Bacterial ribosome

Studies of ribosomal diffusion coefficients using laser light-scattering spectroscopy

Using an optical beating technique, the diffusion coefficients and relative scattered intensity of Escherichia coli 70S, 50S, and 30S ribosomes are measured as a function of temperature and Mg(2+) concentration. For solutions at 10 mM Mg(2+) and between 0 degrees C and about 40 degrees C, the values of D(20,w) obtained are 1.7, 1.9, and approximately 2.1 x 10(-7) cm(2)/s, respectively. Preparative procedures drastically affect these values and equivalent hydrodynamic ellipsoids of revolution models give large axial ratios indicating extensive hydration or a deviation from the assumed shape. Calculations also indicate that the subunits expand upon dissociation. Measurements of D(20,w) vs. temperature indicate that 70S particles undergo a conformational change prior to dissociation and can be heat dissociated at 30-32 degrees C at low concentrations. Treatment of 70S ribosomes with EDTA causes a biphasic dissociation reaction. Addition of Mg(2+) after dissociation with EDTA shows that longer waiting times yield fewer 70S particles and that even short waiting times may yield ribosomes differing from the native conformation. Addition of p-chloromercuribenzoic acid (PCMB) is shown to dissociate 70S particles, but to a lesser extent than ethylenediaminetetraacetic acid (EDTA).

Development of auxotrophy by streptomycin-resistant mutation

Several streptomycin-resistant mutants of Escherichia coli have been isolated which require exogenous isoleucine for growth. The majority of these strains were of streptomycin-dependent phenotype. If grown in the absence of streptomycin, these streptomycin-dependent auxotrophs (Sm(d-aux)) strains were unable to produce beta-galactosidase and aldolase activities and also failed to exhibit donor properties in conjugation. Genetic analysis indicated that the isoleucine requirement of these strains could be caused by a mutation at the strA locus.

The role of ribonuclease II in the maturation of precursor 16S ribosomal ribonucleic acid in Escherichia coli

The suggested involvement of ribonuclease II in the maturation of rRNA has been examined directly by determining the activity of the enzyme and the amount of p16S rRNA in cell-free extracts from Escherichia coli A19 and its temperature-sensitive derivative N464 grown under experimental conditions designed to vary the amounts of enzyme and precursor independently. In strain A19 the enzyme showed maximum activity in circumstances where the amount of p16S rRNA was normal (e.g. exponential-phase cells) or raised eight times (e.g. during inhibition of growth by methionine starvation of the relaxed auxotroph or by chloramphenicol or puromycin treatment). In strain N464 at the non-permissive temperature the ribonuclease II activity may be decreased by 50% without effect upon the amount of p16S rRNA, whereas in methionine starvation of this strain the enzyme activity is at a maximum and the p16S rRNA is eight times that in exponential-phase cells. These observations are discussed in relation to the previously implied role of ribonuclease II in the maturation of rRNA within ribosome precursors.

Mutations in Escherichia coli K-12 decreasing the rate of streptomycin uptake: synergism with R-factor-mediated capacity to inactivate streptomycin

Escherichia coli K-12 carrying the R-factor R1 or R6K is resistant to streptomycin. The resistance is due to R-factor-coded enzymes that metabolize the drug. Streptomycin can be inactivated in two ways, either by adenylylation or by phosphorylation; both reactions require adenosine 5'-triphosphate. In this work we show that the R-factor R1 codes for an enzyme that adenylylates streptomycin and that the enzyme activity is located in the periplasmic volume, whereas the R-factor R6K codes for a streptomycin phosphorylase, which is mainly cytoplasmic. From a strain without any R-factor or carrying different R-factors, mutants were isolated that are 10 times more resistant to streptomycin than the parent strains. This increased resistance is not due to increased amounts of metabolizing enzymes. The mutants have a decreased rate of uptake of streptomycin and an altered response to other antibacterial agents as well. The mutations are located on the chromosome and not on the plasmid. It is likely that the mutations cause changes in the outer layers of the cell envelope and that the increased resistance is due to the synergistic effect of an efficient penetration barrier and a low activity of inactivating enzyme.

Mutation in Saccharomyces cerevisiae conferring streptomycin and cold sensitivity by affecting ribosome formation and function

A cold-sensitive, streptomycin-sensitive mutant of Saccharomyces cerevisiae accumulates a 28S ribonucleoprotein particle when grown at low temperature. This particle contains 17S ribosomal ribonculeic acid which is degraded when exposed to ribonuclease. The particle does not serve as a precursor to 60 and 40S ribosomal subunits nor is it turned over when growth is allowed to resume at the permissive temperature; rather it is only diluted by growth. That streptomycin sensitivity (allelic with cold sensitivity) is ribosomal is evidenced by the inhibition of protein synthesis in vitro by streptomycin and the binding of labeled streptomycin to the mutant but not the parental 40S ribosomal subunit.

Genetic analysis of cold-sensitive ribosome maturation mutants of Escherichia coli

Four cold-sensitive mutants of Escherichia coli, which have defects in the maturation of the 50S ribosomal subunit, were isolated. Each of the mutations was shown to map at a different locus. The loci were assigned the name rim (ribosome maturation) and were shown to map as follows: rimA is co-transduced with ilvD and with pyrE; rimB is co-transduced with aroD; conjugation experiments limited rimD to a region between ilv and malB, and conjugation experiments limited rimC to the 22 to 30 min region of the chromosome. In merodiploids heterozygous for rimA, rimB, or rimD, the wild-type allele was shown to be dominant to the mutant allele. The observation that the rim loci lie outside the strA region and separate from each other, as well as the recessive character of the rim loci, suggests that the mutants may be defective in ribosome maturation factors rather than being defective in ribosomal structural proteins.

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.

NH2-terminal amino acid distribution and amino acid composition of Streptococcus faecalis R soluble and ribosomal proteins

The NH(2)-terminal amino acid distribution of Streptococcus faecalis R soluble and ribosomal proteins isolated from cells at different stages of growth on either folate-sufficient or folate-deficient medium was determined by the dinitrophenyl method. The NH(2)-terminal residues do not follow the random distribution observed for the total amino acid composition of S. faecalis soluble and ribosomal proteins. Methionine and alanine occur most frequently; serine, threonine, aspartic and glutamic acids, and glycine are also present at the NH(2)-terminal position of S. faecalis R proteins. The absence of folic acid yields cells that are incapable of formylating methionyl-transfer ribonucelic acid tRNA(f) (Met), but does not affect either the qualitative or quantitative NH(2)-terminal distribution of total soluble or total ribosomal proteins compared to cells grown with folate. A small quantitative difference was observed in the frequency of distribution of certain amino acids at the NH(2)-termini between log and stationary phase soluble proteins. The amino acid residues found at the NH(2)-terminal position of S. faecalis proteins are qualitatively similar to those reported for several other organisms.

Cold-sensitive mutants of Neurospora crassa

Cold-sensitive mutants of the eucaryote Neurospora crassa have been isolated by a modification of the filtration-enrichment technique of Catcheside. The mutants include osmotic remedial, auxotrophic, transport, and incorporation deficient isolates.

Assembly of bacterial ribosomes

I have not mentioned the remarkable progress made mainly by Fellner and his co-workers (86) in the elucidation of the primary structure of rRNA's and by Wittmann and his co-workers (87) in determining the structure of several ribosomal proteins. Such knowledge of primary structures is certainly the basis of complete understanding of the structure of the ribosome. With the current progress in technology, complete elucidation of the primary structure of all the ribosomal components is probably a matter of time. As indicated in this article, a rough approximation of the three-dimensional structure of ribosomes is likely to emerge soon. Although not mentioned in this article, studies of ribosomes from higher organisms are also progressing. We must, therefore, consider what further studies should be conducted and what kinds of questions we would like to solve. Some groups of investigators aim to elucidate the complete three-dimensional structure of ribosomes and to find out how these complex cell organelles function; they hope to determine the conformational changes of many of the component molecules within the ribosome structure in response to external macromolecules and cofactors engaged in protein synthesis. Such knowledge will also be important in enabling us to understand the regulation of translation of genetic messages. Other groups of investigators aim to elucidate the complex series of events which originate in the transcription of the more than 60 genes and culminate in the formation of the specific structure of the organelle. Complete reproduction in vitro of all the assembly events that occur in vivo should not be difficult to achieve in principle. It should then become possible to study in vitro any factor regulating the biogenesis of the organelle. Although we do not know whether such studies would reveal any new fundamental principle that governs the complex circuits of interconnected macromolecular interactions, the achievement of such a complete in vitro system would represent a necessary step in the comprehensive understanding of biogenesis of organelles, and eventually, of the more complex behavior and genesis of cells (89).

A native ribonucleoprotein complex from Escherichia coli ribosomes

An RNA-protein complex was isolated from the 50S subunit of E. coli ribosomes after trypsin digestion. The complex contains only one protein, L24. Treatment of the complex with pancreatic ribonuclease results in digestion of most of the RNA; however, an RNA fragment of about 100 nucleotides in length is stable to nuclease digestion and remains bound to the protein. It is also possible to reconstitute a complex from 23S RNA and isolated L24; nuclease digestion of this complex produces a resistant RNA fragment of the same size as the native complex. The protein can still bind to 23S RNA after N-methylation of about 20% of its lysine residues. Thus, by use of N-methylated L24 labeled with either (14)C or (3)H, the binding stoichiometry of the reconstituted complex was established; binding of L24 to RNA once again renders the protein trypsin-resistant. This would appear to be a good system for the study of RNA-protein interactions.

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.

Ribosomal RNA genes of Neurospora: isolation and characterization

DNA sequences in Neurospora crassa that code for ribosomal RNA have been isolated in a highly purified state by DNA-RNA hybridization. About 100 separate ribosomal RNA genes exist in each nucleus. These genes are composed of repeated sequences that are present about 100 times per nucleus. The individual members of this group of DNA sequences are essentially identical.

In vitro complementation as an assay for new proteins required for bacteriophage T4 DNA replication: purification of the complex specified by T4 genes 44 and 62

We have developed an in vitro complementation assay for six T4 bacteriophage gene products believed to be components of the T4 DNA replication apparatus. This assay is based upon the fact that DNA synthesis in an infected cell lysate that lacks a given gene product is specifically stimulated by addition of the missing product. By the use of such an assay, two proteins that appear to be the products of T4 genes 44 and 62 have been purified to electrophoretic homogeneity as a single complex of the two polypeptide chains.

Ribosomal ribonucleic acid synthesis and maturation in the blue-green alga Anacystis nidulans

Methods are described for preparation of pulse-labeled ribonucleic acid (RNA) from the blue-green alga Anacystis nidulans. Synthesis of labeled RNA was found to be in part dependent on concurrent photosynthesis and was inhibited by the antibiotic streptolydigin. Mature 23S ribosomal RNA (rRNA) appeared before mature 16S rRNA. Formation of either molecule was inhibited by chloramphenicol, and RNA species of lesser mobility accumulated. These species may be precursors of the mature forms. Maturation of 16S rRNA was also inhibited by streptolydigin. (The effect of this antibiotic on 23S rRNA maturation was not examined). In many respects, ribosomal RNA synthesis and maturation in this blue-green alga appear to follow the pattern already established for bacteria.

Accumulation of 70S monoribosomes in Escherichia coli after energy source shift-down

When Escherichia coli is shifted from glucose-minimal to succinate-minimal medium, a transient inhibition of protein synthesis and a time-dependent redistribution of ribosomes from polysomes to 70S monosomes occurs. These processes are reversed by a shift-up with glucose. In a lysate made from a mixture of log-phase and down-shifted cells, the 70S monosomes are derived solely from the down-shifted cells and are therefore not produced by polysome breakage during preparation. This conclusion is supported by the absence of nascent proteins from the 70S peak. The monosomes are not dissociated by NaCl or by a crude ribosome dissociation factor, so they behave as "complexed" rather than "free" particles. When down-shifted cells are incubated with rifampin to block ribonucleic acid (RNA) synthesis, the 70S monosomes disappear with a half-life of 15 min. When glucose is also added this half-life decreases to 3 min. The 70S particles are stable in the presence of rifampin when chloramphenicol is added to block protein synthesis. We interpret these data to mean that the existence of the 70S monosomes depends on the continued synthesis of messenger RNA and their conversion to free ribosomes (which dissociate under our conditions) is a result of their participation in protein synthesis. Finally, a significant fraction of the RNA labeled during a brief pulse of (3)H-uracil is found associated with the 70S peak. These results are consistent with the hypothesis that the 70S monosomes are initiation complexes of single ribosomes and messenger RNA, which do not initiate polypeptide synthesis during a shift-down.

Expression of ribosomal protein genes as analyzed by bacteriophage Mu-induced mutations

The organization of ribosomal protein genes and the gene (fus) for a protein chain elongation factor, EF G, in Escherichia coli were studied with a merodiploid strain that has an episome with genetic markers, ery(r), spc(r), str(r), and fus(r), and a chromosome with markers ery(s), spc(s), str(s), and fus(s). The ery locus determines a 50S ribosomal protein and the spc and str loci determine 30S ribosomal proteins. The phenotype of the diploid strain is sensitive to all of the four antibiotics, erythromycin (Ery), spectinomycin (Spc), streptomycin (Str), and fusidic acid (Fus). Analysis of antibiotic-resistant mutants induced by bacteriophage Mu in the diploid strain indicates that these four genes, and probably many other ribosomal protein genes linked to them, are transcribed as a single unit, and the direction of the transcription is in the order of ery, spc, str, and fus.

Ribosome maturation of Escherichia coli growing at different growth rates

The data reported here are consistent with the hypothesis that the rate of ribosome assembly in vivo approximates a constant fraction of the generation time for the four rates studied. This conclusion is indicated by the following. (i) There is an increased lag period before radioisotopically labeled uracil appears in 23 and 16S ribosomal ribonucleic acid of 70S ribosomes as a function of growth rate. (ii) The time necessary for (3)H-uracil in the 43S ribonucleoprotein precursor to the 50S subunit to assume a position at 50S in sucrose gradients is greatly increased inversely to the growth rate.

Covalent attachment of a peptidyl-transfer RNA analog to the 50S subunit of Escherichia coli ribosomes

The peptidyl-tRNA analog, N-bromo-acetyl-Phenylalanyl-tRNA(Phe) has been prepared. Its binding to the 70S ribosome of E. coli is totally dependent upon polyuridylic acid. The analog becomes covalently attached to the 50S particle. It is associated with only one protein fraction after polyacrylamide-gel separation of total 50S proteins. The analog also reacts with 23S ribosomal RNA or a protein that remains tightly bound to this RNA after treatment with LiCl-urea and sodium dodecyl sulfate. The analog can function as a peptidyl-tRNA for at least one peptide transfer, but it then inhibits further chain elongation. This result strongly suggests that this analog becomes covalently bound at the P-site of the ribosome.

Ribosomal alterations controlling alkaline phosphatase isozymes in Escherichia coli

Different patterns of isozymes were obtained by starch-gel electrophoresis of alkaline phosphatase from Escherichia coli strains differing only by strA or ram mutations, or both, in the 30S ribosomal subunit. The isozyme spread was reduced in strA and increased in ram strains; this strictly parallels the restriction and enhancement of translational ambiguity produced by these mutations. Streptomycin present during growth had an effect similar to ram on both isozymes and ambiguity. The three isozymes analyzed have different N-terminal residues: aspartic acid, valine, and threonine. Different patterns of isozymes were also obtained in a wild-type strain through the specific action of exogenous arginine. A link between the mechanism of the effect of arginine and that of the ribosome is not obvious. The possibility is discussed that in both cases, although by different mechanisms, N-terminals are formed with different sensitivity to limited degradative attack.

Ribosomal proteins of Rhodopseudomonas palustris

Sodium dodecyl sulfate-polyacrylamide gel electrophoresis of ribosomal proteins of Rhodopseudomonas palustris revealed that the 29S subunit lacked a high-molecular-weight protein. It is suggested that a high-molecular-weight protein may function in protecting ribosomal ribonucleic acid from ribonuclease degradation.

Selection of ribosomal mutants by antibiotic suppression in yeast

Wild-type Saccharomyces cerevisiae is highly resistant to streptomycin. A histidine auxotroph was found which could grow without histidine in the presence of high concentrations of streptomycin. Selection for derivatives of this strain which could be suppressed by much lower concentrations of streptomycin yielded streptomycin-sensitive mutants which are cold-sensitive and have altered ribosomal profiles.