Crosslinking of N-acetyl-phenylalanyl [s4U]tRNAPhe to protein S10 in the ribosomal P site

Deficiency of mitoribosomal S10 protein affects translation and splicing in Arabidopsis mitochondria

The ribosome is not only a protein-making machine, but also a regulatory element in protein synthesis. This view is supported by our earlier data showing that Arabidopsis mitoribosomes altered due to the silencing of the nuclear RPS10 gene encoding mitochondrial ribosomal protein S10 differentially translate mitochondrial transcripts compared with the wild-type. Here, we used ribosome profiling to determine the contribution of transcriptional and translational control in the regulation of protein synthesis in rps10 mitochondria compared with the wild-type ones. Oxidative phosphorylation system proteins are preferentially synthesized in wild-type mitochondria but this feature is lost in the mutant. The rps10 mitoribosomes show slightly reduced translation efficiency of most respiration-related proteins and at the same time markedly more efficiently synthesize ribosomal proteins and MatR and TatC proteins. The mitoribosomes deficient in S10 protein protect shorter transcript fragments which exhibit a weaker 3-nt periodicity compared with the wild-type. The decrease in the triplet periodicity is particularly drastic for genes containing introns. Notably, splicing is considerably less effective in the mutant, indicating an unexpected link between the deficiency of S10 and mitochondrial splicing. Thus, a shortage of the mitoribosomal S10 protein has wide-ranging consequences on mitochondrial gene expression.

Suppressor mutations in ribosomal proteins and FliY restore Bacillus subtilis swarming motility in the absence of EF-P

Translation elongation factor P (EF-P) alleviates ribosome pausing at a subset of motifs encoding consecutive proline residues, and is required for growth in many organisms. Here we show that Bacillus subtilis EF-P also alleviates ribosome pausing at sequences encoding tandem prolines and ribosomes paused within several essential genes without a corresponding growth defect in an efp mutant. The B. subtilis efp mutant is instead impaired for flagellar biosynthesis which results in the abrogation of a form of motility called swarming. We isolate swarming suppressors of efp and identify mutations in 8 genes that suppressed the efp mutant swarming defect, many of which encode conserved ribosomal proteins or ribosome-associated factors. One mutation abolished a translational pause site within the flagellar C-ring component FliY to increase flagellar number and restore swarming motility in the absence of EF-P. Our data support a model wherein EF-P-alleviation of ribosome pausing may be particularly important for macromolecular assemblies like the flagellum that require precise protein stoichiometries.

Recombinant photoreactive tRNA molecules as probes for cross-linking studies

Photoreactive tRNA derivatives have been used extensively for investigating the interaction of tRNA molecules with their ligands and substrates. Recombinant RNA technology facilitates the construction of such tRNA probes through site-specific incorporation of photoreactive nucleosides. The general strategy involves preparation of suitable tRNA fragments and their ligation either to a photoreactive nucleotide or to each other. tRNA fragments can be prepared by site-specific cleavage of native tRNAs, or synthesized by enzymatic and chemical means. A number of photoreactive nucleosides suitable for incorporation into tRNA are presently available. Joining of tRNA fragments is accomplished either by RNA ligase or by DNA ligase in the presence of a DNA splint. The application of this methodology to the study of tRNA binding sites on the ribosome is discussed, and a model of the tRNA-ribosome complex is presented.

A consonant model of the tRNA-ribosome complex during the elongation cycle of translation

Chemical and photochemical affinity techniques have been used extensively to determine the positions of the tRNA binding sites on the Escherichia coli ribosome. Recent advances in our understanding of ribosome structure and function prompted us to critically review the data that have accumulated on tRNA-ribosome cross-links. As a result, we propose a new model of the tRNA-ribosome complex that accounts for nearly all of the pertinent evidence.

An electrophoretic method for the purification of RNA regions involved in protein crosslinking

Direct information about structural interactions in ribonucleoprotein complexes can be obtained from crosslinking data. The purification of specific complexes, i.e., their separation from noncrosslinked proteins, from free RNA, and from other complexes, is essential for the identification of the bound proteins and the precise localization of their attachment sites in RNA. We describe a two-dimensional denaturing gel system which achieves this purification; in the first dimension basic proteins do not enter the gel and RNA--protein complexes are slowed down compared to protein free RNA, and in the second dimension sodium dodecyl sulfate improves the separation between the different complexes on the basis of their protein content.

Structural arrangement of tRNA binding sites on Escherichia coli ribosomes, as revealed from data on affinity labelling with photoactivatable tRNA derivatives

A systematic study of protein environment of tRNA in ribosomes in model complexes representing different translation steps was carried out using the affinity labelling of the ribosomes with tRNA derivatives bearing aryl azide groups scattered statistically over tRNA guanine residues. Analysis of the proteins crosslinked to tRNA derivatives showed that the location of the derivatives in the aminoacyl (A) site led to the labelling of the proteins S5 and S7 in all complexes studied, whereas the labelling of the proteins S2, S8, S9, S11, S14, S16, S17, S18, S19, S21 as well as L9, L11, L14, L15, L21, L23, L24, L29 depended on the state of tRNA in A site. Similarly, the location of tRNA derivatives in the peptidyl (P) site resulted in the labelling of the proteins L27, S11, S13 and S19 in all states, whereas the labelling of the proteins S5, S7, S9, S12, S14, S20, S21 as well as L2, L13, L14, L17, L24, L27, L31, L32, L33 depended on the type of complex. The derivatives of tRNA(fMet) were found to crosslink to S1, S3, S5, S7, S9, S14 and L1, L2, L7/L12, L27. Based on the data obtained, a general principle of the dynamic functioning of ribosomes has been proposed: (i) the formation of each type of ribosomal complex is accompanied by changes in mutual arrangement of proteins - 'conformational adjustment' of the ribosome - and (ii) a ribosome can dynamically change its internal structure at each step of initiation and elongation; on the 70 S ribosome there are no rigidly fixed structures forming tRNA-binding sites (primarily A and P sites).

Effect of spermine on the efficiency and fidelity of the codon-specific binding of tRNA to the ribosomes

Binding of the yeast Tyr-tRNA and Phe-tRNA to the A site, and the binding of their acetyl derivatives to the P site of poly(U11,A)-programmed Escherichia coli ribosomes was studied. Spermine stimulated the rate of binding of both tRNAs at least threefold, enabling more than 90% final saturation of both ribosomal binding sites. The effect is observed when the tRNAs, but not ribosomes or poly(U11,A), are preincubated with polyamine. Regardless of the binding site, optimal saturation was reached at spermine/tRNA molar ratios of 3 for tRNA(Phe) and 5 for tRNA(Tyr). The same low spermine/tRNA ratios were previously reported to stabilize the conformation of these tRNAs in solution. On the other hand, the messenger-free, EF-Tu- and EF-G-dependent polymerization of lysine from E. coli Lys-tRNA is drastically reduced, while the poly(A)-directed polymerization is stimulated by spermine through a wide range of Mg2+ concentrations. Misreading of UUU codons as isoleucine, assayed by the A-site binding of E. coli Ile-tRNA, is also inhibited by spermine. All these results demonstrate that spermine increases the efficiency and accuracy of a series of macromolecular interactions leading to the correct incorporation of an amino acid into protein, at the same time preventing some unspecific or erroneous interactions. From the analogy with its known structural effects, it can be inferred that spermine does so by conferring on the tRNA a specific biologically functional conformation.

Substitution of uridine in vivo by the intrinsic photoactivable probe 4-thiouridine in Escherichia coli RNA. Its use for E. coli ribosome structural analysis

In vivo incorporation of the uridine-photoactivable analogue, 4-thiouridine, into the ribosomal RNA of an Escherichia coli pyrD strain has been demonstrated. It is highly dependent on the exogenous uridine and 4-thiouridine concentrations as well as on temperature. We have defined conditions allowing the substitution of 13 +/- 2% of the uridine residues in bulk RNA by 4-thiouridine. On a high-Mg2+ sucrose gradient, 33 +/- 3% of ribonucleic particles sediment as 70S ribosomes, the remaining being in the form of non-associated 50S and 30S particles containing immature rRNA. The thiolated 70S ribosomes tolerate a 4-5% substitution level (40 thiouridine molecules/particle). Surprisingly, 3-4% of ribosomal proteins, about two protein molecules/particle, were spontaneously covalently bound to 4-thiouridine-substituted rRNA. Specific 366-nm photoactivation increased this proportion to 10-12%, i.e. up to six or seven ribosomal protein molecules/particle. The photochemical cross-linking proceeds with apparent first-order kinetics with a quantum yield close to 5 X 10(-3). Although extensive photodynamic breakage of rRNA occurs under aerobic conditions, both the kinetics and yield of ribosomal protein cross-linking were independent of oxygenation conditions. The thiolated (4.5%) 70S ribosomes allowed the poly(U)-directed poly(Phe)synthesis at 48% the control rate. Photoactivation decreased this activity to 28% and 10% when performed under nitrogen and in aerated conditions, respectively.

Three-dimensional arrangement of the Escherichia coli 16 S ribosomal RNA

A model for the arrangement of the Escherichia coli 16 S ribosomal RNA in the 30 S ribosomal subunit is given. This model is based on the 16 S ribosomal RNA secondary structure, intramolecular RNA crosslinking results, protein-RNA interactions, and the locations of proteins within the 30 S subunit. These considerations allow placement of most of the RNA helices in approximate positions. The overall shape (that of an asymmetric Y) is very reminiscent of the description of the shape of the RNA made by direct determinations and is reasonably correlated to the appearance of the 30 S subunit. The identities of the three major secondary-structure domains of the 16 S ribosomal RNA are, for the most part, preserved. In addition, many close contacts between the 5' and middle RNA domains occur in the body of the particle. The 3'-terminal domain is situated in the central part of the model. This position corresponds to the region between the head and the platform structure in the 30 S subunit. The regions that represent the general locations of the messenger RNA and transfer RNA binding sites can be identified in the model.

Chemical synthesis of 5-azacytidine nucleotides and preparation of tRNAs containing 5-azacytidine in its 3'-terminus

5-azacytidine-5'-triphosphate prepared from 5-azacytidine by chemical phosphorylation is a substrate for AMP (CMP) tRNA nucleotidyl transferase from yeast. tRNAsPhe from yeast containing 5-azacytidine in their 3'-termini were prepared enzymatically. tRNAPhe-Cpn5CpA and tRNAPhe-n5Cpn5CpA can be aminoacylated by phenylalanyl-tRNA synthetase from yeast and they are active in the poly(U)-dependent synthesis of poly(Phe) on E. coli ribosomes. The decomposition of 5-azacytidine via hydrolysis of the triazine ring is significantly accelerated by a phosphate group on the 5'-position of the nucleotide. After the incorporation of 5-azacytidine-5'-phosphate into a polynucleotide chain the rate of hydrolysis of the triazine ring decreases considerably.

Chemical conversion of cytidine residues into 4-thiouridines in yeast tRNAPhe. Determination of the modified cytidines

Treatment of yeast phenylalanine tRNA with pressurized hydrogen sulfide results in conversion of cytidine residues into 4-thiouridine residues. Under conditions leading to an average modification of one cytidine per tRNA molecule 9 positions are thiolated. The 4-thiouridine residues are distributed along the tRNA molecule. Four of the reactive cytidines are located in single-stranded regions: Cm32 , C60 , C74 and C75 . The five others are located in base pairs: C2, C27, C56 , C61 and C63 . Importance of replacement of an amino group by a thiol group on hydrogen bonding and on biological activity of the modified tRNA is discussed.

Location of tRNA on the ribosome

Electron microscopy results of Lake [J. Mol. Biol. (1976) 105, 131-159] and Vasiliev et al. [FEBS Lett. (1983) 155, 167-172] suggest that the 70 S ribosome has an open pocket or a cavity at the base of the L7/L12 stalk of the 50 S subunit, on the side of the 30 S subunit opposite to its bulge or platform. It is this pocket that is proposed here to be the site for binding and retention of two L-shaped tRNA molecules on the ribosome. The model proposed is consistent with the facts about interactions of the protein L7/L12 with the elongation factors (EF-Tu and EF-G) involved in tRNA binding and translocation, as well as with the data available on the participation of proteins S3, S5, S10, S14 and S19 in the formation of tRNA sites.