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At least 1,225 records · Page 68Linked to original sources
PubMed1993

Alterations in DNA sequence and RNA transcription of the Bam HI-H fragment accompany attenuation of oncogenic Marek's disease herpesvirus.

The nucleotide sequences of the BamHI-H fragment of the HPRS16 strain of Marek's disease virus (MDV) and of its attenuated derivative HPRS16/att have been determined. The results show that in addition to the tandem expansion of a 132 bp sequence from two copies in HPRS16 virus to eight copies in HPRS16/att, nucleotide substitutions, deletions, and insertions were also noted. Several potential open reading frames (ORFs) were identified. One of these (ORF 13) encoded a deduced protein, mol wt 32 kD, which is likely to be the serotype-1 specific phosphoprotein expressed in tumours (1) and mapped to an EcoRI fragment within BamHI-H (2). Our results suggest that this ORF is unlikely to be the B antigen (3). ORF 4, which had some similarity to CD4 and immunoglobulin M heavy chain, was encoded by a transcript that originated within the first copy of the 132 bp repeat. ORF 21, which mapped entirely within UL, encoded a deduced protein at least 322 amino acids long that had some similarity to varicella zoster virus (VZV) alpha trans-inducing protein. None of these ORFs was altered significantly by attenuation, except ORF 4 and another small ORF (ORF 3), 5' of the 132 bp repeats, which would probably fail to be transcribed because of truncation of an RNA transcript.

Amino Acid Sequence↗
PubMed1995

Determination and comparative analysis of the small RNA genomic sequences of California encephalitis, Jamestown Canyon, Jerry Slough, Melao, Keystone and Trivittatus viruses (Bunyaviridae, genus Bunyavirus, California serogroup).

The nucleotide sequences of the small (S) genomic RNAs of six California (CAL) serogroup bunyaviruses (Bunyaviridae: genus Bunyavirus) were determined. The S RNAs of two California encephalitis virus strains, two Jamestown Canyon virus strains, Jerry Slough virus, Melao virus, Keystone virus and Trivittatus virus contained the overlapping nucleocapsid (N) and non-structural (NSs) protein open reading frames (ORFs) as described previously for the S RNAs of other CAL serogroup viruses. All N protein ORFs were 708 nucleotides in length and encoded a putative 235 amino acid gene product. The NSs ORFs were found to be of two lengths, 279 and 294 nucleotides, which potentially encode 92 and 97 amino acid proteins, respectively. The complementary termini and a purine-rich sequence in the 3' non-coding region (genome-complementary sense) were highly conserved amongst CAL serogroup bunyavirus S RNAs. Phylogenetic analyses of N ORF sequences indicate that the CAL serogroup bunyaviruses can be divided into three monophyletic lineages corresponding to three of the complexes previously derived by serological classification. The truncated version of the NSs protein, which is found in five CAL serogroup bunyaviruses, appears to have arisen twice during virus evolution.

Amino Acid Sequence↗
PubMed1990

RNA primary sequence or secondary structure in the translational initiation region controls expression of two variant interferon-beta genes in Escherichia coli.

Efficient expression in Escherichia coli (E. coli) of the human interferon-beta gene (IFN-beta) gene and of a chemically synthesized IFN-beta gene variant (506 base pairs; synIFN-beta) adapted to the E. coli codon usage, both fused to the E. coli atpE ribosome-binding site, is controlled either by primary sequence or by mRNA secondary-structure in the translational initiation region. High level expression of the natural human atpE/IFN-beta gene fusion is governed by the nucleotide composition preceding the initiator codon AUG. A single U----C exchange in the -2 or -1 position preceding the initiator codon AUG reduces the translational efficiency from 18% of total cellular protein to only 8% or 4%, respectively, while both U----C substitutions reduce IFN-beta expression below 1%. These sequence alterations interfere with efficient ribosome binding as revealed by toeprinting. They provide further evidence for the influence of the anticodon-flanking regions of tRNA(fMet) upon the initiation rate of translation. In contrast, translation of the synthetic variant atpE/synIFN-beta gene fusion is controlled by a moderately stable stem-loop structure (delta G = -4 kcal/mol; 37 degrees C) located within the coding region and overlapping the 30 S ribosomal subunit attachment site. That the stability of the hairpin interferes with the initiation of translation is inferred from site-directed mutagenesis and toeprint analyses. mRNA half-life in these variants is positively correlated with the rate of translation and involves two major endonucleolytic cleavage site 5'-upstream of the Shine-Dalgarno region.

Base Sequence↗
PubMed1982

Euglena gracilis chloroplast small subunit rRNA. Sequence and base pairing potential of the 3' terminus, cleavage by colicin E3.

RNA sequencing methods have been used to determine sequences at the 3' ends of the small subunit RNAs from Euglena gracilis cytoplasmic and chloroplast ribosomes. The cytoplasmic rRNA sequence, AUCAU psi GOH, has features typical of eukaryotic 18 S rRNAs. The sequence at the 3' terminus of the chloroplast 17 S rRNA, AACAACUCCCOH, differs in several positions from nucleotides conserved in both prokaryotic and eukaryotic small subunit rRNAs, but it does terminate with a pyrimidine tract. Like prokaryotic ribosomes, the chloroplast ribosome displays highly specific binding to purine-rich oligonucleotides. The 30 S subunits select from a random mixture of oligonucleotides only those that contain the sequence GGGAG, which is complementary to the 3' end of 17 S rRNA. The 68S chloroplast ribosome has been shown to be a substrate in vitro for colicin E3. Colicin E3 introduces a cleavage at a position in the chloroplast 17 S rRNA that corresponds exactly to that hydrolyzed in Escherichia coli S rRNA. These results suggest that the 3'-terminal region of 17 S rRNA has an arrangement in the 68 S chloroplast ribosome that may be equivalent to that of the prokaryotic ribosome, with the 3' end exposed in the 30 S subunit for interactions with complementary RNA sequences.

Base Composition↗
PubMed1996

RNA pseudoknot modeling using intersections of stochastic context free grammars with applications to database search.

A model based on intersections of stochastic context free grammars is presented to allow for the modeling of RNA pseudoknot structures. The model runs relatively fast, having the same order running time as stochastic context free grammar parsers. The model is shown to be able to perform database searches and find RNA sequences which resemble RNA pseudoknots which bind biotin. The problem domain of RNA biotin binders has significance in the support of the RNA world model of early life on earth.

Base Sequence↗
PubMed2005

RNALOSS: a web server for RNA locally optimal secondary structures.

RNAomics, analogous to proteomics, concerns aspects of the secondary and tertiary structure, folding pathway, kinetics, comparison, function and regulation of all RNA in a living organism. Given recently discovered roles played by micro RNA, small interfering RNA, riboswitches, ribozymes, etc., it is important to gain insight into the folding process of RNA sequences. We describe the web server RNALOSS, which provides information about the distribution of locally optimal secondary structures, that possibly form kinetic traps in the folding process. The tool RNALOSS may be useful in designing RNA sequences which not only have low folding energy, but whose distribution of locally optimal secondary structures would suggest rapid and robust folding. Website: http://clavius.bc.edu/~clotelab/RNALOSS/.

Algorithms↗
PubMed2004

A short insert in the leader sequence of RNA 3L, a long variant of Alfalfa mosaic virus RNA3, introduces two unidentified reading frames.

N20-RNA 3L, a large form of RNA 3 associated with Alfalfa mosaic virus (AMV) strain N20 comprises 2281 nt and has approximately 97% overall sequence similarity to the longest previously described RNA 3 of AMV strain YSMV (YSMV-RNA 3; 2188 nt). Compared with YSMV-RNA 3, N20-RNA 3L contains an additional 97 nt in the 5' leader upstream of the open reading frames for movement protein (MP) and coat protein (CP). Two overlapping unidentified reading frames (URF1 and URF2) result from this modification, each of which code for putative translation products of 21 amino acids. The URF1 putative peptide has a hydrophilic N-terminus and a hydrophobic C-terminus, indicating a possible association with both host cell membrane and cytosol whereas the putative URF2 product is predominantly hydrophobic. A further structural modification found in N20-RNA 3L is a new tandem repeat of 243 nts which overlaps with the MP open reading frame.

5' Untranslated Regions↗
PubMed1990

RNA enzymes (ribozymes) as antiviral therapeutic agents.

Among the landmark discoveries of recent years are ribozymes, RNA molecules which possess enzymatic, self-cleaving activities. The concept of exploiting the ribozyme catalytic center for cleaving (inactivating) a specific RNA transcript is now emerging as a potential therapeutic or preventative strategy in human diseases, veterinary medicine and agriculture. Linked to the catalytic center of the ribozyme are RNA sequences which are complementary to, and thus serve to target the ribozyme to, a unique RNA sequence. Specific association of the ribozyme with its target via base pairing, cleavage of the RNA substrate and subsequent recycling of the ribozyme make these catalytic RNA molecules attractive as antiviral agents. Theoretically, ribozymes can be adapted for the destruction of any RNA species, whatever its origin.

Animals↗
PubMed1976

3' non-coding region sequences in eukaryotic messenger RNA.

The sequence A-A-U-A-A-A is present in six different purified messenger RNA molecules (specifically the alpha-and beta-globulin mRNAs of rabbit and human, the immunoglobulin light chain mRNA of mouse (MOPC 21) and the ovalbumin mRNA of chicken) about 20 residues away from the 3'-terminal poly (A) sequence. In addition, a large selection of the 3' non-coding regions of rabbit and human globulin mRNAs (both the alpha and beta globin mRNAs) are 85% homologous, demonstrating that this region is significantly conserved in evolution.

Animals↗
PubMed1997

A novel homologue of the prokaryotic htrA gene is differentially expressed in the alga Haematococcus pluvialis following stress.

The alga Haematococcus pluvialis is able to respond to environmental stress by changing from the motile, vegetative green cell form to red stationary aplanospores. This differentiation program is accompanied by dramatic morphological changes that must result, at least in part, from differential gene expression. To begin to identify genes that are differentially expressed as a response to stress, we applied the differential display technique to identify and isolate differentially expressed RNA sequences. Here we report on the isolation and characterization of one such RNA sequence that codes for Haematococcus htrA, a member of a heat shock serine protease family previously described only in prokaryotes. Interestingly, database searches of mouse and human cDNA sequences showed that a previously unreported homologue is also found in a number of tissues. htrA mRNA was not detectable in vegetative cells, but was found at high levels in developing aplanospores. Evidence presented suggests that RNA transcripts encoding this protein are differentially spliced, and that the different splice products are differentially expressed during the developmental process. These experiments provide the groundwork upon which the developmental program of H. pluvialis can be investigated. In addition, they indicate that the htrA family of heat shock serine proteases may play an important role in stress response in higher organisms as well as in bacteria.

Amino Acid Sequence↗
PubMed2000

Phylogenetic relationships of Acanthocephala based on analysis of 18S ribosomal RNA gene sequences.

Acanthocephala (thorny-headed worms) is a phylum of endoparasites of vertebrates and arthropods, included among the most phylogenetically basal tripoblastic pseudocoelomates. The phylum is divided into three classes: Archiacanthocephala, Palaeacanthocephala, and Eoacanthocephala. These classes are distinguished by morphological characters such as location of lacunar canals, persistence of ligament sacs in females, number and type of cement glands in males, number and size of proboscis hooks, host taxonomy, and ecology. To understand better the phylogenetic relationships within Acanthocephala, and between Acanthocephala and Rotifera, we sequenced the nearly complete 18S rRNA genes of nine species from the three classes of Acanthocephala and four species of Rotifera from the classes Bdelloidea and Monogononta. Phylogenetic relationships were inferred by maximum-likelihood analyses of these new sequences and others previously determined. The analyses showed that Acanthocephala is the sister group to a clade including Eoacanthocephala and Palaeacanthocephala. Archiacanthocephala exhibited a slower rate of evolution at the nucleotide level, as evidenced by shorter branch lengths for the group. We found statistically significant support for the monophyly of Rotifera, represented in our analysis by species from the clade Eurotatoria, which includes the classes Bdelloidea and Monogononta. Eurotatoria also appears as the sister group to Acanthocephala.

Acanthocephala↗
PubMed1976

Evolutionary trends in 18S ribosomal RNA nucleotide sequences of rat, mouse, hamster and man.

The large T1 ribonuclease fragments of 18S ribosomal RNA from four mammalian species, rat, mouse, hamster and man, were compared by two-dimensional homochromatography fingerprinting. The nucleotide sequences of the large T1 ribonuclease fragments, polypyrimidines and polypurines which were different among the four mammalian species were determined and compared. The method used for determining nucleotide sequences utilizes 32p-labeling of oligonucleotides at their 5'-termini by polynucleotide kinase, partial digestion by ribonucleases and analysis of labeled spots by homochromatography-fingerprinting. Several examples of point mutations were detected. It was of interest that the 18S rRNA of Chinese hamster has more oligonucleotide sequences in common with those of man that rat or mouse.

Animals↗
PubMed1999

Identification and characterization of T3/T7 bacteriophage-like RNA polymerase sequences in wheat.

Using PCR-based methods, we assembled two wheat cDNA sequences, wheat-G and wheat-C, that encode T3/T7 bacteriophage-like RNA polymerases (RNAPs) sharing 45% amino acid identity. In phylogenetic analyses using maximum likelihood, parsimony and distance methods, the predicted protein sequence of wheat-G (1005 amino acids, 113 kDa) clusters with sequences of previously assigned mitochondrial RNAPs from dicotyledonous plants (Arabidopsis thaliana, Chenopodium album); likewise, in such analyses, the wheat-C sequence (949 amino acids, 107 kDa) affiliates specifically with the Arabidopsis sequence that encodes a phage-like RNAP thought to function in chloroplasts. To confirm biochemically the assignment of the gene encoding the putative wheat mitochondrial RNAP, we isolated a ca. 100 kDa wheat mitochondrial protein that is enriched in fractions displaying specific in vitro transcription activity and that reacts with an antibody raised against a recombinant maize phage-type RNAP. Internal peptide sequence information obtained from the 100-kDa polypeptide revealed that it corresponds to the predicted wheat-G cDNA sequence, providing direct evidence that the wheat-G gene (which we propose to call RpoTm) encodes the wheat mitochondrial RNAP.

Amino Acid Sequence↗
PubMedDate not supplied

[Reaction of pyrophosphorolysis catalyzed by Escherichia coli RNA polymerase].

E. coli RNA polymerase is shown to be capable of catalyzing consecutive DNA-dependent pyrophosphorolysis of RNA in the presence of inorganic pyrophosphate and Mg2+. Active ternary complex of the enzyme with DNA and nascent RNA is needed for the reaction, the mixure of all the components can not carry out pyrophosphorolysis. The reaction was realized in the absence of added nucleoside triphosphates. Nucleoside triphosphates are low molecular mass products of the reaction. The rate of pyrophosphorolysis of the RNA synthesised for the AI promoter of the DNA of wild type T7 phage and delta D III T7 mutant phage was followed as a function of primary structure of the DNA, temperature, ionic strength and inorganic pyrophosphate concentration. The relative rate pyrophosphorolysis for particular nucleotides in different regions of the RNA can differ by several orders of magnitude depending on the primary structure of the RNA that undergoes pyrophosphorolysis. Ternary complex containing partially pyrophosphorilised RNA is active on the RNA synthesis when pyrophosphate is removed and nucleoside triphosphates are added to the reaction mixture. RNA as short as 70-8 nucleotides long can be produced at the conditions used. It seems that efficient dissociation in this region of RNA limits the pyrophosphorolysis to proceed up to the 5' end of RNA. Ternary complex of RNA polymerase with nascent RNA and DNA is shown to undergo site specific dissociation. The specificity of the dissociation is shown to be a function of the primary structure of RNA and the direction of the reaction. Dissociation occurs at different places along RNA sequence when the RNA is synthesised and when it is pyrophosphorilised.

Base Sequence↗
PubMed2003

Intercalation activating fluorescence DNA probe and its application to homogeneous quantification of a target sequence by isothermal sequence amplification in a closed vessel.

We developed a completely homogeneous and isothermal method of detecting RNA sequences and demonstrated ultrarapid and direct quantification of pathogenic gene expression with high sensitivity. The assay is based on performing isothermal RNA sequence amplification in the presence of our novel DNA probe, an intercalation activating fluorescence DNA probe, and measuring the fluorescence intensity of the reaction mixture. When detecting mecA gene expression of methicillin-resistant Staphylococcus aureus, we quantified starting copies ranging from 10 to 10(7) copies within 10min. The primer sequences were designed to bind to secondary structure-free sites of the target RNA, which enabled a totally isothermal protocol to quantify mRNA specifically in a sample of existing genomic DNA. When we applied this to quantifying the expression of marker genes of Vibrio parahaemolyticus and Mycobacterium bovis BCG strain, the results correlated well with the viability of each bacterium. We also demonstrated monitoring Pab gene expression of M. bovis BCG during cultivation with antibiotics. The present method can potentially realize rapid antimicrobial susceptibility testing of slowly growing organisms, such as tuberculosis.

Base Sequence↗
PubMed1989

Nucleotide sequence of potato leafroll luteovirus RNA.

A sequence of 5987 nucleotides is reported for the RNA of potato leafroll luteovirus (PLRV). The sequence contains six large open reading frames, and non-coding regions of 174 nucleotides at the 5' end, 141 nucleotides at the 3' end and 197 nucleotides between two large blocks of coding sequences. The 5' coding region encodes two polypeptides of 28,000 (28K) and 70K which overlap in different reading frames and circumstantial evidence suggests that the third open reading frame in the 5' block is translated by frameshift readthrough near the end of the 70K polypeptide to give a 118K polypeptide. The C-terminal part of the 118K protein contains the consensus sequence for RNA-dependent RNA polymerases. In vitro translation of PLRV RNA resulted in the synthesis mainly of 28K and 70K polypeptides and the largest product made was about 125K; these sizes are similar to those predicted for the translation products of the 5' block of coding sequence. The 3' block of coding sequence codes for three polypeptides: a 23K coat protein, a 17K polypeptide which is encoded in a different frame, and a 53K polypeptide which immediately follows the coat protein coding sequence, and is in the same reading frame. Circumstantial evidence suggests that the 53K polypeptide is translated by readthrough of the amber termination codon of the coat protein gene. The amino acid sequences encoded by the 3' block of coding sequence show many similarities with analogous polypeptides translated from the nucleotide sequences of RNA of barley yellow dwarf virus, PAV strain (BYDV) and, in particular, beet western yellows virus (BWYV). The 118K polypeptide has some similarities with the putative polymerase of southern bean mosaic virus and much more extensive similarities with the corresponding BWYV polypeptide but almost none with that of BYDV. In contrast, the amino acid sequence of the 28K polypeptide is not like that of proteins of the other luteoviruses or of viruses in other groups. The nucleotide sequences reported will appear in the EMBL, GenBank and DDBJ databases under the accession number X14600.

Amino Acid Sequence↗
PubMed1966

Heterogeneity of the conserved ribosomal ribonucleic acid sequences of Bacillus subtilis.

Doi, Roy H. (University of California, Davis), and Richard T. Igarashi. Heterogeneity of the conserved ribosomal ribonucleic acid sequences of Bacillus subtilis. J. Bacteriol. 92:88-96. 1966.-Hybrid formation was demonstrated between Bacillus subtilis ribosomal ribonucleic acid (RNA) and deoxyribonucleic acid (DNA) from various bacterial species. The high degree of complementarity between B. subtilis ribosomal RNA and the DNA from B. cereus and B. stearothermophilus suggested a method to test whether the same RNA sequences were hybridizing with the DNA from these two species. Saturation studies with 16S and 23S RNA preparations from B. subtilis showed that a definite number of complementary sites was present in each DNA. Base composition analyses of the RNA in the hybrid demonstrated that ribosomal RNA sequences were involved. Hybrid competition studies revealed that B. stearothermophilus ribosomal RNA could compete totally against B. subtilis ribosomal RNA for B. stearothermophilus DNA, although it could compete only partially against the B. subtilis ribosomal RNA hybridizing with B. cereus DNA. These observations were made independently with both 16S and 23S ribosomal RNA preparations. These results revealed that different nucleotide sequences of B. subtilis ribosomal RNA were hybridizing with the DNA from B. cereus and B. stearothermophilus. Two possible interpretations of these results are: (i) different nucleotide sequences from a homogeneous ribosomal RNA population are hybridizing with heterologous DNA preparations, and (ii) ribosomal RNA cistrons are heterogeneous.

Adenine↗
PubMed1981

Complementary DNA copies of leukemia and sarcoma virus RNA contain sequences of deoxycytidylate and deoxyguanylate.

Single-stranded complementary DNA (cDNA) of the RNA of Gazdar murine sarcoma virus, Gz-MSV/MuLV; Moloney murine leukemia virus, M-MuLV; mouse mammary tumor virus, MMTV; and simian sarcoma virus, SSV-1, were synthesized in endogenous reverse transcriptase reaction. Gz-MSV/MuLV cDNA was also synthesized in exogenous in vitro reverse transcriptase reactions. In the endogenous reaction, 30-35S, or 6.0- to 7.9-kilobase-length cDNA transcripts were synthesized in high yield. In comparison, transcripts synthesized in exogenous reactions were 6.7S, or 0.39 kilobases. The complementarity of the transcripts was verified by both RNA/DNA hybridization and protection studies. dG and dC sequences were detected in 50-77% of the cDNA molecules by affinity chromatography, by annealing and masking studies, and by resistance to S1 nuclease. dT and dA sequences were not detected in the transcripts. These findings are discussed in relation to the possible selective blocking of transcription of retrovirus genes without interfering significantly with the transcription of cellular genes.

Base Sequence↗