A method for the rapid isolation of nuclear membranes from rat liver. Characterisation of the membrane preparation and its associated DNA polymerase

A general method for quantitative fractionation of mammalian cells

Subcellular fractionation in combination with mass spectrometry-based proteomics is a powerful tool to study localization of key proteins in health and disease. Here we offered a reliable and rapid method for mammalian cell fractionation, tuned for such proteomic analyses. This method proves readily applicable to different cell lines in which all the cellular contents are accounted for, while maintaining nuclear and nuclear envelope integrity. We demonstrated the method's utility by quantifying the effects of a nuclear export inhibitor on nucleoplasmic and cytoplasmic proteomes.

Measuring Inaccessible Chromatin Genome-Wide Using Protect-seq

Chromatin accessibility has been an immensely powerful metric for identifying and understanding regulatory elements in the genome. Many important regulatory elements, such as enhancers and transcriptional start sites, are characterized by "open" or nucleosome-free regions. Understanding the areas of the genome that are not considered open chromatin has been more difficult. Protect-seq is a genomics technique that aims to identify inaccessible chromatin associated with the nuclear periphery. These regions are enriched for histone modifications associated with transcriptional repression and correlate with loci identified by other techniques measuring heterochromatin and peripheral localization. Here, we discuss the protocol and best practices to perform Protect-seq.

Computational analyses reveal spatial relationships between nuclear pore complexes and specific lamins

Nuclear lamin isoforms form fibrous meshworks associated with nuclear pore complexes (NPCs). Using datasets prepared from subpixel and segmentation analyses of 3D-structured illumination microscopy images of WT and lamin isoform knockout mouse embryo fibroblasts, we determined with high precision the spatial association of NPCs with specific lamin isoform fibers. These relationships are retained in the enlarged lamin meshworks of Lmna-/- and Lmnb1-/- fibroblast nuclei. Cryo-ET observations reveal that the lamin filaments composing the fibers contact the nucleoplasmic ring of NPCs. Knockdown of the ring-associated nucleoporin ELYS induces NPC clusters that exclude lamin A/C fibers but include LB1 and LB2 fibers. Knockdown of the nucleoporin TPR or NUP153 alters the arrangement of lamin fibers and NPCs. Evidence that the number of NPCs is regulated by specific lamin isoforms is presented. Overall the results demonstrate that lamin isoforms and nucleoporins act together to maintain the normal organization of lamin meshworks and NPCs within the nuclear envelope.

The Quest for the Blueprint of the Nuclear Pore Complex

During my postdoc interview in June of 1998, I asked Günter why he was moving more towards the nucleus in his latest studies. He said, "Well Joe, that's where everything starts." By the end of the interview, I accepted the postdoc. He had a way of making everything sound so cool. Günter's progression was natural, since the endoplasmic reticulum and the nucleus are the only organelles that share the same membrane. The nuclear envelope extends into a double membrane system with nuclear pore complexes embedded in the pore membrane openings. Even while writing this review, I remember Günter stressing; it is the nuclear pore complex. Just saying nuclear pore doesn't encompass the full magnitude of its significance. The nuclear pore complex is one of the largest collection of proteins that fit together for an overall function: transport. This review will cover the Blobel lab contributions in the quest for the blueprint of the nuclear pore complex from isolation of the nuclear envelope and nuclear lamin to the ring structures.

LAP2 Proteins Chaperone GLI1 Movement between the Lamina and Chromatin to Regulate Transcription

Understanding transcription factor navigation through the nucleus remains critical for developing targeted therapeutics. The GLI1 transcription factor must maintain maximal Hedgehog pathway output in basal cell carcinomas (BCCs), and we have previously shown that resistant BCCs increase GLI1 deacetylation through atypical protein kinase Cι/λ (aPKC) and HDAC1. Here we identify a lamina-associated polypeptide 2 (LAP2) isoform-dependent nuclear chaperoning system that regulates GLI1 movement between the nuclear lamina and nucleoplasm to achieve maximal activation. LAP2β forms a two-site interaction with the GLI1 zinc-finger domain and acetylation site, stabilizing an acetylation-dependent reserve on the inner nuclear membrane (INM). By contrast, the nucleoplasmic LAP2α competes with LAP2β for GLI1 while scaffolding HDAC1 to deacetylate the secondary binding site. aPKC functions to promote GLI1 association with LAP2α, promoting egress off the INM. GLI1 intranuclear trafficking by LAP2 isoforms represents a powerful signal amplifier in BCCs with implications for zinc finger-based signal transduction and therapeutics.

Isolation and preliminary characterization of herpes simplex virus 1 primary enveloped virions from the perinuclear space

Herpes simplex virus 1 (HSV-1) nucleocapsids exit the nucleus by budding into the inner nuclear membrane, where they exist briefly as primary enveloped virions. These virus particles subsequently fuse their envelopes with the outer nuclear membrane, permitting nucleocapsids to then enter the cytoplasm and complete assembly. We have developed a method to isolate primary enveloped virions from HSV-1-infected cells and subjected the primary enveloped virion preparation to MALDI-MS/MS (matrix-assisted laser desorption ionization-tandem mass spectrometry) analyses. We identified most capsid proteins, a tegument protein (VP22), a glycoprotein (gD), and a cellular protein (annexin A2) in the primary enveloped virion preparation. We determined that annexin A2 does not play an essential role in infection under our experimental conditions. Elucidating the structure and biochemical properties of this unique virus assembly intermediate will provide new insights into HSV-1 biology.

Isolation of nuclei and nuclear membranes from animal tissues

The vast majority of methods for the isolation of nuclei and nuclear membranes use soft mammalian tissues (particularly rat liver) as the biological source; however, the protocols described in this unit should be applicable generally to any tissue type, cultured cells, or cells of lower eukaryotes or plants, so long as a suitable homogenization method is available. Generally, a buffered isoosmotic medium containing KCl and MgCl2 is used to stabilize the nuclei of mammalian tissues. Some of the media used for cultured animal cells and nonmammalian sources are also described. After homogenization the nuclei are purified using a sucrose barrier of 2.3 M. The use of OptiPrep overcomes the viscosity and osmolarity problems associated with the use of high molarity sucrose, and it permits the use of a high-speed centrifuge and much shorter centrifugation times. OptiPrep is also used isolate plant cell (i.e., wheat germ) nuclei, because it is able to resolve nuclei from the denser starch granules.

Isolation and fractionation of rat liver nuclear envelopes and nuclear pore complexes

The nuclear envelope is a double lipid bilayer that physically separates the functions of the nucleus and the cytoplasm of eukaryotic cells. Regulated transport of molecules between the nucleus and the cytoplasm is essential for normal cell metabolism and is mediated by large protein complexes, termed nuclear pore complexes (NPCs), which span the inner and outer membranes of the nuclear envelope. Significant progress has been made in the past 10 years in identifying the protein composition of NPCs and the basic molecular mechanisms by which these complexes facilitate the selective exchange of molecules between the nucleus and the cytoplasm. However, many fundamentally important questions about the functions of NPCs, the specific functions of individual NPC-associated proteins, and the assembly and disassembly of NPCs, remain unanswered. This review describes approaches for isolating and characterizing nuclear envelopes and NPC-associated proteins from mammalian cells. It is anticipated that these procedures can be used as a starting point for further molecular and biochemical analysis of the mammalian nuclear envelope, NPCs, and NPC-associated proteins.

Identification of Li+ binding sites and the effect of Li+ treatment on phospholipid composition in human neuroblastoma cells: a 7Li and 31P NMR study

Li(+) binding in subcellular fractions of human neuroblastoma SH-SY 5 Y cells was investigated using (7)Li NMR spin-lattice (T(1)) and spin-spin (T(2)) relaxation measurements, as the T(1)/T(2) ratio is a sensitive parameter of Li(+) binding. The majority of Li(+) binding occurred in the plasma membrane, microsomes, and nuclear membrane fractions as demonstrated by the Li(+) binding constants and the values of the T(1)/T(2) ratios, which were drastically larger than those observed in the cytosol, nuclei, and mitochondria. We also investigated by (31)P NMR spectroscopy the effects of chronic Li(+) treatment for 4--6 weeks on the phospholipid composition of the plasma membrane and the cell homogenate and found that the levels of phosphatidylinositol and phosphatidylserine were significantly increased and decreased, respectively, in both fractions. From these observations, we propose that Li(+) binding occurs predominantly to membrane domains, and that chronic Li(+) treatment alters the phospholipid composition at these membrane sites. These findings support those from clinical studies that have indicated that Li(+) treatment of bipolar patients results in irregularities in Li(+) binding and phospholipid metabolism. Implications of our observations on putative mechanisms of Li(+) action, including the cell membrane abnormality, the inositol depletion and the G-protein hypotheses, are discussed.

p44/42ERK1/2 MAPK and PLD activation by PGD2 preserves papillary phosphatidylcholine homeostasis

Previous works from our laboratory demonstrated that PGD(2) modulates phosphatidylcholine (PC) biosynthesis in renal papillary tissue. In the present work, we have evaluated the mechanism by which PGD(2) exerts this action. PGD(2) caused two stimulatory waves in PC synthesis which were reproduced by its full-agonist BW245C. At 1min stimulation, PGD(2) increased PC synthesis by 131%; this increase was blocked by neomycin and ethanol, cheleritrine and U0126, PLD, PKC, and MEK1/2 inhibitors, respectively. A second PC synthesis increase (100%) was observed after 15min, which was blocked by PLD inhibitors. PGD(2) also increased phospho-ERK1/2 MAPK in a biphasic-fashion, which was abolished by PLC and PKC inhibitors but not by ethanol, which overincreased phospho-ERK1/2, suggesting that PGD(2)-induced ERK1/2 activation requires previous PLC-PKC activation while PLD down-regulates it. Our results indicate that PGD(2) stimulatory effect involves both PLD and ERK1/2-MAPK activation, and both pathways operate independently of PC synthesis homeostasis.

COX-2-mediated PGD2 synthesis regulates phosphatidylcholine biosynthesis in rat renal papillary tissue

Phosphatidylcholine (PC) is the major membrane phospholipid in mammalian cells. Previous works from our laboratory demonstrated a close metabolic relationship between the maintenance of PC biosynthesis and the prostaglandins endogenously synthesized by cyclooxygenase (COX) in rat renal papilla. In the present work, we studied the COX isoform involved in papillary PC biosynthesis regulation. The incorporation of [methyl-3H]choline and [32P]orthophosphate to PC was determined in the absence and presence of SC-560 and NS-398, COX-1 and COX-2 specific inhibitors. PC synthesis was highly sensitive to COX-2 inhibition, while COX-1 inhibition only reduced PC synthesis at high SC-560 concentration. The analysis of choline-containing metabolites showed that COX-2 inhibition affected the formation of CDP-choline intermediary. The evaluation of PC biosynthetic enzymes revealed that microsomal, as well as nuclear, CTP:phosphocholine cytidylyltransferase (CCT), and nuclear-CDP-choline:1,2-diacylglycerol cholinephosphotransferase (CTP) activities were affected by COX-2 inhibition. The addition of exogenous prostaglandin D(2) (PGD(2)) restored nuclear-CCT and -CPT activities but not microsomal CCT. Papillary synthesis of PGD(2) was only detected in nuclear fraction where it was blocked by COX-2 inhibitor NS-398, but not by COX-1 inhibitor. All together, the present results demonstrated that COX-2-mediated PGD(2) synthesis is a PC biosynthesis regulator in rat renal papilla. Considering the importance of the maintenance of PC biosynthesis for the preservation of cell membrane homeostasis to ensure cell viability, and the extensive use of COX-2 inhibitors in therapeutics, the present results could have great pharmacological implications, and can constitute a biochemical explanation for the nephrotoxic effect of non-steroidal anti-inflammatory drugs.

Phospholipase C inhibitors and prostaglandins differentially regulate phosphatidylcholine synthesis in rat renal papilla. Evidence of compartmental regulation of CTP:phosphocholine cytidylyltransferase and CDP-choline:1,2-diacylglycerol cholinephosphotransferase

Phosphatidylcholine (PC) is the most abundant phospholipid in mammalian cell membranes. Several lines of evidence support that PC homeostasis is preserved by the equilibrium between PC biosynthetic enzymes and phospholipases catabolic activities. We have previously shown that papillary synthesis of PC depends on prostaglandins (PGs) that modulate biosynthetic enzymes. In papillary tissue, under bradikynin stimulus, arachidonic acid (AA) mobilization (the substrate for PG synthesis) requires a previous phospholipase C (PLC) activation. Thus, in the present work, we study the possible involvement of PLC in PC biosynthesis and its relationship with PG biosynthetic pathway on the maintenance of phospholipid renewal in papillary membranes; we also evaluated the relevance of CDP-choline pathway enzymes compartmentalization. To this end, neomycin, U-73122 and dibutiryl cyclic AMP, reported as PLC inhibitors, were used to study PC synthesis in rat renal papilla. All the PLC inhibitors assayed impaired PC synthesis. PG synthesis was also blocked by PLC inhibitors without affecting cyclooxygenase activity, indicating a metabolic connection between both pathways. However, we found that PC biosynthesis decrease in the presence of PLC inhibitors was not a consequence of PG decreased synthesis, suggesting that basal PLC activity and PGs exert their effect on different targets of PC biosynthetic pathway. The study of PC biosynthetic enzymes showed that PLC inhibitors affect CTP:phosphocholine cytidylyltransferase (CCT) activity while PGD(2) operates on CDP-choline:1,2-diacylglycerol cholinephosphotransferase (CPT), both activities associated to papillary enriched-nuclei fraction. The present results suggest that renal papillary PC synthesis is a highly regulated process under basal conditions. Such regulation might occur at least at two different levels of the CDP-choline pathway: on the one hand, PLC operates on CCT activity; on the other, while PGs regulate CPT activity.

Functional analysis and intracellular localization of p53 modified by SUMO-1

p53 tumor suppressor is a subject of several post-translational modifications, including phosphorylation, ubiquitination and acetylation, which regulate p53 function. A new covalent modification of p53 at lysine 386 by SUMO-1 was recently identified. To elucidate the function of sumoylated p53, we compared the properties of wild type p53 and sumoylation-deficient p53 mutant, K386R. No differences were found between wild type p53 and K386R mutant of p53 in transactivation or growth suppression assays. Moreover, overexpression of SUMO-1 has no effect on p53-regulated transcription. Biochemical fractionation showed that sumoylated p53 is localized in the nucleus and is tightly bound to chromatin structures. p53 and SUMO-1 co-localized in PML nuclear bodies in 293 cells and the nucleoli in MCF7 and HT1080 cells. However, sumoylation-deficient p53 mutant showed a similar pattern of intranuclear localization, suggesting that SUMO-1 does not target p53 to subnuclear structures. These data indicate that SUMO-1 modification of p53 at lysine 386 may not be essential for p53's cellular localization, transcriptional activation, or growth regulation.

Demonstration of equilibrative nucleoside transporters (hENT1 and hENT2) in nuclear envelopes of cultured human choriocarcinoma (BeWo) cells by functional reconstitution in proteoliposomes

The equilibrative nucleoside transporters (ENTs) are a newly recognized family of membrane proteins of which hENT1 is the nitrobenzylmercaptopurine ribonucleoside (NBMPR)-sensitive (es) and hENT2 the NBMPR-insensitive (ei) transporter of human cells. BeWo cells exhibit large numbers (>10(7)/cell) of NBMPR-binding sites and high es and ei nucleoside transport activities relative to other cell types. In this work, we have demonstrated that proliferating BeWo cells possess (i) mRNA encoding hENT1 and hENT2 and (ii) hENT1-specific immunoepitopes. We examined NBMPR binding and its inhibition of uridine transport in various BeWo membrane fractions and proteoliposomes derived therefrom to determine if NBMPR binding to intracellular membranes represented interaction with functional es transporters. Unfractionated membranes and fractions enriched 5-fold in plasma membranes relative to postnuclear supernatants exhibited high NBMPR binding activity. Intact nuclei and nuclear envelopes also exhibited abundant quantities of NBMPR-binding sites with affinities similar to those of enriched plasma membranes (Kd = 0.4-0.9 nM). When proteoliposomes were made from octyl glucoside-solubilized membranes, high affinity NBMPR-binding sites were not only observed in crude membrane preparations and plasma membrane-enriched fractions but also in nuclear envelope fractions. Proteoliposomes prepared from either unfractionated membranes or nuclear envelopes exhibited both hENT1-mediated (82-85%) and hENT2-mediated (15-18%) transport of [3H]uridine. These results provided evidence for the presence of functional es and ei transporters in nuclear membranes and endoplasmic reticulum, suggesting that hENT1 and hENT2 may function in the translocation of nucleosides between the cytosol and the luminal compartments of one or both of these membrane types.

5 alpha-Reductase type 1 is localized to the outer nuclear membrane

The subcellular distribution of the two isozymes of 5 alpha-reductase has been controversial. To resolve this issue which could provide clues about the respective functions of the two isozymes, two antisera were generated, one which was specific for the Type 1 5 alpha-reductase and one which recognized both isozymes. In COS cells transfected separately with the Type 1 or Type 2 cDNA, both isozymes were detected on Western blots at an M(r) of 26,000. Subfractionation of the COS cells resulted in the partitioning of both isozymes between the crude nuclear and cytosolic fractions, while cytoimmunofluorescence localized both reductases to the nuclear periphery. In rat liver homogenate, the 5 alpha-reductase was also detected at M(r) 26,000. The 5 alpha-reductase immunoreactivity was increased after castration of the animals with no further effect when castrated animals were treated with androgens. Although the rat liver expresses only the Type 1 5 alpha-reductase, the 5 alpha-reductase was distributed about equally between crude nuclear and cytosolic subfractions; this distribution could be shifted to the cytosolic fractions with harsher homogenization procedures. Further extensive subfractionation and extraction studies identified the rat liver Type 1 5 alpha-reductase as an integral membrane protein present in the outer nuclear membrane of the nuclear envelope and in rough endoplasmic reticulum. Thus, the subfractionation and cytoimmunofluorescence studies are consistent with the localization of the Type 1 5 alpha-reductase to the outer nuclear membrane of the nuclear envelope which is continuous with and indistinguishable from the endoplasmic reticulum. This study is the first to localize rat liver Type 1 5 alpha-reductase to the nuclear envelope to which the prostatic 5 alpha-reductase activity previously had been localized. We conclude that, contrary to previous tissue distribution studies, but consistent with investigations in transfected cells, both isozymes are similarly localized to the nuclear periphery.

NAP57, a mammalian nucleolar protein with a putative homolog in yeast and bacteria

We report the identification and molecular characterization of a novel nucleolar protein of rat liver. As shown by coimmunoprecipitation this protein is associated with a previously identified nucleolar protein, Nopp140, in an apparently stoichiometric complex and has therefore been termed NAP57 (Nopp140-associated protein of 57 kD). Immunofluorescence and immunogold electron microscopy with NAP57 specific antibodies show colocalization with Nopp140 to the dense fibrillar component of the nucleolus, to coiled bodies, and to the nucleoplasm. Immunogold staining in the nucleoplasm is occasionally seen in the form of curvilinear tracks between the nucleolus and the nuclear envelope, similar to those previously reported for Nopp140. These data suggest that Nopp140 and NAP57 are indeed associated with each other in these nuclear structures. The cDNA deduced primary structure of NAP57 shows a protein of a calculated molecular mass of 52,070 that contains a putative nuclear localization signal near its amino and carboxy terminus and a hydrophobic amino acid repeat motif extending across 84 residues. Like Nopp140, NAP57 lacks any of the known consensus sequences for RNA binding which are characteristic for many nucleolar proteins. Data bank searches revealed that NAP57 is a highly conserved protein. A putative yeast (S. cerevisiae) homolog is 71% identical. Most strikingly, there also appears to be a smaller prokaryotic (E. coli and B. subtilis) homolog that is nearly 50% identical to NAP57. This indicates that NAP57 and its putative homologs might serve a highly conserved function in both pro- and eukaryotes such as chaperoning of ribosomal proteins and/or of preribosome assembly.

A 46 kDa NTPase common to rat liver nuclear envelope, mitochondria, plasma membrane, and endoplasmic reticulum

A 46 kDa ATP binding polypeptide of the nuclear envelope, virtually identical to the nuclear envelope NTPase putatively involved in mRNA efflux [6], is present in all rat liver cell membranes. Its presence in nuclear envelope is not the result of cross contamination during isolation.

Effect of dietary butylated hydroxytoluene on nuclear envelope cytochrome P-450 during the initiation and promotion stages of hepatocarcinogenesis

The anticarcinogenic effect of the dietary antioxidant butylated hydroxytoluene (BHT) correlates with a preservation of nuclear envelope (NE) cytochrome P-450 in rats undergoing chemically induced hepatocarcinogenesis. This effect of BHT on NE cytochrome P-450 was observed during both the initiation and the promotion stages of hepatocarcinogenesis. Complex interactions between the two different mechanisms of action of BHT (i.e., enzyme induction and antioxidant activity) may account for some of the differences between the patterns of response to BHT observed during initiation and promotion.

Prevention of 2-acetylaminofluorene-induced loss of nuclear envelope cytochrome P450 by the simultaneous administration of 3-methylcholanthrene

Rats fed a basal diet containing 0.05% (w/w) 2-acetylaminofluorene (AAF) for 3 weeks showed a 50% loss of hepatic nuclear envelope cytochrome P450, whereas microsomal P450 remained at control levels. A similar dietary treatment with 0.004% (w/w) 3-methylcholanthrene (MC) caused moderate losses (20-25%) of cytochrome P450 in both nuclear envelopes and microsomes. Administration of the basal diet supplemented with a mixture of AAF (0.05%) plus MC (0.004%) resulted in a preservation of control levels of nuclear envelope cytochrome P450 and a 30% elevation of microsomal P450. Immunoblot analysis revealed that AAF alone, or in concert with MC, induced comparable levels of the P450d form. Induction of cytochrome P450c by dietary MC was detected only when MC was fed together with AAF. As previously found for butylated hydroxytoluene (BHT), the protective effect of dietary MC against hepatocarcinogenesis in AAF-fed rats correlated with a preservation of nuclear envelope cytochrome P450 content and with the induction of cytochrome P450c.

Influence of genotype on diet-induced changes in membrane phosphatidylcholine and phosphatidylethanolamine composition of splenocytes, liver nuclear envelope and liver mitochondria

Inbred congenic mice of strains MRL/Mp-lpr/lpr (lpr/lpr) and MRL/Mp(-)+/+ (+/+) were fed nutritionally adequate semipurified diets containing 20% (w/w) fat and differing in linoleic acid content. Levels of linoleic acid (18:2n-6) and arachidonic acid (20:4n-6) in phospholipids of splenocytes, liver mitochondria and liver nuclear envelopes were determined. Membranes of lpr/lpr mice exhibited significantly lower levels of 18:2n-6 and 20:4n-6 in phospholipids compared with the +/+ strain. The high linoleic acid diet increased incorporation of 18:2n-6 and 20:4n-6 in most phospholipid fractions of these membranes. These observations indicate that genotype as well as dietary 18:2n-6 content significantly influenced incorporation of 18:2n-6 and 20:4n-6 into membrane phospholipids. The results also suggest that membrane compositional abnormalities found in the lpr/lpr mice, which develop lymphoma and age faster than +/+ mice, are not restricted to the immune system but also extend to other organs. Differences observed in phospholipid fatty acid composition in splenocytes and liver subcellular membranes for mice fed diets differing in linoleic acid content suggest that the early expression of the lpr gene resulting in progression of autoimmunity may be delayed through dietary manipulation.

A nuclear localization signal binding protein in the nucleolus

We used functional wild-type and mutant synthetic nuclear localization signal peptides of SV-40 T antigen cross-linked to human serum albumin (peptide conjugates) to assay their binding to proteins of rat liver nuclei on Western blots. Proteins of 140 and 55 kD (p140 and p55) were exclusively recognized by wild-type peptide conjugates. Free wild-type peptides competed for the wild-type peptide conjugate binding to p140 and p55 whereas free mutant peptides, which differed by a single amino acid from the wild type, competed less efficiently. The two proteins were extractable from nuclei by either low or high ionic strength buffers. We purified p140 and raised polyclonal antibodies in chicken against the protein excised from polyacrylamide gels. The anti-p140 antibodies were monospecific as judged by their reactivity with a single nuclear protein band of 140 kD on Western blots of subcellular fractions of whole cells. Indirect immunofluorescence microscopy on fixed and permeabilized Buffalo rat liver (BRL) cells with anti-p140 antibodies exhibited a distinct punctate nucleolar staining. Rhodamine-labeled wild-type peptide conjugates also bound to nucleoli in a similar pattern on fixed and permeabilized BRL cells. Based on biochemical characterization, p140 is a novel nucleolar protein. It is possible that p140 shuttles between the nucleolus and the cytoplasm and functions as a nuclear import carrier.

Characterization of high affinity and low affinity dexamethasone binding sites on male rat liver nuclear envelopes

Steroids must traverse the nuclear envelope before exerting their action at the chromatin. However, few studies have been done to elucidate the mechanism by which steroids traverse this membrane barrier. As first steps towards investigating the mechanism, we have characterized the binding sites for dexamethasone on male rat liver nuclear envelopes. The nuclear envelopes, prepared in the presence of dithiothreitol, were isolated from purified nuclei after treatment with DNase 1 at high pH. Binding of dexamethasone to the nuclear envelopes was measured after 16 h of incubation at 0-4 degrees C. At pH 7.4, only a single high capacity, low affinity binding site for dexamethasone was identified. However, at pH 8.6, two sites were identified; a low capacity, high affinity site and a high capacity, low affinity site. Adrenalectomy of the animal before preparation of the membranes caused loss of the high affinity site and reduction in the number of the lower affinity sites. Acute dexamethasone treatment of adrenalectomized rats resulted in the reappearance of the high affinity site but long term treatment with dexamethasone was required for complete restoration of the high affinity sites and reappearance of any of the low affinity sites. The steroid specificity of these nuclear envelope binding sites was different from that of the cytosolic glucocorticoid receptor, generally showing broader specificity. However, triamcinolone acetonide, which is a potent competitor for binding to the glucocorticoid receptor, did not complete effectively. The binding sites were sensitive to protease treatment and salt extraction studies revealed that the dexamethasone binding sites do not represent proteins non-specifically bound to the nuclear envelope. The affinity and the hormone responsiveness of the high affinity site are similar to those of the nuclear glucocorticoid receptor. Therefore, the nuclear envelope may be a site of action of glucocorticoids.

Induction of rat liver microsomal and nuclear cytochrome P-450 by dietary 2-acetylaminofluorene and butylated hydroxytoluene

The influence of dietary 2-acetylaminofluorene (AAF) on the cytochrome P-450 content of rat liver microsomal and nuclear fractions was immunochemically probed with monoclonal and polyclonal antibodies to cytochromes P-450c and P-450d. Cytochrome P-450d but not P-450c was immunodetected in microsomes, nuclear envelopes, and nuclei from untreated rats. The levels of both cytochromes P-450c and P-450d were elevated after a diet of either 0.1% AAF for 1 week or 0.05% AAF for 3 weeks. However, the level of cytochrome P-450c relative to P-450d was lower after the more prolonged AAF feeding. Supplementation of AAF-containing diets with 0.3% butylated hydroxytoluene (BHT), which affords protection against AAF hepatocarcinogenesis in high-fat fed rats, protected and/or induced total (spectral) nuclear envelope cytochrome P-450 content. Immunochemical studies of liver fractions showed that BHT enhanced the AAF-dependent induction of cytochrome P-450c, but not of P-450d. This was a concerted effect of AAF + BHT since dietary BHT by itself did not affect the levels of cytochrome P-450c or P-450d as compared to control rats. Since 1- to 3-week dietary AAF had little effect on total (spectral analyses) microsomal cytochrome P-450 but markedly reduced total P-450 in nuclear envelopes, the coordinated induction of specific cytochrome P-450s in the different fractions suggests selective induction and depression of different forms of cytochrome P-450 and provides additional evidence for independent regulation of the drug-metabolizing system in nuclear envelope and microsomes. In addition, these results suggest that regulation of cytochrome P-450 may play a crucial role in the nutritional modulation of AAF hepatocarcinogenesis.

Hepatic nuclear envelope cytochrome P-450 in rats fed 2-acetylaminofluorene. Effect of dietary fats and butylated hydroxytoluene

Early losses of nuclear envelope (NE) cytochrome P-450 occur during 2-acetylaminofluorene (AAF)-hepatocarcinogenesis. Butylated hydroxytoluene (BHT), which protects against AAF in rats fed high fat diets, preserves NE P-450 suggesting that the latter may be required for AAF detoxification. AAF-hepatocarcinogenesis is enhanced by increasing the amount or degree of unsaturation of dietary fats. The present studies show that in rats fed AAF in high fat diets BHT preservation of NE P-450 is considerably shorter (3 weeks) with polyunsaturated than with saturated fat (9 weeks). In rats fed AAF in a low fat diet, where BHT does not modify the low tumor incidence, there is a bimodal effect on NE P-450. In controls and AAF-fed rats, BHT causes significant induction of NE P-450 at 1-3 weeks. At 9-16 weeks BHT has no effect on controls and only partially preserves NE P-450 in AAF-fed rats. Due to time constraints, livers could not be utilized fresh, but they were kept frozen at -80 degrees C until processed. Thus, specimens from all groups underwent identical treatment for purposes of comparative studies.

Ribonucleic acid efflux from isolated mouse liver nuclei is altered by diet and genotypically determined change in nuclear envelope composition

Differences in immunological abnormalities like autoimmunity, abnormal T cell proliferative disorders and accelerated ageing occur between MRL/Mp-lpr/lpr(lpr/lpr) and MRL/Mp-+/+(+/+) mice as a consequence of one gene. The present study was designed to assess the effect of these differences in genotype and diet on the composition and function of the liver nuclear envelope. Mice of both strains were fed nutritionally adequate diets differing only in fatty acid composition for 4 weeks. Phospholipid fatty acid composition of the liver nuclear envelope was determined and the effect of altering the lipid composition of the nuclear membrane on nucleoside-triphosphatase (NTPase) activity, ribonucleic acid (RNA) efflux and binding of L-triiodothyronine (L-T3) was determined. Strain of mouse and level of dietary linoleic acid exhibited significant effects on the phospholipid fatty acid composition of the nuclear envelope. Levels of 18:1(n - 9) and 18:2(n - 6) were lower and 20:4(n - 6) content was higher in nuclear envelope phospholipids of lpr/lpr mice compared with mice of the +/+ strain. Mice fed the high linoleic acid diet exhibited higher levels of 18:0, 18:2(n - 6) and 20:4(n - 6) and lower levels of 16:0 and 18:1(n - 9) in liver nuclear envelope phospholipids, compared with mice fed the low linoleic acid diet. These changes in membrane composition were reflected in alteration of NTPase activity and efflux of RNA from isolated mouse liver nuclei. Nucleoside triphosphatase activity and efflux of ribonucleic acid from isolated nuclei were significantly higher in livers of the lpr/lpr strain. NTPase activity and RNA efflux from isolated nuclei were higher in the high linoleic acid fed group compared with the low linoleic acid group. A single class of binding sites for L-T3 was present in liver nuclear envelopes of these mice and Kd values were not influenced by strain or dietary linoleic acid levels. Nuclear envelopes prepared from +/+ animals exhibited a significantly higher number of binding sites for L-T3 compared with the lpr/lpr group. These observations indicate that the single gene difference characterizing lpr/lpr mice from +/+ mice results in alterations in the composition and function of the nuclear envelope. This genetic difference also alters the response of this membrane to dietary factors known to modulate characteristics and functions of the nuclear envelope.

Monoclonal antibodies identify a group of nuclear pore complex glycoproteins

Using monoclonal antibodies we identified a group of eight polypeptides of rat liver nuclear envelopes that have common epitopes. Most or all of these proteins are structurally distinct, as shown by tryptic peptide mapping and analysis with polyclonal antibodies. While these polypeptides are relatively tightly bound to nuclear membranes, only one is an integral membrane protein. The eight antigens cofractionate with the nuclear pore complex under various conditions of ionic strength and detergent. It can be seen by immunofluorescence microscopy that the monoclonal antibodies reacting with these antigens stain the nuclear surface of interphase cells in a finely punctate pattern. When the nuclear envelope is disassembled and subsequently reformed during mitosis, the proteins are reversibly dispersed throughout the cytoplasm in the form of minute foci. By EM immunogold localization on isolated nuclear envelopes, the monoclonal antibodies label exclusively the nuclear pore complex, at both its nucleoplasmic and cytoplasmic margins. Considered together, our biochemical and localization data indicate that the eight nuclear envelope polypeptides are pore complex components. As shown in the accompanying paper (Holt, G. D., C. M. Snow, A. Senior, R. S. Haltiwanger, L. Gerace, and G. W. Hart, J. Cell Biol., 104:1157-1164) these eight polypeptides contain a novel form of glycosylation, O-linked N-acetylglucosamine. The relative abundance and disposition of these O-linked glycoproteins in the pore complex are consistent with their having a role in nucleocytoplasmic transport.

Epidermal growth factor and insulin stimulate nuclear pore-mediated macromolecular transport in isolated rat liver nuclei

Fluorescence photobleaching was used to measure the effect of epidermal growth factor (EGF), insulin, and glucagon on the nuclear transport of fluorescent-labeled dextrans across the nuclear pore complex. EGF and insulin were found to stimulate transport approximately 200%, while boiling these polypeptide growth factors greatly diminished this enhancement activity. Glucagon demonstrated no enhancement effect. The nuclear transport enhancement effects were observed at EGF and insulin concentrations that elicit the various physiological responses, e.g., nanomolar range.

Dietary butylated hydroxytoluene protects cytochrome P-450 in hepatic nuclear membranes of rats fed 2-acetylaminofluorene

We previously reported that during hepatocarcinogenesis which is induced by feeding 2-acetylaminofluorene (AAF) there is an early loss of cytochrome P-450 in the nuclear envelope (Carubelli et al., Chem. Biol. Interact. 58, 125-136, 1986). Cytochrome P-450 participates in the activation in addition to the detoxification of xenobiotics; therefore, these findings suggested that AAF may cause the loss of an important defense for the protection of the genetic material of the nucleus against carcinogenic metabolites of AAF generated by microsomal P-450 which, in contrast to the nuclear envelope cytochrome P-450, remains essentially undiminished during early stages of AAF feeding. Because dietary butylated hydroxytoluene (BHT) affords good protection against AAF carcinogenicity, we decided to investigate the possibility that the BHT effect could be mediated through the preservation of nuclear envelope cytochrome P-450. AAF (0.05% wt/wt) was administered in a purified diet with a high content of polyunsaturated fat (20% wt/wt corn oil), which is known to enhance AAF carcinogenicity. These studies showed that BHT supplementation (0.3% wt/wt) of control in addition to the AAF-containing diets resulted in higher levels of nuclear envelope cytochrome P-450. After 16 weeks of AAF feeding, nuclear envelope cytochrome P-450 could not be detected in rats fed BHT-free diet, whereas in the rats fed the diet containing AAF and BHT, measurable amounts of nuclear envelope P-450 were observed. These results are compatible with the hypothesis that nuclear envelope cytochrome P-450 is needed for protection against AAF and that BHT protects nuclear envelope cytochrome P-450.

Preparation and characterization of nuclear-envelope vesicles from rat liver nuclei

We describe a procedure for the preparation of sealed nuclear-envelope vesicles from rat liver nuclei. These vesicles are strikingly similar in their polypeptide composition when compared with those of nuclear envelopes prepared conventionally using deoxyribonuclease I. Subfractionation analysis by means of extraction with high salt and urea show that the components of the nuclear envelope, e.g. the pore-complex/lamina fraction, are present. The residual DNA content is only 1.5%, and typical preparations consist of about 80% vesicles, with the vesicular character of these envelopes shown by microscopic and biochemical studies. The vesicles can be obtained in high yield, are tight and stable for at least two days and are enriched in a nucleoside triphosphatase thought to be involved in nucleocytoplasmic transport processes. Because the vesicles are largely free of components of the nuclear interior, but retain properties of intact nuclei, we believe that they are a valuable model system to study nucleocytoplasmic transport. Although in transport studies with isolated nuclei interference from intranuclear events has to be considered, the nuclear-envelope vesicles provide the possibility of studying translocation alone. Furthermore, the less complex nature of these vesicles compared with whole nuclei should facilitate investigation of the components involved in the regulation of nuclear transport processes.

Loss of cytochrome P-450 from hepatic nuclear membranes of rats fed 2-acetylaminofluorene

The cytochrome P-450 content of nuclear membranes isolated from the livers of male Sprague-Dawley rats fed a semipurified diet containing 0.05% w/w 2-acetylaminofluorene (AAF) for 3 weeks, was only about 20% of the values in control rats fed the same diet devoid of AAF. This effect was apparent after only 1 week of AAF treatment and persisted in nuclear membranes from isolated hyperplastic nodules (HPN) generated by 4 cycles of interrupted AAF-feeding. The microsomal cytochrome P-450 content, on the other hand, remained at control levels after 1 week of AAF treatment, and it was only slightly decreased after 3 weeks. In contrast, microsomes from HPN generated by prolonged AAF treatment had markedly decreased amounts of cytochrome P-450. The AAF treatment also caused changes in cholesterol epoxide hydrolase activity, which paralleled those observed for cytochrome P-450 content. Nuclear membranes from livers of rats fed AAF for 3 weeks, and from isolated HPN, had only 30-50% of the cholesterol epoxide hydrolase activity present in controls, whereas the microsomal enzyme activity remained at control levels after 3 weeks of AAF feeding but was 50% depressed in microsomes from HPN. The selective loss of cytochrome P-450 and of cholesterol epoxide hydrolase in hepatic nuclear membrane, but not in microsomes, of rats fed AAF for 3 weeks suggests independent control for these enzymes in these two membrane fractions. Cytochrome P-450 plays a role both in the activation of AAF (N-hydroxylation) as well as in its detoxification (ring hydroxylation) whereas cholesterol epoxide hydrolase initiates the detoxification of cholesterol epoxide. Therefore, our findings suggest the hypothesis that AAF treatment causes an early loss, at the surface of the nucleus, of the last line of defense for detoxification of transforming or promoting metabolites generated by microsomal activation of natural substances such as cholesterol and of xenobiotics such as AAF.

Chemical factors that influence nucleocytoplasmic transport: a fluorescence photobleaching study

The technique of fluorescence redistribution after photobleaching was used to measure the translocation rate of fluorescein-labeled dextrans across the nuclear pore complex in isolated rat liver nuclei. A transport assay system was established that could monitor the effect of biologically active molecules, e.g., ATP, GTP, cAMP on the translocation process. The results show that ATP, phosphoinositides, RNA, and insulin can enhance transport rates from 195 to 432%. It was further demonstrated that concanavalin A, but not wheat germ or soybean agglutinin, can block dextran transport completely. The effectors of dextran transport are similar to substances demonstrated to effect the efflux of RNA from isolated nuclei. A model for translocation through the nuclear pore is now presented that incorporates data from protein influx and RNA efflux experiments into a single pathway controlled by ATP.

Nuclear actin and myosin as control elements in nucleocytoplasmic transport

Fluorescence redistribution after photobleaching (FRAP) was used to examine the role of actin and myosin in the transport of dextrans through the nuclear pore complex. Anti-actin antibodies added to isolated rat liver nuclei significantly reduced the flux rate of fluorescently labeled 64-kD dextrans. The addition of 3 mM ATP to nuclei, which enhances the flux rate in control nuclei by approximately 250%, had no enhancement effect in the presence of either anti-actin or anti-myosin antibody. Phalloidin (10 microM) and cytochalasin D (1 micrograms/ml) individually inhibited the ATP stimulation of transport. Rabbit serum, anti-fibronectin, and anti-lamins A and C antibodies had no effect on transport. These results suggest a model for nuclear transport in which actin/myosin are involved in an ATP-dependent process that alters the effective transport rate across the nuclear pore complex.

Survival strategies of the yeast plasmid two-micron circle

The multicopy yeast plasmid 2-micron circle uses a number of strategies to insure its persistence in its host. The plasmid confers no selective phenotype to the cell in which it is resident. Nonetheless, the plasmid is lost at less than 1 per 10(5) cell divisions during continuous exponential growth. We have determined that the plasmid persists at least in part due to the ability of the plasmid to amplify its mean copy number when its cellular copy level is low and to distribute plasmid molecules equally between mother and daughter cells at mitosis. We have found that amplification of plasmid copy number occurs by a novel mechanism in which site-specific recombination induces a transient shift in the mode of replication from theta to rolling circle. Equitable partitioning of plasmid molecules requires plasmid-encoded proteins and a centromere-like segment on the plasmid. We have accumulated evidence consistent with a model of partitioning in which the partitioning proteins form a transnuclear structure that is responsible for distributing plasmid molecules throughout the nucleus prior to cell division. In this chapter we describe evidence supporting the existence and mode of action of these two plasmid strategies and discuss the extent to which these strategies may be a pervasive facet of the biology of eukaryotic extrachromosomal elements.

Androgen interactions with intact nuclear envelopes from the rat ventral prostate

Intact nuclear envelopes containing nuclear pore complexes have been prepared from the rat ventral prostate. The polypeptide profile of the nuclear envelopes from the rat prostate resembled that of nuclear envelopes prepared from the male rat liver. Isolation of the nuclear envelopes after incubation of purified nuclei with radioactive dihydrotestosterone results in labelling of the membrane. More dihydrotestosterone is bound after incubations at 22 degrees C for 18 h than at 2 degrees C for 18 h or 22 degrees C for 2 h. Scatchard analysis revealed a class of binding sites with an apparent Kd of 46 nM. Dihydrotestosterone, testosterone, cyproterone acetate and methyltrienolone were effective as competitors of labelled dihydrotestosterone binding to the nuclear envelopes, while estradiol did not compete. Castration of the rats 24, 48 and 96 h prior to preparation of nuclei resulted in loss of androgen binding to the membranes. Extraction with 0.6 M NaCl resulted in the loss of 72% of the androgen binding.

Lateral diffusion in nuclear membranes

Chemical modification of rat liver nuclei with citraconic anhydride selectively removed outer nuclear membrane. This conclusion was based on (a) transmission electron microscopy, (b) lipid analysis, (c) lamin B as an inner membrane-associated marker, and (d) the demonstration of phospholipid lateral mobility on outer membrane-depleted nuclei as a criteria for inner membrane integrity. Addition of urea or N-ethylmaleimide resulted in the additional disruption of inner membrane. Fluorescence photobleaching was used to determine the long range (greater than 4 microns) lateral transport of lectin receptors and a phospholipid analog in both membranes. The diffusion coefficient for wheat germ agglutinin on whole nuclei was 3.9 X 10(-10) cm2/s whereas the diffusion coefficient for wheat germ agglutinin in outer membrane-depleted nuclei was less than or equal to 10(-12) cm2/s. Phospholipid mobilities were the same in whole and outer membrane-depleted nuclei (3.8 X 10(-9) cm2/s). The protein diffusion differences observed between whole and outer membrane-depleted nuclei may be interpreted in the context of two functionally different membrane systems that compose the double bilayer of the nucleus.

Effect of benzo[a]pyrene on DNA synthesis and DNA polymerase activity of rat liver nuclei

When benzo[a]pyrene (B[a]P) was administered intraperitoneally to rats 48 hr before they were killed, the DNA-synthesizing capability of isolated rat liver nuclei was decreased as compared with control animals. B[a]P also inhibited in vitro DNA synthesis in nuclei purified from control animals; this effect was enhanced by NADPH. DNA polymerases solubilized from purified nuclei of B[a]P-treated animals were less active than those of control animals. DNA polymerase alpha was more inhibited than DNA polymerase beta. Purified rat liver nuclei devoid of cytoplasmic contamination possess an NADPH-dependent B[a]P hydroxylase activity. The observed inhibition of DNA synthesis in nuclei isolated from B[a]P-treated rats was increased by NADPH. Moreover, there was an increased inhibition of DNA polymerase activity by nuclear membranes obtained from B[a]P-treated animals when the incubations were performed in the presence of NADPH. Also, the derivative B[a]P-trans-9,10-dihydrodiol was a potent inhibitor of DNA polymerase alpha under conditions where DNA polymerase beta was less affected. These results suggest that nuclear B[a]P hydroxylase might be involved in the inhibition of DNA synthesis probably at the level of DNA polymerase alpha. As in the in vivo studies, the nuclear polymerase most affected by the hydrocarbon in vitro was DNA polymerase alpha.

The isolation of nuclear envelopes. Effects of thiol-group oxidation and of calcium ions

The effects of (a) oxidative cross-linking of protein thiol groups and (b) the presence or absence of Ca2+ ions on rat liver nuclear-envelope isolation were studied. Two envelope-isolation procedures were compared: a well characterized low-ionic-strength method and a recently developed high-ionic-strength method. The latter method seems preferable to the former in respect of lower intranuclear contamination of the envelopes, suppression of endogenous serine proteinase, and maintenance of high specific activities of envelope-associated enzymes. In both procedures, however, the presence of Ca2+ gave rise to a rapid, apparently irreversible, contamination of the envelopes by intranuclear material. This effect was half-maximal at 20 microM-Ca2+. In addition, the envelopes became contaminated with intranuclear material by a Ca2+-independent mechanism, apparently resulting from N-ethylmaleimide-sensitive intermolecular disulphide-bond formation. This oxidative process seemed to have two major kinetic components (half-life, t1/2, approx. 2 min and 10 min). In view of these findings, it is recommended that (i) for most purposes, nuclear envelopes be isolated by the newly developed high-ionic-strength procedure, (ii) irrespective of the method used, Ca2+-chelators be included in all the buffers, (iii) thiol-group oxidation be prevented or reversed during the procedure.

Correlation of androgen-responsiveness of Shionogi mouse mammary carcinoma cell lines with binding of dihydrotestosterone to nuclear envelopes

Purified nuclear envelopes have been isolated from an androgen-responsive and two androgen-unresponsive cell lines of the Shionogi mouse mammary carcinoma. The binding of dihydrotestosterone to nuclear envelope fractions isolated from the three variant cell lines is correlated with the androgen-responsiveness of the cell line. Nuclear envelopes prepared from the two androgen-unresponsive cell lines did not bind dihydrotestosterone specifically following incubation with radioactive dihydrotestosterone from 2.5 to 45.0 nM at 20 degrees C for 18 h. Under the same binding conditions, nuclear envelopes prepared from the androgen-responsive cell line demonstrated saturable, specific binding of dihydrotestosterone. Scatchard analysis revealed a class of binding sites with an apparent Kd of 14.2 nM and a maximum binding capacity of 28.7 fmol/mg protein. Proteinase and heat treatments resulted in the complete loss of androgen-binding activity, whereas DNAase treatment resulted in the loss of 38% of the binding activity. The binding sites were specific for dihydrotestosterone. Testosterone was only a weak competitor and estradiol did not compete. Extraction with concentrations of KCl up to 1.0 M did not result in loss of androgen binding.

A widely distributed nuclear protein immunologically related to the microtubule-associated protein MAP1 is associated with the mitotic spindle

A 280-kDa protein (p280) confined to the nucleus of interphase cells becomes associated with the mitotic spindle during cell division. p280 is immunologically related to the microtubule-associated protein MAP1, as shown by cross-reactivity with monoclonal (8D12) and polyclonal antibodies raised against MAP1. However, p280 is distinct from MAP1 as judged by its lower molecular size, proteolytic degradation products, presence in preparations of purified nuclei from which MAP1 is absent, and absence from the cytosol fraction that contains MAP1. Immunofluorescence microscopy of cells in interphase using 8D12 reveals punctate staining of the nucleus, cytoplasmic microtubules, and the microtubule organizing center. Dividing cells display strong staining of the spindle, centrioles, and mid-body. The only exception to this staining pattern is marsupial Pt k2 cells that contain p280 in the nucleus and lack MAP1. These cells exhibit fluorescent staining of the nucleus and the microtubule organizing center when in interphase, of spindle and centrioles in mitosis, and show no staining of cytoplasmic and mid-body microtubules.

A subset of non-histone nuclear proteins reversibly stabilized by the sulfhydryl cross-linking reagent tetrathionate. Polypeptides of the internal nuclear matrix

When rat liver nuclei are isolated in the presence of the irreversible sulfhydryl-blocking reagent iodoacetamide, digested with DNase I and RNase A, and extracted with 1.6 M NaCl, nuclear envelope (NE) spheres depleted of intranuclear material, as analysed by thin-section electron microscopy, are obtained. Two-dimensional isoelectric focusing (IEF)/SDS-PAGE and non-equilibrium pH gradient electrophoresis (NEPHGE)/SDS-PAGE reveal that the predominant polypeptides are lamins A, B and C. Nuclei isolated in the absence of sulfhydryl blocking reagents yield salt- and nuclease-resistant structures which contain sparse but demonstrable intranuclear material. A number of non-histone polypeptides are seen in addition to the lamins. Nuclei treated with the sulfhydryl cross-linking reagent sodium tetrathionate (NaTT) yield, after exposure to nucleases and 1.6 M NaCl, nuclear matrix-like structures containing an extensive intranuclear network and components of the nucleolus in addition to the NE. Increased amounts of the non-lamin, non-histone polypeptides are recovered with these structures. Subsequent treatment of these NaTT-cross-linked structures with reducing agents in 1.0 M NaCl selectively solubilizes the intranuclear components but leaves the nuclear envelope apparently intact. The lamins remain sedimentable and are virtually absent from the soluble (intranuclear) material. Instead, the major solubilized polypeptides are (a) 68 and 63 kD polypeptides which migrate in the vicinity of lamins B and C, respectively, but are distinguishable from the lamins by immunoblotting and by uni-dimensional peptide mapping; (b) a series of basic 60-70 kD polypeptides (pI greater than 8.0) which are not recognized by anti-lamin antisera; (c) an acidic (pI 5.3) 38 kD polypeptide; and (d) a number of high molecular mass (greater than 100 kD) polypeptides. These observations not only suggest a convenient method for fractionating matrix structures from rat liver nuclei into biochemically and morphologically discrete components, but also identify a subset of major non-lamin, non-histone nuclear polypeptides (comprising approx. 20% of the total nuclear protein) whose intermolecular interactions can be reversibly stabilized apparently by intermolecular disulfide bond formation by NaTT.

Characterization of a phosphatidylinositol 4-phosphate-specific phosphomonoesterase in rat liver nuclear envelopes

Incubation of rat liver nuclear envelopes with [gamma-32P]ATP resulted in the synthesis of phosphatidylinositol-[4-32P]phosphate (PIP). Degradation of endogenously labeled PIP was observed upon the dilution of the labeled ATP with an excess of unlabeled ATP. This degradation was most rapid in the presence of EDTA, and was inhibited by MgCl2 and CaCl2. To further characterize the degradative activity, phosphatidylinositol[4-32P]phosphate and phosphatidylinositol [4,5-32P]bisphosphate (PIP2) were synthesized and isolated from erythrocyte plasma membranes. The 32P-labeled phospholipids were then resuspended in 0.4% Tween 80, a detergent that did not inhibit degradation of endogenously labeled PIP, and mixed with nuclear envelopes. [32P]PIP and [32P]PIP2 were degraded at rates of 2.25 and 0.04 nmol min-1 mg nuclear envelope protein-1, respectively. Only 32P was released from phosphatidyl[2-3H]inositol-[4-32P]phosphate, indicating that hydrolysis of PIP was due to a phosphomonoesterase activity (EC 3.1.3.36) in nuclear envelopes. Similarly, anion-exchange chromatographic analysis of the water-soluble products released from [32P]PIP indicated that inorganic phosphate was the sole 32P-labeled product. Hydrolysis of PIP was most rapid at neutral pH, and was not affected by inhibitors of acid phosphatase or alkaline phosphatase. Hydrolysis of PIP was also not inhibited by nonspecific phosphatase substrates, such as glycerophosphate, p-nitrophenylphosphate, AMP, or glucose 6-phosphate. Hydrolysis was stimulated by putrescine, and was inhibited by inositol 2-phosphate, spermidine, spermine, and neomycin.

Spatial distribution of DNA loop attachment and replicational sites in the nuclear matrix

Biochemical fractionation was combined with high resolution electron microscopic autoradiography to study the localization in rat liver nuclear matrix of attached DNA fragments, in vivo replicated DNA, and in vitro synthesized DNA. In particular, we determined the distribution of these DNA components with the peripheral nuclear lamina versus more internally localized structural elements of isolated nuclear matrix. Autoradiography demonstrated that the bulk of in vivo newly replicated DNA associated with the nuclear matrix (71%) was found within internal matrix regions. A similar interior localization was observed in isolated nuclei and in situ in whole liver tissue. Likewise, isolated nuclear lamina contained only a small amount (12%) of the total matrix-bound, newly replicated DNA. The structural localization of matrix-bound DNA fragments was examined following long-term in vivo labeling of the DNA. The radioactive DNA fragments were found predominantly within interior regions of the matrix structure (77%), and isolated nuclear lamina contained less than 15% of the total nuclear matrix-associated DNA. Most of the endogenous DNA template sites for the replicative enzyme DNA polymerase alpha (approximately 70%) were also sequestered within interior regions of the matrix. In contrast, a majority of the endogenous DNA template sites for DNA polymerase beta (a presumptive repair enzyme) were closely associated with the peripheral nuclear lamina. A similar spatial distribution for both polymerase activities was measured in isolated nuclei before matrix fractionation. Furthermore, isolated nuclear lamina contained only a small proportion of total matrix-bound DNA polymerase alpha endogenous and exogenous template activities (3-12%), but a considerable amount of the corresponding beta polymerase activities (47-52%). Our results support the hypothesis that DNA loops are both anchored and replicated at nuclear matrix-bound sites that are predominantly but not exclusively associated with interior components of the matrix structure. Our results also suggest that the sites of nuclear DNA polymerase beta-driven DNA synthesis are uniquely sequestered within the characteristic peripheral heterochromatin shell and associated nuclear envelope structure, where they may potentially participate in DNA repair and/or replicative functions.