Does streptomycin cause an error catastrophe?

Recombinant TP-84 Bacteriophage Glycosylase-Depolymerase Confers Activity against Thermostable Geobacillus stearothermophilus via Capsule Degradation

The TP-84 bacteriophage, which infects Geobacillus stearothermophilus strain 10 (G. stearothermophilus), has a genome size of 47.7 kilobase pairs (kbps) and contains 81 predicted protein-coding ORFs. One of these, TP84_26 encodes a putative tail fiber protein possessing capsule depolymerase activity. In this study, we cloned the TP84_26 gene into a high-expression Escherichia coli (E. coli) system, modified its N-terminus with His-tag, expressed both the wild type gene and His-tagged variant, purified the recombinant depolymerase variants, and further evaluated their properties. We developed a direct enzymatic assay for the depolymerase activity toward G. stearothermophilus capsules. The recombinant TP84_26 protein variants effectively degraded the existing bacterial capsules and inhibited the formation of new ones. Our results provide insights into the novel TP84_26 depolymerase with specific activity against thermostable G. stearothermophilus and its role in the TP-84 life cycle. The identification and characterization of novel depolymerases, such as TP84_26, hold promise for innovative strategies to combat bacterial infections and improve various industrial processes.

Translation error clusters induced by aminoglycoside antibiotics

Aminoglycoside antibiotics target the ribosome and induce mistranslation, yet which translation errors induce bacterial cell death is unclear. The analysis of cellular proteins by quantitative mass spectrometry shows that bactericidal aminoglycosides induce not only single translation errors, but also clusters of errors in full-length proteins in vivo with as many as four amino acid substitutions in a row. The downstream errors in a cluster are up to 10,000-fold more frequent than the first error and independent of the intracellular aminoglycoside concentration. The prevalence, length, and composition of error clusters depends not only on the misreading propensity of a given aminoglycoside, but also on its ability to inhibit ribosome translocation along the mRNA. Error clusters constitute a distinct class of misreading events in vivo that may provide the predominant source of proteotoxic stress at low aminoglycoside concentration, which is particularly important for the autocatalytic uptake of the drugs.

Aminoglycoside antibiotics target the ribosome and induce misreading, yet which translation errors induce bacterial cell death is unclear. Here authors use quantitative mass spectrometry and show that bactericidal aminoglycosides induce clusters of errors in full-length proteins in vivo with as many as four amino acid substitutions in a row.

Miscoding-induced stalling of substrate translocation on the bacterial ribosome

Directional transit of the ribosome along the messenger RNA (mRNA) template is a key determinant of the rate and processivity of protein synthesis. Imaging of the multistep translocation mechanism using single-molecule FRET has led to the hypothesis that substrate movements relative to the ribosome resolve through relatively long-lived late intermediates wherein peptidyl-tRNA enters the P site of the small ribosomal subunit via reversible, swivel-like motions of the small subunit head domain within the elongation factor G (GDP)-bound ribosome complex. Consistent with translocation being rate-limited by recognition and productive engagement of peptidyl-tRNA within the P site, we now show that base-pairing mismatches between the peptidyl-tRNA anticodon and the mRNA codon dramatically delay this rate-limiting, intramolecular process. This unexpected relationship between aminoacyl-tRNA decoding and translocation suggests that miscoding antibiotics may impact protein synthesis by impairing the recognition of peptidyl-tRNA in the small subunit P site during EF-G-catalyzed translocation. Strikingly, we show that elongation factor P (EF-P), traditionally known to alleviate ribosome stalling at polyproline motifs, can efficiently rescue translocation defects arising from miscoding. These findings help reveal the nature and origin of the rate-limiting steps in substrate translocation on the bacterial ribosome and indicate that EF-P can aid in resuming translation elongation stalled by miscoding errors.

Conformational Response of 30S-bound IF3 to A-Site Binders Streptomycin and Kanamycin

Aminoglycoside antibiotics are widely used to treat infectious diseases. Among them, streptomycin and kanamycin (and derivatives) are of importance to battle multidrug-resistant (MDR) Mycobacterium tuberculosis. Both drugs bind the small ribosomal subunit (30S) and inhibit protein synthesis. Genetic, structural, and biochemical studies indicate that local and long-range conformational rearrangements of the 30S subunit account for this inhibition. Here, we use intramolecular FRET between the C- and N-terminus domains of the flexible IF3 to monitor real-time perturbations of their binding sites on the 30S platform. Steady and pre-steady state binding experiments show that both aminoglycosides bring IF3 domains apart, promoting an elongated state of the factor. Binding of Initiation Factor IF1 triggers closure of IF3 bound to the 30S complex, while both aminoglycosides revert the IF1-dependent conformation. Our results uncover dynamic perturbations across the 30S subunit, from the A-site to the platform, and suggest that both aminoglycosides could interfere with prokaryotic translation initiation by modulating the interaction between IF3 domains with the 30S platform.

Aminoglycoside activity observed on single pre-translocation ribosome complexes

Aminoglycoside-class antibiotics bind directly to ribosomal RNA, imparting pleiotropic effects on ribosome function. Despite in-depth structural investigations of aminoglycoside-RNA oligonucleotide and aminoglycoside-ribosome interactions, mechanisms explaining the unique ribosome inhibition profiles of chemically similar aminoglycosides remain elusive. Here, using single-molecule fluorescence resonance energy transfer (smFRET) methods, we show that high-affinity aminoglycoside binding to the conserved decoding site region of the functional pre-translocation ribosome complex specifically remodels the nature of intrinsic dynamic processes within the particle. The extents of these effects, which are distinct for each member of the aminoglycoside class, strongly correlate with their inhibition of EF-G-catalyzed translocation. Neomycin, a 4,5-linked aminoglycoside, binds with lower affinity to one or more secondary binding sites, mediating distinct structural and dynamic perturbations that further enhance translocation inhibition. These new insights help explain why closely related aminoglycosides elicit pleiotropic translation activities and demonstrate the potential utility of smFRET as a tool for dissecting the mechanisms of antibiotic action.

Polypeptide chain termination and stop codon readthrough on eukaryotic ribosomes

During protein translation, a variety of quality control checks ensure that the resulting polypeptides deviate minimally from their genetic encoding template. Translational fidelity is central in order to preserve the function and integrity of each cell. Correct termination is an important aspect of translational fidelity, and a multitude of mechanisms and players participate in this exquisitely regulated process. This review explores our current understanding of eukaryotic termination by highlighting the roles of the different ribosomal components as well as termination factors and ribosome-associated proteins, such as chaperones.

Hyper-susceptibility of a fusidic acid-resistant mutant of Salmonella to different classes of antibiotics

Fusidic acid resistance (Fus(R)) in Salmonella enterica serovar Typhimurium is caused by mutations in fusA, encoding elongation factor G (EF-G). Pleiotropic phenotypes are observed in Fus(R) mutants. Thus, the fusA1 allele (EF-G P413L) is associated with slow growth rate, reduced ppGpp and RpoS levels, reduced heme levels, and increased sensitivity to oxidative stress. The fusA1-15 allele, (EF-G P413L and T423I) derived from fusA1 in a selection for growth rate compensation, is partially compensated in each of these phenotypic defects but maintains its resistance to fusidic acid. We show here that the fusA1 allele is associated with sensitivity to ultraviolet light and increased susceptibility to the inhibitory action of several unrelated antibiotic classes (beta-lactam, fluoroquinolone, aminoglycoside, rifampicin, and chloramphenicol). The fusA1-15 allele, in contrast, is less susceptible to UV and to other antibiotics than fusA1. The hyper-susceptibility to multiple antibiotics associated with fusA1 and fusA1-15 is revealed in a novel growth competition assay at sub-MIC concentrations, but not in a standard MIC assay.

Expression of mutant alanine tRNAs increases spontaneous mutagenesis in Escherichia coli

The expression of mutA, an allele of the glycine tRNA gene glyV, can confer a novel mutator phenotype that correlates with its ability to promote Asp-->Gly mistranslation. Both activities are mediated by a single base change within the anticodon such that the mutant tRNA can decode aspartate codons (GAC/U) instead of the normal glycine codons (GCC/U). Here, we investigate whether specific Asp-->Gly mistranslation is required for the unexpected mutator phenotype. To address this question, we created and expressed 18 individual alleles of alaV, the gene encoding an alanine tRNA, in which the alanine anticodon was replaced with those specifying other amino acids such that the mutant (alaVX) tRNAs are expected to potentiate X-->Ala mistranslation, where X is one of the other amino acids. Almost all alaVX alleles proved to be mutators in an assay that measured the frequency of rifampicin-resistant mutants, with one allele (alaVGlu) being a stronger mutator than mutA. The alaVGlu mutator phenotype resembles that of mutA in mutational specificity (predominantly transversions), as well as SOS independence, but in a puzzling twist differs from mutA in that it does not require a functional recA gene. Our results suggest that general mistranslation (as opposed to Asp-->Gly alone) can induce a mutator phenotype. Furthermore, these findings predict that a large number of conditions that increase translational errors, such as genetic defects in the translational apparatus, as well as environmental and physiological stimuli (such as amino acid starvation or exposure to antibiotics) are likely to activate a mutator response. Thus, both genetic and epigenetic mechanisms can accelerate the acquisition of mutations.

The evolutionary design of error-rates, and the fast fixation enigma

Genetic and non-genetic error-rates are analyzed in parallel for a lower and a higher organism (E. coli and man, respectively). From the comparison of mutation with fixation rates, contrasting proposals are made, concerning the arrangement of error-rates in the two organisms. In E. coli, reproduction is very conservative, but genetic variability is high within populations. Most mutations are discarded by selection, yet single mutational variants of a gene have, on average, little impact on fitness. In man, the mutation rate per generation is high, the variability generated in the population is comparatively low, and most mutations are fixed by drift rather than selection. The variants of a gene are in general more deleterious than in E. coli. There is a discrepancy in the published mutation rates: the rate of mutation fixations in human populations is twice or four times higher than the individual rate of mutation production, a feature which is not consistent with current population genetics models. Two, not mutually exclusive, hypotheses may explain this 'fast fixation enigma': (i) Mutation rates have substantially decreased in recent human evolution and (ii) A substantial fraction of the fixed mutations were generated in a process-such as gene conversion-that violates the principle of independence of mutation events.

The two main states of the elongating ribosome and the role of the alpha-sarcin stem-loop structure of 23S RNA

According to the allosteric three-site model of the elongation cycle the ribosome oscillates between two main-functional states, viz the pre-translocational state with occupied A and P sites (E site with low affinity) and the post-translocational state with occupied P and E sites (A site with low affinity). This proposition could be confirmed by a determination of the thermodynamic parameters. High activation-energy barriers were found between both states, namely about 90 kJ mol-1 at 15 mM Mg2+ for either transition (post----pre transition = A-site binding and pre----post transition = translocation). The various A-site states (binding of ternary complex, EF-Tu dependent GTP cleavage, peptide-bond formation) are not separated by significant activation-energy barriers. The rate-limiting step of the elongation cycle is A-site binding, and not translocation as assumed previously. The principal role of both elongation factors is the reduction of the respective activation-energy barrier, thus accelerating the rate of the elongation cycle by several orders of magnitude. Cleavage of a single phosphodiester bond after G2661 of 23S rRNA by the RNase alpha-sarcin abolishes the functions of both elongation factors on the ribosome. This observation implies that the alpha-sarcin stem-loop structure plays an important role in the ribosomal conformational changes involved in the allosteric transitions. Indeed we could demonstrate that suitable oligodeoxynucleotide probes complementary to the alpha-sarcin region induce a conformational change in the 50S subunits; this conformational change causes an irreversible dissociation of tightly coupled ribosomes upon sucrose-gradient centrifugation.(ABSTRACT TRUNCATED AT 250 WORDS)

Connections between translation, transcription and replication error-rates

The analysis of published data from E coli suggests that in all three processes of translation, transcription, and replication, a minority of errors are produced by sub-classes of error-prone components. These add to the basal level of errors a noise of about 10 to 30%. Each one of the three processes contributes to the noisiness of the two others in a loose manner: a large increase in one error-rate produces a moderate increase in another error-rate. The strongest influence is that of transcription on translation errors. There it is possible that a majority of the misacylation errors are produced during the encounter of a correct amino acyl-tRNA ligase with a mistranscribed tRNA. Extreme mutator mutants are expected to produce a moderate increase in translation errors.

Senescence and the accumulation of abnormal proteins

Mammalian cells can produce abnormal proteins in a number of different ways. These include random errors during protein synthesis, spontaneous or metabolite-induced modifications of amino acid sidechains and changes in polypeptide folding. The evidence that such alterations occur in proteins during growth and senescence is discussed. An important function controlling the accumulation of abnormal proteins is the rate at which they are hydrolysed by proteases. Modified proteins are much better protease substrates than their normal parent molecules, but in spite of this sensitivity to proteolysis they accumulate during ageing. This indicates a drop during senescence in the activity of those proteases degrading abnormal polypeptides. Ways in which abnormal proteins could inhibit cell growth and how these inhibitions may be negated during the immortalisation of diploid cells are discussed.

Codon preferences in free-living microorganisms

A popular interpretation of the major codon preference is that it reflects the operation of a regulatory device that controls the expression of individual proteins. In this popular model, rapidly translated codons are thought to promote the accumulation of the highly expressed proteins and slowly translated codons are thought to retard the expression of poorly expressed proteins. However, this widely accepted model is not supported by kinetic theory or by experimental results. A less fashionable model in which the major codon preference has nothing to do with the expression level of the individual proteins is forwarded. In this model, the major codon preference is viewed as a global strategy to support the efficient function of the translation system and thereby to maximize the growth rates of cells under favorable conditions.

The allosteric three-site model for the ribosomal elongation cycle: features and future

The ribosome contains three binding sites for tRNA, viz., the A site for aminoacyl-tRNA (decoding site), the P site for peptidyl-tRNA, and the E site for deacylated tRNA (E for exit). The surprising finding of an allosteric linkage between the E and A sites in the sense of a negative cooperativity has three consequences: (a) it improves the proper selection of aminoacyl-tRNAs while preventing interference from noncognate aminoacyl-tRNAs in the decoding process, (b) it provides an explanation for the ribosomal accuracy without having to resort to the proofreading hypothesis, and (c) it has deepened our understanding of the mode of action of some antibiotics.

Contribution of normal and error-prone ribosomes to translational error formation in vivo

Introduction of tRNA missense suppressors, and/or a protease deficiency into Escherichia coli strains has no significant effect on misreading of non-sense codons. An increased cellular level of faulty proteins therefore does not seem to have much secondary effect on translational accuracy. A genetic test system with two UGA non-sense mutations in the same fused lacIlacZ gene does not demonstrate any enrichment of error-prone ribosomes after read-through of the first non-sense codon in such strains. In contrast, the addition of sublethal amounts of streptomycin to a wild type strain appears to enrich error-prone ribosomes at the second non-sense codon, indicating the existence of a subpopulation of streptomycin-binding ribosomes. Ribosomes in a ribosomal ambiguity mutant strain (rpsD) with or without tRNA missense suppressors appear to be functionally homogeneous with respect to error production, as judged by read-through of the double UGA codons. The results that the major contribution to translational error formation in vivo originates from normal ribosomes and not from error-prone defective particles. An increased translational error in a bacterium results in very little, if any, increased functional heterogeneity of the ribosomal population with respect to error production. This suggests that an autocatalytic formation of translational errors is unlikely to occur in a growing bacterium.