Codon-specific Binding of Deacylated Transfer Ribonucleic Acid to Ribosomes

Functional effects of deleting the coiled-coil motif in Escherichia coli elongation factor Ts

Elongation factor Ts (EF-Ts) is the guanine nucleotide-exchange factor for elongation factor Tu (EF-Tu) that is responsible for promoting the binding of aminoacyl-tRNA to the mRNA-programmed ribosome. The structure of the Escherichia coli EF-Tu-EF-Ts complex reveals a protruding antiparallel coiled-coil motif in EF-Ts, which is responsible for the dimerization of EF-Ts in the crystal. In this study, the sequence encoding the coiled-coil motif in EF-Ts was deleted from the genome in Escherichia coli by gene replacement. The growth rate of the resulting mutant strain was 70-95% of that of the wild-type strain, depending on the growth conditions used. The mutant strain sensed amino acid starvation and synthesized the nucleotides guanosine 5'-diphosphate 3'-diphosphate and guanosine 5'-triphosphate 3'-diphosphate at a lower cell density than the wild-type strain. Deletion of the coiled-coil motif only partially reduced the ability of EF-Ts to stimulate the guanine nucleotide exchange in EF-Tu. However, the concentration of guanine nucleotides (GDP and GTP) required to dissociate the mutant EF-Tu-EF-Ts complex was at least two orders of magnitude lower than that for the wild-type complex. The results show that the coiled-coil motif plays a significant role in the ability of EF-Ts to compete with guanine nucleotides for the binding to EF-Tu. The present results also indicate that the deletion alters the competition between EF-Ts and kirromycin for the binding to EF-Tu.

Differential regulation of opposing RelMtb activities by the aminoacylation state of a tRNA.ribosome.mRNA.RelMtb complex

Rel(Mtb) of Mycobacterium tuberculosis is responsible for the intracellular regulation of (p)ppGpp and the consequent ability of the organism to survive long-term starvation, indicating a possible role in the pathogenesis of tuberculosis. Purified Rel(Mtb) is a dual-function enzyme carrying out ATP: GTP/GDP/ITP 3'-pyrophosphoryltransferase and (p)ppGpp 3'-pyrophosphohydrolase reactions. Here we show that in the absence of biological regulators, Rel(Mtb) simultaneously catalyzes both transferase and hydrolysis at the maximal rate for each reaction, indicating the existence of two distinct active sites. The differential regulation of the opposing activities of Rel(Mtb) is dependent on the ratio of uncharged to charged tRNA and the association of Rel(Mtb) with a complex containing tRNA, ribosomes, and mRNA. A 20-fold increase in the k(cat) and a 4-fold decrease in K(ATP) and K(GTP) from basal levels for transferase activity occur when Rel(Mtb) binds to a complex containing uncharged tRNA, ribosomes, and mRNA (Rel(Mtb) activating complex or RAC). The k(cat) for hydrolysis, however, is reduced 2-fold and K(m) for pppGpp increased 2-fold from basal levels in the presence of the Rel(Mtb) activating complex. The addition of charged tRNA to this complex has the opposite effect by inhibiting transferase activity and activating hydrolysis activity. Differential control of Rel(Mtb) gives the Mtb ribosomal complex a new regulatory role in controlling cellular metabolism in response to stringent growth conditions that may be present in the dormant Mtb lesion.

Chromosomal mutations causing resistance to tetracycline in Bacillus subtilis

We have isolated, after ethylmethanesulfonate mutagenesis, several chromosomal mutations causing resistance to tetracycline in Bacillus subtilis. These mutations fall into two classics, tetA and tetB. 30 S ribosomal protein S10 shows an altered mobility on two-dimensional acrylamide gels in cells bearing the former type of mutation. Ribosomes from these cells show elevated levels of resistance to tetracycline in vitro as measured by polyuridine dependent polyphenylalanine synthesis. The tetA locus maps adjacent to the tuf gene in the B. subtilis ribosomal protein gene cluster. Cells with the tetB mutation do not show any altered ribosomal protein, and their ribosomes are as sensitive, in vitro, to tetracycline as ribosomes isolated from wild type cells. The tetB mutation has been mapped proximal to cysA14.

Codon-specific interaction of uncharged transfer-RNA with eukaryotic ribosomes

Rat liver ribosomes bound [32P]tRNAPhe in both a codon-dependent and codon-independent manner. The codon-dependent binding was studied further by utilising the ability of the unchanged tRNAPhe to inhibit the poly(U)-directed binding of [3H]Phe-tRNA to ribosomes. At least part of the codon-dependent binding of uncharged tRNA appears to be to the ribosomal A-site.

Codon-dependent rearrangement of the three-dimensional structure of phenylalanine tRNA, exposing the T-psi-C-G sequence for binding to the 50S ribosomal subunit

Codon-anticodon interaction induces an allosteric rearrangement of the three-dimensional structure of Phe-tRNAPhe that exposes the T-psi-C-G sequence for binding to the C-G-A-A sequence of the 5S rRNA within the 50S ribosomal subunit. The conformational change in the tRNAPhe structure was followed by the binding of C-G-[3H]A-[3H]A to the T-psi-C-G sequence, as measured by equilibrium dialysis at 10 mM Mg2+. C-G-A-A (14 pmol) was bound to tRNAPhe in the complete system containing elongation factor Tu-GTP-Phe-tRNA-(uridylyl-3',5')7-uridine-30S ribosomes (100 pmol). At a Mg2+ concentration lower than 5 mM the rearrangement was dependent on elongation factor-Tu, whereas GTP could be replaced by guanylyl imidodiphosphonate. In the absence of elongation factor-Tu-GTP a sigmoidal C-G-A-A binding curve with respect to Mg2+ concentration was obtained, showing half-saturation at 6 mM Mg2+. To achieve the change in the tRNAPhe structure in the absence of 30S ribosomes, a twofold higher concentration of (uridylyl-3',5')7-uridine had to be used. A sigmoidal curve was obtained again when the Mg2+ dependence of the C-G-A-A binding was followed, with 12 pmol of C-G-A-A being bound to 200 pmol of Phe-tRNA. Since T-psi-C-G exposure should influence the binding of Phe-tRNA to 70S ribosomes, Phe-tRNA binding to 70S ribosomes was examined. In the "nonenzymatic" binding (i.e., no elongation factor-Tu-GTP) of Phe-tRNA a sigmoidal Mg2+ dependence was found, whereas the "enzymatic" binding (elongation factor-Tu-GTP present) showed a hyperbolic curve. With 30S ribosomes as controls, only hyperbolic binding curves were found. The Mg2+ dependence of AA-tRNA binding thus reflects the rearrangement of the tRNA structure.

Studies on the in vitro synthesis of ppGpp and pppGpp

The effect of a number of inhibitors of protein synthesis on ppGpp and pppGpp synthesis in vitro has been examined. As expected from in vivo results, chloramphenicol is without effect on this reaction. Aurintricarboxylic acid and chlortetracycline, on the other hand rapidly and specifically inhibit ppGpp synthesis. Fusidic acid in the presence of saturating amounts of EF G also inhibits the reaction completely, suggesting that an empty ribosomal acceptor site is necessary for this reaction. On the other hand, the 50-S subunit proteins L7 and L12 are not required for stringent factor activity. Ribosomes from Pseudomonas fluorescens can replace those from Escherichia coli in the complete system, while ribosomes from Ehrlich ascites cannot. A small but reproducible synthesis of ppGpp is observed when the ribosomal wash from E. coli is complemented with ribosomes from wheat germ cytoplasm.

Magic spot metabolism in an Escherichia coli mutant temperature sensitive in elongation factor Ts

A temperature-sensitive mutant of Escherichia coli HAK88 which has been shown to have a lesion in elongation factor Ts (EFTs) was studied with repsect to its metabolism of guanosine 5'-diphosphate, 2'(3')-diphosphate (ppGpp) and the associated failure of ribosomal ribonucleic acid (rRNA) accumulation at the nonpermissive temperature. Results reported here show that (i) when EFTs is nonfunctional, a full complement of charged transfer RNA (tRNA) cannot prevent accumulation of ppGpp (magic spot) and the stringent failure of rRNA accumulation; (ii) chloramphenicol prevents magic spot (MS) formation and the stringent response not by increasing the percentage of charged tRNA, but possibly by somehow interfering directly with the synthesis of MS; and (iii) tetracycline can lead to MS disappearance without resumption of RNA synthesis. Thus, the absence of MS and the presence of a functional RNA polymerase and charged tRNA are not sufficient to support rRNA accumulation in vivo. An additional element in the regulatory system is suggested.