Phenotype masking and streptomycin dependence

The parable of the caveman and the Ferrari: protein synthesis and the RNA world

The basic steps of protein synthesis are carried out by the ribosome, a very large and complex ribonucleoprotein particle. In keeping with its proposed emergence from an RNA world, all three of its core mechanisms-aminoacyl-tRNA selection, catalysis of peptide bond formation and coupled translocation of mRNA and tRNA-are embodied in the properties of ribosomal RNA, while its proteins play a supportive role.This article is part of the themed issue 'Perspectives on the ribosome'.

Correcting direct effects of ethanol on translation and transcription machinery confers ethanol tolerance in bacteria

The molecular mechanisms of ethanol toxicity and tolerance in bacteria, although important for biotechnology and bioenergy applications, remain incompletely understood. Genetic studies have identified potential cellular targets for ethanol and have revealed multiple mechanisms of tolerance, but it remains difficult to separate the direct and indirect effects of ethanol. We used adaptive evolution to generate spontaneous ethanol-tolerant strains of Escherichia coli, and then characterized mechanisms of toxicity and resistance using genome-scale DNAseq, RNAseq, and ribosome profiling coupled with specific assays of ribosome and RNA polymerase function. Evolved alleles of metJ, rho, and rpsQ recapitulated most of the observed ethanol tolerance, implicating translation and transcription as key processes affected by ethanol. Ethanol induced miscoding errors during protein synthesis, from which the evolved rpsQ allele protected cells by increasing ribosome accuracy. Ribosome profiling and RNAseq analyses established that ethanol negatively affects transcriptional and translational processivity. Ethanol-stressed cells exhibited ribosomal stalling at internal AUG codons, which may be ameliorated by the adaptive inactivation of the MetJ repressor of methionine biosynthesis genes. Ethanol also caused aberrant intragenic transcription termination for mRNAs with low ribosome density, which was reduced in a strain with the adaptive rho mutation. Furthermore, ethanol inhibited transcript elongation by RNA polymerase in vitro. We propose that ethanol-induced inhibition and uncoupling of mRNA and protein synthesis through direct effects on ribosomes and RNA polymerase conformations are major contributors to ethanol toxicity in E. coli, and that adaptive mutations in metJ, rho, and rpsQ help protect these central dogma processes in the presence of ethanol.

The central role of protein S12 in organizing the structure of the decoding site of the ribosome

The ribosome decodes mRNA by monitoring the geometry of codon-anticodon base-pairing using a set of universally conserved 16S rRNA nucleotides within the conformationally dynamic decoding site. By applying single-molecule FRET and X-ray crystallography, we have determined that conditional-lethal, streptomycin-dependence mutations in ribosomal protein S12 interfere with tRNA selection by allowing conformational distortions of the decoding site that impair GTPase activation of EF-Tu during the tRNA selection process. Distortions in the decoding site are reversed by streptomycin or by a second-site suppressor mutation in 16S rRNA. These observations encourage a refinement of the current model for decoding, wherein ribosomal protein S12 and the decoding site collaborate to optimize codon recognition and substrate discrimination during the early stages of the tRNA selection process.

Sensitivity and Resistance to Spectinomycin in Escherichia coli

Inhibition of growth and division of Escherichia coli by spectinomycin is reversible, and the kinetics of its interference with deoxyribonucleic and ribonucleic acid synthesis may be interpreted as secondary effects of inhibition of protein synthesis on the ribosome. Spontaneous mutations to spectinomycin resistance occur in E. coli K-12 at a rate of about 2 x 10(-10). Resistance is transducible with a discrete lag in phenotypic expression, and the kinetics of its development is about the same as that for streptomycin resistance. All spectinomycin-resistant mutants tested contain resistant ribosomes, and all map in a locus (spc) counterclockwise to and 70% cotransducible with the classical str locus. Differences in the residual drug sensitivity of various spectinomycin-resistant mutants, and of their ribosomes, indicate the existence of more than one phenotypic class of resistance.

Structural insights into translational fidelity

The underlying basis for the accuracy of protein synthesis has been the subject of over four decades of investigation. Recent biochemical and structural data make it possible to understand at least in outline the structural basis for tRNA selection, in which codon recognition by cognate tRNA results in the hydrolysis of GTP by EF-Tu over 75 A away. The ribosome recognizes the geometry of codon-anticodon base pairing at the first two positions but monitors the third, or wobble position, less stringently. Part of the additional binding energy of cognate tRNA is used to induce conformational changes in the ribosome that stabilize a transition state for GTP hydrolysis by EF-Tu and subsequently result in accelerated accommodation of tRNA into the peptidyl transferase center. The transition state for GTP hydrolysis is characterized, among other things, by a distorted tRNA. This picture explains a large body of data on the effect of antibiotics and mutations on translational fidelity. However, many fundamental questions remain, such as the mechanism of activation of GTP hydrolysis by EF-Tu, and the relationship between decoding and frameshifting.

Conformational changes in the ribosome induced by translational miscoding agents

Ribosomes are dynamic complexes responsible for translating the genetic information encoded in mRNAs to proteins. The accuracy of this process is vital to the survival of an organism, and is often compromised by translational miscoding agents. Aminoglycosides are a group of miscoding agents that bind to the ribosome and reduce the fidelity of translation. Previous studies have shown that aminoglycosides alter the higher order structure of the ribosome. Here, we used a toeprinting assay to how that streptomycin, neomycin, kanamycin, gentamycin, and hygromycin B trigger conformational changes within Escherichia coli ribosome. Miscoding agents viomycin and 30% ethanol also cause similar structural changes within the ribosome. In contrast, antibiotics that do not cause miscoding, such as tetracycline, chloramphenicol, erythromycin, fusidic acid and spectinomycin, do not induce the conformational changes triggered by miscoding agents. Furthermore, ribosomes isolated from strains that are either streptomycin resistant or dependent for growth do not show these conformational changes in the presence of streptomycin. These results correlate structural changes in the ribosome induced by miscoding agents in vitro with their in vivo phenotype.

Interaction between 16S ribosomal RNA and ribosomal protein S12: differential effects of paromomycin and streptomycin

Strains containing a series of restrictive and non-restrictive mutations in ribosomal protein S12 have been transformed with plasmids carrying the rrnB operon with mutations at positions 1409 and 1491 in 16S rRNA. The effects of the double-mutant constructs have been measured by growth rate, paromomycin and streptomycin sensitivity, resistance and dependence. The results demonstrate a functional interaction between the 1409-1491 region of rRNA and ribosomal protein S12.

Effects of mutagenesis of C912 in the streptomycin binding region of Escherichia coli 16S ribosomal RNA

Four different mutations were produced at position 912 of Escherichia coli 16S rRNA in the multicopy plasmid pKK3535. Cells transformed with the mutant plasmids were assayed for growth in steptomycin. The U912 mutant conferred low level streptomycin resistance as reported originally by Montandon and co-workers (EMBO J 1986; 5:3705-3708). The G912 mutant also gave low level resistance but, unlike U912, caused significant retardation in growth rate and tended to select for fast-growing revertants. The A912 mutant was without effect on growth rate or streptomycin sensitivity, while deletion of C912 was lethal. Cells with U912 were selected for increased streptomycin resistance (MIC up to 160 micrograms/ml) and then cured of the plasmid. The cured cells retained a higher level of streptomycin resistance (MIC: 80 micrograms/ml) than the original wild type strain (MIC: 10 micrograms/ml), but sequencing by reverse transcriptase showed no evidence of U912 in the cellular 16S rRNA. Thus, recombination of the plasmid-coded U912 mutation into host rrn operons was not the mechanism by which increased streptomycin resistance occurred. The plasmid with U912 was transformed into three different streptomycin-dependent strains to determine whether the rRNA mutation, which presumably alters streptomycin binding, was compatible with S12 mutations which require bound streptomycin in order to function properly. In one strain, no transformants could be isolated, indicating that the plasmid was lethal. The two other streptomycin-dependent strains were transformed, but ribosomes containing the mutant rRNA were non-functional.

Maintenance of bacterial plasmids: comparison of theoretical calculations and experiments with plasmid R1 in Escherichia coli

Plasmid R1 was tested for stable maintenance in Escherichia coli K12. Populations carrying a transfer-negative derivative of plasmid R1drd-19 were grown exponentially for 72 generations in LB medium. Out of nearly 5000 cells none had lost the plasmid; hence the rate of loss of the plasmid is less than 3 X 10(-6) per cell and cell generation. Other experiments showed that the loss rate was less than or equal to 10(-7) per cell and cell generation. Plasmid R1 replication is controlled so that, on average, n copies are synthesized per cell and cell generation irrespective of the copy number (as long as it is at least one). A theoretical analysis was performed, based on the assumption that there is a Poissonian spread around n in each class of cells (each class defined by the number of R1 copies at birth). Two models for partitioning were analyzed, Equi-partitioning and Pair Site Partitioning; in the latter, each daughter is guaranteed one plasmid copy, whereas the rest of the copies are assumed to be randomly distributed. The copy number distribution was found to be fairly narrow in both cases, with at least 90% of the population in the range n/2-3n/2 for baby cells and in the range n-3n for cells just before cell division. Plasmid-free cells were estimated to appear at a frequency which for the copy number of R1 (n = 3-4) was 1.5 X 10(-3) - 8 X 10(-5) for equipartitioning and 6 X 10(-3) - 6 X 10(-4) for pair site partitioning, respectively.(ABSTRACT TRUNCATED AT 250 WORDS)

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.

Transcription-translation coupling and polarity: a possible role of cyclic AMP

Using specific mutants exhibiting altered translational rates we found that when the rate of protein synthesis is reduced the polarity of the lactose and galactose operons is increased. This polarity is in part relieved by cyclic AMP. On the basis of in vitro hybridization experiments were propose that the cyclic AMP-CAP complex and the ribosomes display similar functions, namely destabilization of the RNA-DNA hybrid formed during transcription.

Phenotypic instability in a tif-1 Mutant of Escherichia coli. I. Impairment in ribosomal function

The mutant T44(lambda) of Escherichia coli K12, grown in the presence of adenine, develops an increased tolerance to streptomycin. In cultures grown on streptomycin, the ts character (tif) may temporarily be suppressed but, on further transfer, both the temperature-sensitive phenotype and streptomycin tolerance disappear. In a cell-free system, the relative efficiency of translation of MS2 and poly U messenger RNAs was, respectively, 75 and 50% lower in extracts from cultures grown at 37 degrees with adenine than in extracts from 30 degrees cultures. Similar results were obtained when adenine was added in vitro to an extract from a culture grown at 37 degrees in the absence of adenine, using MS2 RNA as messenger. Moreover, the 37 degrees extracts showed a much lower misincorporation of isoleucine into polyphenylalanine in the poly U system. In addition, the Mg++ concentration required for optimal translational acitvity was higher for the 37 degrees than for the 30 degrees extracts. Extracts from a culture grown in L medium at 37 degrees or from a tif-/F'tif+ merodiploid grown at 37 degrees with adenine behaved similarly to that from the 30 degrees culture when poly U was used as messenger RNA. It is suggested that the tif+ gene product may play a regulatory role in ribosomal function and the pleiotropic nature of the tif-1 mutation could be due to impairment of translational activity augmented by elevated temperature or by adenine.

Paromomycin and dihydrostreptomycin binding to Escherichia coli ribosomes

Paromomycin binds specifically to a single type of binding site on the 70-S streptomycin-sensitive Escherichia coli ribosome. This site is different from that of dihydrostreptomycin since paromomycin binds to streptomycin-resistant ribosomes and sine dihydrostreptomycin does not compete for paromomycin binding. Paromomycin binding, unlike dihydrostreptomycin binding, is independent of changes in ribosome concentration but influenced by magnesium ion concentration. Moreover, paromomycin does not bind to the 30-S subunit of the streptomycin-sensitive ribosome, except in the presence of dihydrostreptomycin, which probably induces the conformational changes necessary for a paromomycin binding site. This induction does not occur with streptomycin-resistant ribosomes. Neither antibiotic binds to the 50-S subunit. In general, binding of the one antibiotic increases the number of sites available for binding of the other. Both antibiotics exhibit marked non-specific binding at high antibiotic/ribosome ratios. Competition studies have enabled the classification of other aminoglycosides according to their ability to compete for the paromomycin and dihydrostreptomycin binding sites. Derivatives structurally related to paromomycin compete for its binding, the degree of competition being related to antibacterial activity, but do not compete for dihydrostreptomycin binding; they, on the contrary, increase the number of dihydrostreptomycin binding sites. Neither gentamicin nor kanamycin derivatives, which induce a high level of misreading, nor kasugamycin and spectinomycin, which do not induce misreading, compete for paromomycin or dihydrostreptomycin binding sites. Other sites may be involved in the binding of these aminoglycosides and in inducing misreading.

Suppression of spectinomycin resistance in a mutant of Escherichia coli K-12

A mutant of Escherichia coli has been isolated which exhibits partial suppression of spectinomycin resistance. The site of mutation is in the streptomycin (strA) region and is closely linked to the spcA gene. However, this gene, which we propose to call mod, is phenotypically distinguishable from both the neomycin-kanamycin (nek) and the ribosomal ambiguity gene (ram). The relative gene order is mod spcA strA. In a cell-free protein synthesizing system, altered ribosomes appear to be responsible for the suppression of spectinomycin resistance caused by mod.

The effects of streptomycin or dihydrostreptomycin binding to 16S RNA or to 30S ribosomal subunits

Evidence is presented suggesting that streptomycin binds to 16S RNA or to 30S ribosomal subunits at the same topographical site located on the RNA chain. The equally bactericidal dihydrostreptomycin binds to the same site as streptomycin but with lower affinity. The effect of drug binding to 16S RNA (measured by reconstitution inhibition) is readily reversible, while that of drug binding to 30S subunits (measured by misreading) persists after removal of the drug. Binding of the drug is not a necessary and sufficient reason for killing.

Mutation to erythromycin dependence in Escherichia coli K-12

A nitrosoguanidine-induced mutant of Escherichia coli K-12 strain JC12 was absolutely dependent on erythromycin or related macrolide antibiotics for growth. The only other drugs which permitted growth (lincomycin and chloramphenicol) are, like the macrolides, inhibitors of the 50S ribosome. The order of relative effectiveness of these drugs was macrolides > lincomycin > chloramphenicol. Rates of growth with all drugs were concentration dependent. Erythromycin starvation was followed by normal rates of increase in cell mass and macromolecular synthesis for approximately one mass-doubling time, after which macromolecular synthesis abruptly ceased and cell lysis and death occurred. The dependent mutant gave rise spontaneously to revertants to independence with very high frequency (10(-4)). The gene (mac) for macrolide dependence is located near minute 25 on the E. coli chromosome; it does not result in increased resistance to these drugs. A separate gene for erythromycin resistance (eryA) is located in the cluster of ribosomal structural genes near spc, close to minute 63. Dependence on macrolides was most clearly evident in strains carrying mutations at both eryA and mac.

Ribosomal assembly influenced by growth in the presence of streptomycin

Translational leakiness (i.e., nonspecific suppression) of nonsense mutants of bacteriophage T4 is increased in cells of certain streptomycin-resistant strains previously grown in the presence of streptomycin. Concomitantly, ribosomes extracted from these streptomycin-grown cells possess a high level of misreading. Increased suppression ability as well as ribosomes that highly misread accumulate with kinetics expected for a constant differential rate of synthesis of a new product induced by drug action. The misreading ribosomes do not contain appreciable amounts of streptomycin and the misreading property is lost by exposure to high salt concentrations. It is suggested that streptomycin (or dihydrostreptomycin, or paromomycin) induces a reversible modification in 30S subunit assembly without physically participating in the modified structure. The extent of this modification appears dependent upon the strA allele.

The attachment site of streptomycin to the 30S ribosomal subunit

The 16S RNA dissociated from 30S ribosomal subunits of Escherichia coli strains either sensitive or resistant to streptomycin contains the attachment sites for two streptomycin molecules, as does the undissociated particle from a streptomycin-sensitive strain. Since no streptomycin binds to undissociated 30S subunits from a streptomycin-resistant strain, it is suggested that protein P10, specified by the strA locus-known to be responsible for drug sensitivity-controls the availability to streptomycin of the attachment sites. These sites remain exposed in the strA(+) wild-type, and become masked in strA streptomycin-resistant mutants. The 16S RNA molecule binds streptomycin specifically; it binds two drug molecules in its native state, binds many more after its secondary structure is unfolded by melting out, and again binds two molecules after reannealing. The binding is stable to exhaustive dialysis, but it is reversed by exposure of the streptomycin-RNA complex to high-salt concentration. The complex can not be used to reconstitute functional ribosomes, but the 16S RNA reacquires this property after streptomycin elimination. The biological significance of this stable streptomycin binding is questioned, since in strA mutants exhibiting phenotypic masking, exposure to streptomycin induces a modified 30S behavior that persists even after streptomycin has been dialyzed away, and is reversed only by exposure of the modified RNA to high-salt concentration.

Alteration of a 30S ribosomal protein accompanying the ram mutation in Escherichia coli

The functional peculiarities of ram mutants correlate with an observed alteration in chromatographic mobility of P4(a), a specific protein of the 30S ribosomal subunit. This finding is supported by ribosomal reconstitution experiments. These facts, together with the known location of the ram mutational site in the vicinity of other 30S genetic determinants, suggest that ram is the structural gene for P4(a). The known contrasting roles of ram and strA in determining translational efficiency require that the function of P4(a) should be explained in relation to P10 (the 30S-subunit protein defined by strA). One consequence of altering P4(a), a key protein in ribosome assembly, might be to change the interaction of P10 with the 30S subunit. The functional interrelationship of P4(a) and P10 is discussed in terms of the possible roles of these two proteins in regulating access of tRNA molecules to the decoding site.

The dominance of streptomycin sensitivity re-examined

Several aspects of the strA phenotype were studied in strains of Escherichia coli diploid in the strA chromosomal region. It was found that alleles causing different levels of interference with amber suppression can complement each other, the less restrictive effects being predominant. The sensitive strA(+) allele determines two responses to streptomycin: a dominant effect consisting of a sudden, complete, but reversible inhibition of growth, and a recessive effect manifested as cell killing. Both restriction of suppression and inhibition of growth reflect ribosomal involvement in translation.

Coresistance to neomycin and kanamycin by mutations in an Escherichia coli locus that affects ribosomes

Mutant strains resistant to neomycin or to kanamycin sulfate were isolated from Escherichia coli K-12. Nine mutants were analyzed; all were resistant to both antibiotics (about 150 and 100 mug/ml, respectively), and were designated nek. In the mutant strains, the ribosomes are changed from those of the parental strain; for when they were used in assays for polypeptide formation directed by polyadenylic acid or polycytidylic acid, coding fidelity in presence of the drugs was increased and inhibition of synthesis by the drugs was lessened. Mating experiments and transduction tests showed that all of the nine nek mutants are either closely linked or allelic, and the nek locus is closely linked to two genes-str (streptomycin) and spc (spectinomycin)-known to affect the 30S ribosome. The two nek mutants tested were recessive to the sensitive, wild-type allele. When the nek mutants were compared to the parental strain, pleiotropic effects of the nek mutations were observed. Resistance to low levels of streptomycin and spectinomycin was increased, whereas resistance to chloramphenicol was decreased. Also, the mutants were less able to adapt to high concentrations of lincomycin, and could no longer show phenotypic suppression of an arginine requirement by neomycin or kanamycin. Such pleiotropic effects are suggested to be the rule for mutations in genes that participate in the biosynthesis of a cellular organelle.