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At least 19 recordsLinked to original sources
PubMed1995

Sequence analysis of a 44 kb DNA fragment of yeast chromosome XV including the Tyl-H3 retrotransposon, the suf1(+) frameshift suppressor gene for tRNA-Gly, the yeast transfer RNA-Thr-1a and a delta element.

We have sequenced on both strands a 44,019 bp fragment located on the left arm of Saccharomyces cerevisiae chromosome XV. The sequenced segment contains 22 open reading frames (ORFs) of at least 100 amino acids long, one of which probably contains an intron. Six of the 22 ORFs correspond to known proteins: the multicopy suppressor of Snf1 protein 1, the two Tyl-H3 transposon proteins TyA and TyB, the myo-inositol transporter 2, the transcription factor protein Ino4 and the 3,4-dihydroxy-5-hexaprenylbenzoate methyltransferase. Of the 16 remaining ORFs, two show highest homologies with the yeast serine/threonine protein kinase Ste20 and the human tryptophanyl-tRNA synthetase. Eight ORFs show slight similarities with protein sequences described in data banks. DNA sequence comparison reveals also the presence of three known sequences: the Tyl-H3 transposable element, the yeast suf1(+) frameshift suppressor gene for tRNA-Gly and the yeast transfer RNA-Thr-1a. A fourth DNA sequence shows striking identities with the yeast delta elements.

Amino Acid Sequence↗
PubMed1993

Gel retardation analysis of E. coli M1 RNA-tRNA complexes.

We have analyzed complexes between tRNA and E. coli M1 RNA by electrophoresis in non-denaturing polyacrylamide gels. The RNA subunit of E. coli RNase P formed a specific complex with mature tRNA molecules. A derivative of the tRNA(Gly), endowed with the intron of yeast tRNA(ile) (60 nt), was employed to improve separation of complexed and unbound M1 RNA. Binding assays with tRNA(Gly) and intron-tRNA(Gly) as well as analysis of intron-tRNA/M1 RNA complexes on denaturing gels showed that one tRNA is bound per molecule of M1 RNA. A tRNA carrying a truncation as small as the 5'-nucleotide had a strongly reduced affinity to M1 RNA and was also a weak competitor in the cleavage reaction, suggesting that nucleotide +1 is a major determinant of tRNA recognition and that the thermodynamically stable tRNA-M1 RNA complex is relevant for enzyme function. Binding was shown to be dependent on the M1 RNA concentration in a cooperative fashion. Only a fraction of M1 RNAs (50-60%) readily formed a complex with intron-tRNA(Gly), indicating that distinct conformational subpopulations of M1 RNA may exist. Formation of the M1 RNA-tRNA(Gly), complex was very similar at 100 mM Mg++ and Ca++, corroborating earlier data that Ca++ is competent in promoting M1 RNA folding and tRNA binding. Determination of apparent equilibrium constants (app Kd) for tRNA(Gly) as a function of the Mg++ concentration supports an uptake of at least two additional Mg++ ions upon complex formation. At 20-30 mM Mg++, highest cleavage rates but strongly reduced complex formation were observed. This indicates that tight binding of the tRNA to the catalytic RNA at higher magnesium concentrations retards product release and therefore substrate turnover.

Base Sequence↗
PubMed1997

Insights into the interaction between tRNA and primer binding site from characterization of a unique HIV-1 virus which stably maintains dual PBS complementary to tRNA(Gly) and tRNA(His).

Previously our laboratory constructed an HIV-1 which stably maintained a primer binding site (PBS) complementary to tRNA(His) by mutating the region of the provirus within U5 postulated to interact with the anticodon of tRNA(His) (J. Wakefield, S-M Kang, and C. D. Morrow, 1996, J. Virol, 70, 966-975). From the analysis of the virus obtained after long-term culture, we identified an unusual proviral DNA in which the U5-PBS region contained a dual PBS complementary to tRNA(Gly) and tRNA(His), respectively, separated by a 21-nucleotide intervening sequence. To determine if this U5-PBS region containing the dual PBS would give rise to an infectious virus, the mutant U5-PBS containing the dual PBS was subcloned into an infectious HIV-1 proviral clone, pHXB2; the resultant proviral DNA was designated as pHXB2(Gly-His). Transfection of pHXB2(Gly-His) into cells gave rise to infectious virus. Analysis of the U5-PBS region revealed that the virus stably maintained the dual PBS rather than revert back to the wild-type PBS. In addition to genomes with the PBS complementary to tRNA(Gly) and tRNA(His), proviral genomes were identified after extended in vitro culture which contained dual PBS complementary to tRNA(Gly) and tRNA(Phe). To determine which PBS could be used for reverse transcription, we utilized an endogenous reverse transcription/PCR method which could discriminate (based on molecular size of the products) between the minus strand DNA initiated from the two PBSs. The results of this assay demonstrated that either the PBS complementary to tRNA(Gly) or tRNA(His) could be used for the initiation of reverse transcription. The results of our study highlight the complex interrelationship between U5-PBS and primer tRNA required for positioning the tRNA at the PBS and provides new insights into how the tRNA primer used to initiate reverse transcription is selected.

Animals↗
PubMed1991

Chromosomal assignment of a large tRNA gene cluster (tRNA(Leu), tRNA(Gln), tRNA(Lys), tRNA(Arg), tRNA(Gly)) to 17p13.1.

A cluster of tRNA genes (tRNA(UAGLeu), tRNA(CUGGln), tRNA(UUULys), tRNA(UCUArg)) and an adjacent tRNA(GCCGly) have been assigned to human chromosome 17p12-p13.1 by in situ hybridization using a 4.2 kb human DNA fragment for tRNA(Leu), tRNA(Gln), tRNA(Lys), tRNA(Arg), and, for tRNA(Gly), 1.3 kb and 0.58 kb human DNA fragments containing these genes as probes. This localization was confirmed and refined to 17p13.100-p13.105 using a somatic cell hybrid mapping panel. Preliminary experiments with the biotinylated tRNA Leu, Gln, Lys, Arg probe and metaphase spreads from other great apes suggest the presence of a hybridization site on the long arm of gorilla (Gorilla gorilla) chromosome 19 and the short arm of orangutan (Pongo pygmaeus) chromosome 19 providing further support for homology between HSA17, GGO19 and PPY19.

Animals↗
PubMed1990

Genes for tRNA(Gly), tRNA(His), tRNA(Lys), tRNA(Phe), tRNA(Ser) and tRNA(Tyr) are encoded in Oenothera mitochondrial DNA.

The genes coding for tRNA(Gly), tRNA(His), tRNA(Lys), tRNA(Phe), tRNA(Ser) and tRNA(Tyr) have been identified in Oenothera mitochondrial DNA. Sequence analysis of these genes and their surrounding sequences are presented and compared with other known tRNA genes from plant mitochondria. All six deduced tRNA sequences can be folded into the classical cloverleaf structure model. Only the tRNA(His) gene shows high homology with the corresponding chloroplast gene and thus appears to be derived from a transfer event of chloroplast sequences into the mitochondrial genome. The sequences surrounding this gene, however, show little similarity with the chloroplast genome. The other five deduced tRNAs display a much lower similarity with their chloroplast counterparts and thus appear to be genuine mitochondrial tRNAs. These tRNAs are highly conserved between monocots and dicots with maximally three nucleotides differing between the Oenothera sequences and their wheat homologues. A purine-rich sequence is found upstream of each tRNA gene in Oenothera, similar to wheat mitochondrial tRNA genes, that could be involved in transcription signalling.

Base Sequence↗
PubMed2006

Diversity of the abundant pKLC102/PAGI-2 family of genomic islands in Pseudomonas aeruginosa.

The known genomic islands of Pseudomonas aeruginosa clone C strains are integrated into tRNA(Lys) (pKLC102) or tRNA(Gly) (PAGI-2 and PAGI-3) genes and differ from their core genomes by distinctive tetranucleotide usage patterns. pKLC102 and the related island PAPI-1 from P. aeruginosa PA14 were spontaneously mobilized from their host chromosomes at frequencies of 10% and 0.3%, making pKLC102 the most mobile genomic island known with a copy number of 30 episomal circular pKLC102 molecules per cell. The incidence of islands of the pKLC102/PAGI-2 type was investigated in 71 unrelated P. aeruginosa strains from diverse habitats and geographic origins. pKLC102- and PAGI-2-like islands were identified in 50 and 31 strains, respectively, and 15 and 10 subtypes were differentiated by hybridization on pKLC102 and PAGI-2 macroarrays. The diversity of PAGI-2-type islands was mainly caused by one large block of strain-specific genes, whereas the diversity of pKLC102-type islands was primarily generated by subtype-specific combination of gene cassettes. Chromosomal loss of PAGI-2 could be documented in sequential P. aeruginosa isolates from individuals with cystic fibrosis. PAGI-2 was present in most tested Cupriavidus metallidurans and Cupriavidus campinensis isolates from polluted environments, demonstrating the spread of PAGI-2 across habitats and species barriers. The pKLC102/PAGI-2 family is prevalent in numerous beta- and gammaproteobacteria and is characterized by high asymmetry of the cDNA strands. This evolutionarily ancient family of genomic islands retained its oligonucleotide signature during horizontal spread within and among taxa.

Gene Transfer, Horizontal↗
PubMed1995

Rp-phosphorothioate modifications in RNase P RNA that interfere with tRNA binding.

We have used Rp-phosphorothioate modifications and a binding interference assay to analyse the role of phosphate oxygens in tRNA recognition by Escherichia coli ribonuclease P (RNase P) RNA. Total (100%) Rp-phosphorothioate modification at A, C or G positions of RNase P RNA strongly impaired tRNA binding and pre-tRNA processing, while effects were less pronounced at U positions. Partially modified E. coli RNase P RNAs were separated into tRNA binding and non-binding fractions by gel retardation. Rp-phosphorothioate modifications that interfered with tRNA binding were found 5' of nucleotides A67, G68, U69, C70, C71, G72, A130, A132, A248, A249, G300, A317, A330, A352, C353 and C354. Manganese rescue at positions U69, C70, A130 and A132 identified, for the first time, sites of direct metal ion coordination in RNase P RNA. Most sites of interference are at strongly conserved nucleotides and nine reside within a long-range base-pairing interaction present in all known RNase P RNAs. In contrast to RNase P RNA, 100% Rp-phosphorothioate substitutions in tRNA showed only moderate effects on binding to RNase P RNAs from E. coli, Bacillus subtilis and Chromatium vinosum, suggesting that pro-Rp phosphate oxygens of mature tRNA contribute relatively little to the formation of the tRNA-RNase P RNA complex.

Base Sequence↗
PubMed2002

Molecular phylogeny of a circum-global, diverse gastropod superfamily (Cerithioidea: Mollusca: Caenogastropoda): pushing the deepest phylogenetic limits of mitochondrial LSU rDNA sequences.

The Cerithioidea is a very diverse group of gastropods with ca. 14 extant families and more than 200 genera occupying, and often dominating, marine, estuarine, and freshwater habitats. While the composition of Cerithioidea is now better understood due to recent anatomical and ultrastructural studies, the phylogenetic relationships among families remain chaotic. Morphology-based studies have provided conflicting views of relationships among families. We generated a phylogeny of cerithioideans based on mitochondrial large subunit rRNA and flanking tRNA gene sequences (total aligned data set 1873 bp). Nucleotide evidence and the presence of a unique pair of tRNA genes (i.e., threonine + glycine) between valine-mtLSU and the mtSSU rRNA gene support conclusions based on ultrastructural data that Vermetidae and Campanilidae are not Cerithioidea, certain anatomical similarities being due to convergent evolution. The molecular phylogeny shows support for the monophyly of the marine families Cerithiidae [corrected], Turritellidae, Batillariidae, Potamididae, and Scaliolidae as currently recognized. The phylogenetic data reveal that freshwater taxa evolved on three separate occasions; however, all three recognized freshwater families (Pleuroceridae, Melanopsidae, and Thiaridae) are polyphyletic. Mitochondrial rDNA sequences provide valuable data for testing the monophyly of cerithioidean [corrected] families and relationships within families, but fail to provide strong evidence for resolving relationships among families. It appears that the deepest phylogenetic limits for resolving caenogastropod relationships is less than about 245--241 mya, based on estimates of divergence derived from the fossil record.

Animals↗
PubMed1986

Mosquito mitochondrial transfer RNAs for valine, glycine and glutamate: RNA and gene sequences and vicinal genome organization.

We report the sequences of 3 transfer RNAs from mosquito (Aedes albopictus) mitochondria, those for valine (anticodon UAC), glutamic acid (anticodon UUC) and glycine (anticodon UCC), as well as sequences for the corresponding genes and for some neighboring mitochondrial genes. TRNAval is notable for its high level of psi, tRNAglu for its low level of G and C, and tRNAgly is notable in that it appears as two species widely separated in gel electrophoresis, differing only in modification status. TRNAglu is the first sequenced insect mitochondrial tRNA that would be expected to engage in U.R wobble (where U is a modified U in the first position of the anticodon, and R is G or A in the third position of codons), if the insect system followed the modified wobble rules proposed for mammalian and fungal mitochondria; and the sequence determined does fit the proposal. The gene for tRNAval follows immediately that for 12S ribosomal RNA. The gene for tRNAglu occurs in a cluster of 6 tRNA genes that is separated from the gene for tRNAgly by a short reading frame. Features of the DNA sequences are discussed with reference to Drosophila, and mammalian, mitochondrial genome organization.

Aedes↗
PubMed1988

Different mitochondrial gene orders among insects: exchanged tRNA gene positions in the COII/COIII region between an orthopteran and a dipteran species.

We have cloned and sequenced a 2.65 kb segment of the mtDNA molecule of the orthopteran insect Locusta migratoria. It harbors the genes for four mitochondrial tRNAs, for cytochrome c oxidase subunits II and III and for ATPase subunits 6 and 8. The order of the locust genes resembles that of Drosophila yakuba: in both insects the genes for COII and ATPase 8 are separated from each other by the genes encoding tRNA(lys) and tRNA(asp), but in the locust, the positions of the two tRNA genes are reversed. This leads to a different mitochondrial gene order in the two insects.

Amino Acid Sequence↗
PubMedDate not supplied

Population characteristics of Irish Helicobacter pylori isolates: a tRNA-associated locus.

BACKGROUND: A strain-variable transfer RNA-associated-locus (trl) was present in 50% of Irish Helicobacter pylori (H. pylori), isolates and did not correlate with the origin of the isolates. AIM: To associate a particular genotype or phenotype to trl status in H. pylori by further screening the isolates from the original study for the presence of known genotypic and phenotypic characteristics. METHODS: Forty two clinical isolates were screened for the presence of the cagA, vacA, iceA1 and vapD genes by Southern or DNA dot blot analysis. Western blot analysis was performed using antibodies to CagA, VacA, Lewis X (Le(x)) and Lewis Y (Le(y)). Plasmids were identified by the alkaline lysis method. RESULTS: The cagA gene was present in 29 (69%) of isolates screened and 21 (50%) produced the CagA protein. The vacA gene was detected in all of the isolates while VacA was expressed in 71.4%. The iceA1 and vapD loci were detected in 73.8% and 71.4% respectively. Le(x) was expressed in 42.9% and Le(y) in 38.1% of the isolates. Expression of both Lewis antigens was detected in 7.1% while in 30.9% neither antigen was detected. Plasmids were present in 47.6%. There was no association between the trl status of isolates and any of the above. There were no significant associations between the phenotypic and genotypic characteristics studied and peptic ulcer disease or non-ulcer dyspepsia. CONCLUSION: The strain-variable tRNA-associated locus is independent of the vacA/VacA, cagA/CagA, Lewis X, Lewis Y, iceA1, vapD and plasmid status in the population of Irish H. pylori isolates studied.

Bacterial Proteins↗
PubMed1998

Processing of plant mitochondrial tRNAGly and tRNASer(GCU) is independent of RNA editing.

The genes encoding pea and potato mitochondrial tRNAGly and pea mitochondrial tRNASer(GCU) were analyzed with particular respect to their expression. Secondary-structure models deduced from the identical potato and pea tRNAGly gene sequences revealed A7:C66 mismatches in the seventh base pair at the base of the acceptor stems of both tRNAs. Sequence analyses of tRNAGly cDNA clones showed that these mispairings are not corrected by C66 to U66 conversions, as observed in plant mitochondrial tRNAPhe. Likewise, a U6:C67 mismatch identified in the acceptor stem of the pea tRNASer(GCU) is not altered by RNA editing to a mismatched U:U pair, which is created by RNA editing in Oenothera mitochondrial tRNACys. In vitro processing reactions with the respective tRNAGly and tRNASer(GCU) precursors show that such conversions are not necessary for 5' and 3' end maturation of these tRNAs. These results demonstrate that not all C:A (A:C) or U:C (C:U) mismatches in double-stranded regions of tRNAs are altered by RNA editing. An RNA editing event in plant mitochondrial tRNAs is thus not generally indicated by the presence of a mismatch but may depend on additional parameters.

Cloning, Molecular↗
PubMed1989

Genomic organisation of nuclear tRNAGly and tRNALeu genes in Trypanosoma brucei.

We have isolated a 0.3-kb HaeIII restriction fragment from Trypanosoma brucei which contains two tRNA genes. Secondary structure models predict that the two genes identified encode tRNA molecules which specify glycine (anticodon UCC) and leucine (anticodon CAG). The two genes are separated by 86 nucleotides, transcribed in the same direction and contain features of conventional RNA polymerase III transcription units. Southern blot analysis indicates the presence of multicopy tRNa gene families in T. brucei.

Animals↗
PubMed1989

Localization of three DNA segments encompassing tRNA genes to human chromosomes 1, 5, and 16: proposed mechanism and significance of tRNA gene dispersion.

The chromosomal locations of three cloned human DNA fragments encompassing tRNA genes have been determined by Southern analysis of human-rodent somatic cell hybrid DNAs with subfragments from these cloned genes and flanking sequences used as hybridization probes. These three DNA segments have been assigned to human chromosomes 1, 5, and 16, and homologous sequences are probably located on chromosome 14 and a separate locus on chromosome 1. These studies, combined with previous results, indicate that tRNA genes and pseudogenes are dispersed on at least seven different human chromosomes and suggest that these sequences will probably be found on most, if not all, human chromosomes. Short (8-12 nucleotide) direct terminal repeats flank many of the dispersed tRNA genes. The presence of these flanking repeats, combined with the dispersion of tRNA genes throughout the human genome, suggests that many of these genes may have arisen by an RNA-mediated retroposition mechanism. The possible functional significance of this gene dispersion is considered.

Animals↗
PubMed2002

tRNA-mediated transcription antitermination in vitro: codon-anticodon pairing independent of the ribosome.

Uncharged tRNA acts as the effector for transcription antitermination of genes in the T box family in Bacillus subtilis and other Gram-positive bacteria. Genetic studies suggested that expression of these genes is induced by stabilization of an antiterminator element in the leader RNA of each target gene by the cognate uncharged tRNA. The specificity of the tRNA response is dependent on a single codon in the leader, which was postulated to pair with the anticodon of the corresponding tRNA. It was not known whether the leader RNA-tRNA interaction requires additional factors. We show here that tRNA-dependent antitermination occurs in vitro in a purified transcription system, in the absence of ribosomes or accessory factors, demonstrating that the RNA-RNA interaction is sufficient to control gene expression by antitermination. The tRNA response exhibits similar specificity in vivo and in vitro, and the antitermination reaction in vitro is independent of NusA and functions with either B. subtilis or Escherichia coli RNA polymerase.

Anticodon↗