Aminoacyl-tRNA binding at the recognition site is the first step of the elongation cycle of protein synthesis

The transorientation hypothesis for codon recognition during protein synthesis

During decoding, a codon of messenger RNA is matched with its cognate aminoacyl-transfer RNA and the amino acid carried by the tRNA is added to the growing protein chain. Here we propose a molecular mechanism for the decoding phase of translation: the transorientation hypothesis. The model incorporates a newly identified tRNA binding site and utilizes a flip between two tRNA anticodon loop structures, the 5'-stacked and the 3'-stacked conformations. The anticodon loop acts as a three-dimensional hinge permitting rotation of the tRNA about a relatively fixed codon-anticodon pair. This rotation, driven by a conformational change in elongation factor Tu involving GTP hydrolysis, transorients the incoming tRNA into the A site from the D site of initial binding and decoding, where it can be proofread and accommodated. The proposed mechanisms are compatible with the known structures, conformations and functions of the ribosome and its component parts including tRNAs and EF-Tu, in both the GTP and GDP states.

Transit of tRNA through the Escherichia coli ribosome. Cross-linking of the 3' end of tRNA to specific nucleotides of the 23 S ribosomal RNA at the A, P, and E sites

When bound to Escherichia coli ribosomes and irradiated with near-UV light, various derivatives of yeast tRNA(Phe) containing 2-azidoadenosine at the 3' terminus form cross-links to 23 S rRNA and 50 S subunit proteins in a site-dependent manner. A and P site-bound tRNAs, whose 3' termini reside in the peptidyl transferase center, label primarily nucleotides U2506 and U2585 and protein L27. In contrast, E site-bound tRNA labels nucleotide C2422 and protein L33. The cross-linking patterns confirm the topographical separation of the peptidyl transferase center from the E site domain. The relative amounts of label incorporated into the universally conserved residues U2506 and U2585 depend on the occupancy of the A and P sites by different tRNA ligands and indicates that these nucleotides play a pivotal role in peptide transfer. In particular, the 3'-adenosine of the peptidyl-tRNA analogue, AcPhe-tRNA(Phe), remains in close contact with U2506 regardless of whether its anticodon is located in the A site or P site. Our findings, therefore, modify and extend the hybrid state model of tRNA-ribosome interaction. We show that the 3'-end of the deacylated tRNA that is formed after transpeptidation does not immediately progress to the E site but remains temporarily in the peptidyl transferase center. In addition, we demonstrate that the E site, defined by the labeling of nucleotide C2422 and protein L33, represents an intermediate state of binding that precedes the entry of deacylated tRNA into the F (final) site from which it dissociates into the cytoplasm.

Calculation of the relative geometry of tRNAs in the ribosome from directed hydroxyl-radical probing data

The many interactions of tRNA with the ribosome are fundamental to protein synthesis. During the peptidyl transferase reaction, the acceptor ends of the aminoacyl and peptidyl tRNAs must be in close proximity to allow peptide bond formation, and their respective anticodons must base pair simultaneously with adjacent trinucleotide codons on the mRNA. The two tRNAs in this state can be arranged in two nonequivalent general configurations called the R and S orientations, many versions of which have been proposed for the geometry of tRNAs in the ribosome. Here, we report the combined use of computational analysis and tethered hydroxyl-radical probing to constrain their arrangement. We used Fe(II) tethered to the 5' end of anticodon stem-loop analogs (ASLs) of tRNA and to the 5' end of deacylated tRNA(Phe) to generate hydroxyl radicals that probe proximal positions in the backbone of adjacent tRNAs in the 70S ribosome. We inferred probe-target distances from the resulting RNA strand cleavage intensities and used these to calculate the mutual arrangement of A-site and P-site tRNAs in the ribosome, using three different structure estimation algorithms. The two tRNAs are constrained to the S configuration with an angle of about 45 degrees between the respective planes of the molecules. The terminal phosphates of 3'CCA are separated by 23 A when using the tRNA crystal conformations, and the anticodon arms of the two tRNAs are sufficiently close to interact with adjacent codons in mRNA.

Ribosomal tRNA binding sites: three-site models of translation

The first models of translation described protein synthesis in terms of two operationally defined tRNA binding sites, the P-site for the donor substrate, the peptidyl-tRNA, and the A-site for the acceptor substrates, the aminoacyl-tRNAs. The discovery and analysis of the third tRNA binding site, the E-site specific for deacylated tRNAs, resulted in the allosteric three-site model, the two major features of which are (1) the reciprocal relationship of A-site and E-site occupation, and (2) simultaneous codon-anticodon interactions of both tRNAs present at the elongating ribosome. However, structural studies do not support the three operationally defined sites in a simple fashion as three topographically fixed entities, thus leading to new concepts of tRNA binding and movement: (1) the hybrid-site model describes the tRNAs' movement through the ribosome in terms of changing binding sites on the 30S and 50S subunits in an alternating fashion. The tRNAs thereby pass through hybrid binding states. (2) The alpha-epsilon model introduces the concept of a movable tRNA-binding domain comprising two binding sites, termed alpha and epsilon. The translocation movement is seen as a result of a conformational change of the ribosome rather than as a diffusion process between fixed binding sites. The alpha-epsilon model reconciles most of the experimental data currently available.

Movement of the 3'-end of tRNA through the peptidyl transferase centre and its inhibition by antibiotics

Determining how antibiotics inhibit ribosomal activity requires a detailed understanding of the interactions and relative movement of tRNA, mRNA and the ribosome. Recent models for the formation of hybrid tRNA binding sites during the elongation cycle have provided a basis for re-evaluating earlier experimental data and, especially, those relevant to substrate movements through the peptidyl transferase centre. With the exception of deacylated tRNA, which binds at the E-site, ribosomal interactions of the 3'-ends of the tRNA substrates generate only a small part of the total free energy of tRNA-ribosome binding. Nevertheless, these relatively weak interactions determine the unidirectional movement of tRNAs through the ribosome and, moreover, they appear to be particularly susceptible to perturbation by antibiotics. Here we summarise current ideas relating particularly to the movement of the 3'-ends of tRNA through the ribosome and consider possible inhibitory mechanisms of the peptidyl transferase antibiotics.

Analysis of interactions between the codon-anticodon duplexes within the ribosome: their role in translation

Computer graphics simulation of interactions between the codon-anticodon duplexes formed by normal elongator tRNAs at the ribosomal A, P and E-sites (the AP and PE interduplex interactions) was made. This demonstrated that only the correct duplexes at the A-site are compatible with the AP interduplex interaction. The selection of synonymous codons and anticodon wobble bases, together with the AP interduplex interaction, prevents frameshifting. In the absence of this interaction the efficiency of the selection falls off sharply. This suggests that the AP interduplex interaction should be retained during translocation and in the post-translocation state, i.e. the PE interduplex interaction that is identical with that of AP should exist to avoid frameshifting. In such a model the P-site duplex provides an indirect linkage between the A and E-site duplexes. The indirect linkage prohibits the simultaneous existence of the A and E-site duplexes. The wobble pairs of the P and E-site duplexes can affect the rate of the A-site occupation via the AP interduplex interaction and the AE interduplex indirect linkage. It is demonstrated that frameshifting can occur from the AP or PE codon-anticodon complex destabilization caused, for example, by small mobility of the wobble pairs, misreading of the codon, unmodified adenine and guanine at tRNA positions 34 (wobble) and 37, respectively. The results obtained can be subjected to direct experimental tests.

Initial binding of the elongation factor Tu.GTP.aminoacyl-tRNA complex preceding codon recognition on the ribosome

The first step in the sequence of interactions between the ribosome and the complex of elongation factor Tu (EF-Tu), GTP, and aminoacyl-tRNA, which eventually leads to A site-bound aminoacyl-tRNA, is the codon-independent formation of an initial complex. We have characterized the initial binding and the resulting complex by time-resolved (stopped-flow) and steady-state fluorescence measurements using several fluorescent tRNA derivatives. The complex is labile, with rate constants of 6 x 10(7) M-1 s-1 and 24 s-1 (20 degrees C, 10 mM Mg2+) for binding and dissociation, respectively. Both thermodynamic and activation parameters of initial binding were determined, and five Mg2+ ions were estimated to participate in the interaction. While a cognate ternary complex proceeds form initial binding through codon recognition to rapid GTP hydrolysis, the rate constant of GTP hydrolysis in the non-cognate complex is 4 orders of magnitude lower, despite the rapid formation of the initial complex in both cases. Hence, the ribosome-induced GTP hydrolysis by EF-Tu is strongly affected by the presence of the tRNA. This suggests that codon-anticodon recognition, which takes place after the formation of the initial binding complex, provides a specific signal that triggers fast GTP hydrolysis by EF-Tu on the ribosome.

Transient conformational states of aminoacyl-tRNA during ribosome binding catalyzed by elongation factor Tu

Conformational transitions of Phe-tRNA(Phe) that take place during elongation factor Tu (EF-Tu)-dependent binding to the A site of Escherichia coli ribosomes were followed by transient fluorescence measurements. The fluorescence signal of proflavin replacing dihydrouracil at position 16 or 17 in yeast tRNA(Phe) was utilized to monitor changes of the conformation of the D loop. The ternary complex EF-Tu.GTP.Phe-TRNA(Phe)(Pf16/17) was purified by gel filtration. Upon binding of the complex to the A site of poly(U)-programmed, P-site-blocked ribosomes, the fluorescence changes in several steps. First, the rapid formation of an initial complex gives rise to a small fluorescence increase. Subsequent codon-anticodon recognition leads to a conformational rearrangement of the D loop of the tRNA that is reflected in a major fluorescence increase. Fluorescence-quenching data indicate an unfolding of the D loop in this state. The latter conformational state is short-lived, and the aminoacyl-tRNA refolds during the following rearrangement that occurs after GTP hydrolysis and accompanies the release of the aminoacyl-tRNA from EF-Tu.GDP and/or its accommodation in the A site. Further experiments show that the status of the P site influences the binding to the A site in that the two rearrangement steps are slowed down when the P site is unoccupied and even more so when it is occupied with the near-cognate tRNA(Leu2). In contrast, the occupancy of the E site has no influence on A-site binding, and vice versa, thus excluding any coupling between the two sites.

Evidence for a conformational change in the exit site of the Escherichia coli ribosome upon tRNA binding

The exit (E) site of the Escherichia coli ribosome was investigated using oligodeoxyribonucleotides complementary to single-stranded regions of ribosomal RNA suggested to be involved in tRNA binding in the E site [Moazed, D., & Noller, H. (1989) Cell 57, 585-597]. Radiolabeled DNA oligomers (probes) were hybridized in situ to complementary sites on the ribosomal RNA of ribosomes or ribosomal subunits, and the effects of simultaneous tRNA or antibiotic binding on probe binding were measured using a nitrocellulose filtration binding assay. Site specificity of probe binding was assured using ribonuclease H to cleave the ribosomal RNA at the site of probe binding. When 50S subunits were hybridized with a probe spanning bases 2109-2119 and deacylated tRNA was added incrementally, probe binding decreased, suggesting that the probe and tRNA competed for the same binding site or that tRNA was allosterically affecting the probe binding site. When 70S ribosomes were substituted for 50S subunits, probe binding to this site initially increased and then decreased at higher concentrations of deacylated tRNA. Titrating probe-ribosome complexes with acylated tRNA, N-acetyl-acylated tRNA, tetracycline, or chloramphenicol had no effect on probe binding. The data presented provide evidence for tRNA/rRNA interaction at or near the E site of the E. coli ribosome and suggest that a conformational change occurs in the E site when deacylated tRNA is bound to the P site. The data suggest that deacylated tRNA in the P site serves as a translocational trigger by causing the E site to change conformations, making it more available for tRNA (and probe) binding and therefore promoting translocation.(ABSTRACT TRUNCATED AT 250 WORDS)

How are tRNAs and mRNA arranged in the ribosome? An attempt to correlate the stereochemistry of the tRNA-mRNA interaction with constraints imposed by the ribosomal topography

Two tRNA molecules at the ribosomal A- and P-sites, with a relatively small angle between the planes of the L-shaped molecules, can be arranged in two mutually exclusive orientations. In one (the 'R'-configuration), the T-loop of the A-site tRNA faces the D-loop of the P-site tRNA, whereas in the other (the 'S'-configuration) the D-loop of the A-site tRNA faces the T-loop of the P-site tRNA. A number of stereochemical arguments, based on the crystal structure of 'free' tRNA, favour the R-configuration. In the ribosome, the CCA-ends of the tRNA molecules are 'fixed' at the base of the central protuberance (the peptidyl transferase centre) of the 50S subunit, and the anticodon loops lie in the neck region (the decoding site) of the 30S subunit. The translocation step is essentially a rotational movement of the tRNA from the A- to the P-site, and there is convincing evidence that the A-site must be located nearest to the L7/L12 protuberance of the 50S subunit. The mRNA in the two codon-anticodon duplexes lies on the 'inside' of the 'elbows' of the tRNA molecules (in both the S-type and R-type configurations), and runs up between the two molecules from the A- to the P-site in the 3' to 5'-direction. These considerations have the consequence that in the S-configuration the mRNA in the codon-anticodon duplexes is directed towards the 50S subunit, whereas in the R-configuration it is directed towards the 30S subunit. The results of site-directed cross-linking experiments, in particular cross-links to mRNA at positions within or very close to the codons interacting with A- or P-site tRNA, favour the latter situation. This conclusion is in direct contradiction to other current models for the arrangement of mRNA and tRNA on the ribosome.

Movement of tRNA but not the nascent peptide during peptide bond formation on ribosomes

The results from experiments involving nonradiative energy transfer indicate that a fluorescent probe on the 5'-end of tRNA(Phe) moves more than 20 A towards probes on ribosomal protein L1 as a peptide bond is formed during the peptidyl transferase reaction on Escherichia coli ribosomes. The peptide itself moves no more than a few angstroms during peptide bond formation, as judged by the movement of fluorescent probes attached to the phenylalanine amino group of phenylalanyl-tRNA. Other results demonstrate that an analogue of peptidyl-tRNA, deacylated tRNA, and puromycin can be bound simultaneously to the same ribosome, indicating that there are three physically distinct sites to which tRNA is bound during the reaction steps by which peptides are elongated. The results appear to be consistent with the displacement model of peptide elongation.

A single base change at 726 in 16S rRNA radically alters the pattern of proteins synthesized in vivo

A single base change in 16S rRNA (C-726 to G) was constructed by site-directed mutagenesis and cloned into the multicopy plasmid pKK3535 (generating pKK726G) which contains the complete rrnB operon from Escherichia coli. The mutant 16S rRNA was found predominantly in the 30S subunit fraction but was present in the 70S ribosomes. Protein analyses of the free 30S subunits revealed a decrease in the levels of ribosomal proteins S2 and S21 while the composition of the 70S ribosomes was as the wild-type. Transformants of pKK726G were temperature sensitive for growth, although the mutant ribosomes themselves were translationally active in vivo at 37 and 42 degrees C. Two-dimensional gel electrophoresis of the proteins translated in vivo revealed an altered protein profile which included novel proteins, changes in the levels of normal proteins, and the presence of heat shock proteins (HSPs) at 30 degrees C. Inactivation of the host encoded wild-type ribosomes coincided with a significant decrease in the synthesis of the HSPs. We therefore believe the induction of the HSPs to be a secondary response by the cells to the presence of the abnormal proteins.

Intermediate states in the movement of transfer RNA in the ribosome

Direct chemical 'footprinting' shows that translocation of transfer RNA occurs in two discrete steps. During the first step, which occurs spontaneously after the formation of the peptide bond, the acceptor end of tRNA moves relative to the large ribosomal subunit resulting in 'hybrid states' of binding. During the second step, which is promoted by elongation factor EF-G, the anticodon end of tRNA, along with the messenger RNA, moves relative to the small ribosomal subunit.

Reactivity of the P-site-bound donor in ribosomal peptide-bond formation

The puromycin reaction, catalyzed by the ribosomal peptidyltransferase, has been carried out so as to make the definition of two distinct parameters of this reaction possible. These are (a) the final degree of the reaction which gives the proportion of peptidyl (P)-site binding of the donor and (b) the reactivity of the donor substrate expressed as an apparent rate constant (kobs). This kobs varies with the concentration of puromycin; the maximal value (k3) of the kobs, at saturating concentrations of puromycin, gives the reactivity of the donor independently of the concentrations of both the donor and puromycin. k3 is also a measure of the activity of peptidyltransferase expressed as its catalytic rate constant (kcat). If we assume that the puromycin-reactive donor is bound at the ribosomal P site, we observe the following, depending on the conditions of the experiment: the proportion of P-site binding of the donor substrates AcPhe-tRNA or fMet-tRNA can be the same and close to 100%, while there is a tenfold increase in the reactivity of the donor (k3 = 0.8 min-1 versus 8.3 min-1). On the other hand there are conditions, under which the proportion of P-site binding increases from 30% to 100% while k3 remains low and equal to 0.8 min-1. Using the puromycin reaction it was also found that an increase of Mg2+ from 10 mM to 20 mM reduces the reactivity of the donor and, hence, the activity of peptidyltransferase, provided that this change in Mg2+ occurs during the binding of the donor but not when it occurs during peptide bond formation per se. The fact that the donor substrate may exist in various states of reactivity in this cell-free system raises the possibility that the rate of peptide bond formation may not be uniform during protein synthesis.

Models for two tRNAs bound to successive codons on mRNA on the ribosome

We have investigated the structural changes necessary to build a model complex of two molecules of phenylalanine transfer RNA (tRNA(Phe) bound to successive codons in a short segment of a model messenger RNA (mRNA), consisting of U6. We keep the mRNA in an ideal helical conformation, deforming the tRNAs as necessary to eliminate steric overlaps while bringing the two 3' termini together. The resulting model has the two tRNAs oriented relative to one another in a manner that is very similar to a model developed by McDonald and Rein (1) in which the tRNAs maintain their ideal crystallographic conformations and all of the deformations are introduced into the mRNA. Consequently, regardless of how one divides the deformations between the tRNAs and the mRNA it is clear that, on the ribosome, the tRNA in the P site has its "front" side (that side with the variable loop) close to the "back" side of the tRNA in the A site (that side with the D loop). The space between the two molecules must be left free on the ribosome, in order to facilitate the transition from the A site to the P site. A detailed pathway is also proposed for changing the anticodon loop structure from that of the A site to that of the P site. The anticodon loop is always kept in a 3'-stacked conformation, since we find that the shift between the 3'-stacked and 5'-stacked structures proposed by Woese (2) is not feasible.

Conformational change of the L-shaped tRNA(Phe) molecule

Fluorophore of proflavine was introduced onto the 3'-terminal ribose moiety of yeast tRNA(Phe). The distance between the fluorophore and the fluorescent Y base in the anticodon of yeast tRNA(Phe) was measured by a singlet-singlet energy transfer. Conformational changes of tRNA(Phe) with binding of tRNA(2Glu), which has the anticodon UUC complementary to the anticodon GAA of tRNA(Phe), were investigated. The distance obtained at the ionic strength of 100 mM K+ and 10 mM Mg2+ is very close to the distance from x-ray diffraction, while the distance obtained in the presence of tRNA(2Glu) is significantly smaller. Further, using a fluorescent probe of 4-bromomethyl-7-methoxycoumarin introduced onto pseudouridine residue psi 55 in the T psi C loop of tRNA(Phe), Stern-Volmer quenching experiments for the probe with or without added tRNA(2Glu) were carried out. The results showed greater access of the probe to the quencher with added tRNA(2Glu). These results suggest that both arms of the L-shaped tRNA structure tend to bend inside with binding of tRNA(2Glu) and some structural collapse occurs at the corner of the L-shaped structure.

A mutation in the 530 loop of Escherichia coli 16S ribosomal RNA causes resistance to streptomycin

Oligonucleotide-directed mutagenesis was used to introduce an A to C transversion at position 523 in the 16S ribosomal RNA gene of Escherichia coli rrnB operon cloned in plasmid pKK3535. E. coli cells transformed with the mutated plasmid were resistant to streptomycin. The mutated ribosomes isolated from these cells were not stimulated by streptomycin to misread the message in a poly(U)-directed assay. They were also restrictive to the stimulation of misreading by other error-promoting related aminoglycoside antibiotics such as neomycin, kanamycin or gentamicin, which do not compete for the streptomycin binding site. The 530 loop where the mutation in the 16S rRNA is located has been mapped at the external surface of the 30S subunit, and is therefore distal from the streptomycin binding site at the subunit interface. Our results support the conclusion that the mutation at position 523 in the 16S rRNA does not interfere with the binding of streptomycin, but prevents the drug from inducing conformational changes in the 530 loop which account for its miscoding effect. Since this effect primarily results from a perturbation of the translational proofreading control, our results also provide evidence that the 530 loop of the 16S rRNA is involved in this accuracy control.

Covalent cross-linking of poly(A) to Escherichia coli ribosomes, and localization of the cross-link site within the 16S RNA

Poly(A) can be cross-linked to E. coli 70S ribosomes in the presence of tRNALys by mild ultraviolet irradiation. The cross-linking reaction is exclusively with the 30S subunit, and involves primarily the RNA moiety. Following a partial nuclease digestion, cross-linked complexes containing poly(A) and fragments of the 16S RNA were isolated by affinity chromatography on oligo(dT)-cellulose. The complexes were purified by gel electrophoresis and subjected to oligonucleotide analysis, which revealed a single cross-link site within positions 1394-1399 of the 16S RNA. The same pattern of cross-linking, at about one-fifth of the intensity, was observed in the absence of tRNALys. The cross-link site to poly(A), together with other sites in the 16S RNA that have been implicated in ribosomal function, is discussed in the framework of our recent model for the three-dimensional structure of 16S RNA; all of the functional sites are clustered together in two distinct groups in the model.

Extension of Watson's model for the elongation cycle of protein biosynthesis

The scheme for the elongation cycle of protein biosynthesis is proposed based on modern quantitative data on the interactions of mRNA and different functional forms of tRNA with 70S ribosomes and their 30S and 50S subunits. This scheme takes into account recently discovered third ribosomal (E) site with presumable exit function. The E site is introduced into 70S ribosome by its 50S subunit, the codon-anticodon interaction does not take place at the E site, and the affinity of tRNA for the E site is considerably lower than that for the P site. On the other hand, the P and A sites are located mainly on a 30S subunit, the codon-anticodon interactions being realized on both these sites. An mRNA molecule is placed exclusively on a 30S subunit where it makes U-turn. The proposed scheme does not contradict to any data but includes all main postulates of the initial Watson's model (J. D. Watson, Bull. Soc. Chim. Biol. 46, 1399 (1964), and is considered as a natural extension of the later according to modern experimental data.

Structural characteristics and classification of some tRNA-binding sites of elongating Escherichia coli ribosome

Ultraviolet(254 nm)-irradiation-induced cross-linkages in ribosomal complexes allowed identification of proteins in contact with tRNA at different elongation steps. Both the set and the ratio of cross-linked proteins, i.e. the structural characteristics of the tRNA-binding sites of the ribosome, were shown to depend strongly not only on the position of the mRNA codon with which tRNA interacts as a component of a ribosomal complex, but also on its functional state, i.e. on the elongation step. A new classification of tRNA-binding sites of ribosome is suggested.

Conformational dynamics of the anticodon loop in yeast tRNAPhe as sensed by the fluorescence of wybutine

Conformational and dynamic properties of the anticodon loop of yeast tRNAPhe were investigated by analyzing the time resolved fluorescence of wybutine serving as a local structural probe adjacent to the anticodon GmAA on its 3' side. The influence of Mg2+, important for stabilizing the tertiary structure of tRNA, and of the complementary anticodon s2UUC of E. coli tRNA2Glu were investigated. Fluorescence lifetimes and anisotropies were measured with ps time resolution using time correlated single photon counting and a mode locked synchronously pumped and frequency doubled dye laser as excitation source. From the analysis of lifetimes (tau) and rotational relaxation times (tau R) we conclude that wybutine occurs in various structural states: one stacked conformation where the base has no free mobility and the only rotational motion reflects the mobility of the whole tRNA molecule (tau = 6 ns, tau R = 19 ns), an unstacked conformation where the base can freely rotate (tau = 100 ps, tau R = 370 ps) and an intermediary state (tau = 2 ns, tau R = 1.6 ns). Under biological conditions, i.e. in the presence of Mg2+ and neutral salts, wybutine is found in a stacked and immobile state which is consistent with the crystallographic picture. In the presence of the complementary codon however, as exemplified by the E. coli-tRNA2Glu anticodon, our analysis indicates that the codon-anticodon complex exists in an equilibrium of structural states with different rotational mobility of wybutine. The conformation with wybutine freely mobile is the predominant one and suggests that this conformation of the codon-anticodon structure differs from the canonical 3'-5' stack.

The nucleotide sequence of a cytoplasmic tRNAPhe from Scenedesmus obliquus and comparison with a tRNATyr species

The nucleotide sequence of a cytoplasmic tRNAPhe from the eukaryotic green alga Scenedesmus obliquus was determined as: pG-G-C-U-U-G-A-U-A-m2G-C-U-C-A-G-C-D-Gm-G-G-A-G-A-G-C-m22G-p si-psi-A-G-A-Cm-U-G - A-A-m1G-A-psi-C-U-A-C-A-G-m7G-N-m5C-C-C-C-A-G-T-psi-C-G-m1A-U-m5C-Cm-U-G -G-G-U- C A-G-G-C-C-A-C-C-A-OH. The structure has some notable features. Unlike other tRNAPhe species from plant sources, it has an unmodified G as the first residue of the anticodon and m1G rather than a Y derivative as the residue following the anticodon. The sequence m5C(60)-Cm(61) is unique to this tRNA. The sequence of S. obliquus tRNAPhe shows close homology with S. obliquus tRNATyr.

40 S subunits from rat liver ribosomes contain two codon-dependent sites for transfer RNA

40 S subunits from rat liver ribosomes are able to bind, after heat activation, two molecules of either Phe-tRNAPhe, Ac-Phe-tRNAPhe or deacylated tRNAPhe. Addition of 60 S subunits to the quaternary complex 40 S.poly(U).(Phe-tRNAPhe)2 results in quantitative formation of (Phe)2-tRNAPhe. This indicates that the two binding sites for tRNA on 40 S subunits should be considered as the constituent of P and A sites of 80 S ribosomes.

Identification of the site of cross-linking in 16S rRNA of an aromatic azide photoaffinity probe attached to the 5'-anticodon base of A site bound tRNA

The site of Escherichia coli 16S ribosomal RNA cross-linked to the 5'-anticodon base of A site bound E. coli valyl-tRNA was identified. Cross-linking was via the affinity probe 6-[(2-nitro-4-azidophenyl)amino]caproate (NAK) or 3-[[2-[(2-nitro-4-azidophenyl)amino]ethyl]dithio]propionate (SNAP) attached to the carboxyl group of the 5'-anticodon base 5-(carboxyethoxy)uridine via an ethylenediamine spacer [Gornicki, P., Ciesiolka, J., & Ofengand, J. (1985) Biochemistry (preceding paper in this issue)]. With both probes, RNase T1 digestion of the isolated 16S RNA-tRNA covalent complex, 5'-32P postlabeling, and gel electrophoresis yielded two oligonucleotides larger than any fragments from non-cross-linked tRNA or rRNA. Appearance of the oligomers was dependent on the presence of the probe on the tRNA. Unmodified tRNA in the A and/or P sites did not yield any product. The presence of elongation factor Tu in the incubation mixture was also required. Dithiothreitol (DDT) treatment of the SNAP-induced covalent complex prior to electrophoresis also abolished the oligomers. Only the larger of the two oligomers (present in a 3:1 ratio) was sequenced. The SNAP dimer was cleaved with DTT, and the rRNA and tRNA oligomers were separated and sequenced as monomers. The NAK dimer was sequenced without cleavage by taking advantage of the differences in electrophoretic mobility among sequence and/or composition isomers of the same length. In both cases, the rRNA oligomer was identified as UACACACCG1401, and the nucleotide cross-linked was shown to be the C1400 residue. The expected tRNA modification site was also identified.(ABSTRACT TRUNCATED AT 250 WORDS)

Intersubunit RNA-protein contacts in pre- and post-translocated E. coli ribosome

Ribosomal proteins participating in intersubunit RNA-protein contacts (directly interacting with RNA of the opposite subunit) were determined by means of ultraviolet-induced cross-links in pre- and post-translocated ribosomal complexes, as well as in the free 70 S ribosome (tight couple) of E. coli. In these 3 complexes at least L1 and L9 proteins interact with 16 S RNA, while S6, S9/11 and S15 react with 23 S RNA. All these proteins ('hinge-joint' proteins) are clustered on the small protuberance of the 50 S subunit and on the platform of the 30 S subunit. Reduction in the number of other (variable) intersubunit RNA-protein contacts in the course of transition from the tight couple to the pre- and, finally, to the post-translocated state, demonstrates gradual loosening of intersubunit interactions in 70 S ribosome. Such a loosening ('opening') of the 70 S ribosome is determined by conformational changes in ribosomal subunits and/or in their relative arrangement, conjugated with alteration of the functional state of the ribosomal complex.

Specific replacement of functional groups of uridine-33 in yeast phenylalanine transfer ribonucleic acid

Functional groups of the highly conserved uridine at position 33 in the anticodon loop of yeast tRNAPhe were altered by a synthetic protocol that replaces U-33 with any desired nucleotide and leaves all other nucleotides of the tRNA intact. The U-33-substituted tRNAs were prepared in an eight-step protocol that begins with partial cleavage of tRNAPhe at U-33 by ribonuclease A. By use of the combined half-molecules as substrate, U-33 was removed from the 5' half-molecule in three steps and then replaced by using RNA ligase to add the desired nucleoside 3',5'-bisphosphate. Each position 33 substituted 5' half-molecule was isolated and annealed to the original 3' half-molecule from the ribonuclease A digestion. The two halves were then rejoined in three steps to give a full-size tRNAPhe variant. This protocol should be applicable to other RNA molecules where a nucleotide substitution is desired at the 5' side of an available unique cleavage site. Seven substituted tRNAPheS containing uridine, pseudouridine, 3-methyluridine, 2'-O-methyluridine, cytidine, deoxycytidine, and purine riboside at position 33 were assayed for aminoacylation with yeast phenylalanyl-tRNA synthetase. Each of the seven tRNAs aminoacylated normally. Thus, unlike the adjacent guanine residue at position 34, U-33 is not involved in the interaction between yeast tRNAPhe and yeast phenylalanyl-tRNA synthetase.

The effect of GTP hydrolysis and transpeptidation on the arrangement of aminoacyl-tRNA at the A-site of Escherichia coli 70 S ribosomes

From the affinity labelling of 70 S ribosomes with a photoreactive derivative of Phe-tRNAPhe bearing an arylazido group on guanine residues, it has been found that different sets of ribosomal proteins are labelled in the course of three successive steps of EF-Tu-dependent binding of aminoacyl-tRNA derivative at the A-site. Proteins S5, S7, S8, S16, S17, L9, L14, L15 and L24 were labelled before GTP hydrolysis; proteins S5, S7, S9, S11, S14, S18, S19, S21, L9, L21 and L29--after GTP hydrolysis; proteins S2, S5, S7, S21, L11 and L23--after GTP hydrolysis and transpeptidation.

[Modification of blood coagulation and fibrinolysis through physical activity]

Physical conditioning appears to protect against the development of vascular disease. Although physical training often evokes favorable alterations in established cardiovascular risk factors, such as plasma lipids and lipoproteins, the metabolic sequelae of regular exercise that mediate a reduction in the risk of cardiovascular disease remain incompletely understood. Studies in recent years have shown physical training to have beneficial effects on blood coagulation and fibrinolytic activity. On general the data support the concept that blood clotting is potentiated by exercise. Mechanisms involved are an increased release of thromboplastine of tissue, increased coagulation with lactate accumulation during exercise, increased concentrations of plasma proteins owing to hemoconcentration, increased concentrations of specific clotting factors, e.g., Factor VIII and fibrinogen, and an alteration in platelet count and platelet function. The acceleration in coagulation is less in the well-exercised individual. There is evidence that an epinephrine mediated mechanism is responsible for the difference between individuals who have a lot of exercise and those who do not. Fibrinolytic activity seems to increase with exercise in a linear relationship with the heart rate during physical activity. An enhancement of the plasma fibrinolytic activity, stimulated experimentally by thrombotic stress such as venous occlusion, could be an important mechanism in the beneficial effect of habitual physical exercise on the risk of cardiovascular disease.

Involvement of the 3' side of the anticodon loop of yeast tRNATyr in messenger-free binding to ribosomes. An electron-spin resonance study

Electron-spin resonance (ESR) spectra of a nitroxide spin-label attached to residue i6A-37 of yeast tRNATyr were measured in complexes of deacylated tRNATyr with Escherichia coli ribosomes. A Scatchard plot, obtained in the absence of mRNA, indicated strong binding with an association constant of 1 X 10(7) l X mol-1, suggesting the P-site binding. The ESR spectrum of free tRNATyr, characteristic for a rapidly tumbling nitroxide, changes to a spectrum with extensively broadened lines in the ribosome-tRNA complex. The original spectrum can be restored upon long incubations of the complex with an excess of extraneous tRNA. ESR spectra suggest that the spin-label motion is drastically perturbed though not completely blocked in the ribosome-tRNATyr complex. Since ESR spectra of a spin-label attached to the opposite, i.e. 5', side of the anticodon loop are only slightly perturbed by the messenger-free binding to ribosomes [Rodriguez et al. (1980) J. Biol. Chem. 255, 8116-8120], it is concluded that the two sides of the anticodon loop face entirely different environments when bound to the P site, the 3' side being oriented towards the surface of the ribosome, and the other side towards its environment or a large cavity.

Testing the classical two-tRNA-site model for the ribosomal elongation cycle

An experimental system where the elongation of a polypeptide (polyphenylalanine) is performed stepwise and synchronously by purified Escherichia coli ribosome in a matrix-coupled poly (U) column is proposed for testing the number of non-overlapping tRNA binding sites on the elongating ribosome. If phenylalanyl[3H]tRNA is introduced into the column and bound with the ribosomes at the beginning of a given elongation cycle, deacylated [3H]tRNA is shown to be released from the ribosomes and comes out from the column at the translocation step of the next elongation cycle. The result obtained is fully predicted by the classical two-tRNA-site model and contradicts any model involving more than two non-overlapping high-affinity tRNA binding sites in the ribosomal elongation cycle.

Uridine-33 in yeast tRNA not essential for amber suppression

The nucleotide at position 33 on the 5' side of the anticodon of almost all tRNAs is a uridine. Crystallographic studies of different tRNAs reveal that although the precise orientation of uridine-33 is not always the same, it connects the anticodon stacked along the 3' side of the loop with the pyrimidine-32 stacked on the 5' side of the loop. The remarkably conserved nature of uridine-33 and its unique position in the anticodon loop structure has led to suggestions that this nucleotide has an essential role in the translational mechanism. We have developed a biochemical procedure to replace nucleotides 33-35 in yeast tRNATyr with any desired sequence and used it to construct amber suppressor tRNAs having different nucleotides at position 33. As all of these synthetic amber suppressor tRNAs functioned well in eukaryotic in vitro suppression assays, we conclude that uridine-33 does not have an obligatory role in the translation mechanism.

Topological arrangement of two transfer RNAs on the ribosome. Fluorescence energy transfer measurements between A and P site-bound tRNAphe

The relative arrangement of two tRNAPhe molecules bound to the A and P sites of poly(U)-programmed Escherichia coli ribosomes was determined from the spatial separation of various parts of the two molecules. Intermolecular distances were calculated from the fluorescence energy transfer between fluorophores in the anticodon and D loops of yeast tRNAPhe. The energy donors were the natural fluorescent base wybutine in the anticodon loop or proflavine in both anticodon (position 37) and D loops (positions 16 and 17). The corresponding energy acceptors were proflavine or ethidium, respectively, at the same positions. Four distances were measured: anticodon loop-anticodon loop, 24(+/- 4) A; anticodon loop (A site)-D loop (P site), 46(+/- 12) A: anticodon loop (P site)-D loop (A site), 38(+/- 10) A: D loop-D loop, 35(+/- 9) A. Assuming that both tRNAs adopt the conformation present in the crystal and that the CCA ends are close to each other, the results are consistent with the two anticodons being bound to contiguous codons and suggest an asymmetric arrangement in which the planes of the two L-shaped molecules enclose an angle of 60 degrees +/- 30 degrees.

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.

Formation and properties of a covalent complex between elongation factor Tu and Phe-tRNA bearing a photoaffinity probe on its 3-(3-amino-3-carboxypropyl)uridine residue

Escherichia coli Phe-tRNA, modified with the photoaffinity reagent 6-(2-nitro-4-azidophenylamino)caproate on the 3-(3-amino-3-carboxypropyl)uridine residue, was crosslinked to E. coli EFTu Section upon irradiation at 0 degree C with visible light at wavelengths greater than 400 nm. Crosslinking was dependent on irradiation, the photoaffinity probe, and was blocked by pre-photolysis. 1 mM-dithiothreitol completely quenched crosslinking. Binding of the tRNA to EFTu was a prerequisite for crosslinking, because neither EFTu . GDP nor AcPhe-tRNA could substitute; EFTu . GDPCP, however, was almost as active as EFTu . GTP. Crosslinking was complete in less than five minutes and was stable to at least 20 minutes of irradiation with a single 650 W tungsten lamp 4 cm away. The crosslinking yield ranged from 15% to 25%. The crosslinked complex possessed several remarkable properties. At 0.5 mM-Mg2+, the complex protected the AA-tRNA link to chemical hydrolysis, stabilized the bound GTP to dissociation or exchange, and was not adsorbed to cellulose nitrate filters. The purified crosslinked complex could be bound to ribosomes with concomitant hydrolysis of GTP. Extensive peptide bond formation with AcPhe-tRNA in the P site occurred despite the presence of the crosslinked EFTu. We conclude that hydrolysis of GTP is sufficient to release the 3' end of the Phe-tRNA from complexation with EFTu. Translocation of the A site bound complex did not occur. The crosslink site on EFTu is probably near the periphery of the molecule, because shortening the probe from 20 A to 14 A completely blocked crosslinking. A similar but shorter 8 A probe, p-azidophenacyl-4-thiouridine located on the opposite face of the tRNA, did not crosslink.

Structural variability of tRNA: small-angle x-ray scattering of the yeast tRNAphe-Escherichia coli tRNAGlu2 complex

The structure of the complex formed in solution between yeast tRNAPhe and Escherichia coli tRNAGlu2 has been studied by small-angle x-ray scattering. The complex has a radius of gyration of 4.0 nm and an electron-pair distance distribution that is incompatible with a model composed to two tRNAs joined at their complementary anticodons and exhibiting the L shape seen in the crystal. Instead a model in which the two tRNAs, still bound via the anticodons, assume a conformation with the acceptor arms folded toward the anticodon arms agrees with the observed scattering curves.

Binding of tRNA in different functional states to Escherichia coli ribosomes as measured by velocity sedimentation

The binding of initiator and elongator tRNAs to 70-S ribosomes and the 30-S subunits was followed by velocity sedimentation in the analytical ultracentrifuge. fMet-tRNAfMet binds to A-U-G-programmed 30-S subunits, but not to free or misprogrammed particles. Both the formylmethione residue and the initiation factors increase the stability of the 30-S x A-U-G x fMet-tRNAfMet complex. fMet-tRNAfMet is bound only to the P site of the 70-S ribosome even in the absence of A-U-G. Two copies of tRNAPhe or Phe-tRNAPhe are bound to the ribosome with similar affinity. In contrast to a recent report [Rheinberger et al. (1981) Proc. Natl Acad. Sci. USA, 78, 5310-5314], it is shown that three copies of tRNA cannot be bound simultaneously to the ribosome with binding constants higher than 2 x 10(4) M-1. Phe-tRNAPhe when present as the ternary complex Phe-tRNAPhe. EF-Tu x guanosine 5'-[beta,gamma-methylene]triphosphate binds exclusively to the A site. The peptidyl-tRNA analogue, acetylphenylalanine-tRNA, can occupy both ribosomal centers, albeit with a more than tenfold higher affinity for the P site. The thermodynamic data obtained under equilibrium conditions confirm the present view of two tRNA binding sites on the ribosome. The association constants determined are discussed in relation to the mechanism of ribosomal protein synthesis.

Ribosomal protein S4 is an internal protein: Localization by immunoelectron microscopy on protein-deficient subribosomal particles

The location of protein S4 in the small ribosomal subunit has been identified by immunoelectron microscopy. Although intact small subunits are not reactive with antibodies directed against protein S4, subribosomal particles reconstituted without proteins S5 and S12 are reactive. By using these "incomplete" subparticles, we have mapped the position of S4. It is located at a single site on the exterior (cytoplasmic) side of the subunit, at the partition that separates the one-third, or head, from two-thirds, or base, of the subunit. In this location, protein S4 is "beneath" proteins S5 and S12. All three proteins are members of a complex on, or near, the external surface of the small ribosomal subunit that plays an important role in regulation of translational fidelity.

High resolution phosphorus NMR spectroscopy of transfer ribonucleic acids

The temperature dependence of the 31P NMR spectra of yeast phenylalanine tRNA, E. coli tyrosine, glutamate (2), and formylmethione tRNA, and bovine liver aspartate (2b) tRNA is presented. The major difference between the 31P NMR spectra of the different acceptor tRNAs is in the main cluster region between -0.5 and -0.3 ppm. This confirms earlier assignment of the main cluster region to the undistorted phosphate diesters in the hair-pin loops and helical stems. In addition the 31P NMR spectra for all tRNAs reveal approximately 16 non-helical diester signals spread over approximately 7 ppm besides the downfield terminal 3'-phosphate monoester. In the presence of 10 mM Mg++, most scattered and main cluster signals do not shift between 22 and 66 degrees C, thus supporting our earlier hypothesis that 31P chemical shifts are sensitive to phosphate ester torsional and bond angles. At greater than 70 degrees, all of the signals merge into a single random coil conformation signal. Measured spin-lattice and spin-spin relaxation times for tRNAPhe reveal another lower temperature transition associated with a conformational change of the anticodon loop besides the thermal denaturation process. A number of the scattered peaks are shifted (0.2--1.7 ppm) and broadened between 22 and 66 degrees C in the presence of Mg++ as a result of this conformational transition. The effects Mg++ and Mn++ ions on the 31P NMR spectra of tRNAPhe have been used to identify some of the scattered signals upfield and downfield from the main cluster signals. The 31P NMR spectrum of the dimer formed between yeast tRNAPhe and E. coli tRNA2Glu is reported. This dimer stimulates codon-anticodon interaction since the anticodon triplets of the two tRNAs are complementary. Evidence is presented that the anticodon-anticodon interaction alters the anticodon conformation and partially disrupts the tertiary structure of the tRNA.

Role of the constant uridine in binding of yeast tRNAPhe anticodon arm to 30S ribosomes

Twenty-two anticodon arm analogues were prepared by joining different tetra, penta, and hexaribonucleotides to a nine nucleotide fragment of yeast tRNAPhe with T4 RNA ligase. The oligomer with the same sequence as the anticodon arm of tRNAPhe bind poly U programmed 30S ribosomes with affinity similar to intact tRNAPhe. Analogues with an additional nucleotide in the loop bind ribosomes with a weaker affinity whereas analogues with one less nucleotide in the loop do not bind ribosomes at all. Reasonably tight binding of anticodon arms with different nucleotides on the 5' side of the anticodon suggest that positions 32 and 33 in the tRNAPhe sequence are not essential for ribosome binding. However, differences in the binding constants for anticodon arms containing modified uridine residues in the "constant uridine" position suggest that both of the internal "U turn" hydrogen bonds predicted by the X-ray crystal structure are necessary for maximal ribosome binding.