Ribosomal function and its inhibition by antibiotics in prokaryotes

Ribosome Assembly as Antimicrobial Target

Many antibiotics target the ribosome and interfere with its translation cycle. Since translation is the source of all cellular proteins including ribosomal proteins, protein synthesis and ribosome assembly are interdependent. As a consequence, the activity of translation inhibitors might indirectly cause defective ribosome assembly. Due to the difficulty in distinguishing between direct and indirect effects, and because assembly is probably a target in its own right, concepts are needed to identify small molecules that directly inhibit ribosome assembly. Here, we summarize the basic facts of ribosome targeting antibiotics. Furthermore, we present an in vivo screening strategy that focuses on ribosome assembly by a direct fluorescence based read-out that aims to identify and characterize small molecules acting as primary assembly inhibitors.

Lincomycin resistance, a new type of maternally inherited mutation in Nicotiana plumbaginifolia

Lincomycin resistant cell lines were screened in monoploid (X = 10 chromosomes) protoplast cultures of Nicotiana plumbaginifolia. Lincomycin is an inhibitor of protein synthesis on plastid ribosomes and normally inhibits greening of cultured cells on RMOP medium. The LR400 line was isolated by its ability to form a green callus on selective medium (RMOP medium containing 1,000 µg ml(-1) lincomycin hydrochloride). Diploid plants regenerated from this line inherited the resistance maternally. The LR400 line is cross-resistant to cleocin (clindamycin), but is sensitive to streptomycin.

Role of mitochondrial ribosome-dependent translation in germline formation in Drosophila embryos

In Drosophila, mitochondrially encoded ribosomal RNAs (mtrRNAs) form mitochondrial-type ribosomes on the polar granules, distinctive organelles of the germ plasm. Since a reduction in the amount of mtrRNA results in the failure of embryos to produce germline progenitors, or pole cells, it has been proposed that translation by mitochondrial-type ribosomes is required for germline formation. Here, we report that injection of kasugamycin (KA) and chloramphenicol (CH), inhibitors for prokaryotic-type translation, disrupted pole cell formation in early embryos. The number of mitochondrial-type ribosomes on polar granules was significantly decreased by KA treatment, as shown by electron microscopy. In contrast, ribosomes in the mitochondria and mitochondrial activity were unaffected by KA and CH. We further found that injection of KA and CH impairs production of Germ cell-less (Gcl) protein, which is required for pole cell formation. The above observations suggest that mitochondrial-type translation is required for pole cell formation, and Gcl is a probable candidate for the protein produced by this translation system.

Ten remarks on peptide bond formation on the ribosome

Peptide-bond formation is the enzymatic activity of the ribosome. The catalytic site is made up of ribosomal RNA, indicating that the ribosome is a ribozyme. This review summarizes the recent progress in understanding the mechanism of peptide bond formation. The results of biochemical and kinetic experiments, mutagenesis studies and ribosome crystallography suggest that the approx. 107-fold rate enhancement of peptide bond formation by the ribosome is mainly due to substrate positioning within the active site, rather than to chemical catalysis.

The nuclear factor HCF145 affects chloroplast psaA-psaB-rps14 transcript abundance in Arabidopsis thaliana

The high chlorophyll fluorescence (hcf)145 mutant of Arabidopsis thaliana is specifically affected in photosystem (PS)I function as judged from spectroscopic analysis of PSII and PSI activity. The defect is because of a severe deficiency of PSI core subunits, whereas levels of the four outer antenna subunits of PSI were less reduced in hcf145. Pulse labelling of chloroplast proteins indicated that synthesis of the two largest PSI reaction-centre polypeptides, Psa (photosystem I subunit) A and PsaB, is significantly affected by the mutation. A comparison of stationary transcript levels with rates of transcription demonstrates that hcf145 induces a decreased stability and, probably, transcription of the tricistronic psaA-psaB-rps (small-subunit ribosomal protein)14 mRNA, which is generated by the plastid-encoded RNA polymerase. Translation inhibition experiments excluded translational defects as primary cause of impaired mRNA stability. Larger primary transcripts, which also contain sequences of the ycf3 (hypothetical chloroplast reading frame) gene located upstream of the psaA-psaB-rps14 operon and generated by the action of the nuclear-encoded RNA polymerase, are not targeted by the mutation. Real-time reverse transcription (RT)-PCR analysis has successfully been applied to quantify defined intervals of the tricistronic transcript and it was established that the psaA region is less stable than the rps14 region in hcf145. The hcf145 gene has been mapped on the upper part of chromosome 5.

lambda bar minigene-mediated inhibition of protein synthesis involves accumulation of peptidyl-tRNA and starvation for tRNA

Expression of the bacteriophage lambda two-codon, AUG AUA, barI minigene (bar+) leads to the arrest of protein synthesis in cells defective in peptidyl-tRNA hydrolase (Pth). It has been hypothesized that translation of the bar+ transcript provokes premature release and accumulation of peptidyl-tRNA (p-tRNA). Inhibition of protein synthesis would then result from either starvation of sequestered tRNA or from toxicity of accumulated p-tRNA. To test this hypothesis and to investigate the cause of arrest, we used a coupled in vitro transcription-translation system primed with DNA containing bar+ and the beta-lactamase-encoding gene of the vector as a reporter. The results show that expression of bar+ minigene severely inhibits beta-lactamase polypeptide synthesis by Pth-defective extracts and partially inhibits synthesis by wild-type extracts. Fractions enriched for Pth, or a homogeneous preparation of Pth, prevented and reversed bar+-mediated inhibition. A mutant minigene, barA702, which changes the second codon AUA (Ile) to AAA (Lys), was also toxic for Pth-defective cells. Expression of barA702 inhibited in vitro polypeptide synthesis by Pth-defective extracts and, as with bar+, exogenous Pth prevented inhibition. Addition of pure tRNALys prevented inhibition by barA702 but not by bar+. Expression of bar+ and barA702 led to release and accumulation of p-tRNAIle and p-tRNALys respectively but bar+ also induced accumulation of p-tRNALys. Finally, bar+ stimulated association of methionine with ribosomes probably as fMet-tRNAfMet and the accumulation of methionine and isoleucine in solution as peptidyl-tRNA (p-tRNA). These results indicate that minigene-mediated inhibition of protein synthesis involves premature release of p-tRNA, misincorporation of amino acyl-tRNA, accumulation of p-tRNAs and possibly sequestration of tRNAs.

Regulation of protein synthesis by minigene expression

Peptidyl-tRNA hydrolase (Pth), an enzyme essential for Escherichia coli viability, scavenges peptidyl-tRNA released during abortive polypeptide chain elongation. Bacterial strains of E coli partially defective in Pth activity are unable to maintain bacteriophage lambda growth. Phage mutations that overcome the bacterial defect have been located to several regions in the lambda genome named bar. Plasmid constructs expressing just the bar region are toxic and cause a general arrest of protein synthesis in Pth-defective cells. Inspection of the nucleotide sequence from two bar regions reveals the short coding sequence AUG AUA Stop, spaced by an AT-rich segment from a Shine Dalgarno-like sequence (S-D). These sequences have been named minigenes. Base changes altering the putative S-D, the two sense codons, or the stop codon have been found to reduce Bar-toxicity. Transcripts containing bar function as mRNA. Upon expression in pth mutants, wild-type (bar+) transcripts are found associated with ribosomes. In addition, bar+ RNA forms ternary complexes with the 30S ribosomal subunit and the initiator tRNA and can be released upon run-off translation in the same way as an authentic mRNA. A cell free system for protein synthesis reproduces the in vivo effects: bar+ expression inhibits protein synthesis, bar+ RNA sequences are associated with ribosomes in the inhibited extracts, addition of purified Pth restores synthesis, and excess of tRNA(Lys), specific for the last sense codon in a mutant toxic minigene, prevents protein synthesis inhibition. Also, bar expression promotes association of methionine with ribosomes possibly in a translation complex. These results are consistent with a model proposing tRNA starvation to explain the behaviour of a pth mutant, thermosensitive for protein synthesis.

Inhibition of Escherichia coli protein synthesis by abortive translation of phage lambda minigenes

Escherichia coli mutants defective in peptidyl-tRNA hydrolase activity are unable to maintain bacteriophage lambda vegetative growth. Phage mutants, named bar, overcome the host limitation to support viral growth. Multicopy expression of lambda wild-type bar regions is deleterious to hydrolase-defective cells because it provokes arrest of protein synthesis. We noticed that the bar regions include minigenes whose transcripts would contain a Shine-Dalgarno-like sequence appropriately spaced for translation from a two codon open reading frame. To investigate the mechanism of bar inhibition, we asked if transcripts of the barI region function as mRNAs in their ribosomal interactions. We found that bar-containing RNA associates with ribosomes, forms ternary initiation complexes, yields a toeprint signal, and can be removed from ribosomes by run-off translation, as authentic mRNA. Since bar-containing RNA has the properties of a messenger, we propose that its translation leads to drop-off and accumulation of peptidyl-tRNA in pth-defective cells. Starvation of the tRNA(s) sequestered in pepidyl-tRNA(s) eventually causes inhibition of protein synthesis.

EMS-induced streptomycin resistance in Solanum melongena

Streptomycin-resistant mutations were induced in Solanum melongena by exposing seeds to ethyl methane sulphonate (EMS). Seed mutagenesis resulted in a high frequency of chlorophyll-deficient mutations and a low frequency of resistant shoots, both of which retained their resistance on subsequent testing. Reciprocal crosses between streptomycin-resistant and -sensitive plants showed a non-Mendelian transmission of the resistance trait. Streptomycin resistance is the first selectable and maternally inherited organelle marker described in brinjal.

Subcellular location of lincomycin resistance in Nicotiana mutants

Lincomycin-resistant Nicotiana plumbaginifolia plastid mutants were considered also to carry mitochondrial mutations on the basis of their ability to grow in the dark under selective conditions. To clarify the role of mitochondria, individual protoplasts of the green, lincomycin-resistant N. plumbaginifolia mutant LR400 were microfused with protoplasts of the N. tabacum plastid albino line 92V37, which possesses N. undulata cytoplasm. the production of lincomycin-resistant albino cybrid lines, with N. undulata plastids and recombinant mitochondria, strongly indicated a determining role for mitochondria in the lincomycin resistance. Sequence analysis of the region encompassing putative mutation sites in the 26S rRNA genes from the LR400 and several other lincomycin-resistant N. plumbaginifolia mutants revealed, however, no differences from the wild-type sequence. As an alternative source of the resistance of the fusion products, the N. tabacum fusion partner was also taken into account. Surprisingly, a natural lincomycin resistance of tobacco was detected, which was inherited as a dominant nuclear trait. This result compromises the interpretation of the fusion data suggested above. Thus, to answer the original question definitively, the mutant LR400 was crossed as a female parent with a N. plumbaginifolia line carrying streptomycin-resistant N. tabacum plastids. Calli were then induced from the seedlings. Occasional paternal plastid transmissions were selected as streptomycin-resistant calli on selective medium. These cell lines were shown by restriction enzyme analysis to contain paternal plastids and maternal mitochondria. They were tested for greening and growing ability in the presence of lincomycin. These resistance traits proved to be genetically linked and exclusively located in the plastids.

Synthesis of chlorophyll a regulates translation of chlorophyll a apoproteins P700, CP47, CP43 and D2 in barley etioplasts

Accumulation of plastid-encoded chlorophyll apoproteins and chlorophyll synthesis are controlled by light in angiosperms. An in vitro system utilizing isolated and lysed barley (Hordeum vulgare L.) etioplasts revealed the specific accumulation of P700, CP47, CP43 and D2 triggered by de novo synthesis of chlorophyll. Accumulation rates of radiolabelled chlorophyll apoproteins were linear for about 30 min. Pulse/chase translation assays showed that synthesis of chlorophyll does not result in increased chlorophyll apoprotein stability. Instead turnover rates of chlorophyll apoproteins were higher in the presence than in the absence of chlorophyll. Chlorophyll-dependent accumulation of chlorophyll apoproteins must therefore be regulated on the level of translation. Translation of chlorophyll apoproteins was blocked to about 50% by addition of 30-50 microM aurintricarboxylic acid or 20 microM kasugamycin. The kinetics of chlorophyll-dependent translation indicated that the in vitro translation system is capable of translation initiation. The capability of translation initiation was lost in lysed etioplasts after preincubation for at least 5 min without chlorophyll synthesis. The results suggest that initiation is involved in chlorophyll-dependent regulation of translation.

Approaching the molecular structure of ribosomes

Fifteen forms of three-dimensional crystals and three forms of two-dimensional sheets from ribosomal particles have been grown. In all cases only biologically active particles could be crystallized, the crystalline material retaining its integrity and biological activity for months. Cryastallographic data have been collected from crystals of 50 S ribosomal subunits, using synchrotron radiation, at temperatures between 19 and -180 degree C. Although at around 0 degrees C in the synchrotron X-ray beam the crystals rapidly lose their high-resolution reflections, at cryo-temperatures hardly any radiation damage occurs over long periods, and a complete set of diffraction data to about 6 A resolution could be collected from a single crystal. Heavy-atom clusters were used for soaking as well as for specific binding to the surface of the ribosomal subunits prior to crystallization. The 50 S ribosomal subunits from a mutant of Bacillus stearothermophilus which lacks the ribosomal protein BL11 crystallize isomorphously with the native form. Models of the entire 70 S ribosome and of the 50 S subunit have been reconstructed from two-dimensional sheets at 47 and 30 A, respectively. These models demonstrate the overall shape of the particles, the contact areas between large and small subunits, the space where protein biosynthesis may take place and a tunnel through the 50 S subunit which could provide a path for the nascent polypeptide chain.

G-418, an elongation inhibitor of 80 S ribosomes

The mode of action of the aminoglycoside G-418 was studied in wheat-germ, cell-free translation systems programmed with rat-liver polyadenylated RNA. Incorporation of amino acids into protein was effectively inhibited by G-418 in the microM concentration range. The inhibition pattern obtained was not uniform. The synthesis of polypeptides with higher molecular weights was more inhibited than that of smaller polypeptides. An identical inhibition pattern within a similar range of concentrations was obtained with cycloheximide, a known elongation inhibitor. Translation activity was abolished when the wheat-germ 80 S ribosomes were removed and could be partially reconstructed upon addition of the ribosomes. Incubation with G-418 prior to isolation yielded ribosomes defective in their reconstruction ability. The inhibition pattern was not uniform and exhibited again the same relationship between the size of a polypeptide and the extent of inhibition of its synthesis. Therefore, we suggest that in wheat-germ, cell-free translation systems G-418 affects the 80 S ribosomes and inhibits the elongation cycle.

Effects of aminoglycoside antibiotics on the coupling of protein and RNA syntheses in Escherichia coli

The interdependency of protein and RNA syntheses was studied comparatively in bacteria confronted with amino acid starvation or treated separately with various aminoglycoside antibiotics. By contrast with the concomitant inhibition of macromolecular syntheses in cells deprived of an essential amino acid, RNA production was found to continue in drug-treated cells while protein synthesis was arrested. Such uncoupling process was also observed in bacteria subjected simultaneously to amino acid starvation and treatment with certain antibiotics (neomycin, gentamicin, spectinomycin and kasugamycin) but not with others (streptomycin and kanamycin). These results were related to the intracellular concentration of guanosine polyphosphates, ppGpp and pppGpp. They were discussed in terms of interaction of aminoglycosides with ribosomes.

Comparative evaluation of different pairs of DNA repair-deficient and DNA repair-proficient bacterial tester strains for rapid detection of chemical mutagens and carcinogens

The aim of the present study was to evaluate the usefulness of different pairs of DNA repair-deficient and DNA repair-proficient bacterial tester strains in a mutagenicity/carcinogenicity screen, possibly as complements to the Ames test. 70 carcinogenic and non-carcinogenic compounds, representing a variety of chemical structures, were tested for their DNA-damaging effects, using 6 different DNA-repair-deficient bacterial strains. 2 Bacillus subtilis systems, H17/M45 and HLL3g/HJ-15, were used. The susceptibility of Escherichia coli AB1157 was compared with the susceptibility of 4 recombination-deficient mutants, JC5547, JC2921, JC2926 and JC5519. The test compounds were applied onto paper disks (spot test, ST), or incorporated into a top agar layer (agar-incorporation test, AT). The 2 B. subtilis systems were generally found to be more sensitive and reliable than the assays using E coli. The incorporation of the test compounds in the agar increased the sensitivity of the test for polycyclic aromatic hydrocarbons and other poorly water-soluble compounds. Hydrazines and several other highly polar chemicals could be tested more efficiently when applied onto paper disks. About 30% of the test compounds did not induce any growth inhibition and so could not be tested properly. In order to evaluate the ability of these DNA-repair tests to complement the Ames Salmonella mutagenicity test in a genetic toxicology screening program, results from this study were compared with published data both on mutagenicity in the Ames test and on carcinogenicity. 8 carcinogens generally found to be non-mutagenic for Salmonella were tested: 2 showed DNA-damaging properties (mitomycin C, 1,2-dimethylhydrazine), 5 failed to do so (actinomycin D, griseofulvin, thioacetamide, diethylstilbestrol, safrole), and one (thiourea) was not toxic, so that no classification was possible. 2 non-carcinogenic bacterial mutagens were examined; one, sodium azide, was equitoxic for repair-proficient and -deficient strains, while the other, nitrofurantoin, primarily inhibited repair-deficient strains. The DNA-repair tests failed to indicate the mutagenic and carcinogenic properties of acridine orange. Nalidixic acid, a non-mutagenic DNA synthesis inhibitor, damaged bacterial DNA. Apart from the differences summarized above, carcinogenicity was indicated correctly by the Salmonella S9 assay and most sets of DNA-repair-deficient and DNA-repair-proficient tester strains evaluated in this study. Thus, several more carcinogens could be detected by performing the Ames test and the bacterial DNA-repair tests in tandem than by using either test alone. Nevertheless, the use of both bacterial in vitro systems in a battery of short-term tests for mutagenicity/carcinogenicity evaluation is not considered to be ideal, since the Ames test and the pairs of DNA-repair-deficient and DNA-repair-proficient tester strains used had several shortcomings in common under the conditions of this study.

An antibiotic dependent conditional lethal mutant with a lesion affecting transcription and translation

A conditioned lethal mutant of E. coli was isolated which required the presence of either the RNA polymerase targeted antibiotic, rifampicin, or the ribosomally targeted antibiotic, kasugamycin, for survival. This mutant was characterised. The locus of the mutation responsible for the antibiotic dependent phenotype, ridA, was mapped at about 70.5 min on the chromosomal linkage map, between argR and fabE. The mutant was investigated as a candidate for a strain with a lesion in some cellular component acting on both RNA polymerase and the ribosome. A close interaction with RNA polymerase was evident from the interplay arising from the combination of ridA and various rpoB mutations as manifested in the phenotype. The ability of kasugamycin, but not other ribosomally targeted aminoglycoside antibiotics, to relieve the lethality due to the ridA mutation was an indication of the specificity in the interaction of the ridA gene product with the ribosome.

Tetracycline resistance transposon Tn1721: recA-dependent gene amplification and expression of tetracycline resistance

The 7.1-megadalton transposon Tn1721 codes for inducible tetracycline resistance (Tcr). The transposable element consists of a "minor transposon" (3.6 megadaltons) encoding functions required for transposition and a "tet region" (3.5 megadaltons) encoding resistance. Multiple tandem repeats of the tet region can be generated by recA-dependent gene amplification. This feature of Tn1721 has been used to analyze the relationship between gene dosage and Tcr. Derivatives of plasmid R388:Tn1721 containing from one to nine copies of the tet region were isolated and separately transformed into recA host cells, where they are stably maintained. The results of the study of Tcr in these strains were as follows: (i) the uninduced, "basal" level of Tcr was linearly related to gene dosage between 4 and 36 copies of tet per chromosome equivalent; (ii) the underlying mechanism could not be attributed to reduced accumulation of the drug; and (iii) induction with tetracycline elicited a four- to fivefold reduction in drug accumulation, independent of the gene dosage.