Similarity between nuclear matrix proteins of various cells revealed by an improved isolation method

Determination of cell type-specific proteome signatures of primary human leukocytes, endothelial cells, keratinocytes, hepatocytes, fibroblasts and melanocytes by comparative proteome profiling

Cells gain their functional specialization by different protein synthesis. A lot of knowledge with respect to cell type-specific proteins has been collected during the last thirty years. This knowledge was built mainly by using antibodies. Nowadays, modern MS, which supports comprehensive proteome analyses of biological samples, may render possible the search for cell type-specific proteins as well. However, a therefore necessary systematic MS study comprising many different cell types has not been performed until now. Here we present a proteome analysis strategy supporting the automated and meaningful comparison of any biological samples. We have presently applied this strategy to six different primary human cell types, namely leukocytes, endothelial cells, keratinocytes, hepatocytes, fibroblasts, and melanocytes. Comparative analysis of the resulting proteome profiles allowed us to select proteins specifically identified in one of the six cell types and not in any of the five others. Based on these results, we designated cell type-specific proteome signatures consisting each of six such characteristic proteins. These signatures independently reproduced well-known marker proteins already established for FACS analyses in addition to novel candidate marker proteins. We applied these signatures for the interpretation of proteome profiles obtained from the analyses of hepatocellular carcinoma-associated tissue homogenates and normal liver tissue homogenates. The identification of members of the above described signatures gave us an indication of the presence of characteristic cells in the diseased tissues and thus supported the interpretation of the proteomics data of these complex biological samples.

Unravelling the nuclear matrix proteome

The nuclear matrix (NM) model posits the presence of a protein/RNA scaffold that spans the mammalian nucleus. The NM proteins are involved in basic nuclear function and are a promising source of protein biomarkers for cancer. Importantly, the NM proteome is operationally defined as the proteins from cells and tissue that are extracted following a specific biochemical protocol; in brief, the soluble proteins and lipids, cytoskeleton, and chromatin elements are removed in a sequential fashion, leaving behind the proteins that compose the NM. So far, the NM has not been sufficiently verified as a biological entity and only preliminary at the molecular level. Here, we argue for a combined effort of proteomics, immunodetection and microscopy to unravel the composition and structure of the NM.

Proteomic and targeted analytical identification of BXDC1 and EBNA1BP2 as dynamic scaffold proteins in the nucleolus

The nuclear matrix has classically been assumed to be a solid structure coherently aligning nuclear components, but its real nature remains obscure. We separated the proteins in a ribonucleoprotein-containing nuclear matrix fraction of HeLa cells by reversed-phase HPLC followed by SDS-PAGE, and identified 83 proteins through peptide mass fingerprint (PMF) analysis. Many nucleolar proteins, classical nuclear matrix proteins, RNA binding proteins, cytoskeletal proteins and five uncharacterized proteins were identified in this fraction. Four of the latter proteins were localized to the cell nucleus, BXDC1 and EBNA1BP2 being especially localized to the nucleolus. Fluorescence recovery after photobleaching and RNAi knockdown analyses suggested that BXDC1 and EBNA1BP2 function in a dynamic scaffold for ribosome biogenesis.

Nuclear targeting of the growth hormone receptor results in dysregulation of cell proliferation and tumorigenesis

Growth hormone receptor (GHR) has been demonstrated to be nuclear localized both in vivo and in vitro, but the significance of this observation has remained elusive. Here we show that nuclear GHR is strongly correlated with proliferative status in vivo by using a liver regeneration model. In vitro, nuclear translocation of the GH receptor is GH-dependent and appears to be mediated by the Importin system. Constitutive nuclear targeting of GHR in murine pro-B cells is associated with constitutive activation of STAT5, a transforming agent in lymphoma and other cell types. This activation is abrogated by inhibition of JAK2 and appears to be driven by autocrine murine GH action coupled with enhanced nuclear uptake of phospho-STAT5. Nuclear targeting induces dysregulated cell cycle progression in the pro-B cell line, associated with constitutive up-regulation of the proliferation inducers Survivin and Mybbp, the metastasis related Dysadherin, and other tumor markers. GHR nuclear-targeted cells generate aggressive metastatic tumors when injected into nude mice, which display nuclear localized GHR strikingly similar to that seen in human lymphomas. We conclude that aberrant nuclear localization of GHR is a marker of high proliferative status and is sufficient to induce tumorigenesis and tumor progression.

Knowledge-based proteome profiling: Considering identified proteins to evaluate separation efficiency by 2-D PAGE

Proteome profiling techniques rely on the separation of proteins or peptides and their subsequent quantification. The reliability of this technique is still limited because a proteome profiling result does not necessarily represent the true protein composition of the analysed sample, thus seriously hampering proper data interpretation. Many experimentally observed proteome alterations are biologically not significant. It was the aim of this study to use the knowledge of the biological context of proteins in order to establish optimised proteome profiling protocols. While 2-D spot patterns of total cell protein fractions were found to poorly represent the true protein composition, purified subcellular protein fractions were found to better represent the protein composition of the analysed sample. The application of a standardised protocol to different kinds of cells revealed several striking observations. Firstly, the protein composition of cultured cells of various origins is very similar. Secondly, proteome alterations observed with the described protocols do make sense from a biologic point of view and may thus be considered as truly representative for the analysed samples. Thirdly, primary white blood cells isolated from different donors were found to show minor, but reproducible and significant individual differences. We designate the consideration of known properties of identified proteins in proteome profiles as a knowledge-based approach. The present data suggest that this approach may tremendously help to improve the applied techniques and assess the results. We demonstrate that the fulfilment of well-defined criteria of proteome profiles eventually results in reliable and biologically relevant data.

Correlations between scaffold/matrix attachment region (S/MAR) binding activity and DNA duplex destabilization energy

Scaffold or matrix-attachment regions (S/MARs) are thought to be involved in the organization of eukaryotic chromosomes and in the regulation of several DNA functions. Their characteristics are conserved between plants and humans, and a variety of biological activities have been associated with them. The identification of S/MARs within genomic sequences has proved to be unexpectedly difficult, as they do not appear to have consensus sequences or sequence motifs associated with them. We have shown that S/MARs do share a characteristic structural property, they have a markedly high predicted propensity to undergo strand separation when placed under negative superhelical tension. This result agrees with experimental observations, that S/MARs contain base-unpairing regions (BURs). Here, we perform a quantitative evaluation of the association between the ease of stress-induced DNA duplex destabilization (SIDD) and S/MAR binding activity. We first use synthetic oligomers to investigate how the arrangement of localized unpairing elements within a base-unpairing region affects S/MAR binding. The organizational properties found in this way are applied to the investigation of correlations between specific measures of stress-induced duplex destabilization and the binding properties of naturally occurring S/MARs. For this purpose, we analyze S/MAR and non-S/MAR elements that have been derived from the human genome or from the tobacco genome. We find that S/MARs exhibit long regions of extensive destabilization. Moreover, quantitative measures of the SIDD attributes of these fragments calculated under uniform conditions are found to correlate very highly (r2>0.8) with their experimentally measured S/MAR-binding strengths. These results suggest that duplex destabilization may be involved in the mechanisms by which S/MARs function. They suggest also that SIDD properties may be incorporated into an improved computational strategy to search genomic DNA sequences for sites having the necessary attributes to function as S/MARs, and even to estimate their relative binding strengths.

Inherent growth advantage of (pre)malignant hepatocytes associated with nuclear translocation of pro-transforming growth factor alpha

The pro-peptide of transforming growth factor alpha (proTGFalpha) was recently found in hepatocyte nuclei preparing for DNA replication, which suggests a role of nuclear proTGFalpha for mitogenic signalling. This study investigates whether the nuclear occurrence of the pro-peptide is involved in the altered growth regulation of (pre)malignant hepatocytes. In human hepatocarcinogenesis, the incidence of proTGFalpha-positive and replicating nuclei gradually increased from normal liver, to dysplastic nodules, to hepatocellular carcinoma. ProTGFalpha-positive nuclei almost always were in DNA synthesis. Also, in rat hepatocarcinogenesis, proTGFalpha-positive nuclei occurred in (pre)malignant hepatocytes at significantly higher incidences than in unaltered hepatocytes. For functional studies unaltered (GSTp(-)) and premalignant (GSTp(+)) rat hepatocytes were isolated by collagenase perfusion and cultivated. Again, DNA synthesis occurred almost exclusively in proTGFalpha-positive nuclei. GSTp(+) hepatocytes showed an approximately 3-fold higher frequency of proTGFalpha-positive nuclei and DNA replication than GSTp(-) cells. Treatment of cultures with the mitogen cyproterone acetate (CPA) elevated the incidence of proTGFalpha-positive nuclei and DNA synthesis in parallel. Conversely, transforming growth factor beta1 (TGFbeta1) lowered both. These effects of CPA and TGFbeta1 were significantly more pronounced in GSTp(+) than in GSTp(-) hepatocytes. In conclusion, nuclear translocation of proTGFalpha increases in the course of hepatocarcinogenesis and appears to be involved in the inherent growth advantage of (pre)malignant hepatocytes.

Lamin A and ZMPSTE24 (FACE-1) defects cause nuclear disorganization and identify restrictive dermopathy as a lethal neonatal laminopathy

Restrictive dermopathy (RD), also called tight skin contracture syndrome (OMIM 275210), is a rare disorder mainly characterized by intrauterine growth retardation, tight and rigid skin with erosions, prominent superficial vasculature and epidermal hyperkeratosis, facial features (small mouth, small pinched nose and micrognathia), sparse/absent eyelashes and eyebrows, mineralization defects of the skull, thin dysplastic clavicles, pulmonary hypoplasia, multiple joint contractures and an early neonatal lethal course. Liveborn children usually die within the first week of life. The overall prevalence of consanguineous cases suggested an autosomal recessive inheritance. We explored nine fetuses/newborns children with RD. Two were found to have an heterozygous splicing mutation in the LMNA gene, leading to the complete or partial loss of exon 11 in mRNAs encoding Lamin A and resulting in a truncated Prelamin A protein. Lamins are major constituents of the nuclear lamina, a filamentous meshwork underlying the inner nuclear envelope. In the other seven patients, a unique heterozygous insertion leading to the creation of a premature termination codon was identified in the gene ZMPSTE24, also known as FACE-1 in human. This gene encodes a metalloproteinase specifically involved in the post-translational processing of Lamin A precursor. In all patients carrying a ZMPSTE24 mutation, loss of expression of Lamin A as well as abnormal patterns of nuclear sizes and shapes and mislocalization of Lamin-associated proteins was evidenced. Our results indicate that a common pathogenetic pathway, involving defects of the nuclear lamina and matrix, is involved in all RD cases. RD is thus one of the most deleterious laminopathies identified so far in humans caused by (primary or secondary) A-type Lamin defects and nuclear structural and functional alterations.

Expression and functional significance of mouse paraspeckle protein 1 on spermatogenesis

Paraspeckle protein 1 (PSP1) in humans is a recently identified component protein of a novel nuclear body, paraspeckle. The protein has a DBHS (Drosophila behavior, human splicing) motif that is found in PSF and p54(nrb)/NonO proteins. These DBHS-containing proteins have been reported to be involved in various nuclear events such as DNA replication, transcription, and mRNA processing. Here we show that mouse paraspeckle protein 1 (mPSP1; encoded by the Pspc1 gene) has two isoforms with different C-termini lengths. Abundant expression of the longer isoform (mPSP1-alpha) and the shorter one (mPSP1-beta) were observed in testis and kidney, respectively. Transiently expressed mPSP1-alpha was localized in nuclei, but mPSP1-beta was localized in both nuclei and cytoplasm. These observations suggest that alternative splicing regulates tissue distribution and subcellular localization. Like other DBHS-containing proteins, mPSP1 has RNA-binding activity. In mouse testis, mPSP1-alpha was found in the nuclear matrix fraction. Furthermore, by coimmunoprecipitation, we confirmed that mPSP1 interacts with other DBHS-containing proteins, PSF and p54(nrb)/NonO. Therefore, we conclude that mPSP1 may regulate multiple phases of important nuclear events during spermatogenesis.

Analysis of the Arabidopsis nuclear proteome and its response to cold stress

The nucleus is the subcellular organelle that contains nearly all the genetic information required for the regulated expression of cellular proteins. In this study, we comprehensively characterized the Arabidopsis nuclear proteome. Nuclear proteins were isolated and analyzed using two-dimensional (2D) gel electrophoresis and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Approximately 500-700 spots were detected in reference 2D gels of nuclear proteins. Proteomic analyses led to the identification of 184 spots corresponding to 158 different proteins implicated in a variety of cellular functions. We additionally analyzed the changes in the nuclear proteome in response to cold stress. Of the 184 identified proteins, 54 were up- or downregulated with a greater than twofold change in response to cold treatment. Among these, six proteins were selected for further characterization. Northern analysis data revealed that gene expression of these proteins was also altered by cold stress. Following transient expression in BY-2 protoplasts, two proteins were detected in both the cytoplasm and the nucleus and four others were detected exclusively in the nucleus, which correlates well with the nuclear localization patterns of the proteomic data. Our study provides an initial insight into the Arabidopsis nuclear proteome and its response to cold stress.

A proteomic study of the arabidopsis nuclear matrix

The eukaryotic nucleus has been proposed to be organized by two interdependent nucleoprotein structures, the DNA-based chromatin and the RNA-dependent nuclear matrix. The functional composition and molecular organization of the second component have not yet been resolved. Here, we describe the isolation of the nuclear matrix from the model plant Arabidopsis, its initial characterization by confocal and electron microscopy, and the identification of 36 proteins by mass spectrometry. Electron microscopy of resinless samples confirmed a structure very similar to that described for the animal nuclear matrix. Two-dimensional gel electrophoresis resolved approximately 300 protein spots. Proteins were identified in batches by ESI tandem mass spectrometry after resolution by 1D SDS-PAGE. Among the identified proteins were a number of demonstrated or predicted Arabidopsis homologs of nucleolar proteins such as IMP4, Nop56, Nop58, fibrillarins, nucleolin, as well as ribosomal components and a putative histone deacetylase. Others included homologs of eEF-1, HSP/HSC70, and DnaJ, which have also been identified in the nucleolus or nuclear matrix of human cells, as well as a number of novel proteins with unknown function. This study is the first proteomic approach towards the characterization of a higher plant nuclear matrix. It demonstrates the striking similarities both in structure and protein composition of the operationally defined nuclear matrix across kingdoms whose unicellular ancestors have separated more than one billion years ago.

Proteomic analysis of nuclear proteins from proliferative and differentiated human colonic intestinal epithelial cells

Self-renewing tissues such as the intestine contain progenitor proliferating cells which subsequently differentiate. Cell proliferation and differentiation involve gene regulation processes which take place in the nucleus. A human intestinal epithelial cell line model (Caco2/TC7) which reproduces these dynamic processes has been used to perform proteomic studies on nuclear proteins. Nuclei from Caco2/TC7 cells at proliferative and differentiated stages were purified by subcellular fractionation. After two-dimensional gel electrophoresis separation and ruthenium staining, 400 protein spots were detected by image analysis. Eighty-five spots corresponding to 60 different proteins were identified by matrix-assisted laser desorption/ionization mass spectrometry in nuclei from proliferative cells. Comparison of nuclear proteomes from proliferative or differentiated cells by differential display resulted in the identification of differentially expressed proteins such as nucleolin, hnRNP A2/B1 and hnRNP A1. By using Western blot analysis, we found that the expression and number of specific isoforms of these nuclear proteins decreased in differentiated cells. Immunocytochemistry experiments also showed that in proliferative cells nucleolin was distributed in nucleoli-like bodies. In contrast, hnRNPs A2/B1 and A1 were dispersed throughout the nucleus. This study of the nuclear proteome from intestinal epithelial cells represents the first step towards the establishment of a protein database which will be a valuable resource in future studies on the differential expression of nuclear proteins in response to physiological, pharmacological and pathological modulations.

Interaction in vitro of type III intermediate filament proteins with Z-DNA and B-Z-DNA junctions

The selection of DNA fragments containing simple d(GT)(n) and composite d(GT)(m). d(GA)(n) microsatellites during affinity binding of mouse genomic DNA to type III cytoplasmic intermediate filaments (cIFs) in vitro, and the detection of such repeats, often as parts of nuclear matrix attachment region (MAR)-like DNA, in SDS-stable DNA-vimentin crosslinkage products isolated from intact fibroblasts, prompted a detailed study of the interaction of type III cIF proteins with left-handed Z-DNA formed from d(GT)(17) and d(CG)(17) repeats under the topological tension of negatively supercoiled plasmids. Although d(GT)(n) tracts possess a distinctly lower Z-DNA-forming potential than d(CG)(n) tracts, the filament proteins produced a stronger electrophoretic mobility shift with a plasmid carrying a d(GT)(17) insert than with plasmids containing different d(CG)(n) inserts, consistent with the facts that the B-Z transition of d(GT)(n) repeats requires a higher negative superhelical density than that of d(CG)(n) repeats and the affinity of cIF proteins for plasmid DNA increases with its superhelical tension. That both types of dinucleotide repeat had indeed undergone B-Z transition was confirmed by S1 nuclease and chemical footprinting analysis of the plasmids, which also demonstrated efficient protection by cIF proteins from nucleolytic and chemical attack of the Z-DNA helices as such, as well as of the flanking B-Z junctions. The analysis also revealed sensibilization of nucleotides in the center of one of the two strands of a perfect d(CG)(17) insert toward S1 nuclease, indicating cIF protein-induced bending of the repeat. In all these assays, vimentin and glial fibrillary acidic protein (GFAP) showed comparable activities, versus desmin, which was almost inactive. In addition, vimentin and GFAP exhibited much higher affinities for the Z-DNA conformation of brominated, linear d(CG)(25) repeats than for the B-DNA configuration of the unmodified oligonucleotides. While double-stranded DNA was incapable of chasing the Z-DNA from its protein complexes, and Holliday junction and single-stranded (ss)DNA were distinguished by reasonable competitiveness, phosphatidylinositol (PI) and, particularly, phosphatidylinositol 4,5-diphosphate (PIP(2)) turned out to be extremely potent competitors. Because PIP(2) is an important member of the nuclear PI signal transduction cascade, it might exert a regulatory influence on the binding of cIF proteins to Z- and other DNA conformations. From this interaction of cIF proteins with Z- and bent DNA and their previously detected affinities for MAR-like, ss, triple helical, and four-way junction DNA, it may be concluded that the filament proteins play a general role in such nuclear matrix-associated processes as DNA replication, recombination, repair, and transcription.

Proto-oncoprotein TLS/FUS is associated to the nuclear matrix and complexed with splicing factors PTB, SRm160, and SR proteins

TLS/FUS is a nucleic acid-binding protein whose N-terminal half functions as a transcriptional activator domain in fusion oncoproteins found in human leukemias and liposarcomas. Previous reports have suggested a role for TLS/FUS in transcription and splicing processes. Here we report the association of TLS/FUS with the nuclear matrix and investigate its role in splicing. Splicing of two pre-mRNAs was inhibited in a TLS/FUS-immunodepleted extract and could only be partly restored by addition of recombinant TLS/FUS or/and SR proteins, known interaction partners of TLS/FUS. The subsequent analysis of TLS/FUS immunoprecipitates revealed that, in addition to the SR proteins SC35 and SRp75, the splicing factor PTB (hnRNPI) and the splicing coactivator SRm160 are complexed with TLS/FUS, thus explaining the inability to restore splicing completely. Coimmunolocalization confirmed the nuclear matrix association and interaction of TLS/FUS with PTB, SR proteins, and SRm160. Our results suggest that the matrix protein TLS/FUS plays a role in spliceosome assembly.

Functional proteomic analysis of human nucleolus

The notion of a "plurifunctional" nucleolus is now well established. However, molecular mechanisms underlying the biological processes occurring within this nuclear domain remain only partially understood. As a first step in elucidating these mechanisms we have carried out a proteomic analysis to draw up a list of proteins present within nucleoli of HeLa cells. This analysis allowed the identification of 213 different nucleolar proteins. This catalog complements that of the 271 proteins obtained recently by others, giving a total of approximately 350 different nucleolar proteins. Functional classification of these proteins allowed outlining several biological processes taking place within nucleoli. Bioinformatic analyses permitted the assignment of hypothetical functions for 43 proteins for which no functional information is available. Notably, a role in ribosome biogenesis was proposed for 31 proteins. More generally, this functional classification reinforces the plurifunctional nature of nucleoli and provides convincing evidence that nucleoli may play a central role in the control of gene expression. Finally, this analysis supports the recent demonstration of a coupling of transcription and translation in higher eukaryotes.

Formation of nuclear matrix filaments by p27(BBP)/eIF6

p27(BBP)/eIF6 is an evolutionarily conserved protein necessary for ribosome biogenesis which was cloned in mammals for its ability to bind the cytodomain of beta 4 integrin. In cultured cells, a conspicuous fraction of p27(BBP)/eIF6 is associated with the intermediate filaments/nuclear matrix (IF/NM) cytoskeleton. The mechanism of this association is not known. Here we show that in epidermis p27(BBP)/eIF6 is naturally associated with IF/NM. To analyze the intrinsic capability of p27(BBP)/eIF6 to generate cytoskeletal networks, the properties of the pure, recombinant, untagged protein were studied. Recombinant p27(BBP)/eIF6 binds beta 4 integrin. Upon dialysis against IF buffer, p27(BBP)/eIF6 forms polymers which, strikingly, have a morphology identical to NM filaments. Cross-linking experiments suggested that polymerization is favored by the formation of disulphide bridges. These data suggest that p27(BBP)/eIF6 is associated with the cytoskeleton, and contributes to formation of NM filaments. These findings help to settle the controversy on nuclear matrix.

Concomitant determination of absolute values of cellular protein amounts, synthesis rates, and turnover rates by quantitative proteome profiling

Two-dimensional gel electrophoresis of protein fractions isolated from (35)S-radiolabeled cells provides qualitative information on intracellular amounts, (35)S incorporation rates, protein modifications, and subcellular localizations of up to thousands of individual proteins. In this study we extended proteome profiling to provide quantitative data on synthesis rates of individual proteins. We combined fluorescence detection of radiolabeled proteins with SYPRO ruby(TM) staining and subsequent autoradiography of the same gels, thereby quantifying protein amounts and (35)S incorporation. To calibrate calculation of absolute synthesis rates, we determined the amount and autoradiograph intensity of radiolabeled haptoglobin secreted by interleukin-6 pretreated HepG2 cells. This allowed us to obtain a standard calibration value for (35)S incorporation per autoradiograph intensity unit. This value was used to measure protein synthesis rates during time course experiments of heat-shocked U937 cells. We measured the increasing amounts of hsp70 and calculated it by integration of the determined hsp70 synthesis rates over time. Similar results were obtained by both methods, validating our standardization procedure. Based on the assumption that the synthesis rate of proteins in a steady state of cell metabolism would essentially compensate protein degradation, we calculated biological half-lives of proteins from protein amounts and synthesis rates determined from two-dimensional gels. Calculated protein half-lives were found close to those determined by pulse-chase experiments, thus validating this new method. In conclusion, we devised a method to assess quantitative proteome profiles covering determination of individual amounts, synthesis, and turnover rates of proteins.

Proteome analysis of nuclear matrix proteins during apoptotic chromatin condensation

The nuclear matrix (NM) is considered a proteinaceous scaffold spatially organizing the interphase nucleus, the integrity of which is affected during apoptosis. Caspase-mediated degradation of NM proteins, such as nuclear lamins, precedes apoptotic chromatin condensation (ACC). Nevertheless, other NM proteins remain unaffected, which most likely maintain a remaining nuclear structure devoid of chromatin. We, therefore, screened various types of apoptotic cells for changes of the nuclear matrix proteome during the process of apoptotic ACC. Expectedly, we observed fundamental alterations of known chromatin-associated proteins, comprising both degradation and translocation to the cytosol. Importantly, a consistent set of abundant NM proteins, some (e.g. hNMP 200) of which displaying structural features, remained unaffected during apoptosis and might therefore represent constituents of an elementary scaffold. In addition, proteins involved in DNA replication and DNA repair were found accumulated in the NM fraction before cells became irreversibly committed to ACC, a time point characterized in detail by inhibitor studies with orthovanadate. In general, protein alterations of a consistent set of NM proteins (67 of which were identified), were reproducibly detectable in Fas-induced Jurkat cells, in UV-light treated U937 cells and also in staurosporine-treated HeLa cells. Our data indicate that substantial alterations of proteins linking chromatin to an elementary nuclear protein scaffold might play an intriguing role for the process of ACC.

A novel mechanism for mitogenic signaling via pro-transforming growth factor alpha within hepatocyte nuclei

Transforming growth factor (TGF) alpha, an important mediator of growth stimulation, is known to act via epidermal growth factor receptor (EGF-R) binding in the cell membrane. Here we show by immunohistology, 2-dimensional immunoblotting, and mass spectrometry of nuclear fractions that the pro-protein of wild-type TGF-alpha occurs in hepatocyte nuclei of human, rat, and mouse liver. Several findings show a close association between nuclear pro-TGF-alpha and DNA synthesis. (1) The number of pro-TGF-alpha+ nuclei was low in resting liver and increased dramatically after partial hepatectomy and after application of hepatotoxic chemicals or the primary mitogen cyproterone acetate (CPA); in any case, S phase occurred almost exclusively in pro-TGF-alpha+ nuclei. The same was found in human cirrhotic liver. (2) In primary culture, 7% of hepatocytes synthesized pro-TGF-alpha, which then translocated to the nucleus; 70% of these nuclei subsequently entered DNA replication, whereas only 2% of pro-TGF-alpha- hepatocytes were in S phase. (3) The frequency of hepatocytes coexpressing pro-TGF-alpha and DNA synthesis was increased by the hepatomitogens CPA or prostaglandin E(2) and was decreased by the growth inhibitor TGF-beta1. (4) Treatment with mature TGF-alpha increased DNA synthesis exclusively in pro-TGF-alpha- hepatocytes, which was abrogated by the EGF-R tyrosine kinase inhibitor tyrphostin A25. In conclusion, TGF-alpha gene products may exert mitogenic effects in hepatocytes via 2 different signaling mechanisms: (1) the "classic" pathway of mature TGF-alpha via EGF-R in the membrane and (2) a novel pathway involving the presence of pro-TGF-alpha in the nucleus.

Applied proteomics: mitochondrial proteins and effect on function

The identification of a majority of the polypeptides in mitochondria would be invaluable because they play crucial and diverse roles in many cellular processes and diseases. The endogenous production of reactive oxygen species (ROS) is a major limiter of life as illustrated by studies in which the transgenic overexpression in invertebrates of catalytic antioxidant enzymes results in increased lifespans. Mitochondria have received considerable attention as a principal source---and target---of ROS. Mitochondrial oxidative stress has been implicated in heart disease including myocardial preconditioning, ischemia/reperfusion, and other pathologies. In addition, oxidative stress in the mitochondria is associated with the pathogenesis of Alzheimer's disease, Parkinson's disease, prion diseases, and amyotrophic lateral sclerosis (ALS) as well as aging itself. The rapidly emerging field of proteomics can provide powerful strategies for the characterization of mitochondrial proteins. Current approaches to mitochondrial proteomics include the creation of detailed catalogues of the protein components in a single sample or the identification of differentially expressed proteins in diseased or physiologically altered samples versus a reference control. It is clear that for any proteomics approach prefractionation of complex protein mixtures is essential to facilitate the identification of low-abundance proteins because the dynamic range of protein abundance within cells has been estimated to be as high as 10(7). The opportunities for identification of proteins directly involved in diseases associated with or caused by mitochondrial dysfunction are compelling. Future efforts will focus on linking genomic array information to actual protein levels in mitochondria.

Cytoplasmic intermediate filaments are stably associated with nuclear matrices and potentially modulate their DNA-binding function

The tight association of cytoplasmic intermediate filaments (cIFs) with the nucleus and the isolation of crosslinkage products of vimentin with genomic DNA fragments, including nuclear matrix attachment regions (MARs) from proliferating fibroblasts, point to a participation of cIFs in nuclear activities. To test the possibility that cIFs are complementary nuclear matrix elements, the nuclei of a series of cultured cells were subjected to the Li-diiodosalicylate (LIS) extraction protocol developed for the preparation of nuclear matrices and analyzed by immunofluorescence microscopy and immunoblotting with antibodies directed against lamin B and cIF proteins. When nuclei released from hypotonically swollen L929 suspension cells in the presence of digitonin or Triton X-100 were exposed to such strong shearing forces that a considerable number were totally disrupted, a thin, discontinuous layer of vimentin IFs remained tenaciously adhering to still intact nuclei, in apparent coalignment with the nuclear lamina. Even in broken nuclei, the distribution of vimentin followed that of lamin B in areas where the lamina still appeared intact. The same retention of vimentin together with desmin and glial IFs was observed on the nuclei isolated from differentiating C2C12 myoblast and U333 glioma cells, respectively. Nuclei from epithelial cells shed their residual perinuclear IF layers as coherent cytoskeletal ghosts, except for small fractions of vimentin and cytokeratin IFs, which remained in a dot-to cap-like arrangement on the nuclear surface, in apparent codistribution with lamin B. LIS extraction did not bring about a reduction in the cIF protein contents of such nuclei upon their transformation into nuclear matrices. Moreover, in whole mount preparations of mouse embryo fibroblasts, DNA/chromatin emerging from nuclei during LIS extraction mechanically and chemically cleaned the nuclear surface and perinuclear area from loosely anchored cytoplasmic material with the production of broad, IF-free annular spaces, but left substantial fractions of the vimentin IFs in tight association with the nuclear surface. Accordingly, double-immunogold electron microscopy of fixed and permeabilized fibroblasts disclosed a close neighborhood of vimentin IFs and lamin B, with a minimal distance between the nanogold particles of ca. 30 nm. These data indicate an extremely solid interconnection of cIFs with structural elements of the nuclear matrix, and make them, together with their susceptibility to crosslinkage to MARs and other genomic DNA sequences under native conditions, complementary or even integral constituents of the karyoskeleton.

The Fas-induced apoptosis analyzed by high throughput proteome analysis

The fate of cytosolic proteins was studied during Fas-induced cell death of Jurkat T-lymphocytes by proteome analysis. Among 1000 spots resolved in two-dimensional gels, comparison of control versus apoptotic cells revealed that the signal intensity of 19 spots decreased or even disappeared, whereas 38 novel spots emerged. These proteins were further analyzed with respect to de novo protein synthesis, phosphorylation status, and intracellular localization by metabolic labeling and analysis of subcellular protein fractions in combination with two-dimensional Western blots and mass spectrometry analysis of tryptic digests. We found that e.g. hsp27, hsp70B, calmodulin, and H-ras synthesis was induced upon Fas signaling. 34 proteins were affected by dephosphorylation (e.g. endoplasmin) and phosphorylation (e.g. hsc70, hsp57, and hsp90). Nuclear annexin IV translocated to the cytosol, whereas decreasing cytosolic TCP-1alpha became detectable in the nucleus. In addition, degradation of 12 proteins was observed; among them myosin heavy chain was identified as a novel caspase target. Fas-induced proteome alterations were compared with those of other cell death inducers, indicating specific physiological characteristics of different cell death mechanisms, consequent to as well as independent of caspase activation. Characteristic proteome alterations of apoptotic cells at early time points were found reminiscent of those of malignant cells in vivo.

hNMP 200: a novel human common nuclear matrix protein combining structural and regulatory functions

Previously we have reported about human nuclear matrix proteins (hNMPs) with increased reassembling and potential filament-forming capability [C. Gerner et al., 1999, J. Cell. Biochem. 74, 145-151]. Here, we cloned the cDNA of one of these proteins, hNMP 200, following partial amino acid sequencing of the novel 56-kDa nuclear protein. Sequence alignments show hNMP 200-related proteins in metazoans, plants, and yeast, the homologous Saccharomyces cerevisiae protein prp19 being an accessory, but essential, factor for pre-mRNA processing. Evidence for any enzymatic activity was not detected. However, the hNMP 200 primary sequence contained five consensus WD-repeat sequences, indicative of participation and regulatory function in larger protein assemblies. Northern blot analysis and 2D protein electrophoresis showed ubiquitous expression of hNMP 200 in a variety of cell types. (35)S labeling studies indicated a high metabolic stability of the protein. The hNMP 200 gene was assigned to chromosomal region 11q12.2. Confocal laser scanning microscopy revealed that the intracellular localization conformed with that reported for other structural nuclear proteins. In interphase cells, green fluorescent protein-tagged hNMP 200 was predominantly nucleoplasmic. Structures with speckled appearance extended through several sections of in situ-isolated nuclear matrices. During cell division hNMP 200 became irregularly distributed in prophase, sparing regions of condensing chromatin. In anaphase it was concentrated in the spindle midzone. The putative dual function of the novel NMP is discussed. Being a component of the nuclear framework, it may provide structural support for components of the RNA-processing machinery, thereby also modulating splicing activities.

Caspase-mediated cleavage of the chromosome-binding domain of lamina-associated polypeptide 2 alpha

Lamina-associated polypeptide 2 alpha (LAP2 alpha) is a non-membrane-bound isoform of the LAP2 family involved in nuclear structure organization. Using various cell systems, including Jurkat, HL-60, and HeLa cells, and different death-inducing agents, such as anti-Fas antibody, topoisomerase inhibitors, and staurosporine, we found that LAP2 alpha was cleaved during apoptosis as rapidly as lamin B in a caspase-dependent manner yielding stable N- and C-terminal fragments of approximately 50 and 28 kDa, respectively. Based on fragment size and localization of immunoreactive epitopes, four potential cleavage sites were mapped between amino acids 403–485. These sites were located within a domain that has previously been described to be essential and sufficient for association of LAP2 alpha with chromosomes, suggesting that LAP2 alpha cleavage impairs its chromatin-binding properties. Immunofluorescence microscopy demonstrated that, unlike full length protein, apoptotic fragments did not colocalize with condensed chromatin, but remained in the nuclear compartment as long as a single nucleus was visible. Subfractionation analyses showed that the N-terminal LAP2 alpha fragment was extracted from intranuclear structures in detergent/salt buffers, whereas the C-terminal fragment remained associated with a residual framework devoid of chromatin. Our data suggest that early cleavage of LAP2 alpha) is important for chromatin reorganization during apoptosis.

Proteomics meets cell biology: the establishment of subcellular proteomes

Proteome research aims to unravel the biological complexity encoded by the genome. Due to the complexity of higher eukaryotic cells, single-step characterization of a proteome is likely to be difficult to achieve. However, advantage can be taken of the macromolecular architecture of a cell, e.g., subcellular compartments, organelles, macromolecular structures and multiprotein complexes, to establish subcellular proteomes. This review highlights recent developments in this area of proteomics, namely the establishment of two-dimensional electrophoresis (2-DE) reference maps of subcellular compartments and organelles as well as the characterization of macromolecular structures and multiprotein complexes using a proteomics approach.

The establishment of a human liver nuclei two-dimensional electrophoresis reference map

This short communication describes the establishment of a two-dimensional electrophoresis (2-DE) reference map of nuclear proteins isolated from human liver. The human liver nuclei 2-DE reference map contains 1497 spots. In an initial identification study using peptide mass fingerprinting as a means of protein identification we were able to identify 26 spots corresponding to 15 different proteins. The human liver nuclei 2-DE reference map is now included in the SWISS-2DPAGE database, which can be accessed through the ExPASy server (http://www.expasy.ch/ch2d/).

The fate of the nuclear matrix-associated-region-binding protein SATB1 during apoptosis

Special AT-rich sequence-binding protein 1 (SATB1), predominantly expressed in thymocytes, was identified as a component of the nuclear matrix protein fraction. Programmed cell death of Jurkat T-cells was induced by various stimuli in Fas-dependent and -independent fashion. During apoptosis, but not during necrosis, SATB1 was cleaved, as rapidly as was lamin B, in a caspase-dependent way yielding a stable 70 kDa fragment. The same result was obtained for apoptotic HL60-cells. We constructed various deletion constructs of SATB1, expressing protein chimeras tagged with green fluorescent protein (GFP). Transient transfection of these into Jurkat or HeLa cells followed by initiation of apoptosis allowed us to map the potential caspase-6 cleavage site VEMD to the N-terminal third of SATB1, leaving an intact DNA-binding domain in the C-terminal part of the protein. Our results suggest that apoptosis-specific breakdown of SATB1, a transcriptional activator of the CD8a gene, might be of physiological relevance during thymic clonal deletion and apoptosis of peripheral T-lymphoid cells.

Better approaches to finding the needle in a haystack: optimizing proteome analysis through automation

Recent evidence has demonstrated a lack of correlation between transcriptional profiles and actual protein levels in cells. Proteome analysis has therefore become indispensable and complementary to genomic analysis for an accurate picture of cellular metabolism. Although proteomics is a relatively young discipline, technology for increasing throughput in proteomic projects is rapidly being developed. The operating paradigm in proteome analysis today is a combination of two-dimensional (2-D) gel electrophoresis (for protein resolution) with mass spectrometry (for protein identification). All the intermediary steps in the procedure including gel staining, image analysis, protein spot excision, digestion and mass spectrometry can be automated to increase efficiency and save time. This report reviews the current state of the proteomics technology and discusses approaches to enhance the sensitivity of 2-D gels with fractionation techniques.

A method to produce Ponceau replicas from blots: application for Western analysis

We describe a fast and simple method to produce print-quality like Ponceau replicas from blots. These have many applications for Western analysis, primarily to alleviate localization of antigens in complex protein patterns generated by two-dimensional electrophoresis.

A human common nuclear matrix protein homologous to eukaryotic translation initiation factor 4A

Amino acid sequencing and mass spectrometry revealed identity of a human nuclear matrix protein, termed hNMP 265, with a predicted protein of gene KIAA0111. Two-dimensional electrophoresis and Northern hybridization showed the protein to ubiquitously occur in various human cell types. Exhibiting DEAD-box motifs characteristic for RNA helicases, hNMP 265 is highly similar to the human initiation factors eIF4A-I and -II. On the other hand, hNMP 265 greatly differs from the initiation factors by a N-terminal sequence rich in charged amino acids. Sequence searches and alignments indicate proteins related to hNMP 265 in other eukaryotes. Chimeras between hNMP 265 and green fluorescence protein or hapten appeared as speckles in extranucleolar regions in the nucleus, but not in the cytoplasm. Experiments with tagged deletion mutants indicated that the N-terminal amino acid sequence is necessary for nuclear localization. A putative role of hNMP 265 in pre-mRNA processing is discussed.