The role of the anticodon in the interaction between methionyl-tRNA synthetase and bacterial initiator tRNA?

Complementary and antiparallel oligonucleotides bind to exposed regions of the tRNA molecule. Aminoacylation in the presence of triplets has been used to determine the role of the anticodon in the interaction between methionyl-tRNA synthetase and initiator tRNA. ApUpG has no effect on the charging even when 70% of the tRNA is bound to the triplet, whereas in the presence of GpGpU which binds to the A-C-C sequence adjacent to the 3' terminal adenosine that fraction of the tRNA which is bound to the triplet is completely unavailable for charging. Hence the anticodon is probably not involved in a primary interaction while the A-C-C-A-OH clearly is. This conclusion is supported by the failure of the isolated anticodon loop and stem oligonucleotides to inhibit the aminoacylation reaction.     

Review: transport of tRNA out of the nucleus-direct channeling to the ribosome?

Although tRNA was the first substrate whose export from the nuclei of eukaryotic cells had been shown to be carrier-mediated and active, it has only been in the last 2 years that the first mechanistic details of this nucleocytoplasmic transport pathway have begun to emerge. A member of the importin/karyopherin beta superfamily, Los1p in yeast and Xpo-t in vertebrates, has been shown to export tRNA in cooperation with the small GTPase Ran (Gsp1p) from the nucleus into the cytoplasm, where tRNA becomes available for translation. However, Los1p is not essential for viability in yeast cells, suggesting that alternative tRNA export pathways exist. Recent results show that aminoacylation and a translation factor are also required for efficient nuclear tRNA export. Thus, protein translation and nuclear export of tRNA appear to be coupled processes.     

Does the evolutionary history of aminoacyl-tRNA synthetases explain the loss of mitochondrial tRNA genes?

The importation of cytosolic tRNAs is required for protein synthesis in the mitochondria of the wide variety of eukaryotes that lack a complete set of mitochondrial tRNA genes. The evolutionary history of the process, however, is still enigmatic. The analysis presented here suggests that the loss of distinct mitochondrial tRNA genes was not random and that it might be explained by the differential capabilities of mitochondrial aminoacyl-tRNA synthetases to charge imported eukaryotic-type tRNAs with amino acid.     

A primordial tRNA modification required for the evolution of life?

The evolution of reading frame maintenance must have been an early event, and presumably preceded the emergence of the three domains Archaea, Bacteria and Eukarya. Features evolved early in reading frame maintenance may still exist in present-day organisms. We show that one such feature may be the modified nucleoside 1-methylguanosine (m(1)G37), which prevents frameshifting and is present adjacent to and 3' of the anticodon (position 37) in the same subset of tRNAs from all organisms, including that with the smallest sequenced genome (Mycoplasma genitalium), and organelles. We have identified the genes encoding the enzyme tRNA(m(1)G37)methyltransferase from all three domains. We also show that they are orthologues, and suggest that they originated from a primordial gene. Lack of m(1)G37 severely impairs the growth of a bacterium and a eukaryote to a similar degree. Yeast tRNA(m(1)G37)methyltransferase also synthesizes 1-methylinosine and participates in the formation of the Y-base (yW). Our results suggest that m(1)G37 existed in tRNA before the divergence of the three domains, and that a tRNA(m(1)G37)methyltrans ferase is part of the minimal set of gene products required for life.     

The dynamic NMR structure of the TΨC-loop: Implications for the specificity of tRNA methylation

tRNA (m5U54)-methyltransferase (RUMT) catalyzes the S-adenosylmethionine-dependentmethylation of uridine-54 in the TC-loop of all transfer RNAs in E. coli to form the 54-ribosylthymine residue. However, in all tRNA structures, residue 54 is completely buried andthe question arises as to how RUMT gains access to the methylation site. A 17-mer RNAhairpin consisting of nucleotides 49–65 of the T-loop is a substrate for RUMT.Homonuclear NMR methods in conjunction with restrained molecular dynamics (MD)methods were used to determine the solution structure of the 17-mer T-arm fragment. Theloop of the hairpin exhibits enhanced flexibility which renders the conventional NMR averagestructure less useful compared to the more commonly found situation where a molecule existsin predominantly one major conformation. However, when resorting to softer refinementmethods such as MD with time-averaged restraints, the conflicting restraints in the loop canbe satisfied much better. The dynamic structure of the T-arm is represented as an ensembleof 10 time-clusters. In all of these, U54 is completely exposed. The flexibility of the T-loop in solution in conjunction with extensive binding studies of RUMT with the TC-loop and tRNA suggest that the specificity of the RUMT/tRNA recognition is associated withtRNA tertiary structure elements. For the methylation, RUMT would simply have to breakthe tertiary interactions between the D- and T-loops, leading to a melting of the T-armstructure and making U54 available for methylation.     

Review: Transport of tRNA out of the Nucleus—Direct Channeling to the Ribosome?

Although tRNA was the first substrate whose export from the nuclei of eukaryotic cells had been shown to be carrier-mediated and active, it has only been in the last 2 years that the first mechanistic details of this nucleocytoplasmic transport pathway have begun to emerge. A member of the importin/karyopherin β superfamily, Los1p in yeast and Xpo-t in vertebrates, has been shown to export tRNA in cooperation with the small GTPase Ran (Gsp1p) from the nucleus into the cytoplasm, where tRNA becomes available for translation. However, Los1p is not essential for viability in yeast cells, suggesting that alternative tRNA export pathways exist. Recent results show that aminoacylation and a translation factor are also required for efficient nuclear tRNA export. Thus, protein translation and nuclear export of tRNA appear to be coupled processes.     

A thermal ratchet model of tRNA–mRNA translocation by the ribosome

The translocation of tRNA coupled with mRNA in the ribosome is one of important steps during protein synthesis. Despite extensive experimental studies, the detailed mechanism of the translocation remains undetermined. Here, based on previous biochemical, cryo-electron microscopic and X-ray crystallographic studies, a thermal ratchet model is presented for this translocation. In the model, during one elongation cycle of the protein synthesis, two large conformational transitions of the ribosome are involved, with one being the relative rotation between the two ribosomal subunits following the peptide transfer, which is facilitated by the EF-G.GTP binding, and the other one being the reverse relative rotation between the two ribosomal subunits upon EF-G.GTP hydrolysis. The former conformational change plays an important role in ensuring the completion of the release of the deacylated tRNA from the ribosome before tRNA–mRNA translocation. The latter reverse conformational change upon GTP hydrolysis is followed by rapid tRNA–mRNA translocation and Pi release, both of which take place independently of each other. This is consistent with the previous biochemical experimental data. Also, the model is consistent with other available experimental results such as the suppression of EF-G-dependent translocation in cross-linked ribosomes and frameshifting under some conditions.     

Charging the code — tRNA modification complexes

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Studies of odd bases in yeast mitochondrial tRNA: Absence of the fluorescent “Y” base in mitochondrial DNA coded tRNAPhe, absence of 4-thiouridine

Reversed phase chromatography of mitochondrial [³H] Phe-tRNA from $\text{Saccharomyces cerevisiae}$ shows only one peak which elutes distinctly from cytoplasmic [¹⁴C] Phe-tRNA. Mitochondrial tRNA^Phe from this peak hybridizes specifically with ?⁺ and a ?^? mitochondrial DNA. Search for rare bases in mitochondrial tRNA shows the absence of the eukaryotic “Y” base and of the prokariotic s⁴U base.     

Did tRNA synthetase classes arise on opposite strands of the same gene?

Structural homology of class II aminoacyl-tRNA synthetases to the HSP70 family and the existence of a gene whose sense and antisense strands code for a dehydrogenase and an HSP70 chaperonin justify reconsideration of a possible sense-antisense ancestry for the two synthetase classes.     

Modelling the Efficiency of Codon–tRNA Interactions Based on Codon Usage Bias

The tRNA adaptation index (tAI) is a widely used measure of the efficiency by which a coding sequence is recognized by the intra-cellular tRNA pool. This index includes among others weights that represent wobble interactions between codons and tRNA molecules. Currently, these weights are based only on the gene expression in Saccharomyces cerevisiae. However, the efficiencies of the different codon–tRNA interactions are expected to vary among different organisms. In this study, we suggest a new approach for adjusting the tAI weights to any target model organism without the need for gene expression measurements. Our method is based on optimizing the correlation between the tAI and a measure of codon usage bias. Here, we show that in non-fungal the new tAI weights predict protein abundance significantly better than the traditional tAI weights. The unique tRNA–codon adaptation weights computed for 100 different organisms exhibit a significant correlation with evolutionary distance. The reported results demonstrate the usefulness of the new measure in future genomic studies.     

Variation in the cell cycle time in the crypts of lieberkühn of the mouse

The durations of the phases of the cell cycle were measured at different levels in the jejunal crypts of male Balb/c mice. A mean cell cycle time of 12.3 h was found for the whole crypt. In cell positions 1 and 2, the cell cycle time was 16.7 h, and this time steadily decreased to a value of between 10 and 11 h for cell positions above 11. It is concluded that basally situated crypt cells in the mouse are cycling relatively slowly, and that they form the functional stem cell pool for the crypt. These cells may also compose the potential stem cell pool which repopulates the crypt after death of proliferative cells.     

Change in the power of EEG activity in the α range in response to tonic nociceptive stimulation of the distal joint of the little finger

Examination of 12 healthy volunteers aged 20–56 years was performed to study the EEG changes caused by a tonic squeeze of the distal joint of the little finger of the left and then the right hand. This stimulation caused painful sensations of different intensity (pain on the right was stronger). Spectral power was measured in the ( ₁ (8–10.5 Hz) and (₂ ranges (10.5–13 Hz) under different conditions. Weak pain led to an increase in the power of the (₁ and ₂ ranges in the occipital regions. With strong pain, the power of ₁ waves increased bilaterally in the posterior regions (O ₁, O ₂, T ₆), as well as in the left frontal region (F ₃, F ₇). The powers of the ₁ and ₂ ranges substantially increased relative to the background level after the strong nociceptive stimulation ceased. This finding testified to a latent and inertial character of its effect on the -wave parameters.Translated from Fiziologiya Cheloveka, Vol. 31, No. 2, 2005, pp. 77–84.Original Russian Text Copyright © 2005 by Garkavenko, Gorkovenko, Mankovskaya, Shevko, Lyskov, Kostyukov.     

In vitro hyperprocessing of Drosophila tRNAs by the catalytic RNA of RNase P the cloverleaf structure of tRNA is not always stable?

We have previously reported that the catalytic RNA subunit of RNase P of Escherichia coli (M1 RNA) cleaves Drosophila initiator methionine tRNA (tRNA(Met)i) within the mature tRNA sequence to produce specific fragments. This cleavage was dependent on the occurrence of an altered conformation of the tRNA substrate. We call this further cleavage hyperprocessing. In the present paper, to search for another tRNA that can be hyperprocessed in vitro, we used total mature tRNAs from Drosophila as substrates for the in vitro M1 RNA reaction. We found that some tRNAs can be hyperprocessed by M1 RNA and that two such tRNAs are an alanine tRNA and a histidine tRNA. Using mutant substrates of these tRNAs, we also show that the hyperprocessing by M1 RNA is dependent on the occurrence of altered conformations of these tRNAs. The altered conformations were very similar to that of tRNA(Met)i. We show here that M1 RNA can be used as a powerful tool to detect the alternative conformation of tRNAs. The relationship between these hyperprocessing reactions and stability of the tRNA structure will also be discussed.     

Use of Lead(II) to Probe the Structure of Large RNA's. Conformation of the 3′ Terminal Domain of E. coli 16S rRNA and its Involvement in Building the tRNA Binding Sites

Abstract

The present work shows that lead(II) can be used as a convenient structure probe to map the conformation of large RNA's and to follow discrete conformational changes at different functional states. We have investigated the conformation of the 3′ domain of the E. coli 16S rRNA (nucleotides 1295–1542) in its naked form, in the 30S subunit and in the 70S ribosome. Our study clearly shows a preferential affinity of Pb(II) for interhelical and loop regions and suggests a high sensitivity for dynamic and flexible regions. Within 30S subunits, some cleavages are strongly decreased as the result of protein-induced protection, while others are enhanced suggesting local conformational ajustments. These rearrangements occur at functionally strategic regions of the RNA centered around nucleotides 1337,1400,1500 and near the 3′ end of the RNA The association of 30S and 50S subunits causes further protections at several nucleotides and some enhanced reactivities that can be interpreted in terms of subunits interface and allosteric transitions. The binding of E. coli tRNA-Phe to the 70S ribosome results in message-independent (positions 1337 and 1397) and message-dependent (1399–1400, 1491–1492 and 1505) protections. Athird class ofprotection(1344–1345,1393–1395,1403–1409,1412–1414, 1504, 1506–1507 and 1517–1519) is observed in message-directed 30S subunits, which are induced by both tRNA binding and 50S subunit association. This extensive reduction of reactivity most probably reflects an allosteric transition rather than a direct shielding.     

Zooplankton in the ponds with tropical plants in the greenhouses of the Botanical Garden of the Jagiellonian University in Kraków

The presence of P. tetraurelia was found in the pond in "The Palm-House" greenhouse.     

Methylation of the ß-positions of the furan ring in F-acids

Major incubation products in feeding experiments with the sodium salt of 7-(5-butyl-furan-2-yl)heptanoic acid (3) on suspension cultures of Saccharum spec. are the unusual F-acids (4a) and (4b). They possess in contrast to natural monomethyl substituted F-acids a methyl substituent in the 4-position of the furan ring. Unexpectedly, the dimethyl substituted F-acids (4c) and (4d) were found only in very small amounts. The detection and structure elucidation of the methylation products (4a)–(4d) was achieved predominantly by GC-MS analysis of the corresponding tetrahydrofuran derivatives (5a)–(5d).