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Staneva D, Vasileva B, Podlesniy P, Miloshev G, Georgieva M. Yeast Chromatin Mutants Reveal Altered mtDNA Copy Number and Impaired Mitochondrial Membrane Potential. J Fungi (Basel) 2023; 9:jof9030329. [PMID: 36983497 PMCID: PMC10058930 DOI: 10.3390/jof9030329] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 03/02/2023] [Accepted: 03/04/2023] [Indexed: 03/30/2023] Open
Abstract
Mitochondria are multifunctional, dynamic organelles important for stress response, cell longevity, ageing and death. Although the mitochondrion has its genome, nuclear-encoded proteins are essential in regulating mitochondria biogenesis, morphology, dynamics and function. Moreover, chromatin structure and epigenetic mechanisms govern the accessibility to DNA and control gene transcription, indirectly influencing nucleo-mitochondrial communications. Thus, they exert crucial functions in maintaining proper chromatin structure, cell morphology, gene expression, stress resistance and ageing. Here, we present our studies on the mtDNA copy number in Saccharomyces cerevisiae chromatin mutants and investigate the mitochondrial membrane potential throughout their lifespan. The mutants are arp4 (with a point mutation in the ARP4 gene, coding for actin-related protein 4-Arp4p), hho1Δ (lacking the HHO1 gene, coding for the linker histone H1), and the double mutant arp4 hho1Δ cells with the two mutations. Our findings showed that the three chromatin mutants acquired strain-specific changes in the mtDNA copy number. Furthermore, we detected the disrupted mitochondrial membrane potential in their chronological lifespan. In addition, the expression of nuclear genes responsible for regulating mitochondria biogenesis and turnover was changed. The most pronounced were the alterations found in the double mutant arp4 hho1Δ strain, which appeared as the only petite colony-forming mutant, unable to grow on respiratory substrates and with partial depletion of the mitochondrial genome. The results suggest that in the studied chromatin mutants, hho1Δ, arp4 and arp4 hho1Δ, the nucleus-mitochondria communication was disrupted, leading to impaired mitochondrial function and premature ageing phenotype in these mutants, especially in the double mutant.
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Affiliation(s)
- Dessislava Staneva
- Laboratory of Molecular Genetics, Epigenetics and Longevity, Institute of Molecular Biology "RoumenTsanev", Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Bela Vasileva
- Laboratory of Molecular Genetics, Epigenetics and Longevity, Institute of Molecular Biology "RoumenTsanev", Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Petar Podlesniy
- CiberNed (Centro Investigacion Biomedica en Red Enfermedades Neurodegenerativas), 28029 Barcelona, Spain
| | - George Miloshev
- Laboratory of Molecular Genetics, Epigenetics and Longevity, Institute of Molecular Biology "RoumenTsanev", Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Milena Georgieva
- Laboratory of Molecular Genetics, Epigenetics and Longevity, Institute of Molecular Biology "RoumenTsanev", Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
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Mołoń M, Stępień K, Kielar P, Vasileva B, Lozanska B, Staneva D, Ivanov P, Kula-Maximenko M, Molestak E, Tchórzewski M, Miloshev G, Georgieva M. Actin-Related Protein 4 and Linker Histone Sustain Yeast Replicative Ageing. Cells 2022; 11:cells11172754. [PMID: 36078161 PMCID: PMC9454676 DOI: 10.3390/cells11172754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/27/2022] [Accepted: 08/29/2022] [Indexed: 11/24/2022] Open
Abstract
Ageing is accompanied by dramatic changes in chromatin structure organization and genome function. Two essential components of chromatin, the linker histone Hho1p and actin-related protein 4 (Arp4p), have been shown to physically interact in Saccharomyces cerevisiae cells, thus maintaining chromatin dynamics and function, as well as genome stability and cellular morphology. Disrupting this interaction has been proven to influence the stability of the yeast genome and the way cells respond to stress during chronological ageing. It has also been proven that the abrogated interaction between these two chromatin proteins elicited premature ageing phenotypes. Alterations in chromatin compaction have also been associated with replicative ageing, though the main players are not well recognized. Based on this knowledge, here, we examine how the interaction between Hho1p and Arp4p impacts the ageing of mitotically active yeast cells. For this purpose, two sets of strains were used—haploids (WT(n), arp4, hho1Δ and arp4 hho1Δ) and their heterozygous diploid counterparts (WT(2n), ARP4/arp4, HHO1/hho1Δ and ARP4 HHO1/arp4 hho1Δ)—for the performance of extensive morphological and physiological analyses during replicative ageing. These analyses included a comparative examination of the yeast cells’ chromatin structure, proliferative and reproductive potential, and resilience to stress, as well as polysome profiles and chemical composition. The results demonstrated that the haploid chromatin mutants arp4 and arp4 hho1Δ demonstrated a significant reduction in replicative and total lifespan. These findings lead to the conclusion that the importance of a healthy interaction between Arp4p and Hho1p in replicative ageing is significant. This is proof of the concomitant importance of Hho1p and Arp4p in chronological and replicative ageing.
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Affiliation(s)
- Mateusz Mołoń
- Department of Biochemistry and Cell Biology, Institute of Biology and Biotechnology, University of Rzeszow, 35-601 Rzeszow, Poland
- Correspondence: (M.M.); (M.G.)
| | - Karolina Stępień
- Department of Biochemistry and Cell Biology, Institute of Biology and Biotechnology, University of Rzeszow, 35-601 Rzeszow, Poland
| | - Patrycja Kielar
- Department of Biochemistry and Cell Biology, Institute of Biology and Biotechnology, University of Rzeszow, 35-601 Rzeszow, Poland
| | - Bela Vasileva
- Laboratory of Yeast Molecular Genetics, Institute of Molecular Biology “Acad. R. Tsanev”, Bulgarian Academy of Sciences, 1123 Sofia, Bulgaria
| | - Bonka Lozanska
- Laboratory of Yeast Molecular Genetics, Institute of Molecular Biology “Acad. R. Tsanev”, Bulgarian Academy of Sciences, 1123 Sofia, Bulgaria
| | - Dessislava Staneva
- Laboratory of Yeast Molecular Genetics, Institute of Molecular Biology “Acad. R. Tsanev”, Bulgarian Academy of Sciences, 1123 Sofia, Bulgaria
| | - Penyo Ivanov
- Laboratory of Yeast Molecular Genetics, Institute of Molecular Biology “Acad. R. Tsanev”, Bulgarian Academy of Sciences, 1123 Sofia, Bulgaria
| | - Monika Kula-Maximenko
- The Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Kraków, Poland
| | - Eliza Molestak
- Department of Molecular Biology, Maria Curie-Skłodowska University, 20-033 Lublin, Poland
| | - Marek Tchórzewski
- Department of Molecular Biology, Maria Curie-Skłodowska University, 20-033 Lublin, Poland
| | - George Miloshev
- Laboratory of Yeast Molecular Genetics, Institute of Molecular Biology “Acad. R. Tsanev”, Bulgarian Academy of Sciences, 1123 Sofia, Bulgaria
| | - Milena Georgieva
- Laboratory of Yeast Molecular Genetics, Institute of Molecular Biology “Acad. R. Tsanev”, Bulgarian Academy of Sciences, 1123 Sofia, Bulgaria
- Correspondence: (M.M.); (M.G.)
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Natural Deep Eutectic Extracts of Propolis, Sideritis scardica, and Plantago major Reveal Potential Antiageing Activity during Yeast Chronological Lifespan. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:8368717. [PMID: 36082083 PMCID: PMC9448591 DOI: 10.1155/2022/8368717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 08/05/2022] [Indexed: 11/18/2022]
Abstract
Nowadays, the environmentally friendly approach to everyday life routines including body supplementation with pharma-, nutraceuticals and dietary supplements gains popularity. This trend is implemented in pharmaceutical as well as cosmetic and antiageing industries by adopting a newly developed green chemistry approach. Following this trend, a new type of solvents has been created, called Natural Deep Eutectic Solvents (NADES), which are produced by plant primary metabolites. These solvents are becoming a much better alternative to the already established organic solvents like ethanol and ionic liquids by being nontoxic, biodegradable, and easy to make. An interesting fact about NADES is that they enhance the biological activities of the extracted biological compounds. Here, we present our results that investigate the potential antiageing effect of CiAPD14 as a NADES solvent and three plant extracts with it. The tested NADES extracts are from propolis and two well-known medicinal plants—Sideritis scardica and Plantago major. Together with the solvent, their antiageing properties have been tested during the chronological lifespan of four Saccharomyces cerevisiae yeast strains—a wild type and three chromatin mutants. The chromatin mutants have been previously proven to exhibit characteristics of premature ageing. Our results demonstrate the potential antiageing activity of these NADES extracts, which was exhibited through their ability to confer the premature ageing phenotypes in the mutant cells by ameliorating their cellular growth and cell cycle, as well as by influencing the activity of some stress-responsive genes. Moreover, we have classified their antiageing activity concerning the strength of the observed bioactivities.
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Changes in Chromatin Organization Eradicate Cellular Stress Resilience to UVA/B Light and Induce Premature Aging. Cells 2021; 10:cells10071755. [PMID: 34359924 PMCID: PMC8304177 DOI: 10.3390/cells10071755] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 06/10/2021] [Accepted: 07/08/2021] [Indexed: 11/16/2022] Open
Abstract
Complex interactions among DNA and nuclear proteins maintain genome organization and stability. The nuclear proteins, particularly the histones, organize, compact, and preserve the stability of DNA, but also allow its dynamic reorganization whenever the nuclear processes require access to it. Five histone classes exist and they are evolutionarily conserved among eukaryotes. The linker histones are the fifth class and over time, their role in chromatin has been neglected. Linker histones interact with DNA and the other histones and thus sustain genome stability and nuclear organization. Saccharomyces cerevisiae is a brilliant model for studying linker histones as the gene for it is a single-copy and is non-essential. We, therefore, created a linker histone-free yeast strain using a knockout of the relevant gene and traced the way cells age chronologically. Here we present our results demonstrating that the altered chromatin dynamics during the chronological lifespan of the yeast cells with a mutation in ARP4 (the actin-related protein 4) and without the gene HHO1 for the linker histone leads to strong alterations in the gene expression profiles of a subset of genes involved in DNA repair and autophagy. The obtained results further prove that the yeast mutants have reduced survival upon UVA/B irradiation possibly due to the accelerated decompaction of chromatin and impaired proliferation. Our hypothesis posits that the higher-order chromatin structure and the interactions among chromatin proteins are crucial for the maintenance of chromatin organization during chronological aging under optimal and UVA-B stress conditions.
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Venit T, Mahmood SR, Endara-Coll M, Percipalle P. Nuclear actin and myosin in chromatin regulation and maintenance of genome integrity. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2020; 355:67-108. [DOI: 10.1016/bs.ircmb.2020.05.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/06/2022]
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Klages-Mundt NL, Kumar A, Zhang Y, Kapoor P, Shen X. The Nature of Actin-Family Proteins in Chromatin-Modifying Complexes. Front Genet 2018; 9:398. [PMID: 30319687 PMCID: PMC6167448 DOI: 10.3389/fgene.2018.00398] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 08/31/2018] [Indexed: 01/25/2023] Open
Abstract
Actin is not only one of the most abundant proteins in eukaryotic cells, but also one of the most versatile. In addition to its familiar involvement in enabling contraction and establishing cellular motility and scaffolding in the cytosol, actin has well-documented roles in a variety of processes within the confines of the nucleus, such as transcriptional regulation and DNA repair. Interestingly, monomeric actin as well as actin-related proteins (Arps) are found as stoichiometric subunits of a variety of chromatin remodeling complexes and histone acetyltransferases, raising the question of precisely what roles they serve in these contexts. Actin and Arps are present in unique combinations in chromatin modifiers, helping to establish structural integrity of the complex and enabling a wide range of functions, such as recruiting the complex to nucleosomes to facilitate chromatin remodeling and promoting ATPase activity of the catalytic subunit. Actin and Arps are also thought to help modulate chromatin dynamics and maintain higher-order chromatin structure. Moreover, the presence of actin and Arps in several chromatin modifiers is necessary for promoting genomic integrity and an effective DNA damage response. In this review, we discuss the involvement of actin and Arps in these nuclear complexes that control chromatin remodeling and histone modifications, while also considering avenues for future study to further shed light on their functional importance.
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Affiliation(s)
- Naeh L Klages-Mundt
- Science Park Research Division, Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, United States.,Program in Genetics & Epigenetics, The University of Texas MD Anderson Cancer Center, UTHealth Graduate School of Biomedical Sciences, Houston, TX, United States
| | - Ashok Kumar
- Department of Cellular and Molecular Biology, The University of Texas Health Science Center at Tyler, Tyler, TX, United States
| | - Yuexuan Zhang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Prabodh Kapoor
- Department of Cellular and Molecular Biology, The University of Texas Health Science Center at Tyler, Tyler, TX, United States
| | - Xuetong Shen
- Science Park Research Division, Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, United States.,Program in Genetics & Epigenetics, The University of Texas MD Anderson Cancer Center, UTHealth Graduate School of Biomedical Sciences, Houston, TX, United States
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Miloshev G, Staneva D, Uzunova K, Vasileva B, Draganova-Filipova M, Zagorchev P, Georgieva M. Linker histones and chromatin remodelling complexes maintain genome stability and control cellular ageing. Mech Ageing Dev 2018; 177:55-65. [PMID: 30025887 DOI: 10.1016/j.mad.2018.07.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 07/06/2018] [Accepted: 07/12/2018] [Indexed: 01/08/2023]
Abstract
Linker histones are major players in chromatin organization and per se are essential players in genome homeostasis. As the fifth class of histone proteins the linker histones not only interact with DNA and core histones but also with other chromatin proteins. These interactions prove to be essential for the higher levels of chromatin organization like chromatin loops, transcription factories and chromosome territories. Our recent results have proved that Saccharomyces cerevisiae linker histone - Hho1p, physically interacts with the actin-related protein 4 (Arp4) and that the abrogation of this interaction through the deletion of the gene for the linker histone in arp4 mutant cells leads to global changes in chromatin compaction. Here, we show that the healthy interaction between the yeast linker histone and Arp4p is critical for maintaining genome stability and for controlling cellular sensitivity to different types of stress. The abolished interaction between the linker histone and Arp4p leads the mutant yeast cells to premature ageing phenotypes. Cells die young and are more sensitive to stress. These results unambiguously prove the role of linker histones and chromatin remodelling in ageing by their cooperation in pertaining higher-order chromatin compaction and thus maintaining genome stability.
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Affiliation(s)
- George Miloshev
- Laboratory of Yeast Molecular Genetics, Institute of Molecular Biology "Acad. Roumen Tsanev", Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Dessislava Staneva
- Laboratory of Yeast Molecular Genetics, Institute of Molecular Biology "Acad. Roumen Tsanev", Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Katya Uzunova
- Laboratory of Yeast Molecular Genetics, Institute of Molecular Biology "Acad. Roumen Tsanev", Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Bela Vasileva
- Laboratory of Yeast Molecular Genetics, Institute of Molecular Biology "Acad. Roumen Tsanev", Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | | | - Plamen Zagorchev
- Department of Medical Physics and Biophysics, Faculty of Pharmacy, Medical University, Plovdiv, Bulgaria
| | - Milena Georgieva
- Laboratory of Yeast Molecular Genetics, Institute of Molecular Biology "Acad. Roumen Tsanev", Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria.
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Staneva D, Georgieva M, Miloshev G. Kluyveromyces lactis genome harbours a functional linker histone encoding gene. FEMS Yeast Res 2016; 16:fow034. [PMID: 27189369 DOI: 10.1093/femsyr/fow034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/02/2016] [Indexed: 11/14/2022] Open
Abstract
Linker histones are essential components of chromatin in eukaryotes. Through interactions with linker DNA and nucleosomes they facilitate folding and maintenance of higher-order chromatin structures and thus delicately modulate gene activity. The necessity of linker histones in lower eukaryotes appears controversial and dubious. Genomic data have shown that Schizosaccharomyces pombe does not possess genes encoding linker histones while Kluyveromyces lactis has been reported to have a pseudogene. Regarding this controversy, we have provided the first direct experimental evidence for the existence of a functional linker histone gene, KlLH1, in K. lactis genome. Sequencing of KlLH1 from both genomic DNA and copy DNA confirmed the presence of an intact open reading frame. Transcription and splicing of the KlLH1 sequence as well as translation of its mRNA have been studied. In silico analysis revealed homology of KlLH1p to the histone H1/H5 protein family with predicted three domain structure characteristic for the linker histones of higher eukaryotes. This strongly proves that the yeast K. lactis does indeed possess a functional linker histone gene thus entailing the evolutionary preservation and significance of linker histones. The nucleotide sequences of KlLH1 are deposited in the GenBank under accession numbers KT826576, KT826577 and KT826578.
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Affiliation(s)
- Dessislava Staneva
- Laboratory of Yeast Molecular Genetics, Institute of Molecular Biology, Bulgarian Academy of Sciences, 'Acad. Roumen Tsanev', Sofia 1113, Bulgaria
| | - Milena Georgieva
- Laboratory of Yeast Molecular Genetics, Institute of Molecular Biology, Bulgarian Academy of Sciences, 'Acad. Roumen Tsanev', Sofia 1113, Bulgaria
| | - George Miloshev
- Laboratory of Yeast Molecular Genetics, Institute of Molecular Biology, Bulgarian Academy of Sciences, 'Acad. Roumen Tsanev', Sofia 1113, Bulgaria
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Actin, actin-related proteins and profilin in diatoms: A comparative genomic analysis. Mar Genomics 2015; 23:133-42. [DOI: 10.1016/j.margen.2015.07.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Revised: 06/30/2015] [Accepted: 07/02/2015] [Indexed: 12/24/2022]
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10
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Georgieva M, Staneva D, Uzunova K, Efremov T, Balashev K, Harata M, Miloshev G. The linker histone in Saccharomyces cerevisiae interacts with actin-related protein 4 and both regulate chromatin structure and cellular morphology. Int J Biochem Cell Biol 2015; 59:182-92. [DOI: 10.1016/j.biocel.2014.12.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 12/15/2014] [Indexed: 11/28/2022]
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Georgieva M, Staneva D, Uzunova K, Miloshev G. The Deletion of the Gene for the Linker Histone inARP 4Mutant Yeast Cells is not Deleterious. BIOTECHNOL BIOTEC EQ 2014. [DOI: 10.5504/50yrtimb.2011.0025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Nuclear actin-related protein is required for chromosome segregation in Toxoplasma gondii. Mol Biochem Parasitol 2011; 181:7-16. [PMID: 21963440 DOI: 10.1016/j.molbiopara.2011.09.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2011] [Revised: 09/10/2011] [Accepted: 09/15/2011] [Indexed: 12/30/2022]
Abstract
Apicomplexa parasites use complex cell cycles to replicate that are not well understood mechanistically. We have established a robust forward genetic strategy to identify the essential components of parasite cell division. Here we describe a novel temperature sensitive Toxoplasma strain, mutant 13-20C2, which growth arrests due to a defect in mitosis. The primary phenotype is the mis-segregation of duplicated chromosomes with chromosome loss during nuclear division. This defect is conditional-lethal with respect to temperature, although relatively mild in regard to the preservation of the major microtubule organizing centers. Despite severe DNA loss many of the physical structures associated with daughter budding and the assembly of invasion structures formed and operated normally at the non-permissive temperature before completely arresting. These results suggest there are coordinating mechanisms that govern the timing of these events in the parasite cell cycle. The defect in mutant 13-20C2 was mapped by genetic complementation to Toxoplasma chromosome III and to a specific mutation in the gene encoding an ortholog of nuclear actin-related protein 4. A change in a conserved isoleucine to threonine in the helical structure of this nuclear actin related protein leads to protein instability and cellular mis-localization at the higher temperature. Given the age of this protist family, the results indicate a key role for nuclear actin-related proteins in chromosome segregation was established very early in the evolution of eukaryotes.
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Oma Y, Harata M. Actin-related proteins localized in the nucleus: from discovery to novel roles in nuclear organization. Nucleus 2011; 2:38-46. [PMID: 21647298 PMCID: PMC3104808 DOI: 10.4161/nucl.2.1.14510] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2010] [Revised: 12/15/2010] [Accepted: 12/17/2010] [Indexed: 12/18/2022] Open
Abstract
The actin family consists of conventional actin and actin-related proteins (ARPs), and the members show moderate similarity and share the same basal structure. Following the finding of various ARPs in the cytoplasm in the 1990s, multiple subfamilies that are localized predominantly in the nucleus were identified. Consistent with these cytological observations, subsequent biochemical analyses revealed the involvement of the nuclear ARPs in ATP-dependent chromatin-remodeling and histone acetyltransferase complexes. In addition to their contribution to chromatin remodeling, recent studies have shown that nuclear ARPs have roles in the organization of the nucleus that are independent of the activity of the above-mentioned complexes. Therefore, nuclear ARPs are recognized as novel key regulators of genome function, and affect not only the remodeling of chromatin but also the spatial arrangement and dynamics of chromatin within the nucleus.
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Affiliation(s)
- Yukako Oma
- Laboratory of Molecular Biology, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
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15
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Castano E, Philimonenko VV, Kahle M, Fukalová J, Kalendová A, Yildirim S, Dzijak R, Dingová-Krásna H, Hozák P. Actin complexes in the cell nucleus: new stones in an old field. Histochem Cell Biol 2010; 133:607-26. [PMID: 20443021 DOI: 10.1007/s00418-010-0701-2] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/12/2010] [Indexed: 01/13/2023]
Abstract
Actin is a well-known protein that has shown a myriad of activities in the cytoplasm. However, recent findings of actin involvement in nuclear processes are overwhelming. Actin complexes in the nucleus range from very dynamic chromatin-remodeling complexes to structural elements of the matrix with single partners known as actin-binding proteins (ABPs). This review summarizes the recent findings of actin-containing complexes in the nucleus. Particular attention is given to key processes like chromatin remodeling, transcription, DNA replication, nucleocytoplasmic transport and to actin roles in nuclear architecture. Understanding the mechanisms involving ABPs will definitely lead us to the principles of the regulation of gene expression performed via concerting nuclear and cytoplasmic processes.
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Affiliation(s)
- E Castano
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the ASCR, Prague, Czech Republic
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Gieni RS, Hendzel MJ. Actin dynamics and functions in the interphase nucleus: moving toward an understanding of nuclear polymeric actin. Biochem Cell Biol 2009; 87:283-306. [PMID: 19234542 DOI: 10.1139/o08-133] [Citation(s) in RCA: 112] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Actin exists as a dynamic equilibrium of monomers and polymers within the nucleus of living cells. It is utilized by the cell for many aspects of gene regulation, including mRNA processing, chromatin remodelling, and global gene expression. Polymeric actin is now specifically linked to transcription by RNA polymerase I, II, and III. An active process, requiring both actin polymers and myosin, appears to drive RNA polymerase I transcription, and is also implicated in long-range chromatin movement. This type of mechanism brings activated genes from separate chromosomal territories together, and then participates in their compartmentalization near nuclear speckles. Nuclear speckle formation requires polymeric actin, and factors promoting polymerization, such as profilin and PIP2, are concentrated there. A review of the literature shows that a functional population of G-actin cycles between the cytoplasm and the nucleoplasm. Its nuclear concentration is dependent on the cytoplasmic G-actin pool, as well as on the activity of import and export mechanisms and the availability of interactions that sequester it within the nucleus. The N-WASP-Arp2/3 actin polymer-nucleating mechanism functions in the nucleus, and its mediators, including NCK, PIP2, and Rac1, can be found in the nucleoplasm, where they likely influence the kinetics of polymer formation. The actin polymer species produced are tightly regulated, and may take on conformations not easily recognized by phalloidin. Many of the factors that cleave F-actin in the cytoplasm are present at high levels in the nucleoplasm, and are also likely to affect actin dynamics there. The absolute and relative G-actin content in the nucleoplasm and the cytoplasm of a cell contains information about the homeostatic state of that cell. We propose that the cycling of G-actin between the nucleus and cytoplasm represents a signal transduction mechanism that can function through both extremes of global cellular G-actin content. MAL signalling within the serum response factor pathway, when G-actin levels are low, represents a well-studied example of actin functioning in signal transduction. The translocation of NCK into the nucleus, along with G-actin, during dissolution of the cytoskeleton in response to DNA damage represents another instance of a unique signalling mechanism operating when G-actin levels are high.
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Affiliation(s)
- Randall S Gieni
- Cross Cancer Institute and Department of Oncology, Faculty of Medicine, University of Alberta, Edmonton, ABT6G1Z2, Canada
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Meagher RB, Kandasamy MK, McKinney EC, Roy E. Chapter 5. Nuclear actin-related proteins in epigenetic control. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2009; 277:157-215. [PMID: 19766970 PMCID: PMC2800988 DOI: 10.1016/s1937-6448(09)77005-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
The nuclear actin-related proteins (ARPs) share overall structure and low-level sequence homology with conventional actin. They are indispensable subunits of macromolecular machines that control chromatin remodeling and modification leading to dynamic changes in DNA structure, transcription, and DNA repair. Cellular, genetic, and biochemical studies suggest that the nuclear ARPs are essential to the epigenetic control of the cell cycle and cell proliferation in all eukaryotes, while in plants and animals they also exert epigenetic controls over most stages of multicellular development including organ initiation, the switch to reproductive development, and senescence and programmed cell death. A theme emerging from plants and animals is that in addition to their role in controlling the general compaction of DNA and gene silencing, isoforms of nuclear ARP-containing chromatin complexes have evolved to exert dynamic epigenetic control over gene expression and different phases of multicellular development. Herein, we explore this theme by examining nuclear ARP phylogeny, activities of ARP-containing chromatin remodeling complexes that lead to epigenetic control, expanding developmental roles assigned to several animal and plant ARP-containing complexes, the evidence that thousands of ARP complex isoforms may have evolved in concert with multicellular development, and ARPs in human disease.
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Affiliation(s)
- Richard B Meagher
- Department of Genetics, Davison Life Sciences Building, University of Georgia, Athens, GA 30602, USA
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Conaway RC, Conaway JW. The INO80 chromatin remodeling complex in transcription, replication and repair. Trends Biochem Sci 2008; 34:71-7. [PMID: 19062292 DOI: 10.1016/j.tibs.2008.10.010] [Citation(s) in RCA: 143] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2008] [Revised: 10/28/2008] [Accepted: 10/29/2008] [Indexed: 01/05/2023]
Abstract
The Ino80 ATPase is a member of the SNF2 family of ATPases and functions as an integral component of a multisubunit ATP-dependent chromatin remodeling complex. Although INO80 complexes from yeast and higher eukaryotes share a common core of conserved subunits, the complexes have diverged substantially during evolution and have acquired new subunits with apparently species-specific functions. Recent studies have shown that the INO80 complex contributes to a wide variety of chromatin-dependent nuclear transactions, including transcription, DNA repair and DNA replication.
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Affiliation(s)
- Ronald C Conaway
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; Department of Biochemistry and Molecular Biology, Kansas University Medical Center, Kansas City, KS 66160, USA
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19
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Georgieva M, Harata M, Miloshev G. The nuclear actin-related protein Act3p/Arp4 influences yeast cell shape and bulk chromatin organization. J Cell Biochem 2008; 104:59-67. [PMID: 18004728 DOI: 10.1002/jcb.21600] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
ACT3/ARP4 is an essential gene, coding for the actin-related protein Act3p/Arp4 of Saccharomyces cerevisiae located within the nucleus. Act3p/Arp4 is a stoichiometric component of the NuA4, INO80, and SWR1 chromatin modulating complexes, and recruits these complexes onto chromatin for their proper chromatin functions. Mutated Act3p/Arp4 leads to impairment of the functions of these complexes and affects transcription of specific genes. Our results revealed significant disorder in the cell size and shape of act3/arp4 mutant cells, when grown at permissive temperature. act3/arp4 mutants have also demonstrated an increase in their nuclear diameters, thus suggesting that Act3p/Arp4 is a key regulator in the maintenance of cellular shape and nuclear organization. Furthermore, the use of Chromatin Yeast Comet Assay (ChYCA) for assessment of single-cell bulk chromatin organization in act3/arp4 mutant cells allowed us to detect an elevated sensitivity toward nuclease action, denoting differences in higher-order chromatin structure of the mutants.
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Affiliation(s)
- Milena Georgieva
- Laboratory of Yeast Molecular Genetics, Institute of Molecular Biology, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria.
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20
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Gottschalk AJ, Conaway RC, Conaway JW. New clues to actin function in chromatin regulation. Nat Struct Mol Biol 2008; 15:432-3. [PMID: 18461045 DOI: 10.1038/nsmb0508-432] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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21
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Abstract
In this article, we follow the history of one of the most abundant, most intensely studied proteins of the eukaryotic cells: actin. We report on hallmarks of its discovery, its structural and functional characterization and localization over time, and point to present days’ knowledge on its position as a member of a large family. We focus on the rather puzzling number of diverse functions as proposed for actin as a dual compartment protein. Finally, we venture on some speculations as to its origin.
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22
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Song Z, Wang M, Wang X, Pan X, Liu W, Hao S, Zeng X. Nuclear actin is involved in the regulation of CSF1 gene transcription in a chromatin required, BRG1 independent manner. J Cell Biochem 2008; 102:403-11. [PMID: 17393431 DOI: 10.1002/jcb.21300] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Actin is an important protein in nucleus and has been implicated in transcription, however, the mechanism of its function in transcription is still not clear. In this article, we studied the role of actin in the regulation of human CSF1 gene transcription. Our results showed that nuclear actin stimulates the activity of CSF1 promoter, and the role in augmenting CSF1 gene transcription requires the formation of chromatin and Z-DNA structure. The ATP binding motifs of nuclear actin are essential for its function in regulating CSF1 gene transcription, and upon actin overexpression, there is an increase in the ATPase activity of nuclear proteins. Further investigation revealed that nuclear actin regulates CSF1 gene transcription in a BRG1 independent manner. Together, these original results have provided evidence for further understanding the mechanism of nuclear actin in regulating gene transcription.
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Affiliation(s)
- Zhaoxia Song
- Institute of Genetics and Cytology, Northeast Normal University, Changchun 130024, China
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23
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Actin-related proteins in chromatin-level control of the cell cycle and developmental transitions. Trends Cell Biol 2007; 17:325-32. [PMID: 17643304 DOI: 10.1016/j.tcb.2007.06.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2007] [Revised: 05/10/2007] [Accepted: 06/26/2007] [Indexed: 11/18/2022]
Abstract
Regulating developmental transitions, cell proliferation and cell death through differential gene expression is essential to the ontogeny of all multicellular organisms. Chromatin remodeling is an active process that is necessary for managing the genome-wide suppression of gene activities resulting from DNA compaction. Recent data in plants suggest a general theme, whereby chromatin remodeling complexes containing nuclear actin-related proteins (ARPs) potentiate the activities of crucial regulatory genes involved in plant growth and development, in addition to their basal activities on a much larger set of genes.
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24
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Chen M, Shen X. Nuclear actin and actin-related proteins in chromatin dynamics. Curr Opin Cell Biol 2007; 19:326-30. [PMID: 17467255 DOI: 10.1016/j.ceb.2007.04.009] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2007] [Accepted: 04/16/2007] [Indexed: 11/22/2022]
Abstract
Conventional actin and actin-related proteins (Arps) are members of the actin superfamily and are conserved throughout evolution. Although the cytoskeletal functions of cytoplasmic actin and Arps have been characterized extensively, the functions and mechanisms of nuclear actin and Arps are not yet well understood. Emerging evidence suggest that nuclear actin and Arps are involved in many nuclear processes, such as transcription and chromatin remodeling. Actin and Arps are subunits of multiple chromatin modifying complexes, and functionally contribute to chromatin modifications. Recent progress has been made in understanding nuclear actin and Arps in the context of chromatin regulation, suggesting potential mechanisms for their functions.
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Affiliation(s)
- Mingming Chen
- Department of Carcinogenesis, Science Park Research Division, University of Texas M.D. Anderson Cancer Center, Smithville, Texas 78957, USA
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25
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Ogiwara H, Ui A, Kawashima S, Kugou K, Onoda F, Iwahashi H, Harata M, Ohta K, Enomoto T, Seki M. Actin-related protein Arp4 functions in kinetochore assembly. Nucleic Acids Res 2007; 35:3109-17. [PMID: 17452364 PMCID: PMC1888834 DOI: 10.1093/nar/gkm161] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
The actin-related proteins (Arps) comprise a conserved protein family. Arp4p is found in large multisubunits of the INO80 and SWR1 chromatin remodeling complexes and in the NuA4 histone acetyltransferase complex. Here we show that arp4 (arp4S23A/D159A) temperature-sensitive cells are defective in G2/M phase function. arp4 mutants are sensitive to the microtubule depolymerizing agent benomyl and arrest at G2/M phase at restrictive temperature. Arp4p is associated with centromeric and telomeric regions throughout cell cycle. Ino80p, Esa1p and Swr1p, components of the INO80, NuA4 and SWR1 complexes, respectively, also associate with centromeres. The association of many kinetochore components including Cse4p, a component of the centromere nucleosome, Mtw1p and Ctf3p is partially impaired in arp4 cells, suggesting that the G2/M arrest of arp4 mutant cells is due to a defect in formation of the chromosomal segregation apparatus.
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Affiliation(s)
- Hideaki Ogiwara
- Molecular Cell Biology Laboratory, Graduate School of Pharmaceutical Sciences, Tohoku University, Aoba 6-3, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan, Genetic System Regulation Laboratory, RIKEN, Wako, Saitama 351-0198, Japan, The Graduate School of Science and Engineering, Saitama University, Sakura-ku, Saitama, Saitama 338-8570, Japan, National Institute of Advanced Industrial Science and Technology, Ibaraki, Japan, Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi 981-8555, Japan and Tohoku University 21st Century COE Program “Comprehensive Research and Education Center for Planning of Drug development and Clinical Evaluation”, Sendai, Miyagi 980-8578, Japan
| | - Ayako Ui
- Molecular Cell Biology Laboratory, Graduate School of Pharmaceutical Sciences, Tohoku University, Aoba 6-3, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan, Genetic System Regulation Laboratory, RIKEN, Wako, Saitama 351-0198, Japan, The Graduate School of Science and Engineering, Saitama University, Sakura-ku, Saitama, Saitama 338-8570, Japan, National Institute of Advanced Industrial Science and Technology, Ibaraki, Japan, Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi 981-8555, Japan and Tohoku University 21st Century COE Program “Comprehensive Research and Education Center for Planning of Drug development and Clinical Evaluation”, Sendai, Miyagi 980-8578, Japan
| | - Satoshi Kawashima
- Molecular Cell Biology Laboratory, Graduate School of Pharmaceutical Sciences, Tohoku University, Aoba 6-3, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan, Genetic System Regulation Laboratory, RIKEN, Wako, Saitama 351-0198, Japan, The Graduate School of Science and Engineering, Saitama University, Sakura-ku, Saitama, Saitama 338-8570, Japan, National Institute of Advanced Industrial Science and Technology, Ibaraki, Japan, Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi 981-8555, Japan and Tohoku University 21st Century COE Program “Comprehensive Research and Education Center for Planning of Drug development and Clinical Evaluation”, Sendai, Miyagi 980-8578, Japan
| | - Kazuto Kugou
- Molecular Cell Biology Laboratory, Graduate School of Pharmaceutical Sciences, Tohoku University, Aoba 6-3, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan, Genetic System Regulation Laboratory, RIKEN, Wako, Saitama 351-0198, Japan, The Graduate School of Science and Engineering, Saitama University, Sakura-ku, Saitama, Saitama 338-8570, Japan, National Institute of Advanced Industrial Science and Technology, Ibaraki, Japan, Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi 981-8555, Japan and Tohoku University 21st Century COE Program “Comprehensive Research and Education Center for Planning of Drug development and Clinical Evaluation”, Sendai, Miyagi 980-8578, Japan
| | - Fumitoshi Onoda
- Molecular Cell Biology Laboratory, Graduate School of Pharmaceutical Sciences, Tohoku University, Aoba 6-3, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan, Genetic System Regulation Laboratory, RIKEN, Wako, Saitama 351-0198, Japan, The Graduate School of Science and Engineering, Saitama University, Sakura-ku, Saitama, Saitama 338-8570, Japan, National Institute of Advanced Industrial Science and Technology, Ibaraki, Japan, Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi 981-8555, Japan and Tohoku University 21st Century COE Program “Comprehensive Research and Education Center for Planning of Drug development and Clinical Evaluation”, Sendai, Miyagi 980-8578, Japan
| | - Hitoshi Iwahashi
- Molecular Cell Biology Laboratory, Graduate School of Pharmaceutical Sciences, Tohoku University, Aoba 6-3, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan, Genetic System Regulation Laboratory, RIKEN, Wako, Saitama 351-0198, Japan, The Graduate School of Science and Engineering, Saitama University, Sakura-ku, Saitama, Saitama 338-8570, Japan, National Institute of Advanced Industrial Science and Technology, Ibaraki, Japan, Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi 981-8555, Japan and Tohoku University 21st Century COE Program “Comprehensive Research and Education Center for Planning of Drug development and Clinical Evaluation”, Sendai, Miyagi 980-8578, Japan
| | - Masahiko Harata
- Molecular Cell Biology Laboratory, Graduate School of Pharmaceutical Sciences, Tohoku University, Aoba 6-3, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan, Genetic System Regulation Laboratory, RIKEN, Wako, Saitama 351-0198, Japan, The Graduate School of Science and Engineering, Saitama University, Sakura-ku, Saitama, Saitama 338-8570, Japan, National Institute of Advanced Industrial Science and Technology, Ibaraki, Japan, Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi 981-8555, Japan and Tohoku University 21st Century COE Program “Comprehensive Research and Education Center for Planning of Drug development and Clinical Evaluation”, Sendai, Miyagi 980-8578, Japan
| | - Kunihiro Ohta
- Molecular Cell Biology Laboratory, Graduate School of Pharmaceutical Sciences, Tohoku University, Aoba 6-3, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan, Genetic System Regulation Laboratory, RIKEN, Wako, Saitama 351-0198, Japan, The Graduate School of Science and Engineering, Saitama University, Sakura-ku, Saitama, Saitama 338-8570, Japan, National Institute of Advanced Industrial Science and Technology, Ibaraki, Japan, Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi 981-8555, Japan and Tohoku University 21st Century COE Program “Comprehensive Research and Education Center for Planning of Drug development and Clinical Evaluation”, Sendai, Miyagi 980-8578, Japan
| | - Takemi Enomoto
- Molecular Cell Biology Laboratory, Graduate School of Pharmaceutical Sciences, Tohoku University, Aoba 6-3, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan, Genetic System Regulation Laboratory, RIKEN, Wako, Saitama 351-0198, Japan, The Graduate School of Science and Engineering, Saitama University, Sakura-ku, Saitama, Saitama 338-8570, Japan, National Institute of Advanced Industrial Science and Technology, Ibaraki, Japan, Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi 981-8555, Japan and Tohoku University 21st Century COE Program “Comprehensive Research and Education Center for Planning of Drug development and Clinical Evaluation”, Sendai, Miyagi 980-8578, Japan
| | - Masayuki Seki
- Molecular Cell Biology Laboratory, Graduate School of Pharmaceutical Sciences, Tohoku University, Aoba 6-3, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan, Genetic System Regulation Laboratory, RIKEN, Wako, Saitama 351-0198, Japan, The Graduate School of Science and Engineering, Saitama University, Sakura-ku, Saitama, Saitama 338-8570, Japan, National Institute of Advanced Industrial Science and Technology, Ibaraki, Japan, Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi 981-8555, Japan and Tohoku University 21st Century COE Program “Comprehensive Research and Education Center for Planning of Drug development and Clinical Evaluation”, Sendai, Miyagi 980-8578, Japan
- *To whom correspondence should be addressed. +81-22-795-6875+81-22-795-6873
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26
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Steinboeck F, Krupanska L, Bogusch A, Kaufmann A, Heidenreich E. Novel Regulatory Properties of Saccharomyces cerevisiae Arp4. ACTA ACUST UNITED AC 2006; 139:741-51. [PMID: 16672275 DOI: 10.1093/jb/mvj080] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
ARP4, an essential gene of Saccharomyces cerevisiae, codes for a nuclear actin-related protein. Arp4 is a subunit of several chromatin-modifying complexes and is known to be involved in the transcriptional regulation in yeast. We used a mutant strain with a single amino acid substitution (G161D) in the conserved actin fold domain to investigate the influence of Arp4 on stress and nitrogen catabolite repression genes. The deficiency of functional Arp4 caused a highly increased sensitivity towards nitrogen starvation and to the macrolide antibiotic rapamycin. We show the changes of mRNA levels of selected genes under these conditions. The upregulation of stress genes as a consequence of treatment with rapamycin was largely Msn2p/Msn4p-dependent. The sensitivity towards rapamycin indicates a participation of Arp4 in the regulation of the TOR pathway. Consistently, arp4G161D cells exhibited an affected cell cycle. Long-term cultivation, which leads to a G1 arrest in wild-type cells, provoked arrest in G2/M (more than 60%) in the mutant strain. The same effect was observed upon treatment with rapamycin, indicating an unexpected relationship of Arp4 to TOR-mediated cell cycle arrest.
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Affiliation(s)
- Ferdinand Steinboeck
- Institute of Cancer Research, Department of Medicine I, Medical University of Vienna, A-1090 Vienna, Austria.
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27
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Ohfuchi E, Kato M, Sasaki M, Sugimoto K, Oma Y, Harata M. Vertebrate Arp6, a novel nuclear actin-related protein, interacts with heterochromatin protein 1. Eur J Cell Biol 2006; 85:411-21. [PMID: 16487625 DOI: 10.1016/j.ejcb.2005.12.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2005] [Revised: 12/04/2005] [Accepted: 12/09/2005] [Indexed: 11/16/2022] Open
Abstract
Actin-related proteins (Arps) were recently shown to contribute to the organization and regulation of chromatin structures. The nuclear functions of Arps have been investigated principally in budding yeast in which six of the ten Arp subfamilies are localized in the nucleus. In vertebrates, only two isoforms of Arp4 have so far been identified as showing localization to the nucleus. Here we show the predominant nuclear localization of another Arp subfamily, Arp6, in vertebrate cells. Vertebrate Arp6 directly interacted with heterochromatin protein 1 (HP1) orthologs and the two proteins colocalized in pericentric heterochromatin. Yeast Arp6 is involved in telomere silencing, while Drosophila Arp6 is localized in the pericentric heterochromatin. Our data strongly suggest that Arp6 has an evolutionarily conserved role in heterochromatin formation and also provide new insights into the molecular organization of heterochromatin.
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Affiliation(s)
- Eri Ohfuchi
- Laboratory of Molecular Biology, Department of Molecular and Cell Biology, Division of Life Science, Graduate School of Agricultural Science, Tohoku University, Tsutsumidori-Amamiyamachi 1-1, Aoba-ku, Sendai 981-8555, Japan
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28
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Meagher RB, Deal RB, Kandasamy MK, McKinney EC. Nuclear actin-related proteins as epigenetic regulators of development. PLANT PHYSIOLOGY 2005; 139:1576-85. [PMID: 16339804 PMCID: PMC1310543 DOI: 10.1104/pp.105.072447] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Affiliation(s)
- Richard B Meagher
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA.
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29
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Muller J, Oma Y, Vallar L, Friederich E, Poch O, Winsor B. Sequence and comparative genomic analysis of actin-related proteins. Mol Biol Cell 2005; 16:5736-48. [PMID: 16195354 PMCID: PMC1289417 DOI: 10.1091/mbc.e05-06-0508] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Actin-related proteins (ARPs) are key players in cytoskeleton activities and nuclear functions. Two complexes, ARP2/3 and ARP1/11, also known as dynactin, are implicated in actin dynamics and in microtubule-based trafficking, respectively. ARP4 to ARP9 are components of many chromatin-modulating complexes. Conventional actins and ARPs codefine a large family of homologous proteins, the actin superfamily, with a tertiary structure known as the actin fold. Because ARPs and actin share high sequence conservation, clear family definition requires distinct features to easily and systematically identify each subfamily. In this study we performed an in depth sequence and comparative genomic analysis of ARP subfamilies. A high-quality multiple alignment of approximately 700 complete protein sequences homologous to actin, including 148 ARP sequences, allowed us to extend the ARP classification to new organisms. Sequence alignments revealed conserved residues, motifs, and inserted sequence signatures to define each ARP subfamily. These discriminative characteristics allowed us to develop ARPAnno (http://bips.u-strasbg.fr/ARPAnno), a new web server dedicated to the annotation of ARP sequences. Analyses of sequence conservation among actins and ARPs highlight part of the actin fold and suggest interactions between ARPs and actin-binding proteins. Finally, analysis of ARP distribution across eukaryotic phyla emphasizes the central importance of nuclear ARPs, particularly the multifunctional ARP4.
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Affiliation(s)
- Jean Muller
- Laboratoire de Biologie et Génomique Structurales, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, BP 163, 67404 Illkirch Cedex, France.
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30
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de Lanerolle P, Johnson T, Hofmann WA. Actin and myosin I in the nucleus: what next? Nat Struct Mol Biol 2005; 12:742-6. [PMID: 16142228 DOI: 10.1038/nsmb983] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2005] [Accepted: 08/04/2005] [Indexed: 11/09/2022]
Abstract
Several recent publications have demonstrated the importance of nuclear actin and nuclear myosin I in transcription. Here we review these publications and their implications. In addition, we discuss some important issues that should be addressed to gain a more comprehensive understanding of how these traditionally 'cytoplasmic' proteins are involved in transcription. We propose highly speculative models and mechanisms solely to stimulate thought and experimentation in this area.
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Affiliation(s)
- Primal de Lanerolle
- the Department of Physiology and Biophysics, University of Illinois at Chicago, Chicago, Illinois 60612, USA.
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31
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Minoda A, Saitoh S, Takahashi K, Toda T. BAF53/Arp4 homolog Alp5 in fission yeast is required for histone H4 acetylation, kinetochore-spindle attachment, and gene silencing at centromere. Mol Biol Cell 2005; 16:316-27. [PMID: 15483052 PMCID: PMC539175 DOI: 10.1091/mbc.e04-06-0519] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2004] [Revised: 09/29/2004] [Accepted: 10/04/2004] [Indexed: 11/11/2022] Open
Abstract
Nuclear actin-related proteins play vital roles in transcriptional regulation; however, their biological roles remain elusive. Here, we characterize Alp5, fission yeast homolog of Arp4/BAF53. The temperature-sensitive mutant alp5-1134 contains a single amino acid substitution in the conserved C-terminal domain (S402N) and displays mitotic phenotypes, including chromosome condensation and missegregation. Alp5 forms a complex with Mst1-HAT (histone acetyltransferase). Consistently, inhibition of histone deacetylases (HDACs), by either addition of a specific inhibitor or a mutation in HDAC-encoding clr6+ gene, rescues alp5-1134. Immunoblotting with specific antibodies against acetylated histones shows that Alp5 is required for histone H4 acetylation at lysines 5, 8, and 12, but not histone H3 lysines 9 or 14, and furthermore Clr6 plays an opposing role. Mitotic arrest is ascribable to activation of the Mad2/Bub1 spindle checkpoint, in which both proteins localize to the mitotic kinetochores in alp5-1134. Intriguingly, alp5-1134 displays transcriptional desilencing at the core centromere without altering the overall chromatin structure, which also is suppressed by a simultaneous mutation in clr6+. This result shows that Alp5 is essential for histone H4 acetylation, and its crucial role lies in the establishment of bipolar attachment of the kinetochore to the spindle and transcriptional silencing at the centromere.
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Affiliation(s)
- Aki Minoda
- Laboratory of Cell Regulation, Cancer Research UK, London Research Institute, Lincoln's Inn Fields Laboratories, London WC2A 3PX, United Kingdom
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32
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Ueno M, Murase T, Kibe T, Ohashi N, Tomita K, Murakami Y, Uritani M, Ushimaru T, Harata M. Fission yeast Arp6 is required for telomere silencing, but functions independently of Swi6. Nucleic Acids Res 2004; 32:736-41. [PMID: 14757838 PMCID: PMC373355 DOI: 10.1093/nar/gkh234] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The actin-related proteins (Arps), which are subdivided into at least eight subfamilies, are conserved from yeast to humans. A member of the Arp6 subfamily in Drosophila, Arp4/Arp6, co-localizes with heterochromatin protein 1 (HP1) in pericentric heterochromatin. Fission yeast Schizosaccharomyces pombe possesses both an HP1 homolog and an Arp6 homolog. However, the function of S.pombe Arp6 has not been characterized yet. We found that deletion of arp6(+) impaired telomere silencing, but did not affect centromere silencing. Chromatin immunoprecipitation assays revealed that Arp6 bound to the telomere region. However, unlike Drosophila Arp4/Arp6, S.pombe Arp6 was distributed throughout nuclei. The binding of Arp6 to telomere DNA was not affected by deletion of swi6(+). Moreover, the binding of Swi6 to telomere ends was not affected by deletion of arp6(+). These results suggest that Arp6 and Swi6 function independently at telomere ends. We propose that the Arp6-mediated repression mechanism works side by side with Swi6-based telomere silencing in S.pombe.
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Affiliation(s)
- Masaru Ueno
- Department of Chemistry, Shizuoka University, 836 Oya, Shizuoka 422-8529, Japan.
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33
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Görzer I, Schüller C, Heidenreich E, Krupanska L, Kuchler K, Wintersberger U. The nuclear actin-related protein Act3p/Arp4p of Saccharomyces cerevisiae is involved in transcription regulation of stress genes. Mol Microbiol 2003; 50:1155-71. [PMID: 14622406 DOI: 10.1046/j.1365-2958.2003.03759.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
A mutational analysis of the essential nuclear actin-related protein of Saccharomyces cerevisiae, Act3p/Arp4p, was performed. The five residues chosen for substitution were amino acids conserved between actin and Act3p/Arp4p, the tertiary structure of which most probably resembles that of actin. Two thermosensitive (ts) mutants, a single and a double point mutant, and one lethal double point mutant were obtained. Both ts mutants were formamide-sensitive which supports a structural relatedness of Act3p/Arp4p to actin; they were also hypersensitive against hydroxyurea and ultraviolet irradiation pointing to a possible role of Act3p/Arp4p in DNA replication and repair. Their 'suppressor of Ty' (SPT) phenotype, observed with another ts mutant of Act3p/Arp4p before, suggested involvement of Act3p/Arp4p in transcription regulation. Accordingly, genome-wide expression profiling revealed misregulated transcription in a ts mutant of a number of genes, among which increased expression of various stress-responsive genes (many of them requiring Msn2p/Msn4p for induction) was the most salient result. This provides an explanation for the mutant's enhanced resistance to severe thermal and oxidative stress. Thus, Act3p/Arp4p takes an important part in the repression of stress-induced genes under non-stress conditions.
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Affiliation(s)
- Irene Görzer
- Division of Molecular Genetics, Institute of Cancer Research, University of Vienna, A-1090 Vienna, Austria
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Shen X, Ranallo R, Choi E, Wu C. Involvement of actin-related proteins in ATP-dependent chromatin remodeling. Mol Cell 2003; 12:147-55. [PMID: 12887900 DOI: 10.1016/s1097-2765(03)00264-8] [Citation(s) in RCA: 269] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Actin-related proteins (Arps) and conventional actin are enigmatic components of many chromatin-remodeling enzyme complexes. The yeast INO80 ATP-dependent chromatin-remodeling complex contains stoichiometric amounts of Arp4, Arp5, Arp8, and actin. Here we have revealed functions of Arp5 and Arp8 by analysis of mutants. arp5 Delta and arp8 Delta mutants display an ino80 Delta phenotype. Purification of INO80 complexes from arp5 Delta and arp8 Delta cells shows that protein complexes remain intact but are compromised for INO80 ATPase activity, DNA binding, and nucleosome mobilization. The INO80 (arp8 Delta) complex is strikingly deficient, not only for the Arp8 subunit, but also for Arp4 and actin, suggesting an ordered assembly of Arps. Binding of Arp8 to the INO80 complex requires an N-terminal region of Ino80 adjacent to the conserved ATPase domain. GST-Arp8 binds preferentially to histones H3 and H4 in vitro, suggesting a histone chaperone function. These findings show direct involvement of Arps in the chromatin-remodeling process.
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Affiliation(s)
- Xuetong Shen
- Laboratory of Molecular Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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Kuroda Y, Oma Y, Nishimori K, Ohta T, Harata M. Brain-specific expression of the nuclear actin-related protein ArpNalpha and its involvement in mammalian SWI/SNF chromatin remodeling complex. Biochem Biophys Res Commun 2002; 299:328-34. [PMID: 12437990 DOI: 10.1016/s0006-291x(02)02637-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Actin-related proteins share significant homology with conventional actins and are classified into subfamilies based on the similarity of their sequences and functions. The Arp4 subfamily of Arps is localized in the nucleus, and a mammalian isoform, ArpNbeta (also known as BAF53), is a component of the chromatin remodeling and histone acetyltransferase complexes. Another isoform identified in humans, ArpNalpha has scarcely been characterized yet. We identified mouse ArpNalpha, and showed that ArpNalpha is more similar between humans and mice than ArpNbeta. No difference was observed between ArpNalpha and beta in subcellular localization and interaction with BRM, which is an ATPase subunit of mammalian SWI/SNF chromatin remodeling complex. However, ArpNalpha was expressed exclusively in the brain and its expression was induced during neural differentiation of P19 mouse embryonic carcinoma cells. ArpNalpha is the first brain-specific component of a chromatin remodeling complex to be identified, suggesting that ArpNalpha has conserved and important roles in the differentiation of neural cells through regulation of chromatin structure.
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Affiliation(s)
- Yukiko Kuroda
- Laboratory of Molecular Biology, Department of Molecular and Cell Biology, Division of Life Science, Graduate School of Agricultural Science, Tohoku University, Tsutsumidori-Amamiyamachi 1-1, Aoba-ku, 981-8555, Sendai, Japan
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Abstract
Actin is an abundant protein in most nonmuscle cells. It has often been observed in isolated nuclei, yet cytoplasmic contamination was of course initially regarded as the most plausible origin. Numerous studies on nuclear actin appeared in the 1970s and 1980s, but the picture remained rather muddy. The viewpoint at that time was that actin-shown to move freely between cytoplasm and nucleus-was a mere "thermodynamic wanderer," transiently occupying the nucleus. More recently, evidence has been mounting that actin's presence in the nucleus is not simply governed by the laws of diffusion. The same holds true for the finding of various actin-related proteins in the nucleus, and the case for nuclear myosin, specifically myosin I, is now quite convincing. Moreover, the first intimations of functional roles of nuclear actin are now emerging. Here we examine the overall subject from cell biological and chemical perspectives. The major issue is no longer the presence of actin in the nucleus but rather its supramolecular organization, intranuclear locations, and, of course, functions. These issues interface with recent findings that reveal a surprisingly diverse repertoire of actin conformations and oligomer and polymer forms beyond monomeric G-actin and polymeric F-actin. We present ideas for advancing the nuclear actin field and call for a renewed attack on this major problem in cell biology.
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Affiliation(s)
- Thoru Pederson
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 377 Plantation Street, Worcester, MA 01605-2300, USA.
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Current awareness on yeast. Yeast 2002; 19:995-1002. [PMID: 12125056 DOI: 10.1002/yea.827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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