS, Hasratyan 7, 0014, Yerevan, Armenia
| | - Marusya Ayvazyan
- Laboratory of Antiviral Drug Discovery, Institute of Molecular Biology of NAS, Hasratyan 7, 0014, Yerevan, Armenia
| | | | - Zeynab Fakhar
- Laboratory of Bioinformatics and Drug Design (LBD), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Sajjad Gharaghani
- Laboratory of Bioinformatics and Drug Design (LBD), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Hovakim Zakaryan
- Denovo Sciences Inc, 0060, Yerevan, Armenia.
- Laboratory of Antiviral Drug Discovery, Institute of Molecular Biology of NAS, Hasratyan 7, 0014, Yerevan, Armenia.
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11
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Goradia N, Werner S, Mullapudi E, Greimeier S, Bergmann L, Lang A, Mertens H, Węglarz A, Sander S, Chojnowski G, Wikman H, Ohlenschläger O, von Amsberg G, Pantel K, Wilmanns M. Master corepressor inactivation through multivalent SLiM-induced polymerization mediated by the oncogene suppressor RAI2. Nat Commun 2024; 15:5241. [PMID: 38898011 PMCID: PMC11187106 DOI: 10.1038/s41467-024-49488-3] [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: 11/19/2023] [Accepted: 06/05/2024] [Indexed: 06/21/2024] Open
Abstract
While the elucidation of regulatory mechanisms of folded proteins is facilitated due to their amenability to high-resolution structural characterization, investigation of these mechanisms in disordered proteins is more challenging due to their structural heterogeneity, which can be captured by a variety of biophysical approaches. Here, we used the transcriptional master corepressor CtBP, which binds the putative metastasis suppressor RAI2 through repetitive SLiMs, as a model system. Using cryo-electron microscopy embedded in an integrative structural biology approach, we show that RAI2 unexpectedly induces CtBP polymerization through filaments of stacked tetrameric CtBP layers. These filaments lead to RAI2-mediated CtBP nuclear foci and relieve its corepressor function in RAI2-expressing cancer cells. The impact of RAI2-mediated CtBP loss-of-function is illustrated by the analysis of a diverse cohort of prostate cancer patients, which reveals a substantial decrease in RAI2 in advanced treatment-resistant cancer subtypes. As RAI2-like SLiM motifs are found in a wide range of organisms, including pathogenic viruses, our findings serve as a paradigm for diverse functional effects through multivalent interaction-mediated polymerization by disordered proteins in healthy and diseased conditions.
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Affiliation(s)
- Nishit Goradia
- European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22607, Hamburg, Germany
| | - Stefan Werner
- University Medical Center Hamburg-Eppendorf, Department of Tumor Biology, University Cancer Center Hamburg, Martinistrasse 52, 20246, Hamburg, Germany
- University Medical Center Hamburg-Eppendorf, Mildred Scheel Cancer Career Center HaTriCS4, Martinistrasse 52, 20246, Hamburg, Germany
| | - Edukondalu Mullapudi
- European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22607, Hamburg, Germany
| | - Sarah Greimeier
- University Medical Center Hamburg-Eppendorf, Department of Tumor Biology, University Cancer Center Hamburg, Martinistrasse 52, 20246, Hamburg, Germany
| | - Lina Bergmann
- University Medical Center Hamburg-Eppendorf, Department of Tumor Biology, University Cancer Center Hamburg, Martinistrasse 52, 20246, Hamburg, Germany
| | - Andras Lang
- Leibniz Institute on Aging, Fritz-Lipmann-Institute, Beutenbergstraße 11, 07745, Jena, Germany
| | - Haydyn Mertens
- European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22607, Hamburg, Germany
| | - Aleksandra Węglarz
- University Medical Center Hamburg-Eppendorf, Department of Tumor Biology, University Cancer Center Hamburg, Martinistrasse 52, 20246, Hamburg, Germany
| | - Simon Sander
- University Medical Center Hamburg-Eppendorf, Department of Tumor Biology, University Cancer Center Hamburg, Martinistrasse 52, 20246, Hamburg, Germany
| | - Grzegorz Chojnowski
- European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22607, Hamburg, Germany
| | - Harriet Wikman
- University Medical Center Hamburg-Eppendorf, Department of Tumor Biology, University Cancer Center Hamburg, Martinistrasse 52, 20246, Hamburg, Germany
| | - Oliver Ohlenschläger
- Leibniz Institute on Aging, Fritz-Lipmann-Institute, Beutenbergstraße 11, 07745, Jena, Germany
| | - Gunhild von Amsberg
- Martini Clinic, Martinistrasse 52, 20246, Hamburg, Germany
- Department of Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Klaus Pantel
- University Medical Center Hamburg-Eppendorf, Department of Tumor Biology, University Cancer Center Hamburg, Martinistrasse 52, 20246, Hamburg, Germany.
| | - Matthias Wilmanns
- European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22607, Hamburg, Germany.
- University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany.
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12
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Boyer NP, Sharma R, Wiesner T, Delamare A, Pelletier F, Leterrier C, Roy S. Spectrin condensates provide a nidus for assembling the periodic axonal structure. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.05.597638. [PMID: 38895400 PMCID: PMC11185721 DOI: 10.1101/2024.06.05.597638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Coordinated assembly of individual components into higher-order structures is a defining theme in biology, but underlying principles are not well-understood. In neurons, α/β spectrins, adducin, and actinfilaments assemble into a lattice wrapping underneath the axonal plasma membrane, but mechanistic events leading to this periodic axonal structure (PAS) are unclear. Visualizing PAS components in axons as they develop, we found focal patches in distal axons containing spectrins and adducin (but sparse actin filaments) with biophysical properties reminiscent of biomolecular condensation. Overexpressing spectrin-repeats - constituents of α/β-spectrins - in heterologous cells triggered condensate formation, and preventing association of βII-spectrin with actin-filaments/membranes also facilitated condensation. Finally, overexpressing condensate-triggering spectrin repeats in neurons before PAS establishment disrupted the lattice, presumably by competing with innate assembly, supporting a functional role for biomolecular condensation. We propose a condensation-assembly model where PAS components form focal phase-separated condensates that eventually unfurl into a stable lattice-structure by associating with subplasmalemmal actin. By providing local 'depots' of assembly parts, biomolecular condensation may play a wider role in the construction of intricate cytoskeletal structures.
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13
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Bokor M, Tantos Á. General Characterization of Properties of Ordered and Disordered Proteins by Wide-Line 1H NMR. ACS OMEGA 2024; 9:23468-23475. [PMID: 38854569 PMCID: PMC11154930 DOI: 10.1021/acsomega.4c00517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 05/10/2024] [Accepted: 05/15/2024] [Indexed: 06/11/2024]
Abstract
Wide-line 1H NMR is an efficient spectroscopic method to determine the disorder tendency of a protein. It directly measures the properties of the hydration shell of proteins, delivering exact and measurable values of their disorder/order content. A comparison is performed between several globular and disordered proteins. The common properties of the subzero mobile hydration water of these two groups were investigated. The amount of the mobile hydration water and the shape of the melting diagram at subzero temperatures together provide a possibility to distinguish globular proteins from disordered proteins. The shape of the melting diagram also gives information about the presence of secondary structural elements. The disordered and globular protein regions' fundamentally different structures are reflected in their melting diagrams, allowing one to directly determine the level of disorder in a specific protein structure. Intrinsically disordered proteins bind water more strongly than globular proteins, which is shown by the somewhat higher temperature values where mobile hydration water first appears but with a significantly higher heterogeneity in the energy distributions of protein-water interactions.
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Affiliation(s)
- Mónika Bokor
- Institute
for Solid State Physics and Optics, HUN-REN
Wigner Research Centre for Physics, 1121 Budapest, Hungary
| | - Ágnes Tantos
- HUN-REN
Research Centre for Natural Sciences, Institute
of Enzymology, 1117 Budapest, Hungary
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14
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Li T, Wang Y, Natran A, Zhang Y, Wang H, Du K, Qin P, Yuan H, Chen W, Tu B, Inzé D, Dubois M. C-TERMINAL DOMAIN PHOSPHATASE-LIKE 3 contributes to GA-mediated growth and flowering by interaction with DELLA proteins. THE NEW PHYTOLOGIST 2024; 242:2555-2569. [PMID: 38594216 DOI: 10.1111/nph.19742] [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: 09/26/2023] [Accepted: 03/14/2024] [Indexed: 04/11/2024]
Abstract
Gibberellic acid (GA) plays a central role in many plant developmental processes and is crucial for crop improvement. DELLA proteins, the core suppressors in the GA signaling pathway, are degraded by GA via the 26S proteasomal pathway to release the GA response. However, little is known about the phosphorylation-mediated regulation of DELLA proteins. In this study, we combined GA response assays with protein-protein interaction analysis to infer the connection between Arabidopsis thaliana DELLAs and the C-TERMINAL DOMAIN PHOSPHATASE-LIKE 3 (CPL3), a phosphatase involved in the dephosphorylation of RNA polymerase II. We show that CPL3 directly interacts with DELLA proteins and promotes DELLA protein stability by inhibiting its degradation by the 26S proteasome. Consequently, CPL3 negatively modulates multiple GA-mediated processes of plant development, including hypocotyl elongation, flowering time, and anthocyanin accumulation. Taken together, our findings demonstrate that CPL3 serves as a novel regulator that could improve DELLA stability and thereby participate in GA signaling transduction.
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Affiliation(s)
- Ting Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, 611130, Chengdu, China
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Gent, Belgium
- Center for Plant Systems Biology, VIB, 9052, Gent, Belgium
| | - Yongqin Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, 611130, Chengdu, China
| | - Annelore Natran
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Gent, Belgium
- Center for Plant Systems Biology, VIB, 9052, Gent, Belgium
| | - Yi Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, 611130, Chengdu, China
| | - Hao Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 611130, Chengdu, Sichuan, China
| | - Kangxi Du
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 611130, Chengdu, Sichuan, China
| | - Peng Qin
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 611130, Chengdu, Sichuan, China
| | - Hua Yuan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, 611130, Chengdu, China
| | - Weilan Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 611130, Chengdu, Sichuan, China
| | - Bin Tu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 611130, Chengdu, Sichuan, China
| | - Dirk Inzé
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Gent, Belgium
- Center for Plant Systems Biology, VIB, 9052, Gent, Belgium
| | - Marieke Dubois
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Gent, Belgium
- Center for Plant Systems Biology, VIB, 9052, Gent, Belgium
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15
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Nagy KK, Takács K, Németh I, Varga B, Grolmusz V, Molnár M, Vértessy BG. Novel enzymes for biodegradation of polycyclic aromatic hydrocarbons identified by metagenomics and functional analysis in short-term soil microcosm experiments. Sci Rep 2024; 14:11608. [PMID: 38773163 PMCID: PMC11109138 DOI: 10.1038/s41598-024-61566-6] [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: 12/19/2023] [Accepted: 05/07/2024] [Indexed: 05/23/2024] Open
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are highly toxic, carcinogenic substances. On soils contaminated with PAHs, crop cultivation, animal husbandry and even the survival of microflora in the soil are greatly perturbed, depending on the degree of contamination. Most microorganisms cannot tolerate PAH-contaminated soils, however, some microbial strains can adapt to these harsh conditions and survive on contaminated soils. Analysis of the metagenomes of contaminated environmental samples may lead to discovery of PAH-degrading enzymes suitable for green biotechnology methodologies ranging from biocatalysis to pollution control. In the present study, our goal was to apply a metagenomic data search to identify efficient novel enzymes in remediation of PAH-contaminated soils. The metagenomic hits were further analyzed using a set of bioinformatics tools to select protein sequences predicted to encode well-folded soluble enzymes. Three novel enzymes (two dioxygenases and one peroxidase) were cloned and used in soil remediation microcosms experiments. The experimental design of the present study aimed at evaluating the effectiveness of the novel enzymes on short-term PAH degradation in the soil microcosmos model. The novel enzymes were found to be efficient for degradation of naphthalene and phenanthrene. Adding the inorganic oxidant CaO2 further increased the degrading potential of the novel enzymes for anthracene and pyrene. We conclude that metagenome mining paired with bioinformatic predictions, structural modelling and functional assays constitutes a powerful approach towards novel enzymes for soil remediation.
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Affiliation(s)
- Kinga K Nagy
- Department of Applied Biotechnology and Food Science, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Műegyetem Rkp. 3., 1111, Budapest, Hungary
- Institute of Enzymology, Research Centre for Natural Sciences, Magyar Tudósok Körútja 2., 1117, Budapest, Hungary
| | - Kristóf Takács
- PIT Bioinformatics Group, Eötvös Loránd University, 1117, Budapest, Hungary
| | - Imre Németh
- Department of Applied Biotechnology and Food Science, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Műegyetem Rkp. 3., 1111, Budapest, Hungary
| | - Bálint Varga
- PIT Bioinformatics Group, Eötvös Loránd University, 1117, Budapest, Hungary
| | - Vince Grolmusz
- PIT Bioinformatics Group, Eötvös Loránd University, 1117, Budapest, Hungary
- Uratim Ltd., 1118, Budapest, Hungary
| | - Mónika Molnár
- Department of Applied Biotechnology and Food Science, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Műegyetem Rkp. 3., 1111, Budapest, Hungary.
| | - Beáta G Vértessy
- Department of Applied Biotechnology and Food Science, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Műegyetem Rkp. 3., 1111, Budapest, Hungary.
- Institute of Enzymology, Research Centre for Natural Sciences, Magyar Tudósok Körútja 2., 1117, Budapest, Hungary.
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16
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Mansueto G, Fusco G, Colonna G. A Tiny Viral Protein, SARS-CoV-2-ORF7b: Functional Molecular Mechanisms. Biomolecules 2024; 14:541. [PMID: 38785948 PMCID: PMC11118181 DOI: 10.3390/biom14050541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 04/01/2024] [Accepted: 04/17/2024] [Indexed: 05/25/2024] Open
Abstract
This study presents the interaction with the human host metabolism of SARS-CoV-2 ORF7b protein (43 aa), using a protein-protein interaction network analysis. After pruning, we selected from BioGRID the 51 most significant proteins among 2753 proven interactions and 1708 interactors specific to ORF7b. We used these proteins as functional seeds, and we obtained a significant network of 551 nodes via STRING. We performed topological analysis and calculated topological distributions by Cytoscape. By following a hub-and-spoke network architectural model, we were able to identify seven proteins that ranked high as hubs and an additional seven as bottlenecks. Through this interaction model, we identified significant GO-processes (5057 terms in 15 categories) induced in human metabolism by ORF7b. We discovered high statistical significance processes of dysregulated molecular cell mechanisms caused by acting ORF7b. We detected disease-related human proteins and their involvement in metabolic roles, how they relate in a distorted way to signaling and/or functional systems, in particular intra- and inter-cellular signaling systems, and the molecular mechanisms that supervise programmed cell death, with mechanisms similar to that of cancer metastasis diffusion. A cluster analysis showed 10 compact and significant functional clusters, where two of them overlap in a Giant Connected Component core of 206 total nodes. These two clusters contain most of the high-rank nodes. ORF7b acts through these two clusters, inducing most of the metabolic dysregulation. We conducted a co-regulation and transcriptional analysis by hub and bottleneck proteins. This analysis allowed us to define the transcription factors and miRNAs that control the high-ranking proteins and the dysregulated processes within the limits of the poor knowledge that these sectors still impose.
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Affiliation(s)
- Gelsomina Mansueto
- Dipartimento di Scienze Mediche e Chirurgiche Avanzate, Università della Campania, L. Vanvitelli, 80138 Naples, Italy;
| | - Giovanna Fusco
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, 80055 Portici, Italy;
| | - Giovanni Colonna
- Medical Informatics AOU, Università della Campania, L. Vanvitelli, 80138 Naples, Italy
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17
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Papanikolaou NA, Kakavoulia M, Ladias C, Papavassiliou AG. The ras-related protein RAB22A interacts with hypoxia-inducible factor 1-alpha (HIF-1α) in MDA-MB-231 breast cancer cells in hypoxia. Mol Biol Rep 2024; 51:564. [PMID: 38647725 DOI: 10.1007/s11033-024-09516-3] [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: 02/24/2024] [Accepted: 04/03/2024] [Indexed: 04/25/2024]
Abstract
BACKGROUND Recent studies suggest that hypoxia-inducible factor 1-alpha (HIF-1α) and the small GTPase protein Ras-related protein Rab-22 A (RAB22A) may be colocalized in the cytoplasm and that as a conequence they may enhance the formation of microvesicles in breast cancer cells under hypoxia. Therefore, we sought to determine whether these two proteins are present in intracellular complexes in breast carcinoma cells. METHODS AND RESULTS Evaluation using molecular docking indicated that HIF-1α and RAB22A interact with each other. Co-immunoprecipitation of endogenous or ectopically expressed HIF-1α and RAB22A proteins in MDA-MB-231 breast cancer cells or HEK-293T cells demonstrated that endogenous HIF-1α and RAB22A can form an intracellular complex; however, transiently expressed HIF-1α and RAB22A failed to interact. Investigating RAB22A and HIF-1α interactions in various cancer cell lines under hypoxia may shed light on their roles in cancer cell survival and progression through regulation of intracellular trafficking by HIF-1α under hypoxic conditions. CONCLUSIONS Our study is the first to reveal the potential involvement of HIF-1α in intracellular trafficking through physical interactions with the small GTPase protein RAB22A. We discuss the implications of our work on the role of exosomes and microvesicles in tumor invasiveness.
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Affiliation(s)
- Nikolaos A Papanikolaou
- Laboratory of Biological Chemistry, School of Medicine, Aristotle University of Thessaloniki, 54124, Thessaloniki, Macedonia, Greece.
| | - Maria Kakavoulia
- Laboratory of Biological Chemistry, School of Medicine, Aristotle University of Thessaloniki, 54124, Thessaloniki, Macedonia, Greece
| | - Christos Ladias
- Department of Biological Applications and Technology, University of Ioannina, 45110, Ioannina, Epirus, Greece
| | - Athanasios G Papavassiliou
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527, Athens, Greece
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18
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Maneix L, Iakova P, Lee CG, Moree SE, Lu X, Datar GK, Hill CT, Spooner E, King JCK, Sykes DB, Saez B, Di Stefano B, Chen X, Krause DS, Sahin E, Tsai FTF, Goodell MA, Berk BC, Scadden DT, Catic A. Cyclophilin A supports translation of intrinsically disordered proteins and affects haematopoietic stem cell ageing. Nat Cell Biol 2024; 26:593-603. [PMID: 38553595 PMCID: PMC11021199 DOI: 10.1038/s41556-024-01387-x] [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: 04/25/2022] [Accepted: 02/23/2024] [Indexed: 04/11/2024]
Abstract
Loss of protein function is a driving force of ageing. We have identified peptidyl-prolyl isomerase A (PPIA or cyclophilin A) as a dominant chaperone in haematopoietic stem and progenitor cells. Depletion of PPIA accelerates stem cell ageing. We found that proteins with intrinsically disordered regions (IDRs) are frequent PPIA substrates. IDRs facilitate interactions with other proteins or nucleic acids and can trigger liquid-liquid phase separation. Over 20% of PPIA substrates are involved in the formation of supramolecular membrane-less organelles. PPIA affects regulators of stress granules (PABPC1), P-bodies (DDX6) and nucleoli (NPM1) to promote phase separation and increase cellular stress resistance. Haematopoietic stem cell ageing is associated with a post-transcriptional decrease in PPIA expression and reduced translation of IDR-rich proteins. Here we link the chaperone PPIA to the synthesis of intrinsically disordered proteins, which indicates that impaired protein interaction networks and macromolecular condensation may be potential determinants of haematopoietic stem cell ageing.
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Affiliation(s)
- Laure Maneix
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Cell and Gene Therapy Program at the Dan L. Duncan Comprehensive Cancer Center, Houston, TX, USA
| | - Polina Iakova
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Cell and Gene Therapy Program at the Dan L. Duncan Comprehensive Cancer Center, Houston, TX, USA
| | - Charles G Lee
- Department of BioSciences, Rice University, Houston, TX, USA
| | - Shannon E Moree
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Cell and Gene Therapy Program at the Dan L. Duncan Comprehensive Cancer Center, Houston, TX, USA
| | - Xuan Lu
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Gandhar K Datar
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Cedric T Hill
- Center for Regenerative Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Eric Spooner
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Jordon C K King
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Cell and Gene Therapy Program at the Dan L. Duncan Comprehensive Cancer Center, Houston, TX, USA
| | - David B Sykes
- Center for Regenerative Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Borja Saez
- Center for Applied Medical Research, Hematology-Oncology Unit, Pamplona, Navarra, Spain
| | - Bruno Di Stefano
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Cell and Gene Therapy Program at the Dan L. Duncan Comprehensive Cancer Center, Houston, TX, USA
| | - Xi Chen
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Daniela S Krause
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt am Main, Germany
| | - Ergun Sahin
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, USA
| | - Francis T F Tsai
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Margaret A Goodell
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Cell and Gene Therapy Program at the Dan L. Duncan Comprehensive Cancer Center, Houston, TX, USA
| | - Bradford C Berk
- Department of Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - David T Scadden
- Center for Regenerative Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - André Catic
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA.
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA.
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA.
- Cell and Gene Therapy Program at the Dan L. Duncan Comprehensive Cancer Center, Houston, TX, USA.
- Michael E. DeBakey Veterans Affairs Medical Center, Houston, TX, USA.
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19
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Praveen M. Characterizing the West Nile Virus's polyprotein from nucleotide sequence to protein structure - Computational tools. J Taibah Univ Med Sci 2024; 19:338-350. [PMID: 38304694 PMCID: PMC10831166 DOI: 10.1016/j.jtumed.2024.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 11/27/2023] [Accepted: 01/08/2024] [Indexed: 02/03/2024] Open
Abstract
Objectives West Nile virus (WNV) belongs to the Flaviviridae family and causes West Nile fever. The mechanism of transmission involves the culex mosquito species. Infected individuals are primarily asymptomatic, and few exhibit common symptoms. Moreover, 10 % of neuronal infection caused by this virus cause death. The proteins encoded by these genes had been uncharacterized, although understanding their function and structure is important for formulating antiviral drugs. Methods Herein, we used in silico approaches, including various bioinformatic tools and databases, to analyse the proteins from the WNV polyprotein individually. The characterization included GC content, physicochemical properties, conserved domains, soluble and transmembrane regions, signal localization, protein disorder, and secondary structure features and their respective 3D protein structures. Results Among 11 proteins, eight had >50 % GC content, eight proteins had basic pI values, three proteins were unstable under in vitro conditions, four were thermostable according to >100 AI values and some had negative GRAVY values in physicochemical analyses. All protein-conserved domains were shared among Flaviviridae family members. Five proteins were soluble and lacked transmembrane regions. Two proteins had signals for localization in the host endoplasmic reticulum. Non-structural (NS) 2A showed low protein disorder. The secondary structural features and tertiary structure models provide a valuable biochemical resource for designing selective substrates and synthetic inhibitors. Conclusions WNV proteins NS2A, NS2B, PM, NS3 and NS5 can be used as drug targets for the pharmacological design of lead antiviral compounds.
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Affiliation(s)
- Mallari Praveen
- Department of Zoology, Indira Gandhi National Tribal University, Amarkantak, Madhya Pradesh, India
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20
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Salaikumaran M, Gopal PP. Rational Design of TDP-43 Derived α-Helical Peptide Inhibitors: An In Silico Strategy to Prevent TDP-43 Aggregation in Neurodegenerative Disorders. ACS Chem Neurosci 2024; 15:1096-1109. [PMID: 38466778 PMCID: PMC10959110 DOI: 10.1021/acschemneuro.3c00659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 01/21/2024] [Accepted: 02/19/2024] [Indexed: 03/13/2024] Open
Abstract
TDP-43, an essential RNA/DNA-binding protein, is central to the pathology of neurodegenerative diseases, such as amyotrophic lateral sclerosis and frontotemporal dementia. Pathological mislocalization and aggregation of TDP-43 disrupt RNA splicing, mRNA stability, and mRNA transport, thereby impairing neuronal function and survival. The formation of amyloid-like TDP-43 filaments is largely facilitated by the destabilization of an α-helical segment within the disordered C-terminal region. In this study, we hypothesized that preventing the destabilization of the α-helical domain could potentially halt the growth of these pathological filaments. To explore this, we utilized a range of in silico techniques to design and evaluate peptide-based therapeutics that bind to pathological TDP-43 amyloid-like filament crystal structures and resist β sheet conversion. Our computational approaches, including biophysical and secondary structure property prediction, molecular docking, 3D structure prediction, and molecular dynamics simulations, were used to assess the structure, stability, and binding affinity of these peptides in relation to pathological TDP-43 filaments. The results of our in silico analyses identified a selection of promising peptides which displayed a stable α-helical structure, exhibited an increased number of intramolecular hydrogen bonds within the helical domain, and demonstrated high binding affinities for pathological TDP-43 amyloid-like filaments. Molecular dynamics simulations provided further support for the structural and thermodynamic stability of these peptides, as they exhibited lower root-mean-square deviation and more favorable free energy landscapes over 300 ns. These findings establish α-helical propensity peptides as potential lead molecules for the development of novel therapeutics against TDP-43 aggregation. This structure-based computational approach for the rational design of peptide inhibitors opens a new direction in the search for effective interventions for ALS, FTD, and other related neurodegenerative diseases. The peptides identified as the most promising candidates in this study are currently subject to further testing and validation through both in vitro and in vivo experiments.
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Affiliation(s)
- Muthu
Raj Salaikumaran
- Department
of Pathology, Yale School of Medicine, New Haven, Connecticut 06520, United States
| | - Pallavi P. Gopal
- Department
of Pathology, Yale School of Medicine, New Haven, Connecticut 06520, United States
- Program
in Cellular Neuroscience, Neurodegeneration, and Repair, Yale School of Medicine, New Haven, Connecticut 06520-8055, United States
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21
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Bartlett TM, Sisley TA, Mychack A, Walker S, Baker RW, Rudner DZ, Bernhardt TG. FacZ is a GpsB-interacting protein that prevents aberrant division-site placement in Staphylococcus aureus. Nat Microbiol 2024; 9:801-813. [PMID: 38443581 PMCID: PMC10914604 DOI: 10.1038/s41564-024-01607-y] [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: 04/24/2023] [Accepted: 01/15/2024] [Indexed: 03/07/2024]
Abstract
Staphylococcus aureus is a Gram-positive pathogen responsible for antibiotic-resistant infections. To identify vulnerabilities in cell envelope biogenesis that may overcome resistance, we enriched for S. aureus transposon mutants with defects in cell surface integrity or cell division by sorting for cells that stain with propidium iodide or have increased light-scattering properties, respectively. Transposon sequencing of the sorted populations identified more than 20 previously uncharacterized factors impacting these processes. Cells inactivated for one of these proteins, factor preventing extra Z-rings (FacZ, SAOUHSC_01855), showed aberrant membrane invaginations and multiple FtsZ cytokinetic rings. These phenotypes were suppressed in mutants lacking the conserved cell-division protein GpsB, which forms an interaction hub bridging envelope biogenesis factors with the cytokinetic ring in S. aureus. FacZ was found to interact directly with GpsB in vitro and in vivo. We therefore propose that FacZ is an envelope biogenesis factor that antagonizes GpsB function to prevent aberrant division events in S. aureus.
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Affiliation(s)
- Thomas M Bartlett
- Department of Microbiology Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Tyler A Sisley
- Department of Microbiology Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Aaron Mychack
- Department of Microbiology Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Suzanne Walker
- Department of Microbiology Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Richard W Baker
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - David Z Rudner
- Department of Microbiology Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
| | - Thomas G Bernhardt
- Department of Microbiology Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA.
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22
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Zimmermannová O, Velázquez D, Papoušková K, Průša V, Radová V, Falson P, Sychrová H. The Hydrophilic C-terminus of Yeast Plasma-membrane Na +/H + Antiporters Impacts Their Ability to Transport K . J Mol Biol 2024; 436:168443. [PMID: 38211892 DOI: 10.1016/j.jmb.2024.168443] [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: 10/23/2023] [Revised: 12/18/2023] [Accepted: 01/06/2024] [Indexed: 01/13/2024]
Abstract
Yeast plasma-membrane Na+/H+ antiporters (Nha/Sod) ensure the optimal intracellular level of alkali-metal cations and protons in cells. They are predicted to consist of 13 transmembrane segments (TMSs) and a large hydrophilic C-terminal cytoplasmic part with seven conserved domains. The substrate specificity, specifically the ability to recognize and transport K+ cations in addition to Na+ and Li+, differs among homologs. In this work, we reveal that the composition of the C-terminus impacts the ability of antiporters to transport particular cations. In the osmotolerant yeast Zygosaccharomyces rouxii, the Sod2-22 antiporter only efficiently exports Na+ and Li+, but not K+. The introduction of a negative charge or removal of a positive charge in one of the C-terminal conserved regions (C3) enabled ZrSod2-22 to transport K+. The same mutations rescued the low level of activity and purely Li+ specificity of ZrSod2-22 with the A179T mutation in TMS6, suggesting a possible interaction between this TMS and the C-terminus. The truncation or replacement of the C-terminal part of ZrSod2-22 with the C-terminus of a K+-transporting Nha/Sod antiporter (Saccharomyces cerevisiae Nha1 or Z. rouxii Nha1) also resulted in an antiporter with the capacity to export K+. In addition, in ScNha1, the replacement of three positively charged arginine residues 539-541 in the C3 region with alanine caused its inability to provide cells with tolerance to Li+. All our results demonstrate that the physiological functions of yeast Nha/Sod antiporters, either in salt tolerance or in K+ homeostasis, depend on the composition of their C-terminal parts.
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Affiliation(s)
- Olga Zimmermannová
- Laboratory of Membrane Transport, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic.
| | - Diego Velázquez
- Laboratory of Membrane Transport, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic.
| | - Klára Papoušková
- Laboratory of Membrane Transport, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic.
| | - Vojtěch Průša
- Laboratory of Membrane Transport, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic.
| | - Viktorie Radová
- Laboratory of Membrane Transport, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic.
| | - Pierre Falson
- Drug Resistance Membrane Proteins Group, National Centre for Scientific Research and Lyon I University Laboratory n°5086, Institute of Biology and Chemistry of Proteins, Lyon, France.
| | - Hana Sychrová
- Laboratory of Membrane Transport, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic.
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23
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Chappidi N, Quail T, Doll S, Vogel LT, Aleksandrov R, Felekyan S, Kühnemuth R, Stoynov S, Seidel CAM, Brugués J, Jahnel M, Franzmann TM, Alberti S. PARP1-DNA co-condensation drives DNA repair site assembly to prevent disjunction of broken DNA ends. Cell 2024; 187:945-961.e18. [PMID: 38320550 DOI: 10.1016/j.cell.2024.01.015] [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: 05/09/2023] [Revised: 10/27/2023] [Accepted: 01/12/2024] [Indexed: 02/08/2024]
Abstract
DNA double-strand breaks (DSBs) are repaired at DSB sites. How DSB sites assemble and how broken DNA is prevented from separating is not understood. Here we uncover that the synapsis of broken DNA is mediated by the DSB sensor protein poly(ADP-ribose) (PAR) polymerase 1 (PARP1). Using bottom-up biochemistry, we reconstitute functional DSB sites and show that DSB sites form through co-condensation of PARP1 multimers with DNA. The co-condensates exert mechanical forces to keep DNA ends together and become enzymatically active for PAR synthesis. PARylation promotes release of PARP1 from DNA ends and the recruitment of effectors, such as Fused in Sarcoma, which stabilizes broken DNA ends against separation, revealing a finely orchestrated order of events that primes broken DNA for repair. We provide a comprehensive model for the hierarchical assembly of DSB condensates to explain DNA end synapsis and the recruitment of effector proteins for DNA damage repair.
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Affiliation(s)
- Nagaraja Chappidi
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany
| | - Thomas Quail
- Max Planck Institute of Cell Biology and Genetics (MPI-CBG), Pfotenhauerstr. 108, 01307 Dresden, Germany; Cluster of Excellence Physics of Life, TU Dresden, Arnoldstraße 18, 01307 Dresden, Germany; Max Planck Institute for the Physics of Complex Systems (MPI-PKS), Nöthnitzer Str. 38, 01187 Dresden, Germany; Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Simon Doll
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany; Cluster of Excellence Physics of Life, TU Dresden, Arnoldstraße 18, 01307 Dresden, Germany
| | - Laura T Vogel
- Department of Molecular Physical Chemistry, Heinrich Heine University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Radoslav Aleksandrov
- Institute of Molecular Biology, Bulgarian Academy of Sciences, Acad. G. Bonchev Str, bl.21, 1113 Sofia, Bulgaria
| | - Suren Felekyan
- Department of Molecular Physical Chemistry, Heinrich Heine University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Ralf Kühnemuth
- Department of Molecular Physical Chemistry, Heinrich Heine University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Stoyno Stoynov
- Institute of Molecular Biology, Bulgarian Academy of Sciences, Acad. G. Bonchev Str, bl.21, 1113 Sofia, Bulgaria
| | - Claus A M Seidel
- Department of Molecular Physical Chemistry, Heinrich Heine University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Jan Brugués
- Max Planck Institute of Cell Biology and Genetics (MPI-CBG), Pfotenhauerstr. 108, 01307 Dresden, Germany; Cluster of Excellence Physics of Life, TU Dresden, Arnoldstraße 18, 01307 Dresden, Germany; Max Planck Institute for the Physics of Complex Systems (MPI-PKS), Nöthnitzer Str. 38, 01187 Dresden, Germany
| | - Marcus Jahnel
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany; Cluster of Excellence Physics of Life, TU Dresden, Arnoldstraße 18, 01307 Dresden, Germany
| | - Titus M Franzmann
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany
| | - Simon Alberti
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany.
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24
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Vural A, Lanier SM. Properties of biomolecular condensates defined by Activator of G-protein Signaling 3. J Cell Sci 2024; 137:jcs261326. [PMID: 38264908 PMCID: PMC10911133 DOI: 10.1242/jcs.261326] [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: 05/12/2023] [Accepted: 01/11/2024] [Indexed: 01/25/2024] Open
Abstract
Activator of G-protein signaling 3 (AGS3; also known as GPSM1), a receptor-independent activator of G-protein signaling, oscillates among defined subcellular compartments and biomolecular condensates (BMCs) in a regulated manner that is likely related to the functional diversity of the protein. We determined the influence of cell stress on the cellular distribution of AGS3 and core material properties of AGS3 BMCs. Cellular stress (oxidative, pHi and thermal) induced the formation of AGS3 BMCs in HeLa and COS-7 cells, as determined by fluorescent microscopy. Oxidative stress-induced AGS3 BMCs were distinct from G3BP1 stress granules and from RNA processing BMCs defined by the P-body protein Dcp1a. Immunoblots indicated that cellular stress shifted AGS3, but not the stress granule protein G3BP1 to a membrane pellet fraction following cell lysis. The stress-induced generation of AGS3 BMCs was reduced by co-expression of the signaling protein Gαi3, but not the AGS3-binding partner DVL2. Fluorescent recovery following photobleaching of individual AGS3 BMCs indicated that there are distinct diffusion kinetics and restricted fluidity for AGS3 BMCs. These data suggest that AGS3 BMCs represent a distinct class of stress granules that serve as a previously unrecognized signal processing node.
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Affiliation(s)
- Ali Vural
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Stephen M. Lanier
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI 48201, USA
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25
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Hannon CE, Eisen MB. Intrinsic protein disorder is insufficient to drive subnuclear clustering in embryonic transcription factors. eLife 2024; 12:RP88221. [PMID: 38275292 PMCID: PMC10945700 DOI: 10.7554/elife.88221] [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: 01/27/2024] Open
Abstract
Modern microscopy has revealed that core nuclear functions, including transcription, replication, and heterochromatin formation, occur in spatially restricted clusters. Previous work from our lab has shown that subnuclear high-concentration clusters of transcription factors may play a role in regulating RNA synthesis in the early Drosophila embryo. A nearly ubiquitous feature of eukaryotic transcription factors is that they contain intrinsically disordered regions (IDRs) that often arise from low complexity amino acid sequences within the protein. It has been proposed that IDRs within transcription factors drive co-localization of transcriptional machinery and target genes into high-concentration clusters within nuclei. Here, we test that hypothesis directly, by conducting a broad survey of the subnuclear localization of IDRs derived from transcription factors. Using a novel algorithm to identify IDRs in the Drosophila proteome, we generated a library of IDRs from transcription factors expressed in the early Drosophila embryo. We used this library to perform a high-throughput imaging screen in Drosophila Schneider-2 (S2) cells. We found that while subnuclear clustering does not occur when the majority of IDRs are expressed alone, it is frequently seen in full-length transcription factors. These results are consistent in live Drosophila embryos, suggesting that IDRs are insufficient to drive the subnuclear clustering behavior of transcription factors. Furthermore, the clustering of transcription factors in living embryos was unaffected by the deletion of IDR sequences. Our results demonstrate that IDRs are unlikely to be the primary molecular drivers of the clustering observed during transcription, suggesting a more complex and nuanced role for these disordered protein sequences.
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Affiliation(s)
- Colleen E Hannon
- Howard Hughes Medical Institute, University of CaliforniaBerkeleyUnited States
| | - Michael B Eisen
- Howard Hughes Medical Institute, University of CaliforniaBerkeleyUnited States
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26
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Palumbo RJ, Yang Y, Feigon J, Hanes SD. Catalytic activity of the Bin3/MePCE methyltransferase domain is dispensable for 7SK snRNP function in Drosophila melanogaster. Genetics 2024; 226:iyad203. [PMID: 37982586 PMCID: PMC10763541 DOI: 10.1093/genetics/iyad203] [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: 10/27/2023] [Accepted: 11/13/2023] [Indexed: 11/21/2023] Open
Abstract
Methylphosphate Capping Enzyme (MePCE) monomethylates the gamma phosphate at the 5' end of the 7SK noncoding RNA, a modification thought to protect 7SK from degradation. 7SK serves as a scaffold for assembly of a snRNP complex that inhibits transcription by sequestering the positive elongation factor P-TEFb. While much is known about the biochemical activity of MePCE in vitro, little is known about its functions in vivo, or what roles-if any-there are for regions outside the conserved methyltransferase domain. Here, we investigated the role of Bin3, the Drosophila ortholog of MePCE, and its conserved functional domains in Drosophila development. We found that bin3 mutant females had strongly reduced rates of egg-laying, which was rescued by genetic reduction of P-TEFb activity, suggesting that Bin3 promotes fecundity by repressing P-TEFb. bin3 mutants also exhibited neuromuscular defects, analogous to a patient with MePCE haploinsufficiency. These defects were also rescued by genetic reduction of P-TEFb activity, suggesting that Bin3 and MePCE have conserved roles in promoting neuromuscular function by repressing P-TEFb. Unexpectedly, we found that a Bin3 catalytic mutant (Bin3Y795A) could still bind and stabilize 7SK and rescue all bin3 mutant phenotypes, indicating that Bin3 catalytic activity is dispensable for 7SK stability and snRNP function in vivo. Finally, we identified a metazoan-specific motif (MSM) outside of the methyltransferase domain and generated mutant flies lacking this motif (Bin3ΔMSM). Bin3ΔMSM mutant flies exhibited some-but not all-bin3 mutant phenotypes, suggesting that the MSM is required for a 7SK-independent, tissue-specific function of Bin3.
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Affiliation(s)
- Ryan J Palumbo
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Yuan Yang
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Juli Feigon
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Steven D Hanes
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
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27
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Bianchi G, Mangiagalli M, Ami D, Ahmed J, Lombardi S, Longhi S, Natalello A, Tompa P, Brocca S. Condensation of the N-terminal domain of human topoisomerase 1 is driven by electrostatic interactions and tuned by its charge distribution. Int J Biol Macromol 2024; 254:127754. [PMID: 38287572 DOI: 10.1016/j.ijbiomac.2023.127754] [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: 03/13/2023] [Revised: 10/10/2023] [Accepted: 10/27/2023] [Indexed: 01/31/2024]
Abstract
Liquid-liquid phase separation (LLPS) is pivotal in forming biomolecular condensates, which are crucial in several biological processes. Intrinsically disordered regions (IDRs) are typically responsible for driving LLPS due to their multivalency and high content of charged residues that enable the establishment of electrostatic interactions. In our study, we examined the role of charge distribution in the condensation of the disordered N-terminal domain of human topoisomerase I (hNTD). hNTD is densely charged with oppositely charged residues evenly distributed along the sequence. Its LLPS behavior was compared with that of charge permutants exhibiting varying degrees of charge segregation. At low salt concentrations, hNTD undergoes LLPS. However, LLPS is inhibited by high concentrations of salt and RNA, disrupting electrostatic interactions. Our findings show that, in hNTD, moderate charge segregation promotes the formation of liquid condensates that are sensitive to salt and RNA, whereas marked charge segregation results in the formation of aberrant condensates. Although our study is based on a limited set of protein variants, it supports the applicability of the "stickers-and-spacers" model to biomolecular condensates involving highly charged IDRs. These results may help generate reliable models of the overall LLPS behavior of supercharged polypeptides.
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Affiliation(s)
- Greta Bianchi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy
| | - Marco Mangiagalli
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy
| | - Diletta Ami
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy
| | - Junaid Ahmed
- VIB-VUB Center for Structural Biology, VUB, Pleinlaan 2, 1050 Brussels, Belgium
| | - Silvia Lombardi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy
| | - Sonia Longhi
- Lab. Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Aix-Marseille University, CNRS, 13288 Marseille, France
| | - Antonino Natalello
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy
| | - Peter Tompa
- VIB-VUB Center for Structural Biology, VUB, Pleinlaan 2, 1050 Brussels, Belgium.
| | - Stefania Brocca
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy.
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28
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Marshall AC, Cummins J, Kobelke S, Zhu T, Widagdo J, Anggono V, Hyman A, Fox AH, Bond CS, Lee M. Different Low-complexity Regions of SFPQ Play Distinct Roles in the Formation of Biomolecular Condensates. J Mol Biol 2023; 435:168364. [PMID: 37952770 DOI: 10.1016/j.jmb.2023.168364] [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: 08/30/2023] [Revised: 11/02/2023] [Accepted: 11/07/2023] [Indexed: 11/14/2023]
Abstract
Demixing of proteins and nucleic acids into condensed liquid phases is rapidly emerging as a ubiquitous mechanism underlying the complex spatiotemporal organisation of molecules within the cell. Long disordered regions of low sequence complexity (LCRs) are a common feature of proteins that form liquid-like microscopic biomolecular condensates. In particular, RNA-binding proteins with prion-like regions have emerged as key drivers of liquid demixing to form condensates such as nucleoli, paraspeckles and stress granules. Splicing factor proline- and glutamine-rich (SFPQ) is an RNA- and DNA-binding protein essential for DNA repair and paraspeckle formation. SFPQ contains two LCRs of different length and composition. Here, we show that the shorter C-terminal LCR of SFPQ is the main region responsible for the condensation of SFPQ in vitro and in the cell nucleus. In contrast, we find that the longer N-terminal prion-like LCR of SFPQ attenuates condensation of the full-length protein, suggesting a more regulatory role in preventing aberrant condensate formation in the cell. The compositions of these respective LCRs are discussed with reference to current literature. Our data add nuance to the emerging understanding of biomolecular condensation, by providing the first example of a common multifunctional nucleic acid-binding protein with an extensive prion-like region that serves to regulate rather than drive condensate formation.
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Affiliation(s)
- Andrew C Marshall
- School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - Jerry Cummins
- School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - Simon Kobelke
- School of Human Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - Tianyi Zhu
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Jocelyn Widagdo
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Victor Anggono
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Anthony Hyman
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Archa H Fox
- School of Human Sciences, The University of Western Australia, Crawley, WA 6009, Australia.
| | - Charles S Bond
- School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009, Australia.
| | - Mihwa Lee
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia.
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29
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Malhotra N, Khatri S, Kumar A, Arun A, Daripa P, Fatihi S, Venkadesan S, Jain N, Thukral L. AI-based AlphaFold2 significantly expands the structural space of the autophagy pathway. Autophagy 2023; 19:3201-3220. [PMID: 37516933 PMCID: PMC10621275 DOI: 10.1080/15548627.2023.2238578] [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: 06/07/2022] [Revised: 07/08/2023] [Accepted: 07/14/2023] [Indexed: 07/31/2023] Open
Abstract
ABBREVIATIONS AF2: AlphaFold2; AF2-Mult: AlphaFold2 multimer; ATG: autophagy-related; CTD: C-terminal domain; ECTD: extreme C-terminal domain; FR: flexible region; MD: molecular dynamics; NTD: N-terminal domain; pLDDT: predicted local distance difference test; UBL: ubiquitin-like.
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Affiliation(s)
- Nidhi Malhotra
- Computational Structural Biology Lab, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Shantanu Khatri
- Computational Structural Biology Lab, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research (AcSir), Ghaziabad, India
| | - Ajit Kumar
- Computational Structural Biology Lab, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research (AcSir), Ghaziabad, India
| | - Akanksha Arun
- Computational Structural Biology Lab, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research (AcSir), Ghaziabad, India
| | - Purba Daripa
- Computational Structural Biology Lab, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Saman Fatihi
- Computational Structural Biology Lab, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research (AcSir), Ghaziabad, India
| | | | - Niyati Jain
- Computational Structural Biology Lab, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Lipi Thukral
- Computational Structural Biology Lab, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research (AcSir), Ghaziabad, India
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30
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Hu S, Zhang Y, Yi Q, Yang C, Liu Y, Bai Y. Time-resolved proteomic profiling reveals compositional and functional transitions across the stress granule life cycle. Nat Commun 2023; 14:7782. [PMID: 38012130 PMCID: PMC10682001 DOI: 10.1038/s41467-023-43470-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 11/09/2023] [Indexed: 11/29/2023] Open
Abstract
Stress granules (SGs) are dynamic, membrane-less organelles. With their formation and disassembly processes characterized, it remains elusive how compositional transitions are coordinated during prolonged stress to meet changing functional needs. Here, using time-resolved proteomic profiling of the acute to prolonged heat-shock SG life cycle, we identify dynamic SG proteins, further segregated into early and late proteins. Comparison of different groups of SG proteins suggests that their biochemical properties help coordinate SG compositional and functional transitions. In particular, early proteins, with high phase-separation-propensity, drive the rapid formation of the initial SG platform, while late proteins are subsequently recruited as discrete modules to further functionalize SGs. This model, supported by immunoblotting and immunofluorescence imaging, provides a conceptual framework for the compositional transitions throughout the acute to prolonged SG life cycle. Additionally, an early SG constituent, non-muscle myosin II, is shown to promote SG formation by increasing SG fusion, underscoring the strength of this dataset in revealing the complexity of SG regulation.
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Affiliation(s)
- Shuyao Hu
- School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China.
| | - Yufeng Zhang
- School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China
| | - Qianqian Yi
- School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China
| | - Cuiwei Yang
- School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China
| | - Yanfen Liu
- School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China.
| | - Yun Bai
- School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China.
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31
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Morgan MA, Mohammad Parast S, Iwanaszko M, Aoi Y, Yoo D, Dumar ZJ, Howard BC, Helmin KA, Liu Q, Thakur WR, Zeidner JM, Singer BD, Eichler EE, Shilatifard A. ELOA3: A primate-specific RNA polymerase II elongation factor encoded by a tandem repeat gene cluster. SCIENCE ADVANCES 2023; 9:eadj1261. [PMID: 37992162 PMCID: PMC10664989 DOI: 10.1126/sciadv.adj1261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 10/19/2023] [Indexed: 11/24/2023]
Abstract
The biological role of the repetitive DNA sequences in the human genome remains an outstanding question. Recent long-read human genome assemblies have allowed us to identify a function for one of these repetitive regions. We have uncovered a tandem array of conserved primate-specific retrogenes encoding the protein Elongin A3 (ELOA3), a homolog of the RNA polymerase II (RNAPII) elongation factor Elongin A (ELOA). Our genomic analysis shows that the ELOA3 gene cluster is conserved among primates and the number of ELOA3 gene repeats is variable in the human population and across primate species. Moreover, the gene cluster has undergone concerted evolution and homogenization within primates. Our biochemical studies show that ELOA3 functions as a promoter-associated RNAPII pause-release elongation factor with distinct biochemical and functional features from its ancestral homolog, ELOA. We propose that the ELOA3 gene cluster has evolved to fulfil a transcriptional regulatory function unique to the primate lineage that can be targeted to regulate cellular hyperproliferation.
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Affiliation(s)
- Marc A. J. Morgan
- Department of Biochemistry and Molecular Genetics, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Saeid Mohammad Parast
- Department of Biochemistry and Molecular Genetics, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Marta Iwanaszko
- Department of Biochemistry and Molecular Genetics, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Yuki Aoi
- Department of Biochemistry and Molecular Genetics, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - DongAhn Yoo
- Department of Genome Sciences, University of Washington School of Medicine; Seattle, WA 98195, USA
| | - Zachary J. Dumar
- Department of Biochemistry and Molecular Genetics, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Benjamin C. Howard
- Department of Biochemistry and Molecular Genetics, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Kathryn A. Helmin
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Qianli Liu
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - William R. Thakur
- Department of Biochemistry and Molecular Genetics, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Jacob M. Zeidner
- Department of Biochemistry and Molecular Genetics, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Benjamin D. Singer
- Department of Biochemistry and Molecular Genetics, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington School of Medicine; Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
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32
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Qiu C, Zhang Z, Wine RN, Campbell ZT, Zhang J, Hall TMT. Intra- and inter-molecular regulation by intrinsically-disordered regions governs PUF protein RNA binding. Nat Commun 2023; 14:7323. [PMID: 37953271 PMCID: PMC10641069 DOI: 10.1038/s41467-023-43098-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 10/30/2023] [Indexed: 11/14/2023] Open
Abstract
PUF proteins are characterized by globular RNA-binding domains. They also interact with partner proteins that modulate their RNA-binding activities. Caenorhabditis elegans PUF protein fem-3 binding factor-2 (FBF-2) partners with intrinsically disordered Lateral Signaling Target-1 (LST-1) to regulate target mRNAs in germline stem cells. Here, we report that an intrinsically disordered region (IDR) at the C-terminus of FBF-2 autoinhibits its RNA-binding affinity by increasing the off rate for RNA binding. Moreover, the FBF-2 C-terminal region interacts with its globular RNA-binding domain at the same site where LST-1 binds. This intramolecular interaction restrains an electronegative cluster of amino acid residues near the 5' end of the bound RNA to inhibit RNA binding. LST-1 binding in place of the FBF-2 C-terminus therefore releases autoinhibition and increases RNA-binding affinity. This regulatory mechanism, driven by IDRs, provides a biochemical and biophysical explanation for the interdependence of FBF-2 and LST-1 in germline stem cell self-renewal.
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Affiliation(s)
- Chen Qiu
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Zihan Zhang
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Robert N Wine
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Zachary T Campbell
- Department of Anesthesiology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Jun Zhang
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Traci M Tanaka Hall
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA.
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33
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Ghosh A, Ganguly D. Structural impairment of p53 C-terminal due to the effect of phosphorylation and acetylation: a study on the interdependence of PTM. J Biomol Struct Dyn 2023:1-10. [PMID: 37937769 DOI: 10.1080/07391102.2023.2279270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 10/30/2023] [Indexed: 11/09/2023]
Abstract
The C-terminal of tumor suppressor protein p53 is intrinsically disordered while unbound. This particular segment often shows structural plasticity when bound to other binding partners. The disordered component undergoes a disordered to ordered transition upon recognition. Post-translational modifications (PTMs), namely phosphorylation and acetylation, significantly alter the structural motifs of the segment. Among the various types of PTMs, phosphorylation, and acetylation of p53 at both N- and C- terminals lead to stabilization and activation. It has been noted experimentally that phosphorylation often regulates (enhances or reduces) the acetylation at specific sites. The phosphorylation of Thr377 and Ser378 reduces the acetylation of Lys373 and Lys382. Mutations of Thr377 and Ser378 to neutral Ala enhance and phospho mimic Asp reduce the acetylation of Lys373 and Lys382. Simulations of several single-point and pair-wise mutated systems have been generated to compare how the presence or absence of phosphorylation favors or disfavors the acetylation by thermodynamic and conformational analysis. We are using implicit solvent replica exchange molecular dynamics simulations to get 200 ns well-converged conformational ensembles of each system. Different sets of systems having both single and double PTMs are simulated. The results admit the appreciable change in the secondary structural level upon specific PTM. Also, the residual structure of the unbound p53 with single-point PTM varies significantly with pair-wise modifications. These observations further shed light on the relationship between the interdependencies of the specific PTM sites and the secondary structural levels.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Anamika Ghosh
- Centre for Health Science and Technology, JIS Institute of Advanced Studies and Research Kolkata, JIS University, Kolkata, India
| | - Debabani Ganguly
- Centre for Health Science and Technology, JIS Institute of Advanced Studies and Research Kolkata, JIS University, Kolkata, India
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34
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Kuwayama N, Kujirai T, Kishi Y, Hirano R, Echigoya K, Fang L, Watanabe S, Nakao M, Suzuki Y, Ishiguro KI, Kurumizaka H, Gotoh Y. HMGA2 directly mediates chromatin condensation in association with neuronal fate regulation. Nat Commun 2023; 14:6420. [PMID: 37828010 PMCID: PMC10570362 DOI: 10.1038/s41467-023-42094-9] [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: 01/09/2023] [Accepted: 09/27/2023] [Indexed: 10/14/2023] Open
Abstract
Identification of factors that regulate chromatin condensation is important for understanding of gene regulation. High-mobility group AT-hook (HMGA) proteins 1 and 2 are abundant nonhistone chromatin proteins that play a role in many biological processes including tissue stem-progenitor cell regulation, but the nature of their protein function remains unclear. Here we show that HMGA2 mediates direct condensation of polynucleosomes and forms droplets with nucleosomes. Consistently, most endogenous HMGA2 localized to transposase 5- and DNase I-inaccessible chromatin regions, and its binding was mostly associated with gene repression, in mouse embryonic neocortical cells. The AT-hook 1 domain was necessary for chromatin condensation by HMGA2 in vitro and in cellulo, and an HMGA2 mutant lacking this domain was defective in the ability to maintain neuronal progenitors in vivo. Intrinsically disordered regions of other proteins could substitute for the AT-hook 1 domain in promoting this biological function of HMGA2. Taken together, HMGA2 may regulate neural cell fate by its chromatin condensation activity.
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Grants
- This research was supported by AMED-CREST and AMED-PRIME of the Japan Agency for Medical Research and Development (JP22gm1310004, JP22gm6110021), SECOM Science and Technology Foundation SECOM Science and Technology Foundation (for Y.K.), Platform Project for Supporting Drug Discovery and Life Science Research from AMED JP21am0101076 and (for H.K.), Research Support Project for Life Science and Drug Discovery from AMED JP22ama121009 (for H.K.), Japan Science and Technology Agency ERATO JPMJER1901 (for H.K.) and by KAKENHI grants from the Ministry of Education, Culture, Sports, Science, and Technology of Japan and the Japan Society for the Promotion of Science (JP21J14115 for N.K.; JP22K15033 for T.K.;16H06279, 20H03179, 21H00242 and 22H04687 for Y.K.; 20K07589 for S.W.; JP20H00449, JP18H05534 for H.K.; JP22H00431, JP16H06279 and JP22H04925 for Y.G.)
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Affiliation(s)
- Naohiro Kuwayama
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, 113-0033, Japan
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Tomoya Kujirai
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan
| | - Yusuke Kishi
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan
| | - Rina Hirano
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan
| | - Kenta Echigoya
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan
| | - Lingyan Fang
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Sugiko Watanabe
- Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, 860-0811, Japan
| | - Mitsuyoshi Nakao
- Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, 860-0811, Japan
| | - Yutaka Suzuki
- Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8561, Japan
| | - Kei-Ichiro Ishiguro
- Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, 860-0811, Japan
| | - Hitoshi Kurumizaka
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan.
| | - Yukiko Gotoh
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, 113-0033, Japan.
- International Research Center for Neurointelligence (WPI-IRCN), The University of Tokyo, Tokyo, 113-0033, Japan.
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35
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Valverde JM, Dubra G, Phillips M, Haider A, Elena-Real C, Fournet A, Alghoul E, Chahar D, Andrés-Sanchez N, Paloni M, Bernadó P, van Mierlo G, Vermeulen M, van den Toorn H, Heck AJR, Constantinou A, Barducci A, Ghosh K, Sibille N, Knipscheer P, Krasinska L, Fisher D, Altelaar M. A cyclin-dependent kinase-mediated phosphorylation switch of disordered protein condensation. Nat Commun 2023; 14:6316. [PMID: 37813838 PMCID: PMC10562473 DOI: 10.1038/s41467-023-42049-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 09/28/2023] [Indexed: 10/11/2023] Open
Abstract
Cell cycle transitions result from global changes in protein phosphorylation states triggered by cyclin-dependent kinases (CDKs). To understand how this complexity produces an ordered and rapid cellular reorganisation, we generated a high-resolution map of changing phosphosites throughout unperturbed early cell cycles in single Xenopus embryos, derived the emergent principles through systems biology analysis, and tested them by biophysical modelling and biochemical experiments. We found that most dynamic phosphosites share two key characteristics: they occur on highly disordered proteins that localise to membraneless organelles, and are CDK targets. Furthermore, CDK-mediated multisite phosphorylation can switch homotypic interactions of such proteins between favourable and inhibitory modes for biomolecular condensate formation. These results provide insight into the molecular mechanisms and kinetics of mitotic cellular reorganisation.
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Affiliation(s)
- Juan Manuel Valverde
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, 3584 CH, Utrecht, Netherlands
- Netherlands Proteomics Center, Padualaan 8, 3584 CH, Utrecht, Netherlands
| | - Geronimo Dubra
- IGMM, CNRS, University of Montpellier, INSERM, Montpellier, France
- Equipe Labellisée LIGUE 2018, Ligue Nationale Contre le Cancer, Paris, France
| | - Michael Phillips
- Department of Physics and Astronomy, University of Denver, Denver, Co, 80208, USA
| | - Austin Haider
- Department of Molecular and Cellular Biophysics, University of Denver, 80208, Denver, Co, USA
| | | | - Aurélie Fournet
- CBS, CNRS, University of Montpellier, INSERM, Montpellier, France
| | - Emile Alghoul
- IGH, CNRS, University of Montpellier, Montpellier, France
| | - Dhanvantri Chahar
- IGMM, CNRS, University of Montpellier, INSERM, Montpellier, France
- Equipe Labellisée LIGUE 2018, Ligue Nationale Contre le Cancer, Paris, France
| | - Nuria Andrés-Sanchez
- IGMM, CNRS, University of Montpellier, INSERM, Montpellier, France
- Equipe Labellisée LIGUE 2018, Ligue Nationale Contre le Cancer, Paris, France
| | - Matteo Paloni
- Department of Physics and Astronomy, University of Denver, Denver, Co, 80208, USA
| | - Pau Bernadó
- CBS, CNRS, University of Montpellier, INSERM, Montpellier, France
| | - Guido van Mierlo
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, 6525 GA, The Netherlands
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, 6525 GA, The Netherlands
| | - Henk van den Toorn
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, 3584 CH, Utrecht, Netherlands
- Netherlands Proteomics Center, Padualaan 8, 3584 CH, Utrecht, Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, 3584 CH, Utrecht, Netherlands
- Netherlands Proteomics Center, Padualaan 8, 3584 CH, Utrecht, Netherlands
| | | | | | - Kingshuk Ghosh
- Department of Physics and Astronomy, University of Denver, Denver, Co, 80208, USA
- Department of Molecular and Cellular Biophysics, University of Denver, 80208, Denver, Co, USA
| | - Nathalie Sibille
- CBS, CNRS, University of Montpellier, INSERM, Montpellier, France
| | - Puck Knipscheer
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center, Utrecht, 3584 CT, Netherlands
| | - Liliana Krasinska
- IGMM, CNRS, University of Montpellier, INSERM, Montpellier, France
- Equipe Labellisée LIGUE 2018, Ligue Nationale Contre le Cancer, Paris, France
| | - Daniel Fisher
- IGMM, CNRS, University of Montpellier, INSERM, Montpellier, France.
- Equipe Labellisée LIGUE 2018, Ligue Nationale Contre le Cancer, Paris, France.
| | - Maarten Altelaar
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, 3584 CH, Utrecht, Netherlands.
- Netherlands Proteomics Center, Padualaan 8, 3584 CH, Utrecht, Netherlands.
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36
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Djulbegovic M, Taylor Gonzalez DJ, Antonietti M, Uversky VN, Shields CL, Karp CL. Intrinsic disorder may drive the interaction of PROS1 and MERTK in uveal melanoma. Int J Biol Macromol 2023; 250:126027. [PMID: 37506796 PMCID: PMC11182630 DOI: 10.1016/j.ijbiomac.2023.126027] [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: 11/28/2022] [Revised: 07/23/2023] [Accepted: 07/25/2023] [Indexed: 07/30/2023]
Abstract
BACKGROUND Class 2 uveal melanomas are associated with the inactivation of the BRCA1 ((breast cancer type 1 susceptibility protein)-associated protein 1 (BAP1)) gene. Inactivation of BAP1 promotes the upregulation of vitamin K-dependent protein S (PROS1), which interacts with the tyrosine-protein kinase Mer (MERTK) receptor on M2 macrophages to induce an immunosuppressive environment. METHODS We simulated the interaction of PROS1 with MERTK with ColabFold. We evaluated PROS1 and MERTK for the presence of intrinsically disordered protein regions (IDPRs) and disorder-to-order (DOT) regions to understand their protein-protein interaction (PPI). We first evaluated the structure of each protein with AlphaFold. We then analyzed specific sequence-based features of the PROS1 and MERTK with a suite of bioinformatics tools. RESULTS With high-resolution, moderate confidence, we successfully modeled the interaction between PROS1 and MERTK (predicted local distance difference test score (pDLLT) = 70.68). Our structural analysis qualitatively demonstrated IDPRs (i.e., spaghetti-like entities) in PROS1 and MERK. PROS1 was 23.37 % disordered, and MERTK was 23.09 % disordered, classifying them as moderately disordered and flexible proteins. PROS1 was significantly enriched in cysteine, the most order-promoting residue (p-value <0.05). Our IUPred analysis demonstrated that there are two disorder-to-order transition (DOT) regions in PROS1. MERTK was significantly enriched in proline, the most disorder-promoting residue (p-value <0.05), but did not contain DOT regions. Our STRING analysis demonstrated that the PPI network between PROS1 and MERTK is more complex than their assumed one-to-one binding (p-value <2.0 × 10-6). CONCLUSION Our findings present a novel prediction for the interaction between PROS1 and MERTK. Our findings show that PROS1 and MERTK contain elements of intrinsic disorder. PROS1 has two DOT regions that are attractive immunotherapy targets. We recommend that IDPRs and DOT regions found in PROS1 and MERTK should be considered when developing immunotherapies targeting this PPI.
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Affiliation(s)
- Mak Djulbegovic
- Bascom Palmer Eye Institute, University of Miami, Miami, FL, USA
| | | | | | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Carol L Shields
- Ocular Oncology Service, Wills Eye Hospital, Thomas Jefferson University, Philadelphia, PA, USA
| | - Carol L Karp
- Bascom Palmer Eye Institute, University of Miami, Miami, FL, USA.
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Cherney RE, Eberhard QE, Giri G, Mills CA, Porrello A, Zhang Z, White D, Trotman JB, Herring LE, Dominguez D, Calabrese JM. SAFB associates with nascent RNAs and can promote gene expression in mouse embryonic stem cells. RNA (NEW YORK, N.Y.) 2023; 29:1535-1556. [PMID: 37468167 PMCID: PMC10578485 DOI: 10.1261/rna.079569.122] [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: 12/21/2022] [Accepted: 06/23/2023] [Indexed: 07/21/2023]
Abstract
Scaffold attachment factor B (SAFB) is a conserved RNA-binding protein that is essential for early mammalian development. However, the functions of SAFB in mouse embryonic stem cells (ESCs) have not been characterized. Using RNA immunoprecipitation followed by RNA-seq (RIP-seq), we examined the RNAs associated with SAFB in wild-type and SAFB/SAFB2 double-knockout ESCs. SAFB predominantly associated with introns of protein-coding genes through purine-rich motifs. The transcript most enriched in SAFB association was the lncRNA Malat1, which also contains a purine-rich region in its 5' end. Knockout of SAFB/SAFB2 led to differential expression of approximately 1000 genes associated with multiple biological processes, including apoptosis, cell division, and cell migration. Knockout of SAFB/SAFB2 also led to splicing changes in a set of genes that were largely distinct from those that exhibited changes in expression level. The spliced and nascent transcripts of many genes whose expression levels were positively regulated by SAFB also associated with high levels of SAFB, implying that SAFB binding promotes their expression. Reintroduction of SAFB into double-knockout cells restored gene expression toward wild-type levels, an effect again observable at the level of spliced and nascent transcripts. Proteomics analysis revealed a significant enrichment of nuclear speckle-associated and RS domain-containing proteins among SAFB interactors. Neither Xist nor Polycomb functions were dramatically altered in SAFB/2 knockout ESCs. Our findings suggest that among other potential functions in ESCs, SAFB promotes the expression of certain genes through its ability to bind nascent RNA.
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Affiliation(s)
- Rachel E Cherney
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- RNA Discovery Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Quinn E Eberhard
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- RNA Discovery Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Gilbert Giri
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- RNA Discovery Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Christine A Mills
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Proteomics Core Facility, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Alessandro Porrello
- RNA Discovery Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Zhiyue Zhang
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - David White
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Jackson B Trotman
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- RNA Discovery Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Laura E Herring
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Proteomics Core Facility, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Daniel Dominguez
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- RNA Discovery Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - J Mauro Calabrese
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- RNA Discovery Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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Martinez-Goikoetxea M, Lupas AN. New protein families with hendecad coiled coils in the proteome of life. J Struct Biol 2023; 215:108007. [PMID: 37524272 DOI: 10.1016/j.jsb.2023.108007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/30/2023] [Accepted: 07/28/2023] [Indexed: 08/02/2023]
Abstract
Coiled coils are a widespread and well understood protein fold. Their short and simple repeats underpin considerable structural and functional diversity. The vast majority of coiled coils consist of 7-residue (heptad) sequence repeats, but in essence most combinations of 3- and 4-residue segments, each starting with a residue of the hydrophobic core, are compatible with coiled-coil structure. The most frequent among these other repeat patterns are 11-residue (hendecad, 3 + 4 + 4) repeats. Hendecads are frequently found in low copy number, interspersed between heptads, but some proteins consist largely or entirely of hendecad repeats. Here we describe the first large-scale survey of these proteins in the proteome of life. For this, we scanned the protein sequence database for sequences with 11-residue periodicity that lacked β-strand prediction. We then clustered these by pairwise similarity to construct a map of potential hendecad coiled-coil families. Here we discuss these according to their structural properties, their potential cellular roles, and the evolutionary mechanisms shaping their diversity. We note in particular the continuous amplification of hendecads, both within existing proteins and de novo from previously non-coding sequence, as a powerful mechanism in the genesis of new coiled-coil forms.
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Affiliation(s)
| | - Andrei N Lupas
- Department of Protein Evolution, Max Planck Institute for Biology, 72076 Tübingen, Germany.
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Bhopatkar AA, Kayed R. Flanking regions, amyloid cores, and polymorphism: the potential interplay underlying structural diversity. J Biol Chem 2023; 299:105122. [PMID: 37536631 PMCID: PMC10482755 DOI: 10.1016/j.jbc.2023.105122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 07/10/2023] [Accepted: 07/28/2023] [Indexed: 08/05/2023] Open
Abstract
The β-sheet-rich amyloid core is the defining feature of protein aggregates associated with neurodegenerative disorders. Recent investigations have revealed that there exist multiple examples of the same protein, with the same sequence, forming a variety of amyloid cores with distinct structural characteristics. These structural variants, termed as polymorphs, are hypothesized to influence the pathological profile and the progression of different neurodegenerative diseases, giving rise to unique phenotypic differences. Thus, identifying the origin and properties of these structural variants remain a focus of studies, as a preliminary step in the development of therapeutic strategies. Here, we review the potential role of the flanking regions of amyloid cores in inducing polymorphism. These regions, adjacent to the amyloid cores, show a preponderance for being structurally disordered, imbuing them with functional promiscuity. The dynamic nature of the flanking regions can then manifest in the form of conformational polymorphism of the aggregates. We take a closer look at the sequences flanking the amyloid cores, followed by a review of the polymorphic aggregates of the well-characterized proteins amyloid-β, α-synuclein, Tau, and TDP-43. We also consider different factors that can potentially influence aggregate structure and how these regions can be viewed as novel targets for therapeutic strategies by utilizing their unique structural properties.
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Affiliation(s)
- Anukool A Bhopatkar
- Mitchell Center for Neurodegenerative Diseases, University of Texas Medical Branch, Galveston, Texas, USA; Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Rakez Kayed
- Mitchell Center for Neurodegenerative Diseases, University of Texas Medical Branch, Galveston, Texas, USA; Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, Texas, USA.
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Antonietti M, Gonzalez DJT, Djulbegovic M, Dayhoff GW, Uversky VN, Shields CL, Karp CL. Intrinsic disorder in PRAME and its role in uveal melanoma. Cell Commun Signal 2023; 21:222. [PMID: 37626310 PMCID: PMC10463658 DOI: 10.1186/s12964-023-01197-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 06/13/2023] [Indexed: 08/27/2023] Open
Abstract
INTRODUCTION The PReferentially expressed Antigen in MElanoma (PRAME) protein has been shown to be an independent biomarker for increased risk of metastasis in Class 1 uveal melanomas (UM). Intrinsically disordered proteins and regions of proteins (IDPs/IDPRs) are proteins that do not have a well-defined three-dimensional structure and have been linked to neoplastic development. Our study aimed to evaluate the presence of intrinsic disorder in PRAME and the role these structureless regions have in PRAME( +) Class 1 UM. METHODS A bioinformatics study to characterize PRAME's propensity for the intrinsic disorder. We first used the AlphaFold tool to qualitatively assess the protein structure of PRAME. Then we used the Compositional Profiler and a set of per-residue intrinsic disorder predictors to quantify the intrinsic disorder. The Database of Disordered Protein Prediction (D2P2) platform, IUPred, FuzDrop, fIDPnn, AUCpred, SPOT-Disorder2, and metapredict V2 allowed us to evaluate the potential functional disorder of PRAME. Additionally, we used the Search Tool for the Retrieval of Interacting Genes (STRING) to analyze PRAME's potential interactions with other proteins. RESULTS Our structural analysis showed that PRAME contains intrinsically disordered protein regions (IDPRs), which are structureless and flexible. We found that PRAME is significantly enriched with serine (p-value < 0.05), a disorder-promoting amino acid. PRAME was found to have an average disorder score of 16.49% (i.e., moderately disordered) across six per-residue intrinsic disorder predictors. Our IUPred analysis revealed the presence of disorder-to-order transition (DOT) regions in PRAME near the C-terminus of the protein (residues 475-509). The D2P2 platform predicted a region from approximately 140 and 175 to be highly concentrated with post-translational modifications (PTMs). FuzDrop predicted the PTM hot spot of PRAME to be a droplet-promoting region and an aggregation hotspot. Finally, our analysis using the STRING tool revealed that PRAME has significantly more interactions with other proteins than expected for randomly selected proteins of the same size, with the ability to interact with 84 different partners (STRING analysis result: p-value < 1.0 × 10-16; model confidence: 0.400). CONCLUSION Our study revealed that PRAME has IDPRs that are possibly linked to its functionality in the context of Class 1 UM. The regions of functionality (i.e., DOT regions, PTM sites, droplet-promoting regions, and aggregation hotspots) are localized to regions of high levels of disorder. PRAME has a complex protein-protein interaction (PPI) network that may be secondary to the structureless features of the polypeptide. Our findings contribute to our understanding of UM and suggest that IDPRs and DOT regions in PRAME may be targeted in developing new therapies for this aggressive cancer. Video Abstract.
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Affiliation(s)
- Michael Antonietti
- Bascom Palmer Eye Institute, University of Miami, 900 NW 17th Street, Miami, FL, 33136, USA
| | | | - Mak Djulbegovic
- Bascom Palmer Eye Institute, University of Miami, 900 NW 17th Street, Miami, FL, 33136, USA
| | - Guy W Dayhoff
- Department of Chemistry, College of Art and Sciences, University of South Florida, FL, 33612, Tampa, USA
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, FL, 33612, Tampa, USA
| | - Carol L Shields
- Ocular Oncology Service, Wills Eye Hospital, Thomas Jefferson University, PA, Philadelphia, USA
| | - Carol L Karp
- Bascom Palmer Eye Institute, University of Miami, 900 NW 17th Street, Miami, FL, 33136, USA.
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Patel CK, Rani C, Kumar R, Mukherjee TK. Macromolecular Crowding Promotes Re-entrant Liquid-Liquid Phase Separation of Human Serum Transferrin and Prevents Surface-Induced Fibrillation. Biomacromolecules 2023; 24:3917-3928. [PMID: 37503577 DOI: 10.1021/acs.biomac.3c00550] [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: 07/29/2023]
Abstract
Protein aggregation and inactivation upon surface immobilization are major limiting factors for analytical applications in biotechnology-related fields. Protein immobilization on solid surfaces often requires multi-step surface passivation, which is time-consuming and inefficient. Herein, we have discovered that biomolecular condensates of biologically active human serum transferrin (Tf) can effectively prevent surface-induced fibrillation and preserve the native-like conformation of phase-separated Tf over a period of 30 days. It has been observed that macromolecular crowding promotes homotypic liquid-liquid phase separation (LLPS) of Tf through enthalpically driven multivalent hydrophobic interactions possibly via the involvement of its low-complexity domain (residues 3-20) containing hydrophobic amino acids. The present LLPS of Tf is a rare example of salt-mediated re-entrant phase separation in a broad range of salt concentrations (0-3 M) solely via the involvement of hydrophobic interactions. Notably, no liquid-to-solid-like phase transition has been observed over a period of 30 days, suggesting the intact conformational integrity of phase-separated Tf, as revealed from single droplet Raman, circular dichroism, and Fourier transform infrared spectroscopy measurements. More importantly, we discovered that the phase-separated condensates of Tf completely inhibit the surface-induced fibrillation of Tf, illustrating the protective role of these liquid-like condensates against denaturation and aggregation of biomolecules. The cell mimicking compact aqueous compartments of biomolecular condensates with a substantial amount of interfacial water preserve the structure and functionality of Tf. Our present study highlights an important functional aspect of biologically active protein condensates and may have wide-ranging implications in cell physiology and biotechnological applications.
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Affiliation(s)
- Chinmaya Kumar Patel
- Department of Chemistry, Indian Institute of Technology (IIT) Indore, Simrol, Indore 453552, Madhya Pradesh, India
| | - Chanchal Rani
- Department of Physics, Indian Institute of Technology (IIT) Indore, Simrol, Indore 453552, Madhya Pradesh, India
| | - Rajesh Kumar
- Department of Physics, Indian Institute of Technology (IIT) Indore, Simrol, Indore 453552, Madhya Pradesh, India
| | - Tushar Kanti Mukherjee
- Department of Chemistry, Indian Institute of Technology (IIT) Indore, Simrol, Indore 453552, Madhya Pradesh, India
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Chu S, Xie X, Payan C, Stochaj U. Valosin containing protein (VCP): initiator, modifier, and potential drug target for neurodegenerative diseases. Mol Neurodegener 2023; 18:52. [PMID: 37545006 PMCID: PMC10405438 DOI: 10.1186/s13024-023-00639-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 06/27/2023] [Indexed: 08/08/2023] Open
Abstract
The AAA+ ATPase valosin containing protein (VCP) is essential for cell and organ homeostasis, especially in cells of the nervous system. As part of a large network, VCP collaborates with many cofactors to ensure proteostasis under normal, stress, and disease conditions. A large number of mutations have revealed the importance of VCP for human health. In particular, VCP facilitates the dismantling of protein aggregates and the removal of dysfunctional organelles. These are critical events to prevent malfunction of the brain and other parts of the nervous system. In line with this idea, VCP mutants are linked to the onset and progression of neurodegeneration and other diseases. The intricate molecular mechanisms that connect VCP mutations to distinct brain pathologies continue to be uncovered. Emerging evidence supports the model that VCP controls cellular functions on multiple levels and in a cell type specific fashion. Accordingly, VCP mutants derail cellular homeostasis through several mechanisms that can instigate disease. Our review focuses on the association between VCP malfunction and neurodegeneration. We discuss the latest insights in the field, emphasize open questions, and speculate on the potential of VCP as a drug target for some of the most devastating forms of neurodegeneration.
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Affiliation(s)
- Siwei Chu
- Department of Physiology, McGill University, Montreal, HG3 1Y6, Canada
| | - Xinyi Xie
- Department of Physiology, McGill University, Montreal, HG3 1Y6, Canada
| | - Carla Payan
- Department of Physiology, McGill University, Montreal, HG3 1Y6, Canada
| | - Ursula Stochaj
- Department of Physiology, McGill University, Montreal, HG3 1Y6, Canada.
- Quantitative Life Sciences Program, McGill University, Montreal, Canada.
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O'Donoghue L, Comer SP, Hiebner DW, Schoen I, von Kriegsheim A, Smolenski A. RhoGAP6 interacts with COPI to regulate protein transport. Biochem J 2023; 480:1109-1127. [PMID: 37409526 DOI: 10.1042/bcj20230013] [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: 01/16/2023] [Revised: 07/04/2023] [Accepted: 07/05/2023] [Indexed: 07/07/2023]
Abstract
RhoGAP6 is the most highly expressed GTPase-activating protein (GAP) in platelets specific for RhoA. Structurally RhoGAP6 contains a central catalytic GAP domain surrounded by large, disordered N- and C-termini of unknown function. Sequence analysis revealed three conserved consecutive overlapping di-tryptophan motifs close to the RhoGAP6 C-terminus which were predicted to bind to the mu homology domain (MHD) of δ-COP, a component of the COPI vesicle complex. We confirmed an endogenous interaction between RhoGAP6 and δ-COP in human platelets using GST-CD2AP which binds an N-terminal RhoGAP6 SH3 binding motif. Next, we confirmed that the MHD of δ-COP and the di-tryptophan motifs of RhoGAP6 mediate the interaction between both proteins. Each of the three di-tryptophan motifs appeared necessary for stable δ-COP binding. Proteomic analysis of other potential RhoGAP6 di-tryptophan motif binding partners indicated that the RhoGAP6/δ-COP interaction connects RhoGAP6 to the whole COPI complex. 14-3-3 was also established as a RhoGAP6 binding partner and its binding site was mapped to serine 37. We provide evidence of potential cross-regulation between 14-3-3 and δ-COP binding, however, neither δ-COP nor 14-3-3 binding to RhoGAP6 impacted RhoA activity. Instead, analysis of protein transport through the secretory pathway demonstrated that RhoGAP6/δ-COP binding increased protein transport to the plasma membrane, as did a catalytically inactive mutant of RhoGAP6. Overall, we have identified a novel interaction between RhoGAP6 and δ-COP which is mediated by conserved C-terminal di-tryptophan motifs, and which might control protein transport in platelets.
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Affiliation(s)
- Lorna O'Donoghue
- UCD School of Medicine, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield Dublin 4, Ireland
- Irish Centre for Vascular Biology, Royal College of Surgeons in Ireland, 123 St Stephen's Green, Dublin D02 YN77, Ireland
| | - Shane P Comer
- UCD School of Medicine, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield Dublin 4, Ireland
- Irish Centre for Vascular Biology, Royal College of Surgeons in Ireland, 123 St Stephen's Green, Dublin D02 YN77, Ireland
| | - Dishon W Hiebner
- Irish Centre for Vascular Biology, Royal College of Surgeons in Ireland, 123 St Stephen's Green, Dublin D02 YN77, Ireland
- UCD School of Chemical & Bioprocess Engineering, Engineering & Materials Science Centre, University College Dublin, Belfield Dublin 4, Ireland
| | - Ingmar Schoen
- Irish Centre for Vascular Biology, Royal College of Surgeons in Ireland, 123 St Stephen's Green, Dublin D02 YN77, Ireland
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland (RCSI), 123 St Stephen's Green, Dublin D02 YN77, Ireland
| | - Alex von Kriegsheim
- Edinburgh Cancer Research UK Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road South, Edinburgh EH4 2XR, U.K
| | - Albert Smolenski
- UCD School of Medicine, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield Dublin 4, Ireland
- Irish Centre for Vascular Biology, Royal College of Surgeons in Ireland, 123 St Stephen's Green, Dublin D02 YN77, Ireland
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Kosno M, Currie SL, Kumar A, Xing C, Rosen MK. Molecular features driving condensate formation and gene expression by the BRD4-NUT fusion oncoprotein are overlapping but distinct. Sci Rep 2023; 13:11907. [PMID: 37488172 PMCID: PMC10366142 DOI: 10.1038/s41598-023-39102-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 07/20/2023] [Indexed: 07/26/2023] Open
Abstract
Aberrant formation of biomolecular condensates has been proposed to play a role in several cancers. The oncogenic fusion protein BRD4-NUT forms condensates and drives changes in gene expression in Nut Carcinoma. Here we sought to understand the molecular elements of BRD4-NUT and its associated histone acetyltransferase (HAT), p300, that promote these activities. We determined that a minimal fragment of NUT (MIN) in fusion with BRD4 is necessary and sufficient to bind p300 and form condensates. Furthermore, a BRD4-p300 fusion protein also forms condensates and drives gene expression similarly to BRD4-NUT(MIN), suggesting the p300 fusion may mimic certain features of BRD4-NUT. The intrinsically disordered regions, transcription factor-binding domains, and HAT activity of p300 all collectively contribute to condensate formation by BRD4-p300, suggesting that these elements might contribute to condensate formation by BRD4-NUT. Conversely, only the HAT activity of BRD4-p300 appears necessary to mimic the transcriptional profile of cells expressing BRD4-NUT. Our results suggest a model for condensate formation by the BRD4-NUT:p300 complex involving a combination of positive feedback and phase separation, and show that multiple overlapping, yet distinct, regions of p300 contribute to condensate formation and transcriptional regulation.
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Affiliation(s)
- Martyna Kosno
- Department of Biophysics, Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Simon L Currie
- Department of Biophysics, Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Ashwani Kumar
- Eugene McDermott Center for Human Growth and Development, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Chao Xing
- Eugene McDermott Center for Human Growth and Development, UT Southwestern Medical Center, Dallas, TX, 75390, USA
- Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Michael K Rosen
- Department of Biophysics, Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, TX, 75390, USA.
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Li J, Li N, Roellig DM, Zhao W, Guo Y, Feng Y, Xiao L. High subtelomeric GC content in the genome of a zoonotic Cryptosporidium species. Microb Genom 2023; 9:mgen001052. [PMID: 37399068 PMCID: PMC10438818 DOI: 10.1099/mgen.0.001052] [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: 01/06/2023] [Accepted: 05/24/2023] [Indexed: 07/04/2023] Open
Abstract
Cryptosporidium canis is a zoonotic species causing cryptosporidiosis in humans in addition to its natural hosts dogs and other fur animals. To understand the genetic basis for host adaptation, we sequenced the genomes of C. canis from dogs, minks, and foxes and conducted a comparative genomics analysis. While the genomes of C. canis have similar gene contents and organisations, they (~41.0 %) and C. felis (39.6 %) have GC content much higher than other Cryptosporidium spp. (24.3-32.9 %) sequenced to date. The high GC content is mostly restricted to subtelomeric regions of the eight chromosomes. Most of these GC-balanced genes encode Cryptosporidium-specific proteins that have intrinsically disordered regions and are involved in host-parasite interactions. Natural selection appears to play a more important role in the evolution of codon usage in GC-balanced C. canis, and most of the GC-balanced genes have undergone positive selection. While the identity in whole genome sequences between the mink- and dog-derived isolates is 99.9 % (9365 SNVs), it is only 96.0 % (362 894 SNVs) between them and the fox-derived isolate. In agreement with this, the fox-derived isolate possesses more subtelomeric genes encoding invasion-related protein families. Therefore, the change in subtelomeric GC content appears to be responsible for the more GC-balanced C. canis genomes, and the fox-derived isolate could represent a new Cryptosporidium species.
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Affiliation(s)
- Jiayu Li
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, PR China
| | - Na Li
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, PR China
| | - Dawn M. Roellig
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Wentao Zhao
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, PR China
| | - Yaqiong Guo
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, PR China
| | - Yaoyu Feng
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, PR China
| | - Lihua Xiao
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, PR China
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Ramm B, Schumacher D, Harms A, Heermann T, Klos P, Müller F, Schwille P, Søgaard-Andersen L. Biomolecular condensate drives polymerization and bundling of the bacterial tubulin FtsZ to regulate cell division. Nat Commun 2023; 14:3825. [PMID: 37380708 DOI: 10.1038/s41467-023-39513-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 06/07/2023] [Indexed: 06/30/2023] Open
Abstract
Cell division is spatiotemporally precisely regulated, but the underlying mechanisms are incompletely understood. In the social bacterium Myxococcus xanthus, the PomX/PomY/PomZ proteins form a single megadalton-sized complex that directly positions and stimulates cytokinetic ring formation by the tubulin homolog FtsZ. Here, we study the structure and mechanism of this complex in vitro and in vivo. We demonstrate that PomY forms liquid-like biomolecular condensates by phase separation, while PomX self-assembles into filaments generating a single large cellular structure. The PomX structure enriches PomY, thereby guaranteeing the formation of precisely one PomY condensate per cell through surface-assisted condensation. In vitro, PomY condensates selectively enrich FtsZ and nucleate GTP-dependent FtsZ polymerization and bundle FtsZ filaments, suggesting a cell division site positioning mechanism in which the single PomY condensate enriches FtsZ to guide FtsZ-ring formation and division. This mechanism shares features with microtubule nucleation by biomolecular condensates in eukaryotes, supporting this mechanism's ancient origin.
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Affiliation(s)
- Beatrice Ramm
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.
- Department of Physics, Princeton University, Princeton, NJ, 08544, USA.
| | - Dominik Schumacher
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Str. 10, 35043, Marburg, Germany.
| | - Andrea Harms
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Str. 10, 35043, Marburg, Germany
| | - Tamara Heermann
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Philipp Klos
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Str. 10, 35043, Marburg, Germany
| | - Franziska Müller
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Str. 10, 35043, Marburg, Germany
| | - Petra Schwille
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.
| | - Lotte Søgaard-Andersen
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Str. 10, 35043, Marburg, Germany.
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47
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Han X, Hu Z, Surya W, Ma Q, Zhou F, Nordenskiöld L, Torres J, Lu L, Miao Y. The intrinsically disordered region of coronins fine-tunes oligomerization and actin polymerization. Cell Rep 2023; 42:112594. [PMID: 37269287 DOI: 10.1016/j.celrep.2023.112594] [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: 10/18/2022] [Revised: 04/21/2023] [Accepted: 05/16/2023] [Indexed: 06/05/2023] Open
Abstract
Coronins play critical roles in actin network formation. The diverse functions of coronins are regulated by the structured N-terminal β propeller and the C-terminal coiled coil (CC). However, less is known about a middle "unique region" (UR), which is an intrinsically disordered region (IDR). The UR/IDR is an evolutionarily conserved signature in the coronin family. By integrating biochemical and cell biology experiments, coarse-grained simulations, and protein engineering, we find that the IDR optimizes the biochemical activities of coronins in vivo and in vitro. The budding yeast coronin IDR plays essential roles in regulating Crn1 activity by fine-tuning CC oligomerization and maintaining Crn1 as a tetramer. The IDR-guided optimization of Crn1 oligomerization is critical for F-actin cross-linking and regulation of Arp2/3-mediated actin polymerization. The final oligomerization status and homogeneity of Crn1 are contributed by three examined factors: helix packing, the energy landscape of the CC, and the length and molecular grammar of the IDR.
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Affiliation(s)
- Xiao Han
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Zixin Hu
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Wahyu Surya
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Qianqian Ma
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Feng Zhou
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Lars Nordenskiöld
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Jaume Torres
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Lanyuan Lu
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Yansong Miao
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore; Institute for Digital Molecular Analytics and Science, Nanyang Technological University, Singapore 636921, Singapore.
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48
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Mann MW, Fu Y, Gearhart RL, Xu X, Roberts DS, Li Y, Zhou J, Ge Y, Brasier AR. Bromodomain-containing Protein 4 regulates innate inflammation via modulation of alternative splicing. Front Immunol 2023; 14:1212770. [PMID: 37435059 PMCID: PMC10331468 DOI: 10.3389/fimmu.2023.1212770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 06/05/2023] [Indexed: 07/13/2023] Open
Abstract
Introduction Bromodomain-containing Protein 4 (BRD4) is a transcriptional regulator which coordinates gene expression programs controlling cancer biology, inflammation, and fibrosis. In the context of airway viral infection, BRD4-specific inhibitors (BRD4i) block the release of pro-inflammatory cytokines and prevent downstream epithelial plasticity. Although the chromatin modifying functions of BRD4 in inducible gene expression have been extensively investigated, its roles in post-transcriptional regulation are not well understood. Given BRD4's interaction with the transcriptional elongation complex and spliceosome, we hypothesize that BRD4 is a functional regulator of mRNA processing. Methods To address this question, we combine data-independent analysis - parallel accumulation-serial fragmentation (diaPASEF) with RNA-sequencing to achieve deep and integrated coverage of the proteomic and transcriptomic landscapes of human small airway epithelial cells exposed to viral challenge and treated with BRD4i. Results We discover that BRD4 regulates alternative splicing of key genes, including Interferon-related Developmental Regulator 1 (IFRD1) and X-Box Binding Protein 1 (XBP1), related to the innate immune response and the unfolded protein response (UPR). We identify requirement of BRD4 for expression of serine-arginine splicing factors, splicosome components and the Inositol-Requiring Enzyme 1 IREα affecting immediate early innate response and the UPR. Discussion These findings extend the transcriptional elongation-facilitating actions of BRD4 in control of post-transcriptional RNA processing via modulating splicing factor expression in virus-induced innate signaling.
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Affiliation(s)
- Morgan W. Mann
- Department of Medicine, University of Wisconsin – Madison, Madison, WI, United States
| | - Yao Fu
- Department of Medicine, University of Wisconsin – Madison, Madison, WI, United States
| | - Robert L. Gearhart
- Department of Chemistry, University of Wisconsin – Madison, Madison, WI, United States
| | - Xiaofang Xu
- Department of Medicine, University of Wisconsin – Madison, Madison, WI, United States
| | - David S. Roberts
- Department of Chemistry, University of Wisconsin – Madison, Madison, WI, United States
| | - Yi Li
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, United States
| | - Jia Zhou
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, United States
| | - Ying Ge
- Department of Chemistry, University of Wisconsin – Madison, Madison, WI, United States
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, United States
- Human Proteomics Program, University of Wisconsin-Madison, Madison, WI, United States
| | - Allan R. Brasier
- Department of Medicine, University of Wisconsin – Madison, Madison, WI, United States
- Institute for Clinical and Translational Research, University of Wisconsin-Madison, Madison, WI, United States
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49
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Meeussen JVW, Pomp W, Brouwer I, de Jonge WJ, Patel HP, Lenstra TL. Transcription factor clusters enable target search but do not contribute to target gene activation. Nucleic Acids Res 2023; 51:5449-5468. [PMID: 36987884 PMCID: PMC10287935 DOI: 10.1093/nar/gkad227] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 03/06/2023] [Accepted: 03/16/2023] [Indexed: 03/30/2023] Open
Abstract
Many transcription factors (TFs) localize in nuclear clusters of locally increased concentrations, but how TF clustering is regulated and how it influences gene expression is not well understood. Here, we use quantitative microscopy in living cells to study the regulation and function of clustering of the budding yeast TF Gal4 in its endogenous context. Our results show that Gal4 forms clusters that overlap with the GAL loci. Cluster number, density and size are regulated in different growth conditions by the Gal4-inhibitor Gal80 and Gal4 concentration. Gal4 truncation mutants reveal that Gal4 clustering is facilitated by, but does not completely depend on DNA binding and intrinsically disordered regions. Moreover, we discover that clustering acts as a double-edged sword: self-interactions aid TF recruitment to target genes, but recruited Gal4 molecules that are not DNA-bound do not contribute to, and may even inhibit, transcription activation. We propose that cells need to balance the different effects of TF clustering on target search and transcription activation to facilitate proper gene expression.
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Affiliation(s)
- Joseph V W Meeussen
- Division of Gene Regulation, The Netherlands Cancer Institute, Oncode Institute, 1066CX Amsterdam, The Netherlands
| | - Wim Pomp
- Division of Gene Regulation, The Netherlands Cancer Institute, Oncode Institute, 1066CX Amsterdam, The Netherlands
| | - Ineke Brouwer
- Division of Gene Regulation, The Netherlands Cancer Institute, Oncode Institute, 1066CX Amsterdam, The Netherlands
| | - Wim J de Jonge
- Division of Gene Regulation, The Netherlands Cancer Institute, Oncode Institute, 1066CX Amsterdam, The Netherlands
| | - Heta P Patel
- Division of Gene Regulation, The Netherlands Cancer Institute, Oncode Institute, 1066CX Amsterdam, The Netherlands
| | - Tineke L Lenstra
- Division of Gene Regulation, The Netherlands Cancer Institute, Oncode Institute, 1066CX Amsterdam, The Netherlands
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50
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Palumbo RJ, Hanes SD. Catalytic activity of the Bin3/MEPCE methyltransferase domain is dispensable for 7SK snRNP function in Drosophila melanogaster. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.01.543302. [PMID: 37333392 PMCID: PMC10274667 DOI: 10.1101/2023.06.01.543302] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Methylphosphate Capping Enzyme (MEPCE) monomethylates the gamma phosphate at the 5' end of the 7SK noncoding RNA, a modification thought to protect 7SK from degradation. 7SK serves as a scaffold for assembly of a snRNP complex that inhibits transcription by sequestering the positive elongation factor P-TEFb. While much is known about the biochemical activity of MEPCE in vitro, little is known about its functions in vivo, or what roles- if any-there are for regions outside the conserved methyltransferase domain. Here, we investigated the role of Bin3, the Drosophila ortholog of MEPCE, and its conserved functional domains in Drosophila development. We found that bin3 mutant females had strongly reduced rates of egg-laying, which was rescued by genetic reduction of P-TEFb activity, suggesting that Bin3 promotes fecundity by repressing P-TEFb. bin3 mutants also exhibited neuromuscular defects, analogous to a patient with MEPCE haploinsufficiency. These defects were also rescued by genetic reduction of P-TEFb activity, suggesting that Bin3 and MEPCE have conserved roles in promoting neuromuscular function by repressing P-TEFb. Unexpectedly, we found that a Bin3 catalytic mutant (Bin3Y795A) could still bind and stabilize 7SK and rescue all bin3 mutant phenotypes, indicating that Bin3 catalytic activity is dispensable for 7SK stability and snRNP function in vivo. Finally, we identified a metazoan-specific motif (MSM) outside of the methyltransferase domain and generated mutant flies lacking this motif (Bin3ΔMSM). Bin3ΔMSM mutant flies exhibited some-but not all-bin3 mutant phenotypes, suggesting that the MSM is required for a 7SK-independent, tissue-specific function of Bin3.
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Affiliation(s)
- Ryan J Palumbo
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University 750 East Adams Street, 4283 Weiskotten Hall, Syracuse, New York, 13210
| | - Steven D Hanes
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University 750 East Adams Street, 4283 Weiskotten Hall, Syracuse, New York, 13210
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