Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Reading Frames”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

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

At least 199 records · Page 11Linked to original sources
PubMed1984

Birth of a unique enzyme from an alternative reading frame of the preexisted, internally repetitious coding sequence.

The mechanism of gene duplication as the means to acquire new genes with previously nonexistent functions is inherently self limiting in that the function possessed by a new protein, in reality, is but a mere variation of the preexisted theme. As the source of a truly unique protein, I suggest an unused open reading frame of the existing coding sequence. Only those coding sequences that started from oligomeric repeats are likely to retain alternative long open reading frames. Analysis of the published base sequence residing in the pOAD2 plasmid of Flavobacterium Sp. K172 indicated that the 392-amino acid-residue-long bacterial enzyme 6-aminohexanoic acid linear oligomer hydrolase involved in degradation of nylon oligomers is specified by an alternative open reading frame of the preexisted coding sequence that originally specified a 472-residue-long arginine-rich protein.

Amidohydrolases↗
PubMed1993

Sequence of a 4.8 kb fragment of Saccharomyces cerevisiae chromosome II including three essential open reading frames.

The nucleotide sequence of a fragment of 4867 base pairs of Saccharomyces cerevisiae chromosome II has been determined. The sequence contains three complete open reading frames. In addition to the already known gene RPB5, coding for a subunit shared by all three DNA directed RNA polymerases, two new open reading frames could be identified. YBR12.03 codes for a protein of 183 amino acids with homology to one of the proteins of the Bacillus subtilis riboflavin biosynthesis operon (RibG). Deletion mutants of YBR12.03 can germinate but stop growing after five to seven cell divisions on YPD. Supplementation with high concentrations of riboflavin does promote growth. YBR12.05 codes for a protein of 386 amino acids with homology to STI1, a stress-inducible protein of S. cerevisiae. Deletion mutants of YBR12.05 are not viable.

Amino Acid Sequence↗
PubMed2026

Auditing bacterial dark-gene screens for superimposed open reading frame artefacts: A multi-layer analysis of Rv2438A in Mycobacterium tuberculosis.

Essentiality and knockdown-vulnerability screens can promote spurious bacterial open reading frames when those frames overlap essential genes, because such a frame inherits its neighbour's signals undiluted and therefore satisfies the screen's criteria better than a genuine small gene. We present a multi-layer audit that tests this failure mode across genome annotation, transposon mutagenesis, CRISPR interference, homology, transcript mapping, proteomics, and population variation. We apply it to Rv2438A, a 92-codon conserved hypothetical open reading frame of Mycobacterium tuberculosis ranked first by our own dark-gene target screen. Rv2438A is superimposed on the essential NAD synthetase locus nadE: 44% lies within its coding sequence on the opposite strand, and the remainder covers its promoter and transcription start site. Consequently, three of five Himar1 sites lie within nadE, no CRISPRi guide can target Rv2438A without binding nadE, and the cross-species hit maps to the same nadE start junction. Rv2438A lacks its own transcription start site and is absent from every proteomic dataset that detects nadE. A genome-wide scan identifies six short, overlapping, uncharacterised loci among 3907 annotated genes, but only Rv2438A combines overlap and essentiality with non-detection across all proteomic datasets; rare genome-wide, it ranked first among screen hits. We provide an implementable audit workflow and a codon-position control, but measure the control's sensitivity as only two of five genes with attested protein, limiting it to confirmatory use. Overlap coordinates and neighbour-specific experimental resolution should therefore be reported before bacterial dark genes are prioritised.

CRISPR interference↗
PubMed1995

Sequence analysis of a 9873 bp fragment of the left arm of yeast chromosome XV that contains the ARG8 and CDC33 genes, a putative riboflavin synthase beta chain gene, and four new open reading frames.

The DNA sequence of a 9873 bp fragment located near the left telomere of chromosome XV has been determined. Sequence analysis reveals seven open reading frames. One is the ARG8 gene coding for N-acetylornithine aminotransferase. Another corresponds to CDC33, which codes for the initiation factor 4E or cap binding protein. The open reading frame AOE169 can be considered as the putative gene for the Saccharomyces cerevisiae riboflavin synthase beta chain, since its translation product shows strong homology with four prokaryotic riboflavin synthase beta chains.

Amino Acid Sequence↗
PubMed1994

Murine fibroblast growth factor receptor 1 gene generates multiple messenger RNAs containing two open reading frames via alternative splicing.

The arrangement of exons and introns encoding 5'-side of murine fibroblast growth factor (FGF) receptor 1 (FGFR-1) gene was mapped. A large intron with a size of 14 kb was identified between exon 1 and exon 2. In addition, all FGFR-1 subtypes including a unique variant form with 12 amino acids insertion and two amino acids deletion were observed to be able to be generated through alternative splicing. Furthermore, complete sequencing of the 5'-region of FGFR-1 mRNA revealed that a relatively large open reading frame precedes the major open reading frame encoding FGFR-1. These results indicate that FGFR-1 mRNAs are uniquely translated from an internal translation start site.

3T3 Cells↗
PubMed2001

Lupus autoantibodies recognize the product of an alternative open reading frame of SmB/B'.

An unusual feature of the gene for the spliceosomal protein SmB/B' is the presence of an unusually long alternative open reading frame (aORF) which could encode 220 amino acids. We cloned and expressed this aORF protein and used immunological assays to determine its antigenicity in patients with systemic lupus. Sera from 10 of 22 (46%) anti-Sm positive lupus patients showed significant binding to the SmB' aORF protein by ELISA while neither the normal controls nor anti-Sm negative lupus patient controls showed significant reactivity. Antigenicity of the SmB' aORF protein was further localized to the C-terminus using a deletion construct. This is the first known example in which the product of an alternative open reading frame acts as an autoantigen in human disease. These results are consistent with the possibility that generation of anti-Sm autoantibodies in a subset of lupus patients is due to abnormal processing and expression of an aORF SmB/B' message, by an as yet unidentified mechanism.

Adult↗
PubMed1990

Nucleotide sequence of hog cholera virus RNA: properties of the polyprotein encoded by the open reading frame spanning the viral genomic RNA.

Hog cholera virus RNA was cloned and sequenced. A single major open reading frame (ORF), encoding an amino acid sequence of 3898 residues, was found in the second reading frame of the sequence of one of the cDNA strands. We demonstrated that the ORF spans the length of the viral sense RNA, which implies that it is translated into a precursor polyprotein. Several properties of this polyprotein, like hydrophobicity, position of putative protease cleavage sites, distribution of N-linked glycosylation sites, distribution of cysteines and distribution of acidic and basic residues are described and discussed.

Amino Acid Sequence↗
PubMed1995

Translation of the open reading frame encoded by comS, a gene of the srf operon, is necessary for the development of genetic competence, but not surfactin biosynthesis, in Bacillus subtilis.

A small open reading frame, comS of the srf operon, is the site of mutations that impair competence development in Bacillus subtilis. comS open reading frame translation was required for competence, as was confirmed by the suppression of a comS amber mutation [comS(Am)] by the nonsense suppressor sup-3. comS(Am), when introduced into the srf operon, eliminated late competence gene expression but had no significant effect on surfactin production.

Amino Acid Sequence↗
PubMed1987

Mutation to male fertility and toxin insensitivity in Texas (T)-cytoplasm maize is associated with a frameshift in a mitochondrial open reading frame.

Tissue culture-derived mutants of male-sterile and disease toxin-sensitive Texas (T)-cytoplasm maize that exhibit male fertility and toxin insensitivity carry numerous alterations in mitochondrial DNA. In these mutants, a 6.7-kilobase Xho I fragment characteristic of parental T cytoplasm has been rearranged. In the mutant T-4, the parental 6.7-kilobase Xho I fragment contains a guanine to adenine transition adjacent to a 5-base-pair insertion not found in T cytoplasm. The insertion, internal to a 345-base-pair open reading frame (T ORF13), generates a frameshift, resulting in a premature stop codon that terminates the open reading frame at base pair 222. In other mutants, the 345-base-pair ORF is part of a 3-kilobase deletion, which extends into a 5-kilobase repeat characteristic of mtDNA from T but not N male-fertile cytoplasm. Clones specific to T ORF13 hybridize to eight transcripts in T and T-4, yet only hybridize to three transcripts in T-7, a deletion mutant. Transcription of the T ORF13 region appears not to be altered in T-4, but the frameshift mutation in the T ORF13 reading frame indicates that a biologically inactive gene product could be associated with the mutational events. The results suggest that cytoplasmic male sterility and disease toxin sensitivity may be associated with presence of T ORF13 in T-cytoplasm maize.

Journal Article↗
PubMed1995

Transcriptional analysis of the short segment of the feline herpesvirus type 1 genome and insertional mutagenesis of a unique reading frame.

Transcription mapping was performed in the short region of the feline herpesvirus type 1 (FHV-1) genome as a first approach to the functional analysis of open reading frames encoding the homologs of the herpes simplex virus type 1 (HSV-1) gD, gl, gE, US9, and probably also US8.5. All reading frames appeared to be transcribed. Transcripts were grouped into two nested RNA sets; namely, the coterminal transcripts of gD and gl and the coterminal transcripts of gE, US8.5, and US9. This situation was similar to that found in the equivalent region of HSV-1. The FHV-1 ORFs US8.5 and US9 have not been described previously. Sequence analysis and comparison of the putative polypeptide encoded by US8.5 revealed that this ORF was unique to FHV-1. However, US8.5 of FHV-1 might be functionally related to its positional homologs in HSV-1 and equine herpesvirus type 1. In all three viruses, US8.5 does not seem to be critical for virus propagation in cell culture. This was shown for FHV-1 by isolating a mutant containing an insertion in US8.5 and comparing its growth properties in cell culture to those of the parent virus G2620. With regard to US9, conscientious amino acid sequence alignment of FHV-1 US9 and homologs in related herpesviruses suggests that this particular protein could contribute to the virus infectivity in vivo. This speculation was based on the highly conserved C-terminus of US9, starting with a characteristic YYSES motif and followed by a nuclear target sequence and a transmembrane region.

Alphaherpesvirinae↗
PubMed2003

The upstream open reading frame mediates constitutive effects on translation of cytochrome p-450c27 from the seventh in-frame AUG codon in rat liver.

The 2.3-kb mRNA that codes for cytochrome P-450c27 (CYP27) has an unexpectedly long 5'-untranslated region (UTR) that holds six AUGs, leading to several upstream open reading frames (uORFs). The initiation of translation from the seventh AUG forms a putative 55-kDa precursor, which is processed in mitochondria to form a 52-kDa mature protein. The first three AUGs form fully overlapping uORF1, uORF2, and uORF3 that are in-frame with the seventh AUG and next two form fully overlapping uORF4 and uORF5 that are out-of-frame with the seventh AUG. Although not recognized by the scanning ribosomes under normal conditions, the sixth in-frame AUG forms a putative 57-kDa extension of the main open reading frame. The purpose of this study was to identify the elements in the 5'-UTR that direct CYP27 mRNA translation exclusively from the seventh AUG. Expression of 5' deletion mutants in COS cells reveal that the intact 5'-UTR not only directs the initiation of translation from the seventh AUG but also acts as a negative regulator. A 2-kb deletion mutant that lacks uORF1 initiates translation equally from the sixth and the seventh AUGs, forming both 57- and 55-kDa precursor proteins with a 2-fold increase in rate of translation. However, induction in translation does not affect the levels of the mature 52-kDa form in mitochondria but causes accumulation of the precursor form in cytosol not seen in COS cells transfected with wild-type cDNA. Mutation of the stop codon that terminates uORF1 completely shifts the initiation of translation from the seventh to the first AUG, forming a 67-kDa precursor that is processed into a 52-kDa mature protein in mitochondria. Confirmation of the bicistronic nature of CYP27 mRNA by epitope mapping of uORF1 suggests that translation of CYP27 mRNA from the seventh AUG is directed and regulated by uORF1 expression.

5' Untranslated Regions↗
PubMed1994

The urease structural gene ureA in Rhizobium meliloti is preceded by an open reading frame necessary for urease activity.

An open reading frame (ORF1) located upstream of the urease structural gene ureA in Rhizobium meliloti strain AK631 was cloned and characterized by DNA sequencing. Comparison of the amino acid sequence revealed partial homology with the urease accessory gene ureD of Klebsiella aerogenes and Proteus mirabilis. Mutational analysis of ORF1 showed that the gene is necessary for urease activity. Its function is still unknown.

Amino Acid Sequence↗
PubMed1987

Herpes simplex virus 1 protein kinase is encoded by open reading frame US3 which is not essential for virus growth in cell culture.

Earlier reports have described a novel protein kinase in cells infected with herpes simplex or pseudorabies viruses. These novel enzymes were characterized by their acceptance of protamine as a substrate and by their differential chromatographic behavior in anion-exchange chromatography. We report that this activity was not present in extracts of uninfected cells or of cells infected with a mutant constructed so as to contain a deletion in the US3 open reading frame mapping in the small component of herpes simplex virus 1 DNA. The activity was present in extracts of cells infected with wild-type virus and with a recombinant in which the US3 open reading frame had been rescued. Our results are consistent with the observation reported earlier that the coding sequences predict an amino acid motif common to protein kinases and lead to the conclusion that the US3 open reading frame encodes a virus-specific protein kinase that is not required for virus growth in cells in culture.

Amino Acid Sequence↗
PubMed1996

Expression of protein encoded by varicella-zoster virus open reading frame 63 in latently infected human ganglionic neurons.

The ganglionic cell type in which varicella-zoster virus (VZV) is latent in humans was analyzed by using antibodies raised against in vitro-expressed VZV open reading frame 63 protein. VZV open reading frame 63 protein was detected exclusively in the cytoplasm of neurons of latently infected human trigeminal and thoracic ganglia. This is, to our knowledge, the first identification of a herpesvirus protein expressed during latency in the human nervous system.

Adult↗
PubMed1996

Introns and reading frames: correlation between splicing sites and their codon positions.

Computer analyses of the entire GenBank database were conducted to examine correlation between splicing sites and codon positions in reading frames. Intron insertion patterns (i.e., splicing site locations with respect to codon positions) have been analyzed for all of the 74 codons of all the eukaryote taxonomic groups: primates, rodents mammals, vertebrates, invertebrates, and plants. We found that reading frames are interrupted by an intron at a codon boundary (as opposed to the middle of a codon) significantly more often than expected. This observation is consistent with the exon shuffling hypothesis, because exons that end at codon boundaries can be concatenated without causing a frame shift and thus are evolutionarily advantageous. On the other hand, when introns interrupt at the middles of codons, they exist in between the first and second bases much more frequently than between the second and third bases, despite the fact that boundaries between the first and second bases of codons are generally far more important than those between the second and third bases. The reason for this is not clear and yet to be explained. We also show that the length of an exon is a multiple of 3 more frequently than expected. Furthermore, the total length of two consecutive exons is also more frequently a multiple of 3. All the observations above are consistent with results recently published by Long, Rosenberg, and Gilbert (1995).

Algorithms↗
PubMed1998

Growth phase dependent stop codon readthrough and shift of translation reading frame in Escherichia coli.

Nonsense codon readthrough and changed translational reading frame were measured in different growth phases in E. coli. The strains used carry plasmid constructs with a translation assay reporter gene. This reporter gene contains an internal stop codon or a run of U-residues. Termination or frameshifting give rise to stable proteins that can be physically quantified on gels along with the complete protein products. Readthrough of the stop codon UGA by a nearcognate tRNA is several fold higher in active growth than in late exponential phase. In early exponential phase, about 7% of -1 frameshift at a U9 slippery sequence is detectable; upon entry to stationary phase this frameshifting increases to about 40% followed by a decrease in stationary phase. A similar increase is observed in the case of +1 reading frameshift at the U9 sequence, which increases from 13% in early exponential growth phase up to 38% at the beginning of stationary phase followed by a decrease. Thus, the levels of both stop codon readthrough and frameshifting are growth phase dependent, though not in an identical fashion.

Base Sequence↗
PubMed1989

The L1 family of long interspersed repetitive DNA in rabbits: sequence, copy number, conserved open reading frames, and similarity to keratin.

The L1 family of long interspersed repetitive DNA in the rabbit genome (L1Oc) has been studied by determining the sequence of the five L1 repeats in the rabbit beta-like globin gene cluster and by hybridization analysis of other L1 repeats in the genome. L1Oc repeats have a common 3' end that terminates in a poly A addition signal and an A-rich tract, but individual repeats have different 5' ends, indicating a polar truncation from the 5' end during their synthesis or propagation. As a result of the polar truncations, the 5' end of L1Oc is present in about 11,000 copies per haploid genome, whereas the 3' end is present in at least 66,000 copies per haploid genome. One type of L1Oc repeat has internal direct repeats of 78 bp in the 3' untranslated region, whereas other L1Oc repeats have only one copy of this sequence. The longest repeat sequenced, L1Oc5, is 6.5 kb long, and genomic blot-hybridization data using probes from the 5' end of L1Oc5 indicate that a full length L1Oc repeat is about 7.5 kb long, extending about 1 kb 5' to the sequenced region. The L1Oc5 sequence has long open reading frames (ORFs) that correspond to ORF-1 and ORF-2 described in the mouse L1 sequence. In contrast to the overlapping reading frames seen for mouse L1, ORF-1 and ORF-2 are in the same reading frame in rabbit and human L1s, resulting in a discistronic structure. The region between the likely stop codon for ORF-1 and the proposed start codon for ORF-2 is not conserved in interspecies comparisons, which is further evidence that this short region does not encode part of a protein. ORF-1 appears to be a hybrid of sequences, of which the 3' half is unique to and conserved in mammalian L1 repeats. The 5' half of ORF-1 is not conserved between mammalian L1 repeats, but this segment of L1Oc is related significantly to type II cytoskeletal keratin.

Animals↗
PubMed1994

LTE1 of Saccharomyces cerevisiae is a 1435 codon open reading frame that has sequence similarities to guanine nucleotide releasing factors.

The DNA sequence of the LTE1 gene on the left arm of chromosome I of Saccharomyces cerevisiae has been determined. The LTE1 open reading frame comprises 4305 bp that can be translated into 1435 amino acid residues. The position of this open reading frame corresponds well to that of a 4.7 kb transcript that has been mapped to this position. The derived amino acid sequence has significant similarities to the amino acid sequence of the guanine nucleotide releasing factor isolated from a rat brain library. The carboxy-terminus of the LTE1 protein also shows similarities to other guanine nucleotide exchange factors of the S. cerevisiae CDC25 family.

Amino Acid Sequence↗