Assembly of 5S ribosomal RNA is required at a specific step of the pre-rRNA processing pathway

A collection of yeast strains surviving with mutant 5S RNA has been constructed. The mutant strains presented alterations of the nucleolar structure, with less granular component, and a delocalization of the 25S rRNA throughout the nucleoplasm. The 5S RNA mutations affected helix I and resulted in decreased amounts of stable 5S RNA and of the ribosomal 60S subunits. The shortage of 60S subunits was due to a specific defect in the processing of the 27SB precursor RNA that gives rise to the mature 25S and 5.8S rRNA. The processing rate of the 27SB pre-rRNA was specifically delayed, whereas the 27SA and 20S pre-rRNA were processed at a normal rate. The defect was partially corrected by increasing the amount of mutant 5S RNA. We propose that the 5S RNA is recruited by the pre-60S particle and that its recruitment is necessary for the efficient processing of the 27SB RNA precursor. Such a mechanism could ensure that all newly formed mature 60S subunits contain stoichiometric amounts of the three rRNA components.

Fragile X mental retardation protein: nucleocytoplasmic shuttling and association with somatodendritic ribosomes

Fragile X syndrome, a leading cause of inherited mental retardation, is attributable to the unstable expansion of a CGG-repeat within the FMR1 gene that results in the absence of the encoded protein. The fragile X mental retardation protein (FMRP) is a ribosome-associated RNA-binding protein of uncertain function that contains nuclear localization and export signals. We show here detailed cellular localization studies using both biochemical and immunocytochemical approaches. FMRP was highly expressed in neurons but not glia throughout the rat brain, as detected by light microscopy. Although certain structures, such as hippocampus, revealed a strong signal, the regional variation in staining intensity appeared to be related to neuron size and density. In human cell lines and mouse brain, FMRP co-fractionated primarily with polysomes and rough endoplasmic reticulum. Ultrastructural studies in rat brain revealed high levels of FMRP immunoreactivity in neuronal perikarya, where it is concentrated in regions rich in ribosomes, particularly near or between rough endoplasmic reticulum cisternae. Immunogold studies also provided evidence of nucleocytoplasmic shuttling of FMRP, which was localized in neuronal nucleoplasm and within nuclear pores. Moreover, labeling was observed in large- and small-caliber dendrites, in dendritic branch points, at the origins of spine necks, and in spine heads, all known locations of neuronal polysomes. Dendritic localization, which was confirmed by co-fractionation of FMRP with synaptosomal ribosomes, suggests a possible role of FMRP in the translation of proteins involved in dendritic structure or function and relevant for the mental retardation occurring in fragile X syndrome.

Translocation of RNA granules in living neurons

Sorting of RNAs to specific subcellular loci occurs in diverse settings from fly oocytes to mammalian neurons. Using the membrane-permeable nucleic acid stain SYTO 14, we directly visualized the translocation of endogenous RNA in living cells. Labeled RNA was distributed nonrandomly as discrete granules in neuronal processes. The labeled granules colocalized with poly(A+) mRNA, with the 60S ribosomal subunit, and with elongation factor 1alpha, suggesting that granules represent a translational unit. A subset of labeled granules colocalized with beta-actin mRNA. Correlative light and electron microscopy indicated that the fluorescent granules corresponded to clusters of ribosomes at the ultrastructural level. Poststaining of sections with heavy metals confirmed the presence of ribosomes within these granules. In living neurons, a subpopulation of RNA granules was motile during the observation period. They moved at an average rate of 0.1 microm/sec. In young cultures their movements were exclusively anterograde, but after 7 d in culture, one-half of the motile granules moved in the retrograde direction. Granules in neurites were delocalized after treatment with microtubule-disrupting drugs. These results raise the possibility of a cellular trafficking system for the targeting of RNA in neurons.

Translational machinery in dendrites of hippocampal neurons in culture

In neurons, several mRNAs are selectively delivered to dendritic domains where they are presumably translated by local protein synthetic machinery. Although electron microscopy has identified polyribosomes in dendrites, in particular in postsynaptic dendritic compartments, the functional composition of the local protein synthetic apparatus and the scope of its translational capacity have not been analyzed. To ascertain the translational competence of dendrites, we have probed hippocampal neurons in primary culture for various integral and associated factors of the translational apparatus. We report here that dendrites of such neurons are equipped with a spectrum of translational machinery components, including ribosomes, tRNAs, initiation and elongation factors, and elements of the cotranslational signal recognition mechanism. These components are differentially and nonuniformly distributed in dendritic arbors. Their dendritic location illustrates the soma-independent potential of dendrites to synthesize selected proteins in local domains.

Ribosomal frameshifting in yeast viruses

Proper maintenance of translational reading frame by ribosomes is essential for cell growth and viability. In the last 10 years it has been shown that a number of viruses induce ribosomes to shift reading frame in order to regulate the expression of gene products having enzymatic functions. Studies on ribosomal frameshifting in viruses of yeast have been particularly enlightening. The roles of viral mRNA sequences and secondary structures have been elucidated and a picture of how these interact with host chromosomal gene products is beginning to emerge. The efficiency of ribosomal frameshifting is important for viral particle assembly, and has identified ribosomal frameshifting as a potential target for antiviral agents. The availability of mutants of host chromosomal gene products involved in maintaining the efficiency of ribosomal frameshifting bodes well for the use of yeast in future studies of ribosomal frameshifting.

A Cucumis sativus cell-free translation system: preparation, optimization and sensitivity to some antibiotics and ribosome inactivating proteins

A cell-free translation system was prepared from 3- to 5-day-old embryonic axes of gherkin (Cucumis sativus L.). The system was optimized for Mg²⁺ , K⁺ , NH⁺₄ , high speed supernatants, tRNA mixture from wheat germ, time and temperature. The system translates efficiently both endogenous mRNA (using a 30000 g supernatant) and polyuridylic acid (using either a 30000 g supernatant or a 100000 g supernatant supplemented with purified ribosomes). Translation by gherkin ribosomes was inhibited by several well-known eukaryotic inhibitors, antibiotics and ribosome-inactivating proteins. A translational inhibitory activity found in Cucumis sativus L. dry seeds acted on polypeptide synthesis carried out by cell-free systems from several mammals and plants, including gherkin embryonic axes. Our results indicate that the inhibitor is located in the seed bark and cotyledons, and is either blocked or absent in the embryonic axes, thus allowing the isolation of active gherkin ribosomes. The presence of the putative inhibitor appeared to be unevenly distributed in developing plants.

Changes in mitochondrial structure and function in 9l rat brain tumor cells treated in vitro with alpha-difluoromethylornithine, a polyamine biosynthesis inhibitor

Mitochondrial structure and function were studied in 9L rat brain tumor cells depleted of polyamines by alpha-difluoromethylornithine, an enzyme-activated irreversible inhibitor of ornithine decarboxylase. Cells treated with methylglyoxal bis(guanylhydrazone), a reversible inhibitor of S-adenosylmethionine decarboxylase, were used for comparison because this polyamine biosynthesis inhibitor is known to cause structural and functional disruption of mitochondria. A significant increase in mitochondrial size, measured quantitatively, was found in alpha-difluoromethylornithine-treated cells (10 mM for 72 hr) compared with untreated cells (P < 0.001). This increase in mitochondrial size was reversed when putrescine was added to the cultures for 24 hr after alpha-difluoromethylornithine treatment. Putrescine alone had no effect on the size of mitochondria. Treatment of cells with methylglyoxal bis(guanylhydrazone) (80 muM for 48 hr) caused only a slight increase in mitochondrial size compared with mitochondria in untreated cells (P < 0.05) and failed to produce the dramatic ultrastructural changes reported in other cell lines. Ultrastructural examination revealed an increase in cytoplasmic and membrane-associated ribosomes in alpha-difluoromethylornithine-treated cells, an increase in cytoplasmic ribosomes in methylglyoxal bis(guanylhydrazone)-treated cells, and an increase in membrane-bound ribosomes in putrescine-treated cells. In cells treated first with alpha-difluoromethylornithine and then with putrescine, the distribution of ribosomes was normal. The distributions of ribosomes were not quantitatively assessed. Pyruvate utilization, a measure of mitochondrial function, was decreased in cells treated with 10 mM alpha-difluoromethylornithine for 72 hr, compared with untreated cells. Restoration of intracellular polyamine levels by the addition of putrescine 24 hr before analysis reversed this phenomenon. Putrescine treatment alone did not affect pyruvate utilization. Pyruvate utilization in methylglyoxal bis(guanylhydrazone)-treated cells was depressed to a greater extent than that in alpha-difluoromethylornithine-treated cells.

Posttranscriptional modification of mRNA conformation: mechanism that regulates erythromycin-induced resistance

The nucleotide sequence of a gene in plasmid pE194 responsible for erythromycin-induced resistance, including regulation of the resistance phenotype, is reported. A DNA fragment from plasmid pE194, obtained by digestion with Taq I restriction endonuclease, was cloned in Bacillus subtilis by using pC194 as the plasmid cloning vector. Erythromycin-resistant, inducible transformant clones containing the Taq I fragment A were obtained in which the expression of resistance was similar to that found in the original pE194 background; an interpretative model of the regulation of the erythromycin-resistance determinant is proposed based on the sequence of the Taq I A fragment. The cloned Taq I A fragment consists of 1442 base pairs and has open reading frames capable of coding for a peptide and a protein containing 19 and 243 amino acids, respectively, referred to as the "leader peptide" and "29,000 protein." Between the putative transcriptional start site and the ribosome binding site for 29,000-protein synthesis, the promoter region contains four complementary inverted repeat sequences named "1, 2, 3, and 4," respectively, in which 1 is complementary to 2, 2 is complementary to 3, and 3 is complementary to 4. Sequence 1 encodes the COOH-terminal half of the leader peptide, whereas the ribosome binding site for synthesis of 29,000 protein is sequestered in a loop formed by the association of 3 and 4. The 29,000-protein promoter region does not appear to contain any transcription stop signal. We propose a model for regulation of erythromycin resistance according to which ribosomes engaged in leader peptide synthesis are partially inhibited by optimal inducing (i.e., subinhibitory) concentrations of erythromycin that, in turn, cause an accumulation of these partially inhibited ("stalled") ribosomes in sequence 1. During induction, the translationally inactive states of association of the inverted repeats, postulated to be 1 plus 2 and 3 plus 4, respectively, are perturbed by a high level of stalled ribosome occupancy in sequence 1, and in the resultant redistribution, 2 associates with 3, freeing 4 and thereby freeing the ribosome binding site sequestered by the association of 3 and 4. Sequence alterations at the 5' end of the 29,000-protein coding region associated with mutation to constitutive expression have been localized to the inverted complementary repeats, and determination of base changes in eight mutants are all capable of reducing the stability of the postulated stems in a manner consistent with predictions made by the model.

Localization of eukaryotic initiation factor 3 on native small ribosomal subunits

The localization of eukaryotic initiation factor 3(eIF-3) on native small ribosomal subunits has been established by electron microscopy through a comparison of native small ribosomal subunits with derived subunits and with native subunits stripped of eIF-3. Small subunits derived from reticulocyte ribosomes by the puromycin/KCl method are seen in electron micrographs as elongated particles, divided by a heavily stained partition into approximately one-third and two-third domains. Most particles (60-70%) observed in electron micrographs of native small subunit preparations resemble derived small subunits, but have an additional mass attached to one side, thus producing profiles with a three-lobed appearance. The mass measures approximately 160 x 100 x 60 A, and its particle weight is estimated to be about one-third to one-half that of a 40S subunit. The site of attachment of the additional mass is located on a prominence extending from the central part of the small subunit and is separated by a cleft from the smaller third of the subunit. The remaining particles in preparations of native subunits resemble the profiles seen in electron micrographs of derived subunits. After removal of eIF-3 by treatment with high concentrations of salt, profiles observed in electron micrographs of washed, native subunits were indistinguishable from those of derived subunits. Since removal of eIF-3 coincided with removal of a mass of the correct molecular weight, subunits with the three-lobed appearance are identified as native small subunits carrying eIF-3.

Effect of initiation factor 3 binding on the 30S ribosomal subunits of Escherichia coli

Under certain conditions, initiation factor 3 (IF-3) can cause the release of aminoacyl-tRNA bound to 30S ribosomal subunits of E. coli. It is shown that this IF-3-induced aminoacyl-tRNA release cannot be attributed to either nucleolytic attack or competition between IF-3 and aminoacyl-tRNA for the same ribosomal binding site. It was found that the 30S-aminoacyl-tRNA-codon complexes formed in the absence of IF-3 are intrinsically different from those prepared in the presence of IF-3. In the absence of IF-3, the ribosomal binding of aminoacyl-tRNA is a virtually irreversible process, since the bound aminoacyl-tRNA can neither be spontaneously released upon dilution nor exchanged for unbound aminoacyl-tRNA. In the presence of IF-3, the binding of one molecule of IF-3 per 30S ribosome renders the binding of aminoacyl-tRNA reversible upon dilution and promotes exchange between bound and unbound aminoacyl-tRNA. It is suggested that this difference is due to a conformational transition of the 30S ribosomal subunit induced by the binding of IF-3. The possible implications of this finding in relation to the mechanism of action of IF-3 and its functional role in the cell are discussed.

Studies on a factor enhancing colicin E3 activity in vitro

The mechanism of action of colicin E3 (E3) was investigated in an in vitro system. Purified ribosomes are less susceptible to E3 than crude or washed ribosomes. A factor was found in the supernatant fraction of normal Escherichia coli cells that stimulates inactivation of ribosomes by E3, and on addition of this factor, about one tenth as much E3 was required for inactivation of ribosomes. On heating a mixture of E3 and this factor above 60 degrees , the ribosome inactivating activity of E3 increased greatly, and an amount corresponding to 0.01 mug of E3 was sufficient to inactivate 1.0 A(260) unit of ribosomes completely. By this treatment bacteriocidal activity of E3 decreased considerably, as the ratio of the two activities of E3 (ribosome inactivating activity and bacteriocidal activity) increased to 6 x 10(4)-fold. It is evident that the two activities do not run in parallel. This heat-treated product cleaved 16S rRNA in the same way as E3. These results suggest that inactivation of ribosomes is not due to colicin molecules prepared by the standard procedure, but to a modified form of them.

Reversibility of the pyrophosphoryl transfer from ATP to GTP by Escherichia coli stringent factor

The stringent factor-catalyzed, ribosome-dependent synthesis of guanosine polyphosphates is found to be reversible. The reverse reaction specifically requires 5'-AMP as the pyrophosphoryl acceptor, and guanosine 5'-triphosphate-3'-diphosphate is preferentially utilized as the pyrophosphoryl donor. The primary products of the reaction are GTP and ATP. The reverse reaction is strongly inhibited by the antibiotics thiostrepton and tetracycline, and by ATP and beta-gamma-methylene-adenosine-triphosphate, but not by ADP, GTP, and GDP. The reverse reaction occurs under conditions for nonribosomal synthesis. The overall reaction for stringent factor-catalyzed guanosine polyphosphate formation may thus be formulated: (p)pp5'G + ppp5'A right harpoon over left harpoon (p)pp5'G3'pp + p5'A.

Characterization of RNA from noninfectious virions produced by sarcoma positive-leukemia negative transformed 3T3 cells

RNA from noninfectious virions produced by two established clonal lines of sarcoma positive-leukemia negative (S+L-)-transformed 3T3 cells has been characterized. RNA from virions or nucleoids of S+L--(C243) cells consisted of three to four sizes: +/-44 S (6%), 28 S (17%), 18 S (38%), and <18 S (39%). 28S virion RNA contained some virus-specific information demonstrable by RNA.DNA hybridization with a DNA probe derived from the RNA-directed DNA polymerase product of murine sarcoma-leukemia virus, while parallel studies indicated that 28S ribosomal RNA from ribosomal subunits of transformed and nontransformed 3T3 cells did not contain virus-specific information. In contrast to the S+L-(C243) virions, RNA from virions or nucleoids of S+L-(D56) cells consisted of five sizes: 80 S (6%), 68 S (8%), 56 S (5%), 28 S (28%), and <28 S (53%). Thermal dissociation studies suggested that this S+L- genome is comprised of 28S RNA subunits. From these studies we postulate that the 28S viral RNA is most probably the monomeric genome of S+L- virions.

Intervent dilution chromatography: concept for separation of strongly interacting macromolecules

Intervent dilution chromatography separates interacting macromolecules by subjecting them to a dynamic environment in which the association constant is continuously varied. The dynamic environment is produced by using the sieving properties of a gel to repeatedly propel the molecular complex across an intervent boundary. Behind the boundary, at high intervent concentrations, the complex dissociates; ahead of the boundary, the component molecules are separated by adsorption processes. By selective adjustment of the intervent composition of the sample and the conditions of column equilibration, the process is adapted to a particular need. This report describes the chromatographic concept and shows how parameters are adjusted to obtain the desired separation. In this study a particularly difficult separation, i.e., the separation of ribosomal proteins from ribosomal RNA, is chosen to illustrate the power of the procedure.

Mechanism of protein chain termination: further characterization of a mutant defective in a new protein synthesis factor

Mutant N4316 is conditionally lethal at 43 degrees . At 36 degrees it suppresses the termination codons UGA and UAA, but not the UAG codon or a missense mutant of T4 bacteriophage. In vitro, a factor rescues protein synthesis from a temperature-dependent arrest when N4316 extracts are used with RNA from bacteriophage f2. Analyses of the substrate in the arrested synthesis and of the product of the rescue reaction indicate that the factor works at the level of coat protein termination, and that it also affects the synthesis of noncoat protein products. The rescue factor is different from the release factors RF-1, RF-2, and RF-3. Model systems previously used to study release fail to score for at least one vital function in protein chain termination.

Colicin E3: a unique endoribonuclease

The question of whether or not a cellular ribonuclease is involved in the cleavage of 16S ribosomal RNA by colicin E3 was investigated. For this purpose ribosomes from strains devoid of some ribonucleases or ribosomes in which ribonucleases had been inactivated by heat or removed by extensive washings were used for the colicin reaction. Since the 16S RNA of all these different ribosomes, and even of the most extensively washed ribosomes, was cleaved by colicin E3, it is suggested that cellular ribonucleases are not involved in colicin E3 action. Thus, colicin E3 seems to be a unique endoribonuclease.

Release of polypeptide chain initiation factor IF-2 during initiation complex formation

Polypeptide chain initiation factor IF-2 binds to 30S ribosomal subunits. This binding is enhanced by IF-1 and IF-3. During GTP-dependent formation of a 70S initiation complex, IF-2 is released from the ribosome. During 70S initiation complex formation dependent on the methylene analogue of GTP, GMPPCH(2)P, IF-2 is not released, but remains bound to the 70S ribosome. This result suggests that IF-2 release requires GTP hydrolysis. In agreement with this presumed requirement, IF-2 functions catalytically with GTP, but stoichiometrically with GMPPCH(2)P, in bringing about 70S initiation complex formation.

Elongation factor T-dependent hydrolysis of guanosine triphosphate resistant to thiostrepton

Methanol stimulates the hydrolysis of GTP catalyzed by bacterial ribosomes in the presence of the chain elongation factor T (EF-T). The methanol-stimulated activity is uncoupled from aminoacyl-tRNA binding to the ribosomes and does not require the presence of either synthetic polynucleotide messenger or aminoacyl-tRNA. When these reactants are present, along with EF-T, GTP, and methanol, the ribosomal binding of aminoacyl-tRNA is inhibited by thiostrepton but the uncoupled, EF-T-dependent hydrolysis of GTP is resistant to the antibiotic.

A new method for the determination of biological quarternary structure by neutron scattering

Determination of quaternary structure by neutron scattering is proposed. The method gives the identity and relative spatial position of each component of a complex, provided that the complex can be obtained in deuterated form and can be reconstituted from its separated parts. If two components are rich in hydrogen and if the rest of the complex is deuterated, the contrast in scattering power permits the measurement of the separation of the pair from an interference cross term. The structure is obtained by triangulation from a set of measured pair separations.

Translocation of messenger RNA and "accommodation" of fMet-tRNA

Messenger RNA is moved a distance of approximately three nucleotides in the 5' direction relative to the ribosome during the translocation of peptidyl-tRNA from the A to the P site. This movement is catalyzed by G factor and is dependent on the hydrolysis of GTP. In contrast, mRNA is not moved during the f(2)-catalyzed hydrolysis of GTP that is involved in the activation of ribosome-bound fMet-tRNA. This second type of GTP-dependent reaction has been named "Accommodation".

Initial dipeptide formation in hemoglobin biosynthesis

Initiation factors M(1) + M(2) from reticulocyte ribosomes bind Met-tRNA(F) to rabbit reticulocyte ribosomes containing endogenous hemoglobin mRNA. The initial binding of Met-tRNA(F) appears to be to the small ribosomal subunit. The Met-tRNA(F) is able to participate in what is presumed to be the first peptide bond in the formation of hemoglobin, namely the synthesis of a methionyl-valine dipeptide. The formation of this methionyl-valine dipeptide requires Met-tRNA(F), initiation factors M(1), M(2), and M(3), as well as Val-tRNA and T(1). No synthesis of methionyl-valine dipeptide takes place if Met-tRNA(F) is replaced by Met-tRNA(M), or if initiation factor M(3) is omitted. Thus, Met-tRNA(F) appears to be the initiator tRNA for hemoglobin biosynthesis and M(3), although required for the synthesis of the first peptide bond of hemoglobin, does not appear to be necessary, under the experimental conditions studied, for Met-tRNA(F) binding.