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Guo N, Han X, Han G, Dai M, Han Z, Li Q. Bioinformation Analysis of Differential Expression Proteins in Different Processes of COVID-19. Viral Immunol 2024; 37:194-201. [PMID: 38717820 DOI: 10.1089/vim.2023.0094] [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: 05/14/2024] Open
Abstract
COVID-19 is a highly infectious respiratory disease whose progression has been associated with multiple factors. From SARS-CoV-2 infection to death, biomarkers capable of predicting different disease processes are needed to help us further understand the molecular progression of COVID-19 disease. The aim is to find differentially expressed proteins that are associated with the progression of COVID-19 disease or can be potential biomarkers, and to provide a reference for further understanding of the molecular mechanisms of COVID-19 occurrence, progression, and treatment. Data-independent Acquisition (DIA) proteomics to obtain sample protein expression data, using R language screening differentially expressed proteins. Gene Ontology and Kyoto Encyclopedia for Genes and Genomes analysis was performed on differential proteins and protein-protein interaction (PPI) network was constructed to screen key proteins. A total of 47 differentially expressed proteins were obtained from COVID-19 incubation patients and healthy population (L/H), mainly enriched in platelet-related functions, and complement and coagulation cascade reaction pathways, such as platelet degranulation and platelet aggregation. A total of 42 differential proteins were obtained in clinical and latent phase patients (C/L), also mainly enriched in platelet-related functions and in complement and coagulation cascade reactions, platelet activation pathways. A total of 10 differential proteins were screened in recovery and clinical phase patients (R/C), mostly immune-related proteins. The differentially expressed proteins in different stages of COVID-19 are mostly closely associated with coagulation, and key differential proteins, such as FGA, FGB, FGG, ACTB, PFN1, VCL, SERPZNCL, APOC3, LTF, and DEFA1, have the potential to be used as early diagnostic markers.
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Affiliation(s)
- Nana Guo
- Hebei Province Center for Disease Control and Prevention, Shijiazhuang, China
| | - Xu Han
- Hebei Province Center for Disease Control and Prevention, Shijiazhuang, China
| | - Guangyue Han
- Hebei Province Center for Disease Control and Prevention, Shijiazhuang, China
| | - Mingyan Dai
- Hebei Medical University, Shijiazhuang, China
| | - Zhanying Han
- Hebei Province Center for Disease Control and Prevention, Shijiazhuang, China
| | - Qi Li
- Hebei Province Center for Disease Control and Prevention, Shijiazhuang, China
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Rouyère C, Serrano T, Frémont S, Echard A. Oxidation and reduction of actin: Origin, impact in vitro and functional consequences in vivo. Eur J Cell Biol 2022; 101:151249. [PMID: 35716426 DOI: 10.1016/j.ejcb.2022.151249] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/13/2022] [Accepted: 06/06/2022] [Indexed: 11/15/2022] Open
Abstract
Actin is among the most abundant proteins in eukaryotic cells and assembles into dynamic filamentous networks regulated by many actin binding proteins. The actin cytoskeleton must be finely tuned, both in space and time, to fulfill key cellular functions such as cell division, cell shape changes, phagocytosis and cell migration. While actin oxidation by reactive oxygen species (ROS) at non-physiological levels are known for long to impact on actin polymerization and on the cellular actin cytoskeleton, growing evidence shows that direct and reversible oxidation/reduction of specific actin amino acids plays an important and physiological role in regulating the actin cytoskeleton. In this review, we describe which actin amino acid residues can be selectively oxidized and reduced in many different ways (e.g. disulfide bond formation, glutathionylation, carbonylation, nitration, nitrosylation and other oxidations), the cellular enzymes at the origin of these post-translational modifications, and the impact of actin redox modifications both in vitro and in vivo. We show that the regulated balance of oxidation and reduction of key actin amino acid residues contributes to the control of actin filament polymerization and disassembly at the subcellular scale and highlight how improper redox modifications of actin can lead to pathological conditions.
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Affiliation(s)
- Clémentine Rouyère
- Institut Pasteur, Université Paris Cité, CNRS UMR3691, Membrane Traffic and Cell Division Unit, 25-28 rue du Dr Roux, F-75015 Paris, France; Sorbonne Université, Collège Doctoral, F-75005 Paris, France
| | - Thomas Serrano
- Institut Pasteur, Université Paris Cité, CNRS UMR3691, Membrane Traffic and Cell Division Unit, 25-28 rue du Dr Roux, F-75015 Paris, France
| | - Stéphane Frémont
- Institut Pasteur, Université Paris Cité, CNRS UMR3691, Membrane Traffic and Cell Division Unit, 25-28 rue du Dr Roux, F-75015 Paris, France
| | - Arnaud Echard
- Institut Pasteur, Université Paris Cité, CNRS UMR3691, Membrane Traffic and Cell Division Unit, 25-28 rue du Dr Roux, F-75015 Paris, France.
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Simonetta I, Tuttolomondo A, Daidone M, Pinto A. Biomarkers in Anderson-Fabry Disease. Int J Mol Sci 2020; 21:ijms21218080. [PMID: 33138098 PMCID: PMC7662984 DOI: 10.3390/ijms21218080] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 10/25/2020] [Accepted: 10/27/2020] [Indexed: 12/27/2022] Open
Abstract
Fabry disease is a rare lysosomal storage disorder caused by a deficiency of α-galactosidase A, resulting in multisystemic involvement. Lyso-Gb3 (globotriaosylsphingosine), the deacylated form of Gb3, is currently measured in plasma as a biomarker of classic Fabry disease. Intensive research of biomarkers has been conducted over the years, in order to detect novel markers that may potentially be used in clinical practice as a screening tool, in the context of the diagnostic process and as an indicator of response to treatment. An interesting field of application of such biomarkers is the management of female heterozygotes who present difficulty in predictable clinical progression. This review aims to summarise the current evidence and knowledge about general and specific markers that are actually measured in subjects with confirmed or suspected Fabry disease; moreover, we report potential novel markers such as microRNAs. Recent proteomic or metabolomic studies are in progress bringing out plasma proteome profiles in Fabry patients: this assessment may be useful to characterize molecular pathology of the disease, to improve diagnostic process, and to monitor response to treatment. The management of Fabry disease may be improved by the identification of biomarkers that reflect clinical course, severity, and the progression of the disease.
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Heo SH, Kang E, Kim YM, Go H, Kim KY, Jung JY, Kang M, Kim GH, Kim JM, Choi IH, Choi JH, Jung SC, Desnick RJ, Yoo HW, Lee BH. Fabry disease: characterisation of the plasma proteome pre- and post-enzyme replacement therapy. J Med Genet 2017; 54:771-780. [PMID: 28835480 PMCID: PMC5740533 DOI: 10.1136/jmedgenet-2017-104704] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 07/05/2017] [Accepted: 07/24/2017] [Indexed: 01/03/2023]
Abstract
Background Fabry disease is characterised by the progressive accumulation of globotriaosylceramide (Gb3) and related glycosphingolipids in vascular endothelial cells. Enzyme replacement therapy (ERT) clears this accumulation. We analysed plasma proteome profiles before and after ERT to characterise its molecular pathology. Methods Two-dimensional electrophoresis and matrix-assisted laser desorption/ionisation-time of flight tandem mass spectrometry (MALDI-TOF MS) and tandem mass spectrometry (MS/MS) were done using plasma samples before and after ERT in eight patients with classical Fabry disease Results After short-term ERT (4–12 months), the levels of 15 plasma proteins involved in inflammation, oxidative and ischaemic injury, or complement activation were reduced significantly. Among them, β-actin (ACTB), inactivated complement C3b (iC3b), and C4B were elevated significantly in pre-ERT Fabry disease plasma compared with control plasma. After longer-term ERT (46–96 months), iC3b levels gradually decreased, whereas the levels of other proteins varied. The gradual reduction of iC3b was comparable to that of Gb3 levels. In addition, iC3b increased significantly in pre-ERT Fabry disease mouse plasma, and C3 deposits were notable in renal tissues of pre-enzyme replacement therapy patients. Conclusion These results indicated that C3-mediated complement activation might be altered in Fabry disease and ERT might promote its stabilisation.
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Affiliation(s)
- Sun Hee Heo
- Asan Institute for Life Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Eungu Kang
- Department of Pediatrics, Soonchunhyang University Cheonan Hospital, Soonchunhyang University College of Medicine, Cheonan, Korea
| | - Yoon-Myung Kim
- Department of Pediatrics, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul, Korea
| | - Heounjeong Go
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | | | | | - Minji Kang
- Asan Institute for Life Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Gu-Hwan Kim
- Medical Genetics Center, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul, Korea
| | - Jae-Min Kim
- Medical Genetics Center, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul, Korea
| | - In-Hee Choi
- Medical Genetics Center, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul, Korea
| | - Jin-Ho Choi
- Department of Pediatrics, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul, Korea
| | - Sung-Chul Jung
- Department of Biochemistry, School of Medicine, Ewha Womans University, Seoul, Korea
| | - Robert J Desnick
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Han-Wook Yoo
- Department of Pediatrics, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul, Korea
| | - Beom Hee Lee
- Department of Pediatrics, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul, Korea
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Wilson C, Terman JR, González-Billault C, Ahmed G. Actin filaments-A target for redox regulation. Cytoskeleton (Hoboken) 2016; 73:577-595. [PMID: 27309342 DOI: 10.1002/cm.21315] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 06/03/2016] [Accepted: 06/13/2016] [Indexed: 12/21/2022]
Abstract
Actin and its ability to polymerize into dynamic filaments is critical for the form and function of cells throughout the body. While multiple proteins have been characterized as affecting actin dynamics through noncovalent means, actin and its protein regulators are also susceptible to covalent modifications of their amino acid residues. In this regard, oxidation-reduction (Redox) intermediates have emerged as key modulators of the actin cytoskeleton with multiple different effects on cellular form and function. Here, we review work implicating Redox intermediates in post-translationally altering actin and discuss what is known regarding how these alterations affect the properties of actin. We also focus on two of the best characterized enzymatic sources of these Redox intermediates-the NADPH oxidase NOX and the flavoprotein monooxygenase MICAL-and detail how they have both been identified as altering actin, but share little similarity and employ different means to regulate actin dynamics. Finally, we discuss the role of these enzymes and redox signaling in regulating the actin cytoskeleton in vivo and highlight their importance for neuronal form and function in health and disease. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Carlos Wilson
- Department of Biology, Faculty of Sciences, Universidad De Chile, Las Palmeras 3425, Santiago, 7800024, Chile.,Center for Geroscience, Brain Health and Metabolism, Santiago, Chile
| | - Jonathan R Terman
- Department of Neuroscience, The University of Texas Southwestern Medical Center, Dallas, Texas, 75390. .,Department of Pharmacology, The University of Texas Southwestern Medical Center, Dallas, Texas, 75390.
| | - Christian González-Billault
- Department of Biology, Faculty of Sciences, Universidad De Chile, Las Palmeras 3425, Santiago, 7800024, Chile. .,Center for Geroscience, Brain Health and Metabolism, Santiago, Chile. .,The Buck Institute for Research on Aging, Novato, California 94945.
| | - Giasuddin Ahmed
- Department of Neuroscience, The University of Texas Southwestern Medical Center, Dallas, Texas, 75390.,Department of Pharmacology, The University of Texas Southwestern Medical Center, Dallas, Texas, 75390
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Galkina SI, Fedorova NV, Serebryakova MV, Arifulin EA, Stadnichuk VI, Gaponova TV, Baratova LA, Sud'ina GF. Inhibition of the GTPase dynamin or actin depolymerisation initiates outward plasma membrane tubulation/vesiculation (cytoneme formation) in neutrophils. Biol Cell 2015; 107:144-58. [DOI: 10.1111/boc.201400063] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 01/29/2015] [Indexed: 11/30/2022]
Affiliation(s)
- Svetlana I. Galkina
- A. N. Belozersky Institute of Physico-Chemical Biology; Lomonosov Moscow State University; Moscow 119991 Russia
| | - Natalia V. Fedorova
- A. N. Belozersky Institute of Physico-Chemical Biology; Lomonosov Moscow State University; Moscow 119991 Russia
| | - Marina V. Serebryakova
- A. N. Belozersky Institute of Physico-Chemical Biology; Lomonosov Moscow State University; Moscow 119991 Russia
| | - Evgenii A. Arifulin
- A. N. Belozersky Institute of Physico-Chemical Biology; Lomonosov Moscow State University; Moscow 119991 Russia
| | | | - Tatjana V. Gaponova
- FGBU Hematology Research Center; Russian Federation Ministry of Public Health; Moscow 125167 Russia
| | - Ludmila A. Baratova
- A. N. Belozersky Institute of Physico-Chemical Biology; Lomonosov Moscow State University; Moscow 119991 Russia
| | - Galina F. Sud'ina
- A. N. Belozersky Institute of Physico-Chemical Biology; Lomonosov Moscow State University; Moscow 119991 Russia
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Wang QQ, Yu L, Huang GR, Zhang L, Liu YQ, Wang TW, Lin H, Ren Q, Liu P, Huang L, Qin J, Wu GM, Li QN, Li YF, Xiong HY. Polymorphisms of angiotensin converting enzyme and nitric oxide synthase 3 genes as risk factors of high-altitude pulmonary edema: a case-control study and meta-analysis. TOHOKU J EXP MED 2013; 229:255-66. [PMID: 23603420 DOI: 10.1620/tjem.229.255] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
High-altitude pulmonary edema (HAPE) is a non-cardiogenic type of pulmonary edema developing altitudes > 2,500 m. Angiotensin converting enzyme (ACE) and nitric oxide synthase 3 (NOS3) play important roles in regulating pulmonary vascular tone. To assess associations between genetic variants in the ACE and NOS3 genes and HAPE risk, 27 HAPE patients and 108 matched controls were genotyped and analyzed. The indicated HAPE association of the NOS3 G894T (Glu298Asp) single nucleotide polymorphism (SNP), which may change NO production, was further evaluated by a meta-analysis of six studies involving 399 HAPE patients and 495 controls. Odds ratios (ORs) and 95% confidence intervals (CIs) were determined with fixed-effects models. Stratification analyses of ethnicity and geographic location were performed. Significant associations were observed for the dominant model in two ACE tag SNPs influencing serum ACE concentrations (rs8066114 polymorphism: GG+CG vs. CC; rs4461142 polymorphism: TT+CT vs. CC). Furthermore, Single-locus analysis indicated significantly different distributions of G allele frequency between the cases (29.63%) and controls (17.13%) for the ACE rs8066114 polymorphism. The case-control distributions of genotype frequencies and T allele frequency of NOS3 G894T (Glu298Asp) polymorphism were significantly higher in the cases than controls, and the NOS3 G894T (Glu298Asp) SNP showed elevated HAPE risk under the dominant model (TT+GT vs. GG). Meta-analysis showed overall association of NOS3 G894T SNP with HAPE risk under the allele contrast and dominant genetic models, which remained significant for Asians. In conclusion, ACE rs8066114 and rs4461142 and NOS3 rs1799983 (G894T) polymorphisms may be associated with increased HAPE risk in Asians.
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Affiliation(s)
- Qing-Qing Wang
- Department of Epidemiology, College of Preventive Medicine, Third Military Medical University, Chongqing, PR China
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Abstract
Many of the best-studied actin regulatory proteins use non-covalent means to modulate the properties of actin. Yet, actin is also susceptible to covalent modifications of its amino acids. Recent work is increasingly revealing that actin processing and its covalent modifications regulate important cellular events. In addition, numerous pathogens express enzymes that specifically use actin as a substrate to regulate their hosts' cells. Actin post-translational alterations have been linked to different normal and disease processes and the effects associated with metabolic and environmental stressors. Herein, we highlight specific co-translational and post-translational modifications of actin and discuss the current understanding of the role that these modifications play in regulating actin.
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Affiliation(s)
- Jonathan R Terman
- Department of Neuroscience, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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On diphtheria toxin fragment A release into the cytosol—Cytochalasin D effect and involvement of actin filaments and eukaryotic elongation factor 2. Int J Biochem Cell Biol 2011; 43:1365-72. [DOI: 10.1016/j.biocel.2011.05.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Revised: 05/13/2011] [Accepted: 05/26/2011] [Indexed: 11/17/2022]
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Chaturvedi V, Sreedhar AS. Hsp90 inhibition induces destabilization of actin cytoskeleton in tumor cells: functional significance of Hsp90 interaction with F–actin. ASIAN PAC J TROP MED 2010. [DOI: 10.1016/s1995-7645(10)60172-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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Kondrikov D, Fonseca FV, Elms S, Fulton D, Black SM, Block ER, Su Y. Beta-actin association with endothelial nitric-oxide synthase modulates nitric oxide and superoxide generation from the enzyme. J Biol Chem 2010; 285:4319-27. [PMID: 19946124 PMCID: PMC2836036 DOI: 10.1074/jbc.m109.063172] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2009] [Revised: 11/20/2009] [Indexed: 11/06/2022] Open
Abstract
Protein-protein interactions represent an important post-translational mechanism for endothelial nitric-oxide synthase (eNOS) regulation. We have previously reported that beta-actin is associated with eNOS oxygenase domain and that association of eNOS with beta-actin increases eNOS activity and nitric oxide (NO) production. In the present study, we found that beta-actin-induced increase in NO production was accompanied by decrease in superoxide formation. A synthetic actin-binding sequence (ABS) peptide 326 with amino acid sequence corresponding to residues 326-333 of human eNOS, one of the putative ABSs, specifically bound to beta-actin and prevented eNOS association with beta-actin in vitro. Peptide 326 also prevented beta-actin-induced decrease in superoxide formation and increase in NO and L-citrulline production. A modified peptide 326 replacing hydrophobic amino acids leucine and tryptophan with neutral alanine was unable to interfere with eNOS-beta-actin binding and to prevent beta-actin-induced changes in NO and superoxide formation. Site-directed mutagenesis of the actin-binding domain of eNOS replacing leucine and tryptophan with alanine yielded an eNOS mutant that exhibited reduced eNOS-beta-actin association, decreased NO production, and increased superoxide formation in COS-7 cells. Disruption of eNOS-beta-actin interaction in endothelial cells using ABS peptide 326 resulted in decreased NO production, increased superoxide formation, and decreased endothelial monolayer wound repair, which was prevented by PEG-SOD and NO donor NOC-18. Taken together, this novel finding indicates that beta-actin binding to eNOS through residues 326-333 in the eNOS protein results in shifting the enzymatic activity from superoxide formation toward NO production. Modulation of NO and superoxide formation from eNOS by beta-actin plays an important role in endothelial function.
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Affiliation(s)
| | | | | | - David Fulton
- From the Department of Pharmacology and Toxicology
- Vascular Biology Center, and
| | | | - Edward R. Block
- the Department of Medicine, University of Florida College of Medicine, Gainesville, Florida 32610
| | - Yunchao Su
- From the Department of Pharmacology and Toxicology
- Department of Medicine
- Vascular Biology Center, and
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta, Georgia 30912 and
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Molecular basis for G-actin binding to RPEL motifs from the serum response factor coactivator MAL. EMBO J 2008; 27:3198-208. [PMID: 19008859 PMCID: PMC2583105 DOI: 10.1038/emboj.2008.235] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2008] [Accepted: 10/10/2008] [Indexed: 01/13/2023] Open
Abstract
Serum response factor transcriptional activity is controlled through interactions with regulatory cofactors such as the coactivator MAL/MRTF-A (myocardin-related transcription factor A). MAL is itself regulated in vivo by changes in cellular actin dynamics, which alter its interaction with G-actin. The G-actin-sensing mechanism of MAL/MRTF-A resides in its N-terminal domain, which consists of three tandem RPEL repeats. We describe the first molecular insights into RPEL function obtained from structures of two independent RPELMAL peptide:G-actin complexes. Both RPEL peptides bind to the G-actin hydrophobic cleft and to subdomain 3. These RPELMAL:G-actin structures explain the sequence conservation defining the RPEL motif, including the invariant arginine. Characterisation of the RPELMAL:G-actin interaction by fluorescence anisotropy and cell reporter-based assays validates the significance of actin-binding residues for proper MAL localisation and regulation in vivo. We identify important differences in G-actin engagement between the two RPELMAL structures. Comparison with other actin-binding proteins reveals an unexpected similarity to the vitamin-D-binding protein, extending the G-actin-binding protein repertoire.
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