Hideko Kaji

Structural basis for aminoglycoside inhibition of bacterial ribosome recycling.

Aminoglycosides are widely used antibiotics that cause messenger RNA decoding errors, block mRNA and transfer RNA translocation, and inhibit ribosome recycling. Ribosome recycling follows the termination of protein synthesis and is aided by ribosome recycling factor (RRF) in bacteria. The molecular mechanism by which aminoglycosides inhibit ribosome recycling is unknown. Here we show in X-ray crystal structures of the Escherichia coli 70S ribosome that RRF binding causes RNA helix H69 of the large ribosomal subunit, which is crucial for subunit association, to swing away from the subunit interface. Aminoglycosides bind to H69 and completely restore the contacts between ribosomal subunits that are disrupted by RRF. These results provide a structural explanation for aminoglycoside inhibition of ribosome recycling.

Post‐termination complex disassembly by ribosome recycling factor, a functional tRNA mimic

Ribosome recycling factor (RRF) together with elongation factor G (EF‐G) disassembles the post‐ termination ribosomal complex. Inhibitors of translocation, thiostrepton, viomycin and aminoglycosides, inhibited the release of tRNA and mRNA from the post‐termination complex. In contrast, fusidic acid and a GTP analog that fix EF‐G to the ribosome, allowing one round of tRNA translocation, inhibited mRNA but not tRNA release from the complex. The release of tRNA is a prerequisite for mRNA release but partially takes place with EF‐G alone. The data are consistent with the notion that RRF binds to the A‐site and is translocated to the P‐site, releasing deacylated tRNA from the P‐ and E‐sites. The final step, the release of mRNA, is accompanied by the release of RRF and EF‐G from the ribosome. With the model post‐termination complex, 70S ribosomes were released from the post‐termination complex by the RRF reaction and were then dissociated into subunits by IF3.

Binding of dihydrostreptomycin to ribosomal subunits

Abstract Approximately one molecule of dihydrostreptomycin binds to a 30 s ribosomal subunit at 24 °C, but no detectable binding to 50 s ribosomal subunits was observed. This binding was dependent on the presence of uridine- or cytidine-containing polynucleotides. At 37 °C approximately two molecules of dihydro-streptomycin were bound to a 30 s-poly U complex. Incubation of 30 s subunits with [ 3 H]dihydrostreptomycin in the presence of magnesium ions is necessary for the binding. No binding of dihydrostreptomycin to 30 s ribosomal subunits derived from a streptomycin-resistant strain of Escherichia coli was observed.

Effect of temperature on normal and SV40-transformed human fibroblasts

The effect of a temperature shift from low (36 degrees C) to high (40 degrees C) temperature on human fibroblasts (IMR90) at various population doubling levels and IMR90 cells transformed by SV40 virus infection at a population doubling level of 30 (SV40/IMR90) was examined. Both IMR90 and SV40/IMR90 cells showed a decrease in cell saturation density at confluency, whereas an increase in population doubling time and protein content was noted when the cells were shifted up to 40 degrees C from 36 degrees C. The modification of IMR90 chromosomal proteins by arginyl-tRNA transferase was increased by the temperature shift, whereas NH2-terminal arginylation of SV40/IMR90 chromatin was not altered. Similarly, no appreciable change in 2-deoxyglucose uptake was noted with SV40/IMR90 cells at either temperature, although 2-deoxyglucose uptake by IMR90 cells was increased by the temperature shift. Additionally, the rate of 2-deoxyglucose uptake showed no difference between IMR90 and SV40/IMR90 cells. The above results support previous findings that environmental alterations, such as temperature shift can cause acceleration of cellular senescence. These findings also imply that cellular senescence remains fixed when viral transformation occurs and is rendered refractory to further age-associated alterations.

Structural Insights Into Ribosome Recycling Factor Interactions with the 70S Ribosome

At the end of translation in bacteria, ribosome recycling factor (RRF) is used together with elongation factor G to recycle the 30S and 50S ribosomal subunits for the next round of translation. In x-ray crystal structures of RRF with the Escherichia coli 70S ribosome, RRF binds to the large ribosomal subunit in the cleft that contains the peptidyl transferase center. Upon binding of either E. coli or Thermus thermophilus RRF to the E. coli ribosome, the tip of ribosomal RNA helix 69 in the large subunit moves away from the small subunit toward RRF by 8 A, thereby disrupting a key contact between the small and large ribosomal subunits termed bridge B2a. In the ribosome crystals, the ability of RRF to destabilize bridge B2a is influenced by crystal packing forces. Movement of helix 69 involves an ordered-to-disordered transition upon binding of RRF to the ribosome. The disruption of bridge B2a upon RRF binding to the ribosome seen in the present structures reveals one of the key roles that RRF plays in ribosome recycling, the dissociation of 70S ribosomes into subunits. The structures also reveal contacts between domain II of RRF and protein S12 in the 30S subunit that may also play a role in ribosome recycling.

Ribosome recycling step in yeast cytoplasmic protein synthesis is catalyzed by eEF3 and ATP.

After each round of protein biosynthesis, the posttermination complex (PoTC) consisting of a ribosome, mRNA, and tRNA must be disassembled into its components for a new round of translation. Here, we show that a Saccharomyces cerevisiae model PoTC was disassembled by ATP and eukaryotic elongation factor 3 (eEF3). GTP or ITP functioned with less efficiency and adenosine 5γ′-(β,γ-imido)triphosphate did not function at all. The kcat of eEF3 was 1.12 min-1, which is comparable to that of the in vitro initiation step. The disassembly reaction was inhibited by aminoglycosides and cycloheximide. The subunits formed from the yeast model PoTC remained separated under ionic conditions close to those existing in vivo, suggesting that they are ready to enter the initiation process. Based on our experimental techniques used in this paper, the release of mRNA and tRNA and ribosome dissociation took place simultaneously. No 40S•mRNA complex was observed, indicating that eEF3 action promotes ribosome recycling, not reinitiation.

ANTIRETROVIRAL ACTIVITIES OF ANTHRAQUINONES AND THEIR INHIBITORY EFFECTS ON REVERSE TRANSCRIPTASE

Alizarin complexone (AC), alizarin Red S (ARS) and various other anthraquinones were evaluated for their inhibitory effects on Rous-associated virus 2 reverse transcriptase (RAV-2 RT). Some 1,2-dihydroxyanthraquinones were active against this enzyme and AC was the most potent inhibitor among these compounds [50% inhibitory concentration (IC50): 3.8 micrograms/ml]. AC slightly inhibited Rous sarcoma virus RT (RSV RT) and human immunodeficiency virus type 1 RT (HIV-1 RT) (IC50: 100 micrograms/ml and 45 micrograms/ml, respectively). However, AC efficiently inhibited focus formation by Rous sarcoma virus (RSV) and cytopathogenicity of human immunodeficiency virus type 1 (HIV-1). Simultaneous administration of AC with RSV to newborn chickens also delayed tumor induction by RSV.

In vivo effect of inactivation of ribosome recycling factor – fate of ribosomes after unscheduled translation downstream of open reading frame

The post‐termination ribosomal complex is disassembled by ribosome recycling factor (RRF) and elongation factor G. Without RRF, the ribosome is not released from mRNA at the termination codon and reinitiates translation downstream. This is called unscheduled translation. Here, we show that at the non‐permissive temperature of a temperature‐sensitive RRF strain, RRF is lost quickly, and some ribosomes reach the 3′ end of mRNA. However, instead of accumulating at the 3′ end of mRNA, ribosomes are released as monosomes. Some ribosomes are transferred to transfer‐messenger RNA from the 3′ end of mRNA. The monosomes thus produced are able to translate synthetic homopolymer but not natural mRNA with leader and canonical initiation signal. The pellet containing ribosomes appears to be responsible for rapid but reversible inhibition of most but not all of protein synthesis in vivo closely followed by decrease of cellular RNA and DNA synthesis.

The role of GTP in transient splitting of 70S ribosomes by RRF (ribosome recycling factor) and EF-G (elongation factor G)

Ribosome recycling factor (RRF), elongation factor G (EF-G) and GTP split 70S ribosomes into subunits. Here, we demonstrated that the splitting was transient and the exhaustion of GTP resulted in re-association of the split subunits into 70S ribosomes unless IF3 (initiation factor 3) was present. However, the splitting was observed with sucrose density gradient centrifugation (SDGC) without IF3 if RRF, EF-G and GTP were present in the SDGC buffer. The splitting of 70S ribosomes causes the decrease of light scattering by ribosomes. Kinetic constants obtained from the light scattering studies are sufficient to account for the splitting of 70S ribosomes by RRF and EF-G/GTP during the lag phase for activation of ribosomes for the log phase. As the amount of 70S ribosomes increased, more RRF, EF-G and GTP were necessary to split 70S ribosomes. In the presence of a physiological amount of polyamines, GTP and factors, even 0.6 μM 70S ribosomes (12 times higher than the 70S ribosomes for routine assay) were split. Spermidine (2 mM) completely inhibited anti-association activity of IF3, and the RRF/EF-G/GTP-dependent splitting of 70S ribosomes.

Random integration of SV40 in SV40-transformed, immortalized human fibroblasts☆

We have studied the relationship between immortalization of SV40-transformed human embryonic fibroblasts and their SV40 integration sites. From several independently transformed cell pools, we have isolated clones which do not harbor unintegrated SV40 DNA. We have analysed whole-cell DNA from these clones, using the Southern blot method. Our results suggest that no specific integration sites in the cellular genome exist which are a prerequisite for the immortalization process. Although some integration sites were found to be predominant in pre-crisis clones, they could not be detected in the post-crisis clones. This suggests that none of these predominating sites is selected for during the crisis period.