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Li Y, Gong Y, Chen Y, Qu B, Zhang S. Identification and functional characterization of Cofilin-1 as a new member of antimicrobial protein. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2022; 127:104281. [PMID: 34601007 DOI: 10.1016/j.dci.2021.104281] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 09/29/2021] [Accepted: 09/29/2021] [Indexed: 06/13/2023]
Abstract
Cofilin-1 (Cfl1), a member of the ADF/cofilin family, has been identified as one of differentially expressed proteins in human dendritic cells challenged with lipopolysaccharide (LPS), suggesting that it may be involved in immune response. Here we showed that zebrafish cfl1 was markedly up-regulated by LPS and LTA treatment. We also showed that zebrafish recombinant Cfl1 (rCfl1) not only bound to the Gram-negative and positive bacteria A. hydrophila and S. aureus as well as their signature molecules LPS and LTA but also inhibited the growth of the bacteria. Moreover, we found that the heparin-binding motif-containing regions of Cfl1, i.e., Cfl19-25, Cfl134-51 and Cfl1108-125, like rCfl1, were also able to bind to LPS and LTA and to inhibit the bacterial growth. rCfl1, Cfl19-25, Cfl134-51, and Cfl1108-125 were all able to cause bacterial cell destruction, to induce membrane depolarization, and to stimulate intracellular ROS production. Finally, we showed that zebrafish Cfl1 could protect developing embryos/larvae against attack by the potential pathogen A. hydrophila. These data together indicate that zebrafish Cfl1 plays an immune-relevant role as a newly-characterized antimicrobial protein.
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Affiliation(s)
- Yishuai Li
- Department of Marine Biology, Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Yi Gong
- Department of Marine Biology, Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Ying Chen
- Department of Marine Biology, Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Baozhen Qu
- Qingdao Cancer Institute, Qingdao Central Hospital, 127 Siliunan Road, Qingdao, 266042, China.
| | - Shicui Zhang
- Department of Marine Biology, Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266003, China.
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2
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Hou X, Nozumi M, Nakamura H, Igarashi M, Sugiyama S. Coactosin Promotes F-Actin Protrusion in Growth Cones Under Cofilin-Related Signaling Pathway. Front Cell Dev Biol 2021; 9:660349. [PMID: 34235144 PMCID: PMC8256272 DOI: 10.3389/fcell.2021.660349] [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: 01/29/2021] [Accepted: 05/31/2021] [Indexed: 12/03/2022] Open
Abstract
During brain development, axon outgrowth and its subsequent pathfinding are reliant on a highly motile growth cone located at the tip of the axon. Actin polymerization that is regulated by actin-depolymerizing factors homology (ADF-H) domain-containing family drives the formation of lamellipodia and filopodia at the leading edge of growth cones for axon guidance. However, the precise localization and function of ADF-H domain-containing proteins involved in axon extension and retraction remain unclear. We have previously shown that transcripts and proteins of coactosin-like protein 1 (COTL1), an ADF-H domain-containing protein, are observed in neurites and axons in chick embryos. Coactosin overexpression analysis revealed that this protein was localized to axonal growth cones and involved in axon extension in the midbrain. We further examined the specific distribution of coactosin and cofilin within the growth cone using superresolution microscopy, structured illumination microscopy, which overcomes the optical diffraction limitation and is suitable to the analysis of cellular dynamic movements. We found that coactosin was tightly associated with F-actin bundles at the growth cones and that coactosin overexpression promoted the expansion of lamellipodia and extension of growth cones. Coactosin knockdown in oculomotor neurons resulted in an increase in the levels of the inactive, phosphorylated form of cofilin and dysregulation of actin polymerization and axonal elongation, which suggests that coactosin promoted axonal growth in a cofilin-dependent manner. Indeed, the application of a dominant-negative form of LIMK1, a downstream effector of GTPases, reversed the effect of coactosin knockdown on axonal growth by enhancing cofilin activity. Combined, our results indicate that coactosin functions promote the assembly of protrusive actin filament arrays at the leading edge for growth cone motility.
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Affiliation(s)
- Xubin Hou
- Laboratory of Neuronal Development, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan.,Department of Molecular Neurobiology, Graduate School of Life Sciences, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Motohiro Nozumi
- Department of Neurochemistry and Molecular Cell Biology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Harukazu Nakamura
- Department of Molecular Neurobiology, Graduate School of Life Sciences, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Michihiro Igarashi
- Department of Neurochemistry and Molecular Cell Biology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Sayaka Sugiyama
- Laboratory of Neuronal Development, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
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3
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Actin/microtubule crosstalk during platelet biogenesis in mice is critically regulated by Twinfilin1 and Cofilin1. Blood Adv 2021; 4:2124-2134. [PMID: 32407474 DOI: 10.1182/bloodadvances.2019001303] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 03/13/2020] [Indexed: 01/24/2023] Open
Abstract
Rearrangements of the microtubule (MT) and actin cytoskeleton are pivotal for platelet biogenesis. Hence, defects in actin- or MT-regulatory proteins are associated with platelet disorders in humans and mice. Previous studies in mice revealed that loss of the actin-depolymerizing factor homology (ADF-H) protein Cofilin1 (Cof1) in megakaryocytes (MKs) results in a moderate macrothrombocytopenia but normal MK numbers, whereas deficiency in another ADF-H protein, Twinfilin1 (Twf1), does not affect platelet production or function. However, recent studies in yeast have indicated a critical synergism between Twf1 and Cof1 in the regulation of actin dynamics. We therefore investigated platelet biogenesis and function in mice lacking both Twf1 and Cof1 in the MK lineage. In contrast to single deficiency in either protein, Twf1/Cof1 double deficiency (DKO) resulted in a severe macrothrombocytopenia and dramatically increased MK numbers in bone marrow and spleen. DKO MKs exhibited defective proplatelet formation in vitro and in vivo as well as impaired spreading and altered assembly of podosome-like structures on collagen and fibrinogen in vitro. These defects were associated with aberrant F-actin accumulation and, remarkably, the formation of hyperstable MT, which appears to be caused by dysregulation of the actin- and MT-binding proteins mDia1 and adenomatous polyposis coli. Surprisingly, the mild functional defects described for Cof1-deficient platelets were only slightly aggravated in DKO platelets suggesting that both proteins are largely dispensable for platelet function in the peripheral blood. In summary, these findings reveal critical redundant functions of Cof1 and Twf1 in ensuring balanced actin/microtubule crosstalk during thrombopoiesis in mice and possibly humans.
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4
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Scheller I, Stritt S, Beck S, Peng B, Pleines I, Heinze KG, Braun A, Otto O, Ahrends R, Sickmann A, Bender M, Nieswandt B. Coactosin-like 1 integrates signaling critical for shear-dependent thrombus formation in mouse platelets. Haematologica 2019; 105:1667-1676. [PMID: 31582545 PMCID: PMC7271572 DOI: 10.3324/haematol.2019.225516] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 09/26/2019] [Indexed: 11/09/2022] Open
Abstract
Platelet aggregate formation is a multistep process involving receptor-mediated, as well as biomechanical, signaling cascades, which are highly dependent on actin dynamics. We have previously shown that actin depolymerizing factor (ADF)/n-cofilin and Twinfilin 2a, members of the ADF homology (ADF-H) protein family, have distinct roles in platelet formation and function. Coactosin-like 1 (Cotl1) is another ADF-H protein that binds actin and was also shown to enhance biosynthesis of pro-inflammatory leukotrienes (LT) in granulocytes. Here, we generated mice lacking Cotl1 in the megakaryocyte lineage (Cotl1-/- ) to investigate its role in platelet production and function. Absence of Cotl1 had no impact on platelet counts, platelet activation or cytoskeletal reorganization under static conditions in vitro In contrast, Cotl1 deficiency markedly affected platelet aggregate formation on collagen and adhesion to immobilized von Willebrand factor at high shear rates in vitro, pointing to an impaired function of the platelet mechanoreceptor glycoprotein (GP) Ib. Furthermore, Cotl1 -/-platelets exhibited increased deformability at high shear rates, indicating that the GPIb defect may be linked to altered biomechanical properties of the deficient cells. In addition, we found that Cotl1 deficiency markedly affected platelet LT biosynthesis. Strikingly, exogenous LT addition restored defective aggregate formation of Cotl1-/- platelets at high shear in vitro, indicating a critical role of platelet-derived LT in thrombus formation. In vivo, Cotl1 deficiency translated into prolonged tail bleeding times and protection from occlusive arterial thrombus formation. Together, our results show that Cotl1 in platelets is an integrator of biomechanical and LT signaling in hemostasis and thrombosis.
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Affiliation(s)
- Inga Scheller
- Institute of Experimental Biomedicine I, University Hospital, University of Würzburg, Würzburg.,Rudolf Virchow Center, University of Würzburg, Würzburg
| | - Simon Stritt
- Institute of Experimental Biomedicine I, University Hospital, University of Würzburg, Würzburg.,Rudolf Virchow Center, University of Würzburg, Würzburg
| | - Sarah Beck
- Institute of Experimental Biomedicine I, University Hospital, University of Würzburg, Würzburg.,Rudolf Virchow Center, University of Würzburg, Würzburg
| | - Bing Peng
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Lipidomics, Dortmund
| | - Irina Pleines
- Institute of Experimental Biomedicine I, University Hospital, University of Würzburg, Würzburg.,Rudolf Virchow Center, University of Würzburg, Würzburg
| | | | - Attila Braun
- Institute of Experimental Biomedicine I, University Hospital, University of Würzburg, Würzburg.,Rudolf Virchow Center, University of Würzburg, Würzburg
| | - Oliver Otto
- Center for Innovation Competence - Humoral Immune Reactions in Cardiovascular Diseases, Biomechanics, University of Greifswald, Greifswald, Germany
| | - Robert Ahrends
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Lipidomics, Dortmund
| | - Albert Sickmann
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Lipidomics, Dortmund
| | - Markus Bender
- Institute of Experimental Biomedicine I, University Hospital, University of Würzburg, Würzburg.,Rudolf Virchow Center, University of Würzburg, Würzburg
| | - Bernhard Nieswandt
- Institute of Experimental Biomedicine I, University Hospital, University of Würzburg, Würzburg .,Rudolf Virchow Center, University of Würzburg, Würzburg
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5
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Further studies about Coactosin-like protein-1 affecting the migration of mouse neocortical neurons. J Mol Histol 2018; 49:519-530. [PMID: 30128637 DOI: 10.1007/s10735-018-9790-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Accepted: 07/27/2018] [Indexed: 12/18/2022]
Abstract
During the development of mammalian cortex, late neurons generated by neuronal progenitors bypass earlier-born neurons and migrate to reach upper layers of cortical plate in an inner-to-outer fashion. Filamentous-actin (F-actin) can regulate neuronal migration, whereas Coactosin-like protein 1 (Cotl1) modulates F-actin. Lys 75 and Arg 73 of Cotl1 play an important role in binding F-actin; when they are mutated to Glu, Cotl1 cannot bind F-actin, called as a non-actin-binding mutant (ABM). The Lys 131 site of Cotl1, the 5-Lipoxygenase (5LO) binding site, is spatially close to Lys 75, leading to impact the binding of Cotl1 to F-actin. When Lys 131 is mutated to Ala (K131A), Cotl1 cannot bind to 5LO. We have demonstrated that overexpression of Cotl1 inhibited neuronal migration and increased the length of neuronal leading processes. To further explore cellular and molecular mechanisms of Cotl1's effect on neuronal migration, we constructed two mutant vectors-Cotl1-ABM and Cotl1-K131A and studied using in utero electroporation and primary neuronal culture technique. Results indicated that in the Cotl1-ABM group, the neuronal migration and length of the leading process both recovered as control neurons at the postnatal day 1 (P1), while in the Cotl1-K131A group, numerous neurons remained in deeper layers of cortical plate or intermediate zone. However, at P7, most Cotl1-K131A transfected neurons reached their destination. Moreover, we found that overexpression of Cotl1 inhibited the proliferation and mitotic activity of NPs. Therefore, These results demonstrated that Cotl1 played an important role in mouse neocortical development.
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6
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Du J, Wang X, Dong CH, Yang JM, Yao XJ. Computational Study of the Binding Mechanism of Actin-Depolymerizing Factor 1 with Actin in Arabidopsis thaliana. PLoS One 2016; 11:e0159053. [PMID: 27414648 PMCID: PMC4944973 DOI: 10.1371/journal.pone.0159053] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 06/27/2016] [Indexed: 12/15/2022] Open
Abstract
Actin is a highly conserved protein. It plays important roles in cellular function and exists either in the monomeric (G-actin) or polymeric form (F-actin). Members of the actin-depolymerizing factor (ADF)/cofilin protein family bind to both G-actin and F-actin and play vital roles in actin dynamics by manipulating the rates of filament polymerization and depolymerization. It has been reported that the S6D and R98A/K100A mutants of actin-depolymerizing factor 1 (ADF1) in Arabidopsis thaliana decreased the binding affinity of ADF for the actin monomer. To investigate the binding mechanism and dynamic behavior of the ADF1–actin complex, we constructed a homology model of the AtADF1–actin complex based on the crystal structure of AtADF1 and the twinfilin C-terminal ADF-H domain in a complex with a mouse actin monomer. The model was then refined for subsequent molecular dynamics simulations. Increased binding energy of the mutated system was observed using the Molecular Mechanics Generalized Born Surface Area and Poisson–Boltzmann Surface Area (MM-GB/PBSA) methods. To determine the residues that make decisive contributions to the ADF1 actin-binding affinity, per-residue decomposition and computational alanine scanning analyses were performed, which provided more detailed information on the binding mechanism. Root-mean-square fluctuation and principal component analyses confirmed that the S6D and R98A/K100A mutants induced an increased conformational flexibility. The comprehensive molecular insight gained from this study is of great importance for understanding the binding mechanism of ADF1 and G-actin.
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Affiliation(s)
- Juan Du
- Key Laboratory of Plant Biotechnology of Shandong Province, College of Life Science, Qingdao Agricultural University, Qingdao, China
- * E-mail:
| | - Xue Wang
- Key Laboratory of Plant Biotechnology of Shandong Province, College of Life Science, Qingdao Agricultural University, Qingdao, China
| | - Chun-Hai Dong
- Key Laboratory of Plant Biotechnology of Shandong Province, College of Life Science, Qingdao Agricultural University, Qingdao, China
| | - Jian Ming Yang
- Key Laboratory of Plant Biotechnology of Shandong Province, College of Life Science, Qingdao Agricultural University, Qingdao, China
| | - Xiao Jun Yao
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, China
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7
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Koushik AB, Welter BH, Rock ML, Temesvari LA. A genomewide overexpression screen identifies genes involved in the phosphatidylinositol 3-kinase pathway in the human protozoan parasite Entamoeba histolytica. EUKARYOTIC CELL 2014; 13:401-11. [PMID: 24442890 PMCID: PMC3957588 DOI: 10.1128/ec.00329-13] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 01/12/2014] [Indexed: 11/20/2022]
Abstract
Entamoeba histolytica is a protozoan parasite that causes amoebic dysentery and liver abscess. E. histolytica relies on motility, phagocytosis, host cell adhesion, and proteolysis of extracellular matrix for virulence. In eukaryotic cells, these processes are mediated in part by phosphatidylinositol 3-kinase (PI3K) signaling. Thus, PI3K may be critical for virulence. We utilized a functional genomics approach to identify genes whose products may operate in the PI3K pathway in E. histolytica. We treated a population of trophozoites that were overexpressing genes from a cDNA library with a near-lethal dose of the PI3K inhibitor wortmannin. This screen was based on the rationale that survivors would be overexpressing gene products that directly or indirectly function in the PI3K pathway. We sequenced the overexpressed genes in survivors and identified a cDNA encoding a Rap GTPase, a protein previously shown to participate in the PI3K pathway. This supports the validity of our approach. Genes encoding a coactosin-like protein, EhCoactosin, and a serine-rich E. histolytica protein (SREHP) were also identified. Cells overexpressing EhCoactosin or SREHP were also less sensitive to a second PI3K inhibitor, LY294002. This corroborates the link between these proteins and PI3K. Finally, a mutant cell line with an increased level of phosphatidylinositol (3,4,5)-triphosphate, the product of PI3K activity, exhibited increased expression of SREHP and EhCoactosin. This further supports the functional connection between these proteins and PI3K in E. histolytica. To our knowledge, this is the first forward-genetics screen adapted to reveal genes participating in a signal transduction pathway in this pathogen.
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Affiliation(s)
- Amrita B. Koushik
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, USA
- Eukaryotic Pathogens Innovation Center (EPIC), Clemson University, Clemson, South Carolina, USA
| | - Brenda H. Welter
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
- Eukaryotic Pathogens Innovation Center (EPIC), Clemson University, Clemson, South Carolina, USA
| | - Michelle L. Rock
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
- Eukaryotic Pathogens Innovation Center (EPIC), Clemson University, Clemson, South Carolina, USA
| | - Lesly A. Temesvari
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
- Eukaryotic Pathogens Innovation Center (EPIC), Clemson University, Clemson, South Carolina, USA
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The other side of the coin: functional and structural versatility of ADF/cofilins. Eur J Cell Biol 2014; 93:238-51. [PMID: 24836399 DOI: 10.1016/j.ejcb.2013.12.001] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Revised: 11/29/2013] [Accepted: 12/03/2013] [Indexed: 01/20/2023] Open
Abstract
Several cellular processes rely on the fine tuning of actin cytoskeleton. A central component in the regulation of this cellular machinery is the ADF-H domain proteins. Despite sharing the same domain, ADF-H domain proteins produce a diverse functional landscape in the regulation of the actin cytoskeleton. Recent findings emphasize that the functional and structural features of these proteins can differ not only between ADF-H families but even within the same family. The structural and evolutional background of this functional diversity is poorly understood. This review focuses on the specific functional characteristics of ADF-H domain proteins and how these features can be linked to structural differences in the ADF-H domain and also to different conformational transitions in actin. In the light of recent discoveries we pay special attention to the ADF/cofilin proteins to find tendencies along which the functional and structural diversification is governed through the evolution.
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9
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Kim J, Shapiro MJ, Bamidele AO, Gurel P, Thapa P, Higgs HN, Hedin KE, Shapiro VS, Billadeau DD. Coactosin-like 1 antagonizes cofilin to promote lamellipodial protrusion at the immune synapse. PLoS One 2014; 9:e85090. [PMID: 24454796 PMCID: PMC3890291 DOI: 10.1371/journal.pone.0085090] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 11/22/2013] [Indexed: 11/19/2022] Open
Abstract
Actin depolymerizing factor-homology (ADF-H) family proteins regulate actin filament dynamics at multiple cellular locations. Herein, we have investigated the function of the ADF-H family member coactosin-like 1 (COTL1) in the regulation of actin dynamics at the T cell immune synapse (IS). We initially identified COTL1 in a genetic screen to identify novel regulators of T cell activation, and subsequently found that it associates with F-actin and localizes at the IS in response to TCR+CD28 stimulation. Live cell microscopy showed that depletion of COTL1 protein impaired T cell spreading in response to TCR ligation and abrogated lamellipodial protrusion at the T cell – B cell contact site, producing only a band of F-actin. Significantly, re-expression of wild type COTL1, but not a mutant deficient in F-actin binding could rescue these defects. In addition, COTL1 depletion reduced T cell migration. In vitro studies showed that COTL1 and cofilin compete with each other for binding to F-actin, and COTL1 protects F-actin from cofilin-mediated depolymerization. While depletion of cofilin enhanced F-actin assembly and lamellipodial protrusion at the IS, concurrent depletion of both COTL1 and cofilin restored lamellipodia formation. Taken together, our results suggest that COTL1 regulates lamellipodia dynamics in part by protecting F-actin from cofilin-mediated disassembly.
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Affiliation(s)
- Joanna Kim
- Department of Biochemistry and Molecular Biology, College of Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Michael J. Shapiro
- Department of Immunology, College of Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Adebowale O. Bamidele
- Department of Molecular Pharmacology and Experimental Therapeutics, College of Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Pinar Gurel
- Department of Biochemistry, Geisel School of Medicine at Dartmouth, Dartmouth College, Hanover, New Hampshire, United States of America
| | - Puspa Thapa
- Department of Immunology, College of Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Henry N. Higgs
- Department of Biochemistry, Geisel School of Medicine at Dartmouth, Dartmouth College, Hanover, New Hampshire, United States of America
| | - Karen E. Hedin
- Department of Immunology, College of Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Virginia S. Shapiro
- Department of Immunology, College of Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
- * E-mail: (DDB); (VSS)
| | - Daniel D. Billadeau
- Department of Biochemistry and Molecular Biology, College of Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
- Department of Immunology, College of Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
- * E-mail: (DDB); (VSS)
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Ota M, Koike R, Amemiya T, Tenno T, Romero PR, Hiroaki H, Dunker AK, Fukuchi S. An assignment of intrinsically disordered regions of proteins based on NMR structures. J Struct Biol 2012; 181:29-36. [PMID: 23142703 DOI: 10.1016/j.jsb.2012.10.017] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Revised: 10/26/2012] [Accepted: 10/30/2012] [Indexed: 11/24/2022]
Abstract
Intrinsically disordered proteins (IDPs) do not adopt stable three-dimensional structures in physiological conditions, yet these proteins play crucial roles in biological phenomena. In most cases, intrinsic disorder manifests itself in segments or domains of an IDP, called intrinsically disordered regions (IDRs), but fully disordered IDPs also exist. Although IDRs can be detected as missing residues in protein structures determined by X-ray crystallography, no protocol has been developed to identify IDRs from structures obtained by Nuclear Magnetic Resonance (NMR). Here, we propose a computational method to assign IDRs based on NMR structures. We compared missing residues of X-ray structures with residue-wise deviations of NMR structures for identical proteins, and derived a threshold deviation that gives the best correlation of ordered and disordered regions of both structures. The obtained threshold of 3.2Å was applied to proteins whose structures were only determined by NMR, and the resulting IDRs were analyzed and compared to those of X-ray structures with no NMR counterpart in terms of sequence length, IDR fraction, protein function, cellular location, and amino acid composition, all of which suggest distinct characteristics. The structural knowledge of IDPs is still inadequate compared with that of structured proteins. Our method can collect and utilize IDRs from structures determined by NMR, potentially enhancing the understanding of IDPs.
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Affiliation(s)
- Motonori Ota
- Graduate School of Information Sciences, Nagoya University, Nagoya 464-8601, Japan.
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11
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Poukkula M, Kremneva E, Serlachius M, Lappalainen P. Actin-depolymerizing factor homology domain: a conserved fold performing diverse roles in cytoskeletal dynamics. Cytoskeleton (Hoboken) 2011; 68:471-90. [PMID: 21850706 DOI: 10.1002/cm.20530] [Citation(s) in RCA: 110] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2011] [Revised: 06/29/2011] [Accepted: 08/05/2011] [Indexed: 11/09/2022]
Abstract
Actin filaments form contractile and protrusive structures that play central roles in many processes such as cell migration, morphogenesis, endocytosis, and cytokinesis. During these processes, the dynamics of the actin filaments are precisely regulated by a large array of actin-binding proteins. The actin-depolymerizing factor homology (ADF-H) domain is a structurally conserved protein motif, which promotes cytoskeletal dynamics by interacting with monomeric and/or filamentous actin, and with the Arp2/3 complex. Despite their structural homology, the five classes of ADF-H domain proteins display distinct biochemical activities and cellular roles, only parts of which are currently understood. ADF/cofilin promotes disassembly of aged actin filaments, whereas twinfilin inhibits actin filament assembly via sequestering actin monomers and interacting with filament barbed ends. GMF does not interact with actin, but instead binds Arp2/3 complex and promotes dissociation of Arp2/3-mediated filament branches. Abp1 and drebrin are multidomain proteins that interact with actin filaments and regulate the activities of other proteins during various actin-dependent processes. The exact function of coactosin is currently incompletely understood. In this review article, we discuss the biochemical functions, cellular roles, and regulation of the five groups of ADF-H domain proteins.
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Affiliation(s)
- Minna Poukkula
- Program in Cell and Molecular Biology, Institute of Biotechnology, University of Helsinki, Finland
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12
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Goroncy AK, Koshiba S, Tochio N, Tomizawa T, Sato M, Inoue M, Watanabe S, Hayashizaki Y, Tanaka A, Kigawa T, Yokoyama S. NMR solution structures of actin depolymerizing factor homology domains. Protein Sci 2010; 18:2384-92. [PMID: 19768801 DOI: 10.1002/pro.248] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Actin is one of the most conserved proteins in nature. Its assembly and disassembly are regulated by many proteins, including the family of actin-depolymerizing factor homology (ADF-H) domains. ADF-H domains can be divided into five classes: ADF/cofilin, glia maturation factor (GMF), coactosin, twinfilin, and Abp1/drebrin. The best-characterized class is ADF/cofilin. The other four classes have drawn much less attention and very few structures have been reported. This study presents the solution NMR structure of the ADF-H domain of human HIP-55-drebrin-like protein, the first published structure of a drebrin-like domain (mammalian), and the first published structure of GMF beta (mouse). We also determined the structures of mouse GMF gamma, the mouse coactosin-like domain and the C-terminal ADF-H domain of mouse twinfilin 1. Although the overall fold of the five domains is similar, some significant differences provide valuable insights into filamentous actin (F-actin) and globular actin (G-actin) binding, including the identification of binding residues on the long central helix. This long helix is stabilized by three or four residues. Notably, the F-actin binding sites of mouse GMF beta and GMF gamma contain two additional beta-strands not seen in other ADF-H structures. The G-actin binding site of the ADF-H domain of human HIP-55-drebrin-like protein is absent and distorted in mouse GMF beta and GMF gamma.
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Affiliation(s)
- Alexander K Goroncy
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, Japan
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13
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Paavilainen VO, Oksanen E, Goldman A, Lappalainen P. Structure of the actin-depolymerizing factor homology domain in complex with actin. ACTA ACUST UNITED AC 2008; 182:51-9. [PMID: 18625842 PMCID: PMC2447895 DOI: 10.1083/jcb.200803100] [Citation(s) in RCA: 131] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Actin dynamics provide the driving force for many cellular processes including motility and endocytosis. Among the central cytoskeletal regulators are actin-depolymerizing factor (ADF)/cofilin, which depolymerizes actin filaments, and twinfilin, which sequesters actin monomers and caps filament barbed ends. Both interact with actin through an ADF homology (ADF-H) domain, which is also found in several other actin-binding proteins. However, in the absence of an atomic structure for the ADF-H domain in complex with actin, the mechanism by which these proteins interact with actin has remained unknown. Here, we present the crystal structure of twinfilin's C-terminal ADF-H domain in complex with an actin monomer. This domain binds between actin subdomains 1 and 3 through an interface that is conserved among ADF-H domain proteins. Based on this structure, we suggest a mechanism by which ADF/cofilin and twinfilin inhibit nucleotide exchange of actin monomers and present a model for how ADF/cofilin induces filament depolymerization by weakening intrafilament interactions.
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Affiliation(s)
- Ville O Paavilainen
- Program in Cellular Biotechnology, Institute of Biotechnology, University of Helsinki, Helsinki FIN-00014, Finland
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14
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Paavilainen VO, Hellman M, Helfer E, Bovellan M, Annila A, Carlier MF, Permi P, Lappalainen P. Structural basis and evolutionary origin of actin filament capping by twinfilin. Proc Natl Acad Sci U S A 2007; 104:3113-8. [PMID: 17360616 PMCID: PMC1805582 DOI: 10.1073/pnas.0608725104] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Dynamic reorganization of the actin cytoskeleton is essential for motile and morphological processes in all eukaryotic cells. One highly conserved protein that regulates actin dynamics is twinfilin, which both sequesters actin monomers and caps actin filament barbed ends. Twinfilin is composed of two ADF/cofilin-like domains, Twf-N and Twf-C. Here, we reveal by systematic domain-swapping/inactivation analysis that the two functional ADF-H domains of twinfilin are required for barbed-end capping and that Twf-C plays a critical role in this process. However, these domains are not functionally equivalent. NMR-structure and mutagenesis analyses, together with biochemical and motility assays showed that Twf-C, in addition to its binding to G-actin, interacts with the sides of actin filaments like ADF/cofilins, whereas Twf-N binds only G-actin. Our results indicate that during filament barbed-end capping, Twf-N interacts with the terminal actin subunit, whereas Twf-C binds between two adjacent subunits at the side of the filament. Thus, the domain requirement for actin filament capping by twinfilin is remarkably similar to that of gelsolin family proteins, suggesting the existence of a general barbed-end capping mechanism. Furthermore, we demonstrate that a synthetic protein consisting of duplicated ADF/cofilin domains caps actin filament barbed ends, providing evidence that the barbed-end capping activity of twinfilin arose through a duplication of an ancient ADF/cofilin-like domain.
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Affiliation(s)
- Ville O. Paavilainen
- Programs in *Cellular Biotechnology and
- Cytoskeleton Dynamics and Motility, Laboratoire d'Enzymologie et Biochimie Structurale, Centre National de la Recherche Scientifique, 91118 Gif-sur-Yvette, France
| | - Maarit Hellman
- Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, FI-00014, Finland; and
| | - Emmanuèle Helfer
- Cytoskeleton Dynamics and Motility, Laboratoire d'Enzymologie et Biochimie Structurale, Centre National de la Recherche Scientifique, 91118 Gif-sur-Yvette, France
| | | | - Arto Annila
- Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, FI-00014, Finland; and
| | - Marie-France Carlier
- Cytoskeleton Dynamics and Motility, Laboratoire d'Enzymologie et Biochimie Structurale, Centre National de la Recherche Scientifique, 91118 Gif-sur-Yvette, France
| | - Perttu Permi
- Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, FI-00014, Finland; and
- To whom correspondence may be addressed at: Institute of Biotechnology, P.O. Box 56, University of Helsinki, FI-00014 Helsinki, Finland. E-mail: or
| | - Pekka Lappalainen
- Programs in *Cellular Biotechnology and
- To whom correspondence may be addressed at: Institute of Biotechnology, P.O. Box 56, University of Helsinki, FI-00014 Helsinki, Finland. E-mail: or
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15
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Mattinen ML, Hellman M, Permi P, Autio K, Kalkkinen N, Buchert J. Effect of protein structure on laccase-catalyzed protein oligomerization. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2006; 54:8883-90. [PMID: 17090138 DOI: 10.1021/jf062397h] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Laccase-catalyzed oligomerization of proteins was studied using Trametes hirsuta laccase (ThL) and coactosin as a model system. The reaction mechanism was elucidated using free amino acids and the tripeptide Gly-Leu-Tyr as substrates. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and high-performance liquid chromatography (HPLC) as well as oxygen consumption measurements and SDS-PAGE were used to study the reactions. Of the 15 selected amino acids, ThL was found to oxidize tryptophan (Trp), tyrosine (Tyr), and cysteine (Cys), of which the reactions with Tyr and Cys have been described earlier. ThL was able to link four full-length coactosins, whereas coactosin that was truncated from its C-terminus remained unpolymerized. Of the four tyrosine residues present in coactosin, only the tyrosine in the C-terminus was found to be reactive. Polymerization between tyrosine side-chains was unambiguously shown using different oligomers of Gly-Leu-Tyr as parent ions in MALDI-TOF/TOF MS fragment ion analyses.
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16
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Gorbatyuk VY, Nosworthy NJ, Robson SA, Bains NPS, Maciejewski MW, Dos Remedios CG, King GF. Mapping the Phosphoinositide-Binding Site on Chick Cofilin Explains How PIP2 Regulates the Cofilin-Actin Interaction. Mol Cell 2006; 24:511-22. [PMID: 17114056 DOI: 10.1016/j.molcel.2006.10.007] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2006] [Revised: 08/21/2006] [Accepted: 10/04/2006] [Indexed: 11/25/2022]
Abstract
Cofilin plays a key role in the choreography of actin dynamics via its ability to sever actin filaments and increase the rate of monomer dissociation from pointed ends. The exact manner by which phosphoinositides bind to cofilin and inhibit its interaction with actin has proven difficult to ascertain. We determined the structure of chick cofilin and used NMR chemical shift mapping and structure-directed mutagenesis to unambiguously locate its recognition site for phosphoinositides (PIs). This structurally unique recognition site requires both the acyl chain and head group of the PI for a productive interaction, and it is not inhibited by phosphorylation of cofilin. We propose that the interaction of cofilin with membrane-bound PIs abrogates its binding to both actin and actin-interacting protein 1, and facilitates spatiotemporal regulation of cofilin activity.
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Affiliation(s)
- Vitaliy Y Gorbatyuk
- Department of Molecular, Microbial and Structural Biology, University of Connecticut Health Center, Farmington, Connecticut 06032, USA
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17
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Dai H, Huang W, Xu J, Yao B, Xiong S, Ding H, Tang Y, Liu H, Wu J, Shi Y. Binding model of human coactosin-like protein with filament actin revealed by mutagenesis. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2006; 1764:1688-700. [PMID: 17070122 DOI: 10.1016/j.bbapap.2006.06.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2006] [Revised: 06/12/2006] [Accepted: 06/13/2006] [Indexed: 11/25/2022]
Abstract
Human coactosin-like protein (CLP) is a small (MW approximately 17 kDa) evolutionarily conserved actin-binding protein. It can bind to actin filaments but not globular actin and belongs to the fourth class of ADF-H-domain-containing proteins. Human CLP can also bind to 5LO, which plays an important role in cellular leukotriene synthesis. Although the structure of hCLP has been determined by both NMR and X-ray experiments, how hCLP binds to the actin filament is still a controversial question. To obtain insights into the structure of the complex, we studied the three-dimensional structure and backbone dynamics of hCLP using multidimensional NMR spectroscopy. Guided by the solution structure of the protein, a series of site-directed mutants were generated and their F-actin-binding activities were measured by high-speed cosedimentation assays. Furthermore, the structure model of the hCLP-F-actin complex was proposed using computational docking with the docking results filtered by the mutation data. Several previously untested residues (including T66, L89, R91, K102, D116 and E119) in hCLP were found important for the F-actin-binding activity. The extended region of beta4-beta5 of hCLP (residue 66-75) was found very flexible and very important for F-actin binding. The C-terminal residues of hCLP were not involved in F-actin binding, which was different from UNC-60B. Based on our hCLP-F-actin-binding model, different affinities of the four classes of ADF-H domain containing proteins for F-actin were explained.
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Affiliation(s)
- Haiming Dai
- Hefei National Laboratory for Physical Sciences at Microscale, and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
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18
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Würtz P, Hellman M, Tossavainen H, Permi P. Towards unambiguous assignment of methyl-containing residues by double and triple sensitivity-enhanced HCCmHm-TOCSY experiments. JOURNAL OF BIOMOLECULAR NMR 2006; 36:13-26. [PMID: 16964533 DOI: 10.1007/s10858-006-9056-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2006] [Accepted: 07/14/2006] [Indexed: 05/11/2023]
Abstract
Chemical shift assignment of methyl-containing residues is essential in protein NMR spectroscopy, as these residues are abundant in protein interiors and provide the vast majority of long-range NOE connectivities for structure determination. These residues also constitute an integral part of hydrophobic cavities, the surroundings for many enzymatic reactions. Here we present a powerful strategy for the assignment of methyl-containing residues in a uniformly 13C/15N double labeled protein sample. The approach is based on novel four-dimensional HCCmHm-TOCSY experiments, two of them utilizing gradient selection and sensitivity enhancement in all three indirectly detected dimensions. Regardless of the number of dimensions, the proposed experiments can be executed using only one transient per FID, providing outstanding resolution and sensitivity. A complete assignment of the 51 methyl-containing residues in the 16 kDa Mus musculus coactosin was accomplished using a four-dimensional HCCmHm-TOCSY spectrum recorded in 16 hours.
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Affiliation(s)
- Peter Würtz
- Program in Structural Biology and Biophysics, Institute of Biotechnology/NMR Laboratory, University of Helsinki, FI-00014, Helsinki, Finland
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19
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Puttonen E, Tossavainen H, Permi P. Simultaneous determination of one- and two-bond scalar and residual dipolar couplings between 13C', 13Calpha and 15N spins in proteins. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2006; 44 Spec No:S168-76. [PMID: 16823899 DOI: 10.1002/mrc.1836] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Four simple and sensitive HNCO-based methods for measurement of 1J(C'Calpha), 1J(NCalpha) and 2J(NCalpha) coupling constants in protein main chains are presented. Three of these experiments enable the simultaneous measurement of 1J(C'Calpha), 1J(NCalpha) and 2J(NCalpha) couplings. Exploitation of the E.COSY principle provides excellent dispersion of cross peaks in the resulting 3D spectra. The couplings can be retrieved with good accuracy from peak-to-peak separations. Karplus parameterizations are provided for 1J(NCalpha) and 2J(NCalpha), obtained from a nearly complete set of couplings of human ubiquitin. In addition, feasibility of the proposed methodology for measuring several residual dipolar couplings (RDCs) simultaneously is assessed.
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Affiliation(s)
- Eetu Puttonen
- NMR Laboratory, Program in Structural Biology and Biophysics, Institute of Biotechnology, P.O. Box 65, FI-00014, University of Helsinki, Helsinki, Finland
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20
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Quintero-Monzon O, Rodal AA, Strokopytov B, Almo SC, Goode BL. Structural and functional dissection of the Abp1 ADFH actin-binding domain reveals versatile in vivo adapter functions. Mol Biol Cell 2005; 16:3128-39. [PMID: 15872087 PMCID: PMC1165398 DOI: 10.1091/mbc.e05-01-0059] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Abp1 is a multidomain protein that regulates the Arp2/3 complex and links proteins involved in endocytosis to the actin cytoskeleton. All of the proposed cellular functions of Abp1 involve actin filament binding, yet the actin binding site(s) on Abp1 have not been identified, nor has the importance of actin binding for Abp1 localization and function in vivo been tested. Here, we report the crystal structure of the Saccharomyces cerevisiae Abp1 actin-binding actin depolymerizing factor homology (ADFH) domain and dissect its activities by mutagenesis. Abp1-ADFH domain and ADF/cofilin structures are similar, and they use conserved surfaces to bind actin; however, there are also key differences that help explain their differential effects on actin dynamics. Using point mutations, we demonstrate that actin binding is required for localization of Abp1 in vivo, the lethality caused by Abp1 overexpression, and the ability of Abp1 to activate Arp2/3 complex. Furthermore, we genetically uncouple ABP1 functions that overlap with SAC6, SLA1, and SLA2, showing they require distinct combinations of activities and interactions. Together, our data provide the first structural and functional view of the Abp1-actin interaction and show that Abp1 has distinct cellular roles as an adapter, linking different sets of ligands for each function.
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Affiliation(s)
- Omar Quintero-Monzon
- Department of Biology and Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, MA 02454, USA.
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