Isolation and ultrastructural characterization of the residual nuclear matrix in a plant cell system

The plant nuclear lamina proteins NMCP1 and NMCP2 form a filamentous network with lateral filament associations

Plant genomes lack genes encoding intermediate filament proteins, including lamins; however, functional lamin analogues are presumed to exist in plants. Plant-specific coiled-coil proteins, that is, nuclear matrix constituent proteins (NMCPs), are the most likely candidates as the structural elements of the nuclear lamina because they exhibit a lamin-like domain arrangement. They are exclusively localized at the nuclear periphery and have functions that are analogous to those of lamins. However, their assembly into filamentous polymers has not yet been confirmed. In this study, we examined the higher-order structure of NMCP1 and NMCP2 in Apium graveolens cells by using stimulated emission depletion microscopy combined with immunofluorescence cell labelling. Our analyses revealed that NMCP1 and NMCP2 form intricate filamentous networks, which include thick segments consisting of filament bundles, forming a dense filamentous layer extending across the nuclear periphery. Furthermore, the outermost chromatin distribution was found to be in the nucleoplasm-facing region of the nuclear lamina. Recombinant Daucus carota NMCP1 with a His-tag produced in Escherichia coli refolded into dimers and self-assembled into filaments and filament bundles. These results suggest that NMCP1 and NMCP2 organize into the nuclear lamina by forming a filamentous network with filament bundles that localize at the nuclear periphery.

Subnuclear gene positioning through lamina association affects copper tolerance

The nuclear lamina plays an important role in the regulation of chromatin organization and gene positioning in animals. CROWDED NUCLEI (CRWN) is a strong candidate for the plant nuclear lamina protein in Arabidopsis thaliana but its biological function was largely unknown. Here, we show that CRWNs localize at the nuclear lamina and build the meshwork structure. Fluorescence in situ hybridization and RNA-seq analyses revealed that CRWNs regulate chromatin distribution and gene expression. More than 2000 differentially expressed genes were identified in the crwn1crwn4 double mutant. Copper-associated (CA) genes that form a gene cluster on chromosome 5 were among the downregulated genes in the double mutant exhibiting low tolerance to excess copper. Our analyses showed this low tolerance to copper was associated with the suppression of CA gene expression and that CRWN1 interacts with the CA gene locus, enabling the locus to localize at the nuclear lamina under excess copper conditions.

The nuclear lamina regulates chromatin organization and gene positioning. Here the authors show that CROWDED NUCLEI proteins contribute to the meshwork lamina structure in Arabidopsis nuclei and regulate copper tolerance by promoting lamina association and expression of copper response genes.

Is the plant nucleus a mechanical rheostat?

Beyond its biochemical nature, the nucleus is also a physical object. There is accumulating evidence that its mechanics plays a key role in gene expression, cytoskeleton organization, and more generally in cell and developmental biology. Building on data mainly obtained from the animal literature, we show how nuclear mechanics may orchestrate development and gene expression. In other words, the nucleus may play the additional role of a mechanical rheostat. Although data from plant systems are still scarce, we pinpoint recent advances and highlight some differences with animal systems. Building on this survey, we propose a list of prospects for future research in plant nuclear mechanotransduction and development.

Evolutionary history and structure of nuclear matrix constituent proteins, the plant analogues of lamins

Nuclear matrix constituent proteins (NMCPs), the structural components of the plant lamina, are considered to be the analogues of lamins in plants based on numerous structural and functional similarities. Current phylogenetic knowledge suggests that, in contrast to lamins, which are widely distributed in eukaryotes, NMCPs are taxonomically restricted to Streptophyta. At present, most information about NMCPs comes from angiosperms, and virtually no data are available from more ancestral groups. In angiosperms, the NMCP family comprises two phylogenetic groups, NMCP1 and NMCP2, which evolved from the NMCP1 and NMCP2 progenitor genes. Based on sequence conservation and the presence of NMCP-specific domains, we determined the structure and number of NMCP genes present in different Streptophyta clades. We analysed 91 species of embryophytes and report additional NMCP sequences from mosses, liverworts, clubmosses, horsetail, ferns, gymnosperms, and Charophyta algae. Our results confirm an origin of NMCPs in Charophyta (the earliest diverging group of Streptophyta), resolve the number and structure of NMCPs in the different clades, and propose the emergence of additional NMCP homologues by whole-genome duplication events. Immunofluorescence microscopy demonstrated localization of a basal NMCP from the moss Physcomitrella patens at the nuclear envelope, suggesting a functional conservation for basal and more evolved NMCPs.

Characterization of the lamin analogue NMCP2 in the monocot Allium cepa

Nuclear lamina organization is similar in metazoan and plants though the latter lack orthologs of lamins, the main components of the metazoan lamina. Current evidence suggests that Nuclear Matrix Constituent Proteins (NMCPs) are the lamin analogues in plants as these proteins share several key features: higher-order secondary structure and domain layout, subnuclear distribution, and involvement in the regulation of nuclear shape and size, as well as in higher-order chromatin organization. Previously, we studied the NMCP family in flowering plants (angiosperms), in which it comprises two phylogenetic groups: NMCP1 and NMCP2. At present, in silico information about NMCP proteins in embryophytes is relatively advanced, though very few proteins, most of them of the NMCP1 type, have been extensively studied in vivo. We previously characterized the NCMP1 protein in the monocot Allium cepa. Here, we report the key features of a second protein of this species NMCP2, which presents a conserved sequence and domain layout. Immunofluorescence and immunoelectronmicroscopy evidence co-localization of endogenous AcNMCP2 and AcNMCP1 in the lamina, while Western blotting and immunoconfocal microscopy reveal a similar pattern of expression and distribution of both NMCP proteins in different root tissues. Our results provide novel insight about endogenous NMCP2-type proteins and complete the characterization of the NMCP family in A. cepa, thus advancing the current understanding of these structural proteins constituting the plant lamina.

Inside a plant nucleus: discovering the proteins

Nuclear proteins are a vital component of eukaryotic cell nuclei and have a profound effect on the way in which genetic information is stored, expressed, replicated, repaired, and transmitted to daughter cells and progeny. Because of the plethora of functions, nuclear proteins represent the most abundant components of cell nuclei in all eukaryotes. However, while the plant genome is well understood at the DNA level, information on plant nuclear proteins remains scarce, perhaps with the exception of histones and a few other proteins. This lack of knowledge hampers efforts to understand how the plant genome is organized in the nucleus and how it functions. This review focuses on the current state of the art of the analysis of the plant nuclear proteome. Previous proteome studies have generally been designed to search for proteins involved in plant response to various forms of stress or to identify rather a modest number of proteins. Thus, there is a need for more comprehensive and systematic studies of proteins in the nuclei obtained at individual phases of the cell cycle, or isolated from various tissue types and stages of cell and tissue differentiation. All this in combination with protein structure, predicted function, and physical localization in 3D nuclear space could provide much needed progress in our understanding of the plant nuclear proteome and its role in plant genome organization and function.

Localization of Daucus carota NMCP1 to the nuclear periphery: the role of the N-terminal region and an NLS-linked sequence motif, RYNLRR, in the tail domain

Recent ultrastructural studies revealed that a structure similar to the vertebrate nuclear lamina exists in the nuclei of higher plants. However, plant genomes lack genes for lamins and intermediate-type filament proteins, and this suggests that plant-specific nuclear coiled-coil proteins make up the lamina-like structure in plants. NMCP1 is a protein, first identified in Daucus carota cells, that localizes exclusively to the nuclear periphery in interphase cells. It has a tripartite structure comprised of head, rod, and tail domains, and includes putative nuclear localization signal (NLS) motifs. We identified the functional NLS of DcNMCP1 (carrot NMCP1) and determined the protein regions required for localizing to the nuclear periphery using EGFP-fused constructs transiently expressed in Apium graveolens epidermal cells. Transcription was driven under a CaMV35S promoter, and the genes were introduced into the epidermal cells by a DNA-coated microprojectile delivery system. Of the NLS motifs, KRRRK and RRHK in the tail domain were highly functional for nuclear localization. Addition of the N-terminal 141 amino acids from DcNMCP1 shifted the localization of a region including these NLSs from the entire nucleus to the nuclear periphery. Using this same construct, the replacement of amino acids in RRHK or its preceding sequence, YNL, with alanine residues abolished localization to the nuclear periphery, while replacement of KRRRK did not affect localization. The sequence R/Q/HYNLRR/H, including YNL and the first part of the sequence of RRHK, is evolutionarily conserved in a subclass of NMCP1 sequences from many plant species. These results show that NMCP1 localizes to the nuclear periphery by a combined action of a sequence composed of R/Q/HYNLRR/H, NLS, and the N-terminal region including the head and a portion of the rod domain, suggesting that more than one binding site is implicated in localization of NMCP1.

Functional organization and dynamics of the cell nucleus

The eukaryotic cell nucleus enclosed within the nuclear envelope harbors organized chromatin territories and various nuclear bodies as sub-nuclear compartments. This higher-order nuclear organization provides a unique environment to regulate the genome during replication, transcription, maintenance, and other processes. In this review, we focus on the plant four-dimensional nuclear organization, its dynamics and function in response to signals during development or stress.

The intriguing plant nuclear lamina

The nuclear lamina is a complex protein mesh attached to the inner nuclear membrane (INM), which is also associated with nuclear pore complexes. It provides mechanical support to the nucleus and nuclear envelope, and as well as facilitating the connection of the nucleoskeleton to the cytoskeleton, it is also involved in chromatin organization, gene regulation, and signaling. In metazoans, the nuclear lamina consists of a polymeric layer of lamins and other interacting proteins responsible for its association with the INM and chromatin. In plants, field emission scanning electron microscopy of nuclei, and thin section transmission electron microscopy of isolated nucleoskeletons, reveals the lamina to have a similar structure to that of metazoans. Moreover, although plants lack lamin genes and the genes encoding most lamin-binding proteins, the main functions of the lamina are fulfilled in plants. Hence, it would appear that the plant lamina is not based on lamins and that other proteins substitute for lamins in plant cells. The nuclear matrix constituent proteins are the best characterized structural proteins in the plant lamina. Although these proteins do not display strong sequence similarity to lamins, their predicted secondary structure and sub-nuclear distribution, as well as their influence on nuclear size and shape, and on heterochromatin organization, suggest they could be functional lamin analogs. In this review we shall summarize what is currently known about the organization and composition of the plant nuclear lamina and its interacting complexes, and we will discuss the activity of this structure in the plant cell and its nucleus.

Lamin-like analogues in plants: the characterization of NMCP1 in Allium cepa

The nucleoskeleton of plants contains a peripheral lamina (also called plamina) and, even though lamins are absent in plants, their roles are still fulfilled in plant nuclei. One of the most intriguing topics in plant biology concerns the identity of lamin protein analogues in plants. Good candidates to play lamin functions in plants are the members of the NMCP (nuclear matrix constituent protein) family, which exhibit the typical tripartite structure of lamins. This paper describes a bioinformatics analysis and classification of the NMCP family based on phylogenetic relationships, sequence similarity and the distribution of conserved regions in 76 homologues. In addition, NMCP1 in the monocot Allium cepa characterized by its sequence and structure, biochemical properties, and subnuclear distribution and alterations in its expression throughout the root were identified. The results demonstrate that these proteins exhibit many similarities to lamins (structural organization, conserved regions, subnuclear distribution, and solubility) and that they may fulfil the functions of lamins in plants. These findings significantly advance understanding of the structural proteins of the plant lamina and nucleoskeleton and provide a basis for further investigation of the protein networks forming these structures.

NMCP/LINC proteins: putative lamin analogs in plants?

Lamins are the main components of the metazoan lamina, and while the organization of the nuclear lamina of metazoans and plants is similar, there are apparently no genes encoding lamins or most lamin-binding proteins in plants. Thus, the plant lamina is not lamin-based and the proteins that form this structure are still to be characterized. Members of the plant NMCP/LINC/CRWN protein family share the typical tripartite structure of lamins, although the 2 exhibit no sequence similarity. However, given the many similarities between NMCP/LINC/CRWN proteins and lamins (structural organization, position of conserved regions, sub-nuclear distribution, solubility, and pattern of expression), these proteins are good candidates to carry out the functions of lamins in plants. Moreover, functional analysis of NMCP/LINC mutants has revealed their involvement in maintaining nuclear size and shape, another activity fulfilled by lamins. This review summarizes the current understanding of NMCP/LINC proteins and discusses future studies that will be required to demonstrate definitively that these proteins are plant analogs of lamins.

Characterization of a 65 kDa NIF in the nuclear matrix of the monocot Allium cepa that interacts with nuclear spectrin-like proteins

Plant cells have a well organized nucleus and nuclear matrix, but lack orthologues of the main structural components of the metazoan nuclear matrix. Although data is limited, most plant nuclear structural proteins are coiled-coil proteins, such as the NIFs (nuclear intermediate filaments) in Pisum sativum that cross-react with anti-intermediate filament and anti-lamin antibodies, form filaments 6-12 nm in diameter in vitro, and may play the role of lamins. We have investigated the conservation and features of NIFs in a monocot species, Allium cepa, and compared them with onion lamin-like proteins. Polyclonal antisera against the pea 65 kDa NIF were used in 1D and 2D Western blots, ICM (imunofluorescence confocal microscopy) and IEM (immunoelectron microscopy). Their presence in the nuclear matrix was analysed by differential extraction of nuclei, and their association with structural spectrin-like proteins by co-immunoprecipitation and co-localization in ICM. NIF is a conserved structural component of the nucleus and its matrix in monocots with Mr and pI values similar to those of pea 65 kDa NIF, which localized to the nuclear envelope, perichromatin domains and foci, and to the nuclear matrix, interacting directly with structural nuclear spectrin-like proteins. Its similarities with some of the proteins described as onion lamin-like proteins suggest that they are highly related or perhaps the same proteins.

Differential nuclear envelope assembly at the end of mitosis in suspension-cultured Apium graveolens cells

NMCP1 is a plant protein that has a long coiled-coil domain within the molecule. Newly identified NMCP2 of Daucus carota and Apium graveolens showed similar peripheral localization in the interphase nucleus, and the sequence spanning the coiled-coil domain exhibited significant similarity with the corresponding region of NMCP1. To better understand disassembly and assembly of the nuclear envelope (NE) during mitosis, subcellular distribution of NMCP1 and NMCP2 was examined using A. graveolens cells. AgNMCP1 (NMCP1 in Apium) disassembled at prometaphase, dispersed mainly within the spindle, and accumulated on segregating chromosomes, while AgNMCP2 (NMCP2 in Apium), following disassembly at prometaphase with timing similar to that of AgNMCP1, dispersed throughout the mitotic cytoplasm at metaphase and anaphase. The protein accumulated at the periphery of reforming nuclei at telophase. A probe for the endomembrane indicated that the nuclear membrane (NM) disappears at prometaphase and begins to reappear at early telophase. Growth of the NM continued after mitosis was completed. NMCP2 in the mitotic cytoplasm localized in vesicular structures that could be distinguished from the bulk endomembrane system. These results suggest that NMCP1 and NMCP2 are recruited for NE assembly in different pathways in mitosis and that NMCP2 associates with NM-derived vesicles in the mitotic cytoplasm.

The plant nucleoskeleton: ultrastructural organization and identification of NuMA homologues in the nuclear matrix and mitotic spindle of plant cells

In the present work we investigate the structural organization of the nucleoskeleton of Allium cepa meristematic root cells. Resinless sections reveal for the first time a residual filamentous network in plant nuclei. This network is composed of branched knobbed filaments with associated globular structures, connected to the lamina and to the dense aggregates of different sizes. Results of immunoblotting show that many components of this network are homologues of intermediate filament-type proteins. NuMA, a coiled-coil protein related to intermediate filaments, found in animal cells, can also be detected in this plant nuclear matrix system. Immunofluorescence reveals a diffuse distribution of the animal NuMA homologues in plant nuclear core filaments in interphase. Resinless immunoelectron microscopy further reveals a distribution along the extended filaments and the dense aggregates. During mitosis, in contrast to the accumulation at the poles in animal cells, NuMA homologues in plant onion cells show a diffuse pattern, which may correspond to the spindle matrix. Our data are the first report of the conservation in plants of NuMA proteins, which may be involved in both nuclear and mitotic spindle organizations.

Peripheral framework of carrot cell nucleus contains a novel protein predicted to exhibit a long alpha-helical domain

A monoclonal antibody, CML-1, raised against carrot (Daucus carota L.) nuclear-matrix proteins selectively labeled the nuclear periphery of carrot protoplasts when visualized by confocal and electron microscopy. To identify the constituent proteins of higher plant cells structurally homologous to the vertebrate nuclear lamina, we cloned overlapping cDNAs partially encoding a CML-1-recognized protein and determined the entire sequence including the open reading frame. When the deduced amino acid sequence was compared with other known protein sequences contained in major databases, no protein was found to show high sequence identity across the whole region of the protein, while the partial sequence showed strong similarities with myosin, tropomyosin, and some intermediate filament proteins. The protein, designated NMCP1, had an estimated molecular mass of 133.6 kDa and showed three characteristic domains. The central domain contains long alpha-helices exhibiting heptad repeats of apolar residues, demonstrating structural similarity to that of filament-forming proteins. The terminal domains are predominantly nonhelical and contain potential sequence motifs for nuclear localization signals. NMCP1 has many recognition motifs for different types of protein kinases, including cdc2 kinase and PKC. These results suggest that NMCP1 protein forms coiled-coil filaments and is a constituent of the peripheral architecture of the higher plant cell nucleus.

Nuclear degeneration in epidermal cells of drying onion bulb leaf bases

We tested the null hypothesis 'that activated nuclei and nucleoli in outer-epidermal cells of newly exposed equatorial tissue of the turgid leaf bases of white onions (exposed to the ambient atmosphere by removal of two dry and two turgid leaf bases) remained in that state as the tissue dried' by following nuclear macromolecules (total nucleic acid, DNA, RNA, total protein, histone, and non-histone protein; compared with T0 = 100%) and nucleolar morphologies over a 5-day period. The nuclei became activated within 6 h and remained in that state for 2-3 days [increases in RNA, non-histone protein, and volume of major nucleoli occurred by T12 (about 191, 177, and 289%, respectively) and appearance of the minor nucleoli between T12 and T24 (activation of silent rRNA cistrons)]. Combined nucleolar (major and minor) volumes decreased to 228% by T24 and to 150% by T48. Minor nucleoli were visible at T24 and T48. DNA (DAPI) remained unchanged over that period of time. At the T96 sampling, all nuclear indices had decreased to levels below those obtained at the time of exposure to the ambient atmosphere; minor rRNA cistrons had became silent genes; nuclear volume was about 89% of the original volume; and, nucleolar volume (major nucleoli) was about 93%. The percentages for nuclear indices at T120 were DNA, 85% of T0; RNA, 35%; histone, 87%; non-histone protein, 47%; nuclear volume, 81%; and nucleolar volume, 67%. Of interest is the lack of change in major nucleolar morphologies between T96 and T120 although they decreased in volume during that period. We infer that the karyoskeleton (nuclear matrix) had undergone irreversible degeneration after T48 and that the cells had passed the point-of-no-return in the senescence pathway by T120. We propose that this model for cell senescence and death (drying of turgid leaf bases to form the dry, dead outer covering of the bulbs) simulates post-harvest storage conditions and will prove helpful to those studying cellular senescence mechanisms and associated host-pathogen interactions in plants.

Post-mitotic assembly of the nucleolus. I. The internal matrix network is a recruitment site for processing nucleolar components in prenucleolar bodies

The aim of this work was to investigate whether the nuclear matrix could provide the nucleation sites for dispersed parental nucleolar components to form post-mitotic prenucleolar bodies (PNBs). For this purpose, nuclear matrices from asynchronous populations of onion cells were fractionated, and the distribution of the insoluble components of the nucleolar processing complexes in the matrices were analysed by fibrillarin immunolabelling. The ultra-structural organization of the nuclear matrix of cells from late telophase to late G1, corresponding to the period of nucleolar reassembly and activation, was also analysed. Our results demonstrate that PNBs are structural components of the telophasic nuclear matrix and that this structure provides recruitment and assembly sites for the components of the nucleolar processing machinery, and suggests that the telophasic matrix network is involved in the early steps of post-mitotic nucleologenesis.

Nuclear matrix isolated from plant cells

Residual nuclear matrices can be successfully obtained from isolated nuclei of different monocot and dicot plant species using either high ionic or low ionic extraction protocols. The protein composition of isolated nuclear matrices depends on the details of isolation protocols. They are stable and present in all cases, a tripartite organization with a lamina, nucleolar matrix, and internal matrix network, and also maintain some of the basic architectural features of intact nuclei. In situ preparations demonstrate the continuity between the nuclear matrix and the plant cytoskeleton. Two-dimensional separation of isolated plant nuclear matrix proteins reveals a heterogeneous polypeptide composition corresponding rather to a complex multicomponent matrix than to a simple nucleoskeletal structure. Immunological identification of some plant nuclear matrix components such as A and B type lamins, topoisomerase II, and some components of the transcription and splicing machineries, internal intermediate filament proteins, and also specific nucleolar proteins like fibrillarin and nucleolin, which associate to specific matrix domains, establish a model of organization for the plant nuclear matrix similar to that of other eukaryotes. Components of the transcription, processing, and DNA-anchoring complexes are associated with a very stable nucleoskeleton. The plant matrix-attached regions share structural and functional characteristics with those of insects, vertebrates, and yeast, and some of them are active in animal cells. In conclusion, the available data support the view that the plant nuclear matrix is basically similar in animal and plant systems, and has been evolutionarily conserved in eukaryotes.

Effect of abscisic acid, gibberellic acid, indoleacetic acid, and kinetin on selective ribosomal cistron regulation in quiescent and senescent onion leaf base tissue

Small pieces of tissue from the basal, equatorial, near-apical, and apical regions of the third turgid onion leaf base were treated (3 and 6 h in the dark) with abscisic acid (ABA), gibberellic acid (GA3), indoleacetic acid (IAA), and kinetin (K) and compared with responses in water controls. ABA inhibited the activation (increase in size and changes in morphologies from round or oval to elongated-oval and dumbbell) of major nucleolar organizer regions (NORs) in basal, equatorial, and near-apical tissue. GA3 and K activated the major NORs in the basal, equatorial, and near-apical tissue. IAA stimulated the activation of major NORs in basal tissue but inhibited their activation in equatorial and near-apical tissue. No major nucleoli were activated in control or plant growth regulator-treated apical tissue. Minor NORs were not expressed in the control and plant growth regulator-treated tissue in these four locations. Actinomycin D and cycloheximide inhibited major NOR activation in equatorial control and kinetin-treated tissue. We propose that ABA, GA3, IAA, and K are major NOR regulators. We infer that the basal through near-apical cells were quiescent during post-harvest storage and that the cells in the apical tissue had senesced beyond the point of no return (degeneration of the karyoskeleton) in the cellular senescence pathway.

Dinoflagellates have a eukaryotic nuclear matrix with lamin-like proteins and topoisomerase II

Unicellular Dinoflagellates represent the only eukaryotic Phylum lacking histones and nucleosomes. To investigate whether Dinoflagellates do have a nuclear matrix that would modulate the supramolecular organization of their non-nucleosomal DNA and chromosomes, cells of the free-living unarmored Dinoflagellate Amphidinium carterae were encapsulated in agarose microbeads and submitted to sequential extraction with non-ionic detergents, nucleases and 2 M NaCl. Our results demonstrate that this species has a residual nuclear matrix similar to that of vertebrates and higher plants. The cytoskeleton-nuclear matrix complex of A. carterae shows a relatively intricate polypeptide pattern. Immunoblots with different antibodies reveal several intermediate filament types of proteins, one of which is immunologically related to vertebrate lamins, confirming that these proteins are ancestral members of the IF family, which is highly conserved in eukaryotes. A topoisomerase II homologue has also been identified in the nuclear matrix, suggesting that these structures could play a role in organizing the Dinoflagellate DNA in loop domains. Taken together our results demonstrate that the nuclear matrix is an early acquisition of the eukaryotic nucleus, independent of histones and nucleosomes in such a way that the mechanisms controlling the two levels of organization in eukaryotic chromatin would be molecularly and evolutionarily independent.

Effect of ethylene on selective ribosomal cistron regulation in quiescent and senescent onion leaf base tissue

Excised pieces of tissue from four regions (base, equator, near-apex, and apex) of yellow, sweet Spanish onion bulbs were treated with ethylene in an attempt to activate minor nucleolar organizer regions (NORs). In the quiescent equatorial and near-apical regions, major nucleoli in control and ethylene-treated tissue increased in size and changed morphologies. The minor NORs were expressed only in the ethylene-treated tissue. These data confirm and extend our previous findings. In the quiescent basal region, major nucleoli increased in size and changed morphology from round to oval, elongated-oval and dumbbell shapes in both control and ethylene-treated tissue. However, the number of elongated-oval and dumbbell types were one-third that observed in equatorial and near-apical tissue. Minor NORs were not expressed. We infer that the responses of the major nucleoli and the inability to activate minor NORs were due to hormone interactions that affect the expression of rRNA cistrons (methylation-demethylation of CpG sites in the external spacers) in this basal (meristematic) region. In the senescing apical region, major nucleoli in control and ethylene-treated tissue did not change in size or morphology and ethylene had no effect on minor NORs. We infer that the cells in the apical region had passed the point of no return in the senescence pathway. We propose that the inability to activate major and minor NORs in senescing tissue is one of the earliest symptoms of cellular senescence and is associated with karyoskeleton degeneration.

Enhancement of the immunocytochemical detection of antigens by microwave irradiation. Benefits and limitations analysed in isolated plant nuclei and Drosophila embryos in toto

Performing the antibody reaction under controlled heating through microwave irradiation results in significant improvements in the immunovisualization of antigens, such as shortening the times of incubation, lowering the antibody titres used and allowing the detection of difficult, inaccessible antigens. In addition to investigate the basis of the enhancement, we have extended to more intact samples such as isolated plant nuclei and in toto Drosophila embryos the results previously reported only with tissue sections. A drop of heterologous anti-nucleolin antibody covering isolated nuclei from onion root meristems spread on a glass slide was microwave irradiated, resulting in clear immunofluorescent labelling of the nucleoli. This result was never previously obtained in the absence of microwave treatment, even using the complicated procedure previously reported for the homologous identification of this nuclear protein. Using the much larger and to some extent impermeable Drosophila embryos, we were able to show that the incubation time and concentration of the anti-myosin antibody can be strongly reduced by performing the reaction at 45 degrees C under microwave irradiation. The controlled increase in temperature is the main factor responsible for these improvements; the importance of maintaining an adequate mixing of the samples is also emphasized. The proper implementation of these two experimental conditions will require the introduction of appropriate mixing accessories and temperature measuring probes for samples of small volume in current microwave laboratory ovens.

The role of scaffold attachment regions in the structural and functional organization of plant chromatin

Studies on nuclear scaffolds and scaffold attachment regions (SARs) have recently been extended to different plant species and indicate that SARs are involved in the structural and functional organization of the plant genome, as is the case for other eukaryotes. One type of SAR seems to delimit structural chromatin loops and may also border functional units of gene expression and DNA replication. Another group of SARs map close to regulatory elements and may be directly involved in gene expression. In this overview, we summarize the structural and functional properties of plant SARs in comparison with those of SARs from animals and yeast.

Immunological characterization of lamins in the nuclear matrix of onion cells

We have used polyclonal and monoclonal antibodies against different lamins from vertebrates, and the IFA antibody recognizing all kinds of intermediate filament proteins, to investigate the lamins of the nuclear matrix of Allium cepa meristematic root cells. All the antibodies react in the onion nuclear matrix with bands in the range of 60–65 kDa, which are enriched in the nuclear matrix after urea extraction, and do not crossreact with other antibodies recognizing intermediate filaments in plants (AFB, anti-vimentin and MAC 322), ruling out crossreaction with contaminating intermediate filaments of cytoplasmic bundles. In 2-D blots the chicken anti-lamin serum reacts with one spot at 65 kDa and pI 6.8 and the anti B-type lamin antibodies with another one at 64 kDa and pI 5.75. Both crossreact with IFA. The lamin is localized at the nuclear periphery and the lamina by indirect immunofluorescence. Immunogold labelling of nuclear matrix sections reveals that the protein is not only associated with the lamina, but also with the internal matrix. Taken together these results reveal that higher plants, which do not possess an organized network of cytoplasmic intermediate filaments, nevertheless present a well-organized lamina containing lamins in which at least one of them is immunologically related to vertebrate lamin B. Our data confirm that lamins are very old members of the intermediate filament proteins that have been better conserved in plants during evolution than their cytoplasmic counterparts.

Nuclear matrix of the lower eukaryote Physarum polycephalum and the mammalian epithelial LLC-PK1 cell line. A comprehensive investigation of different preparation procedures

Agarose-encapsulated nuclear matrix preparations of the lower eukaryote Physarum polycephalum and the mammalian renal epithelial LLC-PK1 cell line were analyzed after various experimental protocols with respect to the protein composition. The effect of the mode of deproteinization (2 M NaCl, 0.25 M ammonium sulfate or 25 mM lithium diiodosalicylate), presence of 2-mercaptoethanol, Ca2+, Cu2+, chelating agents, the sequence of protein extraction and nuclease digestion, the use of RNase, the temperature at which the experimental manipulations were performed and the use of hypotonic or isotonic conditions was investigated. No significant differences in the final nuclear matrix composition could be observed, regardless of the experimental procedure applied. In Physarum, the major nuclear matrix proteins range over 12-70 kDa with prominent bands at 24, 31, 37 and 45 kDa; the proteins of the matrix in LLC-PK1 cells extend predominantly over 40-80 kDa. Furthermore, no essential differences in the protein composition could be observed when type I and type II nuclear matrices from the highly differentiated LLC-PK1 cell line were compared. The same was found for analogous matrix preparations of Physarum. Therefore, in both systems a distinction between type I/II matrix is questionable. Immunoblotting of the matrix preparations with a variety of antibodies against intermediate filament proteins and with antinuclear autoantibodies revealed the presence of intermediate filament proteins as components of the nuclear matrix. We conclude that the nuclear matrix represents a much more stable and reproducible structure than has been proposed so far, largely independent of changes in the preparation protocol.

The gene structure of Xenopus nuclear lamin A: a model for the evolution of A-type from B-type lamins by exon shuffling

Nuclear lamins are intermediate filament (IF) type proteins that form a fibrillar network underlying the inner nuclear membrane. The existence of multiple subtypes of lamins in vertebrates has been interpreted in terms of functional specialization during cell division and differentiation. The structure of a gene encoding an A-type lamin of Xenopus laevis was analysed. Comparison with that of a B-type lamin of the same species shows remarkable conservation of the exon/intron pattern. In both genes the last exon, only 9-12 amino acids in length, encodes the complete information necessary for membrane targeting of lamins, i.e. a ras-related CaaX motif. The lamin A specific extension of the tail domain is encoded by a single additional exon. The 5' boundary of this exon coincides with the sequence divergence between human lamins A and C, for which an alternative splice mechanism had previously been suggested. Arguments are presented suggesting that B-type lamins represent the ancestral type of lamins and that A-type lamins derived there from by exon shuffling. The acquisition of the new exon might explain the different fates of A- and B-types lamins during cell division.

Ribonucleoprotein components of root meristematic cell nuclei of the tomato characterized by application of mild loosening and immunocytochemistry

Immunocytochemistry and hypotonic-formaldehyde fixation have been used to study the extranucleolar ribonucleoprotein (RNP) constituents of the nucleus of tomato root meristematic cells. The study of the distribution of small nuclear uridine-rich RNPs (snRNP) by means of a monoclonal anti-Sm antibody recognizing a 29-kDa protein in plants, after standard fixation, shows a preferential labeling of the perichromatin region and a lower labeling of the interchromatin space. These results suggest that in the tomato there is a perichromatin region similar to that of animal cells, in which much of the nonnucleolar transcription and splicing takes place. In hypotonic-formaldehyde-detergent-fixed nuclei, fibrogranular polyparticles have been visualized reacting with anti-snRNP antibody. These structures are frequently associated with filaments of extended chromatin characterized by their reaction with an anti-DNA monoclonal antibody.

Intermediate filament antigens of 60 and 65 kDa in the nuclear matrix of plants: their detection and localization

Although the presence of a matrix in plant nuclei has been reported, major questions remain about its structural and biochemical features. We have used an intermediate filament antibody of broad specificity to explore whether Daucus carota (carrot) nuclei and nuclear matrices contain intermediate filament/lamin antigens and, if so, where specifically they are localized. SDS-PAGE and Western blotting revealed two bands, at 60 and 65 kDa, that were highly immunoreactive with the intermediate filament antibody (IFA) of Pruss et al. (1981, Cell 27, 419-428). This pattern was observed consistently, not only with carrot cell-free nuclei and nuclear matrices, but also with nuclear preparations from Vicia faba (broad bean) and Pisum sativum (pea). Immunofluorescence studies with whole carrot nuclei localized the IFA antigens to the nucleoplasm and disclosed no accentuated peripheral labeling. Agarose-embedded nuclear matrices showed not only fluorescence throughout the nucleoplasm but also heavy labeling surrounding the nucleoli and suggestions of peripheral labeling. At the ultrastructural level, immunogold results from pre- and postembedment treatments supported the conclusion that IFA antigens occur throughout the nucleoplasm, with possibly a slight concentration at the periphery. These combined results provide substantial evidence that plant nuclei and their matrices possess at least two major intermediate filament antigens with molecular weights characteristic of animal lamins. Whether or not these antigens represent plant lamins, their nonperipheral localization hints at significant differences among the eukaryotic kingdoms in nuclear organization.

Identification and localization of a nucleolin homologue in onion nucleoli

A protein homologous to nucleolin, a major nucleolar protein with multifunctional features involved in pre-rRNA synthesis and early processing, has been identified and localized in situ in onion root meristematic cells by different techniques, which have included the use of an antibody raised against hamster nucleolin. The protein was identified on Western blots of nucleolar proteins as a 64-kDa band, by means of the anti-nucleolin antibody, bismuth staining, and the silver staining-nucleolar organizer (Ag-NOR) method. The experiments also suggested that nucleolin could be a target of these two cytochemical stainings. Although the 64-kDa band corresponds to a major nucleolar protein, it is a minor one among total nuclear proteins. The same techniques were used in situ at the ultrastructural level, and the immunogold detection of the nucleolin homologue was quantitatively evaluated. The protein accumulates in the transition area from nucleolar fibrillar centers to the dense fibrillar component, which is considered to be the structural result of ribosomal gene transcription. Out of this transition area, the dense fibrillar component may be divided into two regions, proximal and distal with respect to fibrillar centers, which show, respectively, the significant and unsignificant presence of nucleolin; we interpret this fact as the expression of the topological arrangement of pre-rRNA processing. Fibrillar centers themselves showed a weak but significant labeling with the anti-nucleolin antibody. However, bismuth staining was absent from the interior of fibrillar centers, indicating that the nucleolin in them is not phosphorylated. Ag-NOR staining uniformly covered fibrillar centers and the dense fibrillar component (at least in its proximal region), but it did not stain condensed chromatin inclusions in heterogeneous fibrillar centers, showing that the binding of nucleolin to chromatin is associated with its decondensation. This work provides additional evidence of the high phylogenetic conservation of molecular motifs which take part in ribosome biogenesis.

The nucleus: a black box being opened

Until recently our knowledge about the structural and functional organization of the cell nucleus was very limited. Recent technical developments in the field of ultrastructural analysis, combined with ongoing research on the properties of the nuclear matrix, give new insight into how the nucleus is structured. Two types of observations shape our ideas about nuclear organization. First, most nuclear functions (replication, transcription, RNA processing, and RNA transport) are highly localized within the nucleus, rather than diffusely distributed. Moreover, they are associated with the nuclear matrix. Second, chromatin is organized in discrete loops, bordered by nuclear matrix attachment sequences (MARs). Each loop may contain one or several genes. The arrangement of chromatin in loops has profound consequences for the regulation of gene expression.