Alteration of ribosomal proteins in revertants of a valyl-tRNA synthetase mutant of Escherichia coli

Ribosomes lacking protein S20 are defective in mRNA binding and subunit association

The functional significance of ribosomal proteins is still relatively unclear. Here, we examined the role of small subunit protein S20 in translation using both in vivo and in vitro techniques. By means of lambda red recombineering, the rpsT gene, encoding S20, was removed from the chromosome of Salmonella enterica var. Typhimurium LT2 to produce a DeltaS20 strain that grew markedly slower than the wild type while maintaining a wild-type rate of peptide elongation. Removal of S20 conferred a significant reduction in growth rate that was eliminated upon expression of the rpsT gene on a high-copy-number plasmid. The in vitro phenotype of mutant ribosomes was investigated using a translation system composed of highly active, purified components from Escherichia coli. Deletion of S20 conferred two types of initiation defects to the 30S subunit: (i) a significant reduction in the rate of mRNA binding and (ii) a drastic decrease in the yield of 70S complexes caused by an impairment in association with the 50S subunit. Both of these impairments were partially relieved by an extended incubation time with mRNA, fMet-tRNA(fMet), and initiation factors, indicating that absence of S20 disturbs the structural integrity of 30S subunits. Considering the topographical location of S20 in complete 30S subunits, the molecular mechanism by which it affects mRNA binding and subunit docking is not entirely obvious. We speculate that its interaction with helix 44 of the 16S ribosomal RNA is crucial for optimal ribosome function.

Cysteinyl-tRNA(Cys) formation in Methanocaldococcus jannaschii: the mechanism is still unknown

Most organisms form Cys-tRNA(Cys), an essential component for protein synthesis, through the action of cysteinyl-tRNA synthetase (CysRS). However, the genomes of Methanocaldococcus jannaschii, Methanothermobacter thermautotrophicus, and Methanopyrus kandleri do not contain a recognizable cysS gene encoding CysRS. It was reported that M. jannaschii prolyl-tRNA synthetase (C. Stathopoulos, T. Li, R. Longman, U. C. Vothknecht, H. D. Becker, M. Ibba, and D. Söll, Science 287:479-482, 2000; R. S. Lipman, K. R. Sowers, and Y. M. Hou, Biochemistry 39:7792-7798, 2000) or the M. jannaschii MJ1477 protein (C. Fabrega, M. A. Farrow, B. Mukhopadhyay, V. de Crécy-Lagard, A. R. Ortiz, and P. Schimmel, Nature 411:110-114, 2001) provides the "missing" CysRS activity for in vivo Cys-tRNA(Cys) formation. These conclusions were supported by complementation of temperature-sensitive Escherichia coli cysS(Ts) strain UQ818 with archaeal proS genes (encoding prolyl-tRNA synthetase) or with the Deinococcus radiodurans DR0705 gene, the ortholog of the MJ1477 gene. Here we show that E. coli UQ818 harbors a mutation (V27E) in CysRS; the largest differences compared to the wild-type enzyme are a fourfold increase in the K(m) for cysteine and a ninefold reduction in the k(cat) for ATP. While transformants of E. coli UQ818 with archaeal and bacterial cysS genes grew at a nonpermissive temperature, growth was also supported by elevated intracellular cysteine levels, e.g., by transformation with an E. coli cysE allele (encoding serine acetyltransferase) or by the addition of cysteine to the culture medium. An E. coli cysS deletion strain permitted a stringent complementation test; growth could be supported only by archaeal or bacterial cysS genes and not by archaeal proS genes or the D. radiodurans DR0705 gene. Construction of a D. radiodurans DR0705 deletion strain showed this gene to be dispensable. However, attempts to delete D. radiodurans cysS failed, suggesting that this is an essential Deinococcus gene. These results imply that it is not established that proS or MJ1477 gene products catalyze Cys-tRNA(Cys) synthesis in M. jannaschii. Thus, the mechanism of Cys-tRNA(Cys) formation in M. jannaschii still remains to be discovered.

Mutagenesis of ribosomal protein S8 from Escherichia coli: defects in regulation of the spc operon

The structural features of Escherichia coli ribosomal protein S8 that are involved in translational regulation of spc operon expression and, therefore, in its interaction with RNA have been investigated by use of a genetic approach. The rpsH gene, which encodes protein S8, was first inserted into an expression vector under the control of the lac promoter and subsequently mutagenized with methoxylamine or nitrous acid. A screening procedure based on the regulatory role of S8 was used to identify mutants that were potentially defective in their ability to associate with spc operon mRNA and, by inference, 16S mRNA. In this way, we isolated 39 variants of the S8 gene containing alterations at 34 different sites, including 37 that led to single amino acid substitutions and 2 that generated premature termination codons. As the mutations were distributed throughout the polypeptide chain, our results indicate that amino acid residues important for the structural integrity of the RNA-binding domain are not localized to a single segment. Nonetheless, the majority were located within three short sequences at the N terminus, middle, and C terminus that are phylogenetically conserved among all known eubacterial and chloroplast versions of this protein. We conclude that these sites encompass the main structural determinants required for the interaction of protein S8 with RNA.

Uncharged tRNA, protein synthesis, and the bacterial stringent response

Uncharged tRNA has been shown in vivo to have an active role both in the stringent response, and in modulating the rate of translational elongation. Both of these effects appear to be mediated by codon-anticodon interactions on the ribosome. Although the involvement of uncharged tRNA in the stringent response was expected from in vitro experiments, it has only recently been confirmed in vivo. Inhibition of translation by cognate uncharged tRNA was not expected, and a model is proposed in which excess uncharged tRNA competes with charged tRNA (in ternary complex) for the 30S component of the ribosomal A site. When uncharged tRNA is in sufficient excess over charged tRNA, interaction of uncharged tRNA with the 50S component of the A site occurs as well, leading to a stringent response. The cell has a continuum of responses to decreasing aminoacyl-tRNA levels: in moderately limited conditions, the proportion of uncharged tRNA increases, and the translation rate is slowed; under more severe limitations, uncharged tRNA provokes a stringent response, with pleiotropic consequences for the cell.

Streptomyces relC mutants with an altered ribosomal protein ST-L11 and genetic analysis of a Streptomyces griseus relC mutant

Several relaxed (rel) mutants have been obtained from Streptomyces species by selecting colonies resistant to thiopeptin, an analogue of thiostrepton. Using two-dimensional gel electrophoresis, I compared the ribosomal proteins from rel and rel+ pairs of S. antibioticus, S. lavendulae, S. griseoflavus, and S. griseus. It was found that all of the Streptomyces rel mutants thus examined had an altered or missing ribosomal protein, designated tentatively ST-L11. These rel mutants therefore could be classified as relC mutants and were highly sensitive to erythromycin or high temperature. A relC mutant of S. griseus was defective in streptomycin production, but phenotypic reversion of this defect to normal productivity was found at high incidence among progeny of the relC mutant. This phenotypic reversion did not accompany a reappearance of ribosomal protein ST-L11, and furthermore the ability of accumulating ppGpp still remained at a low level, thus suggesting existence of a mutation (named sup) which suppresses the streptomycin deficiency phenotype exhibited by the relC mutant. Genetic analysis revealed that there is a correlation between the rel mutation and the inability to produce streptomycin or aerial mycelia. The sup mutation was found to lie at a chromosomal locus distinct from that of the relC mutation. It was therefore concluded that the dependence of streptomycin production on the normal function of the relC gene could be entirely bypassed by a mutation at the suppressor locus (sup). The suppressing effect of the sup mutation on the relC mutation was blocked when the afs mutation (defective in A-factor synthesis) was introduced into a relC sup double mutant. It is proposed that the sup gene or its product can be direct or indirect target for ppGpp.

Escherichia coli K-12 lysyl-tRNA synthetase mutant with a novel reversion pattern

Fast-growing revertants have been selected from a slow-growing lysyl-tRNA synthetase mutant. All of the revertants had increased lysyl-tRNA synthetase activity compared with the mutant (5- to 85-fold), and in some revertants this amounted to two to three times the wild-type synthetase activity. Two-dimensional gel electrophoresis of a whole-cell extract of revertant IH2018 (1.5- to 2-fold wild-type synthetase activity) showed that the increase in synthetase activity is due to the induction of cryptic lysyl-tRNA synthetase forms and not to a change in the constitutive lysyl-tRNA synthetase. Genetic studies have shown that a locus termed rlu (for regulation of lysU ) which is cotransducible with purF at 49.5 min influences the amount of the cryptic lysyl-tRNA synthetase.

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.

Synthesis of ribosomal proteins in merodiploid strains and in minicells of Escherichia coli

Merodiploid strains of Escherichia coli containing episomes which carry one or several of the ribosomal protein (r-protein) transcriptional units were analysed to see whether the increase in the number of gene copies leads to an increased synthesis of the respective r-proteins. It was found that the amount of ribosomal proteins was (with the only exception of ribosomal protein S20) independent of the number of gene copies present. The comparison of the in vivo stability of r-proteins in haploid and merodiploid strains did not, within the time resolution of the experiment, provide any evidence for an increased rate of degradation of those proteins coded by more than one gene copy. These results indicate a tight coupling between the amount of ribosomal proteins synthesized and the level required irrespective of the number of gene copies present. With the aid of minicells from a strain containing the episome F'101 which carries the thr-leu segment of the chromosome it was demonstrated that (i) in vivo synthesis of r-protein S20 could proceed in the absence of the synthesis of ribosomal RNA and of other r-proteins, and (ii) r-protein S20 was degraded under conditions where it was not assembled into ribosomes.

Cold-sensitive growth of a mutant of Escherichia coli with an altered ribosomal protein S8: analysis of revertants

26 cold-resistant revertants of a cold-sensitive Escherichia coli mutant with an altered ribosomal protein S8 were analyzed for their ribosomal protein pattern by two-dimensional polyacrylamide gel electrophoresis. It was found that 16 of them had acquired the apparent wild-type form of protein S8, one exhibits a more strongly altered SC than the original mutant and two revertants regained the wildtype form of S8 and, in addition, possess alterations in protein L30. The ribosomes of the residual revertants showed no detectable difference from those of the parental S8 mutant. The mutation leading to the more strongly altered S8 was genetically not separable from the primary S8 mutation; this indicates that both mutations are very close to each other or at the same site. The structural gene for ribosomal protein L30 was mapped relative to two other ribosomal protein genes (for proteins S5 and S8) by the aid of one of the L30 mutants: The relative order obtained is: aroE....rpmD(L30)....rpsE(S5)....rpsH(S8)....rpsL(S12). The L30 mutation impairs growth and ribosomal assembly at 20 degrees C and is therefore the first example of a mutant with defined 50S alteration that has (partial) cold-sensitive ribosome assembly. A double mutant was constructed which possesses both the S8 and the L30 mutations. It was found that the L30 mutation had a slight antagonistic effect on the growth inhibition caused by the S8 mutation. Thus the L30 mutants might have possibly arisen from the original S8 mutant first as S8/L30 double mutants which was followed by the loss of the original S8 lesion.

Identity of a gene responsible for suppression of aminoacyl-tRNA synthetase mutations with rpsT, the structural gene for ribosomal protein S20

Sepcialized transducing lines of phage lambda carrying segments between thr and car from the E. coli chromosome have been isolated. With help of these phages it has been shown that the gene sups20 (Böck et al., 1974) corresponds to rpsT, the structural gene for ribosomal protein S20.

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.

A proposal for a uniform nomenclature for the genetics of bacterial protein synthesis

A new genetic nomenclature for the macromolecules involved in bacterial protein synthesis is proposed and explained. Genes for ribosomal proteins are designated rsp, rpl and rpm while genes for ribosomal RNAs are rrs and rrl. Protein synthesis factors and ribosome assembly and modification activities are also consistantly named.

Genetic studies of the ribosomal proteins in Escherichia coli. IX. Mapping of the ribosomal proteins, S2 and S20, by intergeneric mating experiments between Serratia marcescens and Escherichia coli K12

Episomes of E. coli K12, which cover thrleu region of the chromosome, were transferred to Serratia marcescens. Ribosomal proteins from these hybrid strains were analyzed with phosphocellulose column chromatography. Two E. coli 30S ribosomal proteins, S2 and S20, could be detected in the ribosome of the hybrid strain in addition to all ribosomal proteins of S. marcescens.

Determination of the amino-acid sequence of the ribosomal protein S8 of Escherichia coli

The primary structure of protein S8 from the 30-S ribosomal subunit of Escherichia coli was determined mainly by automatic Edman degradation using a modified Beckman protein sequenator and the solid-phase sequentor of Laursen. The complete sequence, containing 109 amino acids, was derived by analysing peptides from tryptic, chymotryptic, thermolysin, staphylococcal protease and cyanogen bromide digestion of the protein. The amino acid composition was found to be (aspartic acid)6, (asparagine)3, (threonine)5, (serine)5, (glutamic acid )7, (glutamine)6, (proline)5, (glycine)6, (alanine)11, (valine)9, (methionine)4, (isoleucine)7, (leucine)9, (tyrosine)3, (phenylalanine)3, (lysine)11, (arginine)8, (cysteine)1. S8 is a basic protein and binds to the 16-S RNA; knowledge of its sequence is necessary for a detailed study of its interaction with the ribosomal RNA.

Localized mutagenesis of the aroE-strA section of the Escherichia coli chromosome coding for ribosomal proteins

In order to obtain E. coli strains altered in ribosomal proteins the following isolation technique was used: Phage P1 grown in a streptomycin resistant E. coli strain, was mutagenized by hydroxylamine or nitrous acid, and was used to transduce into a strain auxotrophic for aroE. Transductants with streptomycin resistance and aroE prototrophy were selected and tested for their growth at various temperatures (20 degrees, 30 degrees and 42 degrees) and their response to different antibiotics. Ribosomes from seventeen transductants with an altered response to temperature or antibiotics were isolated. They were tested for alterations in their ribosomal subunit profiles by sucrose centrifugation and for altered ribosomal proteins by two dimensional gel electrophoresis. Two strains showed accumulation of 50S ribosomal precursors and three strains had an altered 50S protein L18. This protein belongs to the 5S RNA-protein complex having GTPase and ATPase activity.