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Green NM, Talbot D, Tootle TL. Nuclear actin is a critical regulator of Drosophila female germline stem cell maintenance. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.27.609996. [PMID: 39253513 PMCID: PMC11383290 DOI: 10.1101/2024.08.27.609996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/11/2024]
Abstract
Nuclear actin has been implicated in regulating cell fate, differentiation, and cellular reprogramming. However, its roles in development and tissue homeostasis remain largely unknown. Here we uncover the role of nuclear actin in regulating stemness using Drosophila ovarian germline stem cells (GSCs) as a model. We find that the localization and structure of nuclear actin is dynamic in the early germ cells. Nuclear actin recognized by anti-actin C4 is found in both the nucleoplasm and nucleolus of GSCs. The polymeric nucleoplasmic C4 pool is lost after the 2-cell stage, whereas the monomeric nucleolar pool persists to the 8-cell stage, suggesting that polymeric nuclear actin may contribute to stemness. To test this idea, we overexpressed nuclear targeted actin constructs to alter nuclear actin polymerization states in the GSCs and early germ cells. Increasing monomeric nuclear actin, but not polymerizable nuclear actin, causes GSC loss that ultimately results in germline loss. This GSC loss is rescued by simultaneous overexpression of monomeric and polymerizable nuclear actin. Together these data reveal that GSC maintenance requires polymeric nuclear actin. This polymeric nuclear actin likely plays numerous roles in the GSCs, as increasing monomeric nuclear actin disrupts nuclear architecture causing nucleolar hypertrophy, distortion of the nuclear lamina, and heterochromatin reorganization; all factors critical for GSC maintenance and function. These data provide the first evidence that nuclear actin, and in particular, its ability to polymerize, are critical for stem cell function and tissue homeostasis in vivo.
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Affiliation(s)
- Nicole M Green
- Anatomy and Cell Biology, University of Iowa Carver College of Medicine, 51 Newton Rd, 1-500 BSB, Iowa City, IA 52242
- Current affiliation: Biology, Cornell College, 600 First Street SW, Mount Vernon, IA 52314
| | - Danielle Talbot
- Anatomy and Cell Biology, University of Iowa Carver College of Medicine, 51 Newton Rd, 1-500 BSB, Iowa City, IA 52242
- Current affiliation: Biology, University of Iowa, 129 E. Jefferson St, 246 BB, Iowa City, IA 52242
| | - Tina L Tootle
- Anatomy and Cell Biology, University of Iowa Carver College of Medicine, 51 Newton Rd, 1-500 BSB, Iowa City, IA 52242
- Current affiliation: Biology, University of Iowa, 129 E. Jefferson St, 246 BB, Iowa City, IA 52242
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2
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Mokin YI, Povarova OI, Antifeeva IA, Artemov AV, Uversky VN, Turoverov KK, Kuznetsova IM, Fonin AV. Bioinformatics Analysis of Actin Interactome: Characterization of the Nuclear and Cytoplasmic Actin-Binding Proteins. Protein J 2024; 43:675-682. [PMID: 38824467 DOI: 10.1007/s10930-024-10207-y] [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] [Accepted: 05/09/2024] [Indexed: 06/03/2024]
Abstract
Actin is present in the cytoplasm and nucleus of every eukaryotic cell. In the cytoplasm, framework and motor functions of actin are associated with its ability to polymerize to form F-actin. In the nucleus, globular actin plays a significant functional role. For a globular protein, actin has a uniquely large number of proteins with which it interacts. Bioinformatics analysis of the actin interactome showed that only a part of actin-binding proteins are both cytoplasmic and nuclear. There are proteins that interact only with cytoplasmic, or only with nuclear actin. The first pool includes proteins associated with the formation, regulation, and functioning of the actin cytoskeleton predominate, while nuclear actin-binding proteins are involved in the majority of key nuclear processes, from regulation of transcription to DNA damage response. Bioinformatics analysis of the structure of actin-binding proteins showed that these are mainly intrinsically disordered proteins, many of which are part of membrane-less organelles. Interestingly, although the number of intrinsically disordered actin-binding proteins in the nucleus is greater than in the cytoplasm, the drivers for the formation of the membrane-less organelles in the cytoplasm are significantly (four times) greater than in the nucleus.
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Affiliation(s)
- Yakov I Mokin
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064, Russian Federation
| | - Olga I Povarova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064, Russian Federation
| | - Iuliia A Antifeeva
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064, Russian Federation
| | - Alexey V Artemov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064, Russian Federation
| | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, USF Health Byrd Alzheimer's Research Institute, University of South Florida, 12901 Bruce B. Downs Blvd., MDC07, Tampa, FL, 33612, USA.
| | - Konstantin K Turoverov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064, Russian Federation
| | - Irina M Kuznetsova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064, Russian Federation.
| | - Alexander V Fonin
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064, Russian Federation.
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Talbot DE, Vormezeele BJ, Kimble GC, Wineland DM, Kelpsch DJ, Giedt MS, Tootle TL. Prostaglandins limit nuclear actin to control nucleolar function during oogenesis. Front Cell Dev Biol 2023; 11:1072456. [PMID: 36875757 PMCID: PMC9981675 DOI: 10.3389/fcell.2023.1072456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 02/06/2023] [Indexed: 02/19/2023] Open
Abstract
Prostaglandins (PGs), locally acting lipid signals, regulate female reproduction, including oocyte development. However, the cellular mechanisms of PG action remain largely unknown. One cellular target of PG signaling is the nucleolus. Indeed, across organisms, loss of PGs results in misshapen nucleoli, and changes in nucleolar morphology are indicative of altered nucleolar function. A key role of the nucleolus is to transcribe ribosomal RNA (rRNA) to drive ribosomal biogenesis. Here we take advantage of the robust, in vivo system of Drosophila oogenesis to define the roles and downstream mechanisms whereby PGs regulate the nucleolus. We find that the altered nucleolar morphology due to PG loss is not due to reduced rRNA transcription. Instead, loss of PGs results in increased rRNA transcription and overall protein translation. PGs modulate these nucleolar functions by tightly regulating nuclear actin, which is enriched in the nucleolus. Specifically, we find that loss of PGs results in both increased nucleolar actin and changes in its form. Increasing nuclear actin, by either genetic loss of PG signaling or overexpression of nuclear targeted actin (NLS-actin), results in a round nucleolar morphology. Further, loss of PGs, overexpression of NLS-actin or loss of Exportin 6, all manipulations that increase nuclear actin levels, results in increased RNAPI-dependent transcription. Together these data reveal PGs carefully balance the level and forms of nuclear actin to control the level of nucleolar activity required for producing fertilization competent oocytes.
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Affiliation(s)
| | | | | | | | | | | | - Tina L. Tootle
- Anatomy and Cell Biology, University of Iowa Carver College of Medicine, Iowa City, IA, United States
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4
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Wang Z, Bianco V, Pirone D, Memmolo P, Villone MM, Maffettone PL, Ferraro P. Dehydration of plant cells shoves nuclei rotation allowing for 3D phase-contrast tomography. LIGHT, SCIENCE & APPLICATIONS 2021; 10:187. [PMID: 34526484 PMCID: PMC8443563 DOI: 10.1038/s41377-021-00626-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 07/15/2021] [Accepted: 08/27/2021] [Indexed: 05/07/2023]
Abstract
Single-cell phase-contrast tomography promises to become decisive for studying 3D intracellular structures in biology. It involves probing cells with light at wide angles, which unfortunately requires complex systems. Here we show an intriguing concept based on an inherent natural process for plants biology, i.e., dehydration, allowing us to easily obtain 3D-tomography of onion-epidermal cells' nuclei. In fact, the loss of water reduces the turgor pressure and we recognize it induces significant rotation of cells' nuclei. Thanks to the holographic focusing flexibility and an ad-hoc angles' tracking algorithm, we combine different phase-contrast views of the nuclei to retrieve their 3D refractive index distribution. Nucleolus identification capability and a strategy for measuring morphology, dry mass, biovolume, and refractive index statistics are reported and discussed. This new concept could revolutionize the investigation in plant biology by enabling dynamic 3D quantitative and label-free analysis at sub-nuclear level using a conventional holographic setup.
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Affiliation(s)
- Zhe Wang
- Dipartimento di Ingegneria Chimica dei Materiali e della Produzione Industriale, Università degli Studi di Napoli "Federico II", Piazzale Tecchio 80, 80125, Napoli, Italy
- NEAPoLIS, Numerical and Experimental Advanced Program on Liquids and Interface Systems, Joint Research Center CNR - Università degli Studi di Napoli "Federico II", Napoli, Italy
| | - Vittorio Bianco
- NEAPoLIS, Numerical and Experimental Advanced Program on Liquids and Interface Systems, Joint Research Center CNR - Università degli Studi di Napoli "Federico II", Napoli, Italy
- CNR-ISASI, Institute of Applied Sciences and Intelligent Systems "E. Caianiello", Via Campi Flegrei 34, 80078 Pozzuoli, Napoli, Italy
| | - Daniele Pirone
- CNR-ISASI, Institute of Applied Sciences and Intelligent Systems "E. Caianiello", Via Campi Flegrei 34, 80078 Pozzuoli, Napoli, Italy
- Dipartimento di Ingegneria Elettrica e delle Tecnologie dell'Informazione, Università degli Studi di Napoli "Federico II", via Claudio 21, 80125, Napoli, Italy
| | - Pasquale Memmolo
- NEAPoLIS, Numerical and Experimental Advanced Program on Liquids and Interface Systems, Joint Research Center CNR - Università degli Studi di Napoli "Federico II", Napoli, Italy.
- CNR-ISASI, Institute of Applied Sciences and Intelligent Systems "E. Caianiello", Via Campi Flegrei 34, 80078 Pozzuoli, Napoli, Italy.
| | - Massimiliano Maria Villone
- Dipartimento di Ingegneria Chimica dei Materiali e della Produzione Industriale, Università degli Studi di Napoli "Federico II", Piazzale Tecchio 80, 80125, Napoli, Italy
- NEAPoLIS, Numerical and Experimental Advanced Program on Liquids and Interface Systems, Joint Research Center CNR - Università degli Studi di Napoli "Federico II", Napoli, Italy
| | - Pier Luca Maffettone
- Dipartimento di Ingegneria Chimica dei Materiali e della Produzione Industriale, Università degli Studi di Napoli "Federico II", Piazzale Tecchio 80, 80125, Napoli, Italy
- NEAPoLIS, Numerical and Experimental Advanced Program on Liquids and Interface Systems, Joint Research Center CNR - Università degli Studi di Napoli "Federico II", Napoli, Italy
| | - Pietro Ferraro
- NEAPoLIS, Numerical and Experimental Advanced Program on Liquids and Interface Systems, Joint Research Center CNR - Università degli Studi di Napoli "Federico II", Napoli, Italy.
- CNR-ISASI, Institute of Applied Sciences and Intelligent Systems "E. Caianiello", Via Campi Flegrei 34, 80078 Pozzuoli, Napoli, Italy.
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5
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New Insights into Cellular Functions of Nuclear Actin. BIOLOGY 2021; 10:biology10040304. [PMID: 33916969 PMCID: PMC8067577 DOI: 10.3390/biology10040304] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 03/30/2021] [Accepted: 04/01/2021] [Indexed: 12/12/2022]
Abstract
Simple Summary It is well known that actin forms a cytoplasmic network of microfilaments, the part of the cytoskeleton, in the cytoplasm of eukaryotic cells. The presence of nuclear actin was elusive for a very long time. Now, there is a very strong evidence that actin plays many important roles in the nucleus. Here, we discuss the recently discovered functions of the nuclear actin pool. Actin does not have nuclear localization signal (NLS), so its import to the nucleus is facilitated by the NLS-containing proteins. Nuclear actin plays a role in the maintenance of the nuclear structure and the nuclear envelope breakdown. It is also involved in chromatin remodeling, and chromatin and nucleosome movement necessary for DNA recombination, repair, and the initiation of transcription. It also binds RNA polymerases, promoting transcription. Because of the multifaceted role of nuclear actin, the future challenge will be to further define its functions in various cellular processes and diseases. Abstract Actin is one of the most abundant proteins in eukaryotic cells. There are different pools of nuclear actin often undetectable by conventional staining and commercial antibodies used to identify cytoplasmic actin. With the development of more sophisticated imaging and analytical techniques, it became clear that nuclear actin plays a crucial role in shaping the chromatin, genomic, and epigenetic landscape, transcriptional regulation, and DNA repair. This multifaceted role of nuclear actin is not only important for the function of the individual cell but also for the establishment of cell fate, and tissue and organ differentiation during development. Moreover, the changes in the nuclear, chromatin, and genomic architecture are preamble to various diseases. Here, we discuss some of the newly described functions of nuclear actin.
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7
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Abdellatif MEA, Hipp L, Plessner M, Walther P, Knöll B. Indirect visualization of endogenous nuclear actin by correlative light and electron microscopy (CLEM) using an actin-directed chromobody. Histochem Cell Biol 2019; 152:133-143. [PMID: 31154480 PMCID: PMC6675784 DOI: 10.1007/s00418-019-01795-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/15/2019] [Indexed: 12/14/2022]
Abstract
Actin fulfills important cytoplasmic but also nuclear functions in eukaryotic cells. In the nucleus, actin modulates gene expression and chromatin remodeling. Monomeric (G-actin) and polymerized actin (F-actin) have been analyzed by fluorescence microscopy in the nucleus; however, the resolution at the ultrastructural level has not been investigated in great detail. We provide a first documentation of nuclear actin in mouse fibroblasts by electron microscopy (EM). For this, we employed correlative light and electron microscopy on the same section using actin-directed nanobodies recognizing endogenous monomeric and polymeric actin proteins (so-called nuclear Actin-chromobody-GFP; nAC-GFP). Indeed, using this strategy, we could identify actin proteins present in the nucleus. Here, immunogold-labeled actin proteins were spread throughout the entire nucleoplasm. Of note, nuclear actin was complementarily localized to DAPI-positive areas, the latter marking preferentially transcriptionally inactive heterochromatin. Since actin aggregates in rod structures upon cell stress including neurodegeneration, we analyzed nuclear actin at the ultrastructural level after DMSO or UV-mediated cell damage. In those cells the ratio between cytoplasmic and nuclear gold-labeled actin proteins was altered compared to untreated control cells. In summary, this EM analysis (i) confirmed the presence of endogenous nuclear actin at ultrastructural resolution, (ii) revealed the actin abundance in less chromatin-dense regions potentially reflecting more transcriptionally active euchromatin rather than transcriptionally inactive heterochromatin and (iii) showed an altered abundance of actin-associated gold particles upon cell stress.
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Affiliation(s)
- Mohamed E A Abdellatif
- Central Facility for Electron Microscopy, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Lisa Hipp
- Institute of Physiological Chemistry, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Matthias Plessner
- Institute of Experimental and Clinical Pharmacology and Toxicology, University of Freiburg, Albertstr. 25, 79104, Freiburg, Germany
| | - Paul Walther
- Central Facility for Electron Microscopy, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Bernd Knöll
- Institute of Physiological Chemistry, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany.
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8
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Hurst V, Shimada K, Gasser SM. Nuclear Actin and Actin-Binding Proteins in DNA Repair. Trends Cell Biol 2019; 29:462-476. [PMID: 30954333 DOI: 10.1016/j.tcb.2019.02.010] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 02/25/2019] [Accepted: 02/26/2019] [Indexed: 12/27/2022]
Abstract
Nuclear actin has been implicated in a variety of DNA-related processes including chromatin remodeling, transcription, replication, and DNA repair. However, the mechanistic understanding of actin in these processes has been limited, largely due to a lack of research tools that address the roles of nuclear actin specifically, that is, distinct from its cytoplasmic functions. Recent findings support a model for homology-directed DNA double-strand break (DSB) repair in which a complex of ARP2 and ARP3 (actin-binding proteins 2 and 3) binds at the break and works with actin to promote DSB clustering and homology-directed repair. Further, it has been reported that relocalization of heterochromatic DSBs to the nuclear periphery in Drosophila is ARP2/3 dependent and actin-myosin driven. Here we provide an overview of the role of nuclear actin and actin-binding proteins in DNA repair, critically evaluating the experimental tools used and potential indirect effects.
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Affiliation(s)
- Verena Hurst
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland; University of Basel, Faculty of Natural Sciences, CH-4056 Basel, Switzerland
| | - Kenji Shimada
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
| | - Susan M Gasser
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland; University of Basel, Faculty of Natural Sciences, CH-4056 Basel, Switzerland.
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9
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Wineland DM, Kelpsch DJ, Tootle TL. Multiple Pools of Nuclear Actin. Anat Rec (Hoboken) 2018; 301:2014-2036. [PMID: 30312534 PMCID: PMC6293971 DOI: 10.1002/ar.23964] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 04/14/2018] [Accepted: 04/17/2018] [Indexed: 02/06/2023]
Abstract
While nuclear actin was reported ~50 years ago, it's in vivo prevalence and structure remain largely unknown. Here, we use Drosophila oogenesis, that is, follicle development, to characterize nuclear actin. We find that three different reagents-DNase I, anti-actin C4, and anti-actin AC15-recognize distinct pools of nuclear actin. DNase I labels monomeric or G-actin, and, during follicle development, G-actin is present in the nucleus of every cell. Some G-actin is recognized by the C4 antibody. In particular, C4 nuclear actin colocalizes with DNase I to the nucleolus in anterior escort cells, follicle stem cells, some mitotic follicle cells, and a subset of nurse cells during early oogenesis. C4 also labels polymeric nuclear actin in the nucleoplasm of the germline stem cells, early cystoblasts, and oocytes. The AC15 antibody labels a completely distinct pool of nuclear actin from that of DNase I and C4. Specifically, AC15 nuclear actin localizes to the chromatin in the nurse and follicle cells during mid-to-late oogenesis. Within the oocyte, AC15 nuclear actin progresses from localizing to puncta surrounding the DNA, to forming a filamentous cage around the chromosomes. Together these findings reveal that nuclear actin is highly prevalent in vivo, and multiple pools of nuclear actin exist and can be recognized using different reagents. Additionally, our localization studies suggest that nuclear actin may regulate stemness, nucleolar structure and function, transcription, and nuclear structure. Such findings call for further studies to explore the prevalence, diversity, and functions of nuclear actin across tissues and organisms. Anat Rec, 301:2014-2036, 2018. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Dylane M. Wineland
- Anatomy and Cell Biology, University of Iowa Carver College of
Medicine, 51 Newton Rd, 1-500 BSB, Iowa City, IA 52242
| | - Daniel J. Kelpsch
- Anatomy and Cell Biology, University of Iowa Carver College of
Medicine, 51 Newton Rd, 1-500 BSB, Iowa City, IA 52242
| | - Tina L. Tootle
- Anatomy and Cell Biology, University of Iowa Carver College of
Medicine, 51 Newton Rd, 1-500 BSB, Iowa City, IA 52242
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10
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Kelpsch DJ, Tootle TL. Nuclear Actin: From Discovery to Function. Anat Rec (Hoboken) 2018; 301:1999-2013. [PMID: 30312531 PMCID: PMC6289869 DOI: 10.1002/ar.23959] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 04/20/2018] [Accepted: 05/14/2018] [Indexed: 01/02/2023]
Abstract
While actin was discovered in the nucleus over 50 years ago, research lagged for decades due to strong skepticism. The revitalization of research into nuclear actin occurred after it was found that cellular stresses induce the nuclear localization and alter the structure of actin. These studies provided the first hints that actin has a nuclear function. Subsequently, it was established that the nuclear import and export of actin is highly regulated. While the structures of nuclear actin remain unclear, it can function as monomers, polymers, and even rods. Furthermore, even within a given structure, distinct pools of nuclear actin that can be differentially labeled have been identified. Numerous mechanistic studies have uncovered an array of functions for nuclear actin. It regulates the activity of RNA polymerases, as well as specific transcription factors. Actin also modulates the activity of several chromatin remodeling complexes and histone deacetylases, to ultimately impinge on transcriptional programing and DNA damage repair. Further, nuclear actin mediates chromatin movement and organization. It has roles in meiosis and mitosis, and these functions may be functionally conserved from ancient bacterial actin homologs. The structure and integrity of the nuclear envelope and sub-nuclear compartments are also regulated by nuclear actin. Furthermore, nuclear actin contributes to human diseases like cancer, neurodegeneration, and myopathies. Here, we explore the early discovery of actin in the nucleus and discuss the forms and functions of nuclear actin in both normal and disease contexts. Anat Rec, 301:1999-2013, 2018. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Daniel J. Kelpsch
- Anatomy and Cell Biology, University of Iowa Carver College of Medicine, 51 Newton Rd, 1-500 BSB, Iowa City, IA 52242
| | - Tina L. Tootle
- Anatomy and Cell Biology, University of Iowa Carver College of Medicine, 51 Newton Rd, 1-500 BSB, Iowa City, IA 52242
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11
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An actin-based nucleoskeleton involved in gene regulation and genome organization. Biochem Biophys Res Commun 2018; 506:378-386. [DOI: 10.1016/j.bbrc.2017.11.206] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Accepted: 11/30/2017] [Indexed: 12/21/2022]
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12
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Ciska M, de la Espina SMD. Detection of Endogenous Nuclear Proteins in Plant Cells: Localizing Nuclear Matrix Constituent Proteins (NMCPs), the Plant Analogs of Lamins. Methods Mol Biol 2017; 1560:297-311. [PMID: 28155164 DOI: 10.1007/978-1-4939-6788-9_23] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
At present, two complementary approaches are used for in situ protein visualization in plant nuclei. Imaging of transformed fluorescent proteins is the election tool for the analysis of protein movement and interaction. However, this methodology presents several drawbacks for the identification/localization of endogenous nuclear factors, such as over-expression or mislocalization of transformed proteins. In contrast, immunocytochemistry with specific antibodies represents a powerful tool for the localization of endogenous nuclear proteins at their "native" nuclear sub-compartments. In plant cells, the cell wall hampers antibody accessibility during immunocytochemical analysis thereby reducing the effectivity of the technique, particularly in the case of lowly expressed proteins. To overcome this problem in nuclear protein immunodetection, we developed a method based on the in vitro incubation of isolated nuclei with specific antibodies followed by imaging by confocal fluorescence or electron microscopy. Here we describe the application of this methodology to the localization of Nuclear Matrix Constituent Proteins (NMCP), the plant analogs of lamins, of the monocot Allium cepa, using antibodies raised against highly conserved regions of the proteins.
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Affiliation(s)
- Malgorzata Ciska
- Department of Cell and Molecular Biology, Biological Research Center, CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain
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13
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Bancel E, Bonnot T, Davanture M, Branlard G, Zivy M, Martre P. Proteomic Approach to Identify Nuclear Proteins in Wheat Grain. J Proteome Res 2015; 14:4432-9. [DOI: 10.1021/acs.jproteome.5b00446] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Emmanuelle Bancel
- INRA, UMR1095
Genetics, Diversity and Ecophysiology of Cereals, 5 chemin de Beaulieu, F-63 039 Clermont-Ferrand, France
- Blaise Pascal
University, UMR1095 Genetics, Diversity and Ecophysiology of Cereals, Avenue des Landais, F-63 170 Aubière, France
| | - Titouan Bonnot
- INRA, UMR1095
Genetics, Diversity and Ecophysiology of Cereals, 5 chemin de Beaulieu, F-63 039 Clermont-Ferrand, France
- Blaise Pascal
University, UMR1095 Genetics, Diversity and Ecophysiology of Cereals, Avenue des Landais, F-63 170 Aubière, France
| | - Marlène Davanture
- CNRS, PAPPSO, UMR 0320/8120 Génétique
Quantitative et Évolution - Le Moulon, F-91190 Gif-sur-Yvette, France
| | - Gérard Branlard
- INRA, UMR1095
Genetics, Diversity and Ecophysiology of Cereals, 5 chemin de Beaulieu, F-63 039 Clermont-Ferrand, France
- Blaise Pascal
University, UMR1095 Genetics, Diversity and Ecophysiology of Cereals, Avenue des Landais, F-63 170 Aubière, France
| | - Michel Zivy
- CNRS, PAPPSO, UMR 0320/8120 Génétique
Quantitative et Évolution - Le Moulon, F-91190 Gif-sur-Yvette, France
| | - Pierre Martre
- INRA, UMR1095
Genetics, Diversity and Ecophysiology of Cereals, 5 chemin de Beaulieu, F-63 039 Clermont-Ferrand, France
- Blaise Pascal
University, UMR1095 Genetics, Diversity and Ecophysiology of Cereals, Avenue des Landais, F-63 170 Aubière, France
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14
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Ueda K, Xu ZJ, Miyagi N, Ono M, Wabiko H, Masuda K, Inoue M. Isolation and characterization of a carrot nucleolar protein with structural and sequence similarity to the vertebrate PESCADILLO protein. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2013; 208:83-92. [PMID: 23683933 DOI: 10.1016/j.plantsci.2013.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2013] [Revised: 03/29/2013] [Accepted: 04/03/2013] [Indexed: 06/02/2023]
Abstract
The nuclear matrix is involved in many nuclear events, but its protein architecture in plants is still not fully understood. A cDNA clone was isolated by immunoscreening with a monoclonal antibody raised against nuclear matrix proteins of Daucus carota L. Its deduced amino acid sequence showed about 40% identity with the PESCADILLO protein of zebrafish and humans. Primary structure analysis of the protein revealed a Pescadillo N-terminus domain, a single breast cancer C-terminal domain, two nuclear localization signals, and a potential coiled-coil region as also found in animal PESCADILLO proteins. Therefore, we designated this gene DcPES1. Although DcPES1 mRNA was detected in all tissues examined, its levels were highest in tissues with proliferating cells. Immunofluorescence using specific antiserum against the recombinant protein revealed that DcPES1 localized exclusively in the nucleolus. Examination of fusion proteins with green fluorescent protein revealed that the N-terminal portion was important for localization to the nucleoli of tobacco and onion cells. Moreover, when the nuclear matrix of carrot cells was immunostained with an anti-DcPES1 serum, the signal was detected in the nucleolus. Therefore, the DcPES1 protein appears to be a component of or tightly bound to components of the nuclear matrix.
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Affiliation(s)
- Kenji Ueda
- Faculty of Bioresource Sciences, Akita Prefectural University, Akita 010-0195, Japan.
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Ciska M, Moreno Díaz de la Espina S. NMCP/LINC proteins: putative lamin analogs in plants? PLANT SIGNALING & BEHAVIOR 2013; 8:e26669. [PMID: 24128696 PMCID: PMC4091594 DOI: 10.4161/psb.26669] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Lamins are the main components of the metazoan lamina, and while the organization of the nuclear lamina of metazoans and plants is similar, there are apparently no genes encoding lamins or most lamin-binding proteins in plants. Thus, the plant lamina is not lamin-based and the proteins that form this structure are still to be characterized. Members of the plant NMCP/LINC/CRWN protein family share the typical tripartite structure of lamins, although the 2 exhibit no sequence similarity. However, given the many similarities between NMCP/LINC/CRWN proteins and lamins (structural organization, position of conserved regions, sub-nuclear distribution, solubility, and pattern of expression), these proteins are good candidates to carry out the functions of lamins in plants. Moreover, functional analysis of NMCP/LINC mutants has revealed their involvement in maintaining nuclear size and shape, another activity fulfilled by lamins. This review summarizes the current understanding of NMCP/LINC proteins and discusses future studies that will be required to demonstrate definitively that these proteins are plant analogs of lamins.
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16
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Zhang C, Mallery EL, Szymanski DB. ARP2/3 localization in Arabidopsis leaf pavement cells: a diversity of intracellular pools and cytoskeletal interactions. FRONTIERS IN PLANT SCIENCE 2013; 4:238. [PMID: 23874346 PMCID: PMC3709099 DOI: 10.3389/fpls.2013.00238] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Accepted: 06/16/2013] [Indexed: 05/03/2023]
Abstract
In plant cells the actin cytoskeleton adopts many configurations, but is best understood as an unstable, interconnected track that rearranges to define the patterns of long distance transport of organelles during growth. Actin filaments do not form spontaneously; instead filament nucleators, such as the evolutionarily conserved actin-related protein (ARP) 2/3 complex, can efficiently generate new actin filament networks when in a fully activated state. A growing number of genetic experiments have shown that ARP2/3 is necessary for morphogenesis in processes that range from tip growth during root nodule formation to the diffuse polarized growth of leaf trichomes and pavement cells. Although progress has been rapid in the identification of proteins that function in series to positively regulate ARP2/3, less has been learned about the actual function of ARP2/3 in cells. In this paper, we analyze the localization of ARP2/3 in Arabidopsis leaf pavement cells. We detect a pool of ARP2/3 in the nucleus, and also find that ARP2/3 is efficiently and specifically clustered on multiple organelle surfaces and associates with both the actin filament and microtubule cytoskeletons. Our mutant analyses and ARP2/3 and actin double labeling experiments indicate that the clustering of ARP2/3 on organelle surfaces and an association with actin bundles does not necessarily reflect an active pool of ARP2/3, and instead most of the complex appears to exist as a latent organelle-associated pool.
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Affiliation(s)
- Chunhua Zhang
- Department of Agronomy, Purdue UniversityWest Lafayette, IN, USA
| | | | - Daniel B. Szymanski
- Department of Agronomy, Purdue UniversityWest Lafayette, IN, USA
- Department of Biology, Purdue UniversityWest Lafayette, IN, USA
- *Correspondence: Daniel B. Szymanski, Department of Agronomy, Purdue University, Lily Hall of Life Sciences, 915 West State Street, West Lafayette, IN 47907-2054, USA e-mail:
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Characterization of a 65 kDa NIF in the nuclear matrix of the monocot Allium cepa that interacts with nuclear spectrin-like proteins. Cell Biol Int 2012; 36:1097-105. [PMID: 22950797 DOI: 10.1042/cbi20120237] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Plant cells have a well organized nucleus and nuclear matrix, but lack orthologues of the main structural components of the metazoan nuclear matrix. Although data is limited, most plant nuclear structural proteins are coiled-coil proteins, such as the NIFs (nuclear intermediate filaments) in Pisum sativum that cross-react with anti-intermediate filament and anti-lamin antibodies, form filaments 6-12 nm in diameter in vitro, and may play the role of lamins. We have investigated the conservation and features of NIFs in a monocot species, Allium cepa, and compared them with onion lamin-like proteins. Polyclonal antisera against the pea 65 kDa NIF were used in 1D and 2D Western blots, ICM (imunofluorescence confocal microscopy) and IEM (immunoelectron microscopy). Their presence in the nuclear matrix was analysed by differential extraction of nuclei, and their association with structural spectrin-like proteins by co-immunoprecipitation and co-localization in ICM. NIF is a conserved structural component of the nucleus and its matrix in monocots with Mr and pI values similar to those of pea 65 kDa NIF, which localized to the nuclear envelope, perichromatin domains and foci, and to the nuclear matrix, interacting directly with structural nuclear spectrin-like proteins. Its similarities with some of the proteins described as onion lamin-like proteins suggest that they are highly related or perhaps the same proteins.
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18
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Simon DN, Wilson KL. The nucleoskeleton as a genome-associated dynamic 'network of networks'. Nat Rev Mol Cell Biol 2011; 12:695-708. [PMID: 21971041 DOI: 10.1038/nrm3207] [Citation(s) in RCA: 222] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In the cytosol, actin polymers, intermediate filaments and microtubules can anchor to cell surface adhesions and interlink to form intricate networks. This cytoskeleton is anchored to the nucleus through LINC (links the nucleoskeleton and cytoskeleton) complexes that span the nuclear envelope and in turn anchor to networks of filaments in the nucleus. The metazoan nucleoskeleton includes nuclear pore-linked filaments, A-type and B-type lamin intermediate filaments, nuclear mitotic apparatus (NuMA) networks, spectrins, titin, 'unconventional' polymers of actin and at least ten different myosin and kinesin motors. These elements constitute a poorly understood 'network of networks' that dynamically reorganizes during mitosis and is responsible for genome organization and integrity.
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Affiliation(s)
- Dan N Simon
- Department of Cell Biology, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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19
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Silván U, Boiteux C, Sütterlin R, Schroeder U, Mannherz HG, Jockusch BM, Bernèche S, Aebi U, Schoenenberger CA. An antiparallel actin dimer is associated with the endocytic pathway in mammalian cells. J Struct Biol 2011; 177:70-80. [PMID: 21970948 DOI: 10.1016/j.jsb.2011.09.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Revised: 09/15/2011] [Accepted: 09/21/2011] [Indexed: 10/17/2022]
Abstract
The dynamic rearrangement of the actin cytoskeleton plays a key role in several cellular processes such as cell motility, endocytosis, RNA processing and chromatin organization. However, the supramolecular actin structures involved in the different processes remain largely unknown. One of the less studied forms of actin is the lower dimer (LD). This unconventional arrangement of two actin molecules in an antiparallel orientation can be detected by chemical crosslinking at the onset of polymerization in vitro. Moreover, evidence for a transient incorporation of LD into growing filaments and its ability to inhibit nucleation of F-actin filament assembly implicate that the LD pathway contributes to supramolecular actin patterning. However, a clear link from this actin species to a specific cellular function has not yet been established. We have developed an antibody that selectively binds to LD configurations in supramolecular actin structures assembled in vitro. This antibody allowed us to unveil the LD in different mammalian cells. In particular, we show an association of the antiparallel actin arrangement with the endocytic compartment at the cellular and ultrastructural level. Taken together, our results strongly support a functional role of LD in the patterning of supramolecular actin assemblies in mammalian cells.
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Affiliation(s)
- Unai Silván
- M.E. Müller Institute for Structural Biology, Biozentrum, University of Basel, CH-4056 Basel, Switzerland
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20
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Schoenenberger CA, Mannherz HG, Jockusch BM. Actin: from structural plasticity to functional diversity. Eur J Cell Biol 2011; 90:797-804. [PMID: 21820202 DOI: 10.1016/j.ejcb.2011.05.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Accepted: 05/03/2011] [Indexed: 11/17/2022] Open
Abstract
This article addresses the multiple activities of actin. Starting out with the history of actin's discovery, purification and structure, it emphasizes the close relation between structure and function. In this context, we also point to unconventional actin conformations. Their existence in living cells is not yet well documented, however, they seem to play a special role in the supramolecular patterning that underlies some of the physiological functions of actin. Conceivably, such conformations may contribute to actin's diverse activities in the nucleus that are poorly understood so far.
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Affiliation(s)
- Cora-Ann Schoenenberger
- M. E. Mueller Institute for Structural Biology, Biozentrum, University of Basel, CH-4056 Basel, Switzerland
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21
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Abstract
BACKGROUND INFORMATION Although actin is a relevant component of the plant nucleus, only three nuclear ABPs (actin-binding proteins) have been identified in plants to date: cofilin, profilin and nuclear myosin I. Although plants lack orthologues of the main structural nuclear ABPs in animals, such as lamins, lamin-associated proteins and nesprins, their genome does contain sequences with spectrin repeats and N-terminal calponin homology domains for actin binding that might be distant relatives of spectrin. We investigated here whether spectrin-like proteins could act as structural nuclear ABPs in plants. RESULTS We have investigated the presence of spectrins in Allium cepa meristematic nuclei by Western blotting, confocal and electron microscopy, using antibodies against α- and β-spectrin chains that cross-react in plant nuclei. Their role as nuclear ABPs was analysed by co-immunoprecipitation and IF (immunofluorescence) co-localization and their association with the nuclear matrix was investigated by sequential extraction of nuclei with non-ionic detergent, and in low- and high-salt buffers after nuclease digestion. Our results demonstrate the existence of several spectrin-like proteins in the nucleus of onion cells that have different intranuclear distributions in asynchronous meristematic populations and associate with the nuclear matrix. These nuclear proteins co-immunoprecipitate and co-localize with actin. CONCLUSIONS These results reveal that the plant nucleus contains spectrin-like proteins that are structural nuclear components and function as ABPs. Their intranuclear distribution suggests that plant nuclear spectrin-like proteins could be involved in multiple nuclear functions.
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Kandasamy MK, McKinney EC, Meagher RB. Differential sublocalization of actin variants within the nucleus. Cytoskeleton (Hoboken) 2011; 67:729-43. [PMID: 20862689 DOI: 10.1002/cm.20484] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Conventional actin has been implicated in various nuclear processes including chromatin remodeling, transcription, nuclear transport, and overall nuclear structure. Moreover, actin has been identified as a component of several chromatin remodeling complexes present in the nucleus. In animal cells, nuclear actin exists as a dynamic equilibrium of monomers and polymers. Actin-binding proteins (ABPs) such as ADF/cofilin and profilin play a role in actin import and export, respectively. However, very little is known about the localization and roles of nuclear actin in plants. In multicellular plants and animals, actin is comprised of an ancient and divergent family of protein variants. Here, we have investigated the presence and differential localization of two ancient subclasses of actin in isolated Arabidopsis nuclei. Although the subclass 1 variants ACT2 and ACT8 and subclass 2 variant ACT7 were found distributed throughout the nucleoplasm, ACT7 was often found more concentrated in nuclear speckles than subclass 1 variants. The nuclei from the act2-1/act8-2 double null mutant and the act7-5 null mutant lacked their corresponding actin variants. In addition, serial sectioning of several independent nuclei revealed that ACT7 was notably more abundant in the nucleolus than the subclass 1 actins. Profilin and ADF proteins were also found in significant levels in plant nuclei. The possible functions of differentially localized nuclear actin variants are discussed.
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Affiliation(s)
- Muthugapatti K Kandasamy
- Department of Genetics, Davison Life Sciences Complex, University of Georgia, Athens, Georgia 30602, USA
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Philimonenko VV, Janácek J, Harata M, Hozák P. Transcription-dependent rearrangements of actin and nuclear myosin I in the nucleolus. Histochem Cell Biol 2010; 134:243-9. [PMID: 20683608 DOI: 10.1007/s00418-010-0732-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/16/2010] [Indexed: 10/19/2022]
Abstract
Nuclear actin and nuclear myosin I (NMI) are important players in transcription of ribosomal genes. Transcription of rDNA takes place in highly organized intranuclear compartment, the nucleolus. In this study, we characterized the localization of these two proteins within the nucleolus of HeLa cells with high structural resolution by means of electron microscopy and gold-immunolabeling. We demonstrate that both actin and NMI are localized in specific compartments within the nucleolus, and the distribution of NMI is transcription-dependent. Moreover, a pool of NMI is present in the foci containing nascent rRNA transcripts. Actin, in turn, is present both in transcriptionally active and inactive regions of the nucleolus and colocalizes with RNA polymerase I and UBF. Our data support the involvement of actin and NMI in rDNA transcription and point out to other functions of these proteins in the nucleolus, such as rRNA maturation and maintenance of nucleolar architecture.
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Affiliation(s)
- V V Philimonenko
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the AS CR, v.v.i., Vídenská 1083, 142 20 Prague 4, Czech Republic
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Kandasamy MK, McKinney EC, Meagher RB. A single vegetative actin isovariant overexpressed under the control of multiple regulatory sequences is sufficient for normal Arabidopsis development. THE PLANT CELL 2009; 21:701-18. [PMID: 19304937 PMCID: PMC2671709 DOI: 10.1105/tpc.108.061960] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2008] [Revised: 02/12/2009] [Accepted: 02/24/2009] [Indexed: 05/18/2023]
Abstract
The relative significance of gene regulation and protein isovariant differences remains unexplored for most gene families, particularly those participating in multicellular development. Arabidopsis thaliana encodes three vegetative actins, ACT2, ACT7, and ACT8, in two ancient and highly divergent subclasses. Mutations in any of these differentially expressed actins revealed only mild phenotypes. However, double mutants were extremely dwarfed, with altered cell and organ morphology and an aberrant F-actin cytoskeleton (e.g., act2-1 act7-4 and act8-2 act7-4) or totally root-hairless (e.g., act2-1 act8-2). Our studies suggest that the three vegetative actin genes and protein isovariants play distinct subclass-specific roles during plant morphogenesis. For example, during root development, ACT7 was involved in root growth, epidermal cell specification, cell division, and root architecture, and ACT2 and ACT8 were essential for root hair tip growth. Also, genetic complementation revealed that the ACT2 and ACT8 isovariants, but not ACT7, fully rescued the root hair growth defects of single and double mutants. Moreover, we synthesized fully normal plants overexpressing the ACT8 isovariant from multiple actin regulatory sequences as the only vegetative actin in the act2-1 act7-4 background. In summary, it is evident that differences in vegetative actin gene regulation and the diversity in actin isovariant sequences are essential for normal plant development.
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Affiliation(s)
- Muthugapatti K Kandasamy
- Department of Genetics, Davison Life Sciences Complex, University of Georgia, Athens, Georgia 30602, USA
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