1
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Shah R, Panagiotou TC, Cole GB, Moraes TF, Lavoie BD, McCulloch CA, Wilde A. The DIAPH3 linker specifies a β-actin network that maintains RhoA and Myosin-II at the cytokinetic furrow. Nat Commun 2024; 15:5250. [PMID: 38897998 PMCID: PMC11187180 DOI: 10.1038/s41467-024-49427-2] [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: 10/10/2023] [Accepted: 06/03/2024] [Indexed: 06/21/2024] Open
Abstract
Cytokinesis is the final step of the cell division cycle that leads to the formation of two new cells. Successful cytokinesis requires significant remodelling of the plasma membrane by spatially distinct β- and γ-actin networks. These networks are generated by the formin family of actin nucleators, DIAPH3 and DIAPH1 respectively. Here we show that β- and γ-actin perform specialized and non-redundant roles in cytokinesis and cannot substitute for one another. Expression of hybrid DIAPH1 and DIAPH3 proteins with altered actin isoform specificity relocalized cytokinetic actin isoform networks within the cell, causing cytokinetic failure. Consistent with this we show that β-actin networks, but not γ-actin networks, are required for the maintenance of non-muscle myosin II and RhoA at the cytokinetic furrow. These data suggest that independent and spatially distinct actin isoform networks form scaffolds of unique interactors that facilitate localized biochemical activities to ensure successful cell division.
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Affiliation(s)
- Riya Shah
- Department of Biochemistry, University of Toronto, 661 University Ave, Toronto, ON, M5G 1M1, Canada
| | - Thomas C Panagiotou
- Department of Molecular Genetics, University of Toronto, 661 University Ave, Toronto, ON, M5G 1M1, Canada
| | - Gregory B Cole
- Department of Biochemistry, University of Toronto, 661 University Ave, Toronto, ON, M5G 1M1, Canada
| | - Trevor F Moraes
- Department of Biochemistry, University of Toronto, 661 University Ave, Toronto, ON, M5G 1M1, Canada
| | - Brigitte D Lavoie
- Department of Molecular Genetics, University of Toronto, 661 University Ave, Toronto, ON, M5G 1M1, Canada
| | | | - Andrew Wilde
- Department of Biochemistry, University of Toronto, 661 University Ave, Toronto, ON, M5G 1M1, Canada.
- Department of Molecular Genetics, University of Toronto, 661 University Ave, Toronto, ON, M5G 1M1, Canada.
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2
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Sundby LJ, Southern WM, Sun J, Patrinostro X, Zhang W, Yong J, Ervasti JM. Deletion of exons 2 and 3 from Actb and cell immortalization lead to widespread, β-actin independent alterations in gene expression associated with cell cycle control. Eur J Cell Biol 2024; 103:151397. [PMID: 38387258 DOI: 10.1016/j.ejcb.2024.151397] [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: 10/29/2023] [Revised: 02/11/2024] [Accepted: 02/12/2024] [Indexed: 02/24/2024] Open
Abstract
The cytoplasmic actin proteins, β- and γ-actin, are 99% identical but thought to perform non-redundant functions. The nucleotide coding regions of cytoplasmic actin genes, Actb and Actg1, are 89% identical. Knockout (KO) of Actb by Cre-mediated deletion of first coding exons 2 and 3 in mice is embryonic lethal and fibroblasts derived from KO embryos (MEFs) fail to proliferate. In contrast, Actg1 KO MEFs display with a much milder defect in cell proliferation and Actg1 KO mice are viable, but present with increased perinatal lethality. Recent studies have identified important protein-independent functions for both Actb and Actg1 and demonstrate that deletions within the Actb nucleotide sequence, and not loss of the β-actin protein, cause the most severe phenotypes in KO mice and cells. Here, we use a multi-omics approach to better understand what drives the phenotypes of Actb KO MEFs. RNA-sequencing and mass spectrometry reveal largescale changes to the transcriptome, proteome, and phosphoproteome in cells lacking Actb but not those only lacking β-actin protein. Pathway analysis of genes and proteins differentially expressed upon Actb KO suggest widespread dysregulation of genes involved in the cell cycle that may explain the severe defect in proliferation.
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Affiliation(s)
- Lauren J Sundby
- Program in Molecular, Cellular, Developmental Biology, and Genetics, University of Minnesota, Minneapolis, MN 55455, USA
| | - William M Southern
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jiao Sun
- Department of Computer Science, University of Central Florida, Orlando, FL 32816, USA
| | - Xiaobai Patrinostro
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Wei Zhang
- Department of Computer Science, University of Central Florida, Orlando, FL 32816, USA
| | - Jeongsik Yong
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - James M Ervasti
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.
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3
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Greve JN, Marquardt A, Heiringhoff R, Reindl T, Thiel C, Di Donato N, Taft MH, Manstein DJ. The non-muscle actinopathy-associated mutation E334Q in cytoskeletal γ-actin perturbs interaction of actin filaments with myosin and ADF/cofilin family proteins. eLife 2024; 12:RP93013. [PMID: 38446501 PMCID: PMC10942649 DOI: 10.7554/elife.93013] [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] [Indexed: 03/07/2024] Open
Abstract
Various heterozygous cytoskeletal γ-actin mutations have been shown to cause Baraitser-Winter cerebrofrontofacial syndrome, non-syndromic hearing loss, or isolated eye coloboma. Here, we report the biochemical characterization of human cytoskeletal γ-actin carrying mutation E334Q, a mutation that leads to a hitherto unspecified non-muscle actinopathy. Following expression, purification, and removal of linker and thymosin β4 tag sequences, the p.E334Q monomers show normal integration into linear and branched actin filaments. The mutation does not affect thermal stability, actin filament nucleation, elongation, and turnover. Model building and normal mode analysis predict significant differences in the interaction of p.E334Q filaments with myosin motors and members of the ADF/cofilin family of actin-binding proteins. Assays probing the interactions of p.E334Q filaments with human class 2 and class 5 myosin motor constructs show significant reductions in sliding velocity and actin affinity. E334Q differentially affects cofilin-mediated actin dynamics by increasing the rate of cofilin-mediated de novo nucleation of actin filaments and decreasing the efficiency of cofilin-mediated filament severing. Thus, it is likely that p.E334Q-mediated changes in myosin motor activity, as well as filament turnover, contribute to the observed disease phenotype.
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Affiliation(s)
- Johannes N Greve
- Institute for Biophysical Chemistry, Hannover Medical School, Fritz Hartmann Centre for MedicalHannoverGermany
| | - Anja Marquardt
- Institute for Biophysical Chemistry, Hannover Medical School, Fritz Hartmann Centre for MedicalHannoverGermany
| | - Robin Heiringhoff
- Institute for Biophysical Chemistry, Hannover Medical School, Fritz Hartmann Centre for MedicalHannoverGermany
| | - Theresia Reindl
- Institute for Biophysical Chemistry, Hannover Medical School, Fritz Hartmann Centre for MedicalHannoverGermany
| | - Claudia Thiel
- Institute for Biophysical Chemistry, Hannover Medical School, Fritz Hartmann Centre for MedicalHannoverGermany
| | | | - Manuel H Taft
- Institute for Biophysical Chemistry, Hannover Medical School, Fritz Hartmann Centre for MedicalHannoverGermany
| | - Dietmar J Manstein
- Institute for Biophysical Chemistry, Hannover Medical School, Fritz Hartmann Centre for MedicalHannoverGermany
- Division for Structural Biochemistry, Hannover Medical SchoolHannoverGermany
- RESiST, Cluster of Excellence 2155, Hannover Medical SchoolHannoverGermany
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4
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Kyslík J, Born-Torrijos A, Holzer AS, Kosakyan A. RNAi-directed knockdown in the cnidarian fish blood parasite Sphaerospora molnari. Sci Rep 2024; 14:3545. [PMID: 38347054 PMCID: PMC10861503 DOI: 10.1038/s41598-024-54171-0] [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: 12/05/2023] [Accepted: 02/09/2024] [Indexed: 02/15/2024] Open
Abstract
RNA interference (RNAi) is an effective approach to suppress gene expression and monitor gene regulation. Despite its wide application, its use is limited in certain taxonomic groups, including cnidarians. Myxozoans are a unique group of cnidarian parasites that diverged from their free-living ancestors about 600 million years ago, with several species causing acute disease in farmed and wild fish populations. In this pioneering study we successfully applied RNAi in blood stages of the myxozoan Sphaerospora molnari, combining a dsRNA soaking approach, real-time PCR, confocal microscopy, and Western blotting. For proof of concept, we knocked down two unusual actins, one of which is known to play a critical role in S. molnari cell motility. We observed intracellular uptake of dsRNA after 30 min and accumulation in all cells of the typical myxozoan cell-in-cell structure. We successfully knocked down actin in S. molnari in vitro, with transient inhibition for 48 h. We observed the disruption of the cytoskeletal network within the primary cell and loss of the characteristic rotational cell motility. This RNAi workflow could significantly advance functional research within the Myxozoa, offering new prospects for investigating therapeutic targets and facilitating drug discovery against economically important fish parasites.
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Affiliation(s)
- Jiří Kyslík
- Institute of Parasitology, Biology Centre, Academy of Sciences of the Czech Republic, Ceske Budejovice, Czech Republic.
| | - Ana Born-Torrijos
- Institute of Parasitology, Biology Centre, Academy of Sciences of the Czech Republic, Ceske Budejovice, Czech Republic
- Department of Coastal Systems, NIOZ Royal Netherlands Institute for Sea Research, Den Burg, PO Box 59, 1790 AB, Texel, The Netherlands
| | - Astrid S Holzer
- Institute of Parasitology, Biology Centre, Academy of Sciences of the Czech Republic, Ceske Budejovice, Czech Republic
- Fish Health Division, University of Veterinary Medicine, Vienna, Austria
| | - Anush Kosakyan
- Institute of Parasitology, Biology Centre, Academy of Sciences of the Czech Republic, Ceske Budejovice, Czech Republic
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
- National Biodiversity Future Center (NBFC), Palermo, Italy
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5
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Chaung K, Baharav TZ, Henderson G, Zheludev IN, Wang PL, Salzman J. SPLASH: A statistical, reference-free genomic algorithm unifies biological discovery. Cell 2023; 186:5440-5456.e26. [PMID: 38065078 PMCID: PMC10861363 DOI: 10.1016/j.cell.2023.10.028] [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: 08/16/2022] [Revised: 08/31/2023] [Accepted: 10/26/2023] [Indexed: 12/18/2023]
Abstract
Today's genomics workflows typically require alignment to a reference sequence, which limits discovery. We introduce a unifying paradigm, SPLASH (Statistically Primary aLignment Agnostic Sequence Homing), which directly analyzes raw sequencing data, using a statistical test to detect a signature of regulation: sample-specific sequence variation. SPLASH detects many types of variation and can be efficiently run at scale. We show that SPLASH identifies complex mutation patterns in SARS-CoV-2, discovers regulated RNA isoforms at the single-cell level, detects the vast sequence diversity of adaptive immune receptors, and uncovers biology in non-model organisms undocumented in their reference genomes: geographic and seasonal variation and diatom association in eelgrass, an oceanic plant impacted by climate change, and tissue-specific transcripts in octopus. SPLASH is a unifying approach to genomic analysis that enables expansive discovery without metadata or references.
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Affiliation(s)
- Kaitlin Chaung
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA; Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - Tavor Z Baharav
- Department of Electrical Engineering, Stanford University, Stanford, CA 94305, USA
| | - George Henderson
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA; Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - Ivan N Zheludev
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - Peter L Wang
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA; Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - Julia Salzman
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA; Department of Biochemistry, Stanford University, Stanford, CA 94305, USA; Department of Statistics (by courtesy), Stanford University, Stanford, CA 94305, USA; Department of Biology (by courtesy), Stanford University, Stanford, CA 94305, USA.
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6
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Nietmann P, Kaub K, Suchenko A, Stenz S, Warnecke C, Balasubramanian MK, Janshoff A. Cytosolic actin isoforms form networks with different rheological properties that indicate specific biological function. Nat Commun 2023; 14:7989. [PMID: 38042893 PMCID: PMC10693642 DOI: 10.1038/s41467-023-43653-w] [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: 05/03/2023] [Accepted: 11/15/2023] [Indexed: 12/04/2023] Open
Abstract
The implications of the existence of different actins expressed in epithelial cells for network mechanics and dynamics is investigated by microrheology and confocal imaging. γ-actin predominately found in the apical cortex forms stiffer networks compared to β-actin, which is preferentially organized in stress fibers. We attribute this to selective interactions with Mg2+-ions interconnecting the filaments' N-termini. Bundling propensity of the isoforms is different in the presence of Mg2+-ions, while crosslinkers such as α-actinin, fascin, and heavy meromyosin alter the mechanical response independent of the isoform. In the presence of myosin, β-actin networks show a large number of small contraction foci, while γ-actin displays larger but fewer foci indicative of a stronger interaction with myosin motors. We infer that subtle changes in the amino acid sequence of actin isoforms lead to alterations of the mechanical properties on the network level with potential implications for specific biological functions.
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Affiliation(s)
- Peter Nietmann
- Institute of Physical Chemistry, University of Goettingen, Tammannstr. 6, Göttingen, 37077, Germany
| | - Kevin Kaub
- Institute of Physical Chemistry, University of Goettingen, Tammannstr. 6, Göttingen, 37077, Germany
- Max Planck School Matter to Life, Max Planck Institute for Medical Research, Jahnstr. 29, Heidelberg, 69120, Germany
| | - Andrejus Suchenko
- Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - Susanne Stenz
- Institute of Physical Chemistry, University of Goettingen, Tammannstr. 6, Göttingen, 37077, Germany
| | - Claas Warnecke
- Institute of Physical Chemistry, University of Goettingen, Tammannstr. 6, Göttingen, 37077, Germany
| | | | - Andreas Janshoff
- Institute of Physical Chemistry, University of Goettingen, Tammannstr. 6, Göttingen, 37077, Germany.
- Max Planck School Matter to Life, Max Planck Institute for Medical Research, Jahnstr. 29, Heidelberg, 69120, Germany.
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7
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Bai Y, Zhao F, Wu T, Chen F, Pang X. Actin polymerization and depolymerization in developing vertebrates. Front Physiol 2023; 14:1213668. [PMID: 37745245 PMCID: PMC10515290 DOI: 10.3389/fphys.2023.1213668] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 08/22/2023] [Indexed: 09/26/2023] Open
Abstract
Development is a complex process that occurs throughout the life cycle. F-actin, a major component of the cytoskeleton, is essential for the morphogenesis of tissues and organs during development. F-actin is formed by the polymerization of G-actin, and the dynamic balance of polymerization and depolymerization ensures proper cellular function. Disruption of this balance results in various abnormalities and defects or even embryonic lethality. Here, we reviewed recent findings on the structure of G-actin and F-actin and the polymerization of G-actin to F-actin. We also focused on the functions of actin isoforms and the underlying mechanisms of actin polymerization/depolymerization in cellular and organic morphogenesis during development. This information will extend our understanding of the role of actin polymerization in the physiologic or pathologic processes during development and may open new avenues for developing therapeutics for embryonic developmental abnormalities or tissue regeneration.
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Affiliation(s)
- Yang Bai
- Stomatological Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, China
| | - Feng Zhao
- Stomatological Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, China
| | - Tingting Wu
- Stomatological Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, China
| | - Fangchun Chen
- Stomatological Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, China
| | - Xiaoxiao Pang
- Stomatological Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, China
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8
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Lambert C, Schmidt K, Karger M, Stadler M, Stradal TEB, Rottner K. Cytochalasans and Their Impact on Actin Filament Remodeling. Biomolecules 2023; 13:1247. [PMID: 37627312 PMCID: PMC10452583 DOI: 10.3390/biom13081247] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 07/28/2023] [Accepted: 08/06/2023] [Indexed: 08/27/2023] Open
Abstract
The eukaryotic actin cytoskeleton comprises the protein itself in its monomeric and filamentous forms, G- and F-actin, as well as multiple interaction partners (actin-binding proteins, ABPs). This gives rise to a temporally and spatially controlled, dynamic network, eliciting a plethora of motility-associated processes. To interfere with the complex inter- and intracellular interactions the actin cytoskeleton confers, small molecular inhibitors have been used, foremost of all to study the relevance of actin filaments and their turnover for various cellular processes. The most prominent inhibitors act by, e.g., sequestering monomers or by interfering with the polymerization of new filaments and the elongation of existing filaments. Among these inhibitors used as tool compounds are the cytochalasans, fungal secondary metabolites known for decades and exploited for their F-actin polymerization inhibitory capabilities. In spite of their application as tool compounds for decades, comprehensive data are lacking that explain (i) how the structural deviances of the more than 400 cytochalasans described to date influence their bioactivity mechanistically and (ii) how the intricate network of ABPs reacts (or adapts) to cytochalasan binding. This review thus aims to summarize the information available concerning the structural features of cytochalasans and their influence on the described activities on cell morphology and actin cytoskeleton organization in eukaryotic cells.
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Affiliation(s)
- Christopher Lambert
- Molecular Cell Biology Group, Helmholtz Centre for Infection Research (HZI), Inhoffenstrasse 7, 38124 Braunschweig, Germany
- Department of Cell Biology, Helmholtz Centre for Infection Research (HZI), Inhoffenstrasse 7, 38124 Braunschweig, Germany
- Department of Microbial Drugs, Helmholtz Centre for Infection Research and German Centre for Infection Research (DZIF), Partner Site Hannover/Braunschweig, Inhoffenstrasse 7, 38124 Braunschweig, Germany;
| | - Katharina Schmidt
- Department of Cell Biology, Helmholtz Centre for Infection Research (HZI), Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Marius Karger
- Molecular Cell Biology Group, Helmholtz Centre for Infection Research (HZI), Inhoffenstrasse 7, 38124 Braunschweig, Germany
- Division of Molecular Cell Biology, Zoological Institute, Technische Universität Braunschweig, Spielmannstrasse 7, 38106 Braunschweig, Germany
| | - Marc Stadler
- Department of Microbial Drugs, Helmholtz Centre for Infection Research and German Centre for Infection Research (DZIF), Partner Site Hannover/Braunschweig, Inhoffenstrasse 7, 38124 Braunschweig, Germany;
| | - Theresia E. B. Stradal
- Department of Cell Biology, Helmholtz Centre for Infection Research (HZI), Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Klemens Rottner
- Molecular Cell Biology Group, Helmholtz Centre for Infection Research (HZI), Inhoffenstrasse 7, 38124 Braunschweig, Germany
- Department of Cell Biology, Helmholtz Centre for Infection Research (HZI), Inhoffenstrasse 7, 38124 Braunschweig, Germany
- Division of Molecular Cell Biology, Zoological Institute, Technische Universität Braunschweig, Spielmannstrasse 7, 38106 Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), 38106 Braunschweig, Germany
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9
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Chaung K, Baharav TZ, Henderson G, Zheludev IN, Wang PL, Salzman J. [WITHDRAWN] SPLASH: a statistical, reference-free genomic algorithm unifies biological discovery. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.17.549408. [PMID: 37503014 PMCID: PMC10370119 DOI: 10.1101/2023.07.17.549408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
The authors have withdrawn this manuscript due to a duplicate posting of manuscript number BIORXIV/2022/497555. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author. The correct preprint can be found at doi: https://doi.org/10.1101/2022.06.24.497555.
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10
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Chaung K, Baharav TZ, Henderson G, Zheludev IN, Wang PL, Salzman J. SPLASH: a statistical, reference-free genomic algorithm unifies biological discovery. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2022.06.24.497555. [PMID: 35794890 PMCID: PMC9258296 DOI: 10.1101/2022.06.24.497555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
Today's genomics workflows typically require alignment to a reference sequence, which limits discovery. We introduce a new unifying paradigm, SPLASH (Statistically Primary aLignment Agnostic Sequence Homing), an approach that directly analyzes raw sequencing data to detect a signature of regulation: sample-specific sequence variation. The approach, which includes a new statistical test, is computationally efficient and can be run at scale. SPLASH unifies detection of myriad forms of sequence variation. We demonstrate that SPLASH identifies complex mutation patterns in SARS-CoV-2 strains, discovers regulated RNA isoforms at the single cell level, documents the vast sequence diversity of adaptive immune receptors, and uncovers biology in non-model organisms undocumented in their reference genomes: geographic and seasonal variation and diatom association in eelgrass, an oceanic plant impacted by climate change, and tissue-specific transcripts in octopus. SPLASH is a new unifying approach to genomic analysis that enables an expansive scope of discovery without metadata or references.
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Affiliation(s)
- Kaitlin Chaung
- Department of Biomedical Data Science, Stanford University, Stanford, 94305, USA
- Department of Biochemistry, Stanford University, Stanford, 94305, USA
| | - Tavor Z. Baharav
- Department of Electrical Engineering, Stanford University, Stanford, 94305, USA
| | - George Henderson
- Department of Biomedical Data Science, Stanford University, Stanford, 94305, USA
- Department of Biochemistry, Stanford University, Stanford, 94305, USA
| | - Ivan N. Zheludev
- Department of Biochemistry, Stanford University, Stanford, 94305, USA
| | - Peter L. Wang
- Department of Biomedical Data Science, Stanford University, Stanford, 94305, USA
- Department of Biochemistry, Stanford University, Stanford, 94305, USA
| | - Julia Salzman
- Department of Biomedical Data Science, Stanford University, Stanford, 94305, USA
- Department of Biochemistry, Stanford University, Stanford, 94305, USA
- Department of Statistics (by courtesy), Stanford University, Stanford, 94305, USA
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11
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Xu AF, Molinuevo R, Fazzari E, Tom H, Zhang Z, Menendez J, Casey KM, Ruggero D, Hinck L, Pritchard JK, Barna M. Subfunctionalized expression drives evolutionary retention of ribosomal protein paralogs Rps27 and Rps27l in vertebrates. eLife 2023; 12:e78695. [PMID: 37306301 PMCID: PMC10313321 DOI: 10.7554/elife.78695] [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: 03/16/2022] [Accepted: 06/09/2023] [Indexed: 06/13/2023] Open
Abstract
The formation of paralogs through gene duplication is a core evolutionary process. For paralogs that encode components of protein complexes such as the ribosome, a central question is whether they encode functionally distinct proteins or whether they exist to maintain appropriate total expression of equivalent proteins. Here, we systematically tested evolutionary models of paralog function using the ribosomal protein paralogs Rps27 (eS27) and Rps27l (eS27L) as a case study. Evolutionary analysis suggests that Rps27 and Rps27l likely arose during whole-genome duplication(s) in a common vertebrate ancestor. We show that Rps27 and Rps27l have inversely correlated mRNA abundance across mouse cell types, with the highest Rps27 in lymphocytes and the highest Rps27l in mammary alveolar cells and hepatocytes. By endogenously tagging the Rps27 and Rps27l proteins, we demonstrate that Rps27- and Rps27l-ribosomes associate preferentially with different transcripts. Furthermore, murine Rps27 and Rps27l loss-of-function alleles are homozygous lethal at different developmental stages. However, strikingly, expressing Rps27 protein from the endogenous Rps27l locus or vice versa completely rescues loss-of-function lethality and yields mice with no detectable deficits. Together, these findings suggest that Rps27 and Rps27l are evolutionarily retained because their subfunctionalized expression patterns render both genes necessary to achieve the requisite total expression of two equivalent proteins across cell types. Our work represents the most in-depth characterization of a mammalian ribosomal protein paralog to date and highlights the importance of considering both protein function and expression when investigating paralogs.
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Affiliation(s)
- Adele Francis Xu
- Department of Genetics, Stanford UniversityStanfordUnited States
- Medical Scientist Training Program, Stanford School of MedicineStanfordUnited States
| | - Rut Molinuevo
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa CruzSanta CruzUnited States
| | - Elisa Fazzari
- Helen Diller Family Comprehensive Cancer Center, University of California, Los AngelesLos AngelesUnited States
- Department of Cellular and Molecular Pharmacology, University of California, San FranciscoSan FranciscoUnited States
- Department of Urology, University of California, San FranciscoSan FranciscoUnited States
| | - Harrison Tom
- Helen Diller Family Comprehensive Cancer Center, University of California, Los AngelesLos AngelesUnited States
- Department of Cellular and Molecular Pharmacology, University of California, San FranciscoSan FranciscoUnited States
- Department of Urology, University of California, San FranciscoSan FranciscoUnited States
| | - Zijian Zhang
- Department of Chemical and Systems Biology, Stanford UniversityStanfordUnited States
| | - Julien Menendez
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa CruzSanta CruzUnited States
| | - Kerriann M Casey
- Department of Biology, Stanford UniversityStanfordUnited States
- Department of Comparative Medicine, Stanford School of MedicineStanfordUnited States
| | - Davide Ruggero
- Department of Cellular and Molecular Pharmacology, University of California, San FranciscoSan FranciscoUnited States
- Department of Urology, University of California, San FranciscoSan FranciscoUnited States
| | - Lindsay Hinck
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa CruzSanta CruzUnited States
| | | | - Maria Barna
- Department of Genetics, Stanford UniversityStanfordUnited States
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12
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Vedula P, Fina ME, Bell BA, Nikonov SS, Kashina A, Dong DW. β -actin is essential for structural integrity and physiological function of the retina. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.27.534392. [PMID: 37034790 PMCID: PMC10081178 DOI: 10.1101/2023.03.27.534392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Lack of non-muscle β -actin gene (Actb) leads to early embryonic lethality in mice, however mice with β - to γ -actin replacement develop normally and show no detectable phenotypes at young age. Here we investigated the effect of this replacement in the retina. During aging, these mice have accelerated de-generation of retinal structure and function, including elongated microvilli and defective mitochondria of retinal pigment epithelium (RPE), abnormally bulging photoreceptor outer segments (OS) accompanied by reduced transducin concentration and light sensitivity, and accumulation of autofluorescent microglia cells in the subretinal space between RPE and OS. These defects are accompanied by changes in the F-actin binding of several key actin interacting partners, including ezrin, myosin, talin, and vinculin known to play central roles in modulating actin cytoskeleton and cell adhesion and mediating the phagocytosis of OS. Our data show that β -actin protein is essential for maintaining normal retinal structure and function.
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13
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Chen L, Vedula P, Tang HY, Dong DW, Kashina AS. Differential N-terminal processing of beta and gamma actin. iScience 2022; 25:105186. [PMID: 36248738 PMCID: PMC9556930 DOI: 10.1016/j.isci.2022.105186] [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: 04/08/2022] [Revised: 09/02/2022] [Accepted: 09/20/2022] [Indexed: 11/30/2022] Open
Abstract
Cytoplasmic beta- and gamma-actin are ubiquitously expressed in every eukaryotic cell. They are encoded by different genes, but their amino acid sequences differ only by four conservative substitutions at the N-termini, making it difficult to dissect their individual regulation. Here, we analyzed actin from cultured cells and tissues by mass spectrometry and found that beta, unlike gamma actin, undergoes sequential removal of N-terminal Asp residues, leading to truncated actin species found in both F- and G-actin preparations. This processing affects up to ∼3% of beta actin in different cell types. We used CRISPR/Cas-9 in cultured cells to delete two candidate enzymes capable of mediating this type of processing. This deletion abolishes most of the beta actin N-terminal processing and results in changes in F-actin levels, cell spreading, filopodia formation, and cell migration. Our results demonstrate previously unknown isoform-specific actin regulation that can potentially affect actin functions in cells.
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Affiliation(s)
- Li Chen
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA 19104, USA
| | - Pavan Vedula
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA 19104, USA
| | | | - Dawei W. Dong
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA 19104, USA
| | - Anna S. Kashina
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA 19104, USA,Corresponding author
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14
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Ivanov AI, Lechuga S, Marino‐Melendez A, Naydenov NG. Unique and redundant functions of cytoplasmic actins and nonmuscle myosin II isoforms at epithelial junctions. Ann N Y Acad Sci 2022; 1515:61-74. [PMID: 35673768 PMCID: PMC9489603 DOI: 10.1111/nyas.14808] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The integrity and functions of epithelial barriers depend on the formation of adherens junctions (AJs) and tight junctions (TJs). A characteristic feature of AJs and TJs is their association with the cortical cytoskeleton composed of actin filaments and nonmuscle myosin II (NM-II) motors. Mechanical forces generated by the actomyosin cytoskeleton are essential for junctional assembly, stability, and remodeling. Epithelial cells express two different actin proteins and three NM-II isoforms, all known to be associated with AJs and TJs. Despite their structural similarity, different actin and NM-II isoforms have distinct biochemical properties, cellular distribution, and functions. The diversity of epithelial actins and myosin motors could be essential for the regulation of different steps of junctional formation, maturation, and disassembly. This review focuses on the roles of actin and NM-II isoforms in controlling the integrity and barrier properties of various epithelia. We discuss the effects of the depletion of individual actin isoforms and NM-II motors on the assembly and barrier function of AJs and TJs in model epithelial monolayers in vitro. We also describe the functional consequences of either total or tissue-specific gene knockout of different actins and NM-II motors, with a focus on the development and integrity of different epithelia in vivo.
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Affiliation(s)
- Andrei I. Ivanov
- Department of Inflammation and Immunity, Lerner Research InstituteCleveland ClinicClevelandOhioUSA
| | - Susana Lechuga
- Department of Inflammation and Immunity, Lerner Research InstituteCleveland ClinicClevelandOhioUSA
| | - Armando Marino‐Melendez
- Department of Inflammation and Immunity, Lerner Research InstituteCleveland ClinicClevelandOhioUSA
| | - Nayden G. Naydenov
- Department of Inflammation and Immunity, Lerner Research InstituteCleveland ClinicClevelandOhioUSA
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15
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Sundby LJ, Southern WM, Hawbaker KM, Trujillo JM, Perrin BJ, Ervasti JM. Nucleotide- and Protein-Dependent Functions of Actg1. Mol Biol Cell 2022; 33:ar77. [PMID: 35594181 PMCID: PMC9582642 DOI: 10.1091/mbc.e22-02-0054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 05/10/2022] [Accepted: 05/11/2022] [Indexed: 11/11/2022] Open
Abstract
Cytoplasmic β- and γ-actin proteins are 99% identical but support unique organismal functions. The cytoplasmic actin nucleotide sequences Actb and Actg1, respectively, are more divergent but still 89% similar. Actb-/- mice are embryonic lethal and Actb-/- cells fail to proliferate, but editing the Actb gene to express γ-actin (Actbc-g) resulted in none of the overt phenotypes of the knockout revealing protein-independent functions for Actb. To determine if Actg1 has a protein-independent function, we crossed Actbc-g and Actg1-/- mice to generate the bG/0 line, where the only cytoplasmic actin expressed is γ-actin from Actbc-g. The bG/0 mice were viable but showed a survival defect despite expressing γ-actin protein at levels no different from bG/gG with normal survival. A unique myopathy phenotype was also observed in bG/0 mice. We conclude that impaired survival and myopathy in bG/0 mice are due to loss of Actg1 nucleotide-dependent function(s). On the other hand, the bG/0 genotype rescued functions impaired by Actg1-/-, including cell proliferation and auditory function, suggesting a role for γ-actin protein in both fibroblasts and hearing. Together, these results identify nucleotide-dependent functions for Actg1 while implicating γ-actin protein in more cell-/tissue-specific functions.
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Affiliation(s)
- Lauren J. Sundby
- Program in Molecular, Cellular, Developmental Biology, and Genetics, and
| | - William M. Southern
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455
| | - Katelin M. Hawbaker
- Department of Biology, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46022
| | - Jesús M. Trujillo
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455
| | - Benjamin J. Perrin
- Department of Biology, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46022
| | - James M. Ervasti
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455
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16
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Faruangsaeng T, Thaweesapphitak S, Khamwachirapitak C, Porntaveetus T, Shotelersuk V. Comparative transcriptome profiles of human dental pulp stem cells from maxillary and mandibular teeth. Sci Rep 2022; 12:8860. [PMID: 35614192 PMCID: PMC9133121 DOI: 10.1038/s41598-022-12867-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 05/11/2022] [Indexed: 11/09/2022] Open
Abstract
The molecular control of tooth development is different between the maxilla and mandible, contributing to different tooth shapes and locations; however, whether this difference occurs in human permanent teeth is unknown. The aim of this study was to investigate and compare the transcriptome profiles of permanent maxillary and mandibular posterior teeth. Ten participants who had a pair of opposing premolars or molars extracted were recruited. The RNA obtained from cultured dental pulp stem cells underwent RNA-sequencing and qRT-PCR. The transcriptome profiles of two opposing premolar pairs and two molar pairs demonstrated that the upper premolars, lower premolars, upper molars, and lower molars expressed the same top-ranked genes, comprising FN1, COL1A1, COL1A2, ACTB, and EEFIA1, which are involved in extracellular matrix organization, immune system, signal transduction, hemostasis, and vesicle-mediated transport. Comparative transcriptome analyses of each/combined tooth pairs demonstrated that PITX1 was the only gene with different expression levels between upper and lower posterior teeth. PITX1 exhibited a 64-fold and 116-fold higher expression level in lower teeth compared with their upper premolars and molars, respectively. These differences were confirmed by qRT-PCR. Taken together, this study, for the first time, reveals that PITX1 is expressed significantly higher in mandibular posterior teeth compared with maxillary posterior teeth. The difference is more evident in the molars compared with premolars and consistent with its expression pattern in mouse developing teeth. We demonstrate that differences in lower versus upper teeth gene expression during odontogenesis occur in permanent teeth and suggest that these differences should be considered in molecular studies of dental pulp stem cells. Our findings pave the way to develop a more precise treatment in regenerative dentistry such as gene-based therapies for dentin/pulp regeneration and regeneration of different tooth types.
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Affiliation(s)
- Thira Faruangsaeng
- International Graduate Program in Geriatric Dentistry and Special Patients Care, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand.,Center of Excellence in Genomics and Precision Dentistry, Department of Physiology, Faculty of Dentistry, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Sermporn Thaweesapphitak
- Center of Excellence in Genomics and Precision Dentistry, Department of Physiology, Faculty of Dentistry, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Chompak Khamwachirapitak
- Center of Excellence in Genomics and Precision Dentistry, Department of Physiology, Faculty of Dentistry, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Thantrira Porntaveetus
- International Graduate Program in Geriatric Dentistry and Special Patients Care, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand. .,Center of Excellence in Genomics and Precision Dentistry, Department of Physiology, Faculty of Dentistry, Chulalongkorn University, Bangkok, 10330, Thailand.
| | - Vorasuk Shotelersuk
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.,Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, Thailand
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17
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Functional Remodeling of the Contractile Smooth Muscle Cell Cortex, a Provocative Concept, Supported by Direct Visualization of Cortical Remodeling. BIOLOGY 2022; 11:biology11050662. [PMID: 35625390 PMCID: PMC9138025 DOI: 10.3390/biology11050662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/06/2022] [Accepted: 04/24/2022] [Indexed: 11/17/2022]
Abstract
Simple Summary As a key element of the smooth muscle cell contractile apparatus, the actin cytoskeleton participates in the development of force by acting as a molecular track for the myosin cross bridge motor. At the same time, the actin cytoskeleton must transmit the force developed during contraction to the extracellular matrix and, thus, to neighboring cells. This propagation of force to the cell periphery and beyond is initiated in part on specifically localized cellular cortical actin filaments also involved in mechano-chemical transduction. During the contractile process itself and in response to extracellular structural and chemical alterations, the smooth muscle actin cytoskeletal remodels. This indicates that the cytoskeleton is a dynamic cellular organelle that adapts to the changes in cell shape and chemical cues. Current evidence connecting contractile function and mechano-transduction mechanisms to the plasticity of the vascular smooth muscle actin cytoskeleton is reviewed; we then describe new evidence for cytoskeletal remodeling in vascular smooth muscle cells. Here, using immunoelectron microscopy, we visualize the actin binding proteins filamin A, zyxin and talin in these cells and show that they participate in the cortical cell cytoskeletal alteration, thus supporting the premise that smooth muscle cell remodeling occurs during contraction. Abstract Considerable controversy has surrounded the functional anatomy of the cytoskeleton of the contractile vascular smooth muscle cell. Recent studies have suggested a dynamic nature of the cortical cytoskeleton of these cells, but direct proof has been lacking. Here, we review past studies in this area suggesting a plasticity of smooth muscle cells. We also present images testing these suggestions by using the technique of immunoelectron microscopy of metal replicas to directly visualize the cortical actin cytoskeleton of the contractile smooth muscle cell along with interactions by representative cytoskeletal binding proteins. We find the cortical cytoskeletal matrix to be a branched, interconnected network of linear actin bundles. Here, the focal adhesion proteins talin and zyxin were localized with nanometer accuracy. Talin is reported in past studies to span the integrin–cytoplasm distance in fibroblasts and zyxin is known to be an adaptor protein between alpha-actinin and VASP. In response to activation of signal transduction with the alpha-agonist phenylephrine, we found that no movement of talin was detectable but that the zyxin-zyxin spacing was statistically significantly decreased in the smooth muscle cells examined. Contractile smooth muscle is often assumed to have a fixed cytoskeletal structure. Thus, the results included here are important in that they directly support the concept at the electron microscopic level that the focal adhesion of the contractile smooth muscle cell has a dynamic nature and that the protein–protein interfaces showing plasticity are protein-specific.
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18
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Boiero Sanders M, Toret CP, Guillotin A, Antkowiak A, Vannier T, Robinson RC, Michelot A. Specialization of actin isoforms derived from the loss of key interactions with regulatory factors. EMBO J 2022; 41:e107982. [PMID: 35178724 PMCID: PMC8886540 DOI: 10.15252/embj.2021107982] [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: 02/09/2021] [Revised: 01/19/2022] [Accepted: 01/21/2022] [Indexed: 11/09/2022] Open
Abstract
A paradox of eukaryotic cells is that while some species assemble a complex actin cytoskeleton from a single ortholog, other species utilize a greater diversity of actin isoforms. The physiological consequences of using different actin isoforms, and the molecular mechanisms by which highly conserved actin isoforms are segregated into distinct networks, are poorly known. Here, we sought to understand how a simple biological system, composed of a unique actin and a limited set of actin‐binding proteins, reacts to a switch to heterologous actin expression. Using yeast as a model system and biomimetic assays, we show that such perturbation causes drastic reorganization of the actin cytoskeleton. Our results indicate that defective interaction of a heterologous actin for important regulators of actin assembly limits certain actin assembly pathways while reinforcing others. Expression of two heterologous actin variants, each specialized in assembling a different network, rescues cytoskeletal organization and confers resistance to external perturbation. Hence, while species using a unique actin have homeostatic actin networks, actin assembly pathways in species using several actin isoforms may act more independently.
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Affiliation(s)
| | - Christopher P Toret
- CNRS, IBDM, Turing Centre for Living Systems, Aix Marseille Univ, Marseille, France
| | - Audrey Guillotin
- CNRS, IBDM, Turing Centre for Living Systems, Aix Marseille Univ, Marseille, France
| | - Adrien Antkowiak
- CNRS, IBDM, Turing Centre for Living Systems, Aix Marseille Univ, Marseille, France
| | - Thomas Vannier
- CNRS, IBDM, Turing Centre for Living Systems, Aix Marseille Univ, Marseille, France
| | - Robert C Robinson
- Research Institute for Interdisciplinary Science (RIIS), Okayama University, Okayama, Japan.,School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Alphée Michelot
- CNRS, IBDM, Turing Centre for Living Systems, Aix Marseille Univ, Marseille, France
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19
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Bamburg JR, Minamide LS, Wiggan O, Tahtamouni LH, Kuhn TB. Cofilin and Actin Dynamics: Multiple Modes of Regulation and Their Impacts in Neuronal Development and Degeneration. Cells 2021; 10:cells10102726. [PMID: 34685706 PMCID: PMC8534876 DOI: 10.3390/cells10102726] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/06/2021] [Accepted: 10/07/2021] [Indexed: 02/06/2023] Open
Abstract
Proteins of the actin depolymerizing factor (ADF)/cofilin family are ubiquitous among eukaryotes and are essential regulators of actin dynamics and function. Mammalian neurons express cofilin-1 as the major isoform, but ADF and cofilin-2 are also expressed. All isoforms bind preferentially and cooperatively along ADP-subunits in F-actin, affecting the filament helical rotation, and when either alone or when enhanced by other proteins, promotes filament severing and subunit turnover. Although self-regulating cofilin-mediated actin dynamics can drive motility without post-translational regulation, cells utilize many mechanisms to locally control cofilin, including cooperation/competition with other proteins. Newly identified post-translational modifications function with or are independent from the well-established phosphorylation of serine 3 and provide unexplored avenues for isoform specific regulation. Cofilin modulates actin transport and function in the nucleus as well as actin organization associated with mitochondrial fission and mitophagy. Under neuronal stress conditions, cofilin-saturated F-actin fragments can undergo oxidative cross-linking and bundle together to form cofilin-actin rods. Rods form in abundance within neurons around brain ischemic lesions and can be rapidly induced in neurites of most hippocampal and cortical neurons through energy depletion or glutamate-induced excitotoxicity. In ~20% of rodent hippocampal neurons, rods form more slowly in a receptor-mediated process triggered by factors intimately connected to disease-related dementias, e.g., amyloid-β in Alzheimer’s disease. This rod-inducing pathway requires a cellular prion protein, NADPH oxidase, and G-protein coupled receptors, e.g., CXCR4 and CCR5. Here, we will review many aspects of cofilin regulation and its contribution to synaptic loss and pathology of neurodegenerative diseases.
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Affiliation(s)
- James R. Bamburg
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA; (L.S.M.); (O.W.); (L.H.T.); (T.B.K.)
- Correspondence: ; Tel.: +1-970-988-9120; Fax: +1-970-491-0494
| | - Laurie S. Minamide
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA; (L.S.M.); (O.W.); (L.H.T.); (T.B.K.)
| | - O’Neil Wiggan
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA; (L.S.M.); (O.W.); (L.H.T.); (T.B.K.)
| | - Lubna H. Tahtamouni
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA; (L.S.M.); (O.W.); (L.H.T.); (T.B.K.)
- Department of Biology and Biotechnology, The Hashemite University, Zarqa 13115, Jordan
| | - Thomas B. Kuhn
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA; (L.S.M.); (O.W.); (L.H.T.); (T.B.K.)
- Department of Chemistry and Biochemistry, University of Alaska, Fairbanks, AK 99775, USA
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20
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Olivieri JE, Dehghannasiri R, Wang PL, Jang S, de Morree A, Tan SY, Ming J, Ruohao Wu A, Quake SR, Krasnow MA, Salzman J. RNA splicing programs define tissue compartments and cell types at single-cell resolution. eLife 2021; 10:e70692. [PMID: 34515025 PMCID: PMC8563012 DOI: 10.7554/elife.70692] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 09/10/2021] [Indexed: 02/05/2023] Open
Abstract
The extent splicing is regulated at single-cell resolution has remained controversial due to both available data and methods to interpret it. We apply the SpliZ, a new statistical approach, to detect cell-type-specific splicing in >110K cells from 12 human tissues. Using 10X Chromium data for discovery, 9.1% of genes with computable SpliZ scores are cell-type-specifically spliced, including ubiquitously expressed genes MYL6 and RPS24. These results are validated with RNA FISH, single-cell PCR, and Smart-seq2. SpliZ analysis reveals 170 genes with regulated splicing during human spermatogenesis, including examples conserved in mouse and mouse lemur. The SpliZ allows model-based identification of subpopulations indistinguishable based on gene expression, illustrated by subpopulation-specific splicing of classical monocytes involving an ultraconserved exon in SAT1. Together, this analysis of differential splicing across multiple organs establishes that splicing is regulated cell-type-specifically.
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Affiliation(s)
- Julia Eve Olivieri
- Institute for Computational and Mathematical Engineering, Stanford UniversityStanfordUnited States
- Department of Biomedical Data Science, Stanford UniversityStanfordUnited States
- Department of Biochemistry, Stanford UniversityStanfordUnited States
| | - Roozbeh Dehghannasiri
- Department of Biomedical Data Science, Stanford UniversityStanfordUnited States
- Department of Biochemistry, Stanford UniversityStanfordUnited States
| | - Peter L Wang
- Department of Biochemistry, Stanford UniversityStanfordUnited States
| | - SoRi Jang
- Department of Biochemistry, Stanford UniversityStanfordUnited States
| | - Antoine de Morree
- Department of Neurology and Neurological Sciences, Stanford University School of MedicineStanfordUnited States
| | - Serena Y Tan
- Department of Pathology, Stanford University Medical CenterStanfordUnited States
| | - Jingsi Ming
- Academy for Statistics and Interdisciplinary Sciences, Faculty of Economics and Management,East China Normal UniversityShanghaiChina
- Department of Mathematics, The Hong Kong University of Science and TechnologyHong KongChina
| | - Angela Ruohao Wu
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and TechnologyHong KongChina
| | - Stephen R Quake
- Chan Zuckerberg BiohubSan FranciscoUnited States
- Department of Bioengineering, Stanford UniversityStanfordUnited States
| | - Mark A Krasnow
- Department of Biochemistry, Stanford UniversityStanfordUnited States
| | - Julia Salzman
- Department of Biomedical Data Science, Stanford UniversityStanfordUnited States
- Department of Biochemistry, Stanford UniversityStanfordUnited States
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21
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Miyoshi T, Belyantseva IA, Kitajiri SI, Miyajima H, Nishio SY, Usami SI, Kim BJ, Choi BY, Omori K, Shroff H, Friedman TB. Human deafness-associated variants alter the dynamics of key molecules in hair cell stereocilia F-actin cores. Hum Genet 2021; 141:363-382. [PMID: 34232383 DOI: 10.1007/s00439-021-02304-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 06/15/2021] [Indexed: 12/16/2022]
Abstract
Stereocilia protrude up to 100 µm from the apical surface of vertebrate inner ear hair cells and are packed with cross-linked filamentous actin (F-actin). They function as mechanical switches to convert sound vibration into electrochemical neuronal signals transmitted to the brain. Several genes encode molecular components of stereocilia including actin monomers, actin regulatory and bundling proteins, motor proteins and the proteins of the mechanotransduction complex. A stereocilium F-actin core is a dynamic system, which is continuously being remodeled while maintaining an outwardly stable architecture under the regulation of F-actin barbed-end cappers, severing proteins and crosslinkers. The F-actin cores of stereocilia also provide a pathway for motor proteins to transport cargos including components of tip-link densities, scaffolding proteins and actin regulatory proteins. Deficiencies and mutations of stereocilia components that disturb this "dynamic equilibrium" in stereocilia can induce morphological changes and disrupt mechanotransduction causing sensorineural hearing loss, best studied in mouse and zebrafish models. Currently, at least 23 genes, associated with human syndromic and nonsyndromic hearing loss, encode proteins involved in the development and maintenance of stereocilia F-actin cores. However, it is challenging to predict how variants associated with sensorineural hearing loss segregating in families affect protein function. Here, we review the functions of several molecular components of stereocilia F-actin cores and provide new data from our experimental approach to directly evaluate the pathogenicity and functional impact of reported and novel variants of DIAPH1 in autosomal-dominant DFNA1 hearing loss using single-molecule fluorescence microscopy.
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Affiliation(s)
- Takushi Miyoshi
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Porter Neuroscience Research Center, Room 1F-143A, Bethesda, MD, 20892, USA. .,Department of Otolaryngology-Head and Neck Surgery, Graduate School of Medicine, Kyoto University, Kyoto, 606-8507, Japan.
| | - Inna A Belyantseva
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Porter Neuroscience Research Center, Room 1F-143A, Bethesda, MD, 20892, USA
| | - Shin-Ichiro Kitajiri
- Department of Hearing Implant Sciences, Shinshu University School of Medicine, 390-8621, Matsumoto, Japan
| | - Hiroki Miyajima
- Department of Otolaryngology, Shinshu University School of Medicine, Matsumoto, 390-8621, Japan.,Department of Otolaryngology, Aizawa Hospital, Matsumoto, 390-8510, Japan
| | - Shin-Ya Nishio
- Department of Hearing Implant Sciences, Shinshu University School of Medicine, 390-8621, Matsumoto, Japan
| | - Shin-Ichi Usami
- Department of Hearing Implant Sciences, Shinshu University School of Medicine, 390-8621, Matsumoto, Japan
| | - Bong Jik Kim
- Department of Otolaryngology-Head and Neck Surgery, Chungnam National University College of Medicine, Chungnam National University Sejong Hospital, Sejong, 30099, South Korea.,Brain Research Institute, Chungnam National University College of Medicine, Daejeon, 35015, South Korea
| | - Byung Yoon Choi
- Department of Otorhinolaryngology, Seoul National University Bundang Hospital, Seongnam, 13620, South Korea
| | - Koichi Omori
- Department of Otolaryngology-Head and Neck Surgery, Graduate School of Medicine, Kyoto University, Kyoto, 606-8507, Japan
| | - Hari Shroff
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Thomas B Friedman
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Porter Neuroscience Research Center, Room 1F-143A, Bethesda, MD, 20892, USA
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22
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Vedula P, Kurosaka S, MacTaggart B, Ni Q, Papoian G, Jiang Y, Dong DW, Kashina A. Different translation dynamics of β- and γ-actin regulates cell migration. eLife 2021; 10:68712. [PMID: 34165080 PMCID: PMC8328520 DOI: 10.7554/elife.68712] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 06/19/2021] [Indexed: 12/13/2022] Open
Abstract
β- and γ-cytoplasmic actins are ubiquitously expressed in every cell type and are nearly identical at the amino acid level but play vastly different roles in vivo. Their essential roles in embryogenesis and mesenchymal cell migration critically depend on the nucleotide sequences of their genes, rather than their amino acid sequences; however, it is unclear which gene elements underlie this effect. Here we address the specific role of the coding sequence in β- and γ-cytoplasmic actins’ intracellular functions, using stable polyclonal populations of immortalized mouse embryonic fibroblasts with exogenously expressed actin isoforms and their ‘codon-switched’ variants. When targeted to the cell periphery using β-actin 3′UTR; β-actin and γ-actin have differential effects on cell migration. These effects directly depend on the coding sequence. Single-molecule measurements of actin isoform translation, combined with fluorescence recovery after photobleaching, demonstrate a pronounced difference in β- and γ-actins’ translation elongation rates in cells, leading to changes in their dynamics at focal adhesions, impairments in actin bundle formation, and reduced cell anchoring to the substrate during migration. Our results demonstrate that coding sequence-mediated differences in actin translation play a key role in cell migration. Most mammalian cells make both β- and γ-actin, two proteins which shape the cell’s internal skeleton and its ability to migrate. The molecules share over 99% of their sequence, yet they play distinct roles. In fact, deleting the β-actin gene in mice causes death in the womb, while the animals can survive with comparatively milder issues without their γ-actin gene. How two similar proteins can have such different biological roles is a long-standing mystery. A closer look could hold some clues: β- and γ-actin may contain the same blocks (or amino acids), but the genetic sequences that encode these proteins differ by about 13%. This is because different units of genetic information – known as synonymous codons – can encode the same amino acid. These ‘silent substitutions’ have no effect on the sequence of the proteins, yet a cell reads synonymous codons (and therefore produces proteins) at different speeds. To find out the impact of silent substitutions, Vedula et al. swapped the codons for the two proteins, forcing mouse cells to produce β-actin using γ-actin codons, and vice versa. Cells with non-manipulated γ-actin and those with β-actin made using γ-actin codons could move much faster than cells with β-actin. This suggested that silent substitutions were indeed affecting the role of the protein. Vedula et al. found that cells read γ-codons – and therefore made γ-actin – much more slowly than β-codons: this also affected how quickly the protein could be dispatched where it was needed in the cell. Slower production meant that bundles of γ-actin were shorter, which allowed cells to move faster by providing a weaker anchoring system. Overall, this work provides new links between silent substitutions and protein behavior, a relatively new research area which is likely to shed light on other protein families.
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Affiliation(s)
- Pavan Vedula
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, United States
| | - Satoshi Kurosaka
- Institute of Advanced Technology, Kindai University, Kainan, Wakayama, Japan
| | - Brittany MacTaggart
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, United States
| | - Qin Ni
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, United States
| | - Garegin Papoian
- Department of Chemistry, University of Maryland, College Park, United States
| | - Yi Jiang
- Department of Mathematics and Statistics, Georgia State University, Atlanta, United States
| | - Dawei W Dong
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, United States.,Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Anna Kashina
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, United States
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Suresh R, Diaz RJ. The remodelling of actin composition as a hallmark of cancer. Transl Oncol 2021; 14:101051. [PMID: 33761369 PMCID: PMC8008238 DOI: 10.1016/j.tranon.2021.101051] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 02/01/2021] [Accepted: 02/17/2021] [Indexed: 02/06/2023] Open
Abstract
Actin is a key structural protein that makes up the cytoskeleton of cells, and plays a role in functions such as division, migration, and vesicle trafficking. It comprises six different cell-type specific isoforms: ACTA1, ACTA2, ACTB, ACTC1, ACTG1, and ACTG2. Abnormal actin isoform expression has been reported in many cancers, which led us to hypothesize that it may serve as an early biomarker of cancer. We show an overview of the different actin isoforms and highlight mechanisms by which they may contribute to tumorigenicity. Furthermore, we suggest how the aberrant expression of actin subunits can confer cells with greater proliferation ability, increased migratory capability, and chemoresistance through incorporation into the normal cellular F-actin network and altered actin binding protein interaction. Studying this fundamental change that takes place within cancer cells can further our understanding of neoplastic transformation in multiple tissue types, which can ultimately aid in the early-detection, diagnosis and treatment of cancer.
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Affiliation(s)
- Rahul Suresh
- Montreal Neurological Institute, Integrated Program in Neuroscience, McGill University, Montreal, Canada
| | - Roberto J Diaz
- Department of Neurology and Neurosurgery, Montreal Neurological Institute and Hospital, Faculty of Medicine, McGill University, Montreal, Canada.
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24
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Malek N, Michrowska A, Mazurkiewicz E, Mrówczyńska E, Mackiewicz P, Mazur AJ. The origin of the expressed retrotransposed gene ACTBL2 and its influence on human melanoma cells' motility and focal adhesion formation. Sci Rep 2021; 11:3329. [PMID: 33558623 PMCID: PMC7870945 DOI: 10.1038/s41598-021-82074-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 01/08/2021] [Indexed: 01/30/2023] Open
Abstract
We have recently found that β-actin-like protein 2 (actbl2) forms complexes with gelsolin in human melanoma cells and can polymerize. Phylogenetic and bioinformatic analyses showed that actbl2 has a common origin with two non-muscle actins, which share a separate history from the muscle actins. The actin groups' divergence started at the beginning of vertebrate evolution, and actbl2 actins are characterized by the largest number of non-conserved amino acid substitutions of all actins. We also discovered that ACTBL2 is expressed at a very low level in several melanoma cell lines, but a small subset of cells exhibited a high ACTBL2 expression. We found that clones with knocked-out ACTBL2 (CR-ACTBL2) or overexpressing actbl2 (OE-ACTBL2) differ from control cells in the invasion, focal adhesion formation, and actin polymerization ratio, as well as in the formation of lamellipodia and stress fibers. Thus, we postulate that actbl2 is the seventh actin isoform and is essential for cell motility.
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Affiliation(s)
- Natalia Malek
- Department of Cell Pathology, Faculty of Biotechnology, University of Wroclaw, ul. Joliot-Curie 14a, 50-383, Wroclaw, Poland
| | - Aleksandra Michrowska
- Department of Cell Pathology, Faculty of Biotechnology, University of Wroclaw, ul. Joliot-Curie 14a, 50-383, Wroclaw, Poland
| | - Ewa Mazurkiewicz
- Department of Cell Pathology, Faculty of Biotechnology, University of Wroclaw, ul. Joliot-Curie 14a, 50-383, Wroclaw, Poland
| | - Ewa Mrówczyńska
- Department of Cell Pathology, Faculty of Biotechnology, University of Wroclaw, ul. Joliot-Curie 14a, 50-383, Wroclaw, Poland
| | - Paweł Mackiewicz
- Department of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wroclaw, ul. Joliot-Curie 14a, Wroclaw, 50-383, Poland
| | - Antonina J Mazur
- Department of Cell Pathology, Faculty of Biotechnology, University of Wroclaw, ul. Joliot-Curie 14a, 50-383, Wroclaw, Poland.
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25
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Vanslembrouck B, Ampe C, Hengel J. Time for rethinking the different β‐actin transgenic mouse models? Cytoskeleton (Hoboken) 2020; 77:527-543. [DOI: 10.1002/cm.21647] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 11/19/2020] [Accepted: 11/24/2020] [Indexed: 01/23/2023]
Affiliation(s)
- Bieke Vanslembrouck
- Medical Cell Biology Research Group, Department of Human Structure and Repair, Faculty of Medicine and Health Sciences Ghent University Ghent Belgium
| | - Christophe Ampe
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences Ghent University Ghent Belgium
| | - Jolanda Hengel
- Medical Cell Biology Research Group, Department of Human Structure and Repair, Faculty of Medicine and Health Sciences Ghent University Ghent Belgium
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Boiero Sanders M, Antkowiak A, Michelot A. Diversity from similarity: cellular strategies for assigning particular identities to actin filaments and networks. Open Biol 2020; 10:200157. [PMID: 32873155 PMCID: PMC7536088 DOI: 10.1098/rsob.200157] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The actin cytoskeleton has the particularity of being assembled into many functionally distinct filamentous networks from a common reservoir of monomeric actin. Each of these networks has its own geometrical, dynamical and mechanical properties, because they are capable of recruiting specific families of actin-binding proteins (ABPs), while excluding the others. This review discusses our current understanding of the underlying molecular mechanisms that cells have developed over the course of evolution to segregate ABPs to appropriate actin networks. Segregation of ABPs requires the ability to distinguish actin networks as different substrates for ABPs, which is regulated in three different ways: (1) by the geometrical organization of actin filaments within networks, which promotes or inhibits the accumulation of ABPs; (2) by the identity of the networks' filaments, which results from the decoration of actin filaments with additional proteins such as tropomyosin, from the use of different actin isoforms or from covalent modifications of actin; (3) by the existence of collaborative or competitive binding to actin filaments between two or multiple ABPs. This review highlights that all these effects need to be taken into account to understand the proper localization of ABPs in cells, and discusses what remains to be understood in this field of research.
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Affiliation(s)
- Micaela Boiero Sanders
- Aix Marseille University, CNRS, IBDM, Turing Centre for Living Systems, Marseille, France
| | - Adrien Antkowiak
- Aix Marseille University, CNRS, IBDM, Turing Centre for Living Systems, Marseille, France
| | - Alphée Michelot
- Aix Marseille University, CNRS, IBDM, Turing Centre for Living Systems, Marseille, France
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27
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Malek N, Mrówczyńska E, Michrowska A, Mazurkiewicz E, Pavlyk I, Mazur AJ. Knockout of ACTB and ACTG1 with CRISPR/Cas9(D10A) Technique Shows that Non-Muscle β and γ Actin Are Not Equal in Relation to Human Melanoma Cells' Motility and Focal Adhesion Formation. Int J Mol Sci 2020; 21:ijms21082746. [PMID: 32326615 PMCID: PMC7216121 DOI: 10.3390/ijms21082746] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 04/10/2020] [Accepted: 04/10/2020] [Indexed: 12/12/2022] Open
Abstract
Non-muscle actins have been studied for many decades; however, the reason for the existence of both isoforms is still unclear. Here we show, for the first time, a successful inactivation of the ACTB (CRISPR clones with inactivated ACTB, CR-ACTB) and ACTG1 (CRISPR clones with inactivated ACTG1, CR-ACTG1) genes in human melanoma cells (A375) via the RNA-guided D10A mutated Cas9 nuclease gene editing [CRISPR/Cas9(D10A)] technique. This approach allowed us to evaluate how melanoma cell motility was impacted by the lack of either β actin coded by ACTB or γ actin coded by ACTG1. First, we observed different distributions of β and γ actin in the cells, and the absence of one actin isoform was compensated for via increased expression of the other isoform. Moreover, we noted that γ actin knockout had more severe consequences on cell migration and invasion than β actin knockout. Next, we observed that the formation rate of bundled stress fibers in CR-ACTG1 cells was increased, but lamellipodial activity in these cells was impaired, compared to controls. Finally, we discovered that the formation rate of focal adhesions (FAs) and, subsequently, FA-dependent signaling were altered in both the CR-ACTB and CR-ACTG1 clones; however, a more detrimental effect was observed for γ actin-deficient cells. Our research shows that both non-muscle actins play distinctive roles in melanoma cells’ FA formation and motility.
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28
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Kashina AS. Regulation of actin isoforms in cellular and developmental processes. Semin Cell Dev Biol 2020; 102:113-121. [PMID: 32001148 DOI: 10.1016/j.semcdb.2019.12.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 12/02/2019] [Accepted: 12/02/2019] [Indexed: 12/18/2022]
Abstract
Actin is one of the most abundant and essential intracellular proteins that mediates nearly every form of cellular movement and underlies such key processes as embryogenesis, tissue integrity, cell division and contractility of all types of muscle and non-muscle cells. In mammals, actin is represented by six isoforms, which are encoded by different genes but produce proteins that are 95-99 % identical to each other. The six actin genes have vastly different functions in vivo, and the small amino acid differences between the proteins they encode are rigorously maintained through evolution, but the underlying differences behind this distinction, as well as the importance of specific amino acid sequences for each actin isoform, are not well understood. This review summarizes different levels of actin isoform-specific regulation in cellular and developmental processes, starting with the nuclear actin's role in transcription, and covering the gene-level, mRNA-level, and protein-level regulation, with a special focus on mammalian actins in non-muscle cells.
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Affiliation(s)
- Anna S Kashina
- University of Pennsylvania, Philadelphia, PA, 19104, United States.
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29
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A new evolutionary model for the vertebrate actin family including two novel groups. Mol Phylogenet Evol 2019; 141:106632. [DOI: 10.1016/j.ympev.2019.106632] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 09/19/2019] [Accepted: 09/23/2019] [Indexed: 02/06/2023]
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30
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van den Dries K, Nahidiazar L, Slotman JA, Meddens MBM, Pandzic E, Joosten B, Ansems M, Schouwstra J, Meijer A, Steen R, Wijers M, Fransen J, Houtsmuller AB, Wiseman PW, Jalink K, Cambi A. Modular actin nano-architecture enables podosome protrusion and mechanosensing. Nat Commun 2019; 10:5171. [PMID: 31729386 PMCID: PMC6858452 DOI: 10.1038/s41467-019-13123-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 10/11/2019] [Indexed: 01/03/2023] Open
Abstract
Basement membrane transmigration during embryonal development, tissue homeostasis and tumor invasion relies on invadosomes, a collective term for invadopodia and podosomes. An adequate structural framework for this process is still missing. Here, we reveal the modular actin nano-architecture that enables podosome protrusion and mechanosensing. The podosome protrusive core contains a central branched actin module encased by a linear actin module, each harboring specific actin interactors and actin isoforms. From the core, two actin modules radiate: ventral filaments bound by vinculin and connected to the plasma membrane and dorsal interpodosomal filaments crosslinked by myosin IIA. On stiff substrates, the actin modules mediate long-range substrate exploration, associated with degradative behavior. On compliant substrates, the vinculin-bound ventral actin filaments shorten, resulting in short-range connectivity and a focally protrusive, non-degradative state. Our findings redefine podosome nanoscale architecture and reveal a paradigm for how actin modularity drives invadosome mechanosensing in cells that breach tissue boundaries.
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Affiliation(s)
- Koen van den Dries
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Leila Nahidiazar
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, Netherlands
- van Leeuwenhoek Centre of Advanced Microscopy, Amsterdam, Netherlands
| | - Johan A Slotman
- Department of Pathology, Optical imaging center Erasmus MC, Rotterdam, Netherlands
| | - Marjolein B M Meddens
- Department of Physics and Astronomy and Department of Pathology, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Elvis Pandzic
- Biomedical Imaging Facility, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Ben Joosten
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Marleen Ansems
- Radiotherapy & OncoImmunology Laboratory, Department of Radiation Oncology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Joost Schouwstra
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Anke Meijer
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Raymond Steen
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Mietske Wijers
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Jack Fransen
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | | | - Paul W Wiseman
- Departments of Physics and Chemistry, McGill University Otto Maass (OM), Chemistry Building, 801 Sherbrooke Street West, Montreal, QC, H3A 0B8, Canada
| | - Kees Jalink
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, Netherlands
- van Leeuwenhoek Centre of Advanced Microscopy, Amsterdam, Netherlands
| | - Alessandra Cambi
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands.
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31
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Biasoli D, Compston-Garnett L, Ricketts SL, Birand Z, Courtay-Cahen C, Fineberg E, Arendt M, Boerkamp K, Melin M, Koltookian M, Murphy S, Rutteman G, Lindblad-Toh K, Starkey M. A synonymous germline variant in a gene encoding a cell adhesion molecule is associated with cutaneous mast cell tumour development in Labrador and Golden Retrievers. PLoS Genet 2019; 15:e1007967. [PMID: 30901340 PMCID: PMC6447235 DOI: 10.1371/journal.pgen.1007967] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 04/03/2019] [Accepted: 01/16/2019] [Indexed: 02/06/2023] Open
Abstract
Mast cell tumours are the most common type of skin cancer in dogs, representing a significant concern in canine health. The molecular pathogenesis is largely unknown, but breed-predisposition for mast cell tumour development suggests the involvement of inherited genetic risk factors in some breeds. In this study, we aimed to identify germline risk factors associated with the development of mast cell tumours in Labrador Retrievers, a breed with an elevated risk of mast cell tumour development. Using a methodological approach that combined a genome-wide association study, targeted next generation sequencing, and TaqMan genotyping, we identified a synonymous variant in the DSCAM gene on canine chromosome 31 that is associated with mast cell tumours in Labrador Retrievers. DSCAM encodes a cell-adhesion molecule. We showed that the variant has no effect on the DSCAM mRNA level but is associated with a significant reduction in the level of the DSCAM protein, suggesting that the variant affects the dynamics of DSCAM mRNA translation. Furthermore, we showed that the variant is also associated with mast cell tumours in Golden Retrievers, a breed that is closely related to Labrador Retrievers and that also has a predilection for mast cell tumour development. The variant is common in both Labradors and Golden Retrievers and consequently is likely to be a significant genetic contributor to the increased susceptibility of both breeds to develop mast cell tumours. The results presented here not only represent an important contribution to the understanding of mast cell tumour development in dogs, as they highlight the role of cell adhesion in mast cell tumour tumourigenesis, but they also emphasise the potential importance of the effects of synonymous variants in complex diseases such as cancer. The combination of various genetic and environmental risk factors makes the understanding of the molecular circuitry behind complex diseases, like cancer, a major challenge. The homogeneous nature of pedigree dog breed genomes makes these dogs ideal for the identification of both simple disease-causing genetic variants and genetic risk factors for complex diseases. Mast cell tumours are the most common type of canine skin cancer, and one of the most common cancers affecting dogs of most breeds. Several breeds, including Labrador Retrievers (which represent one of the most popular dog breeds), have an elevated risk of mast cell tumour development. Here, by using a methodological approach that combined different techniques, we identified a common inherited synonymous variant, that predisposes Labrador Retrievers to mast cell tumour development. Interestingly, we showed that this variant, despite its synonymous nature, appears to have an effect on translation dynamics as it is associated with reduced levels of DSCAM, a cell adhesion molecule. The results presented here reveal dysregulation of cell adhesion to be an important factor in mast cell tumour pathogenesis, and also highlight the important role that synonymous variants can play in complex diseases.
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Affiliation(s)
| | | | | | | | | | | | - Maja Arendt
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Kim Boerkamp
- Department of Clinical Sciences of Companion Animals, Utrecht University, Utrecht, The Netherlands
| | - Malin Melin
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Michele Koltookian
- Broad Institute of MIT and Harvard, Cambridge, MA, United States of America
| | - Sue Murphy
- Animal Health Trust, Newmarket, United Kingdom
| | - Gerard Rutteman
- Department of Clinical Sciences of Companion Animals, Utrecht University, Utrecht, The Netherlands
- Veterinary Specialist Centre De Wagenrenk, Wageningen, The Netherlands
| | - Kerstin Lindblad-Toh
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Broad Institute of MIT and Harvard, Cambridge, MA, United States of America
| | - Mike Starkey
- Animal Health Trust, Newmarket, United Kingdom
- * E-mail:
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32
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Rodriguez A, Kashina A. Posttranscriptional and Posttranslational Regulation of Actin. Anat Rec (Hoboken) 2018; 301:1991-1998. [PMID: 30312009 DOI: 10.1002/ar.23958] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 04/12/2018] [Accepted: 04/14/2018] [Indexed: 12/14/2022]
Abstract
Actin is one of the most abundant intracellular proteins, essential in every eukaryotic cell type. Actin plays key roles in tissue morphogenesis, cell adhesion, muscle contraction, and developmental reprogramming. Most actin studies have focused on its regulation at the protein level, either directly or through differential interactions with over a hundred intracellular binding partners. However, numerous studies emerging in recent years demonstrate specific types of nucleotide-level regulation that strongly affect non-muscle actins during cell migration and adhesion and are potentially applicable to other members of the actin family. This regulation involves zipcode-mediated actin mRNA targeting to the cell periphery, proposed to mediate local synthesis of actin at the cell leading edge, as well as the recently discovered N-terminal arginylation that specifically targets non-muscle β-actin via a nucleotide-dependent mechanism. Moreover, a study published this year suggests that actin's essential roles at the organismal level may be entirely nucleotide-dependent. This review summarizes the emerging data on actin's nucleotide-level regulation. Anat Rec, 301:1991-1998, 2018. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Alexis Rodriguez
- Department of Biological Sciences, Rutgers University, Newark, New Jersey
| | - Anna Kashina
- Department of Biomedical Sciences, University of Pennsylvania, School of Veterinary Medicine, Philadelphia, Pennsylvania
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33
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Variants in exons 5 and 6 of ACTB cause syndromic thrombocytopenia. Nat Commun 2018; 9:4250. [PMID: 30315159 PMCID: PMC6185941 DOI: 10.1038/s41467-018-06713-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 09/20/2018] [Indexed: 01/08/2023] Open
Abstract
Germline mutations in the ubiquitously expressed ACTB, which encodes β-cytoplasmic actin (CYA), are almost exclusively associated with Baraitser-Winter Cerebrofrontofacial syndrome (BWCFF). Here, we report six patients with previously undescribed heterozygous variants clustered in the 3′-coding region of ACTB. Patients present with clinical features distinct from BWCFF, including mild developmental disability, microcephaly, and thrombocytopenia with platelet anisotropy. Using patient-derived fibroblasts, we demonstrate cohort specific changes to β-CYA filament populations, which include the enhanced recruitment of thrombocytopenia-associated actin binding proteins (ABPs). These perturbed interactions are supported by in silico modeling and are validated in disease-relevant thrombocytes. Co-examination of actin and microtubule cytoskeleton constituents in patient-derived megakaryocytes and thrombocytes indicates that these β-CYA mutations inhibit the final stages of platelet maturation by compromising microtubule organization. Our results define an ACTB-associated clinical syndrome with a distinct genotype-phenotype correlation and delineate molecular mechanisms underlying thrombocytopenia in this patient cohort. Genetic variants in ACTB and ACTG1 have been associated with Baraitser-Winter Cerebrofrontofacial syndrome. Here, the authors report of a syndromic thrombocytopenia caused by variants in ACTB exons 5 or 6 that compromise the organization and coupling of the cytoskeleton, leading to impaired platelet maturation.
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34
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Abstract
The highly similar cytoplasmic β- and γ-actins differ by only four functionally similar amino acids, yet previous in vitro and in vivo data suggest that they support unique functions due to striking phenotypic differences between Actb and Actg1 null mouse and cell models. To determine whether the four amino acid variances were responsible for the functional differences between cytoplasmic actins, we gene edited the endogenous mouse Actb locus to translate γ-actin protein. The resulting mice and primary embryonic fibroblasts completely lacked β-actin protein, but were viable and did not present with the most overt and severe cell and organismal phenotypes observed with gene knockout. Nonetheless, the edited mice exhibited progressive high-frequency hearing loss and degeneration of actin-based stereocilia as previously reported for hair cell-specific Actb knockout mice. Thus, β-actin protein is not required for general cellular functions, but is necessary to maintain auditory stereocilia.
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35
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Vedula P, Kashina A. The makings of the 'actin code': regulation of actin's biological function at the amino acid and nucleotide level. J Cell Sci 2018; 131:131/9/jcs215509. [PMID: 29739859 DOI: 10.1242/jcs.215509] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The actin cytoskeleton plays key roles in every eukaryotic cell and is essential for cell adhesion, migration, mechanosensing, and contractility in muscle and non-muscle tissues. In higher vertebrates, from birds through to mammals, actin is represented by a family of six conserved genes. Although these genes have evolved independently for more than 100 million years, they encode proteins with ≥94% sequence identity, which are differentially expressed in different tissues, and tightly regulated throughout embryogenesis and adulthood. It has been previously suggested that the existence of such similar actin genes is a fail-safe mechanism to preserve the essential function of actin through redundancy. However, knockout studies in mice and other organisms demonstrate that the different actins have distinct biological roles. The mechanisms maintaining this distinction have been debated in the literature for decades. This Review summarizes data on the functional regulation of different actin isoforms, and the mechanisms that lead to their different biological roles in vivo We focus here on recent studies demonstrating that at least some actin functions are regulated beyond the amino acid level at the level of the actin nucleotide sequence.
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Affiliation(s)
- Pavan Vedula
- Department of Biomedical Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Anna Kashina
- Department of Biomedical Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
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37
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Abstract
The differences between β- and γ-actin are deeper than those between the amino acid sequences of these two proteins.
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