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Malaza fastuosus is a lavishly patterned skipper butterfly from a genus that has three described species, all endemic to the mainland of Madagascar. To our knowledge, M. fastuosus has not been collected for nearly 50 years. To evaluate the power of our techniques to recover DNA, we used a single foreleg of an at least 140-year-old holotype specimen from the collection of the Natural History Museum London with no destruction of external morphology to extract DNA and assemble a complete mitogenome from next generation sequencing reads. The resulting 15 540 bp mitogenome contains 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and an A+T rich region, similarly to other Lepidoptera mitogenomes. Here we provide the first mitogenome also for Trapezitinae (Rachelia extrusus). Phylogenetic analysis of available skipper mitogenomes places Malaza outside of Trapezitinae and Barcinae + Hesperiinae, with a possible sister relationship to Heteropterinae. Of these, at least Heteropterinae, Trapezitinae, and almost all Hesperiinae have monocot-feeding caterpillars. Malaza appears to be an evolutionarily highly distinct ancient lineage, morphologically with several unusual hesperiid features. The monotypic subfamily Malazinae Lees & Grishin subfam. nov. (type genus Malaza) is proposed to reflect this morphological and molecular evidence. Key words: next-generation sequencing, phylogeny, Madagascar, ancient DNA, Paul Mabille. Resume : Le Malaza fastuosus est une espece de papillon aux motifs tres colores qui appartient a un genre qui compte trois especes decrites, toutes indigenes de Madagascar. Au meilleur de la connaissance des auteurs, aucun specimen du M. fastuosus n'a ete collecte depuis pres de 50 ans. Pour evaluer la puissance des techniques d'extraction d'ADN, les auteurs ont employe une seule patte avant sur un specimen holotype vieux d'au moins 140 ans, conserve au sein de la collection du Natural History Museum London et qui ne presentait aucun signe morphologique de dommage exterieur, pour extraire de l'ADN et assembler un mitogenome complet a l'aide de sequencage de seconde generation. Le mitogenome obtenu compte 15 540 pb et contient 13 genes codant pour des proteines, 22 genes d'ARN de transfert, deux genes codant pour des ARN ribosomiques et une region riche enA+T, tout comme les autres mitogenomes de lepidopteres. Les auteurs rapportent egalement le premier mitogenome au sein des Trapezitinae (Rachelia extrusus). Une analyse phylogenetique parmi les autres mitogenomes d'hesperides place le genre Malaza a l'exterieur des Trapezitinae et Barcinae + Hesperiinae, mais avec une possible relation proche avec les Heteropterinae. Parmi celles-ci, les Heteropterinae, les Trapezitinae et presque tous les Hesperiinae presentent des chenilles qui se nourrissent de monocotyledones. Le genre Malaza semble former un groupe distinct et ancien sur le plan evolutif, mais qui presente plusieurs caracteristiques morphologiques inhabituelles presentes chez les Hesperiidae. Une sous-famille monotypique, Malazinae Lees & Grishin (genre type Malaza) est propose pour refleter les evidences morphologiques et moleculaires. [Traduit par la Redaction] Mots-cles : sequencage de seconde generation, phylogenie, Madagascar, ADN ancient, Paul Mabille., Introduction Its name translated from Malagasy as 'famous', Malaza Mabille, 1904 is probably the most unusual skipper genus from Madagascar. Three Malagasy endemic species of Malaza have been described (Lees [...]

To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.ajhg.2009.04.013 Byline: Luisa Pereira (1)(2), Fernando Freitas (1), Veronica Fernandes (1), Joana B. Pereira (1), Marta D. Costa (1), Stephanie Costa (1), Valdemar Maximo (1)(2), Vincent Macaulay (3), Ricardo Rocha (4), David C. Samuels (5) Abstract: We analyzed the current status (as of the end of August 2008) of human mitochondrial genomes deposited in GenBank, amounting to 5140 complete or coding-region sequences, in order to present an overall picture of the diversity present in the mitochondrial DNA of the global human population. To perform this task, we developed mtDNA-GeneSyn, a computer tool that identifies and exhaustedly classifies the diversity present in large genetic data sets. The diversity observed in the 5140 human mitochondrial genomes was compared with all possible transitions and transversions from the standard human mitochondrial reference genome. This comparison showed that tRNA and rRNA secondary structures have a large effect in limiting the diversity of the human mitochondrial sequences, whereas for the protein-coding genes there is a bias toward less variation at the second codon positions. The analysis of the observed amino acid variations showed a tolerance of variations that convert between the amino acids V, I, A, M, and T. This defines a group of amino acids with similar chemical properties that can interconvert by a single transition. Author Affiliation: (1) Instituto de Patologia e Imunologia Molecular Universidade do Porto (IPATIMUP), Porto 4200-465, Portugal (2) Faculdade de Medicina da Universidade do Porto, Porto 4200-465, Portugal (3) Department of Statistics, University of Glasgow, Glasgow G12 8QQ, UK (4) Departamento de Ciencias de Computadores, Faculdade de Ciencias da Universidade do Porto, Porto 4169-007, Portugal (5) Center for Human Genetics Research, Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, TN 37232, USA Article History: Received 5 February 2009; Revised 10 April 2009; Accepted 20 April 2009 Article Note: (miscellaneous) Published online: May 7, 2009

To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.cell.2008.11.016 Byline: Florian Brandt (1)(2), Stephanie A. Etchells (2), Julio O. Ortiz (1), Adrian H. Elcock (4), F. Ulrich Hartl (2)(3), Wolfgang Baumeister (1)(3) Keywords: PROTEINS; RNA Abstract: Recent advances have led to insights into the structure of the bacterial ribosome, but little is known about the 3D organization of ribosomes in the context of translating polysomes. We employed cryoelectron tomography and a template-matching approach to map 70S ribosomes in vitrified bacterial translation extracts and in lysates of active E. coli spheroplasts. In these preparations, polysomal arrangements were observed in which neighboring ribosomes are densely packed and exhibit preferred orientations. Analysis of characteristic examples of polysomes reveals a staggered or pseudohelical organization of ribosomes along the mRNA trace, with the transcript being sequestered on the inside, the tRNA entrance sites being accessible, and the polypeptide exit sites facing the cytosol. Modeling of elongating nascent polypeptide chains suggests that this arrangement maximizes the distance between nascent chains on adjacent ribosomes, thereby reducing the probability of intermolecular interactions that would give rise to aggregation and limit productive folding. Author Affiliation: (1) Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried 82152, Germany (2) Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried 82152, Germany (3) Center for Integrated Protein Science Munich, Ludwig-Maximilians-Universitat Munchen, Butenandtstr. 5-13, Munchen 81377, Germany (4) Department of Biochemistry, University of Iowa, 4-530 Bowen Science Building, 51 Newton Road, Iowa City, IA 52242, USA Article History: Received 24 July 2008; Revised 12 October 2008; Accepted 13 November 2008 Article Note: (miscellaneous) Published: January 22, 2009

To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.tibs.2006.08.005 Byline: Alan G. Hinnebusch Abstract: Translation initiation in eukaryotes depends on many eukaryotic initiation factors (eIFs) that stimulate both recruitment of the initiator tRNA, Met-tRNA.sub.i.sup.Met, and mRNA to the 40S ribosomal subunit and subsequent scanning of the mRNA for the AUG start codon. The largest of these initiation factors, the eIF3 complex, organizes a web of interactions among several eIFs that assemble on the 40S subunit and participate in the different reactions involved in translation. Structural analysis suggests that eIF3 performs this scaffolding function by binding to the 40S subunit on its solvent-exposed surface rather than on its interface with the 60S subunit, where the decoding sites exist. This location of eIF3 seems ideally suited for its other proposed regulatory functions, including reinitiating translation on polycistronic mRNAs and acting as a receptor for protein kinases that control protein synthesis. Author Affiliation: Laboratory of Gene Regulation and Development, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA

To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.cell.2006.08.032 Byline: Andrei Korostelev (1), Sergei Trakhanov (1), Martin Laurberg (1), Harry F. Noller (1) Abstract: Our understanding of the mechanism of protein synthesis has undergone rapid progress in recent years as a result of low-resolution X-ray and cryo-EM structures of ribosome functional complexes and high-resolution structures of ribosomal subunits and vacant ribosomes. Here, we present the crystal structure of the Thermus thermophilus 70S ribosome containing a model mRNA and two tRNAs at 3.7 A resolution. Many structural details of the interactions between the ribosome, tRNA, and mRNA in the P and E sites and the ways in which tRNA structure is distorted by its interactions with the ribosome are seen. Differences between the conformations of vacant and tRNA-bound 70S ribosomes suggest an induced fit of the ribosome structure in response to tRNA binding, including significant changes in the peptidyl-transferase catalytic site. Author Affiliation: (1) Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA Article History: Received 13 July 2006; Revised 10 August 2006; Accepted 30 August 2006 Article Note: (miscellaneous) Published online: September 7, 2006

To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.cell.2006.04.028 Byline: Ken-ichi Noma (1), Hugh P. Cam (1), Richard J. Maraia (2), Shiv I.S. Grewal (1) Abstract: Eukaryotic genome complexity necessitates boundary and insulator elements to partition genomic content into distinct domains. We show that inverted repeat (IR) boundary elements flanking the fission yeast mating-type heterochromatin domain contain B-box sequences, which prevent heterochromatin from spreading into neighboring euchromatic regions by recruiting transcription factor TFIIIC complex without RNA polymerase III (Pol III). Genome-wide analysis reveals TFIIIC with Pol III at all tRNA genes, many of which cluster at pericentromeric heterochromatin domain boundaries. However, a single tRNA.sup.phe gene with modest TFIIIC enrichment is insufficient to serve as boundary and requires RNAi-associated element to restrain heterochromatin spreading. Remarkably, we found TFIIIC localization without Pol III at many sites located between divergent promoters. These sites appear to act as chromosome-organizing clamps by tethering distant loci to the nuclear periphery, at which TFIIIC is concentrated into several distinct bodies. Our analyses uncover a general genome organization mechanism involving conserved TFIIIC complex. Author Affiliation: (1) Laboratory of Molecular Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA (2) Laboratory of Molecular Growth Regulation, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA Article History: Received 28 November 2005; Revised 27 February 2006; Accepted 3 April 2006 Article Note: (miscellaneous) Published: June 1, 2006

Results show that the ribosome recycling factor binds to the ribosome in a different orientation than the conventional type exhibited by tRNA, indicating that its mechanism of action is not a mimicry of tRNA.

Research has been conducted on the structure of the specificity domain of the Bacillus subtilis RNase P RNA. The experiments have suggested that this structure is composed of a core, a functional unit of this domain, and a buttress module which provides the structural stability to the core module.

Results indicate that structure of the human tRNA(sup)Lys3UUU anticodon stem coupled with the modified amino acid t(sup)6A(sub)37 facilitates ribosome binding. Data indicate that the modified nucleoside influences anticodon loop conformation, which is mediated by t(sup)6A.

Results point out that it is critical for human tRNA(sup)LysUUU species to undergo anticodon domain modification for its effective binding to AAA-programmed ribosomes and wobbling to AAG codons.

The mitochondrial DNA (mtDNA) control region and flanking tRNAs were sequenced from 76 mice collected at 60 localities extending from Egypt through Turkey, Yemen, Iran, Afghanistan, Pakistan, and Nepal to eastern Asia. Segments of the Y chromosome and of a processed p53 pseudogene ([Psi]p53) were amplified from many of these mice and from others collected elsewhere in Eurasia and North Africa. The 251 mtDNA types, including 54 new ones reported here, now identified from commensal house mice (Mus musculus group) by sequencing this segment can be organized into four major lineages - domesticus, musculus, castaneus, and a new lineage found in Yemen. Evolutionary tree analysis suggested the domesticus mtDNAs as the sister group to the other three commensal mtDNA lineages and the Yemeni mtDNAs as the next oldest lineage. Using this tree and the phylogeographic approach, we derived a new model for the origin and radiation of commensal house mice whose main features are an origin in west-central Asia (within the present-day range of M. domesticus) and the sequential spreading of mice first to the southern Arabian Peninsula, thence eastward and northward into south-central Asia, and later from south-central Asia to north-central Asia (and thence into most of northern Eurasia) and to southeastern Asia. Y chromosomes with and without an 18-bp deletion in the Zfy-2 gene were detected among mice from Iran and Afghanistan, while only undeleted Ys were found in Turkey, Yemen, Pakistan, and Nepal. Polymorphism for the presence of a [Psi]p53 was observed in Georgia, Iran, Turkmenistan, Afghanistan, and Pakistan. Sequencing of a 128-bp [Psi]p53 segment from 79 commensal mice revealed 12 variable sites and implicated [greater than or equal to]14 alleles. The allele that appeared to be phylogenetically ancestral was widespread, and the greatest diversity was observed in Turkey, Afghanistan, Pakistan, and Nepal. Two mice provided evidence for a second [Psi]p53 locus in some commensal populations.

A study of mitochondria from Caenorhabditis elegans which not only has the G:U pair preserved but also proximal nucleotides that inhibits charging by a nonmitochondrial enzyme is presented. Mitochondrial alanyl-tRNA synthetase from C. elegans has been cloned and its microhelix oligonucleotides have been assessed as substrates for aminoacylation. Results show that G:U recognition continues even with an acceptor helix that does not recognize nonmitochondrial systems. The mitochondrial enzyme is similar to other alanine enzymes including the well-studied Escherichia coli protein.

Peptidyl transfer of a growing peptide on a ribosome-bound transfer RNA (tRNA) to an incoming amino acyl tRNA is the central step in translation, and it may be catalyzed primarily by the large subunit (LSU) ribosomal RNA (rRNA). Genetic and biochemical evidence suggests that the central loop of domain V of the LSU rRNA plays a direct role in peptidyl transfer. It was previously found that a single base change at a universally conserved site in this region of the Tetrahymena thermophila LSU rRNA confers anisomycin resistance (an-r) as well as extremely slow growth, cold sensitivity, and aberrant cell morphology. Because anisomycin specifically inhibits peptidyl transfer, possibly by interfering with tRNA binding, it is likely that this mutant rRNA is defective in efficiently completing one of these steps. In the present study, we have isolated an intragenic suppressor mutation located only three bases away from the original mutation that partially reverses the slow growth and cold-sensitive phenotypes. These data imply that the functional interaction of these two bases is necessary for normal rRNA function, perhaps for peptidyl transfer or tRNA binding. These data provide the first demonstration of a functional interaction between bases within this rRNA region.

A study was conducted to determine the ability of Salmonella typhimurium (S typhimurium) to grow on dicarboxylic acids. The S typhimurium strains were cultured in a Luria broth and in a Difco nutrient broth which were treated with morpholine propanesulfonic acid and antibiotics. Results revealed that the ability of the S typhimurium to grow on succinate, fumarate and malate depend on the state of modification in position 37 of the tRNAs which contain ms2io6A37.

Kinetic and thermodynamic analyses were performed to determine the role of the protein component of Bacillus subtilis RNase P in catalytic reactions of B. subtilis precursor tRNA(super Asp) scission. The functional characteristics of ribonuclease P (RNase P) holoenzyme were also correlated to RNase P RNA in 10 millimole magnesium chloride and 100 millimole ammonium chloride. The protein component of RNase P was found to assist recognition of pre-tRNA by supporting the interaction between the enzyme and the 5'-precursor component of the substrate.

The translocation elongation cycle mechanism is characterized by the iterative coupled movement of mRNA and tRNA throughout the elongation phase of protein synthesis. The ribosome provides specific binding sites for mRNA, tRNA and the termination factors. It also stabilizes codon-anticodon interaction and preserves the translational reading frame. Moreover, RNAs bind in the various ribosomal binding states to protect rRNA characteristic bases from chemical probes and to provide structure correlates for the tRNA states during the elongation cycle.

Research was conducted to study the various features associated with the molecular recognition of tRNA by pseudouridine 55 synthase and compare them with those involved in the relationship between tRNA and (m5U54)-methyltransferase. Results showed that the elimination of base pairs in the structure eliminated any form of pseudouridine 55 synthase activity. They also suggested that tRNA mutants located at the base of nucleotide 59 functioned as substrates for the synthase activity.

Research was conducted to investigate the mechanisms of pseudouridine synthases, an enzyme which transforms uridine to pseudouridine in a number of positions. Plasmid pLX1 was turned into BL21(DE3) cells while reaction mixtures were incubated in a buffer. Results showed that the target uracil remained bounded to the enzyme until product formation. They also indicated the importance of fluorouracil in covalent complex formation via 39 target positions.

The universal genetic code is determined by the aminoacylation of tRNAs. In spite of the universality of the code, there are barriers to aminoacylation across taxonomic domains. These barriers are thought to correlate with the co-segregation of sequences of synthetases and tRNAs into distinct taxonomic domains. By contrast, we show here examples of eukaryote-like synthetases that are found in certain prokaryotes. The associated tRNAs have retained their prokaryote-like character in each instance. Thus, co-segregation of domain-specific synthetases and tRNAs does not always occur. Instead, synthetaSes make adaptations of tRNA-protein contacts to cross taxonomic domains.

The importance of the intrinsic ATPase in 80S ribosomes of higher eukaryotes was determined through identification of four binding sites in liver ribosomes of rabbits. Results have shown that the rabbit liver ribosomes contain only three tRNA binding sites A, P and E. The presence of ATP weakened the tight binding of the deacetylated tRNA at the E site. The E site interacted with deacetylated tRNA tightly blocking the binding of aminoacyl-tRNA to the A site.

The role of RNA transfer protein structures as a requirement in modifying enzyme binding, catalysis, and recognition was analyzed through inhibitory studies of structural variants of yeast tRNAasp and Escherichia coli tRNAleu. Results have shown that sequence G36pG37 is an essential identity element particularly in relation to substrate yields of heterologous tRNA species.

The role of RNA tertiary structure in transfer RNA recognition as well as the formation of an RNA tertiary base pair were investigated through identifying the structural determinant of G15*G48. Results have shown that the dependence of the N2*N3 pairing of G15*G48 on A13*A22 indicated the ability to manipulate a G*G base pair through another RNA structural element. The correlation between G15*G48 and A13*A22 indicated a control of an RNA tertiary base pair to modify the function of the RNA.

The influence of the zinc-containing C-terminal region on the binding of isoleucyl-tRNA synthetase was investigated. Gel mobility shift assay was utilized to study the complex formation between the zinc peptide and tRNA. Results have shown that the binding of peptide Zn2+-53C to isoleucyl-transfer RNA synthetase (tRNAIle) was nonspecific and that the peptide binding was zinc-dependent. The same kind of C-terminal when combined with other parts of synthetase can form a specific RNA binding pocket.

The biochemical structure of Thermus thermophilus histidyl-transfer RNA (tRNA) synthetase (HisRSTT)-histidine complex was analyzed by multiple isomorphous replacement (MIR). MIR analysis of the HisRSTT-histidine complex indicated the presence of a crystal structure that was highly homologous to Escherichia coli HisRS complex. The enzyme was also composed of an N-terminal catalytic domain, a 90-residue C-terminal alpha/beta domain and a HisRS-specific alpha-helical domain.

The thiol located at position 443 of Escherichia coli prolyl-tRNA synthetase (ProRS) is not essential for catalysis, but is likely to be in a buried region that forms the prolyl-adenylate substrate binding pocket. This is indicated by results of the chemical modification and site-directed mutagenesis of the single cysteine located at position 443 in motif 3 of Escherichia coli ProRS. It was found that chemical modification of C443 hampers the ability of the enzyme to form the activated aminoacyl-adenylate, which is required for tRNA aminoacylation. Also, the aminoacyl-adenylate binding site is in close proximity to C443 of motif 3.

The nucleoside modification patterns in the unfractionated transfer RNA (tRNA) of ANT-300, Lactobacillus bavaricus, Vibrio sp. strains 5710 and 29-6 were analyzed to characterize the posttranscriptional modification of tRNA. Analysis of nucleoside modification in unfractionated tRNA from psychrotrophic bacteria indicated the presence of significantly elevated levels of dihydrouridine. The presence of dihydrouridine in the tRNA of the psychrotrophic bacteria also indicated the role of the nucleoside in the promotion of conformational flexibility in RNA.

The thermodynamic effects of coaxial stacking of helixes with GA and CC mismatches were analyzed by utilizing model systems with four- or five-nucleotide overhangs on a hairpin stem. The coaxial stacking of helices stabilizes GA mismatches and CC mismatches during helix interfaces. Furthermore, energetic preference for 5' or 3' break in the phosphate backbone adjacent to the GA mismatch was not detected in the mismatch interface systems.

A revised model was developed for the polypeptide chain elongation cycle in which a discriminatory role is ascribed to the conformational differences of cognate and near-cognate transfer ribonucleic acids (tRNA). The model for protein elongation begins with the post-translocation of the peptidyl-tRNA ternary complex to the ribosomal P site. The post-translocation process initiates the release of aa-tRNA and EF-Tu.guanine diphosphate (GDP) due to the hydrolysis of guanine triphosphate.

High affinity binding of trivalent arsenicals to arginyl aminoacyl-tRNA transferase can occur by a thiol-independent mechanism. The presence of vicinal thiol groups is indicated by the reversible enzyme inhibition by phenylarsenoxides. The characterization of all mutant enzymes is carried out and the ability to bind a radioiodinated phenylarsenoxide derivative is retained. The blocking of the binding of the radiolabeled phenylarsenoxide due to the reaction of the enzyme with the bifunctional reagent indicates the binding of the two reagents at a single common site.

The structural conformation of tyrosyl-tRNA synthase, a 370 amino acid polypeptide from a eukaryotic pathogen, can attain transversion in a critical acceptor helix base pair which is responsible for species selective microhelix aminoacylation. The enzyme contains class I aminoacyl-tRNA synthetase and aligns with prokaryotic tyrosyl-tRNA synthetase in the class-defining active site region indicating that species selective microhelix can be used as species-specific inhibitor of tRNA synthetase.

To analyse the function of C-terminal domain, one of the domain of class I tRNA synthetase, in specific RNA binding, the anticodon binding of Escherichia coli methionyl tRNA synthetase was fused to maltose binding protein. This experiment revealed that the fusion protein and the isolated domain are stable and has native-like structural characteristics. Both the fusion protein and isolated domain specifically bind to a small RNA hairpin oligonucleotide.

Byline: William G. Scott, John T. Finch, Aaron Klug Abstract: We have solved the crystal structure of an all-RNA hammerhead ribozyme having a single 2'-O-methyl cytosine incorporated at the active site to prevent cleavage. The conditions used differ from those in another recent solution in four significant ways: first, it is an all-RNA ribozyme rather than a DNA-RNA hybrid; second, the connectivity of the ribozyme backbone strands is different; third, the crystals were grown in the presence of a much lower concentration of salt; and fourth, the crystal packing scheme is very different. Nevertheless, the three-dimensional structure of the all-RNA hammerhead ribozyme is similar to the previous structure. Five potential Mg(II)-binding sites are identified, including one positioned near the ribozyme catalytic pocket. Upon this basis, as well as upon comparisons with the metal-binding sites in the structurally homologous uridine turn of tRNA.sup.Phe, we propose a mechanism for RNA catalytic cleavage. Author Affiliation: Medical Research Council Laboratory of Molecular Biology Hills Road Cambridge CB2 2QH England, UK

A study revealed that lysyl-tRNA synthetase activity is inducible in Escherichia coli B, eight Escherichia coli reference collection (ECOR) isolates, Shigella flexneri, Klebsiella pneumoniae and Enterobacter aerogenes as well as in Escherichia coli K-12, and in each of them two lysU homologs were discernible. The genus Enterobacter was found to be the most ancestral to E. coli in which two lysU homologs could be detected.

X-ray analysis of cross-transplantation and cross-aminoacylation between Escherichia coli class I glutaminyl- and class II aspartyl-tRNA synthetases reveals that both tRNAs share three identity nucleotides, G73, G10 and V35. Transplantation experiments reveal the feasibility of transplantation between Class I and class II systems and that conversion of aspartate to glutamine needs more sequence changes than conversion of glutamine to aspartate. Transplantation studies identify a new identity nucleotide C38 in yeast tRNA (Asp) for aspartylation.

Analysis of the crystal structure of unchanged tRNA(Gln), complexed with glutaminyl-tRNA synthetase from Escherichia coli and ATP, reveals the importance of pseudouridinylation for the stabilization of tRNA through water-regulated connection of the changed bases. The absence of water molecules, which cross-link the N5 of pseudo-uridines to their 5'-phosphate, is the notable change in unmodified tRNA.

The intron processing tRNA enzymes of archaeal Haloferax volcanii differ from their eukaryal counterparts in that factors beyond exon-intron boundary structure are required for intron processing. Changing the U6-U67 pair of the yeast tRNA proacceptor stem to A6-U67 effects RNase P cleavage and restores 5' and 3' flanking sequences in H. volcanii.

HemA is the gene encoding glutamyl tRNA reductase (GTR) and is required for 5-aminolevulinic acid (ALA) synthesis. A plasmid containing both hemA and another gene hemM gives normal colonies of ALA. HemM gene is a regulatory subunit of GTR.

A comparison of the intermediates of selenocysteine tRNA's precursor reveals that selenium affects tRNA (ser)(sec) stability and methylation. Selenocysteine also affects the methylation of the mcm U residue's ribose portion. The precusor tRNA used in the comparison lacks nucleoside modification. The microinjection method incorporates either one of the tRNAs into Xenopus oocytes.