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At least 1,099 records · Page 61Linked to original sources
PubMed1994

A series of integrative plasmids for Bacillus subtilis containing unique cloning sites in all three open reading frames for translational lacZ fusions.

Two sets of three plasmids each were constructed based on integrative plasmids for Bacillus subtilis. Each set encodes resistance to either chloramphenicol or kanamycin. The plasmids contain a cassette consisting of the resistance gene, BamHI and SmaI cloning sites, and the promoterless lacZ gene. The cassette is flanked by the 3' and 5' ends of the amyE gene (encoding amylase) allowing integration of the cassette into that locus in the B. subtilis chromosome. For propagation and selection in Escherichia coli, the plasmids contain the pBR322 origin of replication and the beta-lactamase-encoding gene. Within a set, each of the three plasmids carries the unique SmaI and BamHI restriction sites in a different reading frame relative to the 'lacZ gene. These sets of plasmids allow the easy construction of translational fusions with lacZ and single-copy integration at the amyE locus of B. subtilis.

Amino Acid Sequence↗
PubMed2006

Telomeric silencing of an open reading frame in Saccharomyces cerevisiae.

The endmost chromosome I ORF is silenced by a natural telomere position effect. YAR073W/IMD1 was found to be transcribed at much higher levels in sir3 mutants and when its adjacent telomere was removed from it. These results suggest that telomeres play a role in silencing actual genes.

Base Sequence↗
PubMed2003

Maintenance of the correct open reading frame by the ribosome.

During translation, a string of non-overlapping triplet codons in messenger RNA is decoded into protein. The ability of a ribosome to decode mRNA without shifting between reading frames is a strict requirement for accurate protein biosynthesis. Despite enormous progress in understanding the mechanism of transfer RNA selection, the mechanism by which the correct reading frame is maintained remains unclear. In this report, evidence is presented that supports the idea that the translational frame is controlled mainly by the stability of codon-anticodon interactions at the P site. The relative instability of such interactions may lead to dissociation of the P-site tRNA from its codon, and formation of a complex with an overlapping codon, the process known as P-site tRNA slippage. We propose that this process is central to all known cases of +1 ribosomal frameshifting, including that required for the decoding of the yeast transposable element Ty3. An earlier model for the decoding of this element proposed 'out-of-frame' binding of A-site tRNA without preceding P-site tRNA slippage.

Anticodon↗
PubMed2001

Proteomics reveals open reading frames in Mycobacterium tuberculosis H37Rv not predicted by genomics.

Genomics revealed the sequence of 3924 genes of the H37Rv strain of Mycobacterium tuberculosis. Proteomics complements genomics in showing which genes are really expressed, and here we show the expression of six genes not predicted by genomics, as proved by two-dimensional electrophoresis and matrix-assisted laser desorption ionization and nano-electrospray mass spectrometry.

Amino Acid Sequence↗
PubMed2000

A vestigial X open reading frame in duck hepatitis B virus.

Duck hepatitis B virus (DHBV) appears to lack a homologue of the X protein found in mammalian hepadnaviruses. By replacing stop codons in the corresponding region of the DHBV genome, a hypothetical protein which closely matches the hydrophilicity profile of X proteins can be predicted, despite limited sequence homology. We conclude that a full-length X protein was once a common feature of the hepadnaviruses, conserved in structure but not sequence.

Amino Acid Sequence↗
PubMedDate not supplied

Conservation of an open-reading frame as an element affecting 5' splice site selection.

Splice site selection is a key element of pre-mRNA splicing and involves specific recognition of consensus sequences at the 5(') and 3(') splice sites. Evidently, the compliance of a given sequence with the consensus 5(') splice site sequence is not sufficient to define it as a functional 5(') splice site, because not all sequences that conform with the consensus are used for splicing. We have previously hypothesized that the necessity to avoid the inclusion of premature termination codons within mature mRNAs may serve as a criterion that differentiates normal 5(') splice sites from unused (latent) ones. We further provided experimental support to this idea, by analyzing the splicing of pre-mRNAs in which in-frame stop codons upstream of a latent 5(') splice site were mutated, and showing that splicing using the latent site is indeed activated by such mutations. Here we evaluate this hypothesis by a computerized survey for latent 5(') splice sites in 446 protein-coding human genes. This data set contains 2311 introns, in which we found 10490 latent 5(') splice sites. The utilization of 10045 (95.8%) of these sites for splicing would have led to the inclusion of an in-frame stop codon within the resultant mRNA. The validity of this finding is confirmed here by statistical analyses. This finding, together with our previous experimental results, invokes a nuclear scanning mechanism, as part of the splicing machine, which identifies in-frame stop codons within the pre-mRNA and prevents splicing that could lead to the formation of a prematurely terminated protein.

Algorithms↗
PubMed1999

Compositional correlation between open reading frames with opposite transcriptional orientations in Escherichia coli.

This paper analyzes correlations in base composition between pairs of neighboring genes in Escherichia coli. The G + C contents of nearby, but convergently or divergently transcribed, genes show weak but significant correlations, and this is attributed to compositional variation among genomic regions. The finding that the base composition varies among intergenic regions, depending upon whether the adjacent genes are transcribed convergently, divergently, or in the same orientation, seems to indicate that transcription affects the patterns of mutation and, therefore, the overall base composition of the region.

Base Composition↗
PubMed1993

An open reading frame in the Rhodospirillum rubrum plasmid, pKY1, similar to algA, encoding the bifunctional enzyme phosphomannose isomerase-guanosine diphospho-D-mannose pyrophosphorylase (PMI-GMP).

The nucleotide sequence of a BglII fragment (3188 bp) from the plasmid pKY1 of Rhodospirillum rubrum was determined. A significant similarity was found between the amino acid sequences deduced from the nucleotide sequence of BglII fragment with that of algA, encoding the bifunctional enzyme with both the activities of phosphomannose isomerase and guanosine diphospho-D-mannose pyrophosphorylase of Pseudomonas aeruginosa.

Amino Acid Sequence↗
PubMed2005

Characterization of the Tupaia rhabdovirus genome reveals a long open reading frame overlapping with P and a novel gene encoding a small hydrophobic protein.

Rhabdoviruses are negative-stranded RNA viruses of the order Mononegavirales and have been isolated from vertebrates, insects, and plants. Members of the genus Lyssavirus cause the invariably fatal disease rabies, and a member of the genus Vesiculovirus, Chandipura virus, has recently been associated with acute encephalitis in children. We present here the complete genome sequence and transcription map of a rhabdovirus isolated from cultivated cells of hepatocellular carcinoma tissue from a moribund tree shrew. The negative-strand genome of tupaia rhabdovirus is composed of 11,440 nucleotides and encodes six genes that are separated by one or two intergenic nucleotides. In addition to the typical rhabdovirus genes in the order N-P-M-G-L, a gene encoding a small hydrophobic putative type I transmembrane protein of approximately 11 kDa was identified between the M and G genes, and the corresponding transcript was detected in infected cells. Similar to some Vesiculoviruses and many Paramyxovirinae, the P gene has a second overlapping reading frame that can be accessed by ribosomal choice and encodes a protein of 26 kDa, predicted to be the largest C protein of these virus families. Phylogenetic analyses of the tupaia rhabdovirus N and L genes show that the virus is distantly related to the Vesiculoviruses, Ephemeroviruses, and the recently characterized Flanders virus and Oita virus and further extends the sequence territory occupied by animal rhabdoviruses.

Amino Acid Sequence↗
PubMed2006

Revised model for Enterococcus faecalis fsr quorum-sensing system: the small open reading frame fsrD encodes the gelatinase biosynthesis-activating pheromone propeptide corresponding to staphylococcal agrd.

Gelatinase biosynthesis-activating pheromone (GBAP) is an autoinducing peptide involved in Enterococcus faecalis fsr quorum sensing, and its 11-amino-acid sequence has been identified in the C-terminal region of the 242-residue deduced fsrB product (J. Nakayama et al., Mol. Microbiol. 41:145-154, 2001). In this study, however, we demonstrated the existence of fsrD, encoding the GBAP propeptide, which is in frame with fsrB but is translated independently of fsrB. It was also demonstrated that FsrB', an FsrD segment-truncated FsrB, functions as a cysteine protease-like processing enzyme to generate GBAP from FsrD. This revised model is consistent with the staphylococcal agr system.

Amino Acid Sequence↗
PubMed2004

A previously unidentified MECP2 open reading frame defines a new protein isoform relevant to Rett syndrome.

Rett syndrome is caused by mutations in the gene MECP2 in approximately 80% of affected individuals. We describe a previously unknown MeCP2 isoform. Mutations unique to this isoform and the absence, until now, of identified mutations specific to the previously recognized protein indicate an important role for the newly discovered molecule in the pathogenesis of Rett syndrome.

Base Sequence↗
PubMed2006

An alloplasmic male-sterile line of Brassica oleracea harboring the mitochondria from Diplotaxis muralis expresses a novel chimeric open reading frame, orf72.

Nuclear so-called fertility-restorer genes reverse the pollen sterility of cytoplasmic male-sterile (CMS) plants caused by disturbed mitochondrial-nuclear interactions. We identified a CMS-associated chimeric mitochondrial gene in an alloplasmic CMS line of Brassica oleracea in the 'mur' system. This novel chimeric gene, orf72, was found in the mitochondrial genome of donor cytoplasm. It was located downstream of normal rps7 and contained part of atp9 (atp9-b). It was expressed specifically on the nuclear background of CMS B. oleracea, partially suppressed in the fertility-restored line and entirely suppressed in the cytoplasmic donor.

Amino Acid Sequence↗
PubMed1992

Both open reading frames of the linear plasmid pMC3-2 from the ascomycete Morchella conica are transcribed in vivo.

Mitochondrial RNA was isolated from the morel strain Morchella conica 3 harbouring the linear plasmid pMC3-2 and subjected to gel electrophoresis followed by a Northern analysis using cloned fragments of the plasmid pMC3-2 as probes. Hybridization was obtained only with central parts of pMC3-2 and specific bands of mtRNA. The hybridization bands (2.8 kb and 1.0 kb) correspond in size to the length of the two ORFs of pMC3-2 which were deduced from nucleotide-sequence data. Thus, both ORFs, one encoding a DNA polymerase and the other a yet unknown protein, are transcribed in the mitochondria of the plasmid-bearing Morchella conica strain.

Ascomycota↗
PubMed2002

Highly sensitive assay for human herpesvirus 8 antibodies that uses a multiple antigenic peptide derived from open reading frame K8.1.

The immunodominant region of the human herpesvirus 8 (HHV-8), the antibody-binding site of glycoprotein K8.1A, was mapped to the N-terminal region by using overlapping peptides and a residue replacement method. The main epitope was located within residues 44 to 56 (GQVYQDWL----C). Based on this information, we developed an enzyme immunoassay to detect HHV-8 antibodies in human sera using a four-branch multiple antigenic peptide as the antigen. The sensitivity and specificity of the assay were 96 and 99.4%, respectively. This assay should be useful for population-based, epidemiological studies of HHV-8 infection.

Amino Acid Sequence↗
PubMed1992

Two homologous mitochondrial introns from closely related Saccharomyces species differ by only a few amino acid replacements in their Open Reading Frames: one is mobile, the other is not.

We have undertaken a comprehensive study of the gene conversion of all the mitochondrial introns of Saccharomyces capensis. The approach used involved the measurements of intron transmission amongst the progeny of crosses between a recipient strain (Saccharomyces cerevisiae intronless mitochondria) and various donor strains (Saccharomyces capensis, with various combinations of mitochondrial introns). We have shown that the S. capensis second intron (bi2 of cytochrome b gene) is extremely active as a donor in gene conversion whereas its homologous S. cerevisiae intron is not. Determination of sequence of the S. capensis intron demonstrates that it differs from that of the homologous S. cerevisiae intron (bi2) by a very small number of nucleotide substitutions.

Amino Acid Sequence↗
PubMed1991

Deletion of 55 open reading frames from the termini of vaccinia virus.

Each copy of the inverted terminal repeat of vaccinia virus consists of 8 kb of DNA containing 9 ORFS flanked near the terminus of the genome by 4 kb of repetitive DNA which in turn contains blocks of tandem repeats. Using plasmids containing repetitive DNA as the external arm, we have generated deletions at both the left and the right termini of the vaccinia genome. We report here the engineered deletion within a single vaccinia virus of 32.7 kb of DNA (including 38 ORFS) from the left terminus and 14.9 kb of DNA (including 17 ORFS) from the right terminus.

Base Sequence↗
PubMed1995

Characterization of human aortic smooth muscle cells expressing HPV16 E6 and E7 open reading frames.

A comparative study of human papillomavirus type 16 E6E7-transfected and normal human aortic smooth muscle cells by morphological, electron microscopic, immunofluorescent, and biochemical analyses demonstrated that the E6E7-expressing cells retained much of the phenotype of normal aortic smooth muscle cells, including expression of smooth muscle markers and appropriate growth responses to PDGF and heparin. These cells differed from normal vascular smooth muscle cells in that they had slightly altered morphology and a higher growth rate that was not due to an autocrine response to secreted PDGF, and they contained more polyribosomes than normal smooth muscle cells.

Aorta↗