Restriction, de-restriction and mistranslation in missense suppression. Ribosomal discrimination of transfer RNA's

System-wide optimization of an orthogonal translation system with enhanced biological tolerance

Over the past two decades, synthetic biological systems have revolutionized the study of cellular physiology. The ability to site-specifically incorporate biologically relevant non-standard amino acids using orthogonal translation systems (OTSs) has proven particularly useful, providing unparalleled access to cellular mechanisms modulated by post-translational modifications, such as protein phosphorylation. However, despite significant advances in OTS design and function, the systems-level biology of OTS development and utilization remains underexplored. In this study, we employ a phosphoserine OTS (pSerOTS) as a model to systematically investigate global interactions between OTS components and the cellular environment, aiming to improve OTS performance. Based on this analysis, we design OTS variants to enhance orthogonality by minimizing host process interactions and reducing stress response activation. Our findings advance understanding of system-wide OTS:host interactions, enabling informed design practices that circumvent deleterious interactions with host physiology while improving OTS performance and stability. Furthermore, our study emphasizes the importance of establishing a pipeline for systematically profiling OTS:host interactions to enhance orthogonality and mitigate mechanisms underlying OTS-mediated host toxicity.

Translational fidelity and mistranslation in the cellular response to stress

Faithful translation of mRNA into the corresponding polypeptide is a complex multistep process, requiring accurate amino acid selection, transfer RNA (tRNA) charging and mRNA decoding on the ribosome. Key players in this process are aminoacyl-tRNA synthetases (aaRSs), which not only catalyse the attachment of cognate amino acids to their respective tRNAs, but also selectively hydrolyse incorrectly activated non-cognate amino acids and/or misaminoacylated tRNAs. This aaRS proofreading provides quality control checkpoints that exclude non-cognate amino acids during translation, and in so doing helps to prevent the formation of an aberrant proteome. However, despite the intrinsic need for high accuracy during translation, and the widespread evolutionary conservation of aaRS proofreading pathways, requirements for translation quality control vary depending on cellular physiology and changes in growth conditions, and translation errors are not always detrimental. Recent work has demonstrated that mistranslation can also be beneficial to cells, and some organisms have selected for a higher degree of mistranslation than others. The aims of this Review Article are to summarize the known mechanisms of protein translational fidelity and explore the diversity and impact of mistranslation events as a potentially beneficial response to environmental and cellular stress.

Genetic evidence for a polycistronic unit of transcription in the complex locus ‘14’ inPodospora anserinaII. Genetic analysis of informational suppressors

Forty-one suppressors obtained after NG and EMS mutagenesis of two ‘polar’ mutants of segment ‘29’ inPodospora anserinawere genetically analysed. Three classes of suppressor could be distinguished on spectrum pattern criteria. One representative suppressor of each class was demonstrated to be non-gene specific. The class I suppressor was dominant and only suppressed polar mutants in segment ‘29’ and non-ICR-induced ones in genes where polarity cannot be determined. Class II and III suppressors were partially dominant and they suppressed polar, non-polar and even ICR-induced mutants. The difference between classes II and III seems to be only quantitative. According to whether class II and III suppressors are considered strongly or weakly allele-specific, two hypotheses are considered. First,tRNAs could be involved in all three classes of suppression: class I would be nonsense-specific and classes II and III would be nonsense-missense suppressors. Secondly,tRNA could be involved only in class I suppression, while ribosomal ambiguity could be responsible for class II and III suppression.

The length of the 5' leader of Escherichia coli tRNA precursors influences bacterial growth

Based on a computational analysis of the 5' regions of tRNA-encoding genes, the average length of the 5' leaders in tRNA precursors in Escherichia coli appears to be 17-18 residues long. An in vivo assay based on tRNA nonsense suppression was developed and used to investigate the function of the 5' leader of the tRNA precursors on tRNA processing and bacterial growth. Our data indicate that the 5' leader influences bacterial growth but is surprisingly not absolutely necessary for growth. These findings are consistent with previous in vitro data where it was demonstrated that the 5' leader plays a role in the interaction with RNase P, the endoribonuclease responsible for removing the 5' leader in the cell. We discuss the plausible role of the 5' leader in processing and tRNA gene expression.

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.

Streptomycin revisited: molecular action in the microbial cell

The key event for antimicrobial action begins when streptomycin binds to the 30S subunit (S12 protein) of a ribosome. Lysine 42 and lysine 87 are involved. It is proposed that antagonism of acetyl coenzyme A carboxylase by streptomycin results in faulty fatty acids, lipids and derivatives marked exclusively for cell membrane synthesis. Streptomycin-sensitive growing cells are fatally wounded when defective membranes leak K(+) ions, then amino acids, nucleotides, oligonucleotides and proteins as increasing amounts of streptomycin enter the cell.

Self-description and the origin of the genetic code

The genetic code presents an important conceptual challenge within the broader context of the origin of life. Translation of genetic information captures a fundamental property of living systems, i.e. the ability of decoding proteins (e.g. aminoacyl-tRNA synthetases) to reproduce themselves from self-contained RNA/DNA descriptors. Silvano Colombano and I, as graduate students with Howard Pattee in the 1970s, focused on achieving this closure of self-description and self-reproduction in the genetic code. Simulation and analysis of competitive models that allowed alternate code assignments, exploring initial conditions, arbitrary descriptor-catalyst relationships, and degree of non-linearity, indicated that these dynamical systems undergo bifurcations, transforming initial ambiguous stable states to unstable states. New, stable, steady states, progressively closer to a code, became available as the descriptor parameters were varied. The efficiency of utilization of raw materials for the production of a coding family of catalysts is proposed as a selection criterion that drives such systems towards a coded state.

Mutations in yeast ribosomal proteins S28 and S4 affect the accuracy of translation and alter the sensitivity of the ribosomes to paromomycin

Ribosomal proteins S12, S5 and S4 of Escherichia coli are essential for the control of translational accuracy. Their yeast equivalents, i.e., S28, S4 and S13, have also been implicated in this process. Using a poly(U)-dependent cell-free translation system, we determined the accuracy of translation and the sensitivity to antibiotic paromomycin of yeast ribosomes carrying mutant ribosomal proteins S28 and/or S4. Our results confirm by quantitative biochemical methods previous genetic data showing that proteins S28 and S4 are involved in the decoding activity of the ribosome and interact to control translational accuracy. We find that the suppressor mutation SUP44 in yeast S4, decreased the accuracy of translation. To examine the effect of mutant S28, we disrupted RPS28B and introduced in RPS28A the same substitutions that cause hyperaccurate translation or antibiotic resistance in bacteria. Three of these substitutions (Lys-62-->Asn, Thr or Gln) similarly increased translational accuracy in vitro or antibiotic resistance. In the presence of the SUP44 mutation, these substitutions partially reversed the decrease of translational accuracy caused by SUP44. However, the Lys-62-->Arg substitution decreased translational accuracy and caused antibiotic sensitivity both in nonsuppressor and in SUP44 haploids. These results establish the role of Lys-62 of S28 in optimizing translational accuracy and provide a more precise view of the functional role of two important ribosomal proteins.

Dual functions of ribosome recycling factor in protein biosynthesis: disassembling the termination complex and preventing translational errors

We summarize in this communication the data supporting the two functions of ribosome recycling factor (RRF, originally called ribosome releasing factor). The first described role involves the disassembly of the termination complex which consists of mRNA, tRNA and the ribosome bound to the mRNA at the termination codon. This process is catalyzed by two factors, elongation factor G (EF-G) and RRF. RRF stimulated protein synthesis as much as eight-fold in the in vitro lysozyme synthesis system, when ribosomes were limiting. In the absence of RRF, ribosomes remain mRNA-bound at the termination codon and translate downstream codons. In the in vitro system, the site of reinitiation is the triplet codon 3' to the termination codon. RRF is an essential protein for bacterial life. Temperature sensitive (ts) RRF mutants were isolated and in vivo translational reinitiation due to inactivation of ts RRF was demonstrated using the beta-galactosidase reporter gene placed downstream from the termination codon. A second function of RRF involves preventing errors in translation. In polyphenylalanine synthesis programmed by polyuridylic acid, misincorporation of isoleucine, leucine or a mixture of amino acids was stimulated upto 17-fold when RRF was omitted from the in vitro system. RRF did not influence the large error (10-fold increase) induced by streptomycin. This means that RRF participates not only in the disassembly of the termination complex but also in peptide elongation. Extending this concept and its conventional role for releasing ribosomes from mRNA, involvement of RRF in the reinitiation in the 3A' system (a construct using S aureus protein A, a collaborative work with Dr Isaksson), in programmed frame shifting, in trans-translation with 10Sa RNA (collaborative work with Dr Muto), and in the reinitiation downstream from the ORF A of the IS 3 (insertion sequence of a transposon, collaborative work with Dr Sekine) are discussed on the basis of preliminary data to be published elsewhere. Finally, we review the known RRF sequences from various organisms including eukaryotes and discuss the possible mechanism for disassembly of the eukaryotic termination complex.

An accuracy center in the ribosome conserved over 2 billion years

The accuracy of translation in Escherichia coli is profoundly influenced by three interacting ribosomal proteins, S12, S4, and S5. Mutations at lysine-42 of S12, originally isolated as causing resistance to streptomycin, increase accuracy. Countervailing "ribosomal ambiguity mutations" (ram) in S4 or S5 decrease accuracy. In the eukaryotic ribosome of Saccharomyces cerevisiae, mutations in SUP46 and SUP44, encoding the proteins equivalent to S4 and S5, lead to omnipotent suppression--i.e., to less accurate translation. The evolution of ribosomal protein S12 can be traced, by comparison with archaebacteria and Tetrahymena, to S28 of S. cerevisiae, even though the two proteins share only very limited regions of homology. However, one region that has been conserved contains a lysine residue whose mutation leads to increased accuracy in E. coli. We have introduced into S28 of yeast the same amino acid substitutions that led to the original streptomycin-resistant mutations in E. coli. We find that they have a profound effect on the accuracy of translation and interact with SUP44 and SUP46, just as predicted from the E. coli model. Thus, the interplay of these three proteins to provide the optimal level of accuracy of translation has been conserved during the 2 billion years of evolution that separate E. coli from S. cerevisiae.

Streptomycin inhibits splicing of group I introns by competition with the guanosine substrate

Streptomycin is an aminocyclitol glycoside antibiotic, which interferes with prokaryotic protein synthesis by interacting with the ribosomal RNA. We report here that streptomycin is also able to inhibit self splicing of the group I intron of the thymidylate synthase gene of phage T4. The inhibition is kinetically competitive with the substrate guanosine. Streptomycin and guanosine have in common a guanidino group, which has been shown to undergo hydrogen bonds with the ribozyme (Bass & Cech, Biochemistry, 25, 1986, 4473). The inhibitory effect of streptomycin extends to other group I introns, but does not affect group II introns. Mutating the bulged nucleotide in the conserved P7 secondary structure element of the td intron alters the affinity of the ribozyme for both guanosine and streptomycin. Myomycin, an antibiotic with similar effects on protein synthesis as streptomycin, is also able to inhibit splicing. In contrast, bluensomycin, which is structurally related to streptomycin, but contains only one guanidino group does not inhibit splicing. We discuss these findings in support of an evolutionary model that stresses the antiquity of antibiotics (J. Davies, Molecular Microbiology 4, 1990, 1227).

Temperature sensitivity caused by missense suppressor supH and amber suppressor supP in Escherichia coli

The temperature-sensitive missense suppressor supH and amber suppressor supP in Escherichia coli are mutations of the serU and leuX genes, respectively. The supH tRNA, tRNA(SerCAA), is expected to recognize UUG codons, which are normally read by tRNA(LeuCAA) and tRNA(LeuUAA), coded for by the leuX gene and the leuZ gene, respectively. We show that supP and supH are incompatible and that strains carrying both supP and a restrictive rpsL allele are temperature sensitive. It is suggested that the temperature sensitivity of both supH and supP strains is caused by deficient reading of UUG codons by tRNA(LeuUAA).

Is efficiency of suppressor tRNAs controlled at the level of ribosomal proofreading in vivo?

Ribosomal rpsD mutations did not stimulate nonsense suppressor tRNAs in a general manner according to their increased ribosomal ambiguity and decreased proofreading efficiency. Streptomycin, which stimulates error production by blocking proofreading in vitro, did not increase efficiency of suppressor tRNAs in strains with normal or streptomycin-resistant (rpsL) ribosomes. It did so only in combination with one rpsL mutation which is associated with streptomycin pseudodependence.

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.

Interaction of antibiotics with functional sites in 16S ribosomal RNA

Chemical footprinting shows that several classes of antibiotics (streptomycin, tetracycline, spectinomycin, edeine, hygromycin and the neomycins) protect concise sets of highly conserved nucleotides in 16S ribosomal RNA when bound to ribosomes. These findings have strong implications for the mechanism of action of these antibiotics and for the assignment of functions to specific structural features of 16S rRNA.

Functional interactions in vivo between suppressor tRNA and mutationally altered ribosomal protein S4

Ribosomal mutants (rpsD) which are associated with a generally increased translational ambiguity were investigated for their effects in vivo on individual tRNA species using suppressor tRNAs as models. It was found that nonsense suppression is either increased, unaffected or decreased depending on the codon context and the rpsD allele involved as well as the nature of the suppressor tRNA. Missense suppression of AGA and AGG by glyT(SuAGA/G) tRNA as well as UGG by glyT(SuUGG-8) tRNA is unaffected whereas suppression of UGG by glyT(SuUGA/G) or glyV(SuUGA/G) tRNA is decreased in the presence of an rpsD mutation. The effects on suppressor tRNA are thus not correlated with the ribosomal ambiguity (Ram) phenotype of the rpsD mutants used in this study. It is suggested that the mutationally altered ribosomes are changed in functional interactions with the suppressor tRNA itself rather than with the competing translational release factor(s) or cognate aminoacyl tRNA. The structure of suppressor tRNA, particularly the anticodon loop, and the suppressed codon as well as the codon context determine the allele specific functional interactions with these ribosomal mutations.

Primary structures of mutationally altered ribosomal protein L7/L12 and their effects on cellular growth and translational accuracy

The amino acid sequences of mutationally altered ribosomal protein L7/L12 from four different rplL mutants of Escherichia coli were determined and correlated with some features of the mutant ribosomes. Two of the rplL mutations are deletions around position 40, which give rise to a shortened hinge region between the two domains of L7/L12. The other two mutants harbor point mutations at position 74 (Gly----Asp) or at position 82 (Glu----Lys), which are in or close to an evolutionarily conserved sequence in the C-terminal domain. The two latter mutations are associated with decreased rates of growth and translational elongation. All four mutants show increased nonsense codon read-through in vivo. Ribosomes from one of the deletion mutants show clearly increased missense error rates in vitro.

The accuracy of Q beta RNA translation. 2. Errors during the synthesis of Q beta proteins by cell-free Escherichia coli extracts

The accuracy of Q beta translation by Escherichia coli extracts in polymix and a conventional Tris/Mg2+ system has been followed. Misinsertions of histidine and of tryptophan into the phage coat protein were less frequent in polymix than in Tris/Mg2+, as were errors leading to a change in the coat protein pI. Even the lowest Q beta error rates, however, were still an order of magnitude greater than those for poly(U) or poly(U-G) translation. Comparing Q beta translational errors made in vitro to those found in whole cells, histidine misinsertions were almost twice as frequent, errors leading to a coat protein charge change six times more frequent and tryptophan misinsertions at least 15 times more frequent in vitro. The relation of these findings to measurements of translational accuracy and to factors affecting fidelity is discussed.

The accuracy of Q beta RNA translation. 1. Errors during the synthesis of Q beta proteins by intact Escherichia coli cells

The fidelity of Q beta RNA translation by intact Escherichia coli cells has been studied. After infection, host protein synthesis was eliminated by adding rifampicin and the radioactive, phage-specified, proteins separated by one or two-dimensional gel electrophoresis. Labelled histidine and tryptophan were incorporated into the phage coat protein, whose message does not specify these amino acids, at a frequency of 0.09-0.13 per molecule. Errors leading to a change in the pI of the coat protein occurred at a rate of 0.05 per molecule, while the coat protein UGA stop codon was misread 6.5% of the time. These error rates are similar to data in some recent publications but much higher than the canonical 3-4 X 10(-4). They further provide a reference point in vivo to which the translation of the same message by E. coli extracts can be compared.

Translational efficiency of transfer RNA's: uses of an extended anticodon

Transfer RNA's are probably very strongly selected for translational efficiency. In this article, the argument is presented that the coding performance of the triplet anticodon is enhanced by selection of a matching anticodon loop and stem sequence. the anticodon plus these nearby sequence features (the extended anticodon) therefore contains more coding information than the anticodon alone and can perform more efficiently and accurately at the ribosome. This idea successfully accounts for the relative efficiencies of many transfer RNA's.

Genetic analysis of a streptomycin-resistant Escherichia coli mutant temperature-sensitive for nonsense suppression

Continuing the genetic and biochemical characterization of the streptomycin-resistant Escherichia coli mutant LD1, we confirmed that LD1 is temperature-sensitive for suppression of nonsense codons, and that this phenotype of the mutant and its streptomycin-resistance are genetically linked and are probably caused by a single mutation, strA(LD1). We also isolated a spontaneous revertant, called LD1-R, which partially relieves the restriction of nonsense suppression caused by the strA(LD1) mutation. LD1-R is derived by an additional mutation (revA) which is closely linked to strA(LD1). We further demonstrate that the weak suppression of a lacZUGA mutation in a suppressor-free strain, which probably takes place by normal tRNA1rp, can be detected by the use of the chromagenic substance x-gal (5-Bromo-4-chloro-3-indolyl-beta-D-Galactopyranoside).

The possible role of assignment catalysts in the origin of the genetic code

A model is presented for the emergence of a primitive genetic code through the selection of a family of proteins capable of executing the code and catalyzing their own formation from polynucleotide templates. These proteins are assignment catalysts capable of modulating the rate of incorporation of different amino acids at the position of different codons. The starting point of the model is a polynucleotide based polypeptide construction process which maintains colinearity between template and product, but may not maintain a coded relationship between amino acids and codons. Among the primitive proteins made are assumed to be assignment catalysts characterized by structural and functional parameters which are used to formulate the production kinetics of these catalysts from available templates. Application of the model to the simple case of two letter codon and amino acid alphabets has been analyzed in detail. As the structural, functional, and kinetic parameters are varied, the dynamics undergoes many bifurcations, allowing an initially ambiguous system of catalysts to evolve to a coded, self-reproductive system. The proposed selective pressure of this evolution is the efficiency of utilization of monomers and energy. The model also simulates the qualitative features of suppression, in which a deleterious mutation is partly corrected by the introduction of translation error.

A novel form of suppression due to an altered RNA polymerase

A group of mutants isolated from E coli K12(tif-1) display a very pleiotropic phenotype. The main characteristic of these mutants, temporarily designated 'S' strains, is their ability to suppress a large number of mutations. High efficiency of suppression is correlated with increased thermolability of cellular proteins, indicating an impairment in the fidelity of protein synthesis. Efficient suppression is also accompanied by the appearance of new characteristics like simultaneous resistance to several antibiotic drugs (Sm, Spc, and Mer), and plasmid-like DNA circles. Genetic studies show that the suppressor character is located in the rpoBC region. In a large number of spontaneous Rifr mutants, isolated from these strains, suppression or resistance to drugs is lost. The findings suggest that the phenotype of 'S' strains is due to an altered RNA polymerase causing erroneous transcription.

Speed-accuracy relationships during in vitro and in vivo protein biosynthesis

Poly U-directed incorporation of phenylalanine and leucine into polypeptide has been described in at least 50 papers since 1961. In general, high translation activities are associated with high accuracies, and vice-versa. Moreover, a vast body of independent experimental data (effect of ethanol, temperature, urea, aminoglycosides, etc... on protein synthesis) put together here suggests that, in many circumstances, speed and accuracy of elongation are correlated. This result is to be contrasted with the view that the speed and the fidelity of protein synthesis are two opposing parameters. In this report, recent experimental data on the nature and effect of ribosomal ambiguity (ram) and streptomycin resistance (Strr) mutations are reexamined. Models on the action of streptomycin and other misreading-inducing antibiotics, as well as long-standing ideas on the control of misreading in mammalian systems are critically evaluated. An explanation is provided for the long-befuddling data on the action of gentamicin.

Bacterial ribosomes with two ambiguity mutations: effects of translational fidelity, on the response to aminoglycosides and on the rate of protein synthesis

A set of mutants affected in translational fidelity was constructed by transduction within an otherwise isogenic Escherichia coli B argF40 argR11 background. Alterations in ribosomal proteins S4, S5, S12 and L6 either as single mutations or in various combinations were compared for their effects on aminoglycoside phenotypes, on in vivo and in vitro misreading and on the rate of peptide bond formation. Results may be summarized as follows: (i) Strains carrying two ambiguity mutations on the ribosome without any restrictive mutation are viable. When together, they only weakly increase the level of mistranslation as judged by several in vivo and in vitro test systems. (ii) The combination of two ram mutations causes a very strong cooperative increase of streptomycin sensitivity, irrespective of whether the strains have a wild-type S12 or mutationally altered S12 proteins (of the drug-resistant or -dependent types) on their ribosomes; (iii) The S4 and S5 ram mutations do not alter the response of the ribosome to aminoglycosides of the 2-desoxystreptamine group which are structurally unrelated to streptomycin. This is interpreted in terms of an effect of these ram mutations on the streptomycin binding site but not on the site(s) of binding of the other aminoglycosides. (iv) The rate of polypeptide bond formation which was determined from the kinetics of beta-galactosidase induction is not significantly changed in strains bearing the ram and the strA (streptomycin-resistant) alleles. In contrast, the L6 and the strA (streptomycin-dependent) alleles strongly reduce the rate of polypeptide elongation which mechanistically might be connected with restriction of ambiguity (Nino, 1974) in these cases.

Analysis of rpsD mutations in Escherichia coli. III. Effects of rpsD mutations on expression of some ribosomal protein genes

Relative rates of production and steady state levels of ribosomal proteins were determined in a temperature sensitive rpsD (S4) mutant of Escherichia coli. Some proteins (S4, S12, S13) were overproduced in the mutant at permissive temperature but steady state levels of all examined ribosomal proteins were normal. In a rpsD+/rpsD+ homodiploid strain the relative rates of production of ribosomal proteins were not affected by the increased gene dose. In a rpsD+/rpsD heterodiploid strain only wild type, but not mutant S4, was found. In such a strain S4, S7, S12 and probably S13 is overproduced. It is implied that S4 is involved in the regulation of expression of proximal genes of the two transcriptional units including the genes coding for S4 itself and S12, respectively. A degradation system for ribosomal proteins, which is rapid enough to be of regulatory significance, is demonstrated.

A mutation that increases the activity of nonsense suppressors in Escherichia coli

We have isolated a new mutation, ups, that amplifies the suppressor activity of all the nonsense suppressors we have tested so far at low but not at high temperature. The properties of ups make it a very useful tool to improve the systems of temperature sensitive suppressors thus far described. ups maps between 25 to 27 min on the E. coli genetic map (Bachmann et al., 1976) and has no suppressor activity of its own. Its effects on translational fidelity are not influenced by mutations for ribosomal drug resistance. Thus, ups is different from ram which exhibits cooperative control of translation with other ribosomal proteins. The possible functions of ups in the cell are discussed.

Conditional lethal mutants of bacteriophage T4 unable to grow on a streptomycin resistant mutant of Escherichia coli

Sixteen conditional lethal mutants of bacteriophage T4D have been isolated which grow on Escherichia coli CR63 (a su+ streptomycin-sensitive K12 strain) but are restricted by CR/s (a streptomycin-resistant derivative of CR63). These mutants have been given the prefix str. Four of these mutants are amber and 12 appear to be missense. Eleven of the 12 missense mutants appear to be "pseudo-amber" (i.e. they are restricted by a su- E. coli B strain but not by a su- K12 strain); the other missense mutant was not restricted by either B or K12. The str mutations mapped in 12 different genes. Most were clustered in a region of early genes (gene 56 to gene 47). Fifty-eight amber and 10 "pseudo-amber" mutants isolated previously for their inability to grow on E. coli B were tested for restriction by CR/s. All the amber mutants grew normally on CR/s, whereas all 10 "pseudo-amber" mutants were restricted by CR/s. This implies that the phenotype of the "pseudo-amber" mutants is the result of a ribosomal difference between the permissive host CR63 and the restrictive hosts B and CR/s. These str mutants should prove to be useful alternatives to amber mutants for genetic and biochemical studies of bacteriophage T4 and for studies of the E. coli ribosome. It should be possible ot isolate similar mutants in other bacteriophages provided that streptomycin resistant hosts are available.

An investigation of mistranslation in vivo induced by streptomycin by an examination of the susceptibility of abnormal proteins to degradation

Proteolysis rates in vivo were measured in Escherichia coli cultures during treatment with dihydrostreptomycin and under various other conditions. Dihydrostreptomycin treatment caused an increase in the proteolysis rate, compared to untreated controls. The proteolytic system in vivo responsible for the elevated proteolysis in the early stages of dihydrostreptomycin treatment, or that during canavanine and puromycin treatment, were not inhibited by addition of phenylmethanesulphonyl fluoride. This agent did inhibit proteolysis rates in cultures whose growth was inhibited by starvation, or had been completely stopped by dihydrostreptomycin. It seems, therefore, that the extremely high proteolysis rates in cultures at this stage of dihydrostreptomycin treatment were due to the action of two protease systems: the one concerned with the breakdown of abnormal proteins, and the other concerned with normal protein turnover and active during a non-specific decline of growth. The proteolytic rate at complete growth inhibition brought about by dihydrostreptomycin was intermediate between those induced by canavanine and puromycin at the same stage of treatment. This indicated a similar hierarchy in the extent and nature of abnormality in the proteins synthesized under these conditions. The relationship between the abnormality of proteins induced by dihydrostreptomycin and the importance of this in the antibiotic mechanism is discussed.

Ribosome editing and the error catastrophe hypothesis of cellular aging

Ribosome editing involves the dissociation during protein synthesis of inappropriate peptidyl-tRNA's, ones whose structure does not correctly complement the codon of the mRNA. This process is one of three stages in protein biosynthesis in which the frequency of errors in cellular proteins is controlled. These stages are reviewed and the implications of ribosome editing are described. A model for stability of the translation apparatus is criticized. Calculations using a revision of the model and experimentally reasonable values for the various parameters show varying time courses for error catastrophes.

Suppression of temperature-sensitive aminoacyl-tRNA synthetase mutations by ribosomal mutations: a possible mechanism

The biochemical basis of suppression of a temperature-sensitive alanyl-tRNA synthetase (alaS) mutation by mutational alterations of the ribosome has been investigated. Measurement of the polyU-dependent polyphenylalanine synthesis showed that ribosomes from the suppressor strains are less active than ribosomes from the unsuppressed aminoacyl-tRNA synthetase mutant. In this system no increased translational ambiguity could be detected for the suppressor ribosomes. This fact and also the findings that the ram-1 mutation is not able to suppress the aminoacyl-tRNA synthetase mutation and that presence of the suppressor allele is not accompanied by a measureably improved alanyl-tRNA synthetase activity argue against the possibility that suppression might be due to increased translational misreading rates of the alanyl-tRNA synthetase mRNA. It has been further found that partial suppression of temperature sensitive growth of the alaS mutation can be achieved by independent ribosomal mutations leading to reduced growth rates because of a mutation to antibiotic resistance. Addition of low concentrations of a variety of antibiotics acting at the ribosomal level can also partially revert the temperature-sensitive phenotype of the alaS mutant. Although the possibility cannot be excluded that suppression is due to the stabilisation or activation of the mutant enzyme by some indirect effect of the suppressor ribosomal mutations, the following working hypothesis is favoured at the moment: It is assumed that limitation of the aminoacyl-tRNA synthetase activity in a certain range of the restrictive temperature causes growth inhibition by the premature termination of polypeptide synthesis at the ribosome or by the unbalanced synthesis of the individual cellular proteins under this condition. The mechanism of suppression by ribosomal mutations is proposed to consist of the release of this growth inhibition by the reduction of the rate of polypeptide synthesis, which would keep amino acid incorporation from exceeding the slow charging of tRNA and thus exhausting the pool of charged tRNA. In the suppressor strains, therefore, growth at the semi-restrictive temperature is no longer limited by the aminoacylation of tRNA but by the translational process at the mutated ribosome. This influence of the ribosomal mutation on the speed of translation could be directly or indirectly coupled with an effect on translational fidelity resulting in the prevention of the binding of uncharged or non-cognate charged tRNA or in the tighter binding of peptidyl-tRNA when cognate aminoacyl-tRNA is limiting.

Genetic evidence of ribosomal antisuppressors in Podospora anserina

Antisuppressors were screened for with the help of informational suppressors in Podospores anserina. Four mutations in the AS1 locus and two in the AS2 locus were isolated, using allele non specific suppressors supposed to be ribosomal ambiguity mutations. Four mutations in the AS3 locus and 45 in the AS4 locus were obtained, using a nonsense (t-RNA like) suppressor. All antisuppressors are partially dominant. Most mutations in the AS4 locus are lethal. The four mutants at the AS3 locus and 6 out of the 8 viable mutants at the AS4 locus are cold sensitive. Phenotypic properties and action spectra of the antisuppressors suggest that they are restrictive ribosomal mutations.

Cooperative control of translational fidelity by ribosomal proteins in Escherichia coli. III. A ram mutation in the structural gene for protein S5 (rpx E)

The effect on translational fidelity of a particular mutation in the gene coding for protein S5(rpxE) has been investigated. This mutation has the opposite effect of a restrictive strA mutation; in vivo, it relieves the restriction imposed by strA on the suppression of T4 nonsense mutants and results in hypersensitivity to streptomycin; in vitro, the presence of the altered S5 protein in 30S ribosomes results in increased intrinsic misreading. It is concluded that this mutation, ramC319, acts as a ribosomal ambiguity mutation similar to certain mutations of protein S4 (ramA).

Kinetic amplification of enzyme discrimination

The dependence of the accuracy of enzymatic systems on the mechanism of the catalyzed reaction is investigated, using a probabilistic approach. Certain mechanisms of reaction, involving a delay in one of the steps act as kinetic amplifiers of molecular discriminations. The relationship between our scheme for a delayed reaction [1] and Hopfield's scheme [i] is discussed.