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PubMed1975

Localized mutagenesis of the aroE-strA section of the Escherichia coli chromosome coding for ribosomal proteins.

In order to obtain E. coli strains altered in ribosomal proteins the following isolation technique was used: Phage P1 grown in a streptomycin resistant E. coli strain, was mutagenized by hydroxylamine or nitrous acid, and was used to transduce into a strain auxotrophic for aroE. Transductants with streptomycin resistance and aroE prototrophy were selected and tested for their growth at various temperatures (20 degrees, 30 degrees and 42 degrees) and their response to different antibiotics. Ribosomes from seventeen transductants with an altered response to temperature or antibiotics were isolated. They were tested for alterations in their ribosomal subunit profiles by sucrose centrifugation and for altered ribosomal proteins by two dimensional gel electrophoresis. Two strains showed accumulation of 50S ribosomal precursors and three strains had an altered 50S protein L18. This protein belongs to the 5S RNA-protein complex having GTPase and ATPase activity.

Chromosome Mapping↗

PubMed1974

Thermostability of mammalian brain ribosomes and the effects of nucleoside triphosphates on their heat-sensitivity.

Mammalian brain ribosomes were found to be heat-labile. On preincubation of the ribosomes at 37 degrees C, their ability to participate in polypeptide-synthesis reactions was substantially diminished. Despite the sensitivity of ribosomal protein synthesis to heat-inactivation, preincubation resulted in no significant alterations in ribosomal sedimentation profiles or changes in the integrity of the ribosomal RNA. The thermolability of brain ribosomes was shown to be associated with their inability to bind both template RNA and aminoacyl-tRNA. Similar experiments with brain ribosomal subunits demonstrated that the small (40S) subunit was more sensitive to heat-inactivation than the large (60S) subunit. The presence of ATP (1mm) protected ribosomes from thermal inactivation, although this protection was shown to be temporary. The protection appeared to be specific to nucleoside triphosphates, since GTP and UTP also stabilized ribosomes to thermal denaturation whereas nucleoside diphosphates (ADP) and nucleoside monophosphates (AMP and cyclic AMP) did not alter ribosomal sensitivity to heat. Although 1mm concentrations of nucleoside triphosphates protected ribosomes from heat-inactivation, the presence of higher concentrations resulted in complete inactivation of ribosomal activity.

Adenosine Triphosphate↗

PubMed1977

Analysis by two-dimensional polyacrylamide gel electrophoresis of liver ribosomal subunnit proteins obtained from free and membrane-bound polysomes of unfasted animals.

Ribosomal proteins were analyzed by means of two-dimensional gel electrophoresis. To insure that the analysis included only that fraction of the ribosome actively participating in protein synthesis, only polysomal-bound ribosomes were used. This differs from previously reported analyses of liver ribosomal proteins. The ribosomal proteins were prepared from ribosomes of polysomal origin from membrane-bound and free polysomes. Membrane-bound and free liver polysomes were isolated from unfasted mice. The polysomes were purified on hydroxyapatite under conditions known to result in polysomes and ribosomes that are active in both endogenous and synthetic mRNA translation. Moreover, this is the first time that liver ribosomal protein was obtained and analyzed from animals that have not been starved prior to sacrifice. The puromycin-released ribosomes were dissociated into subunits and ribosomal proteins were analyzed by means of two-dimensional polyacrylamide gel electrophoresis. When 100-200 mug samples of the ribosomal subunit proteins were analyzed by two-dimensional electrophoresis, approximately 32 major proteins were detected for the 60 S ribosomal subunit and 25 major proteins for the 40 S ribosomal subunit. A total of 13 "fractional" ribosomal proteins was also detected in the ribosomal subunit profiles. No differences in number or mobility of the ribosomal proteins were found between the membrane-bound and free ribosome populations. We describe a system in which all ribosomal proteins are completely solubilized and quantitatively move from the first to the second dimension gel. Thus the total sample is separated and fractionated. This procedure elimates artifacts due to incomplete solubilization of ribosomal proteins, which is common for the transfer from the first- to second-dimension gel. Therefore, a more detailed and accurate analysis is achieved.

Animals↗

PubMed1995

Phenotypic and genotypic analysis of variability in Aspergillus fumigatus.

Sixty-one isolates and collection strains of Aspergillus fumigatus were compared for their phenotypic (morphological features and isoenzyme profiles) and genotypic (restriction enzyme-generated mitochondrial DNA and ribosomal DNA profiles and random amplified polymorphic DNA patterns) features. The examined strains exhibited highly variable colony morphologies and growth rates at different temperatures, but their micromorphologies and conidial diameters were characteristic of the species. Of the isoenzymes studied, the beta-arylesterase and phosphatase patterns were the most divergent, and the 61 strains could be classified into seven groups. The glucose 6-phosphate dehydrogenase and catalase isoenzyme patterns displayed only a limited variability, while the profiles of superoxide dismutase, lactate dehydrogenase, and glutamate dehydrogenase were highly conserved. The HaeIII-generated mitochondrial DNA patterns and SmaI-digested repetitive DNA and ribosomal DNA hybridization patterns of almost all strains were also invariable. The level of variation was much higher when random amplified polymorphic DNA analysis was applied. Although the patterns of the strains were very similar with most of the primers, the application of some primers made it possible to cluster the A. fumigatus isolates into several groups. The results indicate that the random amplified polymorphic DNA technique could be used more efficiently than isoenzyme analysis for typing A. fumigatus isolates. A good correlation was found between the dendrograms obtained from the isoenzyme and random amplified polymorphic DNA data, but the isoenzyme and amplified DNA patterns did not correlate with the pathogenicity, pigment production, or geographical origin of the strains. One "A. fumigatus" strain (strain FRR 1266) exhibited unique isoenzyme, mitochondrial DNA, ribosomal DNA, and random amplified polymorphic DNA patterns; it is proposed that this strain represents a new species of the section Fumigati.

Aspergillus fumigatus↗

PubMed1977

Denaturation of mouse satellite and ribosomal DNA during hydroxyapatite thermal chromatography of chromatin.

Mouse DNA and chromatin were melted on hydroxyapatite and the denaturation profiles of ribosomal and satellite DNAs were followed by hybridization with their complementary RNAs. Neither ribosomal nor bulk DNA had significantly different melting profiles in chromatin as compared to DNA. However, most of satellite DNA eluted at higher temperature from chromatin than from purified DNA. One explaination for the higher melting temperature of mouse satellite DNA in chromatin suggests that the complex between this particular DNA component and at least some proteins in chromatin is more stable than the average DNA-protein interaction.

Animals↗

PubMed2026

Ribosome stalling position, spacing, and A-site occupancy impact translation and cotranslational mRNA decay in plants.

Ribosomes can pause during mRNA translation, but what causes pausing, how pauses affect protein production, and whether they trigger cotranslational mRNA decay are poorly understood in plants. Here, we investigate the causes and consequences of ribosome pausing in Arabidopsis and maize. This is accomplished by sizing, mapping, and quantifying footprints of individual ribosomes (monosomes) and closely spaced ribosome pairs (disomes) at single-codon resolution on open reading frames (ORFs). Ribosome footprinting was combined with 5'P-degradome-seq to examine the coincidence of pausing with cotranslational decay under control conditions and brief hypoxia in Arabidopsis. The data resolve two monosome conformations and three disome configurations. These include monosomes with a vacant or occupied A-site and disomes that have collided or are separated by one or two codons. Pausing is prevalent at initiation, termination, and di-Proline codons. Di-Proline pauses do not trigger cotranslational decay but appear important in cotranslational protein processing. Brief hypoxia induces stalling of A-site vacant ribosomes at Aspartate codons, often coinciding with 5'P peaks, indicating that rate-limiting decoding can trigger cotranslational mRNA decay. Notably, actively transcribed and translated hypoxia-response mRNAs accumulate 1- to 2-codon-separated disomes and are actively degraded. Comparative analysis of footprints in the two species reveals ribosome conformations and codon-specific pausing can be conserved or lineage-specific, as exemplified by pausing at di-Prolines and on Conserved Peptide upstream ORFs. In sum, the stalling of ribosomes at specific codons, coupled with ribosome A-site occupancy and disome spacing, modulates protein production and cotranslational mRNA decay in plants.

Ribosomes↗

PubMed1979

Protein synthesis in rat brain in hypoxia, anoxia and hypoglycemia.

The effect of cerebral hypoxia on protein synthesis was investigated by exposing rats to 5% O2, and examining polypeptide synthesis and size distribution profiles of ribosomes. The findings were compared with the results from cerebral anoxia (decapitation) and hypoglycemia. In cerebral hypoxia there was suppression of polypeptide synthesis, though to a lesser extent than in cerebral anoxia, while no effect was detected in hypoglycemia. Among 4 different ribosomal fractions used for polypeptide synthesis, the microsome was the most sensitive for hypoxia and anoxia, and the polyribosome after short centrifugation was the least sensitive. The size distribution profiles of 3 different ribosomes revealed an increase in the size of the monomere-dimer complex and a decrease of the polysome peak both in cerebral hypoxia and anoxia. Comparison of the energy state and the extent of lactic acidosis in cerebral hypoxia, anoxia and hypoglycemia available in the literature and the functional and structural state of polyribosomes in the present investigation suggests that intracellular acidosis may be the main cause of the suppression of polypeptide synthesis and disaggregation of polyribosomes in hypoxia, and the depletion of energy reserve may be the main cause in anoxia-ischemia.

Animals↗

PubMed2004

Clustered bottlenecks in mRNA translation and protein synthesis.

Using a model based on the totally asymmetric exclusion process, we investigate the effects of slow codons along messenger RNA. Ribosome density profiles near neighboring clusters of slow codons interact, enhancing suppression of ribosome throughput when such bottlenecks are closely spaced. Increasing the slow codon cluster size beyond approximately 3-4 codons does not significantly reduce the ribosome current. Our results are verified by both extensive Monte Carlo simulations and numerical calculation, and provide a biologically motivated explanation for the experimentally observed clustering of low-usage codons.

Algorithms↗

PubMed1987

Effect of essential amino acids on the phosphorylation of a 40S ribosomal protein and protein synthesis in Acanthamoeba castellanii.

Reversible and multiple phosphorylation of a 40S ribosomal protein is observed in a variety of eukaryotic cells. In the primitive eukaryote Acanthamoeba, one or three phosphorylated S3 derivatives are observed during growth phase in nondefined nutrient medium (ND cells) or in chemically defined nutrient medium (D cells), respectively. In both cases, stationary phase cells exhibit nonphosphorylated S3; however, transfer of these cells into the respective fresh nutrient media results in a transient accumulation of four phosphorylated S3 derivatives. Transfer of D cells into nutrient medium, deficient in all or any single essential amino acids, leads to reversible inhibition of S3 phosphorylation and growth arrest. The low level of phosphorylated S3 is not simply the consequence of growth arrest, since in cells where growth is arrested differently, the level of phosphorylated S3 can be high. In response to amino acid deficiency, a number of other changes can be observed. These include a 2-3-fold decrease of total protein synthesis, 13 changes in the cellular protein pattern, and specific alterations in the ribosome absorbance profiles and in the distribution of poly-A+ RNA within subribosomal and ribosomal fractions. While the rate of total protein synthesis seems to be associated with the level of phosphorylated S3, the level of the synthesis of at least 10 of the particular proteins can be dissociated from the level of S3 phosphorylation.

Amino Acids, Essential↗

PubMed2002

Nep1p (Emg1p), a novel protein conserved in eukaryotes and archaea, is involved in ribosome biogenesis.

The essential Saccharomyces cerevisiae gene YLR186w [ NEP1 (nucleolar essential protein 1), also recently named EMG1 (essential for mitotic growth 1)] is highly conserved in eukaryotes and archaea. In S. cerevisiae, Nep1p is localized in the nucleus with a rod-shaped morphology, which first suggested a spindle/microtubule association for ScNEP1 (S. cerevisiae NEP1). However, in Candida albicans and in HeLa cells, Nep1p is a protein of the nucleoli. CaNEP1 (C. albicans NEP1) and HsNEP1 (Homo sapiens NEP1) heterologously complement the essential phenotype in a S. cerevisiae nep1 deletion mutant. However, the ScNEP1 spindle/microtubule phenotype is not found with HsNEP1 and CaNEP1, which shows that the spindle/microtubule association is specific for ScNep1p and that it is not the primary essential function of Nep1p. A temperature-sensitive ScNEP1 (ts1) allele was isolated and revealed a strongly increased sensitivity to paromomycin, a translational inhibitor which binds to RNA, indicating that ribosome biogenesis within the nucleolus is probably affected. This was confirmed by polysome profile and ribosomal subunit analysis, showing a ribosomal subunit imbalance with a decrease in 40S subunits, due to reduced amounts of native 18S rRNA. Furthermore, ScSAM2, encoding S-adenosylmethionine synthetase, was isolated as a multicopy-suppressor of the ScNEP1 (ts1) mutant allele and medium supplementation with S-adenosylmethionine restored its growth. For the first time, these results identified a novel protein with an essential function in ribosomal biogenesis which directly or indirectly interferes with a methylation reaction during the early steps of pre-rRNA processing necessary for the generation of 40S ribosomal subunits.

Amino Acid Sequence↗

PubMed2006

Phylogenetic analysis of a biofilm bacterial population in a water pipeline in the Gulf of Mexico.

The aim of this study was to assess the bacterial diversity associated with a corrosive biofilm in a steel pipeline from the Gulf of Mexico used to inject marine water into the oil reservoir. Several aerobic and heterotrophic bacteria were isolated and identified by 16S rRNA gene sequence analysis. Metagenomic DNA was also extracted to perform a denaturing gradient gel electrophoresis analysis of ribosomal genes and to construct a 16S rRNA gene metagenomic library. Denaturing gradient gel electrophoresis profiles and ribosomal libraries exhibited a limited bacterial diversity. Most of the species detected in the ribosomal library or isolated from the pipeline were assigned to Proteobacteria (Halomonas spp., Idiomarina spp., Marinobacter aquaeolei, Thalassospira sp., Silicibacter sp. and Chromohalobacter sp.) and Bacilli (Bacillus spp. and Exiguobacterium spp.). This is the first report that associates some of these bacteria with a corrosive biofilm. It is relevant that no sulfate-reducing bacteria were isolated or detected by a PCR-based method. The diversity and relative abundance of bacteria from water pipeline biofilms may contribute to an understanding of the complexity and mechanisms of metal corrosion during marine water injection in oil secondary recovery.

Bacteria↗

PubMed1996

Species attribution and strain typing of Oenococcus oeni (formerly Leuconostoc oenos) with restriction endonuclease fingerprints.

In several wines, malolactic fermentation is required to improve the organoleptic characters and to stabilize the final product. In order to establish a controlled malolactic fermentation in wine, easy identification and sensitive typing of strains of Oenococcus oeni (new name of the malolactic bacterium Leuconostoc oenos) used as starter cultures are necessary. To accomplish these tasks, several strains of Oenococcus oeni isolated from wines of the Chianti region (Italy), along with reference strains and strains of L. mesenteroides subsp. mesenteroides, L. carnosum, L. fallax, L. pseudomesenteroides, L. lactis and Weisella paramesenteroides, were studied with RFLP of ribosomal genes and ultrasensitive total DNA restriction pattern analysis performed on polyacrylamide gel. With each of four restriction endonucleases used, identical restriction profiles of ribosomal genes were obtained for all strains of O. oeni. These ribopatterns, being strongly dissimilar to profiles of the other lactic acid bacteria tested, appear to be well suited for the attribution of wine lactic acid bacteria to the species O. oeni. Cluster analysis performed on two total DNA restriction profile data sets showed that the species O. oeni possesses a good degree of genomic homogeneity. Very sensitive typing of strains of O. oeni was obtained with total DNA restriction profiles. The potential of an integrated approach using restriction profiles for species assignment and typing of selected malolactic bacteria is demonstrated.

Bacterial Typing Techniques↗

PubMed1997

Acetylation of ribosomal protein S5 affected by defects in the central pseudoknot in 16S ribosomal RNA?

We have analyzed the ribosomal protein profile of Escherichia coli 30S subunits with the mutation C18A in the central pseudoknot of their 16S ribosomal RNA. This mutation was shown to inhibit translational activity in vivo and to affect ribosome stability in vitro. The majority of the mutant 30S particles were present as free subunits in which a reproducible decrease in amount of proteins S1, S2, S18 and S21 was observed. The protein gels also showed the appearance of a satellite band next to S5. This band reacted with anti-S5 antibodies and had a slightly increased positive charge. The simplest interpretation of these findings, also considering published data, is that the satellite band is S5 with a non-acetylated N-terminal alanine. Underacetylation of S5 due to mutations in the 16S rRNA implies that the modification is performed on the ribosome.

Acetylation↗

PubMed1975

Variations in the cell-free translating apparatus of cultured animal cells as a function of time during cell growth.

Vero M3 cells, a line derived from the kidney of an African Green Monkey, display certain alterations in their protein synthetic apparatus as a function of time during a growth cycle. (Growth cycle here refers to exponential growth of unsynchronized cells in culture and their subsequent passage into the stationary phase.) The capacity of cytoplasmic extracts of these cells to promote endogeneous mRNA-mediated polypeptide synthesis or poly U-mediated polyphenylalanine synthesis declines from the second day after the initiation of the growth cycle. The ribosome sedimentation profile indicates that after the second day of growth a decrease also occurs in the total amount of ribosomes per cell, and that a shift occurs from predominantly polyribosome structures to predominantly subunits and monoribosomes structures. The activity of the translation factor, elongation factor 1, also progressively decreases after the second day of growth. Furthermore, when crude factor preparations from cells in the second day of growth (Exponential phase) and from cells in the fifth day of growth (Stationary phase) are compared for leucyl-tRNA synthetase and prolyl-tRNA synthetase activities, it is found that the extracts from fifth-day cells have significantly less activity. The activity of another enzyme, acid phosphatase, remains relatively unaffected as a function of time during the cell growth cycle. When HeLa S3 plating cells are grown under the same conditions, they do not display the same responses.

Acid Phosphatase↗

PubMed1980

Acute effects of growth hormone on the function of ribosomes of rat skeletal muscle.

The effect of the acute intravenous administration of bovine growth hormone (bGH) to female hypophysectomized rats on the ability of ribosomes isolated from their thigh muscles to incorporate 3H-leucine and 3H-puromycin into protein in vitro was studied. Ribosomes prepared from the muscles of animals that had received bGH (200 microgram) 30 min before sacrifice were more active in incorporating leucine and puromycin into protein than the controls. However, no effect of the hormone on leucine incorporation was seen 15 min after its injection, suggesting some lag period in its course of action on ribosome function. In experiments dealing with the ability of the ribosome preparations to incorporation puromycin into protein, it was found that at the completion of the reaction, ribosomes made from the muscles of bGH-treated rats had incorporated 22% more tracer into protein than the controls, suggesting that these preparations contained a larger population of ribosomes actively engaged in protein synthesis. This conclusion was also supported by the finding that sucrose density gradient profiles of ribosome preparations from the hormone-treated rats had a greater proportion of ribosomes in the polyribosome fraction than those of the controls. From these and other observations made in this study, it would appear that the acute effect of growth hormone on the function of rat skeletal muscle ribosomes is to increase the fraction of ribosomes active in peptide synthesis.

Animals↗

PubMed1989

Red nucleus of Macaca fascicularis: an electron microscopic study of its synaptic organization.

The parvicellular and magnocellular divisions of the red nucleus of the old world monkey, Macaca fascicularis, were analyzed at an electron microscopic level to examine the morphology of the synaptic profiles terminating on rubral neurons and to categorize them by their individual characteristics. The parvicellular division, or anterior two-thirds of the nucleus, is composed of small (10-15 microns) and medium-size (20-30 microns) cells, which are uniformly distributed with high packing density throughout this portion of the nucleus. These cells have invaginated nuclei and are often indented by blood vessels and glial cell somata (satellite cells) that lie in close proximity. The magnocellular portion, occupying the caudal one-third of the nucleus, is composed of an additional population of large cells, ranging from 50-90 microns in diameter, which often contain prominent lipofuscin granules and are frequently indented by blood vessels. Satellite glial cells are not a prominent feature in the magnocellularis portion of the nucleus. The large cells are separated one from the other by fields of myelinated axons either coursing through the nucleus or projecting to and from the nucleus itself. Although the divisions of the nucleus in the Macaca fascicularis are spatially distinct, each possesses a morphological similarity in regard to the categories of synaptic profiles seen at the electron microscopic level. These synaptic profiles are classified as follows: large terminals containing numerous, predominantly rounded vesicles (LR), which can often be seen to form the central profile in a synaptic glomerular arrangement; terminals of similar size with predominantly rounded vesicles but with a pale axoplasmic matrix (LRP); small profiles with rounded vesicles (SR); profiles containing granular dense-cored vesicles (DCV); profiles with numerous flattened vesicles (F); profiles containing pleomorphic vesicles (PL), some of which can be interpreted as presynaptic dendrites (PSD) because they are seen to be postsynaptic and contain ribosomes; and profiles with rounded synaptic vesicles, which are associated with subsynaptic Taxi bodies (T). Most of the various synaptic profile types were found to have similar distributions on the dendritic arbors of rubral neurons in both divisions of the nucleus. However, the LRP-type terminal predominates on the cell bodies and proximal dendrites of the large neurons in magnocellularis. Unlike other regions in the nervous system, F type terminals are rarely seen to contact neuronal somata. This study provides a basis for future experimental studies of afferents to the nucleus in this species.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗

PubMed1975

Terbium binding to ribosomes and ribosomal RNA.

Terbium binding to rat liver ribosomes and ribosomal RNA (rRNA) was examined by equilibrium dialysis and fluorescence spectroscopy. Upon binding to ribosomes and rRNA, the enhancement of terbium fluorescence emission at both 488 and 541 nm was dependent only upon the amount of bound terbium and independent of ionic strength. Binding profiles for ribosomes and rRNA suggested that terbium was bound to ribosomes primarily through rRNA interactions. Data suggested that terbium mimicked characteristics previously described for interactions between ribosomes and magnesium. It is proposed, therefore, that fluorescence of terbium bound to ribosomes may prove useful in studies on the nature and extent of interactions between ribosomes and magnesium.

Animals↗

PubMed1996

Functional Escherichia coli 23S rRNAs containing processed and unprocessed intervening sequences from Salmonella typhimurium.

We have introduced the intervening sequence (IVS) from 23S rRNA of the rrnD operon of Salmonella typhimurium into the equivalent position of Escherichia coli 23S rRNA. Salmonella typhimurium 23S rRNA is fragmented due to the RNase III-dependent removal of the approximately 100 nt stem-loop structure that comprises the IVS. In this study, we have found that insertion of the S. typhimurium IVS into E. coli 23S rRNA causes fragmentation of the RNA but does not affect ribosome function. Cells expressing the fragmented 23S rRNA exhibited wild-type growth rates. Fragmented RNA was found in the actively translating polysome pool and did not alter the sedimentation profile of ribosomal subunits, 70S ribosomes or polysomes. Finally, hybrid 23S rRNA carrying the A2058G mutation conferred high level erythromycin resistance indistinguishable from that of intact 23S rRNA carrying this mutation. These observations indicate that the presence of this IVS and its removal are phenotypically silent. As observed in an RNase III-deficient strain, processing of the IVS was not required for the production of functional ribosomes.

Base Sequence↗