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Bulangalire N, Claeyssen C, Douffi S, Agbulut O, Cieniewski-Bernard C. A novel 2D-electrophoresis method for the simultaneous visualization of phosphorylated and O-GlcNAcylated proteoforms of a protein. Electrophoresis 2024. [PMID: 38700120 DOI: 10.1002/elps.202400043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 04/16/2024] [Indexed: 05/05/2024]
Abstract
Post-translational modifications (PTMs), such as phosphorylation and O-N-acetyl-β-d-glucosaminylation (O-GlcNAcylation), are involved in the fine spatiotemporal regulation of protein functions, and their dynamic interplay is at the heart of protein language. The coexistence of phosphorylation and O-GlcNAcylation on a protein leads to the diversification of proteoforms. It is therefore essential to decipher the phosphorylation/O-GlcNAcylation interplay on protein species that orchestrates cellular processes in a specific physiological or pathophysiological context. However, simultaneous visualization of phosphorylation and O-GlcNAcylation patterns on a protein of interest remains a challenge. To map the proteoforms of a protein, we have developed an easy-to-use two-dimensional electrophoresis method with a single sample processing permitting simultaneous visualization of the phosphorylated and the O-GlcNAcylated forms of the protein of interest. This method, we termed 2D-WGA-Phos-tag-PAGE relies on proteoforms retardation by affinity gel electrophoresis. With this novel approach, we established the cartography of phospho- and glycoforms of αB-crystallin and desmin in the whole extract and the cytoskeleton protein subfraction in skeletal muscle cells. Interestingly, we have shown that the pattern of phosphorylation and O-GlcNAcylation depends of the subcellular subfraction. Moreover, we have also shown that proteotoxic stress condition increased the complexity of the pattern of PTMs on αB-crystallin.
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Affiliation(s)
- Nathan Bulangalire
- Univ. Lille, Univ. Artois, Univ. Littoral Côte d'Opale, ULR 7369 - URePSSS - Unité de Recherche Pluridisciplinaire Sport Santé Société, F-59000, Lille, France
- CHU Lille, Université de Lille, F-59000, Lille, France
- Sorbonne Université, Institut de Biologie Paris-Seine (IBPS), CNRS UMR 8256, Inserm ERL U1164, Biological Adaptation and Ageing, 75005, Paris, France
| | - Charlotte Claeyssen
- Univ. Lille, Univ. Artois, Univ. Littoral Côte d'Opale, ULR 7369 - URePSSS - Unité de Recherche Pluridisciplinaire Sport Santé Société, F-59000, Lille, France
| | - Sana Douffi
- Univ. Lille, Univ. Artois, Univ. Littoral Côte d'Opale, ULR 7369 - URePSSS - Unité de Recherche Pluridisciplinaire Sport Santé Société, F-59000, Lille, France
| | - Onnik Agbulut
- Sorbonne Université, Institut de Biologie Paris-Seine (IBPS), CNRS UMR 8256, Inserm ERL U1164, Biological Adaptation and Ageing, 75005, Paris, France
| | - Caroline Cieniewski-Bernard
- Univ. Lille, Univ. Artois, Univ. Littoral Côte d'Opale, ULR 7369 - URePSSS - Unité de Recherche Pluridisciplinaire Sport Santé Société, F-59000, Lille, France
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Bulangalire N, Claeyssen C, Agbulut O, Cieniewski-Bernard C. Impact of MG132 induced-proteotoxic stress on αB-crystallin and desmin phosphorylation and O-GlcNAcylation and their partition towards cytoskeleton. Biochimie 2024:S0300-9084(24)00079-8. [PMID: 38636798 DOI: 10.1016/j.biochi.2024.04.004] [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: 01/16/2024] [Revised: 03/19/2024] [Accepted: 04/14/2024] [Indexed: 04/20/2024]
Abstract
Small Heat Shock Proteins are considered as the first line of defense when proteostasis fails. Among them, αB-crystallin is expressed in striated muscles in which it interacts with desmin intermediate filaments to stabilize them, maintaining cytoskeleton's integrity and muscular functionalities. Desmin is a key actor for muscle health; its targeting by αB-crystallin is thus crucial, especially in stress conditions. αB-crystallin is phosphorylated and O-GlcNAcylated. Its phosphorylation increases consecutively to various stresses, correlated with its recruitment for cytoskeleton's safeguarding. However, phosphorylation as unique signal for cytoskeleton translocation remains controversial; indeed, O-GlcNAcylation was also proposed to be involved. Thus, there are still some gaps for a deeper comprehension of how αB-crystallin functions are finely regulated by post-translational modifications. Furthermore, desmin also bears both post-translational modifications; while desmin phosphorylation is closely linked to desmin intermediates filaments turnover, it is unclear whereas its O-GlcNAcylation could impact its proper function. In the herein paper, we aim at identifying whether phosphorylation and/or O-GlcNAcylation are involved in αB-crystallin targeting towards cytoskeleton in proteotoxic stress induced by proteasome inhibition in C2C12 myotubes. We demonstrated that proteotoxicity led to αB-crystallin's phosphorylation and O-GlcNAcylation patterns changes, both presenting a dynamic interplay depending on protein subfraction. Importantly, both post-translational modifications showed a spatio-temporal variation correlated with αB-crystallin translocation towards cytoskeleton. In contrast, we did not detect any change of desmin phosphorylation and O-GlcNAcylation. All together, these data strongly support that αB-crystallin phosphorylation/O-GlcNAcylation interplay rather than changes on desmin is a key regulator for its cytoskeleton translocation, preserving it towards stress.
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Affiliation(s)
- Nathan Bulangalire
- Univ. Lille, Univ. Artois, Univ. Littoral Côte d'Opale, ULR 7369 - URePSSS - Unité de Recherche Pluridisciplinaire Sport Santé Société, F-59000, Lille, France; CHU Lille, Université de Lille, F-59000, Lille, France; Sorbonne Université, Institut de Biologie Paris-Seine (IBPS), CNRS UMR 8256, Inserm ERL U1164, Biological Adaptation and Ageing, 75005, Paris, France
| | - Charlotte Claeyssen
- Univ. Lille, Univ. Artois, Univ. Littoral Côte d'Opale, ULR 7369 - URePSSS - Unité de Recherche Pluridisciplinaire Sport Santé Société, F-59000, Lille, France
| | - Onnik Agbulut
- Sorbonne Université, Institut de Biologie Paris-Seine (IBPS), CNRS UMR 8256, Inserm ERL U1164, Biological Adaptation and Ageing, 75005, Paris, France
| | - Caroline Cieniewski-Bernard
- Univ. Lille, Univ. Artois, Univ. Littoral Côte d'Opale, ULR 7369 - URePSSS - Unité de Recherche Pluridisciplinaire Sport Santé Société, F-59000, Lille, France.
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Kruglova N, Filatov A. Detecting PTP Protein-Protein Interactions by Fluorescent Immunoprecipitation Analysis (FIPA). Methods Mol Biol 2024; 2743:181-194. [PMID: 38147216 DOI: 10.1007/978-1-0716-3569-8_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
Identifying protein-protein interactions is crucial for revealing protein functions and characterizing cellular processes. Manipulating PPIs has become widespread in treating human diseases such as cancer, autoimmunity, and infections. It has been recently applied to the regulation of protein tyrosine phosphatases (PTPs) previously considered undruggable. A broad panel of methods is available for studying PPIs. To complement the existing toolkit, we developed a simple method called fluorescent immunoprecipitation analysis (FIPA). This method is based on coimmunoprecipitation followed by protein gel electrophoresis and fluorescent imaging to visualize components of a protein complex simultaneously on a gel. The FIPA allows the detection of proteins expressed under native conditions and is compatible with mass spectrometry identification of protein bands.
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Affiliation(s)
- Natalia Kruglova
- Cell and Gene Technology Group, Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology RAS, Moscow, Russia
- National Research Center, Institute of Immunology of Federal Medical Biological Agency of Russia, Moscow, Russia
| | - Alexander Filatov
- National Research Center, Institute of Immunology of Federal Medical Biological Agency of Russia, Moscow, Russia
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Prakash A, Paunikar S, Webber M, McDermott E, Vellanki SH, Thompson K, Dockery P, Jahns H, Brown JAL, Hopkins AM, Bourke E. Centrosome amplification promotes cell invasion via cell-cell contact disruption and Rap-1 activation. J Cell Sci 2023; 136:jcs261150. [PMID: 37772773 PMCID: PMC10629695 DOI: 10.1242/jcs.261150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 09/19/2023] [Indexed: 09/30/2023] Open
Abstract
Centrosome amplification (CA) is a prominent feature of human cancers linked to tumorigenesis in vivo. Here, we report mechanistic contributions of CA induction alone to tumour architecture and extracellular matrix (ECM) remodelling. CA induction in non-tumorigenic breast cells MCF10A causes cell migration and invasion, with underlying disruption of epithelial cell-cell junction integrity and dysregulation of expression and subcellular localisation of cell junction proteins. CA also elevates expression of integrin β-3, its binding partner fibronectin-1 and matrix metalloproteinase enzymes, promoting cell-ECM attachment, ECM degradation, and a migratory and invasive cell phenotype. Using a chicken embryo xenograft model for in vivo validation, we show that CA-induced (+CA) MCF10A cells invade into the chick mesodermal layer, with inflammatory cell infiltration and marked focal reactions between chorioallantoic membrane and cell graft. We also demonstrate a key role of small GTPase Rap-1 signalling through inhibition using GGTI-298, which blocked various CA-induced effects. These insights reveal that in normal cells, CA induction alone (without additional oncogenic alterations) is sufficient to confer early pro-tumorigenic changes within days, acting through Rap-1-dependent signalling to alter cell-cell contacts and ECM disruption.
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Affiliation(s)
- Anu Prakash
- Lambe Institute for Translational Research, Discipline of Pathology, Centre for Chromosome Biology, University of Galway, Galway H91 V4AY, Ireland
| | - Shishir Paunikar
- Lambe Institute for Translational Research, Discipline of Pathology, Centre for Chromosome Biology, University of Galway, Galway H91 V4AY, Ireland
| | - Mark Webber
- Lambe Institute for Translational Research, Discipline of Pathology, Centre for Chromosome Biology, University of Galway, Galway H91 V4AY, Ireland
| | - Emma McDermott
- Centre for Microscopy and Imaging, Discipline of Anatomy, School of Medicine, University of Galway, Galway H91 W5P7, Ireland
| | - Sri H. Vellanki
- Department of Surgery, Beaumont Hospital, Royal College of Surgeons in Ireland, Dublin D09 DK19, Ireland
| | - Kerry Thompson
- Centre for Microscopy and Imaging, Discipline of Anatomy, School of Medicine, University of Galway, Galway H91 W5P7, Ireland
| | - Peter Dockery
- Centre for Microscopy and Imaging, Discipline of Anatomy, School of Medicine, University of Galway, Galway H91 W5P7, Ireland
| | - Hanne Jahns
- Pathobiology Section, School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - James A. L. Brown
- Department of Biological Sciences, University of Limerick, Limerick V94T9PX, Ireland
- Limerick Digital Cancer Research Centre (LDCRC) and Health Research Institute, University of Limerick, Limerick V94T9PX, Ireland
| | - Ann M. Hopkins
- Department of Surgery, Beaumont Hospital, Royal College of Surgeons in Ireland, Dublin D09 DK19, Ireland
| | - Emer Bourke
- Lambe Institute for Translational Research, Discipline of Pathology, Centre for Chromosome Biology, University of Galway, Galway H91 V4AY, Ireland
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Maddala R, Eldawy C, Bachman W, Soderblom EJ, Rao PV. Glypican-4 regulated actin cytoskeletal reorganization in glucocorticoid treated trabecular meshwork cells and involvement of Wnt/PCP signaling. J Cell Physiol 2023; 238:631-646. [PMID: 36727620 DOI: 10.1002/jcp.30953] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/30/2022] [Accepted: 01/10/2023] [Indexed: 02/03/2023]
Abstract
A common adverse response to the clinical use of glucocorticoids (GCs) is elevated intraocular pressure (IOP) which is a major risk factor for glaucoma. Elevated IOP arises due to impaired outflow of aqueous humor (AH) through the trabecular meshwork (TM). Although GC-induced changes in actin cytoskeletal dynamics, contractile characteristics, and cell adhesive interactions of TM cells are believed to influence AH outflow and IOP, the molecular mechanisms mediating changes in these cellular characteristics are poorly understood. Our studies focused on evaluating changes in the cytoskeletal and cytoskeletal-associated protein (cytoskeletome) profile of human TM cells treated with dexamethasone (Dex) using label-free mass spectrometric quantification, identified elevated levels of specific proteins known to regulate actin stress fiber formation, contraction, actin networks crosslinking, cell adhesion, and Wnt signaling, including LIMCH1, ArgBP2, CNN3, ITGBL1, CTGF, palladin, FAT1, DIAPH2, EPHA4, SIPA1L1, and GPC4. Several of these proteins colocalized with the actin cytoskeleton and underwent alterations in distribution profile in TM cells treated with Dex, and an inhibitor of Abl/Src kinases. Wnt/Planar Cell Polarity (PCP) signaling agonists-Wnt5a and 5b were detected prominently in the cytoskeletome fraction of TM cells, and studies using siRNA to suppress expression of glypican-4 (GPC4), a known modulator of the Wnt/PCP pathway revealed that GPC4 deficiency impairs Dex induced actin stress fiber formation, and activation of c-Jun N-terminal Kinase (JNK) and Rho kinase. Additionally, while Dex augmented, GPC4 deficiency suppressed the formation of actin stress fibers in TM cells in the presence of Dex and Wnt5a. Taken together, these results identify the GPC4-dependent Wnt/PCP signaling pathway as one of the crucial upstream regulators of Dex induced actin cytoskeletal reorganization and cell adhesion in TM cells, opening an opportunity to target the GPC4/Wnt/PCP pathway for treatment of ocular hypertension in glaucoma.
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Affiliation(s)
- Rupalatha Maddala
- Department of Ophthalmology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Camelia Eldawy
- Department of Ophthalmology, Duke University School of Medicine, Durham, North Carolina, USA
| | - William Bachman
- Department of Ophthalmology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Erik J Soderblom
- Proteomics and Metabolomics Shared Resource, Duke University School of Medicine, Duke Center for Genomic and Computational Biology, Durham, North Carolina, USA
| | - Ponugoti V Rao
- Department of Ophthalmology, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina, USA
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Opposing roles of ZEB1 in the cytoplasm and nucleus control cytoskeletal assembly and YAP1 activity. Cell Rep 2022; 41:111452. [DOI: 10.1016/j.celrep.2022.111452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 07/12/2022] [Accepted: 09/14/2022] [Indexed: 11/16/2022] Open
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Global O-GlcNAcylation changes impact desmin phosphorylation and its partition toward cytoskeleton in C2C12 skeletal muscle cells differentiated into myotubes. Sci Rep 2022; 12:9831. [PMID: 35701470 PMCID: PMC9198038 DOI: 10.1038/s41598-022-14033-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 05/31/2022] [Indexed: 11/09/2022] Open
Abstract
Desmin is the guardian of striated muscle integrity, permitting the maintenance of muscle shape and the efficiency of contractile activity. It is also a key mediator of cell homeostasis and survival. To ensure the fine regulation of skeletal muscle processes, desmin is regulated by post-translational modifications (PTMs). It is more precisely phosphorylated by several kinases connecting desmin to intracellular processes. Desmin is also modified by O-GlcNAcylation, an atypical glycosylation. However, the functional consequence of O-GlcNAcylation on desmin is still unknown, nor its impact on desmin phosphorylation. In a model of C2C12 myotubes, we modulated the global O-GlcNAcylation level, and we determined whether the expression, the PTMs and the partition of desmin toward insoluble material or cytoskeleton were impacted or not. We have demonstrated in the herein paper that O-GlcNAcylation variations led to changes in desmin behaviour. In particular, our data clearly showed that O-GlcNAcylation increase led to a decrease of phosphorylation level on desmin that seems to involve CamKII correlated to a decrease of its partition toward cytoskeleton. Our data showed that phosphorylation/O-GlcNAcylation interplay is highly complex on desmin, supporting that a PTMs signature could occur on desmin to finely regulate its partition (i.e. distribution) with a spatio-temporal regulation.
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Applications of Tandem Mass Spectrometry (MS/MS) in Protein Analysis for Biomedical Research. Molecules 2022; 27:molecules27082411. [PMID: 35458608 PMCID: PMC9031286 DOI: 10.3390/molecules27082411] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 04/05/2022] [Accepted: 04/06/2022] [Indexed: 01/27/2023] Open
Abstract
Mass Spectrometry (MS) allows the analysis of proteins and peptides through a variety of methods, such as Electrospray Ionization-Mass Spectrometry (ESI-MS) or Matrix-Assisted Laser Desorption Ionization-Mass Spectrometry (MALDI-MS). These methods allow identification of the mass of a protein or a peptide as intact molecules or the identification of a protein through peptide-mass fingerprinting generated upon enzymatic digestion. Tandem mass spectrometry (MS/MS) allows the fragmentation of proteins and peptides to determine the amino acid sequence of proteins (top-down and middle-down proteomics) and peptides (bottom-up proteomics). Furthermore, tandem mass spectrometry also allows the identification of post-translational modifications (PTMs) of proteins and peptides. Here, we discuss the application of MS/MS in biomedical research, indicating specific examples for the identification of proteins or peptides and their PTMs as relevant biomarkers for diagnostic and therapy.
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O'Sullivan LR, Ajaykumar AP, Dembicka KM, Murphy A, Grennan EP, Young PW. Investigation of calmodulin-like and rod domain mutations suggests common molecular mechanism for α-actinin-1-linked congenital macrothrombocytopenia. FEBS Lett 2019; 594:161-174. [PMID: 31365757 DOI: 10.1002/1873-3468.13562] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 07/22/2019] [Accepted: 07/29/2019] [Indexed: 11/11/2022]
Abstract
Actinin-1 mutations cause dominantly inherited congenital macrothrombocytopenia (CMTP), with mutations in the actin-binding domain increasing actinin's affinity for F-actin. In this study, we examined nine CMTP-causing mutations in the calmodulin-like and rod domains of actinin-1. These mutations increase, to varying degrees, actinin's ability to bundle actin filaments in vitro. Mutations within the calmodulin-like domain decrease its thermal stability slightly but do not dramatically affect calcium binding, with mutant proteins retaining calcium-dependent regulation of filament bundling in vitro. The G764S and E769K mutations increase cytoskeletal association of actinin in cells, and all mutant proteins colocalize with F-actin in cultured HeLa cells. Thus, CMTP-causing actinin-1 mutations outside the actin-binding domain also increase actin association, suggesting a common molecular mechanism underlying actinin-1 related CMTP.
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Affiliation(s)
- Leanne Rose O'Sullivan
- School of Biochemistry and Cell Biology, Western Gateway Building, University College Cork, Cork, Ireland
| | | | - Kornelia Maria Dembicka
- School of Biochemistry and Cell Biology, Western Gateway Building, University College Cork, Cork, Ireland
| | - Aidan Murphy
- School of Biochemistry and Cell Biology, Western Gateway Building, University College Cork, Cork, Ireland
| | - Eamonn Paul Grennan
- School of Biochemistry and Cell Biology, Western Gateway Building, University College Cork, Cork, Ireland
| | - Paul William Young
- School of Biochemistry and Cell Biology, Western Gateway Building, University College Cork, Cork, Ireland
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Wasik AA, Schiller HB. Functional proteomics of cellular mechanosensing mechanisms. Semin Cell Dev Biol 2017; 71:118-128. [DOI: 10.1016/j.semcdb.2017.06.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 06/23/2017] [Accepted: 06/25/2017] [Indexed: 10/19/2022]
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Murphy ACH, Lindsay AJ, McCaffrey MW, Djinović-Carugo K, Young PW. Congenital macrothrombocytopenia-linked mutations in the actin-binding domain of α-actinin-1 enhance F-actin association. FEBS Lett 2016; 590:685-95. [PMID: 26879394 DOI: 10.1002/1873-3468.12101] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 02/09/2016] [Accepted: 02/11/2016] [Indexed: 01/21/2023]
Abstract
Mutations in the actin cross-linking protein actinin-1 were recently linked to dominantly inherited congenital macrothrombocytopenia. Here, we report that several disease-associated mutations that are located within the actinin-1 actin-binding domain cause increased binding of actinin-1 to actin filaments and enhance filament bundling in vitro. These actinin-1 mutants are also more stably associated with the cytoskeleton in cultured cells, as assessed by biochemical fractionation and fluorescence recovery after photobleaching experiments. For two mutations the disruption of contacts between the calponin homology domains within the actinin actin-binding domain may explain increased filament binding--providing mechanistic and structural insights into the basis of actinin-1 dysfunction in congenital macrothrombocytopenia.
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Affiliation(s)
- Anita C H Murphy
- School of Biochemistry and Cell Biology, University College Cork, Ireland
| | - Andrew J Lindsay
- Molecular Cell Biology Laboratory, School of Biochemistry and Cell Biology, Biosciences Institute, University College Cork, Ireland
| | - Mary W McCaffrey
- Molecular Cell Biology Laboratory, School of Biochemistry and Cell Biology, Biosciences Institute, University College Cork, Ireland
| | - Kristina Djinović-Carugo
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Austria.,Department of Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Slovenia
| | - Paul W Young
- School of Biochemistry and Cell Biology, University College Cork, Ireland
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