The actin-related protein Act3p of Saccharomyces cerevisiae is located in the nucleus

Actin, actin-binding proteins, and actin-related proteins in the nucleus

Extensive research in the past decade has significantly broadened our view about the role actin plays in the life of the cell and added novel aspects to actin research. One of these new aspects is the discovery of the existence of nuclear actin which became evident only recently. Nuclear activities including transcriptional activation in the case of all three RNA polymerases, editing and nuclear export of mRNAs, and chromatin remodeling all depend on actin. It also became clear that there is a fine-tuned equilibrium between cytoplasmic and nuclear actin pools and that this balance is ensured by an export-import system dedicated to actin. After over half a century of research on conventional actin and its organizing partners in the cytoplasm, it was also an unexpected finding that the nucleus contains more than 30 actin-binding proteins and new classes of actin-related proteins which are not able to form filaments but had evolved nuclear-specific functions. The actin-binding and actin-related proteins in the nucleus have been linked to RNA transcription and processing, nuclear transport, and chromatin remodeling. In this paper, we attempt to provide an overview of the wide range of information that is now available about actin, actin-binding, and actin-related proteins in the nucleus.

Selection and Validation of Reference Genes for Quantitative Real-time PCR in Gentiana macrophylla

Real time quantitative PCR (RT-qPCR or qPCR) has been extensively applied for analyzing gene expression because of its accuracy, sensitivity, and high throughput. However, the unsuitable choice of reference gene(s) can lead to a misinterpretation of results. We evaluated the stability of 10 candidates - five traditional housekeeping genes (UBC21, GAPC2, EF-1α4, UBQ10, and UBC10) and five novel genes (SAND1, FBOX, PTB1, ARP, and Expressed1) - using the transcriptome data of Gentiana macrophylla. Common statistical algorithms ΔC t, GeNorm, NormFinder, and BestKeeper were run with samples collected from plants under various experimental conditions. For normalizing expression levels from tissues at different developmental stages, GAPC2 and UBC21 had the highest rankings. Both SAND1 and GAPC2 proved to be the optimal reference genes for roots from plants exposed to abiotic stresses while EF-1α4 and SAND1 were optimal when examining expression data from the leaves of stressed plants. Based on a comprehensive ranking of stability under different experimental conditions, we recommend that SAND1 and EF-1α4 are the most suitable overall. In this study, to find a suitable reference gene and its real-time PCR assay for G. macrophylla DNA content quantification, we evaluated three target genes including WRKY30, G10H, and SLS, through qualitative and absolute quantitative PCR with leaves under elicitors stressed experimental conditions. Arbitrary use of reference genes without previous evaluation can lead to a misinterpretation of the data. Our results will benefit future research on the expression of genes related to secoiridoid biosynthesis in this species under different experimental conditions.

Actin-related proteins localized in the nucleus: from discovery to novel roles in nuclear organization

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.

Actin-related protein Arp6 influences H2A.Z-dependent and -independent gene expression and links ribosomal protein genes to nuclear pores

Actin-related proteins are ubiquitous components of chromatin remodelers and are conserved from yeast to man. We have examined the role of the budding yeast actin-related protein Arp6 in gene expression, both as a component of the SWR1 complex (SWR-C) and in its absence. We mapped Arp6 binding sites along four yeast chromosomes using chromatin immunoprecipitation from wild-type and swr1 deleted (swr1Delta) cells. We find that a majority of Arp6 binding sites coincide with binding sites of Swr1, the catalytic subunit of SWR-C, and with the histone H2A variant Htz1 (H2A.Z) deposited by SWR-C. However, Arp6 binding detected at centromeres, the promoters of ribosomal protein (RP) genes, and some telomeres is independent of Swr1 and Htz1 deposition. Given that RP genes and telomeres both show association with the nuclear periphery, we monitored the ability of Arp6 to mediate the localization of chromatin to nuclear pores. Arp6 binding is sufficient to shift a randomly positioned locus to nuclear periphery, even in a swr1Delta strain. Arp6 is also necessary for the pore association of its targeted RP promoters possibly through cell cycle-dependent factors. Loss of Arp6, but not Htz1, leads to an up-regulation of these RP genes. In contrast, the pore-association of GAL1 correlates with Htz1 deposition, and loss of Arp6 reduces both GAL1 activation and peripheral localization. We conclude that Arp6 functions both together with the nucleosome remodeler Swr1 and also without it, to mediate Htz1-dependent and Htz1-independent binding of chromatin domains to nuclear pores. This association is shown to have modulating effects on gene expression.

Cooperation between the INO80 complex and histone chaperones determines adaptation of stress gene transcription in the yeast Saccharomyces cerevisiae

In yeast, environmental stresses provoke sudden and dramatic increases in gene expression at stress-inducible loci. Stress gene transcription is accompanied by the transient eviction of histones from the promoter and the transcribed regions of these genes. We found that mutants defective in subunits of the INO80 complex, as well as in several histone chaperone systems, exhibit extended expression windows that can be correlated with a distinct delay in histone redeposition during adaptation. Surprisingly, Ino80 became associated with the ORFs of stress genes in a stress-specific way, suggesting a direct function in the repression during adaptation. This recruitment required elongation by RNA polymerase (Pol) II but none of the histone modifications that are usually associated with active transcription, such as H3 K4/K36 methylation. A mutant lacking the Asf1-associated H3K56 acetyltransferase Rtt109 or Asf1 itself also showed enhanced stress-induced transcript levels. Genetic data, however, suggest that Asf1 and Rtt109 function in parallel with INO80 to restore histone homeostasis, whereas Spt6 seems to have a function that overlaps that of the chromatin remodeler. Thus, chromatin remodeling by INO80 in cooperation with Spt6 determines the shape of the expression profile under acute stress conditions, possibly by an elongation-dependent mechanism.

Chapter 5. Nuclear actin-related proteins in epigenetic control

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.

The nuclear actin-related protein Act3p/Arp4 influences yeast cell shape and bulk chromatin organization

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.

ACTIN-RELATED PROTEIN8 encodes an F-box protein localized to the nucleolus in Arabidopsis

Arabidopsis encodes six nuclear actin-related proteins (ARPs), among them ARP8 is unique in having an F-box domain and an actin homology domain. Analysis of the ARP8 promoter-beta-glucuronidase (GUS) fusion suggests that ARP8 is ubiquitously expressed in all organs and cell types. Immunocytochemical analysis with ARP8-specific monoclonal antibodies revealed that ARP8 protein is localized to the nucleolus in interphase cells and dispersed in the cytoplasm in mitotic cells. The cell cycle-dependent subcellular patterns of distribution of ARP8 are conserved in other members of Brassicaceae. Our findings provide the first insight into the possible contributions of plant ARP8 to nucleolar functions.

The actin-related protein hArp8 accumulates on the mitotic chromosomes and functions in chromosome alignment

The actin family consists of conventional actin and various actin-related proteins (Arps). Some of these Arps are localized in the nucleus, and a fraction of each of these nuclear Arps is functionally involved in chromatin remodeling and histone acetyltransferase complexes. On the other hand, in mitotic cells, the localization and function of the nuclear Arps are largely unknown. Human Arp8 (hArp8), an ortholog of yeast nuclear Arp8, was recently found to be associated with the hINO80-chromatin remodeling complex along with hArp5. Here we report that hArp8, but not hArp5, accumulates on mitotic chromosomes. This is the first example where a member of the actin family is found to be associated with mitotic chromosomes. Expression of truncated hArp8 proteins and depletion of endogenous hArp8 by RNA interference caused misalignment of mitotic chromosomes, suggesting that chromosome-associated hArp8 has a role in chromosome behavior. In contrast, depletion of hIno80 and hArp5 did not cause misalignment of chromosomes, suggesting that the role of hArp8 at mitotic chromosomes is independent of the activity of hINO80 complexes. These findings provide the first insight into a novel function of actin family members in mitosis.

Nuclear actin and actin-related proteins in chromatin dynamics

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.

Actin-related protein Arp4 functions in kinetochore assembly

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.

The nuclear actin-related protein of Saccharomyces cerevisiae, Arp4, directly interacts with the histone acetyltransferase Esa1p

Ten actin-related proteins are known in Saccharomyces cerevisiae, classified into Arps1-10 according to their relatedness to actin. Arp4, a nuclear protein, essential for viability of S. cerevisiae, is a component of at least three chromatin-modifying complexes, one of which is the histone acetyltransferase (HAT) complex NuA4. Since recent data point to a role for Arp4 in the recruitment to specific sites of interaction, we tested if Arp4 directly interacts with the HAT Esa1p that is the catalytic subunit of NuA4. We observed that Arp4 directly binds to Esa1p, whereas Act1p, which is also a component of the NuA4 complex, does not interact with Esa1p. The interaction of Arp4 and Esa1p was not abolished by a deletion of one or both of the specific insertions present in the ARP4 gene. We propose that the interaction of Arp4 with Esa1p is crucial for proper functioning and targeting of the NuA4 complex.

Novel Regulatory Properties of Saccharomyces cerevisiae Arp4

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.

Vertebrate Arp6, a novel nuclear actin-related protein, interacts with heterochromatin protein 1

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.

Sequence and comparative genomic analysis of actin-related proteins

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.

The nuclear actin-related protein Act3p/Arp4p is involved in the dynamics of chromatin-modulating complexes

Chromatin remodelling and histone-modifying complexes govern the modulation of chromatin structure. While components of these complexes are diverse, nuclear actin-related proteins (Arps) have been repeatedly found in these complexes from yeast to mammals. In most cases, Arps are required for functioning of the complexes, but the molecular mechanisms of nuclear Arps have as yet been largely unknown. The Arps and actin, sharing a common ancestor, are supposed to be highly similar in the three-dimensional structure of their core regions, including the ATP-binding pocket. The Arp Act3p/Arp4p of Saccharomyces cerevisiae exists within the nucleus, partly as a component of several high molecular mass complexes, including the NuA4 histone acetyltransferase (HAT) complex, and partly as uncomplexed molecules. We observed that mutations in the putative ATP-binding pocket of Act3p/Arp4p increased its concentration in the high molecular mass complexes and, conversely, that an excess of ATP or ATPgammaS led to the release of wild-type Act3p/Arp4p from the complexes. These results suggest a requirement of ATP binding by Act3p/Arp4p for its dissociation from the complexes. In accordance, a mutation in the putative ATP binding site of Act3p/Arp4p inhibited the conversion of the NuA4 complex into the smaller piccoloNuA4, which does not contain Act3p/Arp4p and exhibits HAT activity distinct from that of NuA4. Although the in vitro binding activity of ATP by recombinant Act3p/Arp4p was found to be rather weak, our observations, taken together, suggest that the ATP-binding pocket of Act3p/Arp4p is involved in the function of chromatin modulating complexes by regulating their dynamics.

Plant actin-related proteins

Actin-related proteins (ARPs) constitute a family of divergent and evolutionarily ancient eukaryotic proteins whose primary sequences display homology to conventional actins. Whereas actins play well-characterized cytoskeletal roles, the ARPs are implicated in various cellular functions in both the cytoplasm and in the nucleus. Cytoplasmic ARPs, for example, are known to participate in the assembly of branched actin filaments and dynein-mediated movement of vesicles in many eukaryotes. Nuclear ARPs, by contrast, are enigmatic components of various chromatin-modifying complexes involved in transcriptional regulation. Here, we review homologs to several known classes of ARPs and two distinct ARP classes in plants, and summarize recent work elucidating the biological functions of ARPs in eukaryotes.

Fission yeast Arp6 is required for telomere silencing, but functions independently of Swi6

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.

The nuclear actin-related protein Act3p/Arp4p of Saccharomyces cerevisiae is involved in transcription regulation of stress genes

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.

Series of vectors to evaluate the position and the order of two different affinity tags for purification of protein complexes

A series of protein expression vectors with dual-affinity tags has been developed. With these constructed vectors, FLAG and hexahistidine tags were fused to a given protein at either the N- or the C-terminal ends or both, for a total of six combinations. Three auxotrophy markers were introduced into each construct, thus yielding 18 different vectors. These vectors allow evaluation of different positions and orders of two different tags. To confirm the efficacy of these vectors, we purified a histone acetyltransferase (Esa1p)-containing complex. First, an appropriate position of the tags was selected through small-scale purification. Next, large-scale purification was done for the selected construct, yielding an Esa1p-containing complex that was comparable to an Esa1p-containing complex (NuA4) obtained by a conventional activity-based purification. These vectors provide a convenient way to select the best position of tags for efficient purification of protein complexes also applicable in proteomics studies.

Cell cycle-dependent association of Arabidopsis actin-related proteins AtARP4 and AtARP7 with the nucleus

Arabidopsis encodes at least eight actin-related proteins (ARPs) most of which have orthologs in other distant organisms. To gain insight into the role of ARPs in plants, we have examined the spatial expression and subcellular distribution of two highly divergent Arabidopsis ARPs, AtARP4 and AtARP7. AtARP4 is a homolog of human BAF53 and yeast Arp4, and AtARP7 is a novel, ancient and plant-specific actin-related protein that is not distinctly related to any known ARPs from other kingdoms. Analysis of both these proteins with AtARP4- and AtARP7-specific antibodies revealed that they were most abundant in young meristematic and floral tissues, but were expressed constitutively in all organs and cell types irrespective of their developmental stage. Immunofluorescence studies showed that both AtARP4 and AtARP7 were localized predominantly to the nucleus during interphase. In mitotic cells lacking a nuclear envelope (e.g. metaphase, anaphase, and early telophase stages), these ARPs were excluded from the condensed chromosomes and dispersed throughout the cytoplasm. In contrast, a putative Arabidopsis histone H2B protein remained associated with the interphase nuclei as well as chromosomes throughout the cell cycle. Based on our results and data on the yeast ortholog of AtARP4, these two nuclear plant ARPs may be involved in the modulation of chromatin structure and transcriptional regulation mainly in interphase cells.

The brain-specific actin-related protein ArpN alpha interacts with the transcriptional co-repressor CtBP

Actin-related protein (Arp) is found in many chromatin remodeling and histone acetyltransferase complexes. We previously identified ArpN alpha as an isoform of ArpN beta/BAF53, which is included in mammalian SWI/SNF chromatin remodeling complex, and showed that ArpN alpha is a potential component of the complex. Although it has a structure highly similar to ArpN beta/BAF53, ArpN alpha is expressed exclusively in brain and in neural differentiated embryonal carcinoma cells. Since ArpN alpha possesses a region that shows low similarity to ArpN beta/BAF53, we hypothesized that proteins interacting with this region contribute to the ArpN alpha-specific function in brain. Here we showed that ArpN alpha, but not ArpN beta/BAF53, interacts with the transcriptional co-repressor CtBP (C-terminal binding protein). Transactivation by the SWI/SNF complex and glucocorticoid receptor was repressed by the CtBP in the presence of ArpN alpha. These findings suggest that SWI/SNF complex containing ArpN alpha might regulate certain genes involved in brain development and/or its function differently from SWI/SNF complex containing ArpN beta/BAF53.

Brain-specific expression of the nuclear actin-related protein ArpNalpha and its involvement in mammalian SWI/SNF chromatin remodeling complex

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.

Nuclear actin and actin-related proteins in chromatin remodeling

The existence and function of actin in the nucleus has been hotly debated for forty years. Recently, beta-actin was found to be a component of mammalian SWI/SNF-like BAF chromatin remodeling complexes and still more recently other SWI/SNF-related chromatin remodeling complexes in yeast, flies, and man. Although the function of actin in these chromatin remodeling complexes is only starting to be explored, the fact that actin is one of the most regulated proteins in the cell suggests that control of nuclear actin may be a critical regulatory point in the control of chromatin remodeling. Actin rapidly shuttles between the nucleus and the cytoplasm offering additional sites and modes of regulation. In addition, actin-related proteins (Arps) are also components of these chromatin remodeling complexes and have been implicated in transcriptional control in yeast. The observation that the BAF chromatin remodeling complex in which actin was originally identified, is also a human tumor suppressor complex necessary for the actions of the retinoblastoma protein indicates that the study of nuclear actin is likely to contribute to understanding cell growth control.

Remodeling of organelle-bound actin is required for yeast vacuole fusion

Actin participates in several intracellular trafficking pathways. We now find that actin, bound to the surface of purified yeast vacuoles in the absence of cytosol or cytoskeleton, regulates the last compartment mixing stage of homotypic vacuole fusion. The Cdc42p GTPase is known to be required for vacuole fusion. We now show that proteins of the Cdc42p-regulated actin remodeling cascade (Cdc42p --> Cla4p --> Las17p/Vrp1p --> Arp2/3 complex --> actin) are enriched on isolated vacuoles. Vacuole fusion is dramatically altered by perturbation of the vacuole-bound actin, either by mutation of the ACT1 gene, addition of specific actin ligands such as latrunculin B or jasplakinolide, antibody to the actin regulatory proteins Las17p (yeast Wiskott-Aldrich syndrome protein) or Arp2/3, or deletion of actin regulatory genes. On docked vacuoles, actin is enriched at the "vertex ring" membrane microdomain where fusion occurs and is required for the terminal steps leading to membrane fusion. This role for actin may extend to other trafficking systems.

Correlation between chromatin association and transcriptional regulation for the Act3p/Arp4 nuclear actin-related protein of Saccharomyces cerevisiae

Actin-related proteins (Arps), which share a basal structure with actin but have distinct functions, have been found in a wide variety of organisms. While their functions are not yet clear, some Arps are localized in the nucleus and are suggested to contribute to the regulation of transcription. An essential gene of Saccharomyces cerevisiae, Act3p/Arp4, encodes the first identified nuclear Arp, which has been shown to bind to core histones in vitro. Here we have analyzed the in vivo function of Act3p/Arp4 on the his4-912delta promoter. Chromatin immunoprecipitation assays show that Act3p/Arp4 is bound to the entire his4-912delta promoter region. Conditional act3/arp4 mutations affect transcription from the his4-912delta promoter, where decreased Act3p/Arp4 binding and a change in nuclease sensitivity of chromatin were observed, showing the involvement of Act3p/Arp4 in the regulation of gene expression through the organization of chromatin structure. Taken together with the presence of Act3p/Arp4 in chromatin remodeling and histone acetyltransferase complexes, it is suggested that Act3p/Arp4 functions in transcriptional regulation to recruit chromatin remodeling and histone acetyltransferase complexes onto chromatin.

Identification of two cDNAs for human actin-related proteins (Arps) that have remarkable similarity to conventional actin

We identified two cDNAs coding for the novel human actin-related proteins (Arps) hArpM1 and hArpM2. Both of them show remarkable similarity to conventional actin, and the ATP-binding motif and nuclear-export signals of actin are highly conserved. Their mRNAs are expressed in all tested human tissues, but in smaller amounts than that of actin. These features suggest that hArpM1 and M2 are involved in cytoskeletal organization like other cytoplasmic Arp subfamilies.

Generation of the dominant-negative mutant of hArpNbeta: a component of human SWI/SNF chromatin remodeling complex

hArpNbeta, an actin-related protein located within the nucleus, is a subunit of the human SWI/SNF chromatin remodeling complex. hArpNbeta has been proposed to regulate the assembly and activity of the hSWI/SNF complex. Sequence comparisons of the potential ArpN homologs with beta-actin showed that the ArpNs have the divergent subdomains Ib and IIb in addition to the unique N-terminal short insert, MS(G/A)-(V/L)YGG. Since the proposed function of hArpNbeta requires more than two distinct but concurrently operating surfaces, we examined whether the disruption of one operating surface of hArpNbeta results in dominant-negative phenotype. When overexpressed in HeLa or 293T cells, the subdomain Ib or IIb hybrids, in which the subdomain Ib or IIb of hArpNbeta was replaced with that of beta-actin, respectively, showed no effect on cell survival. On the other hand, the overexpression of the N-terminal deletion mutant of hArpNbeta resulted in cell death probably through apoptotic process. These results indicate that the proper function of hArpNbeta is essential for cell survival in human cells. Furthermore, they suggests the possibility that the N-terminal short sequence is indispensable for the chromatin remodeling activity or the assembly of the hSWI/SNF complex after the binding of hArpNbeta with functionally essential partner proteins.

Novel actin-related proteins in vertebrates: similarities of structure and expression pattern to Arp6 localized on Drosophila heterochromatin

Actin-related proteins (Arps), which share a basal structure with actin isoforms but possess different functions, have been identified in a wide variety of organisms. The Arps are classified into subfamilies based on the relatedness of their sequences and functions. Recently, several Arp subfamilies have been shown to be localized in the nucleus and included in protein complexes involved in the organization of chromatin structure, for example, in chromatin remodeling and histone acetyltransferase complexes. A member of the Arp6 subfamily in Drosophila, dArp6, is localized on centric heterochromatin together with heterochromatin protein 1 (HP1). We have identified the first examples of the Arp6 subfamily in vertebrates, novel human and chicken Arps, hArp6 and gArp6, respectively. They are closely related to each other (98% similar) and show apparent similarity to dArp6 (70%). In addition, the hArp6 gene possesses evolutionarily conserved exon/intron structures compared with genes for members of the Arp6 subfamily in invertebrates. Like Drosophila dArp6, gArp6 is expressed abundantly in the early developmental stages, when heterochromatin condensation and nuclear maturation occur. The finding of a conserved Arp6 subfamily in vertebrates will contribute to the understanding of molecular mechanisms of heterochromatin organization.

Functional analysis of six genes from chromosomes XIV and XV of Saccharomyces cerevisiae reveals YOR145c as an essential gene and YNL059c/ARP5 as a strain-dependent essential gene encoding nuclear proteins

We report here basic functional analysis of strains deleted for six open reading frames (ORFs), YNL059c and YNL148c from chromosome XIV and YOR145c, YOR152c, YOR161c and YOR162c from chromosome XV of Saccharomyces cerevisiae. ORFs were replaced with the KanMX4 resistance marker using a long flanking homology PCR strategy in FY1679 and W303 diploid strains. Replacement cassettes were constructed in plasmid pUG7 and the cognate wild-type genes were recovered by gap repair. Sporulation and tetrad analysis revealed that deletion of YNL059c/ARP5 was lethal for vegetative growth in strain W303 and caused severe growth defects in strain FY1679 while YOR145c was essential for growth in both strains. Fusion of the green fluorescent protein (GFP) gene to the 3' ends of the YNL059c/ARP5 and YOR145c coding sequences created functional chimeric genes at the respective chromosomal loci. Both Arp5-GFP and Yor145-GFP localized to the nucleus, Yor145-GFP concentrating in the nucleolus. The vectors containing the deletion cassettes and the cognate wild-type genes, the oligonucleotides, and the deletant strains are available from the EUROFAN resource centre EUROSCARF (Frankfurt).

Actin-related proteins (Arps): conformational switches for chromatin-remodeling machines?

The actin superfamily of ATPases includes cytoskeletal actins, the stress 70 proteins (e.g. hsc70), sugar kinases, glycerol kinase, and several prokaryotic cell cycle proteins. Although these proteins share limited sequence identity, they all appear to maintain a similar tertiary structure, the "actin fold", which may serve to couple ATP hydrolysis to protein conformational changes. Recently, an actin-related protein (Arp) subfamily has been identified based on sequence homology to conventional actin. Although some Arps are clearly involved in cytoskeletal functions, both actin and/or Arps have been found as stoichiometric subunits of several nuclear chromatin-remodeling enzymes. Here we present two related models in which actin and/or Arps function as conformational switches that control either the activity or the assembly of chromatin-remodeling machines.

Multiple links between the NuA4 histone acetyltransferase complex and epigenetic control of transcription

NuA4 is an essential histone H4/H2A acetyltransferase complex that interacts with activators and stimulates transcription in vitro. We have identified three novel NuA4 subunits: Act3/Arp4, an actin-related protein implicated in epigenetic control of transcription, Act1, and Epl1, a protein homologous to Drosophila Enhancer of Polycomb. Act3/Arp4 binds nucleosomes in vitro and is required for NuA4 integrity in vivo. Mutations in ACT3 and acetyltransferase-encoding ESA1 cause gene-specific transcription defects. Accordingly, NuA4 is localized in precise loci within the nucleus and does not overlap with the silent chromatin marker Sir3. These data along with the known epigenetic roles of Act3/Arp4 and homologs of Epl1 and Esa1 strongly support an essential role for chromatin structure modification by NuA4 in transcription regulation in vivo.

Further characterization of the actin-related protein Act3p/Arp4 of S. cerevisiae through mutational analysis

In the course of functional analysis of the yeast ARP4 (ACT3) gene, we further characterized the role of its protein product Arp4p in the cell. We report that although it is localized in the nucleus, Arp4p performs its function independently of binding to DNA directly. The roles of the core actin structure (the ATP-binding pocket) and a putative Nuclear Localization Signal (NLS) of Arp4p were tested by targeted mutagenesis. The results suggest that under normal conditions, the ATPase activity and the NLS are dispensable for the essential function of this protein in the cell. Furthermore, the use of reporter genes confirmed that Arp4p could be involved in some general mechanism of transcriptional regulation.

Actin-related proteins

Actin-related proteins (Arps) participate in a diverse array of cellular processes. They modulate assembly of conventional actin, contribute to microtubule-based motility catalyzed by dynein, and serve as integral components of large protein complexes required for gene expression. We highlight here recent work aimed at understanding the roles played by Arps in each of these processes.

The Arabidopsis actin-related protein 2 (AtARP2) promoter directs expression in xylem precursor cells and pollen

To investigate the role of the actin cytoskeleton in plant growth and development, we have cloned and determined the DNA sequence of a gene encoding an actin-related protein (arp) from Arabidopsis thaliana (AtARP2) and studied its expression patterns. A. thaliana appears to have only one AtARP2 gene which contains 14 introns, an unusually large number when compared to 4 or 5 introns in the actin genes isolated so far. The predicted protein shows high homology to and shares typical peptide insertions with arp2 proteins from other organisms. The AtARP2 transcript is present in all plant tissues, at a very low level, and is down-regulated by light. Promoter-GUS expression studies showed that the AtARP2 promoter directs activity predominantly in a very small number of cells immediately adjacent to the xylem in all organs. In addition, strong expression was observed in pollen grains. We discuss the potential role of an arp2/3 complex in plant development.

The nuclear actin-related protein of Saccharomyces cerevisiae, Act3p/Arp4, interacts with core histones

Act3p/Arp4, an essential actin-related protein of Saccharomyces cerevisiae located within the nucleus, is, according to genetic data, involved in transcriptional regulation. In addition to the basal core structure of the actin family members, which is responsible for ATPase activity, Act3p possesses two insertions, insertions I and II, the latter of which is predicted to form a loop-like structure protruding from beyond the surface of the molecule. Because Act3p is a constituent of chromatin but itself does not bind to DNA, we hypothesized that insertion II might be responsible for an Act3p-specific function through its interaction with some other chromatin protein. Far Western blot and two-hybrid analyses revealed the ability of insertion II to bind to each of the core histones, although with somewhat different affinities. Together with our finding of coimmunoprecipitation of Act3p with histone H2A, this suggests the in vivo existence of a protein complex required for correct expression of particular genes. We also show that a conditional act3 mutation affects chromatin structure of an episomal DNA molecule, indicating that the putative Act3p complex may be involved in the establishment, remodeling, or maintenance of chromatin structures.

Identification and characterization of Schizosaccharomyces pombe asp1(+), a gene that interacts with mutations in the Arp2/3 complex and actin

The Arp2/3 complex is an essential component of the actin cytoskeleton in yeast and is required for the movement of actin patches. In an attempt to identify proteins that interact with this complex in the fission yeast Schizosaccharomyces pombe, we sought high-copy suppressors of the S. pombe arp3-c1 mutant, and have identified one, which we have termed asp1(+). The asp1(+) open reading frame (ORF) predicts a highly conserved protein of 921 amino acids with a molecular mass of 106 kD that does not contain motifs of known function. Neither asp1(+) nor its apparent Saccharomyces cerevisiae ortholog, VIP1, are essential genes. However, disruption of asp1(+) leads to altered morphology and growth properties at elevated temperatures and defects in polarized growth. The asp1 disruption strain also is hypersensitive to Ca+ ions and to low pH conditions. Although Asp1p is not stably associated with the Arp2/3 complex nor localized in any discrete structure within the cytoplasm, the asp1 disruption mutant was synthetically lethal with mutations in components of the Arp2/3 complex, arp3-c1 and sop2-1, as well as with a mutation in actin, act1-48. Moreover, the vip1 disruption strain showed a negative genetic interaction with a las17Delta strain. We conclude that Asp1p/Vip1p is important for the function of the cortical actin cytoskeleton.

Conformational difference between nuclear and cytoplasmic actin as detected by a monoclonal antibody

Using a reconstituted complex of profilin and skeletal muscle actin as an antigen, we generated a monoclonal mouse antibody against actin, termed 2G2. As revealed by immunoblots of proteolytic actin fragments and by pepscan analysis, the antibody recognises a nonsequential epitope on actin which is located within three different regions of the sequence, consisting of aa131-139, aa155-169, and aa176-187. In the actin model derived from X-ray diffraction, these sequences lie spatially close together in the region of the nucleotide-binding cleft, but do not form a coherent patch. In immunoblots, 2G2 reacts with all SDS-denatured actin isoforms and with actins of many vertebrates. In contrast, its immunofluorescence reactivity is highly selective and fixation-dependent. In fibroblasts and myogenic cells, fixed and extracted by formaldehyde/detergent, stress fibres or myofibrils, respectively, remained unstained. Likewise, after microinjection into living cells, 2G2 did not bind to such microfilament bundles. Extraction of myosin and tropomyosin did not alter this pattern indicating that the lack in reactivity is probably not due to epitope-masking by actin-binding proteins. More likely, the reason for the lack of reactivity with filamentous actin is that its epitope is not accessible in F-actin. However, the antibody revealed a distinct pattern of nuclear dots in differentiated myogenic cells but not in myoblasts, and of fibrillar structures in nuclei of Xenopus oocytes. In contrast, after methanol treatment, a 2G2-specific staining of stress fibres and myofibrils was observed, but no nuclear dot staining. We conclude that 2G2, in addition to binding to SDS- and methanol-denatured actin, recognises a specific conformation of native actin which is present in the nucleus and specified by compaction of the antibody-reactive region into a coherent patch. This conformation is apparently present in differentiated myogenic cells and oocytes, but not in cytoplasmic actin filament bundles.

Subunits of the yeast SWI/SNF complex are members of the actin-related protein (ARP) family

The yeast SWI/SNF chromatin remodeling complex is comprised of 11 tightly associated polypeptides (SWI1, SWI2, SWI3, SNF5, SNF6, SNF11, SWP82, SWP73, SWP59, SWP61, and SWP29). We have used matrix-assisted laser desorption ionization time-of-flight mass spectrometry to identify the genes that encode the SWP59 and SWP61 subunits. Surprisingly, we find that SWP59 and SWP61 are encoded by the ARP9 and ARP7 genes, respectively, which encode members of the actin-related protein (ARP) family. Sequence analyses have shown that ARP9 and ARP7 are 24-26% identical (48-51% similar) to yeast actin and that they are likely to maintain the overall actin fold. Deletion of either the ARP9 or ARP7 gene causes typical swi/snf phenotypes, including growth defects on media containing galactose, glycerol, or sucrose as sole carbon sources. ARP9 and ARP7 are also required for expression of an HO-lacZ fusion gene and for full transcriptional enhancement by the GAL4 activator. The identification of two ARP family members as crucial subunits of the SWI/SNF complex suggests that the complex may contain a total of three different ATPase subunits; furthermore, the similarity of ARP7 and ARP9 to the HSP and HSC family of ATPases suggests the possibility that chromatin remodeling by SWI/SNF may involve chaperone-like activities.

Peripheral nuclear matrix actin forms perinuclear shells

Perinuclear actin shells have been reported in a variety of organisms. The shells have been identified by staining perinuclear material with fluorescently-labelled phalloidin, but have not been localized to a specific subcellular compartment at the ultrastructural level. We show here that the shells of 3T3 cells lie in the peripheral nuclear matrix. Nuclear shells and matrix actin in other parts of the nucleus are not usually detected by immunohistochemical staining because they are inaccessible to antibodies or to phalloidin. Immunohistochemical detection of nuclear actin is only possible during its deposition at the end of mitosis, or in interphase nuclei that have been extracted with detergent, digested with nucleases and washed with high salt buffers.

Immunofluorescent localization of actin in relation to transcription sites in mouse pronuclei

Previous biochemical and morphological studies have shown the presence of actin in the nucleus of different cell types where its role remains unclear. In this work, through fluorescence microscopy we studied the localization of actin in the nuclei of early mouse embryos with particular attention to its possible involvement in the onset of transcription occurring at the late one-cell stage. Fluorescent labelling of embryo sections showed that nuclear actin in abundant, in a non-filamentous state, in the whole nucleoplasm excluding the nucleolar precursor bodies. Immunofluorescence on permeabilized embryos revealed that insoluble nuclear actin accumulates in a few large aggregates in transcriptionally inert early one-cell embryos and progressively redistributes into many small aggregates in transcriptionally active late one-cell embryos. Interestingly, these actin aggregates clearly colocalize with transcription sites. Treatment of late one-cell embryos with cytochalasin D induces the formation of actin bundles network in the nucleoplasm but has no apparent effect on the transcriptional activity. In addition, the inhibition of transcription by alpha-amanitin does not modify the nuclear actin distribution. Hence, there does not appear to be a direct causal relationship between transcriptional activity and nuclear actin organization at the one-cell stage although nuclear actin aggregates appear associated with transcription sites.

The role of the dynactin complex in intracellular motility

Dynactin is a multisubunit complex that binds to the minus-end-directed microtubule motor cytoplasmic dynein and may provide a link between the motor and its cargo. Results from genetic studies in Saccharomyces cerevisiae, Neurospora crassa, Aspergillus nidulans, and Drosophila have suggested that cytoplasmic dynein and dynactin function in the same cellular pathways. p150Glued, a vertebrate homologue of the Drosophila gene Glued, is the largest polypeptide in the dynactin complex with multiple protein interactions. Centractin, the most abundant dynactin subunit polypeptide, forms an actin-like filament at the base of the complex. Studies on dynamitin, the 50-kDa dynactin subunit, predict a role for dynactin in mitotic spindle assembly. Other subunits of dynactin have also been cloned and characterized; these studies have provided insight into the role of the complex in essential cellular processes.

Nuclear assembly

We review old and new insights into the structure of the nuclear envelope and the components responsible for its dynamic reassembly during mitosis. New information is coming to light about several of the proteins that mediate nuclear reassembly. These proteins include the lamins and their emerging relationship with proteins such as otefin and the MAN antigens: peripheral proteins that might participate in lamina structure. There are four identified proteins localized to the inner nuclear membrane: the lamina-associated proteins LAP1 and LAP2, emerin, and the lamin B receptor (LBR). LBR can interact independently with lamin B and a chromodomain protein, Hp1, and appears to be a central player in targeting nuclear membranes to chromatin. Intermediates in the assembly of nuclear pore complexes (NPCs) can now be studied biochemically and visualized by high resolution scanning electron microscopy. We discuss the possibility that the filament-forming proteins Tpr/p270, NuMA, and perhaps actin may have roles in nuclear assembly.

Interphase chromosomes undergo constrained diffusional motion in living cells

BACKGROUND

Structural studies of fixed cells have revealed that interphase chromosomes are highly organized into specific arrangements in the nucleus, and have led to a picture of the nucleus as a static structure with immobile chromosomes held in fixed positions, an impression apparently confirmed by recent photobleaching studies. Functional studies of chromosome behavior, however, suggest that many essential processes, such as recombination, require interphase chromosomes to move around within the nucleus.

RESULTS

To reconcile these contradictory views, we exploited methods for tagging specific chromosome sites in living cells of Saccharomyces cerevisiae with green fluorescent protein and in Drosophila melanogaster with fluorescently labeled topoisomerase ll. Combining these techniques with submicrometer single-particle tracking, we directly measured the motion of interphase chromatin, at high resolution and in three dimensions. We found that chromatin does indeed undergo significant diffusive motion within the nucleus, but this motion is constrained such that a given chromatin segment is free to move within only a limited subregion of the nucleus. Chromatin diffusion was found to be insensitive to metabolic inhibitors, suggesting that it results from classical Brownian motion rather than from active motility. Nocodazole greatly reduced chromatin confinement, suggesting a role for the cytoskeleton in the maintenance of nuclear architecture.

CONCLUSIONS

We conclude that chromatin is free to undergo substantial Brownian motion, but that a given chromatin segment is confined to a subregion of the nucleus. This constrained diffusion is consistent with a highly defined nuclear architecture, but also allows enough motion for processes requiring chromosome motility to take place. These results lead to a model for the regulation of chromosome interactions by nuclear architecture.

Purification and nucleic-acid-binding properties of a Saccharomyces cerevisiae protein involved in the control of ploidy

Scp160p (Saccharomyces cerevisiae protein involved in the control of ploidy), a polypeptide with a molecular mass of around 160 kDa, is associated with the nuclear envelope and the endoplasmic reticulum. The most noteworthy phenotype of SCP160 deletion mutants is a decrease in viability and an increased number of chromosomes in the surviving cells [Wintersberger, U., Kühne, C. & Karwan, A. (1995) Yeast 11, 929-944]. Scp160p contains 14 KH domains, conserved motifs that have lately been identified in a variety of RNA-binding proteins. In this report, we demonstrate that the Scp160p sequence shows nearly perfect colinearity with the putative gene product of C08H9.2 from the nematode Caenorhabditis elegans as well as with the vigilins, vertebrate RNA-binding proteins with a cellular location similar to that of Scp160p. Moreover, we found that Scp160p contains a potential nuclear-export signal (NES) near its N-terminus and a potential nuclear-localization signal (NLS) between KH domains 3 and 4. To determine whether the protein is able to bind to RNA, we purified Scp160p from yeast cell extract by DNA-cellulose and anti-Scp160p affinity chromatography. In northwestern blotting experiments, the electrophoretically homogeneous protein bound to ribohomopolymers and ribosomal RNA as well as to single-stranded and double-stranded DNA. Subcellular fractionation studies revealed that the major part of Scp160p is membrane associated via ionic interactions and can be released from the membrane fraction under conditions that lead to a dissociation of ribosomes. Together, our findings suggest that Scp160p is the yeast homologue of the vigilins, and point to a role for Scp160p in nuclear RNA export or in RNA transport within the cytoplasm.

Who's who among the Saccharomyces cerevisiae actin-related proteins? A classification and nomenclature proposal for a large family

Inspection of the complete Saccharomyces cerevisiae genome sequence and analysis of the actin-related proteins (ARPs) found therein revealed seven proteins, in addition to the previously designated actin-related proteins Arp1, Arp2 and Arp3, which contained substantial blocks of conservation relative to a chosen sub-set of actins. We have ordered the new ARPs relative to this group of actins and propose to name the more distantly related ARP members, according to their amino acid identity and similarity, Arp4-Arp10. Most of these proteins appear to represent the first example of new classes of ARPs, each of which may have specific localization(s) and cellular function(s). Recently reported ARPs from other species have also been included in the phylogenetic tree derived from the overall alignment of 29 actins and 28 ARPs.