1
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Mukherjee S, Poudyal M, Dave K, Kadu P, Maji SK. Protein misfolding and amyloid nucleation through liquid-liquid phase separation. Chem Soc Rev 2024; 53:4976-5013. [PMID: 38597222 DOI: 10.1039/d3cs01065a] [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: 04/11/2024]
Abstract
Liquid-liquid phase separation (LLPS) is an emerging phenomenon in cell physiology and diseases. The weak multivalent interaction prerequisite for LLPS is believed to be facilitated through intrinsically disordered regions, which are prevalent in neurodegenerative disease-associated proteins. These aggregation-prone proteins also exhibit an inherent property for phase separation, resulting in protein-rich liquid-like droplets. The very high local protein concentration in the water-deficient confined microenvironment not only drives the viscoelastic transition from the liquid to solid-like state but also most often nucleate amyloid fibril formation. Indeed, protein misfolding, oligomerization, and amyloid aggregation are observed to be initiated from the LLPS of various neurodegeneration-related proteins. Moreover, in these cases, neurodegeneration-promoting genetic and environmental factors play a direct role in amyloid aggregation preceded by the phase separation. These cumulative recent observations ignite the possibility of LLPS being a prominent nucleation mechanism associated with aberrant protein aggregation. The present review elaborates on the nucleation mechanism of the amyloid aggregation pathway and the possible early molecular events associated with amyloid-related protein phase separation. It also summarizes the recent advancement in understanding the aberrant phase transition of major proteins contributing to neurodegeneration focusing on the common disease-associated factors. Overall, this review proposes a generic LLPS-mediated multistep nucleation mechanism for amyloid aggregation and its implication in neurodegeneration.
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Affiliation(s)
- Semanti Mukherjee
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
| | - Manisha Poudyal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
| | - Kritika Dave
- Sunita Sanghi Centre of Aging and Neurodegenerative Diseases, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Pradeep Kadu
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
| | - Samir K Maji
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
- Sunita Sanghi Centre of Aging and Neurodegenerative Diseases, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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2
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Wenninger N, Chaiyo S, Kollau A, Kalcher K, Ortner A. Paper-based electrochemical immunosensor for the determination of symmetric dimethylarginine. Biosens Bioelectron 2023; 237:115481. [PMID: 37379792 DOI: 10.1016/j.bios.2023.115481] [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: 03/01/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 06/30/2023]
Abstract
In this work, we present the development of an immunosensor for the direct, selective, and sensitive determination of symmetric dimethylarginine (SDMA) in urine, in view of the emerging role of this molecule as a biomarker for renal disease. SDMA is almost completely excreted by the kidneys, hence in renal dysfunction, the excretion is decreased, resulting in accumulation in plasma. Reference values for plasma or serum have already been established in small animal practice. Values < 15 μg/dL are considered normal, 15-19 μg/dL are values of concern, and at values > 20 μg/dL kidney disease is likely. The proposed electrochemical paper-based sensing platform uses anti-SDMA antibodies for targeted detection of SDMA. Quantification is related to a decrease in the signal of a redox indicator due to the formation of an immunocomplex that interferes with electron transfer. Square wave voltammetry measurements showed a linear correlation of the peak decline for 50 nM - 1 μM SDMA with a detection limit of 15 nM. The influence of common physiological interferences caused no significant peak reduction, indicating excellent selectivity. The proposed immunosensor was successfully applied for the quantification of SDMA in human urine of healthy individuals. Surveillance of SDMA concentration in urine could prove to be very valuable in the diagnosis or monitoring of renal disease.
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Affiliation(s)
- Nadine Wenninger
- Institute of Pharmaceutical Sciences, Department of Pharmaceutical Chemistry, University of Graz, Schubertstraße 1, Graz, 8010, Austria
| | - Sudkate Chaiyo
- Institute of Biotechnology and Genetic Engineering, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Alexander Kollau
- Institute of Pharmaceutical Sciences, Department of Pharmacology and Toxicology, University of Graz, Humboldtstraße 46/I, Graz, 8010, Austria
| | - Kurt Kalcher
- Institute of Chemistry, Department of Analytical Chemistry, University of Graz, Universitätsplatz 1, Graz, 8010, Austria
| | - Astrid Ortner
- Institute of Pharmaceutical Sciences, Department of Pharmaceutical Chemistry, University of Graz, Schubertstraße 1, Graz, 8010, Austria.
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3
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Skowron KJ, Baliga C, Johnson T, Kremiller KM, Castroverde A, Dean TT, Allen AC, Lopez-Hernandez AM, Aleksandrova EV, Klepacki D, Mankin AS, Polikanov YS, Moore TW. Structure-Activity Relationships of the Antimicrobial Peptide Natural Product Apidaecin. J Med Chem 2023; 66:11831-11842. [PMID: 37603874 PMCID: PMC10768847 DOI: 10.1021/acs.jmedchem.3c00406] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
Abstract
With the growing crisis of antimicrobial resistance, it is critical to continue to seek out new sources of novel antibiotics. This need has led to renewed interest in natural product antimicrobials, specifically antimicrobial peptides. Nonlytic antimicrobial peptides are highly promising due to their unique mechanisms of action. One such peptide is apidaecin (Api), which inhibits translation termination through stabilization of the quaternary complex of the ribosome-apidaecin-tRNA-release factor. Synthetic derivatives of apidaecin have been developed, but structure-guided modifications have yet to be considered. In this work, we have focused on modifying key residues in the Api sequence that are responsible for the interactions that stabilize the quaternary complex. We present one of the first examples of a highly modified Api peptide that maintains its antimicrobial activity and interaction with the translation complex. These findings establish a starting point for further structure-guided optimization of Api peptides.
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Affiliation(s)
- Kornelia J Skowron
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois Chicago, Chicago, Illinois 60612, United States
| | - Chetana Baliga
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois Chicago, Chicago, Illinois 60612, United States
| | - Tatum Johnson
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois Chicago, Chicago, Illinois 60612, United States
| | - Kyle M Kremiller
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois Chicago, Chicago, Illinois 60612, United States
| | - Alexandra Castroverde
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois Chicago, Chicago, Illinois 60612, United States
| | - Trevor T Dean
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois Chicago, Chicago, Illinois 60612, United States
| | - A'Lester C Allen
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois Chicago, Chicago, Illinois 60612, United States
| | - Ana M Lopez-Hernandez
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois Chicago, Chicago, Illinois 60612, United States
| | - Elena V Aleksandrova
- Department of Biological Sciences, College of Liberal Arts and Sciences, University of Illinois Chicago, Chicago, Illinois 60607, United States
| | - Dorota Klepacki
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois Chicago, Chicago, Illinois 60612, United States
| | - Alexander S Mankin
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois Chicago, Chicago, Illinois 60612, United States
- Center for Biomolecular Sciences, University of Illinois Chicago, Chicago, Illinois 60612, United States
| | - Yury S Polikanov
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois Chicago, Chicago, Illinois 60612, United States
- Department of Biological Sciences, College of Liberal Arts and Sciences, University of Illinois Chicago, Chicago, Illinois 60607, United States
- Center for Biomolecular Sciences, University of Illinois Chicago, Chicago, Illinois 60612, United States
| | - Terry W Moore
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois Chicago, Chicago, Illinois 60612, United States
- University of Illinois Cancer Center, University of Illinois Chicago, Chicago, Illinois 60612, United States
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4
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Ainani H, Bouchmaa N, Ben Mrid R, El Fatimy R. Liquid-liquid phase separation of protein tau: An emerging process in Alzheimer's disease pathogenesis. Neurobiol Dis 2023; 178:106011. [PMID: 36702317 DOI: 10.1016/j.nbd.2023.106011] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 01/04/2023] [Accepted: 01/21/2023] [Indexed: 01/24/2023] Open
Abstract
Metabolic reactions within cells occur in various isolated compartments with or without borders, the latter being known as membrane-less organelles (MLOs). The MLOs show liquid-like properties and are formed by a process known as liquid-liquid phase separation (LLPS). MLOs contribute to different molecules interactions such as protein-protein, protein-RNA, and RNA-RNA driven by various factors, such as multivalency of intrinsic disorders. MLOs are involved in several cell signaling pathways such as transcription, immune response, and cellular organization. However, disruption of these processes has been found in different pathologies. Recently, it has been demonstrated that protein aggregates, a characteristic of some neurodegenerative diseases, undergo similar phase separation. Tau protein is known as a major neurofibrillary tangles component in Alzheimer's disease (AD). This protein can undergo phase separation to form a MLO known as tau droplet in vitro and in vivo, and this process can be facilitated by several factors, including crowding agents, RNA, and phosphorylation. Tau droplet has been shown to mature into insoluble aggregates suggesting that this process may precede and induce neurodegeneration in AD. Here we review major factors involved in liquid droplet formation within a cell. Additionally, we highlight recent findings concerning tau aggregation following phase separation in AD, along with the potential therapeutic strategies that could be explored in this process against the progression of this pathology.
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Affiliation(s)
- Hassan Ainani
- Institute of Biological Sciences (ISSB), UM6P-Faculty of Medical Sciences (UM6P-FMS), Mohammed VI Polytechnic University, Ben-Guerir, Morocco
| | - Najat Bouchmaa
- Institute of Biological Sciences (ISSB), UM6P-Faculty of Medical Sciences (UM6P-FMS), Mohammed VI Polytechnic University, Ben-Guerir, Morocco
| | - Reda Ben Mrid
- Institute of Biological Sciences (ISSB), UM6P-Faculty of Medical Sciences (UM6P-FMS), Mohammed VI Polytechnic University, Ben-Guerir, Morocco
| | - Rachid El Fatimy
- Institute of Biological Sciences (ISSB), UM6P-Faculty of Medical Sciences (UM6P-FMS), Mohammed VI Polytechnic University, Ben-Guerir, Morocco.
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5
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Matteo Jörgensen A, Knoll P, Haddadzadegan S, Fabian H, Hupfauf A, Gust R, Georg Jörgensen R, Bernkop-Schnürch A. Biodegradable arginine based steroid-surfactants: Cationic green agents for hydrophobic ion-pairing. Int J Pharm 2022; 630:122438. [PMID: 36464112 DOI: 10.1016/j.ijpharm.2022.122438] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 11/18/2022] [Accepted: 11/20/2022] [Indexed: 12/03/2022]
Abstract
The aim of this study was to evaluate the safety and efficacy for hydrophobic ion-pairing of surfactants based on arginine (Arg). The prepared Arg-cholesteryl ester (ACE) and Arg-diosgenyl ester (ADE) were characterized regarding solubility, pKa, critical micellar concentration (CMC), biodegradability as well as membrane- and aquatic toxicity using DOTAP as reference. The ability for hydrophobic ion-pairing was evaluated and the lipophilicity of formed complexes was determined. NMR, FT-IR and MS confirmed successful synthesis of Arg-surfactants. The slightly soluble single-charged Arg-surfactants (pH < pKa3 (ACE = 10.42 ± 0.52; ADE = 10.38 ± 0.27)) showed CMCs of 27.17 µM for ACE and 35.67 µM for ADE. CMCs of the sparingly soluble double-charged species (pH < pKa2 (ACE = 5.30 ± 0.20; ADE = 5.55 ± 0.06)) were determined at concentrations of ≥ 250 µM for ACE and ≥ 850 µM for ADE. The enzymatic- and environmental biodegradability was proven by an entire cleavage of Arg-surfactants within 24 h, whereas DOTAP remained stable. Arg-surfactants exhibited lower membrane- (> 2-fold) and aquatic toxicity (> 15-fold) than DOTAP. The complexes formed with Arg-surfactants and insulin showed higher lipophilicity than the DOTAP-complex. According to these results, Arg-surfactants might be a promising safe tool for the delivery of peptide drugs.
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Affiliation(s)
- Arne Matteo Jörgensen
- Department of Pharmaceutical Technology, University of Innsbruck, Institute of Pharmacy, Center for Chemistry and Biomedicine, Innrain 80-82, 6020 Innsbruck, Austria
| | - Patrick Knoll
- Department of Pharmaceutical Technology, University of Innsbruck, Institute of Pharmacy, Center for Chemistry and Biomedicine, Innrain 80-82, 6020 Innsbruck, Austria
| | - Soheil Haddadzadegan
- Department of Pharmaceutical Technology, University of Innsbruck, Institute of Pharmacy, Center for Chemistry and Biomedicine, Innrain 80-82, 6020 Innsbruck, Austria
| | - Hannah Fabian
- Department of Pharmaceutical Technology, University of Innsbruck, Institute of Pharmacy, Center for Chemistry and Biomedicine, Innrain 80-82, 6020 Innsbruck, Austria
| | - Andrea Hupfauf
- Department of Pharmaceutical Chemistry, University of Innsbruck, Institute of Pharmacy, Center for Chemistry and Biomedicine, Innrain 80-82, 6020 Innsbruck, Austria
| | - Ronald Gust
- Department of Pharmaceutical Chemistry, University of Innsbruck, Institute of Pharmacy, Center for Chemistry and Biomedicine, Innrain 80-82, 6020 Innsbruck, Austria
| | - Rainer Georg Jörgensen
- Soil Biology and Plant Nutrition, University of Kassel, Nordbahnhofstr. 1a, 37023 Witzenhausen, Germany
| | - Andreas Bernkop-Schnürch
- Department of Pharmaceutical Technology, University of Innsbruck, Institute of Pharmacy, Center for Chemistry and Biomedicine, Innrain 80-82, 6020 Innsbruck, Austria.
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6
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Angrand G, Quillévéré A, Loaëc N, Dinh VT, Le Sénéchal R, Chennoufi R, Duchambon P, Keruzoré M, Martins R, Teulade-Fichou MP, Fåhraeus R, Blondel M. Type I arginine methyltransferases are intervention points to unveil the oncogenic Epstein-Barr virus to the immune system. Nucleic Acids Res 2022; 50:11799-11819. [PMID: 36350639 PMCID: PMC9723642 DOI: 10.1093/nar/gkac915] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 10/06/2022] [Indexed: 11/10/2022] Open
Abstract
The oncogenic Epstein-Barr virus (EBV) evades the immune system but has an Achilles heel: its genome maintenance protein EBNA1. Indeed, EBNA1 is essential for viral genome maintenance but is also highly antigenic. Hence, EBV seemingly evolved a system in which the glycine-alanine repeat (GAr) of EBNA1 limits the translation of its own mRNA to the minimal level to ensure its essential function, thereby, at the same time, minimizing immune recognition. Therefore, defining intervention points at which to interfere with GAr-based inhibition of translation is an important step to trigger an immune response against EBV-carrying cancers. The host protein nucleolin (NCL) plays a critical role in this process via a direct interaction with G-quadruplexes (G4) formed in the GAr-encoding sequence of the viral EBNA1 mRNA. Here we show that the C-terminal arginine-glycine-rich (RGG) motif of NCL is crucial for its role in GAr-based inhibition of translation by mediating interaction of NCL with G4 of EBNA1 mRNA. We also show that this interaction depends on the type I arginine methyltransferase family, notably PRMT1 and PRMT3: drugs or small interfering RNA that target these enzymes prevent efficient binding of NCL on G4 of EBNA1 mRNA and relieve GAr-based inhibition of translation and of antigen presentation. Hence, this work defines type I arginine methyltransferases as therapeutic targets to interfere with EBNA1 and EBV immune evasion.
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Affiliation(s)
| | | | | | - Van-Trang Dinh
- Institut National de la Santé et de la Recherche Médicale UMR1078; Université de Bretagne Occidentale, Faculté de Médecine et des Sciences de la Santé; Etablissement Français du Sang (EFS) Bretagne; CHRU Brest, Hôpital Morvan, Laboratoire de Génétique Moléculaire, 22 avenue Camille Desmoulins, F-29200 Brest, France
| | - Ronan Le Sénéchal
- Institut National de la Santé et de la Recherche Médicale UMR1078; Université de Bretagne Occidentale, Faculté de Médecine et des Sciences de la Santé; Etablissement Français du Sang (EFS) Bretagne; CHRU Brest, Hôpital Morvan, Laboratoire de Génétique Moléculaire, 22 avenue Camille Desmoulins, F-29200 Brest, France
| | - Rahima Chennoufi
- Chemistry and Modelling for the Biology of Cancer, CNRS UMR9187 - Inserm U1196, Institut Curie, Université Paris-Saclay, Orsay, Campus universitaire, Bat. 110, F-91405, France
| | - Patricia Duchambon
- Chemistry and Modelling for the Biology of Cancer, CNRS UMR9187 - Inserm U1196, Institut Curie, Université Paris-Saclay, Orsay, Campus universitaire, Bat. 110, F-91405, France
| | - Marc Keruzoré
- Institut National de la Santé et de la Recherche Médicale UMR1078; Université de Bretagne Occidentale, Faculté de Médecine et des Sciences de la Santé; Etablissement Français du Sang (EFS) Bretagne; CHRU Brest, Hôpital Morvan, Laboratoire de Génétique Moléculaire, 22 avenue Camille Desmoulins, F-29200 Brest, France
| | | | - Marie-Paule Teulade-Fichou
- Chemistry and Modelling for the Biology of Cancer, CNRS UMR9187 - Inserm U1196, Institut Curie, Université Paris-Saclay, Orsay, Campus universitaire, Bat. 110, F-91405, France
| | - Robin Fåhraeus
- Cibles Thérapeutiques, Institut National de la Santé et de la Recherche Médicale UMR1162, Institut de Génétique Moléculaire, Université Paris 7, Hôpital St. Louis, 27 rue Juliette Dodu, F-75010 Paris, France,RECAMO, Masaryk Memorial Cancer Institute, Zluty kopec 7, 65653 Brno, Czech Republic
| | - Marc Blondel
- To whom correspondence should be addressed. Tel: +33 2 98 01 83 88;
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7
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Ren J, Zhang Z, Zong Z, Zhang L, Zhou F. Emerging Implications of Phase Separation in Cancer. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2202855. [PMID: 36117111 PMCID: PMC9631093 DOI: 10.1002/advs.202202855] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 08/26/2022] [Indexed: 05/19/2023]
Abstract
In eukaryotic cells, biological activities are executed in distinct cellular compartments or organelles. Canonical organelles with membrane-bound structures are well understood. Cells also inherently contain versatile membrane-less organelles (MLOs) that feature liquid or gel-like bodies. A biophysical process termed liquid-liquid phase separation (LLPS) elucidates how MLOs form through dynamic biomolecule assembly. LLPS-related molecules often have multivalency, which is essential for low-affinity inter- or intra-molecule interactions to trigger phase separation. Accumulating evidence shows that LLPS concentrates and organizes desired molecules or segregates unneeded molecules in cells. Thus, MLOs have tunable functional specificity in response to environmental stimuli and metabolic processes. Aberrant LLPS is widely associated with several hallmarks of cancer, including sustained proliferative signaling, growth suppressor evasion, cell death resistance, telomere maintenance, DNA damage repair, etc. Insights into the molecular mechanisms of LLPS provide new insights into cancer therapeutics. Here, the current understanding of the emerging concepts of LLPS and its involvement in cancer are comprehensively reviewed.
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Affiliation(s)
- Jiang Ren
- School of MedicineZhejiang University City CollegeHangzhou215123China
- The Eighth Affiliated HospitalSun Yat‐sen UniversityShenzhen518033China
| | - Zhenyu Zhang
- Department of NeurosurgeryThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouHenan450003China
| | - Zhi Zong
- MOE Key Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling NetworkLife Sciences InstituteZhejiang UniversityHangzhou310058China
| | - Long Zhang
- MOE Key Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling NetworkLife Sciences InstituteZhejiang UniversityHangzhou310058China
- International Biomed‐X Research Center, Second Affiliated Hospital of Zhejiang University School of MedicineZhejiang UniversityHangzhouChina
- Cancer CenterZhejiang UniversityHangzhou215123China
| | - Fangfang Zhou
- School of MedicineZhejiang University City CollegeHangzhou215123China
- Institutes of Biology and Medical SciencesSoochow UniversitySuzhou215123China
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8
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Schmidt A, Frei J, Poetsch A, Chittka A, Zhang H, Aßmann C, Lehmkuhl A, Bauer UM, Nuber UA, Cardoso MC. MeCP2 heterochromatin organization is modulated by arginine methylation and serine phosphorylation. Front Cell Dev Biol 2022; 10:941493. [PMID: 36172281 PMCID: PMC9510713 DOI: 10.3389/fcell.2022.941493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 08/19/2022] [Indexed: 11/23/2022] Open
Abstract
Rett syndrome is a human intellectual disability disorder that is associated with mutations in the X-linked MECP2 gene. The epigenetic reader MeCP2 binds to methylated cytosines on the DNA and regulates chromatin organization. We have shown previously that MECP2 Rett syndrome missense mutations are impaired in chromatin binding and heterochromatin reorganization. Here, we performed a proteomics analysis of post-translational modifications of MeCP2 isolated from adult mouse brain. We show that MeCP2 carries various post-translational modifications, among them phosphorylation on S80 and S421, which lead to minor changes in either heterochromatin binding kinetics or clustering. We found that MeCP2 is (di)methylated on several arginines and that this modification alters heterochromatin organization. Interestingly, we identified the Rett syndrome mutation site R106 as a dimethylation site. In addition, co-expression of protein arginine methyltransferases (PRMT)1 and PRMT6 lead to a decrease of heterochromatin clustering. Altogether, we identified and validated novel modifications of MeCP2 in the brain and show that these can modulate its ability to bind as well as reorganize heterochromatin, which may play a role in the pathology of Rett syndrome.
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Affiliation(s)
- Annika Schmidt
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Jana Frei
- Stem Cell and Developmental Biology, Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Ansgar Poetsch
- Queen Mary School, Medical College, Nanchang University, Nanchang, China
- Plant Biochemistry, Ruhr University Bochum, Bochum, Germany
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Alexandra Chittka
- Division of Medicine, The Wolfson Institute for Biomedical Research, University College London, London, United Kingdom
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Hui Zhang
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Chris Aßmann
- Institute of Molecular Biology and Tumor Research, Philipps University Marburg, Marburg, Germany
| | - Anne Lehmkuhl
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Uta-Maria Bauer
- Institute of Molecular Biology and Tumor Research, Philipps University Marburg, Marburg, Germany
| | - Ulrike A. Nuber
- Stem Cell and Developmental Biology, Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
- *Correspondence: Ulrike A. Nuber, ; M. Cristina Cardoso,
| | - M. Cristina Cardoso
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
- *Correspondence: Ulrike A. Nuber, ; M. Cristina Cardoso,
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9
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Liu J, Zhorabek F, Zhang T, Lam JWY, Tang BZ, Chau Y. Multifaceted Cargo Recruitment and Release from Artificial Membraneless Organelles. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2201721. [PMID: 35596607 DOI: 10.1002/smll.202201721] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/15/2022] [Indexed: 06/15/2023]
Abstract
Liquid-liquid phase separation (LLPS) drives membraneless organelles (MLOs) formation for organizing biomolecules. Artificial MLOs (AMLOs) have been constructed mostly via the LLPS of engineered proteins capable of regulating limited types of biomolecules. Here, leveraging a minimalist AMLO, driven by LLPS of polymer-oligopeptide hybrids, enrichment, recruitment, and release of multifaceted cargoes are quantitatively shown, including small fluorescent molecules, fluorophore-containing macromolecules, proteins, DNAs, and RNAs. Cargoes show up to 105 -fold enrichment, whilst recruitment and release are triggered by variations of temperature, pH, and/or ionic strength. Also, the first efficacious, rapid, and reversible control of aggregation-induced emission with over 30 folds of modulation of overall fluorescence intensity is achieved, by intensifying the aggregation of luminogens in AMLO. The AMLO is a simple yet versatile platform for potential drug delivery and biosensor applications.
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Affiliation(s)
- Jianhui Liu
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, P. R. China
| | - Fariza Zhorabek
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, P. R. China
| | - Tianfu Zhang
- Department of Chemistry and Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, P. R. China
| | - Jacky W Y Lam
- Department of Chemistry and Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, P. R. China
| | - Ben Zhong Tang
- Department of Chemistry and Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, P. R. China
- School of Science and Engineering, Shenzhen Key Laboratory of Functional Aggregate Materials, The Chinese University of Hong Kong, Shenzhen, Shenzhen City, Guangdong, 518172, P. R. China
| | - Ying Chau
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, P. R. China
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10
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Liu J, Zhorabek F, Dai X, Huang J, Chau Y. Minimalist Design of an Intrinsically Disordered Protein-Mimicking Scaffold for an Artificial Membraneless Organelle. ACS CENTRAL SCIENCE 2022; 8:493-500. [PMID: 35505868 PMCID: PMC9052801 DOI: 10.1021/acscentsci.1c01021] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Indexed: 05/05/2023]
Abstract
Liquid-liquid phase separation (LLPS) is an emerging and universal mechanism for intracellular organization, particularly, by forming membraneless organelles (MLOs) hosting intrinsically disordered proteins (IDPs) as scaffolds. Genetic engineering is generally applied to reconstruct IDPs harboring over 100 amino acid residues. Here, we report the first design of synthetic hybrids consisting of short oligopeptides of fewer than 10 residues as "stickers" and dextran as a "spacer" to recapitulate the characteristics of IDPs, as exemplified by the multivalent FUS protein. Hybrids undergo LLPS into micron-sized liquid droplets resembling LLPS in vitro and in living cells. Moreover, the droplets formed are capable of recruiting proteins and RNAs and providing a favorable environment for a biochemical reaction with highly enriched components, thereby mimicking the function of natural MLOs. This simple yet versatile model system can help elucidate the molecular interactions implicated in MLOs and pave ways to a new type of biomimetic materials.
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Affiliation(s)
- Jianhui Liu
- Department
of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Fariza Zhorabek
- Department
of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Xin Dai
- Department
of Chemistry, The Hong Kong University of
Science and Technology, Clear Water
Bay, Kowloon, Hong Kong SAR, China
| | - Jinqing Huang
- Department
of Chemistry, The Hong Kong University of
Science and Technology, Clear Water
Bay, Kowloon, Hong Kong SAR, China
| | - Ying Chau
- Department
of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
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11
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Ma Z, Liu X, Nie J, Zhao H, Li W. Nano-Antimicrobial Peptides Based on Constitutional Isomerism-Dictated Self-Assembly. Biomacromolecules 2022; 23:1302-1313. [DOI: 10.1021/acs.biomac.1c01532] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Zhiyuan Ma
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Qianjin Avenue 2699, Changchun 130012, China
| | - Xiaohuan Liu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Qianjin Avenue 2699, Changchun 130012, China
| | - Junlian Nie
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Qianjin Avenue 2699, Changchun 130012, China
| | - He Zhao
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Qianjin Avenue 2699, Changchun 130012, China
| | - Wen Li
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Qianjin Avenue 2699, Changchun 130012, China
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12
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Lee J, An S, Lee SJ, Kang JS. Protein Arginine Methyltransferases in Neuromuscular Function and Diseases. Cells 2022; 11:364. [PMID: 35159176 PMCID: PMC8834056 DOI: 10.3390/cells11030364] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 01/17/2022] [Accepted: 01/19/2022] [Indexed: 02/07/2023] Open
Abstract
Neuromuscular diseases (NMDs) are characterized by progressive loss of muscle mass and strength that leads to impaired body movement. It not only severely diminishes the quality of life of the patients, but also subjects them to increased risk of secondary medical conditions such as fall-induced injuries and various chronic diseases. However, no effective treatment is currently available to prevent or reverse the disease progression. Protein arginine methyltransferases (PRMTs) are emerging as a potential therapeutic target for diverse diseases, such as cancer and cardiovascular diseases. Their expression levels are altered in the patients and molecular mechanisms underlying the association between PRMTs and the diseases are being investigated. PRMTs have been shown to regulate development, homeostasis, and regeneration of both muscle and neurons, and their association to NMDs are emerging as well. Through inhibition of PRMT activities, a few studies have reported suppression of cytotoxic phenotypes observed in NMDs. Here, we review our current understanding of PRMTs' involvement in the pathophysiology of NMDs and potential therapeutic strategies targeting PRMTs to address the unmet medical need.
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Affiliation(s)
- Jinwoo Lee
- Research Institute for Aging-Related Diseases, AniMusCure Inc., Suwon 16419, Korea;
| | - Subin An
- Department of Molecular Cell Biology, School of Medicine, Sungkyunkwan University, Suwon 16419, Korea;
- Single Cell Network Research Center, Sungkyunkwan University, Suwon 16419, Korea
| | - Sang-Jin Lee
- Research Institute for Aging-Related Diseases, AniMusCure Inc., Suwon 16419, Korea;
| | - Jong-Sun Kang
- Department of Molecular Cell Biology, School of Medicine, Sungkyunkwan University, Suwon 16419, Korea;
- Single Cell Network Research Center, Sungkyunkwan University, Suwon 16419, Korea
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13
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Warmerdam Z, Kamba BE, Le MH, Schrader T, Isaacs L, Bayer P, Hof F. Binding Methylarginines and Methyllysines as Free Amino Acids: A Comparative Study of Multiple Host Classes*. Chembiochem 2021; 23:e202100502. [PMID: 34758178 PMCID: PMC9299052 DOI: 10.1002/cbic.202100502] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 11/09/2021] [Indexed: 01/18/2023]
Abstract
Methylated free amino acids are an important class of targets for host‐guest chemistry that have recognition properties distinct from those of methylated peptides and proteins. We present comparative binding studies for three different host classes that are each studied with multiple methylated arginines and lysines to determine fundamental structure‐function relationships. The hosts studied are all anionic and include three calixarenes, two acyclic cucurbiturils, and two other cleft‐like hosts, a clip and a tweezer. We determined the binding association constants for a panel of methylated amino acids using indicator displacement assays. The acyclic cucurbiturils display stronger binding to the methylated amino acids, and some unique patterns of selectivity. The two other cleft‐like hosts follow two different trends, shallow host (clip) following similar trends to the calixarenes, and the other more closed host (tweezer) binding certain less‐methylated amino acids stronger than their methylated counterparts. Molecular modelling sheds some light on the different preferences of the various hosts. The results identify hosts with new selectivities and with affinities in a range that could be useful for biomedical applications. The overall selectivity patterns are explained by a common framework that considers the geometry, depth of binding pockets, and functional group participation across all host classes.
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Affiliation(s)
- Zoey Warmerdam
- Department of Chemistry and the Centre for, Advanced Materials and Related Technology, University of Victoria, 3800 Finnerty Rd, V8W 3V6, Victoria, BC, Canada
| | - Bianca E Kamba
- Department of Structural and Medicinal Biochemistry, Universität Duisburg Essen, Universitätstrasse 2, 45141, Essen, Germany
| | - My-Hue Le
- Department of Chemistry, Universität Duisburg Essen, Universitätstrasse 7, 45117, Essen, Germany
| | - Thomas Schrader
- Department of Chemistry, Universität Duisburg Essen, Universitätstrasse 7, 45117, Essen, Germany
| | - Lyle Isaacs
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, College Park, USA
| | - Peter Bayer
- Department of Structural and Medicinal Biochemistry, Universität Duisburg Essen, Universitätstrasse 2, 45141, Essen, Germany
| | - Fraser Hof
- Department of Chemistry and the Centre for, Advanced Materials and Related Technology, University of Victoria, 3800 Finnerty Rd, V8W 3V6, Victoria, BC, Canada
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14
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Xu J, Richard S. Cellular pathways influenced by protein arginine methylation: Implications for cancer. Mol Cell 2021; 81:4357-4368. [PMID: 34619091 PMCID: PMC8571027 DOI: 10.1016/j.molcel.2021.09.011] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/24/2021] [Accepted: 09/08/2021] [Indexed: 02/07/2023]
Abstract
Arginine methylation is an influential post-translational modification occurring on histones, RNA binding proteins, and many other cellular proteins, affecting their function by altering their protein-protein and protein-nucleic acid interactions. Recently, a wealth of information has been gathered, implicating protein arginine methyltransferases (PRMTs), enzymes that deposit arginine methylation, in transcription, pre-mRNA splicing, DNA damage signaling, and immune signaling with major implications for cancer therapy, especially immunotherapy. This review summarizes this recent progress and the current state of PRMT inhibitors, some in clinical trials, as promising drug targets for cancer.
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Affiliation(s)
- Jian Xu
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, CA, USA; Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, and Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
| | - Stéphane Richard
- Segal Cancer Center, Lady Davis Institute for Medical Research, Gerald Bronfman Department of Oncology, and Departments of Medicine, Human Genetics, and Biochemistry, McGill University, Montréal, QC H3T 1E2, Canada.
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15
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Ismail H, Liu X, Yang F, Li J, Zahid A, Dou Z, Liu X, Yao X. Mechanisms and regulation underlying membraneless organelle plasticity control. J Mol Cell Biol 2021; 13:239-258. [PMID: 33914074 PMCID: PMC8339361 DOI: 10.1093/jmcb/mjab028] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 03/31/2021] [Accepted: 04/06/2021] [Indexed: 12/11/2022] Open
Abstract
Evolution has enabled living cells to adopt their structural and functional complexity by organizing intricate cellular compartments, such as membrane-bound and membraneless organelles (MLOs), for spatiotemporal catalysis of physiochemical reactions essential for cell plasticity control. Emerging evidence and view support the notion that MLOs are built by multivalent interactions of biomolecules via phase separation and transition mechanisms. In healthy cells, dynamic chemical modifications regulate MLO plasticity, and reversible phase separation is essential for cell homeostasis. Emerging evidence revealed that aberrant phase separation results in numerous neurodegenerative disorders, cancer, and other diseases. In this review, we provide molecular underpinnings on (i) mechanistic understanding of phase separation, (ii) unifying structural and mechanistic principles that underlie this phenomenon, (iii) various mechanisms that are used by cells for the regulation of phase separation, and (iv) emerging therapeutic and other applications.
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Affiliation(s)
- Hazrat Ismail
- MOE Key Laboratory for Membraneless Organelles & Cellular Dynamics and CAS Center for Excellence in Molecular Cell Science, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230027, China
| | - Xu Liu
- MOE Key Laboratory for Membraneless Organelles & Cellular Dynamics and CAS Center for Excellence in Molecular Cell Science, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230027, China
- Keck Center for Organoids Plasticity Control, Atlanta, GA 30310, USA
| | - Fengrui Yang
- MOE Key Laboratory for Membraneless Organelles & Cellular Dynamics and CAS Center for Excellence in Molecular Cell Science, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230027, China
- Keck Center for Organoids Plasticity Control, Atlanta, GA 30310, USA
| | - Junying Li
- MOE Key Laboratory for Membraneless Organelles & Cellular Dynamics and CAS Center for Excellence in Molecular Cell Science, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230027, China
- Anhui Key Laboratory for Cellular Dynamics & Chemical Biology, Hefei 230027, China
| | - Ayesha Zahid
- MOE Key Laboratory for Membraneless Organelles & Cellular Dynamics and CAS Center for Excellence in Molecular Cell Science, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230027, China
| | - Zhen Dou
- MOE Key Laboratory for Membraneless Organelles & Cellular Dynamics and CAS Center for Excellence in Molecular Cell Science, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230027, China
| | - Xing Liu
- MOE Key Laboratory for Membraneless Organelles & Cellular Dynamics and CAS Center for Excellence in Molecular Cell Science, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230027, China
- Anhui Key Laboratory for Cellular Dynamics & Chemical Biology, Hefei 230027, China
| | - Xuebiao Yao
- MOE Key Laboratory for Membraneless Organelles & Cellular Dynamics and CAS Center for Excellence in Molecular Cell Science, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230027, China
- Anhui Key Laboratory for Cellular Dynamics & Chemical Biology, Hefei 230027, China
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16
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Li WJ, He YH, Yang JJ, Hu GS, Lin YA, Ran T, Peng BL, Xie BL, Huang MF, Gao X, Huang HH, Zhu HH, Ye F, Liu W. Profiling PRMT methylome reveals roles of hnRNPA1 arginine methylation in RNA splicing and cell growth. Nat Commun 2021; 12:1946. [PMID: 33782401 PMCID: PMC8007824 DOI: 10.1038/s41467-021-21963-1] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 02/12/2021] [Indexed: 02/05/2023] Open
Abstract
Numerous substrates have been identified for Type I and II arginine methyltransferases (PRMTs). However, the full substrate spectrum of the only type III PRMT, PRMT7, and its connection to type I and II PRMT substrates remains unknown. Here, we use mass spectrometry to reveal features of PRMT7-regulated methylation. We find that PRMT7 predominantly methylates a glycine and arginine motif; multiple PRMT7-regulated arginine methylation sites are close to phosphorylations sites; methylation sites and proximal sequences are vulnerable to cancer mutations; and methylation is enriched in proteins associated with spliceosome and RNA-related pathways. We show that PRMT4/5/7-mediated arginine methylation regulates hnRNPA1 binding to RNA and several alternative splicing events. In breast, colorectal and prostate cancer cells, PRMT4/5/7 are upregulated and associated with high levels of hnRNPA1 arginine methylation and aberrant alternative splicing. Pharmacological inhibition of PRMT4/5/7 suppresses cancer cell growth and their co-inhibition shows synergistic effects, suggesting them as targets for cancer therapy. Arginine methyltransferases (PRMTs) are involved in the regulation of various physiological and pathological conditions. Using proteomics, the authors here profile the methylation substrates of PRMTs 4, 5 and 7 and characterize the roles of these enzymes in cancer-associated splicing regulation.
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Affiliation(s)
- Wen-Juan Li
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China.,Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China
| | - Yao-Hui He
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China.,Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China
| | - Jing-Jing Yang
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China.,Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China
| | - Guo-Sheng Hu
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China.,Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China
| | - Yi-An Lin
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China.,Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China
| | - Ting Ran
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China.,Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China
| | - Bing-Ling Peng
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China.,Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China
| | - Bing-Lan Xie
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China.,Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China
| | - Ming-Feng Huang
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China.,Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China
| | - Xiang Gao
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China
| | - Hai-Hua Huang
- Department of Pathology, The Second Affiliated Hospital, Shantou University Medical College, Shantou, Guangdong, China
| | - Helen He Zhu
- Department of Urology, Ren Ji Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Feng Ye
- Department of Medical Oncology, The First Affiliated Hospital of Xiamen University, Fujian, China
| | - Wen Liu
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China. .,Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China. .,State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China.
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17
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Zbinden A, Pérez-Berlanga M, De Rossi P, Polymenidou M. Phase Separation and Neurodegenerative Diseases: A Disturbance in the Force. Dev Cell 2021; 55:45-68. [PMID: 33049211 DOI: 10.1016/j.devcel.2020.09.014] [Citation(s) in RCA: 213] [Impact Index Per Article: 71.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 09/09/2020] [Accepted: 09/13/2020] [Indexed: 12/12/2022]
Abstract
Protein aggregation is the main hallmark of neurodegenerative diseases. Many proteins found in pathological inclusions are known to undergo liquid-liquid phase separation, a reversible process of molecular self-assembly. Emerging evidence supports the hypothesis that aberrant phase separation behavior may serve as a trigger of protein aggregation in neurodegeneration, and efforts to understand and control the underlying mechanisms are underway. Here, we review similarities and differences among four main proteins, α-synuclein, FUS, tau, and TDP-43, which are found aggregated in different diseases and were independently shown to phase separate. We discuss future directions in the field that will help shed light on the molecular mechanisms of aggregation and neurodegeneration.
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Affiliation(s)
- Aurélie Zbinden
- Department of Quantitative Biomedicine, University of Zürich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Manuela Pérez-Berlanga
- Department of Quantitative Biomedicine, University of Zürich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Pierre De Rossi
- Department of Quantitative Biomedicine, University of Zürich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Magdalini Polymenidou
- Department of Quantitative Biomedicine, University of Zürich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
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18
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A conserved arginine residue is critical for stabilizing the N2 FeS cluster in mitochondrial complex I. J Biol Chem 2021; 296:100474. [PMID: 33640456 PMCID: PMC8042128 DOI: 10.1016/j.jbc.2021.100474] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 02/18/2021] [Accepted: 02/24/2021] [Indexed: 11/22/2022] Open
Abstract
Respiratory complex I (NADH:ubiquinone oxidoreductase), the first enzyme of the electron-transport chain, captures the free energy released by NADH oxidation and ubiquinone reduction to translocate protons across an energy-transducing membrane and drive ATP synthesis during oxidative phosphorylation. The cofactor that transfers the electrons directly to ubiquinone is an iron–sulfur cluster (N2) located in the NDUFS2/NUCM subunit. A nearby arginine residue (R121), which forms part of the second coordination sphere of the N2 cluster, is known to be posttranslationally dimethylated but its functional and structural significance are not known. Here, we show that mutations of this arginine residue (R121M/K) abolish the quinone-reductase activity, concomitant with disappearance of the N2 signature from the electron paramagnetic resonance (EPR) spectrum. Analysis of the cryo-EM structure of NDUFS2-R121M complex I at 3.7 Å resolution identified the absence of the cubane N2 cluster as the cause of the dysfunction, within an otherwise intact enzyme. The mutation further induced localized disorder in nearby elements of the quinone-binding site, consistent with the close connections between the cluster and substrate-binding regions. Our results demonstrate that R121 is required for the formation and/or stability of the N2 cluster and highlight the importance of structural analyses for mechanistic interpretation of biochemical and spectroscopic data on complex I variants.
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19
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Di Blasi R, Blyuss O, Timms JF, Conole D, Ceroni F, Whitwell HJ. Non-Histone Protein Methylation: Biological Significance and Bioengineering Potential. ACS Chem Biol 2021; 16:238-250. [PMID: 33411495 DOI: 10.1021/acschembio.0c00771] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Protein methylation is a key post-translational modification whose effects on gene expression have been intensively studied over the last two decades. Recently, renewed interest in non-histone protein methylation has gained momentum for its role in regulating important cellular processes and the activity of many proteins, including transcription factors, enzymes, and structural complexes. The extensive and dynamic role that protein methylation plays within the cell also highlights its potential for bioengineering applications. Indeed, while synthetic histone protein methylation has been extensively used to engineer gene expression, engineering of non-histone protein methylation has not been fully explored yet. Here, we report the latest findings, highlighting how non-histone protein methylation is fundamental for certain cellular functions and is implicated in disease, and review recent efforts in the engineering of protein methylation.
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Affiliation(s)
- Roberto Di Blasi
- Department of Chemical Engineering, Faculty of Engineering, Imperial College London, London, U.K
- Imperial College Centre for Synthetic Biology, Imperial College London, London, U.K
| | - Oleg Blyuss
- School of Physics, Astronomy and Mathematics, University of Hertfordshire, Hatfield, U.K
- Department of Paediatrics and Paediatric Infectious Diseases, Sechenov First Moscow State Medical University, Moscow, Russia
- Department of Applied Mathematics, Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia
| | - John F Timms
- Department of Women's Cancer, EGA Institute for Women's Health, University College London, London, U.K
| | - Daniel Conole
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, U.K
| | - Francesca Ceroni
- Department of Chemical Engineering, Faculty of Engineering, Imperial College London, London, U.K
- Imperial College Centre for Synthetic Biology, Imperial College London, London, U.K
| | - Harry J Whitwell
- Department of Applied Mathematics, Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia
- National Phenome Centre and Imperial Clinical Phenotyping Centre, Department of Metabolism, Digestion and Reproduction, IRDB Building, Imperial College London, Hammersmith Campus, London, W12 0NN, U.K
- Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Sir Alexander Fleming Building, Imperial College London, Hammersmith Campus, London, SW7 2AZ, U.K
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20
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Price OM, Hevel JM. Toward Understanding Molecular Recognition between PRMTs and their Substrates. Curr Protein Pept Sci 2021; 21:713-724. [PMID: 31976831 DOI: 10.2174/1389203721666200124143145] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 10/08/2019] [Accepted: 12/04/2019] [Indexed: 11/22/2022]
Abstract
Protein arginine methylation is a widespread eukaryotic posttranslational modification that occurs with as much frequency as ubiquitinylation. Yet, how the nine different human protein arginine methyltransferases (PRMTs) recognize their respective protein targets is not well understood. This review summarizes the progress that has been made over the last decade or more to resolve this significant biochemical question. A multipronged approach involving structural biology, substrate profiling, bioorthogonal chemistry and proteomics is discussed.
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Affiliation(s)
- Owen M Price
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322, United States
| | - Joan M Hevel
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322, United States
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21
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Scopino K, Dalgarno C, Nachmanoff C, Krizanc D, Thayer KM, Weir MP. Arginine Methylation Regulates Ribosome CAR Function. Int J Mol Sci 2021; 22:ijms22031335. [PMID: 33572867 PMCID: PMC7866298 DOI: 10.3390/ijms22031335] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/25/2021] [Accepted: 01/26/2021] [Indexed: 11/16/2022] Open
Abstract
The ribosome CAR interaction surface is hypothesized to provide a layer of translation regulation through hydrogen-bonding to the +1 mRNA codon that is next to enter the ribosome A site during translocation. The CAR surface consists of three residues, 16S/18S rRNA C1054, A1196 (E. coli 16S numbering), and R146 of yeast ribosomal protein Rps3. R146 can be methylated by the Sfm1 methyltransferase which is downregulated in stressed cells. Through molecular dynamics analysis, we show here that methylation of R146 compromises the integrity of CAR by reducing the cation-pi stacking of the R146 guanidinium group with A1196, leading to reduced CAR hydrogen-bonding with the +1 codon. We propose that ribosomes assembled under stressed conditions have unmethylated R146, resulting in elevated CAR/+1 codon interactions, which tunes translation levels in response to the altered cellular context.
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Affiliation(s)
- Kristen Scopino
- Department of Biology, Wesleyan University, Middletown, CT 06459, USA; (K.S.); (C.D.); (C.N.)
| | - Carol Dalgarno
- Department of Biology, Wesleyan University, Middletown, CT 06459, USA; (K.S.); (C.D.); (C.N.)
| | - Clara Nachmanoff
- Department of Biology, Wesleyan University, Middletown, CT 06459, USA; (K.S.); (C.D.); (C.N.)
| | - Daniel Krizanc
- Department of Mathematics and Computer Science, Wesleyan University, Middletown, CT 06459, USA; (D.K.); (K.M.T.)
- College of Integrative Sciences, Wesleyan University, Middletown, CT 06459, USA
| | - Kelly M. Thayer
- Department of Mathematics and Computer Science, Wesleyan University, Middletown, CT 06459, USA; (D.K.); (K.M.T.)
- College of Integrative Sciences, Wesleyan University, Middletown, CT 06459, USA
- Department of Chemistry, Wesleyan University, Middletown, CT 06459, USA
| | - Michael P. Weir
- Department of Biology, Wesleyan University, Middletown, CT 06459, USA; (K.S.); (C.D.); (C.N.)
- College of Integrative Sciences, Wesleyan University, Middletown, CT 06459, USA
- Correspondence:
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22
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Miclotte G, Martens K, Fostier J. Computational assessment of the feasibility of protonation-based protein sequencing. PLoS One 2020; 15:e0238625. [PMID: 32915813 PMCID: PMC7485799 DOI: 10.1371/journal.pone.0238625] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 08/20/2020] [Indexed: 02/05/2023] Open
Abstract
Recent advances in DNA sequencing methods revolutionized biology by providing highly accurate reads, with high throughput or high read length. These read data are being used in many biological and medical applications. Modern DNA sequencing methods have no equivalent in protein sequencing, severely limiting the widespread application of protein data. Recently, several optical protein sequencing methods have been proposed that rely on the fluorescent labeling of amino acids. Here, we introduce the reprotonation-deprotonation protein sequencing method. Unlike other methods, this proposed technique relies on the measurement of an electrical signal and requires no fluorescent labeling. In reprotonation-deprotonation protein sequencing, the terminal amino acid is identified through its unique protonation signal, and by repeatedly cleaving the terminal amino acids one-by-one, each amino acid in the peptide is measured. By means of simulations, we show that, given a reference database of known proteins, reprotonation-deprotonation sequencing has the potential to correctly identify proteins in a sample. Our simulations provide target values for the signal-to-noise ratios that sensor devices need to attain in order to detect reprotonation-deprotonation events, as well as suitable pH values and required measurement times per amino acid. For instance, an SNR of 10 is required for a 61.71% proteome recovery rate with 100 ms measurement time per amino acid.
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Affiliation(s)
| | | | - Jan Fostier
- IDLab, Ghent University-Imec, Ghent, Belgium
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23
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Kiseleva O, Zgoda V, Naryzhny S, Poverennaya E. Empowering Shotgun Mass Spectrometry with 2DE: A HepG2 Study. Int J Mol Sci 2020; 21:E3813. [PMID: 32471280 PMCID: PMC7312985 DOI: 10.3390/ijms21113813] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 05/21/2020] [Accepted: 05/26/2020] [Indexed: 01/07/2023] Open
Abstract
One of the major goals of the Chromosome-Centric Human Proteome Project (C-HPP) is to catalog and annotate a myriad of heterogeneous proteoforms, produced by ca. 20 thousand genes. To achieve a detailed and personalized understanding into proteomes, we suggest using a customized RNA-seq library of potential proteoforms, which includes aberrant variants specific to certain biological samples. Two-dimensional electrophoresis coupled with high-performance liquid chromatography allowed us to downgrade the difficulty of biological mixing following shotgun mass spectrometry. To benchmark the proposed pipeline, we examined heterogeneity of the HepG2 hepatoblastoma cell line proteome. Data are available via ProteomeXchange with identifier PXD018450.
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Affiliation(s)
- Olga Kiseleva
- Institute of Biomedical Chemistry, Moscow 119121, Russia; (V.Z.); (S.N.); (E.P.)
| | - Victor Zgoda
- Institute of Biomedical Chemistry, Moscow 119121, Russia; (V.Z.); (S.N.); (E.P.)
| | - Stanislav Naryzhny
- Institute of Biomedical Chemistry, Moscow 119121, Russia; (V.Z.); (S.N.); (E.P.)
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of NRC “Kurchatov Institute”, Gatchina 188300, Russia
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24
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Liu MY, Hua WK, Chen CJ, Lin WJ. The MKK-Dependent Phosphorylation of p38α Is Augmented by Arginine Methylation on Arg49/Arg149 during Erythroid Differentiation. Int J Mol Sci 2020; 21:ijms21103546. [PMID: 32429593 PMCID: PMC7278938 DOI: 10.3390/ijms21103546] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 05/13/2020] [Accepted: 05/15/2020] [Indexed: 01/03/2023] Open
Abstract
The activation of p38 mitogen-activated protein kinases (MAPKs) through a phosphorylation cascade is the canonical mode of regulation. Here, we report a novel activation mechanism for p38α. We show that Arg49 and Arg149 of p38α are methylated by protein arginine methyltransferase 1 (PRMT1). The non-methylation mutations of Lys49/Lys149 abolish the promotive effect of p38α on erythroid differentiation. MAPK kinase 3 (MKK3) is identified as the major p38α upstream kinase and MKK3-mediated activation of the R49/149K mutant p38α is greatly reduced. This is due to a profound reduction in the interaction of p38α and MKK3. PRMT1 can enhance both the methylation level of p38α and its interaction with MKK3. However, the phosphorylation of p38α by MKK3 is not a prerequisite for methylation. MAPK-activated protein kinase 2 (MAPKAPK2) is identified as a p38α downstream effector in the PRMT1-mediated promotion of erythroid differentiation. The interaction of MAPKAPK2 with p38α is also significantly reduced in the R49/149K mutant. Together, this study unveils a novel regulatory mechanism of p38α activation via protein arginine methylation on R49/R149 by PRMT1, which impacts partner interaction and thus promotes erythroid differentiation. This study provides a new insight into the complexity of the regulation of the versatile p38α signaling and suggests new directions in intervening p38α signaling.
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Affiliation(s)
- Mei-Yin Liu
- Institute of Biopharmaceutical Sciences, National Yang-Ming University, Taipei 112, Taiwan; (M.-Y.L.); (W.-K.H.)
| | - Wei-Kai Hua
- Institute of Biopharmaceutical Sciences, National Yang-Ming University, Taipei 112, Taiwan; (M.-Y.L.); (W.-K.H.)
| | - Chi-Ju Chen
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei 112, Taiwan;
| | - Wey-Jinq Lin
- Institute of Biopharmaceutical Sciences, National Yang-Ming University, Taipei 112, Taiwan; (M.-Y.L.); (W.-K.H.)
- Correspondence: ; Tel.: +886-2-28267257
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25
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Altincekic N, Löhr F, Meier-Credo J, Langer JD, Hengesbach M, Richter C, Schwalbe H. Site-Specific Detection of Arginine Methylation in Highly Repetitive Protein Motifs of Low Sequence Complexity by NMR. J Am Chem Soc 2020; 142:7647-7654. [PMID: 32233470 DOI: 10.1021/jacs.0c02308] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Post-translational modifications of proteins are widespread in eukaryotes. To elucidate the functional role of these modifications, detection methods need to be developed that provide information at atomic resolution. Here, we report on the development of a novel Arg-specific NMR experiment that detects the methylation status and symmetry of each arginine side chain even in highly repetitive RGG amino acid sequence motifs found in numerous proteins within intrinsically disordered regions. The experiment relies on the excellent resolution of the backbone H,N correlation spectra even in these low complexity sequences. It requires 13C, 15N labeled samples.
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Affiliation(s)
- Nadide Altincekic
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, Frankfurt 60438, Germany.,Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt am Main, Frankfurt 60438, Germany
| | - Frank Löhr
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt am Main, Frankfurt 60438, Germany.,Institute of Biophysical Chemistry, Goethe University Frankfurt am Main, Frankfurt 60438, Germany
| | - Jakob Meier-Credo
- Max Planck Institute of Biophysics, Frankfurt am Main, 60438, Germany
| | - Julian D Langer
- Max Planck Institute of Biophysics, Frankfurt am Main, 60438, Germany
| | - Martin Hengesbach
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, Frankfurt 60438, Germany
| | - Christian Richter
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, Frankfurt 60438, Germany.,Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt am Main, Frankfurt 60438, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, Frankfurt 60438, Germany.,Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt am Main, Frankfurt 60438, Germany
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26
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Liu X, Xie X, Du Z, Li B, Wu L, Li W. Aqueous self-assembly of arginine and K 8SiW 11O 39: fine-tuning the formation of a coacervate intended for sprayable anticorrosive coatings. SOFT MATTER 2019; 15:9178-9186. [PMID: 31584062 DOI: 10.1039/c9sm01511f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Coacervates are commonly thought to be formed from the liquid-liquid phase separation of macromolecules, such as oppositely charged polyelectrolytes, proteins or peptides. Unlike conventional systems, we here show an entirely novel coacervate obtained from the self-assembly of arginine (Arg) and K8[α-SiW11O39] (SiW11) in water. The formation of the coacervate Arg/SiW11 is confirmed by combined techniques, including turbidity, rheology, optical microscopy, and scanning and transmission electron microscopy. Assessment of the rheological response reveals that the complex coacervate exhibits shear thinning behaviour. X-ray photoelectron spectroscopy (XPS), Fourier transform infrared (FT-IR) spectroscopy, elemental analysis and thermogravimetric analysis are used to characterize the coacervate. The thermodynamic parameters of the coacervation are monitored by isothermal titration calorimetry (ITC), which identifies that the formation of the coacervate by mixing of Arg and SiW11 is driven by a combination of entropic and enthalpic effects. The resultant coacervate shows a typical upper critical solution temperature (UCST) phenomenon, which is strongly dependent on the concentration of the species. Furthermore, we demonstrate that the coacervation could be tuned by stoichiometry and pH. A phase diagram for the complexation of Arg and SiW11 thus has been constructed using turbidity measurements. Such a phase diagram is a very useful tool for the preparation of coacervates from a specific combination of Arg and SiW11. Finally, the acid induced gelation of the coacervate has been explored to fabricate an anticorrosive coating to protect a copper plate from exposure to acid vapour.
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Affiliation(s)
- Xiaohuan Liu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Qianjin Avenue 2699, Changchun 130012, China.
| | - Xiaoming Xie
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Qianjin Avenue 2699, Changchun 130012, China.
| | - Zhanglei Du
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Qianjin Avenue 2699, Changchun 130012, China.
| | - Bao Li
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Qianjin Avenue 2699, Changchun 130012, China.
| | - Lixin Wu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Qianjin Avenue 2699, Changchun 130012, China.
| | - Wen Li
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Qianjin Avenue 2699, Changchun 130012, China.
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27
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Li ASM, Li F, Eram MS, Bolotokova A, Dela Seña CC, Vedadi M. Chemical probes for protein arginine methyltransferases. Methods 2019; 175:30-43. [PMID: 31809836 DOI: 10.1016/j.ymeth.2019.11.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 11/29/2019] [Accepted: 11/29/2019] [Indexed: 12/28/2022] Open
Abstract
Protein arginine methyltransferases (PRMTs) catalyze the transfer of methyl groups to specific arginine residues of their substrates using S-adenosylmethionine as a methyl donor, contributing to regulation of many biological processes including transcription, and DNA damage repair. Dysregulation of PRMT expression is often associated with various diseases including cancers. Different methods have been used to characterize the activities of PRMTs and determine their kinetic parameters including mass spectrometry, radiometric, and antibody-based assays. Here, we present kinetic characterization of PRMTs using a radioactivity-based assay for better comparison along with previously reported values. We also report on full characterization of PRMT9 activity with SAP145 peptide as substrate. We further review the potent, selective and cell-active PRMT inhibitors discovered in recent years to provide a better understanding of available tools to investigate the roles these proteins play in health and disease.
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Affiliation(s)
- Alice Shi Ming Li
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada; Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Fengling Li
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Mohammad S Eram
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Albina Bolotokova
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Carlo C Dela Seña
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Masoud Vedadi
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada; Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON M5S 1A8, Canada.
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28
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Pieroni L, Iavarone F, Olianas A, Greco V, Desiderio C, Martelli C, Manconi B, Sanna MT, Messana I, Castagnola M, Cabras T. Enrichments of post-translational modifications in proteomic studies. J Sep Sci 2019; 43:313-336. [PMID: 31631532 DOI: 10.1002/jssc.201900804] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 09/23/2019] [Accepted: 10/17/2019] [Indexed: 12/14/2022]
Abstract
More than 300 different protein post-translational modifications are currently known, but only a few have been extensively investigated because modified proteoforms are commonly present in sub-stoichiometry amount. For this reason, improvement of specific enrichment techniques is particularly useful for the proteomic characterization of post-translationally modified proteins. Enrichment proteomic strategies could help the researcher in the challenging issue to decipher the complex molecular cross-talk existing between the different factors influencing the cellular pathways. In this review the state of art of the platforms applied for the enrichment of specific and most common post-translational modifications, such as glycosylation and glycation, phosphorylation, sulfation, redox modifications (i.e. sulfydration and nitrosylation), methylation, acetylation, and ubiquitinylation, are described. Enrichments strategies applied to characterize less studied post-translational modifications are also briefly discussed.
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Affiliation(s)
- Luisa Pieroni
- Laboratorio di Proteomica e Metabolomica, Centro Europeo di Ricerca sul Cervello, IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Federica Iavarone
- Istituto di Biochimica e Biochimica Clinica, Facoltà di Medicina, Università Cattolica del Sacro Cuore, Rome, Italy.,IRCCS Fondazione Policlinico Universitario Agostino Gemelli, Rome, Italy
| | - Alessandra Olianas
- Dipartimento di Scienze della Vita e dell'Ambiente, Università di Cagliari, Cagliari, Italy
| | - Viviana Greco
- Istituto di Biochimica e Biochimica Clinica, Facoltà di Medicina, Università Cattolica del Sacro Cuore, Rome, Italy.,IRCCS Fondazione Policlinico Universitario Agostino Gemelli, Rome, Italy
| | - Claudia Desiderio
- Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Claudia Martelli
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Barbara Manconi
- Dipartimento di Scienze della Vita e dell'Ambiente, Università di Cagliari, Cagliari, Italy
| | - Maria Teresa Sanna
- Dipartimento di Scienze della Vita e dell'Ambiente, Università di Cagliari, Cagliari, Italy
| | - Irene Messana
- Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Massimo Castagnola
- Laboratorio di Proteomica e Metabolomica, Centro Europeo di Ricerca sul Cervello, IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Tiziana Cabras
- Dipartimento di Scienze della Vita e dell'Ambiente, Università di Cagliari, Cagliari, Italy
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29
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Owen I, Shewmaker F. The Role of Post-Translational Modifications in the Phase Transitions of Intrinsically Disordered Proteins. Int J Mol Sci 2019; 20:ijms20215501. [PMID: 31694155 PMCID: PMC6861982 DOI: 10.3390/ijms20215501] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 11/01/2019] [Accepted: 11/02/2019] [Indexed: 12/23/2022] Open
Abstract
Advances in genomics and proteomics have revealed eukaryotic proteomes to be highly abundant in intrinsically disordered proteins that are susceptible to diverse post-translational modifications. Intrinsically disordered regions are critical to the liquid-liquid phase separation that facilitates specialized cellular functions. Here, we discuss how post-translational modifications of intrinsically disordered protein segments can regulate the molecular condensation of macromolecules into functional phase-separated complexes.
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30
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Hartel NG, Chew B, Qin J, Xu J, Graham NA. Deep Protein Methylation Profiling by Combined Chemical and Immunoaffinity Approaches Reveals Novel PRMT1 Targets. Mol Cell Proteomics 2019; 18:2149-2164. [PMID: 31451547 PMCID: PMC6823857 DOI: 10.1074/mcp.ra119.001625] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Indexed: 01/02/2023] Open
Abstract
Protein methylation has been implicated in many important biological contexts including signaling, metabolism, and transcriptional control. Despite the importance of this post-translational modification, the global analysis of protein methylation by mass spectrometry-based proteomics has not been extensively studied because of the lack of robust, well-characterized techniques for methyl peptide enrichment. Here, to better investigate protein methylation, we compared two methods for methyl peptide enrichment: immunoaffinity purification (IAP) and high pH strong cation exchange (SCX). Using both methods, we identified 1720 methylation sites on 778 proteins. Comparison of these methods revealed that they are largely orthogonal, suggesting that the usage of both techniques is required to provide a global view of protein methylation. Using both IAP and SCX, we then investigated changes in protein methylation downstream of protein arginine methyltransferase 1 (PRMT1). PRMT1 knockdown resulted in significant changes to 127 arginine methylation sites on 78 proteins. In contrast, only a single lysine methylation site was significantly changed upon PRMT1 knockdown. In PRMT1 knockdown cells, we found 114 MMA sites that were either significantly downregulated or upregulated on proteins enriched for mRNA metabolic processes. PRMT1 knockdown also induced significant changes in both asymmetric dimethyl arginine (ADMA) and symmetric dimethyl arginine (SDMA). Using characteristic neutral loss fragmentation ions, we annotated dimethylarginines as either ADMA or SDMA. Through integrative analysis of methyl forms, we identified 18 high confidence PRMT1 substrates and 12 methylation sites that are scavenged by other non-PRMT1 arginine methyltransferases in the absence of PRMT1 activity. We also identified one methylation site, HNRNPA1 R206, which switched from ADMA to SDMA upon PRMT1 knockdown. Taken together, our results suggest that deep protein methylation profiling by mass spectrometry requires orthogonal enrichment techniques to identify novel PRMT1 methylation targets and highlight the dynamic interplay between methyltransferases in mammalian cells.
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Affiliation(s)
- Nicolas G Hartel
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089
| | - Brandon Chew
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089
| | - Jian Qin
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, California 90089; Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, California 90089; Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California 90089
| | - Jian Xu
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, California 90089; Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, California 90089; Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California 90089
| | - Nicholas A Graham
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089; Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California 90089.
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31
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Lorton BM, Shechter D. Cellular consequences of arginine methylation. Cell Mol Life Sci 2019; 76:2933-2956. [PMID: 31101937 PMCID: PMC6642692 DOI: 10.1007/s00018-019-03140-2] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 04/22/2019] [Accepted: 05/10/2019] [Indexed: 02/07/2023]
Abstract
Arginine methylation is a ubiquitous post-translational modification. Three predominant types of arginine-guanidino methylation occur in Eukarya: mono (Rme1/MMA), symmetric (Rme2s/SDMA), and asymmetric (Rme2a/ADMA). Arginine methylation frequently occurs at sites of protein-protein and protein-nucleic acid interactions, providing specificity for binding partners and stabilization of important biological interactions in diverse cellular processes. Each methylarginine isoform-catalyzed by members of the protein arginine methyltransferase family, Type I (PRMT1-4,6,8) and Type II (PRMT5,9)-has unique downstream consequences. Methylarginines are found in ordered domains, domains of low complexity, and in intrinsically disordered regions of proteins-the latter two of which are intimately connected with biological liquid-liquid phase separation. This review highlights discoveries illuminating how arginine methylation affects genome integrity, gene transcription, mRNA splicing and mRNP biology, protein translation and stability, and phase separation. As more proteins and processes are found to be regulated by arginine methylation, its importance for understanding cellular physiology will continue to grow.
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Affiliation(s)
- Benjamin M Lorton
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - David Shechter
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
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32
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Grimaldi G, Catara G, Palazzo L, Corteggio A, Valente C, Corda D. PARPs and PAR as novel pharmacological targets for the treatment of stress granule-associated disorders. Biochem Pharmacol 2019; 167:64-75. [PMID: 31102582 DOI: 10.1016/j.bcp.2019.05.019] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 05/13/2019] [Indexed: 12/13/2022]
Abstract
Among the post-translational modifications, ADP-ribosylation has been for long time the least integrated in the scheme of the structural protein modifications affecting physiological functions. In spite of the original findings on bacterial-dependent ADP-ribosylation catalysed by toxins such as cholera and pertussis toxin, only with the discovery of the poly-ADP-ribosyl polymerase (PARP) family the field has finally expanded and the role of ADP-ribosylation has been recognised in both physiological and pathological processes, including cancer, infectious and neurodegenerative diseases. This is now a rapidly expanding field of investigation, centred on the role of the different PARPs and their substrates in various diseases, and on the potential of PARP inhibitors as novel pharmacological tools to be employed in relevant pathological context. In this review we analyse the role that members of the PARP family and poly-ADP-ribose (PAR; the product of PARP1 and PARP5a activity) play in the processes following the exposure of cells to different stresses. The cell response that arises following conditions such as heat, osmotic, oxidative stresses or viral infection relies on the formation of stress granules, which are transient cytoplasmic membrane-less structures, that include untranslated mRNA, specific proteins and PAR, this last one serving as the "collector" of all components (that bind to it in a non-covalent manner). The resulting phenotypes are cells in which translation, intracellular transport or pro-apoptotic pathways are reversibly inhibited, for the time the given stress holds. Interestingly, the formation of defective stress granules has been detected in diverse pathological conditions including neurological disorders and cancer. Analysing the molecular details of stress granule formation under these conditions offers a novel view on the pathogenesis of these diseases and, as a consequence, the possibility of identifying novel drug targets for their treatment.
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Affiliation(s)
- Giovanna Grimaldi
- Institute of Protein Biochemistry, National Research Council of Italy, Via Pietro Castellino 111, Naples 80131, Italy.
| | - Giuliana Catara
- Institute of Protein Biochemistry, National Research Council of Italy, Via Pietro Castellino 111, Naples 80131, Italy
| | - Luca Palazzo
- Institute of Protein Biochemistry, National Research Council of Italy, Via Pietro Castellino 111, Naples 80131, Italy
| | - Annunziata Corteggio
- Institute of Protein Biochemistry, National Research Council of Italy, Via Pietro Castellino 111, Naples 80131, Italy
| | - Carmen Valente
- Institute of Protein Biochemistry, National Research Council of Italy, Via Pietro Castellino 111, Naples 80131, Italy
| | - Daniela Corda
- Institute of Protein Biochemistry, National Research Council of Italy, Via Pietro Castellino 111, Naples 80131, Italy.
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33
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Rubio K, Dobersch S, Barreto G. Functional interactions between scaffold proteins, noncoding RNAs, and genome loci induce liquid-liquid phase separation as organizing principle for 3-dimensional nuclear architecture: implications in cancer. FASEB J 2019; 33:5814-5822. [PMID: 30742773 DOI: 10.1096/fj.201802715r] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The eukaryotic cell nucleus consists of functionally specialized subcompartments. These nuclear subcompartments are biomolecular aggregates built of proteins, transcripts, and specific genome loci. The structure and function of each nuclear subcompartment are defined by the composition and dynamic interaction between these 3 components. The spatio-temporal localization of biochemical reactions into membraneless nuclear subcompartments can be achieved through liquid-liquid phase separation. Based on this organizing principle, nuclear subcompartments are droplet-like structures that adopt spherical shapes, flow, and fuse like liquids or gels. In the present review, we bring into the spotlight seminal works elucidating the functional interactions between scaffold proteins, noncoding RNAs, and genomic loci, thereby inducing liquid-liquid phase separation as an organizing principle for 3-dimensional nuclear architecture. We also discuss the implications in different cancer types as well as the potential use of this knowledge to develop novel therapeutic strategies against cancer.-Rubio, K., Dobersch, S., Barreto, G. Functional interactions between scaffold proteins, noncoding RNAs, and genome loci induce liquid-liquid phase separation as organizing principle for 3-dimensional nuclear architecture: implications in cancer.
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Affiliation(s)
- Karla Rubio
- Lung Cancer Epigenetic, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Stephanie Dobersch
- Lung Cancer Epigenetic, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Guillermo Barreto
- Lung Cancer Epigenetic, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany.,Laboratoire Croissance, Réparation, et Régénération Tissulaires (CRRET), Centre National de la Recherche Scientifique (CNRS) Équipe de Recherche Labellisée (ERL) 9215, Université Paris Est Créteil, Créteil, France.,Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russian Federation.,Excellence Cluster Cardio Pulmonary System (ECCPS), Universities of Giessen-Marburg Lung Center (UGMLC), Giessen, Germany.,German Center of Lung Research, Giessen, Germany
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34
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Hofweber M, Dormann D. Friend or foe-Post-translational modifications as regulators of phase separation and RNP granule dynamics. J Biol Chem 2018; 294:7137-7150. [PMID: 30587571 DOI: 10.1074/jbc.tm118.001189] [Citation(s) in RCA: 227] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Ribonucleoprotein (RNP) granules are membrane-less organelles consisting of RNA-binding proteins (RBPs) and RNA. RNA granules form through liquid-liquid phase separation (LLPS), whereby weak promiscuous interactions among RBPs and/or RNAs create a dense network of interacting macromolecules and drive the phase separation. Post-translational modifications (PTMs) of RBPs have emerged as important regulators of LLPS and RNP granule dynamics, as they can directly weaken or enhance the multivalent interactions between phase-separating macromolecules or can recruit or exclude certain macromolecules into or from condensates. Here, we review recent insights into how PTMs regulate phase separation and RNP granule dynamics, in particular arginine (Arg)-methylation and phosphorylation. We discuss how these PTMs regulate the phase behavior of prototypical RBPs and how, as "friend or foe," they might influence the assembly, disassembly, or material properties of cellular RNP granules, such as stress granules or amyloid-like condensates. We particularly highlight how PTMs control the phase separation and aggregation behavior of disease-linked RBPs. We also review how disruptions of PTMs might be involved in aberrant phase transitions and the formation of amyloid-like protein aggregates as observed in neurodegenerative diseases.
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Affiliation(s)
- Mario Hofweber
- From the BioMedical Center, Cell Biology, Ludwig-Maximilians-University Munich, Grosshaderner Strasse 9, 82152 Planegg-Martinsried.,the Graduate School of Systemic Neurosciences, Ludwig-Maximilians-University Munich, Grosshaderner Strasse 2, 82152 Planegg-Martinsried, and
| | - Dorothee Dormann
- From the BioMedical Center, Cell Biology, Ludwig-Maximilians-University Munich, Grosshaderner Strasse 9, 82152 Planegg-Martinsried, .,the Graduate School of Systemic Neurosciences, Ludwig-Maximilians-University Munich, Grosshaderner Strasse 2, 82152 Planegg-Martinsried, and.,the Munich Cluster for Systems Neurology (SyNergy), Feodor-Lynen-Strasse 17, 81377 Munich, Germany
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35
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Ng V, Kuehne SA, Chan WC. Rational Design and Synthesis of Modified Teixobactin Analogues: In Vitro Antibacterial Activity against Staphylococcus aureus
, Propionibacterium acnes
and Pseudomonas aeruginosa. Chemistry 2018; 24:9136-9147. [DOI: 10.1002/chem.201801423] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Vivian Ng
- School of Pharmacy; Centre for Biomolecular Sciences; University of Nottingham; University Park Nottingham NG7 2RD United Kingdom
| | - Sarah A. Kuehne
- School of Dentistry; Institute for Microbiology and Infection; University of Birmingham; Birmingham B5 7EG United Kingdom
| | - Weng C. Chan
- School of Pharmacy; Centre for Biomolecular Sciences; University of Nottingham; University Park Nottingham NG7 2RD United Kingdom
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36
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Rhoads SN, Monahan ZT, Yee DS, Shewmaker FP. The Role of Post-Translational Modifications on Prion-Like Aggregation and Liquid-Phase Separation of FUS. Int J Mol Sci 2018; 19:ijms19030886. [PMID: 29547565 PMCID: PMC5877747 DOI: 10.3390/ijms19030886] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 03/05/2018] [Accepted: 03/07/2018] [Indexed: 12/13/2022] Open
Abstract
Subcellular mislocalization and aggregation of the human FUS protein occurs in neurons of patients with subtypes of amyotrophic lateral sclerosis and frontotemporal dementia. FUS is one of several RNA-binding proteins that can functionally self-associate into distinct liquid-phase droplet structures. It is postulated that aberrant interactions within the dense phase-separated state can potentiate FUS's transition into solid prion-like aggregates that cause disease. FUS is post-translationally modified at numerous positions, which affect both its localization and aggregation propensity. These modifications may influence FUS-linked pathology and serve as therapeutic targets.
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Affiliation(s)
- Shannon N Rhoads
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA.
| | - Zachary T Monahan
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA.
| | - Debra S Yee
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA.
| | - Frank P Shewmaker
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA.
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37
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赵 娜, 黄 彪, 吴 巧, 唐 勇, 余 曙. 蛋白修饰与炎症性肠病. Shijie Huaren Xiaohua Zazhi 2017; 25:1521-1527. [DOI: 10.11569/wcjd.v25.i17.1521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
近年来炎症性肠病(inflammatory bowel disease, IBD)的发病率明显呈持续上升趋势, 越来越多的证据表明, 肠道内蛋白质的异常表达或蛋白修饰的异常与IBD的发病有关. 蛋白修饰是指蛋白质通过翻译后修饰改变自身的空间构象、活性、稳定性及与其他分子相互作用等方面的性能, 从而参与调节机体多样化的生命过程. 虽然蛋白修饰不会改变DNA的序列, 但可以影响相关基因的表达. 研究显示, 蛋白修饰可能通过患者的饮食、环境及肠道微生物等多方面影响基因表型从而参与IBD的发病过程. 本文就蛋白修饰在IBD发病过程中所起的作用做一综述.
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38
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Rice A, Wereszczynski J. Probing the disparate effects of arginine and lysine residues on antimicrobial peptide/bilayer association. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:1941-1950. [PMID: 28583830 DOI: 10.1016/j.bbamem.2017.06.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 05/08/2017] [Accepted: 06/01/2017] [Indexed: 10/19/2022]
Abstract
Antimicrobial peptides (AMPs) are key components of the innate immune response and represent promising templates for the development of broad-spectrum alternatives to conventional antibiotics. Most AMPs are short, cationic peptides that interact more strongly with negatively charged prokaryotic membranes than net neutral eukaryotic ones. Both AMPs and synthetic analogues with arginine-like side chains are more active against bacteria than those with lysine-like amine groups, though the atomistic mechanism for this increase in potency remains unclear. To examine this, we conducted comparative molecular dynamics simulations of a model negatively-charged membrane system interacting with two mutants of the AMP KR-12: one with lysine residues mutated to arginines (R-KR12) and one with arginine residues mutated to lysine (K-KR12). Simulations show that both partition analogously to the bilayer and display similar preferences for hydrogen bonding with the anionic POPGs. However, R-KR12 binds stronger to the bilayer than K-KR12 and forms significantly more hydrogen bonds, leading to considerably longer interaction times. Additional simulations with methylated R-KR12 and charge-modified K-KR12 mutants show that the extensive interaction seen in the R-KR12 system is partly due to arginine's strong atomic charge distribution, rather than being purely an effect of the greater number of hydrogen bond donors. Finally, free energy simulations reveal that both peptides are disordered in solution but form an amphipathic α-helix when inserted into the bilayer headgroup region. Overall, these results highlight the role of charge and hydrogen bond strength in peptide bilayer insertion, and offer potential insights for designing more potent analogues in the future.
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Affiliation(s)
- A Rice
- Department of Physics and The Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, Chicago, Illinois 60616, USA
| | - J Wereszczynski
- Department of Physics and The Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, Chicago, Illinois 60616, USA.
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39
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Shishkova E, Zeng H, Liu F, Kwiecien NW, Hebert AS, Coon JJ, Xu W. Global mapping of CARM1 substrates defines enzyme specificity and substrate recognition. Nat Commun 2017; 8:15571. [PMID: 28537268 PMCID: PMC5458078 DOI: 10.1038/ncomms15571] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 04/05/2017] [Indexed: 12/14/2022] Open
Abstract
Protein arginine methyltransferases (PRMTs) introduce arginine methylation, a post-translational modification with the increasingly eminent role in normal physiology and disease. PRMT4 or coactivator-associated arginine methyltransferase 1 (CARM1) is a propitious target for cancer therapy; however, few CARM1 substrates are known, and its mechanism of substrate recognition is poorly understood. Here we employed a quantitative mass spectrometry approach to globally profile CARM1 substrates in breast cancer cell lines. We identified >130 CARM1 protein substrates and validated in vitro >90% of sites they encompass. Bioinformatics analyses reveal enrichment of proline-containing motifs, in which both methylation sites and their proximal sequences are frequently targeted by somatic mutations in cancer. Finally, we demonstrate that the N-terminus of CARM1 is involved in substrate recognition and nearly indispensable for substrate methylation. We propose that development of CARM1-specific inhibitors should focus on its N-terminus and predict that other PRMTs may employ similar mechanism for substrate recognition.
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Affiliation(s)
- Evgenia Shishkova
- The Department of Biomolecular Chemistry, University of Wisconsin – Madison, Madison, Wisconsin 53705, USA
| | - Hao Zeng
- McArdle Laboratory for Cancer Research, University of Wisconsin – Madison, Madison, Wisconsin 53705, USA
| | - Fabao Liu
- McArdle Laboratory for Cancer Research, University of Wisconsin – Madison, Madison, Wisconsin 53705, USA
| | - Nicholas W. Kwiecien
- The Genome Center of Wisconsin, University of Wisconsin – Madison, Madison, Wisconsin 53705, USA
| | - Alexander S. Hebert
- The Genome Center of Wisconsin, University of Wisconsin – Madison, Madison, Wisconsin 53705, USA
| | - Joshua J. Coon
- The Department of Biomolecular Chemistry, University of Wisconsin – Madison, Madison, Wisconsin 53705, USA
- The Department of Chemistry, University of Wisconsin – Madison, Madison, Wisconsin 53705, USA
| | - Wei Xu
- McArdle Laboratory for Cancer Research, University of Wisconsin – Madison, Madison, Wisconsin 53705, USA
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40
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Shen Y, Szewczyk MM, Eram MS, Smil D, Kaniskan HÜ, de Freitas RF, Senisterra G, Li F, Schapira M, Brown PJ, Arrowsmith CH, Barsyte-Lovejoy D, Liu J, Vedadi M, Jin J. Discovery of a Potent, Selective, and Cell-Active Dual Inhibitor of Protein Arginine Methyltransferase 4 and Protein Arginine Methyltransferase 6. J Med Chem 2016; 59:9124-9139. [PMID: 27584694 DOI: 10.1021/acs.jmedchem.6b01033] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Well-characterized selective inhibitors of protein arginine methyltransferases (PRMTs) are invaluable chemical tools for testing biological and therapeutic hypotheses. Based on 4, a fragment-like inhibitor of type I PRMTs, we conducted structure-activity relationship (SAR) studies and explored three regions of this scaffold. The studies led to the discovery of a potent, selective, and cell-active dual inhibitor of PRMT4 and PRMT6, 17 (MS049). As compared to 4, 17 displayed much improved potency for PRMT4 and PRMT6 in both biochemical and cellular assays. It was selective for PRMT4 and PRMT6 over other PRMTs and a broad range of other epigenetic modifiers and nonepigenetic targets. We also developed 46 (MS049N), which was inactive in biochemical and cellular assays, as a negative control for chemical biology studies. Considering possible overlapping substrate specificity of PRMTs, 17 and 46 are valuable chemical tools for dissecting specific biological functions and dysregulation of PRMT4 and PRMT6 in health and disease.
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Affiliation(s)
- Yudao Shen
- Department of Pharmacological Sciences and Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Magdalena M Szewczyk
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, M5G 1L7, Canada
| | - Mohammad S Eram
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, M5G 1L7, Canada
| | - David Smil
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, M5G 1L7, Canada
| | - H Ümit Kaniskan
- Department of Pharmacological Sciences and Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | | | - Guillermo Senisterra
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, M5G 1L7, Canada
| | - Fengling Li
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, M5G 1L7, Canada
| | - Matthieu Schapira
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, M5G 1L7, Canada.,Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Peter J Brown
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, M5G 1L7, Canada
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, M5G 1L7, Canada.,Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, Ontario, M5G 2M9, Canada
| | - Dalia Barsyte-Lovejoy
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, M5G 1L7, Canada
| | - Jing Liu
- Department of Pharmacological Sciences and Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Masoud Vedadi
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, M5G 1L7, Canada.,Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Jian Jin
- Department of Pharmacological Sciences and Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
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41
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Larsen SC, Sylvestersen KB, Mund A, Lyon D, Mullari M, Madsen MV, Daniel JA, Jensen LJ, Nielsen ML. Proteome-wide analysis of arginine monomethylation reveals widespread occurrence in human cells. Sci Signal 2016; 9:rs9. [DOI: 10.1126/scisignal.aaf7329] [Citation(s) in RCA: 187] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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42
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Garay PG, Martin OA, Scheraga HA, Vila JA. Detection of methylation, acetylation and glycosylation of protein residues by monitoring (13)C chemical-shift changes: A quantum-chemical study. PeerJ 2016; 4:e2253. [PMID: 27547559 PMCID: PMC4963218 DOI: 10.7717/peerj.2253] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 06/23/2016] [Indexed: 11/20/2022] Open
Abstract
Post-translational modifications of proteins expand the diversity of the proteome by several orders of magnitude and have a profound effect on several biological processes. Their detection by experimental methods is not free of limitations such as the amount of sample needed or the use of destructive procedures to obtain the sample. Certainly, new approaches are needed and, therefore, we explore here the feasibility of using (13)C chemical shifts of different nuclei to detect methylation, acetylation and glycosylation of protein residues by monitoring the deviation of the (13)C chemical shifts from the expected (mean) experimental value of the non-modified residue. As a proof-of-concept, we used (13)C chemical shifts, computed at the DFT-level of theory, to test this hypothesis. Moreover, as a validation test of this approach, we compare our theoretical computations of the (13)Cε chemical-shift values against existing experimental data, obtained from NMR spectroscopy, for methylated and acetylated lysine residues with good agreement within ∼1 ppm. Then, further use of this approach to select the most suitable (13)C-nucleus, with which to determine other modifications commonly seen, such as methylation of arginine and glycosylation of serine, asparagine and threonine, shows encouraging results.
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Affiliation(s)
- Pablo G. Garay
- IMASL-CONICET, Universidad Nacional de San Luis, San Luis, Argentina
| | - Osvaldo A. Martin
- IMASL-CONICET, Universidad Nacional de San Luis, San Luis, Argentina
| | | | - Jorge A. Vila
- IMASL-CONICET, Universidad Nacional de San Luis, San Luis, Argentina
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