The involvement of protein L16 on ribosomal peptidyl transferase activity

The essential GTPase RbgA (YlqF) is required for 50S ribosome assembly inBacillus subtilis

In this paper the essential GTPase YlqF is shown to participate in the biogenesis of the 50S ribosomal subunit in Bacillus subtilis. Cells depleted of YlqF displayed gene expression profiles and nucleoid morphologies that were consistent with a function for YlqF in translation. In addition, YlqF is evolutionarily linked to two eukaryotic GTPases, Nog2p and Nug1p, that are involved in the biogenesis and the nuclear export of the 60S ribosomal subunit. Analysis of ribosomes from cells depleted of YlqF demonstrated that the formation of 70S ribosomes was greatly reduced and the large subunit sedimented at 45S. Cells grown with varying depleted levels of YlqF, yielding doubling times ranging from 38 min to 150 min, all displayed the 45S intermediate. Purified YlqF-His(6) protein associates with the 45S intermediate, but not the mature 50S subunit in vitro. Analysis of proteins from the 45S intermediate indicated that ribosomal protein L16, which is added late during in vitro Escherichia coli 50S ribosome biogenesis, was missing from the 45S intermediate. These results support a model in which YlqF participates in the formation of active 70S ribosomes in the cell by functioning in a late step of 50S subunit biogenesis. Based on these results we propose to rename the ylqF gene rbgA (ribosome biogenesis GTPase A).

Effects of mutations in ribosomal protein L16 on susceptibility and accumulation of evernimicin

Chemical mutagenesis of Staphylococcus aureus RN450 generated two strains that displayed a stable reduction (30- to 60-fold) in susceptibility to evernimicin. Cell-free translation reactions demonstrated that the resistance determinant was located in the ribosomal fraction. Compared to ribosomes isolated from a wild-type strain, ribosomes from the mutant strains displayed an 8- to 10-fold reduction in affinity for [(14)C]evernimicin. In contrast, the mutants displayed no alteration in either binding affinity or in vitro susceptibility to erythromycin. Exponential cultures of the mutant strains accumulated significantly less [(14)C]evernimicin than the wild-type strain, suggesting that accumulation is dependent on the high affinity that evernimicin displays for its binding site. Sequencing rplP (encodes ribosomal protein L16) in the mutant strains revealed a single base change in each strain, which resulted in a substitution of either cysteine or histidine for arginine at residue 51. Introduction of a multicopy plasmid carrying wild-type rplP into the mutant strains restored sensitivity to evernimicin, confirming that the alterations in rplP were responsible for the change in susceptibility. Overexpression of the mutant alleles in S. aureus RN450 had no effect on susceptibility to evernimicin, demonstrating that susceptibility is dominant over resistance.

Mutations in ribosomal protein L16 conferring reduced susceptibility to evernimicin (SCH27899): implications for mechanism of action

A clinical isolate of Streptococcus pneumoniae (SP#5) that showed decreased susceptibility to evernimicin (MIC, 1.5 microgram/ml) was investigated. A 4,255-bp EcoRI fragment cloned from SP#5 was identified by its ability to transform evernimicin-susceptible S. pneumoniae R6 (MIC, 0.03 microgram/ml) such that the evernimicin MIC was 1.5 microgram/ml. Nucleotide sequence analysis of this fragment revealed that it contained portions of the S10-spc ribosomal protein operons. The nucleotide sequences of resistant and susceptible isolates were compared, and a point mutation (thymine to guanine) that causes an Ile52-Ser substitution in ribosomal protein L16 was identified. The role of this mutation in decreasing susceptibility to evernimicin was confirmed by direct transformation of the altered L16 gene. The presence of the L16 mutation in the resistant strain suggests that evernimicin is an inhibitor of protein synthesis. This was confirmed by inhibition studies using radiolabeled substrates, which showed that the addition of evernimicin at sub-MIC levels resulted in a rapid decrease in the incorporation of radiolabeled isoleucine in a susceptible isolate (SP#3) but was much less effective against SP#5. The incorporation of isoleucine showed a linear response to the dose level of evernimicin. The incorporation of other classes of labeled substrates was unaffected or much delayed, indicating that these were secondary effects.

A single nucleotide substitution at the rib2 locus of the yeast mitochondrial gene for 21S rRNA confers resistance to erythromycin and cold-sensitive ribosome assembly

We have studied a mutation (cs23) in the mitochondrial gene for 21S rRNA that affects the peptidyl transferase center of the ribosome and conditionally blocks the assembly of the 54S ribosomal subunit. Strains carrying this mutation are resistant to erythromycin and cold-sensitive for growth on nonfermentable carbon sources (Singh et al. 1978) Mitochondria isolated from mutant cells grown on glucose at 20 degrees C, the nonpermissive temperature, were depleted of the 54S subunit and instead contained a novel 45S ribosomal particle. After mutant cells were shifted from 20 degrees C to 32 degrees C, 54S subunits were assembled, apparently from the 45S particles and pre-existing ribosomal proteins. DNA sequencing revealed that the mutant phenotype is a consequence of a C to A transversion at position 3993 of the 21S rRNA gene. Previously, C to U and C to G mutations have been identified at the same position in the 21S rRNA sequence. This position corresponds to C-2611 in the E. coli 23S RNA, a nucleotide that appears to be conserved in the large rRNA of all erythromycin-sensitive ribosomes.

A plasmid-coded and site-directed mutation in Escherichia coli 23S RNA that confers resistance to erythromycin: implications for the mechanism of action of erythromycin

Primer-directed mutagenesis was employed to introduce an A2058----G transition in plasmid-encoded Escherichia coli 23S RNA at a site that has been implicated, indirectly, in erythromycin binding. The mutation raises the growth tolerance of cells from 30 to 300 micrograms/ml of erythromycin, and cells grown in the presence of erythromycin contain ribosomes with high levels of mutated 23S RNA. In these cells, wild type 50S subunits 'fall off' the message and are selectively degraded, possibly as a result of an erythromycin-induced conformational change. A fast in vitro poly(U) assay revealed minimal effects of erythromycin on elongation beyond tetrapeptides. We correlated these results with the literature data and concluded that erythromycin acts immediately post-initiation and directly, or indirectly, destabilizes mRNA-bound 70S ribosomes, and prevents their recycling by causing 50S subunit degradation.

Purification and characterization of two ribosomal proteins of Saccharomyces cerevisiae. Homologies with proteins from eukaryotic species and with bacterial protein EC L11

Two non-acidic proteins, extracted from the ribosomes of Saccharomyces cerevisiae using 1 M ammonium chloride in the presence of 50% ethanol, have been purified and characterized. Similar proteins are present in other eukaryotic ribosomes tested, as determined by two-dimensional gel electrophoresis and cross-reaction with antisera. One of the two yeast proteins, protein YL23, seems to be very well preserved during evolution, since antisera specific for YL23 cross-react with protein EC L11 from Escherichia coli. The structural similarity between these two proteins parallels a functional equivalence shown by the ability of the bacterial protein to reconstitute the activity of protein-deficient core particles from yeast. However, in contrast to protein EC L11, protein YL23 interacts with the yeast acidic proteins, forming a complex probably similar to the one made by bacterial protein EC L10 with proteins EC L7 and EC L12 in the E. coli ribosome. Protein YL23 might play similar roles to those of proteins EC L10 and EC L11 in bacteria.

Effects of partial deproteinization on the functional properties of 50S ribosomal subunits of E. coli

Sedimentation of E. coli 50S ribosomal subunits through sucrose gradients containing 10 mM Mg2+ and high concentrations of NaCl (0.1-1.0 M) leads to removal of proteins L16 and L25. Analyses of the structural and functional properties of the protein depleted particles shows that removal of L16 and L25 from the 50S subunit causes loss of its ability to bind tRNA, to associate with the 30S subunit and to catalyze peptide bond formation. Reassociation of both L16 and L25 with core particles lacking these proteins is necessary for recovery of peptidyl transferase activity.

How partially inhibitory concentrations of chloramphenicol affect the growth of Escherichia coli

In the presence of up to 6 microM chloramphenicol, balanced exponential growth of Escherichia coli occurred at a reduced rate after an adjustment period. The inhibition of ribosome function by chloramphenicol within growing cells was inferred from measurements of growth rate and cell composition during balanced growth and of pulse-labeling of cells by radioactive proline after a 10-min exposure to chloramphenicol. In each case the results were consistent with simple noncompetitive inhibition of protein synthesis, with 50% inhibition occurring at 2 microM chloramphenicol, the concentration that gave 50% binding of chloramphenicol to purified ribosomes in vitro. The differences between these results and those obtained with cell-free protein synthesizing systems were shown to be in part due to slow binding of chloramphenicol and in part due to the slow rate and lack of saturation of the cell-free protein-synthesizing systems now available. During balanced growth in concentrations of chloramphenicol 1 microM or higher, the net rate of maturation of ribosomal ribonucleic acid was also inhibited (50% at 2.8 microM). The specific growth rate during balanced growth was inhibited by 50% at 1.8 microM chloramphenicol, but at higher concentrations inhibition was greater than expected from the simple noncompetitive dose-response observed for inhibition of polypeptide synthesis. However, the inhibition of maturation of ribosomal ribonucleic acid plus the inhibition of protein synthesis quantitatively accounted for the observed inhibition of growth. Thus, we have presented for the first time an essentially complete account of the effects of partially inhibitory concentrations of an antibiotic on the growth physiology of a bacterium.

Comparative study between prokaryotes and eukaryotes by chemical iodination of ribosomal proteins

Escherichia coli and Saccharomyces cerevisiae ribosomal proteins were chemically iodinated with 125I by chloramine T under conditions in which the proteins were denatured. The labelled proteins were subsequently separated by two-dimensional gel electrophoresis with an excess of untreated ribosomal proteins from the same species. The iodination did not change the electrophoretic mobility of the proteins as shown by the pattern of spots in the stained gel slabs and their autoradiography. The 125I radioactivity incorporated in the proteins was estimated by cutting out the gel spots from the two-dimensional electrophoresis gel slabs. The highest content of 125I was found in the ribosomal proteins L2, L11, L13, L20/S12, S4 and S9 from E. coli, and L2/L3, L4/L6/S7, L5, L19/L20, L22/S17, L29/S27, L35/L37 and S14/S15 from S. cerevisiae. Comparisons between the electrophoretic patterns of E. coli and S. cerevisiae ribosomal proteins were carried out by coelectrophoresis of labelled and unlabelled proteins from both species. E. coli ribosomal proteins L5, L11, L20, S2, S3 and S15/S16 were found to overlap with L15, L11/L16, L36/L37, S3, S10 and S33 from S. cerevisiae, respectively. Similar coelectrophoresis of E. coli 125I-labelled proteins with unlabelled rat liver and wheat germ ribosomal proteins showed the former to overlap with proteins L1, L11, L14, L16, L19, L20 and the latter with L2, L5, L6, L15, L17 from E. coli.

Peptidyl transferase of bacterial ribosome: resistance to proteinase K

70-S ribosomes and 50-S ribosomal subunits from Escherichia coli D10 were treated with proteinase K for increasing periods of time. Peptidyl transferase activity and sparsomycin-induced binding of (U)C-A-C-C-A-[3H]Leu-Ac were tested in the treated particles, the binding of the substrate being more sensitive to the protease than peptide bond formation. Comparison of the amounts of proteins present in the treated particles with the residual activity indicates that only proteins L3 and L14 are released at a similar rate to that at which peptidyl transferase activity is lost. Proteins related to this ribosomal activity by other techniques are lost at a faster rate than the activity itself. In addition, the results indicate that sparsomycin stimulates the binding of the substrate by a different mechanism from that which inhibits peptide bond formation.

The modification of the peptidyl transferase activity of 50-S ribosomal subunits, LiC1-split proteins and L16 ribosomal protein by ethoxyformic anhydride

Ethoxyformic anhydride abolishes the peptidyl transferase activity of 50-S ribosomal subunits, LiC1 split proteins and L16. Hydroxylamine treatment results in reactivation. Erythromycin exhibits significant protection with 50-S ribosomal subunits. With LiC1 split proteins and L16 significant protection was exhibited only after reconstitution. The results indicate that the ethoxyformic anhydride is reacting with approximately six histidines in LiC1 split proteins and one in L16. Since L16 has been reported to contain a single histidine, the results presented indicate the involvement of this histidine in peptidyl transferase activity.