1
|
Cao L, Huang S, Basant A, Mladenov M, Way M. CK-666 and CK-869 differentially inhibit Arp2/3 iso-complexes. EMBO Rep 2024; 25:3221-3239. [PMID: 39009834 PMCID: PMC11316031 DOI: 10.1038/s44319-024-00201-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 05/30/2024] [Accepted: 06/18/2024] [Indexed: 07/17/2024] Open
Abstract
The inhibitors, CK-666 and CK-869, are widely used to probe the function of Arp2/3 complex mediated actin nucleation in vitro and in cells. However, in mammals, the Arp2/3 complex consists of 8 iso-complexes, as three of its subunits (Arp3, ArpC1, ArpC5) are encoded by two different genes. Here, we used recombinant Arp2/3 with defined composition to assess the activity of CK-666 and CK-869 against iso-complexes. We demonstrate that both inhibitors prevent linear actin filament formation when ArpC1A- or ArpC1B-containing complexes are activated by SPIN90. In contrast, inhibition of actin branching depends on iso-complex composition. Both drugs prevent actin branch formation by complexes containing ArpC1A, but only CK-869 can inhibit ArpC1B-containing complexes. Consistent with this, in bone marrow-derived macrophages which express low levels of ArpC1A, CK-869 but not CK-666, impacted phagocytosis and cell migration. CK-869 also only inhibits Arp3- but not Arp3B-containing iso-complexes. Our findings have important implications for the interpretation of results using CK-666 and CK-869, given that the relative expression levels of ArpC1 and Arp3 isoforms in cells and tissues remains largely unknown.
Collapse
Affiliation(s)
- LuYan Cao
- The Francis Crick Institute, London, UK.
| | | | | | | | - Michael Way
- The Francis Crick Institute, London, UK.
- Department of Infectious Disease, Imperial College, London, UK.
| |
Collapse
|
2
|
Liu T, Cao L, Mladenov M, Jegou A, Way M, Moores CA. Cortactin stabilizes actin branches by bridging activated Arp2/3 to its nucleated actin filament. Nat Struct Mol Biol 2024; 31:801-809. [PMID: 38267598 PMCID: PMC11102864 DOI: 10.1038/s41594-023-01205-2] [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: 07/25/2023] [Accepted: 12/18/2023] [Indexed: 01/26/2024]
Abstract
Regulation of the assembly and turnover of branched actin filament networks nucleated by the Arp2/3 complex is essential during many cellular processes, including cell migration and membrane trafficking. Cortactin is important for actin branch stabilization, but the mechanism by which this occurs is unclear. Given this, we determined the structure of vertebrate cortactin-stabilized Arp2/3 actin branches using cryogenic electron microscopy. We find that cortactin interacts with the new daughter filament nucleated by the Arp2/3 complex at the branch site, rather than the initial mother actin filament. Cortactin preferentially binds activated Arp3. It also stabilizes the F-actin-like interface of activated Arp3 with the first actin subunit of the new filament, and its central repeats extend along successive daughter-filament subunits. The preference of cortactin for activated Arp3 explains its retention at the actin branch and accounts for its synergy with other nucleation-promoting factors in regulating branched actin network dynamics.
Collapse
Affiliation(s)
- Tianyang Liu
- Institute of Structural and Molecular Biology, Birkbeck College, London, UK
| | - Luyan Cao
- The Francis Crick Institute, London, UK
| | | | - Antoine Jegou
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, France
| | - Michael Way
- The Francis Crick Institute, London, UK.
- Department of Infectious Disease, Imperial College, London, UK.
| | - Carolyn A Moores
- Institute of Structural and Molecular Biology, Birkbeck College, London, UK.
| |
Collapse
|
3
|
McGuirk ER, Koundinya N, Nagarajan P, Padrick SB, Goode BL. Direct observation of cortactin protecting Arp2/3-actin filament branch junctions from GMF-mediated destabilization. Eur J Cell Biol 2024; 103:151378. [PMID: 38071835 PMCID: PMC10843626 DOI: 10.1016/j.ejcb.2023.151378] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 12/02/2023] [Accepted: 12/02/2023] [Indexed: 01/28/2024] Open
Abstract
How cells tightly control the formation and turnover of branched actin filament arrays to drive cell motility, endocytosis, and other cellular processes is still not well understood. Here, we investigated the mechanistic relationship between two binding partners of the Arp2/3 complex, glia maturation factor (GMF) and cortactin. Individually, GMF and cortactin have opposite effects on the stability of actin filament branches, but it is unknown how they work in concert with each other to govern branch turnover. Using TIRF microscopy, we observe that GMF's branch destabilizing activities are potently blocked by cortactin (IC50 = 1.3 nM) and that this inhibition requires direct interactions of cortactin with Arp2/3 complex. The simplest model that would explain these results is competition for binding Arp2/3 complex. However, we find that cortactin and GMF do not compete for free Arp2/3 complex in solution. Further, we use single molecule analysis to show that cortactin's on-rate (3 ×107 s-1 M-1) and off-rate (0.03 s-1) at branch junctions are minimally affected by excess GMF. Together, these results show that cortactin binds with high affinity to branch junctions, where it blocks the destabilizing effects of GMF, possibly by a mechanism that is allosteric in nature. In addition, the affinities we measure for cortactin at actin filament branch junctions (Kd = 0.9 nM) and filament sides (Kd = 206 nM) are approximately 20-fold stronger than previously reported. These observations contribute to an emerging view of molecular complexity in how Arp2/3 complex is regulated through the integration of multiple inputs.
Collapse
Affiliation(s)
- Emma R McGuirk
- Department of Biology, Rosenstiel Basic Medical Science Research Center, Brandeis University, 415 South Street, Waltham, MA 02454, USA
| | - Neha Koundinya
- Department of Biology, Rosenstiel Basic Medical Science Research Center, Brandeis University, 415 South Street, Waltham, MA 02454, USA
| | - Priyashree Nagarajan
- Department of Biochemistry and Molecular Biology, Drexel University, Philadelphia, PA 19104, USA
| | - Shae B Padrick
- Department of Biochemistry and Molecular Biology, Drexel University, Philadelphia, PA 19104, USA
| | - Bruce L Goode
- Department of Biology, Rosenstiel Basic Medical Science Research Center, Brandeis University, 415 South Street, Waltham, MA 02454, USA.
| |
Collapse
|
4
|
Ghasemi F, Cao L, Mladenov M, Guichard B, Way M, Jégou A, Romet-Lemonne G. Regeneration of actin filament branches from the same Arp2/3 complex. SCIENCE ADVANCES 2024; 10:eadj7681. [PMID: 38277459 PMCID: PMC10816697 DOI: 10.1126/sciadv.adj7681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 12/27/2023] [Indexed: 01/28/2024]
Abstract
Branched actin filaments are found in many key cellular structures. Branches are nucleated by the Arp2/3 complex activated by nucleation-promoting factor (NPF) proteins and bound to the side of preexisting "mother" filaments. Over time, branches dissociate from their mother filament, leading to network reorganization and turnover, but this mechanism is less understood. Here, using microfluidics and purified proteins, we examined the dissociation of individual branches under controlled biochemical and mechanical conditions. We observe that the Arp2/3 complex remains bound to the mother filament after most debranching events, even when accelerated by force. Strikingly, this surviving Arp2/3 complex readily nucleates a new actin filament branch, without being activated anew by an NPF: It simply needs to exchange its nucleotide and bind an actin monomer. The protein glia maturation factor (GMF), which accelerates debranching, prevents branch renucleation. Our results suggest that actin filament renucleation can provide a self-repair mechanism, helping branched networks to sustain mechanical stress in cells over extended periods of time.
Collapse
Affiliation(s)
- Foad Ghasemi
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
| | - LuYan Cao
- The Francis Crick Institute, London, UK
| | | | - Bérengère Guichard
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
| | - Michael Way
- The Francis Crick Institute, London, UK
- Department of Infectious Disease, Imperial College, London, UK
| | - Antoine Jégou
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
| | | |
Collapse
|
5
|
Colin A, Orhant-Prioux M, Guérin C, Savinov M, Cao W, Vianay B, Scarfone I, Roux A, De La Cruz EM, Mogilner A, Théry M, Blanchoin L. Friction patterns guide actin network contraction. Proc Natl Acad Sci U S A 2023; 120:e2300416120. [PMID: 37725653 PMCID: PMC10523593 DOI: 10.1073/pnas.2300416120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 08/09/2023] [Indexed: 09/21/2023] Open
Abstract
The shape of cells is the outcome of the balance of inner forces produced by the actomyosin network and the resistive forces produced by cell adhesion to their environment. The specific contributions of contractile, anchoring and friction forces to network deformation rate and orientation are difficult to disentangle in living cells where they influence each other. Here, we reconstituted contractile actomyosin networks in vitro to study specifically the role of the friction forces between the network and its anchoring substrate. To modulate the magnitude and spatial distribution of friction forces, we used glass or lipids surface micropatterning to control the initial shape of the network. We adapted the concentration of Nucleating Promoting Factor on each surface to induce the assembly of actin networks of similar densities and compare the deformation of the network toward the centroid of the pattern shape upon myosin-induced contraction. We found that actin network deformation was faster and more coordinated on lipid bilayers than on glass, showing the resistance of friction to network contraction. To further study the role of the spatial distribution of these friction forces, we designed heterogeneous micropatterns made of glass and lipids. The deformation upon contraction was no longer symmetric but biased toward the region of higher friction. Furthermore, we showed that the pattern of friction could robustly drive network contraction and dominate the contribution of asymmetric distributions of myosins. Therefore, we demonstrate that during contraction, both the active and resistive forces are essential to direct the actin network deformation.
Collapse
Affiliation(s)
- Alexandra Colin
- Université Grenoble-Alpes, CEA, CNRS, UMR5168, Interdisciplinary Research Institute of Grenoble, CytoMorpho Lab, Grenoble38054, France
| | - Magali Orhant-Prioux
- Université Grenoble-Alpes, CEA, CNRS, UMR5168, Interdisciplinary Research Institute of Grenoble, CytoMorpho Lab, Grenoble38054, France
| | - Christophe Guérin
- Université Grenoble-Alpes, CEA, CNRS, UMR5168, Interdisciplinary Research Institute of Grenoble, CytoMorpho Lab, Grenoble38054, France
| | - Mariya Savinov
- Courant Institute of Mathematical Sciences, New York University, New York, NY10012
| | - Wenxiang Cao
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT06520-8114
| | - Benoit Vianay
- University of Paris, INSERM, Commissariat à l'énergie atomique et aux énergies alternatives, UMRS1160, Institut de Recherche Saint Louis, CytoMorpho Lab, Hôpital Saint Louis, Paris75010, France
| | - Ilaria Scarfone
- Université Grenoble-Alpes, CEA, CNRS, UMR5168, Interdisciplinary Research Institute of Grenoble, CytoMorpho Lab, Grenoble38054, France
| | - Aurélien Roux
- Department of Biochemistry, University of Geneva, CH-1211Geneva, Switzerland
| | - Enrique M. De La Cruz
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT06520-8114
| | - Alex Mogilner
- Courant Institute of Mathematical Sciences, New York University, New York, NY10012
| | - Manuel Théry
- Université Grenoble-Alpes, CEA, CNRS, UMR5168, Interdisciplinary Research Institute of Grenoble, CytoMorpho Lab, Grenoble38054, France
- University of Paris, INSERM, Commissariat à l'énergie atomique et aux énergies alternatives, UMRS1160, Institut de Recherche Saint Louis, CytoMorpho Lab, Hôpital Saint Louis, Paris75010, France
| | - Laurent Blanchoin
- Université Grenoble-Alpes, CEA, CNRS, UMR5168, Interdisciplinary Research Institute of Grenoble, CytoMorpho Lab, Grenoble38054, France
- University of Paris, INSERM, Commissariat à l'énergie atomique et aux énergies alternatives, UMRS1160, Institut de Recherche Saint Louis, CytoMorpho Lab, Hôpital Saint Louis, Paris75010, France
| |
Collapse
|
6
|
Hosseini K, Frenzel A, Fischer-Friedrich E. EMT induces characteristic changes of Rho GTPases and downstream effectors with a mitosis-specific twist. Phys Biol 2023; 20:066001. [PMID: 37652025 DOI: 10.1088/1478-3975/acf5bd] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 08/31/2023] [Indexed: 09/02/2023]
Abstract
Epithelial-mesenchymal transition (EMT) is a key cellular transformation for many physiological and pathological processes ranging from cancer over wound healing to embryogenesis. Changes in cell migration, cell morphology and cellular contractility were identified as hallmarks of EMT. These cellular properties are known to be tightly regulated by the actin cytoskeleton. EMT-induced changes of actin-cytoskeletal regulation were demonstrated by previous reports of changes of actin cortex mechanics in conjunction with modifications of cortex-associated f-actin and myosin. However, at the current state, the changes of upstream actomyosin signaling that lead to corresponding mechanical and compositional changes of the cortex are not well understood. In this work, we show in breast epithelial cancer cells MCF-7 that EMT results in characteristic changes of the cortical association of Rho-GTPases Rac1, RhoA and RhoC and downstream actin regulators cofilin, mDia1 and Arp2/3. In the light of our findings, we propose that EMT-induced changes in cortical mechanics rely on two hitherto unappreciated signaling paths-i) an interaction between Rac1 and RhoC and ii) an inhibitory effect of Arp2/3 activity on cortical association of myosin II.
Collapse
Affiliation(s)
- Kamran Hosseini
- Cluster of Excellence Physics of Life, Technische Universität Dresden, Dresden, Germany
- Biotechnology Center, Technische Universität Dresden, Dresden, Germany
| | - Annika Frenzel
- Cluster of Excellence Physics of Life, Technische Universität Dresden, Dresden, Germany
- Biotechnology Center, Technische Universität Dresden, Dresden, Germany
| | - Elisabeth Fischer-Friedrich
- Cluster of Excellence Physics of Life, Technische Universität Dresden, Dresden, Germany
- Biotechnology Center, Technische Universität Dresden, Dresden, Germany
- Faculty of Physics, Technische Universität Dresden, Dresden, Germany
| |
Collapse
|
7
|
Singh Y, Hocky GM, Nolen BJ. Molecular dynamics simulations support a multistep pathway for activation of branched actin filament nucleation by Arp2/3 complex. J Biol Chem 2023; 299:105169. [PMID: 37595874 PMCID: PMC10514467 DOI: 10.1016/j.jbc.2023.105169] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 08/10/2023] [Accepted: 08/12/2023] [Indexed: 08/20/2023] Open
Abstract
Actin-related protein 2/3 complex (Arp2/3 complex) catalyzes the nucleation of branched actin filaments that push against membranes in processes like cellular motility and endocytosis. During activation by WASP proteins, the complex must bind WASP and engage the side of a pre-existing (mother) filament before a branched filament is nucleated. Recent high-resolution structures of activated Arp2/3 complex revealed two major sets of activating conformational changes. How these activating conformational changes are triggered by interactions of Arp2/3 complex with actin filaments and WASP remains unclear. Here we use a recent high-resolution structure of Arp2/3 complex at a branch junction to design all-atom molecular dynamics simulations that elucidate the pathway between the active and inactive states. We ran a total of ∼4.6 microseconds of both unbiased and steered all-atom molecular dynamics simulations starting from three different binding states, including Arp2/3 complex within a branch junction, bound only to a mother filament, and alone in solution. These simulations indicate that the contacts with the mother filament are mostly insensitive to the massive rigid body motion that moves Arp2 and Arp3 into a short pitch helical (filament-like) arrangement, suggesting actin filaments alone do not stimulate the short pitch conformational change. In contrast, contacts with the mother filament stabilize subunit flattening in Arp3, an intrasubunit change that converts Arp3 from a conformation that mimics an actin monomer to one that mimics a filamentous actin subunit. Our results support a multistep activation pathway that has important implications for understanding how WASP-mediated activation allows Arp2/3 complex to assemble force-producing actin networks.
Collapse
Affiliation(s)
| | - Glen M Hocky
- Department of Chemistry, New York University; Simons Center for Computational Physical Chemistry, New York University.
| | - Brad J Nolen
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon.
| |
Collapse
|
8
|
van Eeuwen T, Boczkowska M, Rebowski G, Carman PJ, Fregoso FE, Dominguez R. Transition State of Arp2/3 Complex Activation by Actin-Bound Dimeric Nucleation-Promoting Factor. Proc Natl Acad Sci U S A 2023; 120:e2306165120. [PMID: 37549294 PMCID: PMC10434305 DOI: 10.1073/pnas.2306165120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 07/03/2023] [Indexed: 08/09/2023] Open
Abstract
Arp2/3 complex generates branched actin networks that drive fundamental processes such as cell motility and cytokinesis. The complex comprises seven proteins, including actin-related proteins (Arps) 2 and 3 and five scaffolding proteins (ArpC1-ArpC5) that mediate interactions with a pre-existing (mother) actin filament at the branch junction. Arp2/3 complex exists in two main conformations, inactive with the Arps interacting end-to-end and active with the Arps interacting side-by-side like subunits of the short-pitch helix of the actin filament. Several cofactors drive the transition toward the active state, including ATP binding to the Arps, WASP-family nucleation-promoting factors (NPFs), actin monomers, and binding of Arp2/3 complex to the mother filament. The precise contribution of each cofactor to activation is poorly understood. We report the 3.32-Å resolution cryo-electron microscopy structure of a transition state of Arp2/3 complex activation with bound constitutively dimeric NPF. Arp2/3 complex-binding region of the NPF N-WASP was fused C-terminally to the α and β subunits of the CapZ heterodimer. One arm of the NPF dimer binds Arp2 and the other binds actin and Arp3. The conformation of the complex is intermediate between those of inactive and active Arp2/3 complex. Arp2, Arp3, and actin also adopt intermediate conformations between monomeric (G-actin) and filamentous (F-actin) states, but only actin hydrolyzes ATP. In solution, the transition complex is kinetically shifted toward the short-pitch conformation and has higher affinity for F-actin than inactive Arp2/3 complex. The results reveal how all the activating cofactors contribute in a coordinated manner toward Arp2/3 complex activation.
Collapse
Affiliation(s)
- Trevor van Eeuwen
- Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Malgorzata Boczkowska
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Grzegorz Rebowski
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Peter J. Carman
- Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Fred E. Fregoso
- Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Roberto Dominguez
- Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| |
Collapse
|
9
|
Cao L, Ghasemi F, Way M, Jégou A, Romet‐Lemonne G. Regulation of branched versus linear Arp2/3-generated actin filaments. EMBO J 2023; 42:e113008. [PMID: 36939020 PMCID: PMC10152144 DOI: 10.15252/embj.2022113008] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 02/01/2023] [Accepted: 03/01/2023] [Indexed: 03/21/2023] Open
Abstract
Activation of the Arp2/3 complex by VCA-motif-bearing actin nucleation-promoting factors results in the formation of "daughter" actin filaments branching off the sides of pre-existing "mother" filaments. Alternatively, when stimulated by SPIN90, Arp2/3 directly nucleates "linear" actin filaments. Uncovering the similarities and differences between these two mechanisms is fundamental to understanding how actin cytoskeleton dynamics are regulated. Here, analysis of individual filaments reveals that, unexpectedly, the VCA motifs of WASP, N-WASP, and WASH destabilize existing branches, as well as SPIN90-Arp2/3 at linear filament ends. Furthermore, branch stabilizer cortactin and destabilizer GMF each have a similar impact on SPIN90-activated Arp2/3. However, unlike branch junctions, SPIN90-Arp2/3 at the ends of linear filaments is not destabilized by piconewton forces and does not become less stable with time. It thus appears that linear and branched Arp2/3-generated filaments respond similarly to the regulatory proteins we have tested, albeit with some differences, but significantly differ in their responses to aging and mechanical stress. These kinetic differences likely reflect the small conformational differences recently reported between Arp2/3 in branch junctions and linear filaments and suggest that their turnover in cells may be differently regulated.
Collapse
Affiliation(s)
- Luyan Cao
- Université Paris Cité, CNRS, Institut Jacques MonodParisFrance
- The Francis Crick InstituteLondonUK
| | - Foad Ghasemi
- Université Paris Cité, CNRS, Institut Jacques MonodParisFrance
| | - Michael Way
- The Francis Crick InstituteLondonUK
- Department of Infectious DiseaseImperial CollegeLondonUK
| | - Antoine Jégou
- Université Paris Cité, CNRS, Institut Jacques MonodParisFrance
| | | |
Collapse
|
10
|
Lappalainen P, Kotila T, Jégou A, Romet-Lemonne G. Biochemical and mechanical regulation of actin dynamics. Nat Rev Mol Cell Biol 2022; 23:836-852. [PMID: 35918536 DOI: 10.1038/s41580-022-00508-4] [Citation(s) in RCA: 77] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/13/2022] [Indexed: 12/30/2022]
Abstract
Polymerization of actin filaments against membranes produces force for numerous cellular processes, such as migration, morphogenesis, endocytosis, phagocytosis and organelle dynamics. Consequently, aberrant actin cytoskeleton dynamics are linked to various diseases, including cancer, as well as immunological and neurological disorders. Understanding how actin filaments generate forces in cells, how force production is regulated by the interplay between actin-binding proteins and how the actin-regulatory machinery responds to mechanical load are at the heart of many cellular, developmental and pathological processes. During the past few years, our understanding of the mechanisms controlling actin filament assembly and disassembly has evolved substantially. It has also become evident that the activities of key actin-binding proteins are not regulated solely by biochemical signalling pathways, as mechanical regulation is critical for these proteins. Indeed, the architecture and dynamics of the actin cytoskeleton are directly tuned by mechanical load. Here we discuss the general mechanisms by which key actin regulators, often in synergy with each other, control actin filament assembly, disassembly, and monomer recycling. By using an updated view of actin dynamics as a framework, we discuss how the mechanics and geometry of actin networks control actin-binding proteins, and how this translates into force production in endocytosis and mesenchymal cell migration.
Collapse
Affiliation(s)
- Pekka Lappalainen
- Institute of Biotechnology and Helsinki Institute of Life Sciences, University of Helsinki, Helsinki, Finland.
| | - Tommi Kotila
- Institute of Biotechnology and Helsinki Institute of Life Sciences, University of Helsinki, Helsinki, Finland
| | - Antoine Jégou
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, France
| | | |
Collapse
|
11
|
PI(4,5)P2: signaling the plasma membrane. Biochem J 2022; 479:2311-2325. [PMID: 36367756 PMCID: PMC9704524 DOI: 10.1042/bcj20220445] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/19/2022] [Accepted: 10/21/2022] [Indexed: 11/13/2022]
Abstract
In the almost 70 years since the first hints of its existence, the phosphoinositide, phosphatidyl-D-myo-inositol 4,5-bisphosphate has been found to be central in the biological regulation of plasma membrane (PM) function. Here, we provide an overview of the signaling, transport and structural roles the lipid plays at the cell surface in animal cells. These include being substrate for second messenger generation, direct modulation of receptors, control of membrane traffic, regulation of ion channels and transporters, and modulation of the cytoskeleton and cell polarity. We conclude by re-evaluating PI(4,5)P2's designation as a signaling molecule, instead proposing a cofactor role, enabling PM-selective function for many proteins.
Collapse
|
12
|
Yan VT, Narayanan A, Wiegand T, Jülicher F, Grill SW. A condensate dynamic instability orchestrates actomyosin cortex activation. Nature 2022; 609:597-604. [PMID: 35978196 PMCID: PMC9477739 DOI: 10.1038/s41586-022-05084-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 07/07/2022] [Indexed: 11/17/2022]
Abstract
A key event at the onset of development is the activation of a contractile actomyosin cortex during the oocyte-to-embryo transition1-3. Here we report on the discovery that, in Caenorhabditis elegans oocytes, actomyosin cortex activation is supported by the emergence of thousands of short-lived protein condensates rich in F-actin, N-WASP and the ARP2/3 complex4-8 that form an active micro-emulsion. A phase portrait analysis of the dynamics of individual cortical condensates reveals that condensates initially grow and then transition to disassembly before dissolving completely. We find that, in contrast to condensate growth through diffusion9, the growth dynamics of cortical condensates are chemically driven. Notably, the associated chemical reactions obey mass action kinetics that govern both composition and size. We suggest that the resultant condensate dynamic instability10 suppresses coarsening of the active micro-emulsion11, ensures reaction kinetics that are independent of condensate size and prevents runaway F-actin nucleation during the formation of the first cortical actin meshwork.
Collapse
Affiliation(s)
- Victoria Tianjing Yan
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Dresden, Germany.,Biotechnology Center, TU Dresden, Dresden, Germany
| | - Arjun Narayanan
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Dresden, Germany. .,Biotechnology Center, TU Dresden, Dresden, Germany. .,Max Planck Institute for the Physics of Complex Systems (MPI-PKS), Dresden, Germany. .,Center for Systems Biology Dresden (CSBD), Dresden, Germany.
| | - Tina Wiegand
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems (MPI-PKS), Dresden, Germany.,Center for Systems Biology Dresden (CSBD), Dresden, Germany
| | - Frank Jülicher
- Max Planck Institute for the Physics of Complex Systems (MPI-PKS), Dresden, Germany. .,Center for Systems Biology Dresden (CSBD), Dresden, Germany. .,Cluster of Excellence Physics of Life, TU Dresden, Dresden, Germany.
| | - Stephan W Grill
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Dresden, Germany. .,Center for Systems Biology Dresden (CSBD), Dresden, Germany. .,Cluster of Excellence Physics of Life, TU Dresden, Dresden, Germany.
| |
Collapse
|
13
|
Hansen SR, White DS, Scalf M, Corrêa IR, Smith LM, Hoskins AA. Multi-step recognition of potential 5' splice sites by the Saccharomyces cerevisiae U1 snRNP. eLife 2022; 11:70534. [PMID: 35959885 PMCID: PMC9436412 DOI: 10.7554/elife.70534] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 08/11/2022] [Indexed: 11/13/2022] Open
Abstract
In eukaryotes, splice sites define the introns of pre-mRNAs and must be recognized and excised with nucleotide precision by the spliceosome to make the correct mRNA product. In one of the earliest steps of spliceosome assembly, the U1 small nuclear ribonucleoprotein (snRNP) recognizes the 5' splice site (5' SS) through a combination of base pairing, protein-RNA contacts, and interactions with other splicing factors. Previous studies investigating the mechanisms of 5' SS recognition have largely been done in vivo or in cellular extracts where the U1/5' SS interaction is difficult to deconvolute from the effects of trans-acting factors or RNA structure. In this work we used colocalization single-molecule spectroscopy (CoSMoS) to elucidate the pathway of 5' SS selection by purified yeast U1 snRNP. We determined that U1 reversibly selects 5' SS in a sequence-dependent, two-step mechanism. A kinetic selection scheme enforces pairing at particular positions rather than overall duplex stability to achieve long-lived U1 binding. Our results provide a kinetic basis for how U1 may rapidly surveil nascent transcripts for 5' SS and preferentially accumulate at these sequences rather than on close cognates.
Collapse
Affiliation(s)
- Sarah R Hansen
- Department of Biochemistry, University of Wisconsin-Madison, Madison, United States
| | - David S White
- Department of Biochemistry, University of Wisconsin-Madison, Madison, United States
| | - Mark Scalf
- Department of Chemistry, University of Wisconsin-Madison, Madison, United States
| | | | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin-Madison, Madison, United States
| | - Aaron A Hoskins
- Department of Biochemistry, University of Wisconsin-Madison, Madison, United States
| |
Collapse
|
14
|
Geometric trade-off between contractile force and viscous drag determines the actomyosin-based motility of a cell-sized droplet. Proc Natl Acad Sci U S A 2022; 119:e2121147119. [PMID: 35857875 PMCID: PMC9335187 DOI: 10.1073/pnas.2121147119] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Cell migration in confined environments is fundamental for diverse biological processes from cancer invasion to leukocyte trafficking. The cell body is propelled by the contractile force of actomyosin networks transmitted from the cell membrane to the external substrates. However, physical determinants of actomyosin-based migration capacity in confined environments are not fully understood. Here, we develop an in vitro migratory cell model, where cytoplasmic actomyosin networks are encapsulated into droplets surrounded by a lipid monolayer membrane. We find that the droplet can move when the actomyosin networks are bound to the membrane, in which the physical interaction between the contracting actomyosin networks and the membrane generates a propulsive force. The droplet moves faster when it has a larger contact area with the substrates, while narrower confinement reduces the migration speed. By combining experimental observations and active gel theory, we propose a mechanism where the balance between sliding friction force, which is a reaction force of the contractile force, and viscous drag determines the migration speed, providing a physical basis of actomyosin-based motility in confined environments.
Collapse
|
15
|
Chung J, Goode BL, Gelles J. Single-molecule analysis of actin filament debranching by cofilin and GMF. Proc Natl Acad Sci U S A 2022; 119:e2115129119. [PMID: 35858314 PMCID: PMC9304009 DOI: 10.1073/pnas.2115129119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 05/31/2022] [Indexed: 01/13/2023] Open
Abstract
Eukaryotic cells contain branched actin networks that are essential for endocytosis, motility, and other key cellular processes. These networks, which are formed by filamentous actin and the Arp2/3 complex, must subsequently be debranched to allow network remodeling and to recycle the Arp2/3 complex. Debranching appears to be catalyzed by two different members of the actin depolymerizing factor homology protein family: cofilin and glial maturation factor (GMF). However, their mechanisms of debranching are only partially understood. Here, we used single-molecule fluorescence imaging of Arp2/3 complex and actin filaments under physiological ionic conditions to observe debranching by GMF and cofilin. We demonstrate that cofilin, like GMF, is an authentic debrancher independent of its filament-severing activity and that the debranching activities of the two proteins are additive. While GMF binds directly to the Arp2/3 complex, cofilin selectively accumulates on branch-junction daughter filaments in tropomyosin-decorated networks just prior to debranching events. Quantitative comparison of debranching rates with the known kinetics of cofilin-actin binding suggests that cofilin occupancy of a particular single actin site at the branch junction is sufficient to trigger debranching. In rare cases in which the order of departure could be resolved during GMF- or cofilin-induced debranching, the Arp2/3 complex left the branch junction bound to the pointed end of the daughter filament, suggesting that both GMF and cofilin can work by destabilizing the mother filament-Arp2/3 complex interface. Taken together, these observations suggest that GMF and cofilin promote debranching by distinct yet complementary mechanisms.
Collapse
Affiliation(s)
- Johnson Chung
- Department of Biochemistry, Brandeis University, Waltham, MA 02454
| | - Bruce L. Goode
- Department of Biology, Brandeis University, Waltham, MA 02454
| | - Jeff Gelles
- Department of Biochemistry, Brandeis University, Waltham, MA 02454
| |
Collapse
|
16
|
Li TD, Bieling P, Weichsel J, Mullins RD, Fletcher DA. The molecular mechanism of load adaptation by branched actin networks. eLife 2022; 11:e73145. [PMID: 35748355 PMCID: PMC9328761 DOI: 10.7554/elife.73145] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 06/07/2022] [Indexed: 11/13/2022] Open
Abstract
Branched actin networks are self-assembling molecular motors that move biological membranes and drive many important cellular processes, including phagocytosis, endocytosis, and pseudopod protrusion. When confronted with opposing forces, the growth rate of these networks slows and their density increases, but the stoichiometry of key components does not change. The molecular mechanisms governing this force response are not well understood, so we used single-molecule imaging and AFM cantilever deflection to measure how applied forces affect each step in branched actin network assembly. Although load forces are observed to increase the density of growing filaments, we find that they actually decrease the rate of filament nucleation due to inhibitory interactions between actin filament ends and nucleation promoting factors. The force-induced increase in network density turns out to result from an exponential drop in the rate constant that governs filament capping. The force dependence of filament capping matches that of filament elongation and can be explained by expanding Brownian Ratchet theory to cover both processes. We tested a key prediction of this expanded theory by measuring the force-dependent activity of engineered capping protein variants and found that increasing the size of the capping protein increases its sensitivity to applied forces. In summary, we find that Brownian Ratchets underlie not only the ability of growing actin filaments to generate force but also the ability of branched actin networks to adapt their architecture to changing loads.
Collapse
Affiliation(s)
- Tai-De Li
- Department of Bioengineering & Biophysics Program, University of California, BerkeleyBerkeleyUnited States
- Division of Biological Systems & Engineering, Lawrence Berkeley National LaboratoryBerkeleyUnited States
- Advanced Science Research Center, City University of New YorkNew YorkUnited States
| | - Peter Bieling
- Division of Biological Systems & Engineering, Lawrence Berkeley National LaboratoryBerkeleyUnited States
- Department of Cellular and Molecular Pharmacology and Howard Hughes Medical Institute, University of California, San FranciscoSan FranciscoUnited States
- Department of Systemic Cell Biology, Max Planck Institute of Molecular PhysiologyDortmundGermany
| | - Julian Weichsel
- Department of Chemistry, University of California, BerkeleyBerkeleyUnited States
| | - R Dyche Mullins
- Department of Cellular and Molecular Pharmacology and Howard Hughes Medical Institute, University of California, San FranciscoSan FranciscoUnited States
| | - Daniel A Fletcher
- Department of Bioengineering & Biophysics Program, University of California, BerkeleyBerkeleyUnited States
- Division of Biological Systems & Engineering, Lawrence Berkeley National LaboratoryBerkeleyUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
| |
Collapse
|
17
|
Liu SL, Narvaez-Ortiz HY, Miner M, Kiemel J, Oberhelman N, Watt A, Wagner AR, Luan Q, Helgeson LA, Nolen BJ. Analysis of functional surfaces on the actin nucleation promoting factor Dip1 required for Arp2/3 complex activation and endocytic actin network assembly. J Biol Chem 2022; 298:102019. [PMID: 35533728 PMCID: PMC9168731 DOI: 10.1016/j.jbc.2022.102019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 05/02/2022] [Accepted: 05/04/2022] [Indexed: 11/30/2022] Open
Abstract
Arp2/3 complex nucleates branched actin filaments that drive processes like endocytosis and lamellipodial protrusion. WISH/DIP/SPIN90 (WDS) proteins form a class of Arp2/3 complex activators or nucleation promoting factors (NPFs) that, unlike WASP family NPFs, activate Arp2/3 complex without requiring preformed actin filaments. Therefore, activation of Arp2/3 complex by WDS proteins is thought to produce the initial actin filaments that seed branching nucleation by WASP-bound Arp2/3 complexes. However, whether activation of Arp2/3 complex by WDS proteins is important for the initiation of branched actin assembly in cells has not been directly tested. Here, we used structure-based point mutations of the Schizosaccharomyces pombe WDS protein Dip1 to test the importance of its Arp2/3-activating activity in cells. Six of thirteen Dip1 mutants caused severe defects in Arp2/3 complex activation in vitro, and we found a strong correlation between the ability of mutants to activate Arp2/3 complex and to rescue endocytic actin assembly defects caused by deleting Dip1. These data support a model in which Dip1 activates Arp2/3 complex to produce actin filaments that initiate branched actin assembly at endocytic sites. Dip1 mutants that synergized with WASP in activating Arp2/3 complex in vitro showed milder defects in cells compared to those that did not, suggesting that in cells the two NPFs may coactivate Arp2/3 complex to initiate actin assembly. Finally, the mutational data reveal important complementary electrostatic contacts at the Dip1-Arp2/3 complex interface and corroborate the previously proposed wedge model, which describes how Dip1 binding triggers structural changes that activate Arp2/3 complex.
Collapse
Affiliation(s)
- Su-Ling Liu
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA
| | - Heidy Y Narvaez-Ortiz
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA
| | - Matt Miner
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA
| | - Jack Kiemel
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA
| | - Nicholas Oberhelman
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA
| | - April Watt
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA
| | - Andrew R Wagner
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA
| | - Qing Luan
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA
| | - Luke A Helgeson
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA
| | - Brad J Nolen
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA.
| |
Collapse
|
18
|
Structure of Arp2/3 complex at a branched actin filament junction resolved by single-particle cryo-electron microscopy. Proc Natl Acad Sci U S A 2022; 119:e2202723119. [PMID: 35622886 DOI: 10.1073/pnas.2202723119] [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] [Indexed: 01/31/2023] Open
Abstract
SignificanceActin filament nucleation by Arp2/3 complex must be triggered by activators like WASP family proteins. Understanding how WASP proteins activate Arp2/3 complex has been a major challenge due to a lack of high-resolution structures of the complex in an activated state. We determined a high-resolution (∼3.9 Å) structure of the WASP-activated Arp2/3 complex at a branch junction and used biochemical, cell biological, and molecular dynamic simulations to understand the mechanism of WASP-mediated activation. This work shows in detail the contacts between the fully activated Arp2/3 complex, the nucleated daughter actin filament, and the mother actin filament and provides important insights into how conformational rearrangements in the Arp2/3 complex are stimulated during activation.
Collapse
|
19
|
Narvaez-Ortiz HY, Nolen BJ. Unconcerted conformational changes in Arp2/3 complex integrate multiple activating signals to assemble functional actin networks. Curr Biol 2022; 32:975-987.e6. [PMID: 35090589 PMCID: PMC8930562 DOI: 10.1016/j.cub.2022.01.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 11/25/2021] [Accepted: 01/04/2022] [Indexed: 11/16/2022]
Abstract
Arp2/3 complex nucleates branched actin filaments important for processes such as DNA repair, endocytosis, and cellular motility. Multiple factors are required to activate branching nucleation by Arp2/3 complex, including a WASP family protein and a pre-existing actin filament. Activation is achieved through two major conformational changes-subunit flattening and movement into the short pitch conformation-that allow the actin-related proteins (Arps) within the complex (Arp2 and Arp3) to mimic filamentous actin subunits, thereby templating new filament assembly. Some models suggest that these changes are concerted and stimulated cooperatively by WASP and actin filaments, but how Arp2/3 complex integrates signals from multiple factors to drive switch-like activation of branching nucleation has been unknown. Here, we use biochemical assays to show that instead of a concerted mechanism, signal integration by Arp2/3 complex occurs via distinct and unconcerted conformational changes; WASP stimulates the short pitch arrangement of Arp2 and Arp3, while actin filaments trigger a different activation step. An engineered Arp2/3 complex that bypasses the need for WASP but not actin filaments in activation potently assembles isotropic actin networks but fails to assemble sustained force-producing actin networks in bead motility assays. The engineered complex, which is crosslinked into the short pitch conformation, fails to target nucleation to the surface of the bead, creating unproductive branching events that deplete unpolymerized actin and halt assembly. Together, our data demonstrate the requirement for multifactor signal integration by Arp2/3 complex and highlight the importance of both the WASP- and actin filament-mediated activation steps in the assembly of functional actin networks.
Collapse
Affiliation(s)
- Heidy Y Narvaez-Ortiz
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
| | - Brad J Nolen
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA.
| |
Collapse
|
20
|
Liu X, Pimm ML, Haarer B, Brawner AT, Henty-Ridilla JL. Biochemical characterization of actin assembly mechanisms with ALS-associated profilin variants. Eur J Cell Biol 2022; 101:151212. [PMID: 35248815 PMCID: PMC10163920 DOI: 10.1016/j.ejcb.2022.151212] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 02/23/2022] [Accepted: 02/25/2022] [Indexed: 12/26/2022] Open
Abstract
Eight separate mutations in the actin-binding protein profilin-1 have been identified as a rare cause of amyotrophic lateral sclerosis (ALS). Profilin is essential for many neuronal cell processes through its regulation of lipids, nuclear signals, and cytoskeletal dynamics, including actin filament assembly. Direct interactions between profilin and actin monomers inhibit actin filament polymerization. In contrast, profilin can also stimulate polymerization by simultaneously binding actin monomers and proline-rich tracts found in other proteins. Whether the ALS-associated mutations in profilin compromise these actin assembly functions is unclear. We performed a quantitative biochemical comparison of the direct and formin mediated impact for the eight ALS-associated profilin variants on actin assembly using classic protein-binding and single-filament microscopy assays. We determined that the binding constant of each profilin for actin monomers generally correlates with the actin nucleation strength associated with each ALS-related profilin. In the presence of formin, the A20T, R136W, Q139L, and C71G variants failed to activate the elongation phase of actin assembly. This diverse range of formin-activities is not fully explained through profilin-poly-L-proline (PLP) interactions, as all ALS-associated variants bind a formin-derived PLP peptide with similar affinities. However, chemical denaturation experiments suggest that the folding stability of these profilins impact some of these effects on actin assembly. Thus, changes in profilin protein stability and alterations in actin filament polymerization may both contribute to the profilin-mediated actin disruptions in ALS.
Collapse
Affiliation(s)
- Xinbei Liu
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Morgan L Pimm
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Brian Haarer
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Andrew T Brawner
- Department of Neuroscience & Physiology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Jessica L Henty-Ridilla
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA; Department of Neuroscience & Physiology, SUNY Upstate Medical University, Syracuse, NY 13210, USA.
| |
Collapse
|
21
|
Abstract
The precise assembly and disassembly of actin filaments is required for several cellular processes, and their regulation has been scrutinized for decades. Twenty years ago, a handful of studies marked the advent of a new type of experiment to study actin dynamics: using optical microscopy to look at individual events, taking place on individual filaments in real time. Here, we summarize the main characteristics of this approach and how it has changed our ability to understand actin assembly dynamics. We also highlight some of its caveats and reflect on what we have learned over the past 20 years, leading us to propose a set of guidelines, which we hope will contribute to a better exploitation of this powerful tool.
Collapse
|
22
|
Ordabayev YA, Friedman LJ, Gelles J, Theobald DL. Bayesian machine learning analysis of single-molecule fluorescence colocalization images. eLife 2022; 11:73860. [PMID: 35319463 PMCID: PMC9183235 DOI: 10.7554/elife.73860] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 03/19/2022] [Indexed: 01/07/2023] Open
Abstract
Multi-wavelength single-molecule fluorescence colocalization (CoSMoS) methods allow elucidation of complex biochemical reaction mechanisms. However, analysis of CoSMoS data is intrinsically challenging because of low image signal-to-noise ratios, non-specific surface binding of the fluorescent molecules, and analysis methods that require subjective inputs to achieve accurate results. Here, we use Bayesian probabilistic programming to implement Tapqir, an unsupervised machine learning method that incorporates a holistic, physics-based causal model of CoSMoS data. This method accounts for uncertainties in image analysis due to photon and camera noise, optical non-uniformities, non-specific binding, and spot detection. Rather than merely producing a binary 'spot/no spot' classification of unspecified reliability, Tapqir objectively assigns spot classification probabilities that allow accurate downstream analysis of molecular dynamics, thermodynamics, and kinetics. We both quantitatively validate Tapqir performance against simulated CoSMoS image data with known properties and also demonstrate that it implements fully objective, automated analysis of experiment-derived data sets with a wide range of signal, noise, and non-specific binding characteristics.
Collapse
Affiliation(s)
| | - Larry J Friedman
- Department of Biochemistry, Brandeis UniversityWalthamUnited States
| | - Jeff Gelles
- Department of Biochemistry, Brandeis UniversityWalthamUnited States
| | | |
Collapse
|
23
|
Gautreau AM, Fregoso FE, Simanov G, Dominguez R. Nucleation, stabilization, and disassembly of branched actin networks. Trends Cell Biol 2021; 32:421-432. [PMID: 34836783 PMCID: PMC9018471 DOI: 10.1016/j.tcb.2021.10.006] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 10/19/2021] [Accepted: 10/22/2021] [Indexed: 12/18/2022]
Abstract
Arp2/3 complex is an actin filament nucleation and branching machinery conserved in all eukaryotes from yeast to human. Arp2/3 complex branched networks generate pushing forces that drive cellular processes ranging from membrane remodeling to cell and organelle motility. Several molecules regulate these processes by directly inhibiting or activating Arp2/3 complex and by stabilizing or disassembling branched networks. Here, we review recent advances in our understanding of Arp2/3 complex regulation, including high-resolution cryoelectron microscopy (cryo-EM) structures that illuminate the mechanisms of Arp2/3 complex activation and branch formation, and novel cellular pathways of branch formation, stabilization, and debranching. We also identify major gaps in our understanding of Arp2/3 complex inhibition and branch stabilization and disassembly.
Collapse
Affiliation(s)
- Alexis M Gautreau
- Laboratoire de Biologie Structurale de la Cellule, CNRS, École Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau, France.
| | - Fred E Fregoso
- Department of Physiology and Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Gleb Simanov
- Laboratoire de Biologie Structurale de la Cellule, CNRS, École Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - Roberto Dominguez
- Department of Physiology and Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| |
Collapse
|
24
|
Mehidi A, Kage F, Karatas Z, Cercy M, Schaks M, Polesskaya A, Sainlos M, Gautreau AM, Rossier O, Rottner K, Giannone G. Forces generated by lamellipodial actin filament elongation regulate the WAVE complex during cell migration. Nat Cell Biol 2021; 23:1148-1162. [PMID: 34737443 DOI: 10.1038/s41556-021-00786-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 09/27/2021] [Indexed: 12/17/2022]
Abstract
Actin filaments generate mechanical forces that drive membrane movements during trafficking, endocytosis and cell migration. Reciprocally, adaptations of actin networks to forces regulate their assembly and architecture. Yet, a demonstration of forces acting on actin regulators at actin assembly sites in cells is missing. Here we show that local forces arising from actin filament elongation mechanically control WAVE regulatory complex (WRC) dynamics and function, that is, Arp2/3 complex activation in the lamellipodium. Single-protein tracking revealed WRC lateral movements along the lamellipodium tip, driven by elongation of actin filaments and correlating with WRC turnover. The use of optical tweezers to mechanically manipulate functional WRC showed that piconewton forces, as generated by single-filament elongation, dissociated WRC from the lamellipodium tip. WRC activation correlated with its trapping, dwell time and the binding strength at the lamellipodium tip. WRC crosslinking, hindering its mechanical dissociation, increased WRC dwell time and Arp2/3-dependent membrane protrusion. Thus, forces generated by individual actin filaments on their regulators can mechanically tune their turnover and hence activity during cell migration.
Collapse
Affiliation(s)
- Amine Mehidi
- University Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297, Bordeaux, France
| | - Frieda Kage
- Division of Molecular Cell Biology, Zoological Institute, Technische Universität Braunschweig, Braunschweig, Germany.,Department of Cell Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Zeynep Karatas
- University Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297, Bordeaux, France
| | - Maureen Cercy
- University Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297, Bordeaux, France
| | - Matthias Schaks
- Division of Molecular Cell Biology, Zoological Institute, Technische Universität Braunschweig, Braunschweig, Germany.,Department of Cell Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Anna Polesskaya
- CNRS, Ecole Polytechnique, Institut Polytechnique de Paris, Palaiseau, France
| | - Matthieu Sainlos
- University Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297, Bordeaux, France
| | - Alexis M Gautreau
- CNRS, Ecole Polytechnique, Institut Polytechnique de Paris, Palaiseau, France
| | - Olivier Rossier
- University Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297, Bordeaux, France
| | - Klemens Rottner
- Division of Molecular Cell Biology, Zoological Institute, Technische Universität Braunschweig, Braunschweig, Germany.,Department of Cell Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Grégory Giannone
- University Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297, Bordeaux, France.
| |
Collapse
|
25
|
Su Q, Mehta S, Zhang J. Liquid-liquid phase separation: Orchestrating cell signaling through time and space. Mol Cell 2021; 81:4137-4146. [PMID: 34619090 DOI: 10.1016/j.molcel.2021.09.010] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 08/16/2021] [Accepted: 09/08/2021] [Indexed: 12/19/2022]
Abstract
Cell signaling is a complex process. The faithful transduction of information into specific cellular actions depends on the synergistic effects of many regulatory molecules, nurtured by their strict spatiotemporal regulation. Over the years, we have gained copious insights into the subcellular architecture supporting this spatiotemporal control, including the roles of membrane-bound organelles and various signaling nanodomains. Recently, liquid-liquid phase separation (LLPS) has been recognized as another potentially ubiquitous framework for organizing signaling molecules with high specificity and precise spatiotemporal control in cells. Here, we review the pervasive role of LLPS in signal transduction, highlighting several key pathways that intersect with LLPS, including examples in which LLPS is controlled by signaling events. We also examine how LLPS orchestrates signaling by compartmentalizing signaling molecules, amplifying signals non-linearly, and moderating signaling dynamics. We focus on the specific molecules that drive LLPS and highlight the known functional and pathological consequences of LLPS in each pathway.
Collapse
Affiliation(s)
- Qi Su
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sohum Mehta
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jin Zhang
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA.
| |
Collapse
|
26
|
Jaqaman K, Ditlev JA. Biomolecular condensates in membrane receptor signaling. Curr Opin Cell Biol 2021; 69:48-54. [PMID: 33461072 PMCID: PMC8058224 DOI: 10.1016/j.ceb.2020.12.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 12/09/2020] [Accepted: 12/10/2020] [Indexed: 12/17/2022]
Abstract
Clustering is a prominent feature of receptors at the plasma membrane (PM). It plays an important role in signaling. Liquid-liquid phase separation (LLPS) of proteins is emerging as a novel mechanism underlying the observed clustering. Receptors/transmembrane signaling proteins can be core components essential for LLPS (such as LAT or nephrin) or clients enriched at the phase-separated condensates (for example, at the postsynaptic density or at tight junctions). Condensate formation has been shown to regulate signaling in multiple ways, including by increasing protein binding avidity and by modulating the local biochemical environment. In moving forward, it is important to study protein LLPS at the PM of living cells, its interplay with other factors underlying receptor clustering, and its signaling and functional consequences.
Collapse
Affiliation(s)
- Khuloud Jaqaman
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Jonathon A Ditlev
- Program in Molecular Medicine, Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada; Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada.
| |
Collapse
|
27
|
Balzer CJ, James ML, Narvaez-Ortiz HY, Helgeson LA, Sirotkin V, Nolen BJ. Synergy between Wsp1 and Dip1 may initiate assembly of endocytic actin networks. eLife 2020; 9:60419. [PMID: 33179595 PMCID: PMC7707826 DOI: 10.7554/elife.60419] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 11/10/2020] [Indexed: 12/30/2022] Open
Abstract
The actin filament nucleator Arp2/3 complex is activated at cortical sites in Schizosaccharomyces pombe to assemble branched actin networks that drive endocytosis. Arp2/3 complex activators Wsp1 and Dip1 are required for proper actin assembly at endocytic sites, but how they coordinately control Arp2/3-mediated actin assembly is unknown. Alone, Dip1 activates Arp2/3 complex without preexisting actin filaments to nucleate ‘seed’ filaments that activate Wsp1-bound Arp2/3 complex, thereby initiating branched actin network assembly. In contrast, because Wsp1 requires preexisting filaments to activate, it has been assumed to function exclusively in propagating actin networks by stimulating branching from preexisting filaments. Here we show that Wsp1 is important not only for propagation but also for initiation of endocytic actin networks. Using single molecule total internal reflection fluorescence microscopy we show that Wsp1 synergizes with Dip1 to co-activate Arp2/3 complex. Synergistic co-activation does not require preexisting actin filaments, explaining how Wsp1 contributes to actin network initiation in cells.
Collapse
Affiliation(s)
- Connor J Balzer
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon, Eugene, United States
| | - Michael L James
- Department of Cell and Developmental Biology, SUNY Upstate Medical University, Syracuse, United States
| | - Heidy Y Narvaez-Ortiz
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon, Eugene, United States
| | - Luke A Helgeson
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon, Eugene, United States
| | - Vladimir Sirotkin
- Department of Cell and Developmental Biology, SUNY Upstate Medical University, Syracuse, United States
| | - Brad J Nolen
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon, Eugene, United States
| |
Collapse
|
28
|
Tang Q, Schaks M, Koundinya N, Yang C, Pollard LW, Svitkina TM, Rottner K, Goode BL. WAVE1 and WAVE2 have distinct and overlapping roles in controlling actin assembly at the leading edge. Mol Biol Cell 2020; 31:2168-2178. [PMID: 32697617 PMCID: PMC7550694 DOI: 10.1091/mbc.e19-12-0705] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
SCAR/WAVE proteins and Arp2/3 complex assemble branched actin networks at the leading edge. Two isoforms of SCAR/WAVE, WAVE1 and WAVE2, reside at the leading edge, yet it has remained unclear whether they perform similar or distinct roles. Further, there have been conflicting reports about the Arp2/3-independent biochemical activities of WAVE1 on actin filament elongation. To investigate this in vivo, we knocked out WAVE1 and WAVE2 genes, individually and together, in B16-F1 melanoma cells. We demonstrate that WAVE1 and WAVE2 are redundant for lamellipodia formation and motility. However, there is a significant decrease in the rate of leading edge actin extension in WAVE2 KO cells, and an increase in WAVE1 KO cells. The faster rates of actin extension in WAVE1 KO cells are offset by faster retrograde flow, and therefore do not translate into faster lamellipodium protrusion. Thus, WAVE1 restricts the rate of actin extension at the leading edge, and appears to couple actin networks to the membrane to drive protrusion. Overall, these results suggest that WAVE1 and WAVE2 have redundant roles in promoting Arp2/3-dependent actin nucleation and lamellipodia formation, but distinct roles in controlling actin network extension and harnessing network growth to cell protrusion.
Collapse
Affiliation(s)
- Qing Tang
- Department of Biology, Brandeis University, Waltham, MA 02454
| | - Matthias Schaks
- Zoological Institute, Technische Universität Braunschweig, 38106 Braunschweig, Germany.,Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Neha Koundinya
- Department of Biology, Brandeis University, Waltham, MA 02454
| | - Changsong Yang
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104
| | | | - Tatyana M Svitkina
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104
| | - Klemens Rottner
- Zoological Institute, Technische Universität Braunschweig, 38106 Braunschweig, Germany.,Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Bruce L Goode
- Department of Biology, Brandeis University, Waltham, MA 02454
| |
Collapse
|
29
|
Shaaban M, Chowdhury S, Nolen BJ. Cryo-EM reveals the transition of Arp2/3 complex from inactive to nucleation-competent state. Nat Struct Mol Biol 2020; 27:1009-1016. [PMID: 32839613 DOI: 10.1038/s41594-020-0481-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 07/10/2020] [Indexed: 12/29/2022]
Abstract
Arp2/3 complex, a crucial actin filament nucleator, undergoes structural rearrangements during activation by nucleation-promoting factors (NPFs). However, the conformational pathway leading to the nucleation-competent state is unclear due to lack of high-resolution structures of the activated state. Here we report a ~3.9 Å resolution cryo-EM structure of activated Schizosaccharomyces pombe Arp2/3 complex bound to the S. pombe NPF Dip1 and attached to the end of the nucleated actin filament. The structure reveals global and local conformational changes that allow the two actin-related proteins in Arp2/3 complex to mimic a filamentous actin dimer and template nucleation. Activation occurs through a clamp-twisting mechanism, in which Dip1 forces two core subunits in Arp2/3 complex to pivot around one another, shifting half of the complex into a new activated position. By showing how Dip1 stimulates activation, the structure reveals how NPFs can activate Arp2/3 complex in diverse cellular processes.
Collapse
Affiliation(s)
- Mohammed Shaaban
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, USA
| | - Saikat Chowdhury
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, USA.
| | - Brad J Nolen
- Institute of Molecular Biology and Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR, USA.
| |
Collapse
|
30
|
Zimmet A, Van Eeuwen T, Boczkowska M, Rebowski G, Murakami K, Dominguez R. Cryo-EM structure of NPF-bound human Arp2/3 complex and activation mechanism. SCIENCE ADVANCES 2020; 6:6/23/eaaz7651. [PMID: 32917641 PMCID: PMC7274804 DOI: 10.1126/sciadv.aaz7651] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 04/16/2020] [Indexed: 05/12/2023]
Abstract
Actin-related protein (Arp) 2/3 complex nucleates branched actin networks that drive cell motility. It consists of seven proteins, including two actin-related subunits (Arp2 and Arp3). Two nucleation-promoting factors (NPFs) bind Arp2/3 complex during activation, but the order, specific interactions, and contribution of each NPF to activation are unresolved. Here, we report the cryo-electron microscopy structure of recombinantly expressed human Arp2/3 complex with two WASP family NPFs bound and address the mechanism of activation. A cross-linking assay that captures the transition of the Arps into the activated filament-like conformation shows that actin binding to NPFs favors this transition. Actin-NPF binding to Arp2 precedes binding to Arp3 and is sufficient to promote the filament-like conformation but not activation. Structure-guided mutagenesis of the NPF-binding sites reveals their distinct roles in activation and shows that, contrary to budding yeast Arp2/3 complex, NPF-mediated delivery of actin at the barbed end of both Arps is required for activation of human Arp2/3 complex.
Collapse
Affiliation(s)
- Austin Zimmet
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Trevor Van Eeuwen
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Malgorzata Boczkowska
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Grzegorz Rebowski
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kenji Murakami
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Roberto Dominguez
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| |
Collapse
|
31
|
Force and phosphate release from Arp2/3 complex promote dissociation of actin filament branches. Proc Natl Acad Sci U S A 2020; 117:13519-13528. [PMID: 32461373 DOI: 10.1073/pnas.1911183117] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Networks of branched actin filaments formed by Arp2/3 complex generate and experience mechanical forces during essential cellular functions, including cell motility and endocytosis. External forces regulate the assembly and architecture of branched actin networks both in vitro and in cells. Considerably less is known about how mechanical forces influence the disassembly of actin filament networks, specifically, the dissociation of branches. We used microfluidics to apply force to branches formed from purified muscle actin and fission yeast Arp2/3 complex and observed debranching events in real time with total internal reflection fluorescence microscopy. Low forces in the range of 0 pN to 2 pN on branches accelerated their dissociation from mother filaments more than two orders of magnitude, from hours to <1 min. Neither force on the mother filament nor thermal fluctuations in mother filament shape influenced debranching. Arp2/3 complex at branch junctions adopts two distinct mechanical states with different sensitivities to force, which we name "young/strong" and "old/weak." The "young/strong" state 1 has adenosine 5'-diphosphate (ADP)-P i bound to Arp2/3 complex. Phosphate release converts Arp2/3 complex into the "old/weak" state 2 with bound ADP, which is 20 times more sensitive to force than state 1. Branches with ADP-Arp2/3 complex are more sensitive to debranching by fission yeast GMF (glia maturation factor) than branches with ADP-P i -Arp2/3 complex. These findings suggest that aging of branch junctions by phosphate release from Arp2/3 complex and mechanical forces contribute to disassembling "old" actin filament branches in cells.
Collapse
|
32
|
Abstract
Cell migration is an essential process, both in unicellular organisms such as amoeba and as individual or collective motility in highly developed multicellular organisms like mammals. It is controlled by a variety of activities combining protrusive and contractile forces, normally generated by actin filaments. Here, we summarize actin filament assembly and turnover processes, and how respective biochemical activities translate into different protrusion types engaged in migration. These actin-based plasma membrane protrusions include actin-related protein 2/3 complex-dependent structures such as lamellipodia and membrane ruffles, filopodia as well as plasma membrane blebs. We also address observed antagonisms between these protrusion types, and propose a model - also inspired by previous literature - in which a complex balance between specific Rho GTPase signaling pathways dictates the protrusion mechanism employed by cells. Furthermore, we revisit published work regarding the fascinating antagonism between Rac and Rho GTPases, and how this intricate signaling network can define cell behavior and modes of migration. Finally, we discuss how the assembly of actin filament networks can feed back onto their regulators, as exemplified for the lamellipodial factor WAVE regulatory complex, tightly controlling accumulation of this complex at specific subcellular locations as well as its turnover.
Collapse
|
33
|
Much More Than a Scaffold: Cytoskeletal Proteins in Neurological Disorders. Cells 2020; 9:cells9020358. [PMID: 32033020 PMCID: PMC7072452 DOI: 10.3390/cells9020358] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 01/27/2020] [Accepted: 01/29/2020] [Indexed: 02/08/2023] Open
Abstract
Recent observations related to the structure of the cytoskeleton in neurons and novel cytoskeletal abnormalities involved in the pathophysiology of some neurological diseases are changing our view on the function of the cytoskeletal proteins in the nervous system. These efforts allow a better understanding of the molecular mechanisms underlying neurological diseases and allow us to see beyond our current knowledge for the development of new treatments. The neuronal cytoskeleton can be described as an organelle formed by the three-dimensional lattice of the three main families of filaments: actin filaments, microtubules, and neurofilaments. This organelle organizes well-defined structures within neurons (cell bodies and axons), which allow their proper development and function through life. Here, we will provide an overview of both the basic and novel concepts related to those cytoskeletal proteins, which are emerging as potential targets in the study of the pathophysiological mechanisms underlying neurological disorders.
Collapse
|
34
|
Obeidy P, Ju LA, Oehlers SH, Zulkhernain NS, Lee Q, Galeano Niño JL, Kwan RY, Tikoo S, Cavanagh LL, Mrass P, Cook AJ, Jackson SP, Biro M, Roediger B, Sixt M, Weninger W. Partial loss of actin nucleator actin-related protein 2/3 activity triggers blebbing in primary T lymphocytes. Immunol Cell Biol 2019; 98:93-113. [PMID: 31698518 PMCID: PMC7028084 DOI: 10.1111/imcb.12304] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 11/03/2019] [Accepted: 11/04/2019] [Indexed: 12/11/2022]
Abstract
T lymphocytes utilize amoeboid migration to navigate effectively within complex microenvironments. The precise rearrangement of the actin cytoskeleton required for cellular forward propulsion is mediated by actin regulators, including the actin‐related protein 2/3 (Arp2/3) complex, a macromolecular machine that nucleates branched actin filaments at the leading edge. The consequences of modulating Arp2/3 activity on the biophysical properties of the actomyosin cortex and downstream T cell function are incompletely understood. We report that even a moderate decrease of Arp3 levels in T cells profoundly affects actin cortex integrity. Reduction in total F‐actin content leads to reduced cortical tension and disrupted lamellipodia formation. Instead, in Arp3‐knockdown cells, the motility mode is dominated by blebbing migration characterized by transient, balloon‐like protrusions at the leading edge. Although this migration mode seems to be compatible with interstitial migration in three‐dimensional environments, diminished locomotion kinetics and impaired cytotoxicity interfere with optimal T cell function. These findings define the importance of finely tuned, Arp2/3‐dependent mechanophysical membrane integrity in cytotoxic effector T lymphocyte activities.
Collapse
Affiliation(s)
- Peyman Obeidy
- Immune Imaging Program, The Centenary Institute, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2050, Australia
| | - Lining A Ju
- School of Biomedical Engineering, The University of Sydney, Sydney, NSW, 2006, Australia.,Heart Research Institute and Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Stefan H Oehlers
- Tuberculosis Research Program, The Centenary Institute, The University of Sydney, Camperdown, NSW, 2050, Australia.,Discipline of Infectious Diseases & Immunology, Marie Bashir Institute, The University of Sydney, Sydney, NSW, 2006, Australia.,Sydney Medical School, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Nursafwana S Zulkhernain
- Immune Imaging Program, The Centenary Institute, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2050, Australia.,Sydney Medical School, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Quintin Lee
- Immune Imaging Program, The Centenary Institute, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2050, Australia
| | - Jorge L Galeano Niño
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences, the ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Kensington, NSW, 2033, Australia
| | - Rain Yq Kwan
- Immune Imaging Program, The Centenary Institute, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2050, Australia
| | - Shweta Tikoo
- Immune Imaging Program, The Centenary Institute, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2050, Australia.,Sydney Medical School, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Lois L Cavanagh
- Immune Imaging Program, The Centenary Institute, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2050, Australia
| | - Paulus Mrass
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, Albuquerque, NM, 87131, USA
| | - Adam Jl Cook
- Immune Imaging Program, The Centenary Institute, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2050, Australia.,Sydney Medical School, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Shaun P Jackson
- Heart Research Institute and Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia.,Central Clinical School, Sydney Medical School, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Maté Biro
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences, the ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Kensington, NSW, 2033, Australia
| | - Ben Roediger
- Immune Imaging Program, The Centenary Institute, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2050, Australia
| | - Michael Sixt
- Institute of Science and Technology, Klosterneuburg, 3400, Austria
| | - Wolfgang Weninger
- Immune Imaging Program, The Centenary Institute, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2050, Australia.,Department of Dermatology, Royal Prince Alfred Hospital, Camperdown, NSW, 2050, Australia.,Discipline of Dermatology, Sydney Medical School, The University of Sydney, Sydney, NSW, 2006, Australia.,Department of Dermatology, Medical University of Vienna, Vienna, 1090, Austria
| |
Collapse
|
35
|
Balzer CJ, Wagner AR, Helgeson LA, Nolen BJ. Single-Turnover Activation of Arp2/3 Complex by Dip1 May Balance Nucleation of Linear versus Branched Actin Filaments. Curr Biol 2019; 29:3331-3338.e7. [PMID: 31564494 DOI: 10.1016/j.cub.2019.08.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 07/12/2019] [Accepted: 08/09/2019] [Indexed: 02/01/2023]
Abstract
Arp2/3 complex nucleates branched actin filaments important for cellular motility, endocytosis, meiosis, and cellular differentiation [1-4]. Wiskott-Aldrich syndrome proteins (WASPs), the prototypical Arp2/3 complex activators, activate Arp2/3 complex only once it is bound to the side of an actin filament [5, 6]. This ensures WASP-activated Arp2/3 complex only nucleates branched actin filaments but means branched actin networks must be seeded with an initial preformed filament. Dip1 and other WISH/DIP/SPIN90 family proteins activate Arp2/3 complex without preformed filaments [7], creating seed filaments that activate WASP-bound Arp2/3 complex [8]. Importantly, Dip1-mediated activation of Arp2/3 complex creates linear filaments instead of branches [7]. Cells may therefore need to limit Dip1 activity relative to WASP to preserve the dendritic nature of actin networks, although it is unclear whether such regulatory mechanisms exist. Here, we use total internal reflection fluorescence (TIRF) microscopy to show that Dip1 causes actin assembled with WASP and Arp2/3 complex to form disconnected networks with many linear filaments rather than highly branched arrays. We discover a key biochemical difference between Dip1 and WASP that may limit linear filament nucleation in cells; although WASP must be released for nucleation, Dip1 stays associated with Arp2/3 complex on the pointed ends of nucleated actin filaments, so Dip1 is consumed in the reaction. Using live-cell imaging of fission yeast, we provide evidence that Dip1 is a single-turnover activator of Arp2/3 complex in vivo, revealing a mechanism by which Dip1 can initiate branched actin networks at endocytic sites without disrupting their branched architectures.
Collapse
Affiliation(s)
- Connor J Balzer
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
| | - Andrew R Wagner
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
| | - Luke A Helgeson
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
| | - Brad J Nolen
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA.
| |
Collapse
|
36
|
Case LB, Zhang X, Ditlev JA, Rosen MK. Stoichiometry controls activity of phase-separated clusters of actin signaling proteins. Science 2019; 363:1093-1097. [PMID: 30846599 DOI: 10.1126/science.aau6313] [Citation(s) in RCA: 294] [Impact Index Per Article: 58.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 01/10/2019] [Indexed: 12/20/2022]
Abstract
Biomolecular condensates concentrate macromolecules into foci without a surrounding membrane. Many condensates appear to form through multivalent interactions that drive liquid-liquid phase separation (LLPS). LLPS increases the specific activity of actin regulatory proteins toward actin assembly by the Arp2/3 complex. We show that this increase occurs because LLPS of the Nephrin-Nck-N-WASP signaling pathway on lipid bilayers increases membrane dwell time of N-WASP and Arp2/3 complex, consequently increasing actin assembly. Dwell time varies with relative stoichiometry of the signaling proteins in the phase-separated clusters, rendering N-WASP and Arp2/3 activity stoichiometry dependent. This mechanism of controlling protein activity is enabled by the stoichiometrically undefined nature of biomolecular condensates. Such regulation should be a general feature of signaling systems that assemble through multivalent interactions and drive nonequilibrium outputs.
Collapse
Affiliation(s)
- Lindsay B Case
- The HHMI Summer Institute, Marine Biological Laboratory, Woods Hole, MA 02543, USA.,Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xu Zhang
- Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jonathon A Ditlev
- The HHMI Summer Institute, Marine Biological Laboratory, Woods Hole, MA 02543, USA.,Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Michael K Rosen
- The HHMI Summer Institute, Marine Biological Laboratory, Woods Hole, MA 02543, USA. .,Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| |
Collapse
|
37
|
Kopitar AN, Markelj G, Oražem M, Blazina Š, Avčin T, Ihan A, Debeljak M. Flow Cytometric Determination of Actin Polymerization in Peripheral Blood Leukocytes Effectively Discriminate Patients With Homozygous Mutation in ARPC1B From Asymptomatic Carriers and Normal Controls. Front Immunol 2019; 10:1632. [PMID: 31379835 PMCID: PMC6646687 DOI: 10.3389/fimmu.2019.01632] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 07/01/2019] [Indexed: 11/26/2022] Open
Abstract
Actin nucleators initiate formation of actin filaments. Among them, the Arp2/3 complex has the ability to form branched actin networks. This complex is regulated by members of the Wiscott-Aldrich syndrome protein (WASp) family. Polymerization of actin filaments can be evaluated through flow cytometry by fluorescent phalloidin staining before and after stimulation with N-formyl-methionyl-leucyl-phenylalanine (fMLP). We identified a missense mutation in the gene ARPC1B (Arp2/3 activator subunit) resulting in defective actin polymerization in four patients (three of them were related). All patients (1 male, 3 female) developed microthrombocytopenia, cellular immune deficiency, eczema, various autoimmune manifestations, recurrent skin abscesses and elevated IgE antibodies. Besides four patients with homozygous mutation in ARPC1B, we also identified six heterozygous carriers without clinical disease (3 males, 3 females) within the same family. We developed a functional test to evaluate Arp2/3 complex function, which consists of flow cytometric detection of intracellular polymerized actin after in vitro fMLP stimulation of leukocytes. Median fluorescence intensities of FITC-phalloidin stained actin were measured in monocytes, neutrophils and lymphocytes of patients, carriers, and healthy control subjects. We detected non-efficient actin polymerization in monocytes and neutrophils of homozygous patients compared to carriers or the healthy subjects. In monocytes, the increase in median fluorescence intensities was significantly lower in patients compared to carriers (104 vs. 213%; p < 0.01) and healthy controls (104 vs. 289%; p < 0.01). Similarly, the increase in median fluorescence intensities in neutrophils was significantly increased in the group with carriers (208%; p < 0.01) and healthy controls (238%; p < 0.01) and significantly decreased in the patient's group (94%). Our functional fMLP/phalloidin test can therefore be used as a practical tool to separate symptomatic patients from asymptomatic mutation associated to actin polymerization.
Collapse
Affiliation(s)
- Andreja N Kopitar
- Faculty of Medicine, Institute of Microbiology and Immunology, University of Ljubljana, Ljubljana, Slovenia
| | - Gašper Markelj
- Department of Allergology, Rheumatology and Clinical Immunology, University Children's Hospital, University Medical Center Ljubljana, Ljubljana, Slovenia
| | - Miha Oražem
- Department of Radiation Oncology, Institute of Oncology Ljubljana, Ljubljana, Slovenia
| | - Štefan Blazina
- Department of Allergology, Rheumatology and Clinical Immunology, University Children's Hospital, University Medical Center Ljubljana, Ljubljana, Slovenia
| | - Tadej Avčin
- Department of Allergology, Rheumatology and Clinical Immunology, University Children's Hospital, University Medical Center Ljubljana, Ljubljana, Slovenia.,Department of Pediatrics, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Alojz Ihan
- Faculty of Medicine, Institute of Microbiology and Immunology, University of Ljubljana, Ljubljana, Slovenia
| | - Maruša Debeljak
- Unit for Special Laboratory Diagnostics, University Children's Hospital, University Medical Center Ljubljana, Ljubljana, Slovenia
| |
Collapse
|
38
|
Colin M, Delporte C, Janky R, Lechon AS, Renard G, Van Antwerpen P, Maltese WA, Mathieu V. Dysregulation of Macropinocytosis Processes in Glioblastomas May Be Exploited to Increase Intracellular Anti-Cancer Drug Levels: The Example of Temozolomide. Cancers (Basel) 2019; 11:cancers11030411. [PMID: 30909495 PMCID: PMC6468498 DOI: 10.3390/cancers11030411] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 03/15/2019] [Accepted: 03/20/2019] [Indexed: 12/16/2022] Open
Abstract
Macropinocytosis is a clathrin-independent endocytosis of extracellular fluid that may contribute to cancer aggressiveness through nutrient supply, recycling of plasma membrane and receptors, and exosome internalization. Macropinocytosis may be notably triggered by epidermal growth factor receptor (EGFR) and platelet-derived growth factor receptor (PDGFR), two well-known markers for glioblastoma aggressiveness. Therefore, we studied whether the expression of key actors of macropinocytosis is modified in human glioma datasets. Strong deregulation has been evidenced at the mRNA level according to the grade of the tumor, and 38 macropinocytosis-related gene signatures allowed discrimination of the glioblastoma (GBM) samples. Honokiol-induced vacuolization was then compared to vacquinol-1 and MOMIPP, two known macropinocytosis inducers. Despite high phase-contrast morphological similarities, honokiol-induced vacuoles appeared to originate from both endocytosis and ER. Also, acridine orange staining suggested differences in the macropinosomes’ fate: their fusion with lysosomes appeared very limited in 3-(5-methoxy -2-methyl-1H-indol-3-yl)-1-(4-pyridinyl)-2-propen-1-one (MOMIPP)-treated cells. Nevertheless, each of the compounds markedly increased temozolomide uptake by glioma cells, as evidenced by LC-MS. In conclusion, the observed deregulation of macropinocytosis in GBM makes them prone to respond to various compounds affecting their formation and/or intracellular fate. Considering that sustained macropinocytosis may also trigger cell death of both sensitive and resistant GBM cells, we propose to envisage macropinocytosis inducers in combination approaches to obtain dual benefits: increased drug uptake and additive/synergistic effects.
Collapse
Affiliation(s)
- Margaux Colin
- Department of Pharmacotherapy and Pharmaceuticals, Faculty of Pharmacy, Université Libre de Bruxelles (ULB), 1050 Brussels, Belgium.
| | - Cédric Delporte
- RD3-Pharmacognosy, Bioanalysis and Drug Discovery Unit and Analytical Platform, Faculty of Pharmacy, Université libre de Bruxelles (ULB), 1050 Brussels, Belgium.
| | | | - Anne-Sophie Lechon
- Department of Pharmacotherapy and Pharmaceuticals, Faculty of Pharmacy, Université Libre de Bruxelles (ULB), 1050 Brussels, Belgium.
| | - Gwendoline Renard
- Department of Pharmacotherapy and Pharmaceuticals, Faculty of Pharmacy, Université Libre de Bruxelles (ULB), 1050 Brussels, Belgium.
| | - Pierre Van Antwerpen
- RD3-Pharmacognosy, Bioanalysis and Drug Discovery Unit and Analytical Platform, Faculty of Pharmacy, Université libre de Bruxelles (ULB), 1050 Brussels, Belgium.
| | - William A Maltese
- Department of Cancer Biology, University of Toledo College of Medicine, Toledo, OH 43614, USA.
| | - Véronique Mathieu
- Department of Pharmacotherapy and Pharmaceuticals, Faculty of Pharmacy, Université Libre de Bruxelles (ULB), 1050 Brussels, Belgium.
- ULB Cancer Research Center, Université libre de Bruxelles (ULB), 1050 Bruxelles, Belgium.
| |
Collapse
|
39
|
Stumper SK, Ravi H, Friedman LJ, Mooney RA, Corrêa IR, Gershenson A, Landick R, Gelles J. Delayed inhibition mechanism for secondary channel factor regulation of ribosomal RNA transcription. eLife 2019; 8:40576. [PMID: 30720429 PMCID: PMC7028371 DOI: 10.7554/elife.40576] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Accepted: 02/04/2019] [Indexed: 11/25/2022] Open
Abstract
RNA polymerases (RNAPs) contain a conserved ‘secondary channel’ which binds regulatory factors that modulate transcription initiation. In Escherichia coli, the secondary channel factors (SCFs) GreB and DksA both repress ribosomal RNA (rRNA) transcription, but SCF loading and repression mechanisms are unclear. We observed in vitro fluorescently labeled GreB molecules binding to single RNAPs and initiation of individual transcripts from an rRNA promoter. GreB arrived and departed from promoters only in complex with RNAP. GreB did not alter initial RNAP-promoter binding but instead blocked a step after conformational rearrangement of the initial RNAP-promoter complex. Strikingly, GreB-RNAP complexes never initiated at an rRNA promoter; only RNAP molecules arriving at the promoter without bound GreB produced transcript. The data reveal that a model SCF functions by a ‘delayed inhibition’ mechanism and suggest that rRNA promoters are inhibited by GreB/DksA because their short-lived RNAP complexes do not allow sufficient time for SCFs to dissociate.
Collapse
Affiliation(s)
- Sarah K Stumper
- Department of Biochemistry, Brandeis University, Waltham, United States
| | - Harini Ravi
- Department of Biochemistry, Brandeis University, Waltham, United States
| | - Larry J Friedman
- Department of Biochemistry, Brandeis University, Waltham, United States
| | - Rachel Anne Mooney
- Department of Biochemistry, University of Wisconsin, Madison, United States
| | | | - Anne Gershenson
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, United States
| | - Robert Landick
- Department of Biochemistry, University of Wisconsin, Madison, United States.,Department of Bacteriology, University of Wisconsin, Madison, United States
| | - Jeff Gelles
- Department of Biochemistry, Brandeis University, Waltham, United States
| |
Collapse
|
40
|
Ganzinger KA, Schwille P. More from less - bottom-up reconstitution of cell biology. J Cell Sci 2019; 132:132/4/jcs227488. [PMID: 30718262 DOI: 10.1242/jcs.227488] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The ultimate goal of bottom-up synthetic biology is recreating life in its simplest form. However, in its quest to find the minimal functional units of life, this field contributes more than its main aim by also offering a range of tools for asking, and experimentally approaching, biological questions. This Review focusses on how bottom-up reconstitution has furthered our understanding of cell biology. Studying cell biological processes in vitro has a long tradition, but only recent technological advances have enabled researchers to reconstitute increasingly complex biomolecular systems by controlling their multi-component composition and their spatiotemporal arrangements. We illustrate this progress using the example of cytoskeletal processes. Our understanding of these has been greatly enhanced by reconstitution experiments, from the first in vitro experiments 70 years ago to recent work on minimal cytoskeleton systems (including this Special Issue of Journal of Cell Science). Importantly, reconstitution approaches are not limited to the cytoskeleton field. Thus, we also discuss progress in other areas, such as the shaping of biomembranes and cellular signalling, and prompt the reader to add their subfield of cell biology to this list in the future.
Collapse
Affiliation(s)
- Kristina A Ganzinger
- Physics of Cellular Interactions Group, AMOLF, 1098 XG Amsterdam, The Netherlands
| | - Petra Schwille
- Department Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| |
Collapse
|
41
|
Higgs HN. A fruitful tree: developing the dendritic nucleation model of actin-based cell motility. Mol Biol Cell 2018. [PMCID: PMC6333179 DOI: 10.1091/mbc.e18-07-0426] [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] [Indexed: 11/30/2022] Open
Abstract
A fundamental question in cell biology concerns how cells move, and this has been the subject of intense research for decades. In the 1990s, a major leap forward was made in our understanding of cell motility, with the proposal of the dendritic nucleation model. This essay describes the events leading to the development of the model, including findings from many laboratories and scientific disciplines. The story is an excellent example of the scientific process in action, with the combination of multiple perspectives leading to robust conclusions.
Collapse
Affiliation(s)
- Henry N. Higgs
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755
| |
Collapse
|
42
|
Kaur H, Jamalidinan F, Condon SGF, Senes A, Hoskins AA. Analysis of spliceosome dynamics by maximum likelihood fitting of dwell time distributions. Methods 2018; 153:13-21. [PMID: 30472247 DOI: 10.1016/j.ymeth.2018.11.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 11/20/2018] [Accepted: 11/21/2018] [Indexed: 11/17/2022] Open
Abstract
Colocalization single-molecule methods can provide a wealth of information concerning the ordering and dynamics of biomolecule assembly. These have been used extensively to study the pathways of spliceosome assembly in vitro. Key to these experiments is the measurement of binding times-either the dwell times of a multi-molecular interaction or times in between binding events. By analyzing hundreds of these times, many new insights into the kinetic pathways governing spliceosome assembly have been obtained. Collections of binding times are often plotted as histograms and can be fit to kinetic models using a variety of methods. Here, we describe the use of maximum likelihood methods to fit dwell time distributions without binning. In addition, we discuss several aspects of analyzing these distributions with histograms and pitfalls that can be encountered if improperly binned histograms are used. We have automated several aspects of maximum likelihood fitting of dwell time distributions in the AGATHA software package.
Collapse
Affiliation(s)
- Harpreet Kaur
- Department of Biochemistry, 433 Babcock Dr., University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Fatemehsadat Jamalidinan
- Department of Biochemistry, 433 Babcock Dr., University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Samson G F Condon
- Department of Biochemistry, 433 Babcock Dr., University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Alessandro Senes
- Department of Biochemistry, 433 Babcock Dr., University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Aaron A Hoskins
- Department of Biochemistry, 433 Babcock Dr., University of Wisconsin-Madison, Madison, WI 53706, USA.
| |
Collapse
|
43
|
Luan Q, Liu SL, Helgeson LA, Nolen BJ. Structure of the nucleation-promoting factor SPIN90 bound to the actin filament nucleator Arp2/3 complex. EMBO J 2018; 37:embj.2018100005. [PMID: 30322896 DOI: 10.15252/embj.2018100005] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 08/31/2018] [Accepted: 09/06/2018] [Indexed: 11/09/2022] Open
Abstract
Unlike the WASP family of Arp2/3 complex activators, WISH/DIP/SPIN90 (WDS) family proteins activate actin filament nucleation by the Arp2/3 complex without the need for a preformed actin filament. This allows WDS proteins to initiate branched actin network assembly by providing seed filaments that activate WASP-bound Arp2/3 complex. Despite their important role in actin network initiation, it is unclear how WDS proteins drive the activating steps that require both WASP and pre-existing actin filaments during WASP-mediated nucleation. Here, we show that SPIN90 folds into an armadillo repeat domain that binds a surface of Arp2/3 complex distinct from the two WASP sites, straddling a hinge point that may stimulate movement of the Arp2 subunit into the activated short-pitch conformation. SPIN90 binds a surface on Arp2/3 complex that overlaps with actin filament binding, explaining how it could stimulate the same structural rearrangements in the complex as pre-existing actin filaments. By revealing how WDS proteins activate the Arp2/3 complex, these data provide a molecular foundation to understand initiation of dendritic actin networks and regulation of Arp2/3 complex by its activators.
Collapse
Affiliation(s)
- Qing Luan
- Institute of Molecular Biology and Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR, USA
| | - Su-Ling Liu
- Institute of Molecular Biology and Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR, USA
| | - Luke A Helgeson
- Institute of Molecular Biology and Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR, USA
| | - Brad J Nolen
- Institute of Molecular Biology and Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR, USA
| |
Collapse
|
44
|
Assembling actin filaments for protrusion. Curr Opin Cell Biol 2018; 56:53-63. [PMID: 30278304 DOI: 10.1016/j.ceb.2018.09.004] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 09/10/2018] [Accepted: 09/17/2018] [Indexed: 12/31/2022]
Abstract
Cell migration entails a plethora of activities combining the productive exertion of protrusive and contractile forces to allow cells to push and squeeze themselves through cell clumps, interstitial tissues or tissue borders. All these activities require the generation and turnover of actin filaments that arrange into specific, subcellular structures. The most prominent structures mediating the protrusion at the leading edges of cells include lamellipodia and filopodia as well as plasma membrane blebs. Moreover, in cells migrating on planar substratum, mechanical support is being provided by an additional, more proximally located structure termed the lamella. Here, we systematically dissect the literature concerning the mechanisms driving actin filament nucleation and elongation in the best-studied protrusive structure, the lamellipodium. Recent work has shed light on open questions in lamellipodium protrusion, including the relative contributions of nucleation versus elongation to the assembly of both individual filaments and the lamellipodial network as a whole. However, much remains to be learned concerning the specificity and relevance of individual factors, their cooperation and their site-specific functions relative to the importance of global actin monomer and filament homeostasis.
Collapse
|
45
|
Conformational changes in Arp2/3 complex induced by ATP, WASp-VCA, and actin filaments. Proc Natl Acad Sci U S A 2018; 115:E8642-E8651. [PMID: 30150414 DOI: 10.1073/pnas.1717594115] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
We used fluorescence spectroscopy and EM to determine how binding of ATP, nucleation-promoting factors, actin monomers, and actin filaments changes the conformation of Arp2/3 complex during the process that nucleates an actin filament branch. We mutated subunits of Schizosaccharomyces pombe Arp2/3 complex for labeling with fluorescent dyes at either the C termini of Arp2 and Arp3 or ArpC1 and ArpC3. We measured Förster resonance energy transfer (FRET) efficiency (ETeff) between the dyes in the presence of the various ligands. We also computed class averages from electron micrographs of negatively stained specimens. ATP binding made small conformational changes of the nucleotide-binding cleft of the Arp2 subunit. WASp-VCA, WASp-CA, and WASp-actin-VCA changed the ETeff between the dyes on the Arp2 and Arp3 subunits much more than between dyes on ArpC1 and ArpC3. Ensemble FRET detected an additional structural change that brought ArpC1 and ArpC3 closer together when Arp2/3 complex bound actin filaments. VCA binding to Arp2/3 complex causes a conformational change that favors binding to the side of an actin filament, which allows further changes required to nucleate a daughter filament.
Collapse
|
46
|
Abp1 promotes Arp2/3 complex-dependent actin nucleation and stabilizes branch junctions by antagonizing GMF. Nat Commun 2018; 9:2895. [PMID: 30042427 PMCID: PMC6057921 DOI: 10.1038/s41467-018-05260-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 06/22/2018] [Indexed: 12/26/2022] Open
Abstract
Formation and turnover of branched actin networks underlies cell migration and other essential force-driven processes. Type I nucleation-promoting factors (NPFs) such as WASP recruit actin monomers to Arp2/3 complex to stimulate nucleation. In contrast, mechanisms of type II NPFs such as Abp1 (also known as HIP55 and Drebrin-like protein) are less well understood. Here, we use single-molecule analysis to investigate yeast Abp1 effects on Arp2/3 complex, and find that Abp1 strongly enhances Arp2/3-dependent branch nucleation by stabilizing Arp2/3 on sides of mother filaments. Abp1 binds dynamically to filament sides, with sub-second lifetimes, yet associates stably with branch junctions. Further, we uncover a role for Abp1 in protecting filament junctions from GMF-induced debranching by competing with GMF for Arp2/3 binding. These data, combined with EM structures of Abp1 dimers bound to Arp2/3 complex in two different conformations, expand our mechanistic understanding of type II NPFs. Abp1, a type II actin nucleation promoting factor, is a known component of branched actin networks but its mechanism remains poorly understood. Here, the authors find that Abp1 enhances Arp2/3-mediated actin branch formation, and blocks ‘debranching’ by GMF, making it a pro-branching factor.
Collapse
|
47
|
Goode BL, Sweeney MO, Eskin JA. GMF as an Actin Network Remodeling Factor. Trends Cell Biol 2018; 28:749-760. [PMID: 29779865 DOI: 10.1016/j.tcb.2018.04.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 04/22/2018] [Accepted: 04/23/2018] [Indexed: 10/24/2022]
Abstract
Glia maturation factor (GMF) has recently been established as a regulator of the actin cytoskeleton with a unique role in remodeling actin network architecture. Conserved from yeast to mammals, GMF is one of five members of the ADF-H family of actin regulatory proteins, which includes ADF/cofilin, Abp1/Drebrin, Twinfilin, and Coactosin. GMF does not bind actin, but instead binds the Arp2/3 complex with high affinity. Through this association, GMF catalyzes the debranching of actin filament networks and inhibits actin nucleation by Arp2/3 complex. Here, we discuss GMF's emerging role in controlling actin filament spatial organization and dynamics underlying cell motility, endocytosis, and other biological processes. Further, we attempt to reconcile these functions with its earlier characterization as a cell differentiation factor.
Collapse
Affiliation(s)
- Bruce L Goode
- Rosenstiel Basic Medical Sciences Research Center, Brandeis University, 415 South Street, Waltham, MA 02454 USA.
| | - Meredith O Sweeney
- Rosenstiel Basic Medical Sciences Research Center, Brandeis University, 415 South Street, Waltham, MA 02454 USA
| | - Julian A Eskin
- Rosenstiel Basic Medical Sciences Research Center, Brandeis University, 415 South Street, Waltham, MA 02454 USA
| |
Collapse
|
48
|
Maziveyi M, Alahari SK. Cell matrix adhesions in cancer: The proteins that form the glue. Oncotarget 2018; 8:48471-48487. [PMID: 28476046 PMCID: PMC5564663 DOI: 10.18632/oncotarget.17265] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 03/27/2017] [Indexed: 12/28/2022] Open
Abstract
The main purposes of Integrin-mediated cell contacts are to interpret bi-directional signals between the extracellular environment and intracellular proteins, as well as, anchor the cell to a matrix. Many cell adhesion molecules have been discovered with a wide spectrum of responsibilities, including recruiting, activating, elongating, and maintaining. This review will perlustrate some of the key incidences that precede focal adhesion formation. Tyrosine phosphorylation is a key signaling initiation event that leads to the recruitment of multiple proteins to focal adhesion sites. Recruitment and concentration of proteins such as Paxillin and Vinculin to Integrin clutches is necessary for focal adhesion development. The assembled networks are responsible for transmitting signals back and forth from the extracellular matrix (ECM) to Actin and its binding proteins. Cancer cells exhibit highly altered focal adhesion dynamics. This review will highlight some key discoveries in cancer cell adhesion, as well as, identify current gaps in knowledge.
Collapse
Affiliation(s)
- Mazvita Maziveyi
- Department of Biochemistry and Molecular Biology, Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | - Suresh K Alahari
- Department of Biochemistry and Molecular Biology, Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, LA, USA
| |
Collapse
|
49
|
Identification of Wiskott-Aldrich syndrome protein (WASP) binding sites on the branched actin filament nucleator Arp2/3 complex. Proc Natl Acad Sci U S A 2018; 115:E1409-E1418. [PMID: 29386393 DOI: 10.1073/pnas.1716622115] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Arp2/3 complex nucleates branched actin filaments important for cellular motility and endocytosis. WASP family proteins are Arp2/3 complex activators that play multiple roles in branching nucleation, but little is known about the structural bases of these WASP functions, owing to an incomplete understanding of how WASP binds Arp2/3 complex. Recent data show WASP binds two sites, and biochemical and structural studies led to models in which the WASP C segment engages the barbed ends of the Arp3 and Arp2 subunits while the WASP A segment binds the back side of the complex on Arp3. However, electron microscopy reconstructions showed density for WASP inconsistent with these models on the opposite (front) side of Arp2/3 complex. Here we use chemical cross-linking and mass spectrometry (XL-MS) along with computational docking and structure-based mutational analysis to map the two WASP binding sites on the complex. Our data corroborate the barbed end and back side binding models and show one WASP binding site on Arp3, on the back side of the complex, and a second site on the bottom of the complex, spanning Arp2 and ARPC1. The XL-MS-identified cross-links rule out the front side binding model and show that the A segment of WASP binds along the bottom side of the ARPC1 subunit, instead of at the Arp2/ARPC1 interface, as suggested by FRET experiments. The identified binding sites support the Arp3 tail release model to explain WASP-mediated activating conformational changes in Arp2/3 complex and provide insight into the roles of WASP in branching nucleation.
Collapse
|
50
|
Molinie N, Gautreau A. The Arp2/3 Regulatory System and Its Deregulation in Cancer. Physiol Rev 2017; 98:215-238. [PMID: 29212790 DOI: 10.1152/physrev.00006.2017] [Citation(s) in RCA: 119] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 05/10/2017] [Accepted: 05/11/2017] [Indexed: 02/07/2023] Open
Abstract
The Arp2/3 complex is an evolutionary conserved molecular machine that generates branched actin networks. When activated, the Arp2/3 complex contributes the actin branched junction and thus cross-links the polymerizing actin filaments in a network that exerts a pushing force. The different activators initiate branched actin networks at the cytosolic surface of different cellular membranes to promote their protrusion, movement, or scission in cell migration and membrane traffic. Here we review the structure, function, and regulation of all the direct regulators of the Arp2/3 complex that induce or inhibit the initiation of a branched actin network and that controls the stability of its branched junctions. Our goal is to present recent findings concerning novel inhibitory proteins or the regulation of the actin branched junction and place these in the context of what was previously known to provide a global overview of how the Arp2/3 complex is regulated in human cells. We focus on the human set of Arp2/3 regulators to compare normal Arp2/3 regulation in untransformed cells to the deregulation of the Arp2/3 system observed in patients affected by various cancers. In many cases, these deregulations promote cancer progression and have a direct impact on patient survival.
Collapse
Affiliation(s)
- Nicolas Molinie
- Ecole Polytechnique, Université Paris-Saclay, CNRS UMR 7654, Palaiseau, France; and Moscow Institute of Physics and Technology, Life Sciences Center, Dolgoprudny, Russia
| | - Alexis Gautreau
- Ecole Polytechnique, Université Paris-Saclay, CNRS UMR 7654, Palaiseau, France; and Moscow Institute of Physics and Technology, Life Sciences Center, Dolgoprudny, Russia
| |
Collapse
|