SEARCH · PubMed Health

Results for “RNA, Transfer, Val”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 91 records · Page 5Linked to original sources

PubMed1993

Identification of a tRNA-like molecule that copurifies with the 7SL RNA of Trypanosoma brucei.

During the purification of Trypanosoma brucei 7SL RNA, we detected a small RNA, 76 nucleotide-long (sRNA-76), that copurified with the 7SL RNP through several different separation steps. In this study, a partial RNA sequence of sRNA-76 was obtained and a complementary oligonucleotide to the RNA sequence was used to clone the corresponding gene. sRNA-76 is very similar to a tRNA molecule and is encoded by a single copy gene. The gene is located next to a tRNA(Val) which has 75.3% homology to T. brucei tRNA(Val) that exists in a different chromosomal locus. The highest homology of sRNA-76 is to mouse and rat tRNA(Asp) (69%), to mouse tRNA(Gly) (68.1%) and to yeast suppressor tRNA(Gly) (69.5%). However, sRNA-76 is neither a tRNA(Asp) nor a tRNA(Gly), since it has a Leu anticodon. In addition, sRNA-76 deviates from the canonical tRNA structure in 3 positions. A potential for base pairing between sRNA-76 and 7SL RNA was found in the 100 nt region of 7SL RNA, which is a highly conserved region in all 7SL RNAs.

Animals↗

PubMed2001

Transport of intracellularly active ribozymes to the cytoplasm.

Ribozymes are RNA molecules with enzymatic activity which selectively bind and cleave specific target RNAs. To date, numerous studies directed toward the application of ribozymes in vivo have been performed and many successful experiments have been reported. However, to induce high-level activities of ribozymes in vivo, several factors must be considered. Here we report that the cytoplasmic localization of ribozymes is important for their intracellular activity in mammalian cells. Northern blot analysis revealed that a tRNA(Val) ribozyme, which can assume a cloverleaf structure similar to that of a native tRNA, is efficiently transported to the cytoplasm. In contrast, the tRNAiMet-driven ribozyme, which does not maintain the cloverleaf structure, remained predominantly in the nucleus. In correlation with the localization, the activity of the exported ribozyme was higher than that of the ribozyme retained in the nucleus. These results should provide insight into the design of ribozymes that have high-level activity in mammalian cells.

Base Sequence↗

PubMed1989

Genes, variant genes and pseudogenes of the human tRNA(Val) gene family. Expression and pre-tRNA maturation in vitro.

Nine different members of the human tRNA(Val) gene family have been cloned and characterized. Only four of the genes code for one of the known tRNA(Val) isoacceptors. The remaining five genes carry mutations, which in two cases even affect the normal three-dimensional tRNA structure. Each of the genes is transcribed by polymerase III in a HeLa cell nuclear extract, but their transcription efficiencies differ by up to an order of magnitude. Conserved sequences immediately flanking the structural genes that could serve as extragenic control elements were not detected. However, short sequences in the 5' flanking region of two genes show striking similarity with sequences upstream from two Drosophila melanogaster tRNA(Val) genes. Each of the human tRNA(Val) genes has multiple, i.e. two to four, transcription initiation sites. In most cases, transcription termination is caused by oligo(T) sequences downstream from the structural genes. However, the signal sequences ATCTT and CTTCTT also serve as effective polymerase III transcription terminators. The precursors derived from the four tRNA(Val) genes coding for known isoacceptors and those derived from two mutant genes are processed first at their 3' and subsequently at their 5' ends to yield mature tRNAs. The precursor derived from a third mutant gene is incompletely maturated at its 3' end, presumably as a consequence of base-pairing between 5' and 3' flanking sequences. Finally, precursors encoded by the genes that carry mutations affecting the tRNA tertiary structure are completely resistant to 5' and 3' processing.

Base Sequence↗

PubMed2000

Evolution of the family of pRN plasmids and their integrase-mediated insertion into the chromosome of the crenarchaeon Sulfolobus solfataricus.

Plasmid pHEN7 from Sulfolobus islandicus was sequenced (7.83 kb) and shown to belong to the archaeal pRN family, which includes plasmids pRN1, pRN2, pSSVx and pDL10 that share a large conserved sequence region. pHEN7 is most closely related to pRN1 in this conserved region. It also shares a large variant region containing several homologous genes with pDL10, which is absent from the other plasmids. The variant region is flanked by the sequence motif TTAGAATGGGGATTC and similar duplicated motifs occur in plasmids pRN1 and pRN2, separated by a few bases. It is inferred that recombination at these sites produces the main genetic variability in the plasmid family. The conserved region of the plasmid, and duplicated copies of the motif, are also present in the genome of Sulfolobus solfataricus P2. Moreover, they are bordered by a partitioned integrase gene (int) and by a 45 bp perfect direct repeat corresponding to the downstream half of a tRNA(Val) gene. The integrase and the direct repeat are highly similar in sequence to the integrase and the chromosomal integration site (att), respectively, of the SSV1 virus, which integrates into the chromosome of Sulfolobus shibatae. Recombination at the att repeats in S. solfataricus would produce a novel plasmid, pXQ1, which carries both an intact integrase gene and a single integration site (att). This strongly suggests that the same mechanism of site-specific integration at a tRNA gene is used for both viruses and plasmids in Sulfolobus.

Attachment Sites, Microbiological↗

PubMed2004

Childhood neurological presentation of a novel mitochondrial tRNA(Val) gene mutation.

We describe a young girl with a novel 1659T>C mutation in the tRNA(Val) gene of mitochondrial DNA (mtDNA) who presented with learning difficulties, hemiplegia, and a movement disorder, together with a raised cerebrospinal fluid (CSF) lactate. The mutation, which was present at high levels of heteroplasmy in patient tissues, interrupts a conserved Watson-Crick basepair in the TPsiC stem and has not previously been described in controls. This report further confirms the frequent association of mitochondrial tRNA mutation with neurological presentations, even in paediatric cases.

Adolescent↗

PubMed2000

tRNA recognition of tRNA-guanine transglycosylase from a hyperthermophilic archaeon, Pyrococcus horikoshii.

In the biosynthesis of archaeosine, archaeal tRNA-guanine transglycosylase (TGT) catalyzes the replacement of guanine at position 15 in the D loop of most tRNAs by a free precursor base. We examined the tRNA recognition of TGT from a hyperthermophilic archaeon, Pyrococcus horikoshii. Mutational studies using variant tRNA(Val) transcripts revealed that both guanine and its location (position 15) were strictly recognized by TGT without any other sequence-specific requirements. It appeared that neither the global L-shaped structure of a tRNA nor the local conformation of the D loop contributed to recognition by TGT. A minihelix composed of the acceptor stem and D arm of tRNA(Val), designed as a potential minimal substrate, failed to serve as a substrate for TGT. Only a minihelix with mismatched nucleotides at the junction between the two domains served as a good substrate, suggesting that mismatched nucleotides in the helix provide the specific information that allows TGT to recognize the guanine in the D loop. Our findings indicate that the tRNA recognition requirements of P. horikoshii TGT are sufficiently limited and specific to allow the enzyme to recognize efficiently any tRNA species whose structure is not fully stabilized in an extremely high temperature environment.

Anticodon↗

PubMed1989

The modulatory element TNNCT affects transcription of a Drosophila tRNA(Val)4 gene without affecting transcription complex stability.

We have previously identified a sequence of the general form TNNCT in the 5'-flanking region of a Drosophila melanogaster tRNA(Val)4 gene which positively modulates in vitro transcription. The pentadeoxynucleotide is also present in the 5'-flank of other Drosophila tRNA genes which direct transcription efficiently in vitro. We have examined transcription of a mutant of this gene further to understand the role of the TNNCT sequence. When template competition experiments were carried out, a template which contained mutations in TNNCT was a better competitor than was the wildtype template. The time-course of transcription and the effects of temperature and ionic strength on transcription indicated that mutating the TNNCT did not alter the efficiency of stable complex formation. It is proposed that the pentadeoxynucleotide TNNCT may influence the rate of transcription initiation by RNA polymerase III bound to transcription complexes.

Animals↗

PubMed2003

The anticodon and the D-domain sequences are essential determinants for plant cytosolic tRNA(Val) import into mitochondria.

In higher plants, one-third to one-half of the mitochondrial tRNAs are encoded in the nucleus and are imported into mitochondria. This process appears to be highly specific for some tRNAs, but the factors that interact with tRNAs before and/or during import, as well as the signals present on the tRNAs, still need to be identified. The rare experiments performed so far suggest that, besides the probable implication of aminoacyl-tRNA synthetases, at least one additional import factor and/or structural features shared by imported tRNAs must be involved in plant mitochondrial tRNA import. To look for determinants that direct tRNA import into higher plant mitochondria, we have transformed BY2 tobacco cells with Arabidopsis thaliana cytosolic tRNA(Val)(AAC) carrying various mutations. The nucleotide replacements introduced in this naturally imported tRNA correspond to the anticodon and/or D-domain of the non-imported cytosolic tRNA(Met-e). Unlike the wild-type tRNA(Val)(AAC), a mutant tRNA(Val) carrying a methionine CAU anticodon that switches the aminoacylation of this tRNA from valine to methionine is not present in the mitochondrial fraction. Furthermore, mutant tRNAs(Val) carrying the D-domain of the tRNA(Met-e), although still efficiently recognized by the valyl-tRNA synthetase, are not imported any more into mitochondria. These data demonstrate that in plants, besides identity elements required for the recognition by the cognate aminoacyl-tRNA synthetase, tRNA molecules contain other determinants that are essential for mitochondrial import selectivity. Indeed, this suggests that the tRNA import mechanism occurring in plant mitochondria may be different from what has been described so far in yeast or in protozoa.

Acylation↗

PubMedDate not supplied

Block-units method for conformational calculations of large nucleic acid chains. II. The two-hierarchical approach and its application to conformational arrangement of the unusual T psi C loop of rabbit tRNA(Val).

The two-level hierarchical methodology is suggested for conformational calculations of large fragments of nucleic acids. The method of the first level is intended for performing a fast screening of the conformational phase space. The high-level method may be used to refine structurally important conformations. The method of the first level is the block-units method, which has been developed specially for these purposes (see part I). It has been shown that the block-units method allows the satisfactory calculation of the structure parameters of the optimal conformations of polynucleotides. The results of the conformational rearrangement calculations of the T psi C loop of the tRNA(Phe) after modification of its sequence are represented.

Animals↗

PubMed2004

A multiplex PCR assay for the identification of animal species in feedstuffs.

A multiplex Polymerase Chain Reaction (PCR) assay was applied to feedstuff analysis for the identification of the most used species in rendering plants (ruminant, poultry, fish and pork materials). Primers were designed in different regions of mitochondrial DNA (12S rRNA, tRNA Val and 16S rRNA) after alignment of the available sequences in the GenBank database. The primers generated specific fragments of 104-106, 183, 220-230 and 290 bp length for ruminants, poultry, fish and pork, respectively. The detection limit was 0.004% for fish primers and 0.002% for ruminants, poultry and pork primers. The multiplex PCR proposed in this study can be considered a valid alternative to the microscopic method for the detection of animal derived materials banned by a European Union Regulation as a preventive measure against the spread of Bovine Spongiform Encephalopathy.

Animal Feed↗

PubMed2002

Impaired expression of a human septin family gene Bradeion inhibits the growth and tumorigenesis of colorectal cancer in vitro and in vivo.

We have identified a novel human septin family gene Bradeion, which is specifically expressed in human colorectal cancer and malignant melanoma. In order to analyze the implications of tumor-specific gene expression, ribozymes and its derivatives were specifically designed and transfected into various colorectal adenocarcinoma cell lines for Bradeion inactivation. We constructed ribozyme expression plasmids controlled by a human tRNA(Val) promoter, and both hammerhead ribozyme and its allosteric derivative maxizyme were used for two different forms of Bradeion mRNA. The sequence-specific cleavage of Bradeion mRNA resulted in significant growth inhibition and G2 arrest in human cancer cell lines, detected by flow cytometry analysis. In addition, in vivo mice studies demonstrated marked tumor growth suppression by the Bradeion-specific ribozymes. Thus, the tumor-specific and selective marker Bradeion also provides valuable tools as a potential target for colorectal cancer therapy.

Animals↗

PubMed2005

Construction of a functional transporter analysis system using MDR1 knockdown Caco-2 cells.

PURPOSE: The efflux transporter, P-glycoprotein (P-gp), located in the brush-border membrane of intestinal absorptive cells, reduces the bioavailability of a wide range of orally administered drugs. Using P-gp inhibitors in transport experiments in Caco-2 cell monolayers is widely accepted as an efficient way to estimate the contribution of P-gp to the intestinal absorption of drugs. However, there still remain some arguments that the inhibitors might affect the function of other proteins. Multidrug resistance 1 gene (MDR1) specifically inhibited Caco-2 cells were constructed, therefore, as a better in vitro evaluation system of intestinal drug absorption. METHODS: The effective sites of RNAi were selected using siRNA libraries and single siRNAs and MDR1 stable knockdown Caco-2 cells were constructed using a tRNA(val)-shRNA expression vector. RESULTS: In siRNA stably expressed Caco-2 cells, the expression level of MDR1 was reduced at mRNA and protein levels. Transcellular transport studies using digoxin revealed that the P-gp function was suppressed completely, similar to that in verapamil-treated cells. CONCLUSIONS: MDR1 stable knockdown Caco-2 cells were successfully constructed by RNAi technology. This will consequently allow the development of a selection system for candidate drugs with improved absorption properties.

Biological Transport, Active↗

PubMed1974

Mercury(II) binding to s4U in E. coli tRNA(Val).

The accessibility of the s(4)U base in native tRNA(Val) from E.coli was monitored by studying the binding of various mercurials. The relative binding order HgBr(2)[unk]HgCl(2)>>CH(3)HgOAc[unk]CH(3)HgCl[unk]PCMB parallels approximately the steric requirements of linear HgX(2) or RHgX compounds for S(N)2 displacement by sulfur, although other factors are operative. Para-chloromercuri-benzoate (PCMB) does not bind the thiolated nucleotide unless the tertiary structure of the tRNA is opened up by removal of Mg(2+) ions and heating to 40 degrees . Under these conditions, equilibrium dialysis measurements using (14)C-labeled PCMB showed one binding site (n = 0.93) with an association constant, K(1), of 9 x 10(4)M(-1).

Binding Sites↗

PubMed2005

Molecular phylogeny and stripe pattern evolution in the cardinalfish genus Apogon.

Cardinalfishes of the genus Apogon (Apogonidae) are one of the most speciose (>200 species) and numerically dominant fishes in coral reefs. Although the genus is divided into 10 subgenera, more than 70% of the species are included in the subgenus Ostorhinchus, most having either horizontal or vertical lines on the body. The phylogenetic relationship among 32 species of subgenus Ostorhinchus and 11 species of four other subgenera of Apogon, based on mitochondrially encoded 12S and 16S ribosomal genes and intervening tRNA(Val) gene, were investigated, using two species of the apogonid genus Fowleria as outgroups. The analyses demonstrated that Ostorhinchus (the most speciose subgenus) was polyphyletic, comprising at least three lineages, Ostorhinchus I, II, and III. Ostorhinchus I included two species, A. (O.) amboinensis and A. (O.) sangiensis, being a sister group to subgenus Zoramia. Ostorhinchus II and III included species with horizontal and vertical lines on the body, respectively. The respective monophylies of the latter two groups, together with a molecular clock calibration, indicated that in the evolutionary history of the genus, basic stripe patterns evolved first (more than 20 million years BP), with subsequent pattern diversification and modification.

Animals↗

PubMed2000

Misactivated amino acids translocate at similar rates across surface of a tRNA synthetase.

Certain aminoacyl-tRNA synthetases have a second active site that destroys (by hydrolysis) errors of amino acid activation. For example, isoleucyl-tRNA synthetase misactivates valine (to produce valyl adenylate or Val-tRNA(Ile)) at its active site. The misactivated amino acid is then translocated to an editing site located >25 A away. The role of the misactivated amino acid in determining the rate of translocation is not known. Valyl-tRNA synthetase, a close homolog of isoleucyl-tRNA synthetase, misactivates threonine, alpha-aminobutyrate, and cysteine. In this paper, we use a recently developed fluorescence-energy-transfer assay to study translocation of misactivated threonine, alpha-aminobutyrate, and cysteine. Although their rates of misactivation are clearly distinct, their rates of translocation are similar. Thus, the rate of translocation is independent of the nature of the misactivated amino acid. This result suggests that the misactivated amino acid per se has little or no role in directing translocation.

Amino Acids↗

PubMed1991

Identity determinants of E. coli tRNA(Val).

In order to study the identity elements of valine tRNA, various transcripts of E. coli valine tRNA mutants were constructed. Both mutations at the second letter A35 of the anticodon and at the discriminator base A73 seriously damaged valine charging activity. Mutations at either the G3-C70 or U4-A69 base pairs in the acceptor stem also affected the activity. Only one nucleotide substitution of the second letter G35 of the anticodon with A35 brought an 18% valine charging activity into alanine tRNA, which acquired an almost full charging activity with valine by introducing an additional change at those two base pairs in the acceptor stem. These results indicate that the second letter A35 of the anticodon, discriminator base and acceptor stem are involved in recognition by valyl-tRNA synthetase.

Base Composition↗

PubMed1992

Constraints on the evolution of plastid introns: the group II intron in the gene encoding tRNA-Val(UAC).

The evolution of the group II intron in the plastid gene encoding tRNA(Val)UAC (trnV) from seven plant taxa was studied by aligning secondary and other structural features. Levels of evolutionary divergence between six angiosperms and a liverwort, Marchantia polymorpha, were compared for the six domains commonly demonstrated for group II introns and were shown to be statistically heterogeneous. Evolutionary rates varied substantially among various domains and other features. Domain II showed the highest evolutionary rate, approaching the synonymous substitution rate reported for cpDNA-encoded genes, while domain VI and the helix and loop region bearing EBS1 evolved at rates similar to those for nonsynonymous substitutions of a number of cpDNA-encoded genes. The minimum free-energy structure of domain I varied among the seven taxa, suggesting that possible protein-RNA or tertiary interactions are important for intron processing.

Base Sequence↗

PubMed2003

Inhibition of type I procollagen production by tRNAVal CTE-HSP47 ribozyme.

BACKGROUND: Fibrosis characteristically occurs in the advanced stages of chronic inflammatory diseases, occasionally as the primary lesion, and frequently determines the disease prognosis. Fibrotic lesions consist mostly of collagen, and therefore it may be possible to prevent or treat fibrosis by inhibiting collagen production. Of the currently available therapeutic approaches, however, none is sufficiently effective and specific for inhibition of collagen. Heat shock protein 47 (HSP47) is a collagen-specific molecular chaperone that has been reported to play a pivotal role in secretion of procollagen molecules. Therefore, we have tried to suppress its function to inhibit these various types of collagen. METHODS: We have developed a novel type of ribozyme by ligating a hammerhead sequence to a tRNA(Val) promoter to facilitate displacing the ribozyme from nucleus to cytoplasm and to constitutive transport element, a binding motif of helicase which unwinds mRNA to render the target sequence on the mRNA accessible to the ribozyme. RESULTS: The ribozyme thus constructed showed strong activity to cleave HSP47 mRNA and suppress the secretion of type I procollagen in the human primary fibroblast. CONCLUSION: We suggest applicability of this ribozyme as a new modality for antifibrosis therapy.

Antisense Elements (Genetics)↗