Aminoacyl-tRNA synthetases optimize both cognate tRNA recognition and discrimination against noncognate tRNAs

Specific protein--nucleic acid interactions are usually the product of sequence-dependent hydrogen bonding. However, in the crystal structure of Escherichia coli glutaminyl-tRNA synthetase (GlnRS) in complex with tRNAGln, leucine 136 (Leu136) stabilizes the disruption of the weak first (U1-A72) base pair in tRNAGln by stacking between A72 and G2. We have demonstrated, by a combined in vivo and in vitro mutational analysis, that Leu136 is important for tRNA specificity despite making no hydrogen bonds with tRNAGln. Both more (L136F) and less (L136V, L136M, L136A, and L136T) mischarging mutants of GlnRS have been identified. GlnRS(L136F) is more mischarging and less specific than wild-type GlnRS in vivo, due not to an increased affinity for the noncognate tRNAs but to a decreased affinity for tRNAGln. Also, unlike other mischarging mutants of GlnRS that have been characterized, it does not exhibit generally relaxed tRNA specificity in vivo and mischarges only a subset of the tRNAs tested. A possible sequence preference for a Py1-Pu72/Pu2-Py71 combination is suggested. The L136A/M/T/V mutants are the first GlnRS variants, including wild-type, expressed on pBR322 which no longer mischarge tyrT(UAG) in vivo. We have shown that, while the L136A mutant is less mischarging than wild-type both in vivo and in vitro, it is not more specific as it also exhibits reduced affinity for its cognate glutamine tRNA. On the basis of these results, we suggest that the aminoacyl-tRNA synthetases have evolved to balance cognate tRNA recognition and discrimination against noncognate tRNAs.     

Codon recognition by artificial tRNA molecules with modified nucleosides in the anticodon

Proteins with unnatural amino acids at specific positions can be produced through cell-free protein synthesis. The synthesis of such molecules can, in principle, be facilitated by improving the codon reading efficiency of the tRNA that inserts the unnatural amino acid. In the present study, we prepared tRNA molecules with 2'-O-methyl nucleosides at the second and third positions of the anticodon and measured their codon-reading efficiencies. The results indicated, contrary to our expectation, that the modification damaged the decoding function completely.     

A tRNA identity switch mediated by the binding interaction between a tRNA anticodon and the accessory domain of a class II aminoacyl-tRNA synthetase

Identity elements in tRNAs and the intracellular balance of tRNAs allow accurate selection of tRNAs by aminoacyl-tRNA synthetases. The histidyl-tRNA from Escherichia coli is distinguished by a unique G-1.C73 base pair that upon exchange with other nucleotides leads to a marked decrease in the rate of aminoacylation in vitro. G-1.C73 is also a major identity element for histidine acceptance, such that the substitution of C73 brings about mischarging by glycyl-, glutaminyl-, and leucyl-tRNA synthetases. These identity conversions mediated by the G-1.C73 base pair were exploited to isolate secondary site revertants in the histidyl-tRNA synthetase from E. coli which restore histidine identity to a histidyl-tRNA suppressor carrying U73. The revertant substitutions confer a 3-4 fold reduction in the Michaelis constant for tRNAs carrying the amber-suppressing anticodon and map to the C-terminal domain of HisRS and its interface with the catalytic core. These findings demonstrate that the histidine tRNA anticodon plays a significant role in tRNA selection in vivo and that the C-terminal domain of HisRS is in large part responsible for recognizing this trinucleotide. The kinetic parameters determined also show a small degree of anticooperativity (delta delta G = -1.24 kcal/mol) between recognition of the discriminator base and the anticodon, suggesting that the two helical domains of the tRNA are not recognized independently. We propose that these effects substantially account for the ability of small changes in tRNA binding far removed from the site of a major determinant to bring about a complete conversion of tRNA identity.     

Differences in the magnesium dependences of the class I and class II aminoacyl-tRNA synthetases from Escherichia coli

The magnesium dependences of the ATP/PPi exchange and tRNA aminoacylation of reactions were measured for six aminoacyl-tRNA synthetases (isoleucyl-, tyrosyl- and arginyl-tRNA synthetases from class I, and histidyl-, lysyl- and phenylalanyl-tRNA synthetases from class II). The measured values were subjected to best-fit analyses using sum square error calculations between the data and the calculated curves in order to find the mode of participation of the Mg2+ and to optimize the sets of the kinetic constants. The following four dependences were observed: the class II synthetases require three Mg2+ for the activation reaction (including the one in MgATP), but the class I synthetases require only one Mg2+ (in MgATP); in class II synthetases both MgPPi and Mg2PPi participate in the pyrophosphorolysis of the aminoacyl adenylate. Arginyl-tRNA synthetase from class I also shows a better fit if also Mg2PPi reacts, but in the isoleucyl- and tyrosyl-tRNA synthetases only MgPPi but not Mg2PPi is used in the pyrophosphorolysis. Different synthetases have different requirements for the tRNA-bound Mg2+ and spermidine, independent of the enzyme class. 1-4 Mg2+ or spermidines are required in the best fit models. At the end of the reaction in all the synthetases analysed the dissociation of Mg2+ from the product aminoacyl-tRNA essentially enhances the subsequent dissociation of the aminoacyl-tRNA from the enzyme. The binding of ATP to the E. aminoacyl-tRNA complex also speeds up the dissociation of the aminoacyl-tRNA from most of these enzymes.     

Determination of the angle between the acceptor and anticodon stems of a truncated mitochondrial tRNA

Significant departures from the canonical (cloverleaf) secondary structure of transfer (t)RNAs can be found among the mitochondrial (m)tRNAs of higher metazoans; these mtRNAs thus pose a challenge to the concept of an invariant, L-shaped tertiary conformation for all tRNAs. For bovine mtRNASer(AGY), which lacks the entire "dihydrouridine" (dhU) arm, two distinct tertiary models have been proposed: the first model preserves the L-shaped conformation at the expense of overall size; the second model preserves the absolute distance between the 3' terminus and the anticodon loop, while allowing the acceptor-anticodon interstem angle to vary. We have tested the central predictions of these two models by performing a series of transient electric birefringence measurements on bovine mtRNASer(AGY) constructs in which the aminoacyl-acceptor and anticodon stems were each extended by approximately 70 bp. This mtRNA species is particularly amenable to analysis, since the native bovine (heart) mtRNA is completely unmodified outside of the anticodon loop. For magnesium ion concentrations above 1 mM, the interstem angle for the extended mtRNA, 120(+/-5) degrees, is approximately 50% larger than the corresponding angle for yeast tRNAPhe (70-80 degrees) under the same ionic conditions. Furthermore, the interstem angles of the two tRNAs exhibit strikingly different responses to the addition of magnesium ions: the interstem angle for yeast tRNAPhe is reduced by nearly 50 % upon addition of 2 mM magnesium ions, whereas the angle for mtRNASer(AGY) increases by about 10%. Our data thus support a central prediction of the second model; namely, that truncated mtRNAs will possess more open interstem angles. In addition, we demonstrate that birefringence amplitude data can be used to provide model-independent estimates for the interstem angles.     

The anticodon and discriminator base are important for aminoacylation of Escherichia coli tRNA(Asn)

A gel shift assay that distinguishes the aminoacylated form from the deacylated form of tRNAs was used to study the requirements for aminoacylation of Escherichia coli tRNA(Asn) in vivo. tRNA(Asn) derivatives containing single base changes in their anticodons or discriminator bases were constructed, and the extent of in vivo aminoacylation was determined directly. Substitution of U35 with C35 or U36 with C36 abolished aminoacylation of the tRNA. Substitution of G34 with C34 converted tRNA(Asn) into a lysine acceptor. Thus, each of the anticodon nucleotides are important for aminoacylation of tRNA(Asn). Substitution of discriminator base G73 with A73 affected the extent of aminoacylation in vivo indicating that the discriminator base also contributes to aminoacylation of tRNA(Asn).     

The chemical synthesis of E. coli tRNA(Lys) anticodon loop fragment and its analogues

E. coli tRNA(Lys) anticodon loop fragment (Umnm5s2UUUt6A) 1 and its analogues 2-6 were synthesized by the classical phosphotriester approach in solution. The preparation of suitably protected derivatives of N6-threonylcarbamoyladenosine 18 is also described.     

The angle between the anticodon and aminoacyl acceptor stems of yeast tRNA(Phe) is strongly modulated by magnesium ions

Many tRNAs undergo tertiary folding transitions at temperatures well below the main thermally induced (hyperchromic) transition. Such transitions are essentially isochromic and isoenthalpic and display an absolute requirement for divalent cations; however, the nature of the structural transition is not known for any tRNA. Using a combination of transient electric birefringence (TEB) and gel electrophoretic measurements, we have characterized the influence of magnesium ions on the apparent angle between the anticodon and acceptor stems of a yeast tRNA(Phe) construct. TEB is a particularly sensitive method for quantifying the bends introduced in RNA by various nonhelix elements. In the current instance, the tRNA construct comprises an unmodified tRNA(Phe) molecule in which the anticodon and acceptor stems have been extended by approximately 70 bp to more effectively "report" the interstem angles. Upon the addition of sub-millimolar concentrations of magnesium ions, the tRNA core undergoes a substantial rearrangement in tertiary structure, passing from an open form with an apparent interstem angle of approximately 150 degrees to a conformation with an interstem angle of approximately 70 degrees (200 microM Mg2+). Further addition of magnesium ions results in a minor adjustment of the apparent interstem angle to approximately 80-90 degrees, in line with earlier results. Finally, the magnesium-induced structural transition is essentially isochromic, in agreement with previous observations with native tRNAs. The current results suggest that changes in local divalent ion concentration in the ribosome could profoundly affect the global conformations of tRNAs during the translation cycle.     

Specific atomic groups and RNA helix geometry in acceptor stem recognition by a tRNA synthetase

Oligonucleotides that recapitulate the acceptor stems of tRNAs are substrates for aminoacylation by many tRNA synthetases in vitro, even though these substrates are missing the anticodon trinucleotides of the genetic code. In the case of tRNAAla a single acceptor stem G.U base pair at position 3.70 is essential, based on experiments where the wobble pair has been replaced by alternatives such as I.U, G.C, and A.U, among others. These experiments led to the conclusion that the minor-groove free 2-amino group (of guanosine) of the G.U wobble pair is essential for charging. Moreover, alanine-inserting tRNAs (amber suppressors) that replace G. U with mismatches such as G.A and C.A are partially active in vivo and can support growth of an Escherichia coli tRNAAla knockout strain, leading to the hypothesis that a helix irregularity and nucleotide functionalities are important for recognition. Herein we investigate the charging in vitro of oligonucleotide and full-length tRNA substrates that contain mismatches at the position of the G.U pair. Although most of these substrates have undetectable activity, G.A and C.A variants retain some activity, which is, nevertheless, reduced by at least 100-fold. Thus, the in vivo assays are much less sensitive to large changes in aminoacylation kinetic efficiency of 3.70 variants than is the in vitro assay system. Although these functional data do not clarify all of the details, it is now clear that specific atomic groups are substantially more important in determining kinetic efficiency than is a helical distortion. By implication, the activity of mutant tRNAs measured in the in vivo assays appears to be more dependent on factors other than aminoacylation kinetic efficiency.     

Binding of a fragment of yeast phenylalanyl tRNA containing an anticodon loop with 30S and 70S ribosomes from Escherichia coli. The role of guanosine-42 in this interaction

Poly(U)-dependent binding of isolated yeast tRNA(Phe) anticodon hairpin (15-nucleotide-long, corresponding to nucleotides 28-42 within the tRNA) and several its derivatives to the P site of Escherichia coli 30S and 70S ribosomes was studied quantitatively. The affinity for the hairpin binding to 70S ribosomes was shown to be only 30-fold weaker than that for the binding of total tRNA(Phe). Within the anticodon hairpin, removal of the 3'-terminal nucleotide corresponding to guanosine-42 in tRNA(Phe) decreases the association constant for the anticodon arm-ribosome interaction 15-fold. Replacement of this guanosine with other nucleosides does not affect the affinity, regardless of involvement in the hairpin secondary structure. These data indicate that G-42 affects the anticodon arm affinity most likely by forming a direct contact with the ribosome. One can assume that this nucleotide within intact tRNA also forms a contact with the P site. Since the 3'-terminal ribose modifications (oxidation, oxidation and reduction) as well as the presence or absence of the 3'-terminal phosphate does not affect the affinity of the anticodon arm fragment, the latter is obviously involved in the interaction through 3'-terminal nucleotide base groups which does not take part in base pairing.     

Kinematic specification of dynamics as an informational basis for person-and-action perception: Expectation, gender recognition, and deceptive intention.

Presents the principle of kinematic specification of dynamics (KSD), which states that movements specify the causal factors of events, in order to challenge the widespread conviction that perceiving another person must rest on ambiguous and falsifiable information. 89 Ss (aged 19–53 yrs), most of whom were undergraduates, participated in 6 experiments. Ss observed actors in action via G. Johansson's (see record 1974-10267-001) patch-light technique and made judgments about the actors' actions and gender. Results show that (a) the influence of an invisible thrown object on the kinematics of the thrower enabled Ss to perceive the length of the throw; (b) the lead-in movements of lifting allowed perception of the weight lifted; (c) an actor lifting a box could not deceive Ss about the weight, but only convey the deception; and (d) gender was recognizable in about 75% of the presentations, and this percentage rose when the actors were not self-conscious about gender. Results demonstrate the considerable effectiveness of kinematic information in enabling perception of persons and actions. The KSD principle therefore appears an appropriate conceptual guide, and the patch-light technique a useful empirical method, for the study of social knowing. (87 ref) (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Word recognition cues used in matching verbal stimuli within and between auditory and visual modalities.

Administered a matching-to-sample task to 60 first graders under 4 conditions, 2 intra- and 2 intermodal. The 5 matching cues (letters and segments) were used differentially within the 4 conditions with the initial segment selected most frequently in all conditions. The 5 cues were also used differentially across the 4 task conditions. Cue choice was related to reading achievement in the visual-to-visual matching condition, with the good readers using the final word segment cue significantly more often than the initial and final consonant cue. The reading achievement of those selecting the reversal, initial word segment, or final word segment did not differ. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Mutations and deletions within the hepatitis B virus core antigen and locations of B cell recognition sites

One or more infants of a multifetal pregnancy occasionally require delivery selectively because of in utero risk of fetal death in circumstances in which the sibling fetus appears well. At 26 weeks 5 days of gestation a small fundally placed twin in a dichorionic gestation had an estimated fetal weight of 650 g with decreased amniotic fluid and ominous Doppler velocity findings in his umbilical artery. A normally grown presenting sibling had reassuring fetal surveillance data. Over a 2-week interval the growth-restricted twin showed no growth, and his status deteriorated. He was selectively delivered by hysterotomy. Selective delivery may offer parents of multifetal gestations an additional option when 1 or more of their fetuses are at high risk for in utero death.     

The effect of catecholaminergic depletion within the prelimbic and infralimbic medial prefrontal cortex on recognition memory for recency, location, and objects.

There is good evidence that the medial prefrontal cortex (mPFC) is involved in different aspects of recognition memory. However, the mPFC is a heterogeneous structure, and the contribution of the prelimbic (PL) and infralimbic (IL) cortices to recognition memory has not been investigated. Similarly, the role of different neuromodulators within the mPFC in these processes is poorly understood. To this end, we tested animals with 6-hydroxydopamine (6-OHDA) lesions of the PL and IL mPFC on three tests of object recognition memory that required judgments about recency, object location, and object identity. In the recency task, lesions to both PL and IL severely impaired animals' ability to differentiate between old (earlier presented) and recently presented familiar objects. Relative to sham and PL animals, the IL lesion also disrupted performance on the object location task. However, both lesions left novel object recognition intact. These data confirm previous reports that the mPFC is not required for discriminations based on the relative familiarity of individual objects. However, these results demonstrate that catecholamines within the PL cortex are crucial for relative recency judgments and suggest a possible role for neural processing within the IL in the integration of information about object location. (PsycINFO Database Record (c) 2011 APA, all rights reserved)     

The exchange of Arg-Gly-Asp (RGD) and Arg-Tyr-Asp (RYD) binding sequences in a recombinant murine Fab fragment specific for the integrin alpha IIb beta 3 does not alter integrin recognition

The murine monoclonal antibody OPG2 is an excellent paradigm of natural RGD ligands and binds specifically to alpha IIb beta 3 integrin. A reactive Arg103-Tyr104-Asp105 (RYD) tripeptide is located in an extended loop, the third complementarity-determining region of the heavy chain (H3). When compared to other RGD ligands, the RYD tripeptide of OPG2 is unique, in that the side chains are fixed in a stable orientation that we have defined by x-ray crystallography. In this study, we express OPG2 H chain segments (Fd) and kappa chains as components of active, Fab heterodimers by coinfection of Spodoptera frugiperda cell lines with recombinant baculoviruses containing cDNA specific for each protein. Recombinant AP7 Fd segments are generated from the parent OPG2 Fd segments by replacement of Tyr104 with Gly, while recombinant AP7E Fd segments are produced from AP7 Fd segments, by exchange of Asp105 with Glu. Neither the free Fd segments nor the free kappa chains of OPG2 or AP7 can bind to alpha IIb beta 3. The AP7 Fab fragment, like the parent OPG2 Fab, binds strongly to purified alpha IIb beta 3 but weakly, if at all, to purified alpha V beta 3. The affinity of OPG2 and AP7 Fab fragments for gel-filtered platelets, whether nonstimulated or activated by 0.2 microM phorbol 12-myristate 13-acetate, is identical. As with other natural RGD ligands, the binding of recombinant OPG2 Fab or AP7 Fab fragments to purified alpha IIb beta 3 or to gel-filtered platelets is completely inhibited by the peptide RGDW or by addition of EDTA, AP7E Fab fragments do not bind at all to either purified alpha IIb beta 3 or platelets. Our results demonstrate, for the first time within a natural protein ligand, that the tripeptides RGD and RYD exhibit equivalent binding capacity and specificity for the integrin alpha IIb beta 3.     

A novel P-selectin glycoprotein ligand-1 monoclonal antibody recognizes an epitope within the tyrosine sulfate motif of human PSGL-1 and blocks recognition of both P- and L-selectin

Interactions between P-selectin and P-selectin glycoprotein ligand-1 (PSGL-1) mediate the earliest "rolling" of leukocytes on the lumenal surface of endothelial cells at sites of inflammation. Previously, PSGL-1 has been shown to be the primary mediator of interactions between neutrophils and P-selectin, but studies on the ability of PSGL-1 to mediate interactions between P-selectin and other subsets of leukocytes have yielded variable and conflicting results. A novel IgG monoclonal antibody (MoAb) to human PSGL-1 was generated, and the specificity of this MoAb was confirmed by both flow cytometric analysis and Western blotting of cells transfected with human PSGL-1. This newly developed MoAb, KPL1, inhibited interactions between P-selectin expressing COS cells and either HL60 cells, neutrophils, or lymphocytes. Furthermore, KPL1 completely inhibited interactions between P-selectin and either purified CD4 T cells or neutrophils in a flow assay under physiological conditions, but had no effect on interactions of T cells or neutrophils with E-selectin. In addition, KPL1 blocked interactions between lymphoid cells transfected with L-selectin and COS cells expressing PSGL-1. The KPL1 epitope was mapped to a site within a consensus tyrosine sulfation motif of PSGL-1, previously shown to be essential for interaction with P-selectin and now shown to be essential for interaction with L-selectin, and to be distinct from the epitope identified by the PL1 function blocking anti-PSGL-1 MoAb. Two-color flow cytometry of normal leukocytes showed that while natural killer (NK) cells (CD16(+)), monocytes, CD4 and CD8 T cells, and alpha/beta and gamma/delta T cells were uniformly positive for PSGL-1, B cells expressed low levels of the KPL1 epitope. This low level of KPL1 staining was also observed immunohistologically in germinal centers, which had no detectable KPL1 staining, whereas T-cell areas (interfollicular region) were positive for KPL1. Interestingly, plasma cells in situ and interleukin-6-dependent myeloma cell lines were KPL1(+). Thus, PSGL-1 is expressed on essentially all blood neutrophils, NK cells, B cells, T cells, and monocytes. Variation in tyrosine sulfation during B-cell differentiation may affect the ability of B cells to interact with P- and L-selectin.