Proteins and RNA in mouse L cell core nucleoli and nucleolar matrix

When intact nucleoli were prepared in the presence of enough leupeptin and phenylmethanesulfonyl fluoride to inhibit protease action, electrophoretic patterns of their constituent proteins were reproducible and very similar for L, HeLa, CHO, and rat hepatoma cells. "Core nucleoli", defined as that nucleolar fraction which remains after extensive DNase I action, had a protein composition similar to that of crude intact nucleoli, but were enriched for snRNA U3. Core nucleolar proteins included all of the histones, ribosomal proteins, and phosphorylated proteins with mobilities corresponding to 110 (protein C23) and 160 kilodaltons (kDa). The presence of protein C23 and of lamins A and C in nucleoli and core nucleoli was further verified by reaction with specific antibodies after one- or two-dimensional electrophoresis. A class of higher molecular weight proteins, ranging from 70 to greater than 200 kDa by mobility, was observed. It included at least 25 specific proteins, almost all of them highly acidic (pI less than 3.5). Treatment of core nucleoli with ethylenediaminetetraacetic acid/hypotonic buffer solubilized 30-35% of the small and large molecular weight proteins. In contrast, washing core nucleoli with 2 M NaCl selectively released U3 snRNA, 95% of the ribosomal RNA, and about half of the proteins, including C23 and most of the histones, ribosomal proteins, and other lower molecular weight proteins. The fraction remaining insoluble, "nucleolar matrix", was enriched for proteins of 34 and 57 kDa, lamins A and C, and most higher molecular weight proteins, as well as a portion of ribosomal spacer DNA.

Irreversible block of the mycelial-to-yeast phase transition of Histoplasma capsulatum

p-Chloromercuriphenylsulfonic acid (PCMS), a sulfhydryl inhibitor, prevented the mycelial-to-yeast transition of the dimorphic fungal pathogen, Histoplasma capsulatum. The effect of PCMS was specific for the mycelial-to-yeast transformation; it had no effect on growth of either the yeast or mycelial forms or on the yeast-to-mycelial transition. The failure of PCMS-treated mycelia to transform to yeast was permanent and irreversible. PCMS-treated mycelia could not infect mice but could stimulate resistance to infection by a pathogenic strain of Histoplasma capsulatum. These results suggest a new general strategy for vaccine development in diseases caused by dimorphic pathogens.

Why is processing of 23 S ribosomal RNA in Escherichia coli not obligate for its function?

In an RNase III-deficient mutant of Escherichia coli, all 23 S ribosomal RNA in ribosomes is present in an unprocessed form with a double-stranded stem at the base of the molecule stable enough to be detected by electron microscopy under conditions where all other secondary structure is denatured. Molecules with variable stem lengths enter freely into polysomes, consistent with the existence of a similar but much shorter stem in mature 23 S rRNA in wild-type ribosomes.

DNase I-resistant nontranscribed spacer segments of mouse ribosomal DNA contain poly(dG-dT).poly(dA-dC)

The nontranscribed spacer regions (NTS) that adjoin the coding portion of mouse ribosomal DNA are protected in nucleoli against exhaustive DNase I digestion. Since these sequences are degraded by the enzyme after they are extracted by phenol, the protection is suggested to result from the binding of specific proteins. The nucleolar structure would thus be organized to protect NTS sequences and expose the coding sequences for transcription. We show here that these protected sequences include tracts of poly(dG-dT).poly(dA-dC). We also report that these sequences are localized in regions flanking the rRNA transcription unit. These sequences can potentially form Z-DNA. The organized DNase I-resistant NTS structure in which they participate could be involved in structuring the nucleolus or in regulating transcription because poly(dG-dT).poly(dA-dC) sequences and portions of spacer rDNA can serve as transcriptional enhancer elements.

Ordered processing of Escherichia coli 23S rRNA in vitro

In an RNase III-deficient strain of E. coli 23S pre-rRNA accumulates unprocessed in 50S ribosomes and in polysomes. These ribosomes provide a substrate for the analysis of rRNA maturation in vitro. S1 nuclease protection analysis of the products obtained in in vitro processing reactions demonstrates that 23S rRNA processing is ordered. The double stranded stem of 23S rRNA is cleaved by RNase III in vitro to two intermediate RNAs at the 5' end and one at the 3' end. Mature termini are then produced by other enzyme(s) in a soluble protein fraction from wild-type cells. The nature of the reaction at the 5' end is not clear, but the reaction at the 3' end is exonucleolytic, producing three heterogeneous mature termini. The two reactions are coordinated; 3' end maturation progresses concurrently with cleavages at the 5' end. Two results suggest a possible link between final maturation and translation: in vitro, mature termini are formed efficiently in the presence of additives required for protein synthesis; and all the processing intermediates detected from in vitro reactions are also found in polysomes from wild-type cells.

Electron microscopy of secondary structure in partially denatured precursor and mature Escherichia coli 16 S and 23 S rRNA

The secondary structure of 16 S and 23 s rRNA sequences in 30 S preribosomal RNA of Escherichia coli was analyzed by electron microscopy after partial denaturation and compared to mature 16 S and 23 S rRNA examined under the same conditions. The sequences in the pre-rRNA notably lack the specific loops that dominate the 5'-terminal regions of mature 16 S and 23 S rRNA. In other respects, the sizes and locations of loops in the 23 S rRNA sequence are qualitatively very similar in mature and pre-rRNA. Eleven of 12 loops outside of the 5'-terminal domain correspond, with the most frequent features in the 3'-half of the molecule. In contrast, the sizes and locations of loops in the 16 S rRNA sequence differ between precursor and mature forms. In the pre-rRNA, instead of the 370-nucleotide 5'-terminal loop of mature rRNA, some 1000-nucleotide terminal loops are observed. The pre-rRNA also shows a frequent 610-nucleotide central loop and a large 1240-nucleotide loop not seen in the mature rRNA. Also, in the 3'-region of the sequence, the largest loops in pre-rRNA are 120 nucleotides shorter than in mature rRNA. We suggest that the structure of pre-rRNA may promote some alternate conformational features, and that these could be important during ribosome formation or function.

Alternative conformations in Escherichia coli 16S ribosomal RNA

Partially denatured 16S rRNA from 30S ribosomes shows features of secondary structure in electron microscopy that correspond to the well accepted secondary structure model derived from chemical modification and phylogenetic data. However, a very different conformation is seen in precursor 16S rRNA sequences contained within 30S pre-rRNA transcripts: the major 5'-terminal loop is absent, and several additional quite stable large loops, symmetrically placed in the molecule, are present. Features of the alternative structure are also seen in mature 16S rRNA from Escherichia coli and from two Bacillus species when heated in certain buffers. Microscopy thus reveals specific features of alternative conformations and their relative stabilities, suggesting a possible transition during ribosome formation.

Localization of specific rDNA spacer sequences to the mouse L-cell nucleolar matrix

Mouse L-cell nucleoli were isolated from sonicated nuclei by centrifugation and extensively treated with pancreatic DNase or micrococcal nuclease to obtain "core nucleoli." Core nucleoli still contained the precursors to rRNA and about 1% of the total nuclear DNA, which remained tightly bound even after the removal of some chromatin proteins with 2 M NaCl. The core nucleolar DNA electrophoresed in a series of discrete bands, 20 to about 200 base pairs in length. Hybridization tests with specific DNA probes showed that the DNA was devoid of sequences complementary to mouse satellite, mouse Alu-like, and 5S RNA sequences. It also lacked sequences coding for cytoplasmic rRNA species, since it did not hybridize to the 18S to 28S portion of rDNA in Northern blot analyses and none of it was protected by hybridization to a 100-fold excess of total cytoplasmic RNA in S1 nuclease assays. However, the core nucleolar DNA did hybridize to nontranscribed and external transcribed spacer rDNA sequences. We infer that specific portions of rDNA are protected from DNase action by a tight association with nucleolar structural proteins.

Electron microscopy of the secondary structure in partially denatured rRNAs of Escherichia coli and Bacillus stearothermophilus

Partially denatured 16S and 23S rRNAs from the thermophile Bacillus stearothermophilus show characteristic loop patterns when observed by electron microscopy. The patterns are very similar to those seen in rRNAs from Escherichia coli. At least 2 of 4 most stable interactions in 16S rRNA and 8 of 12 interactions in 23S rRNA are in common for the two species. These interactions correspond well to features of secondary structure in models inferred for rRNA from phylogenetic sequence comparisons and chemical modification studies. However, two additional large loops, enclosing large portions of the 23S rRNA, have been detected in B. stearothermophilus for the first time, and even though other loops are similar, their relative frequencies vary in the two species. Much of the variation is consistent with relative delta G degree values for putative base-paired stems at the base of different loops; but the 5'-terminal loops in 23S rRNA, for example, are unaccountably far less stable in B. stearothermophilus. Also, in general, structural features are not differentially stabilized in B. stearothermophilus; the relative stability of secondary structure in its ribosomes at elevated growth temperatures must involve interactions with ribosomal proteins or other cellular components.

Escherichia coli 23S ribosomal RNA truncated at its 5' terminus

In a strain of E. coli deficient in RNase III (ABL1), 23S rRNA has been shown to be present in incompletely processed form with extra nucleotides at both the 5' and 3' ends (King et al., 1984, Proc. Natl. Acad. Sci. U.S. 81, 185-188). RNA molecules with four different termini at the 5' end are observed in vivo, and are all found in polysomes. The shortest of these ("C3") is four nucleotides shorter than the accepted mature terminus. In growing cells of both wild-type and mutant strains up to 10% of the 23S rRNA chains contain the 5' C3 terminus. In stationary phase cells, the proportion of C3 termini remains the same in the wild-type cells; but C3 becomes the dominant terminus in the mutant. Species C3 is also one of the 5' termini of 23S rRNA generated in vitro from larger precursors by the action of purified RNase III. We therefore suggest that some form of RNase III may still exist in the mutant; and since no cleavage is detectable at any other RNase III-specific site, the remaining enzyme would have a particular affinity for the C3 cleavage site, especially in stationary phase cells. We raise the question whether the C3 terminus has a special role in cellular metabolism.

Involvement of oxidative damage in erythrocyte lysis induced by amphotericin B

Lysis of human erythrocytes induced by amphotericin B was retarded when the oxygen tension of the incubation mixture was reduced or when the antioxidant catalase was added; lysis was accelerated when cells were preincubated with the prooxidant ascorbate. In the atmosphere of reduced oxygen tension, the erythrocytes containing carboxyhemoglobin lysed at a slower rate than did the cells containing oxyhemoglobin. Consistent with a role for oxidative damage in lysis, the mixture of erythrocytes and amphotericin B showed an increase in malonyldialdehyde, the product of peroxidation, which paralleled the progression of hemolysis. In contrast, the permeabilizing effect of amphotericin B, measured as a decrease in intracellular K+, was not affected by changes in oxygen tension, catalase, or ascorbate treatment. These results imply that oxidant damage is involved in the lytic, but not in the permeabilizing, action of amphotericin B.

Stimulatory, permeabilizing, and toxic effects of amphotericin B on L cells

High concentrations of amphotericin B (AmB) killed mouse L cells, but low concentrations increased plating efficiency and stimulated the incorporation of labeled precursors into DNA and RNA. Thus, there were two disparate effects of AmB on L cells, stimulatory and toxic, and they occurred in distinct dose-related stages. AmB also affected the permeability of L cells. In dose-response studies, increases in cell membrane permeability, measured as the loss of K+ ions, occurred along with the stimulation of [3H]uridine incorporation into RNA. In contrast, stimulation of [3H]thymidine incorporation into DNA was only observed in cells recuperating from AmB-induced permeability changes. When the K+ concentration in the medium was lowered to 0.5 from 4.5 mM, or when 1 mM ouabain was added to the cultures, cell killing was potentiated, but the stimulatory and permeabilizing effects of subtoxic concentrations of AmB were unaffected. Furthermore, etruscomycin, a polyene antibiotic without any permeabilizing effects, nevertheless induced an enhancement of plating efficiency and of incorporation of [3H]uridine into RNA and [3H]thymidine into DNA. Our results suggest that the dose-related stimulatory, permeabilizing, and toxic effects of AmB most probably have distinct mechanisms of action and may be independent of one another.

Electron microscopy of secondary structure in partially denatured Escherichia coli 16S rRNA and 30S subunits

Loops observed in partially denatured 16S rRNA lie within three domains, each about 500 nucleotides long. The loops observed in the 5' and central domains agree well with features of the model proposed by Woese et al. [Woese, C. R., Gutell, R., Gupta, R., & Noller, H. F. (1983) Microbiol. Rev. 47, 621-669]. The structure in the 3' domain is more complex and variable but is still consistent with the model. Published psoralen cross-linking studies have reported one of the observed loops but have also identified loops other than those observed here or predicted by any secondary structure model. These loops are stabilized by increasing concentrations of Mg2+ ions and by bound ribosomal proteins. For example, protein S4 in LiCl core particles stabilizes a loop of 370 nucleotides which forms part of its putative binding site on rRNA. The loop structures are characteristic enough to permit an overall comparison of the most stable of the predicted and observed loops in 16S and 23S rRNAs. Both rRNAs show a stable 5'-terminal loop and a set of subterminal nested loops near the 3' end.

Interaction of plasma proteins and lipoproteins with amphotericin B

Amphotericin B (AmB) binds to the cholesterol in lipoproteins, as determined by comigration in density gradient ultracentrifugation and changes in the circular dichroic spectrum. The saturation curve and Scatchard plots obtained with circular dichroism suggest that four to 10 cholesterol molecules in low-density lipoproteins bind to one molecule of AmB. AmB interacts more rapidly with low- and very-low-density lipoproteins than with high-density lipoproteins, but the circular dichroic spectrum of the complexed species is the same in all three cases. AmB also binds to other proteins in blood, but much higher concentrations of these proteins than of lipoproteins are needed for comparable binding. Interaction with lipoproteins stabilizes the antifungal activity of AmB. Interaction with lipoproteins and with much higher concentrations of other proteins in blood can also inhibit the effects of AmB on red blood cells, which contain cholesterol in their plasma membranes, but not the effects on Candida albicans, whose membranes contain ergosterol. An appropriate inference is that, when used clinically, AmB circulates in blood bound to lipoproteins and other proteins. The toxic and therapeutic effects of AmB in clinical situations are thus contingent on competitive interactions between sterol-containing cellular membranes of the host and the parasite and components of blood, such as lipoproteins and proteins.

RNase III cleavage is obligate for maturation but not for function of Escherichia coli pre-23S rRNA

RNase III makes the initial cleavages that excise Escherichia coli precursor 16S and 23S rRNA from a single large primary transcript. In mutants deficient in RNase III, no species cleaved by RNase III are detected and the processing of 23S rRNA precursors to form mature 23S rRNA fails entirely. Instead, 50S ribosomes are formed with rRNAs up to several hundred nucleotides longer than mature 23S rRNA. Unexpectedly, these aberrant subunits function well enough to participate in protein synthesis and permit cell growth. Consistent with the inference that RNase III cleavages are absolutely required for 23S rRNA maturation, when 50S ribosomes from a strain deficient in RNase III were incubated with a ribosome-free extract from a RNase III+ strain, rRNA species processed by RNase III and species with normal mature 23S rRNA termini were produced.

S1 nuclease mapping analysis of ribosomal RNA processing in wild type and processing deficient Escherichia coli

S1 nuclease mapping was used to assess rRNA processing in Escherichia coli. Single-stranded DNA probes complementary to the sequences bordering each terminus of 16 S and 23 S rRNA were end-labeled, hybridized to total E. coli RNA, and treated with S1 nuclease. The resultant DNA fragments were then displayed on denaturing polyacrylamide gels. Measurements of steady state levels of precursor rRNA species and measurements of the rates of decay of precursors after transcription arrest by rifampicin gave consistent results. 1) The rRNA precursor species identified in wild type cells corresponded to those previously identified by other means. 2) In RNase III-deficient strains, mature 16 S rRNA termini form at the same rate as in wild type cells; but the normal mature termini of 23 S rRNA are never generated. 3) RNase III cleavage at the 5' end of 23 S rRNA can occur before the 3' end of the same molecule is synthesized. 4) The cleavages that generate the mature termini of 16 S rRNA are interdependent; in the BUMMER strain, slow processing at the 5' end is accompanied by slow processing at the 3' end. Thus, the kinetically observed order of processing reactions is obligate for some cleavages but not for others, and the assumption that complete rRNA processing is required for function fails for 23 S rRNA.

Structure of partially denatured Escherichia coli 23 S ribosomal RNA determined by electron microscopy

The secondary structure of 23 S ribosomal RNA was analyzed by electron microscopy after partial denaturation. A reproducible pattern of loops was seen when molecules were spread for electron microscopy in 50% formamide solutions containing various concentrations of Mg2+ and Na+. Some loops were stabilized more than others by Na+ or by Mg2+; but in general, small amounts of Mg2+ (0.5 to 1.0 mM) markedly stabilized all the major loops, as did much greater amounts of Na+ (100 mM). However, at all levels of Mg2+ examined, increasing levels of Na+ destabilized loop structures. These data are consistent with the known salt dependence of double-stranded DNA and transfer RNA structure. The four most frequently observed loops correspond, within the limits of measurement error, to the major loops in the secondary structure models of Noller et al. (1981) and Glotz et al. (1981). These four loops are, in length and position of their midpoints along the 23 S rRNA molecule: 490 +/- 50 at 250 +/- 40; 350 +/- 50 at 1860 +/- 80; 400 +/- 70 at 2330 +/- 150; and 570 +/- 100 at 2350 +/- 100. Three of the four have base-paired stems with delta G0 values among the lowest of all the loops in the two indirect models. At least two are also among the most stable loops found in computer searches of the 23 S rRNA sequence for dyad symmetry. These results demonstrate that partial denaturation mapping can both identify prominent features of secondary structure in rRNA and estimate their relative stability.

Mouse rDNA: sequences and evolutionary analysis of spacer and mature RNA regions

Two regions of mouse rDNA were sequenced. One contained the last 323 nucleotides of the external transcribed spacer and the first 595 nucleotides of 18S rRNA; the other spanned the entire internal transcribed spacer and included the 3' end of 18S rRNA, 5.8S rRNA, and the 5' end of 28S rRNA. The mature rRNA sequences are very highly conserved from yeast to mouse (unit evolutionary period, the time required for a 1% divergence of sequence, was 30 X 10(6) to 100 X 10(6) years). In 18S rRNA, at least some of the evolutionary expansion and increase in G + C content is due to a progressive accretion of discrete G + C-rich insertions. Spacer sequence comparisons between mouse and rat rRNA reveal much more extensive and frequent insertions and substitutions of G + C-rich segments. As a result, spacers conserve overall G + C richness but not sequence (UEP, 0.3 X 10(6) years) or specific base-paired stems. Although no stems analogous to those bracketing 16S and 23S rRNA in Escherichia coli pre-rRNA are evident, certain features of the spacer regions flanking eucaryotic mature rRNAs are conserved and could be involved in rRNA processing or ribosome formation. These conserved regions include some short homologous sequence patterns and closely spaced direct repeats.

Location of the initial cleavage sites in mouse pre-rRNA

The locations of three cleavages that can occur in mouse 45S pre-rRNA were determined by Northern blot hybridization and S1 nuclease mapping techniques. These experiments indicate that an initial cleavage of 45S pre-rRNA can directly generate the mature 5' terminus of 18S rRNA. Initial cleavage of 45S pre-rRNA can also generate the mature 5' terminus of 5.8S rRNA, but in this case cleavage can occur at two different locations, one at the known 5' terminus of 5.8S rRNA and another 6 or 7 nucleotides upstream. This pattern of cleavage results in the formation of cytoplasmic 5.8S rRNA with heterogeneous 5' termini. Further, our results indicate that one pathway for the formation of the mature 5' terminus of 28S rRNA involves initial cleavages within spacer sequences followed by cleavages which generate the mature 5' terminus of 28S rRNA. Comparison of these different patterns of cleavage for mouse pre-rRNA with that for Escherichia coli pre-rRNA implies that there are fundamental differences in the two processing mechanisms. Further, several possible cleavage signals have been identified by comparing the cleavage sites with the primary and secondary structure of mouse rRNA (see W. E. Goldman, G. Goldberg, L. H. Bowman, D. Steinmetz, and D. Schlessinger, Mol. Cell. Biol. 3:1488-1500, 1983).

Regulation of glucose 6-phosphate dehydrogenase expression in CHO-human fibroblast somatic cell hybrids

Human--hamster somatic cell hybrids have been obtained by fusion of a CHO line (NA31) doubly deficient in hypoxanthine guanine phosphoribosyltransferase and glucose 6-phosphate dehydrogenase (G6PD) with normal G6PD(+) human fibroblasts. Analysis of NA31 extracts has revealed that, although G6PD activity is nearly absent, significant activity can be detected with 2-deoxyglucose 6-phosphate as substrate, so that the mutant and normal forms of the enzyme can both be easily detected. The cell hybrids obtained express human G6PD. The human G6PD subunits are distributed in homodimeric molecules as well as in human--hamster heterodimeric molecules. However, whereas the amount of hamster G6PD subunits present in the hybrid is similar to that in the hamster parental cells, the amount of human G6PD subunits is decreased by 3- to 10-fold when compared to the human parental cell. These results indicate that either the expression of the G6PD gene or the stability of the gene product is altered in the hybrid. By mutagenesis and selection in diamide (a substance that oxidizes intracellular glutathione), we have isolated a clone with a 3- to 5-fold increase in human G6PD activity. This derivative may have an increased rate of expression of the human G6PD structural gene.

Electrophoretic elution of nucleic acids from acrylamide and agarose gels

A simple method for electrophoretic elution of nucleic acids from gel slices is described. The procedure utilizes a standard tube gel system and can be completed in as little as one hour. Nucleic acids are recovered in a small volume with almost 100% efficiency. The procedure is applicable equally to acrylamide and agarose gels, and small as well as large RNA and DNA molecules. The eluted nucleic acids are essentially undegraded and are suitable for a variety of structural and biological analyses.

lac Transcription in Escherichia coli cells treated with chloramphenicol

When protein synthesis was blocked by chloramphenicol in vivo, transcription initiation of lac mRNA was severely inhibited. In a promoter mutant (L8-UV5) or in wild-type cells supplemented with adenosine 3',5'-phosphate (greater than or equal to 5 mM), nearly normal initiation could be achieved, and when the mRNA chains formed were extracted, they coded for the 5'-terminal alpha-peptide of the lacZ gene in vitro. However, even under such conditions, only a fraction of RNA polymerases proceeded to the end of the Z gene in the presence of chloramphenicol; as a consequence, a wide range of sizes of mRNA was produced, and very few transcripts were formed all the way to the natural termination site of the operon. In other words, premature transcription termination occurred in chloramphenicol-treated cells, as current models predict, but terminations occurred to variable extents at several intragenic sites and apparently at least one intergenic site. Termination at intragenic sites occurred far less in cells bearing a mutation in the transcription termination factor rho.

RNase III cleavage of Escherichia coli beta-galactosidase and tryptophan operon mRNA

Purified RNase III of Escherichia coli cleaved the initial 479-nucleotide sequence of lac operon mRNA at four specific sites and also gave limited cleavage of trp operon mRNA. This action explains the inactivation of mRNA coding capacity by RNase III in vitro.