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At least 127 records · Page 7Linked to original sources
PubMed1995

Polymorphic sequences encoding the first open reading frame protein from LINE-1 ribonucleoprotein particles.

The mouse LINE-1 (L1) retrotransposon contains two open reading frames (ORFs). Three classes of the protein encoded by the first open reading frame (ORF1) are expressed in the mouse embryonal carcinoma cell line, F9; the apparent molecular sizes of these proteins are 41.3, 43, and 43.5 kDa. Two of these three proteins (41.3 and 43 kDa) are translated in vitro from full-length, sense-strand L1 RNA isolated from ribonucleoprotein particles. A reverse transcription-polymerase chain reaction approach was used to clone the ORF1 region from RNA isolated from ribonucleoprotein particles, then the coding capacity of these clones was examined using in vitro transcription and translation. Multiple sequences that encode ORF1 were recovered by this approach, indicating that multiple loci of L1 in the mouse genome are expressed in F9 cells. In addition, L1 sequences with intact ORF1 regions appear to be selectively enriched in the ribonucleoprotein particles.

Animals↗
PubMed1986

E5 open reading frame of bovine papillomavirus type 1 encodes a transforming gene.

We have previously shown that the early region of the bovine papillomavirus type 1 genome contains two nonoverlapping segments that can independently induce the morphological transformation of cultured cells. The transforming gene from the 5' end of the early region is encoded by the E6 open reading frame. The second transforming segment was previously localized to a 2.3-kilobase fragment (2.3T) from the 3' end of the early region. To determine which of the four open reading frames (E2, E3, E4, and E5) located within 2.3T encodes a transforming gene, we have now introduced a series of insertion and deletion mutations into a clone (pHLB1) in which 2.3T is activated by the Harvey viral long terminal repeat, and we tested the mutants for their ability to induce focal transformation. Our results indicate that the E5 open reading frame, which could encode a low-molecular-weight hydrophobic peptide, is required for pHLB1-induced transformation of NIH 3T3 cells, but that the E2, E3, and E4 open reading frames are not.

Amino Acid Sequence↗
PubMed2003

Gene fusion and overlapping reading frames in the mammalian genes for 4E-BP3 and MASK.

4E-BP3 is a member of the eukaryotic initiation factor (eIF) 4F-binding protein family of translational repressors. eIF4E-binding proteins (4E-BPs) inhibit translation initiation by sequestering eIF4E, the cap-binding protein, from eIF4G thus preventing ribosome recruitment to the mRNA. Previous analysis of 4E-BP3 expression uncovered an 8.5-kb mRNA variant of unknown origin. To study this splice variant, we determined the structure of the genomic locus encoding human 4E-BP3 (EIF4EBP3). EIF4EBP3 is located on human chromosome 5q31.3 and comprises three exons (A, B, and C) and two introns. Exon B contains the region of the open reading frame responsible for eIF4E binding. GenBank searches revealed multiple expressed sequence tags originating from the alternative splicing of exon B with unidentified upstream exons. Further studies revealed that the 8.5-kb transcript arises from the fusion of EIF4EBP3 with the mammalian homologue of Drosophila MASK (multiple ankyrin repeats, single KH domain), which is crucial for photoreceptor differentiation, cell survival, and proliferation. Surprisingly, the open reading frame of the MASK-BP3 transcript is different from that of 4E-BP3, which indicates that exon B is translated using an alternative reading frame. A gene fusion similar to that of MASK and EIF4EBP3 has been reported only once in mammals for the UEV1-Kua transcript. The use of an alternative reading frame is also very rare, having been described for two loci, INK4a/ARF and XLalphas/ALEX. The simultaneous exploitation of both mechanisms underscores the flexibility of mammalian genomes and has important implications for the functional analysis of 4E-BP3 and MASK. Interestingly, both eIF4E and MASK are downstream effectors of the Ras/MAPK pathway, which provides a rationale for the MASK-BP3 fusion in mammals.

Alternative Splicing↗
PubMed1986

The tobacco mitochondrial ATPase subunit 9 gene is closely linked to an open reading frame for a ribosomal protein.

A transcribed segment of mitochondrial DNA (mtDNA) from Nicotiana tabacum contains the F0-ATPase subunit 9 gene, an open reading frame with homology to the E. coli small subunit ribosomal protein S13 and an open reading frame with homology to a portion of the mammalian "URF 1" protein, recently shown to be a component of the NADH:ubiquinone reductase complex (NADH:Q 1). The transcriptional patterns of the tobacco ATPase 9 gene and S13-like open reading frame share eight RNA species indicating the two sequences are part of the same transcriptional unit. A maize mtDNA fragment contains the S13 homologous sequence and the NADH:Q 1 homologous sequence in an orientation similar to tobacco. The S13-like sequence is present as a single copy in maize and tobacco, as two copies in wheat, and is absent in pea and bean. We discuss the distribution and orientation of the S13-like and "URF 1"-like sequences and the possibility that they are active genes.

Mitochondria↗
PubMed1988

Mutants of translational components that alter reading frame by two steps forward or one step back.

External suppressors, sufS, of a -1 frameshift mutant cause ribosomes to shift into the -1 frame when reading the sequence CAG GGA GUG. The resulting product is not Gln-Gly-Val but Gln-Gly-Ser with Ser being encoded by the underlined AGU. The alleles investigated are approximately 2% efficient in causing frameshifting. Two other suppressors, hopR and hopE of the same -1 frameshift mutant, cause some ribosomes reading the sequence GUG UG to decode a single amino acid, Val, from the five nucleotides. The possibility is considered that peptidyl-tRNA(Val) dissociates from the mRNA, but re-pairs in a triplet manner after the mRNA slips forward by two bases.

Amino Acid Sequence↗
PubMed1997

Characterization of two age-induced intracisternal A-particle-related transcripts in the mouse liver. Transcriptional read-through into an open reading frame with similarities to the yeast ccr4 transcription factor.

Intracisternal A-particle (IAP) sequences are endogenous retrovirus-like elements present at 1,000 copies in the mouse genome. We had previously identified IAP-related transcripts of unusual size (6 and 10 kilobases (kb)), which are observed exclusively in the liver of the aging mouse. In this report, using cDNA libraries that we have constructed from the liver mRNAs of an aged DBA/2 mouse, we have cloned and entirely sequenced the corresponding cDNAs. Both are initiated within the 5' long terminal repeat of a type IDelta1 IAP sequence, and correspond to a read-through into a unique flanking cellular sequence containing a 966-nucleotide open reading frame, located 3' to the IAP sequence. The 6-kb IAP-related transcript corresponds to a post-transcriptional modification of the 10-kb mRNA, and is generated by a splicing event with the donor site in the IAP sequence, and the acceptor site 5' to the open reading frame. This open reading frame is located on chromosome 3, is evolutionarily conserved, and discloses significant similarity to the yeast CCR4 transcription factor at the amino acid level. The specific expression of these age-induced transcripts, which account for more than 50% of the IAP-related transcripts in the liver of old mice, is therefore entirely consistent with the induction of a single genomic locus, thus strengthening the importance of position effects for the expression of transposable elements. Characterization of this locus should now allow studies on its chromatin and methylation status, and on the "molecular factors of senescence" possibly involved in its induction.

Aging↗
PubMed1992

Indian hepatitis E virus shows a major deletion in the small open reading frame.

Enterically transmitted non-A, non-B hepatitis virus (HEV), the causative agent for sporadic and large epidemic outbreaks in developing countries, contains a positive-sense single-stranded RNA genome. The genome of the virus encodes three open reading frames (ORF1, ORF2, and ORF3). The gene segment corresponding to the small open reading frame (ORF3), overlapping between ORF1 and ORF2, was synthesized by reverse transcription-polymerase chain reaction (RT-PCR) from a number of previously identified HEV-positive clinical specimens. A DNA fragment of 166 bp was consistently obtained from all the clinical specimens. This small fragment was cloned, sequenced, and found to contain an open reading frame encoding only 41 amino acid residues. Comparison of our results with that of geographically related Burma HEV suggests a major inframe deletion of 246 bp in the ORF3 of Indian strain. The protein encoded by ORF3 does not appear to be useful for early serodiagnosis as a synthetic peptide deduced from the truncated ORF3 failed to show any demonstrable immunoreactivity against HEV-infected acute phase sera in an enzyme-linked immunosorbent assay.

Antibody Formation↗
PubMed1990

Developmental rearrangement of cyanobacterial nif genes: nucleotide sequence, open reading frames, and cytochrome P-450 homology of the Anabaena sp. strain PCC 7120 nifD element.

An 11-kbp DNA element of unknown function interrupts the nifD gene in vegetative cells of Anabaena sp. strain PCC 7120. In developing heterocysts the nifD element excises from the chromosome via site-specific recombination between short repeat sequences that flank the element. The nucleotide sequence of the nifH-proximal half of the element was determined to elucidate the genetic potential of the element. Four open reading frames with the same relative orientation as the nifD element-encoded xisA gene were identified in the sequenced region. Each of the open reading frames was preceded by a reasonable ribosome-binding site and had biased codon utilization preferences consistent with low levels of expression. Open reading frame 3 was highly homologous with three cytochrome P-450 omega-hydroxylase proteins and showed regional homology to functionally significant domains common to the cytochrome P-450 superfamily. The sequence encoding open reading frame 2 was the most highly conserved portion of the sequenced region based on heterologous hybridization experiments with three genera of heterocystous cyanobacteria.

Amino Acid Sequence↗
PubMed1989

The double-stranded RNA genome of yeast virus L-A encodes its own putative RNA polymerase by fusing two open reading frames.

The L-A double-stranded RNA virus of Saccharomyces cerevisiae encodes its major coat protein (80 kDa) and a minor single-stranded RNA binding protein (180 kDa) that has immunological cross-reactivity with the major coat protein. The sequence of L-A cDNA clones revealed two open reading frames (ORF), ORF1 and ORF2. These two reading frames overlap by 130 base pairs and ORF2 is in the -1 reading frame with respect to ORF1. Although the major coat protein of the viral particles is encoded by ORF1, the 180-kDa protein is derived from the entire double-stranded RNA genome by fusing ORF1 and ORF2, probably by a -1 translational frameshift. Within the overlapping region is a sequence similar to that producing a -1 frameshift by "simultaneous slippage" in retroviruses. The coding sequence of ORF2 shows a pattern characteristic of viral RNA-dependent RNA polymerases of icosahedral (+)-strand RNA viruses. Thus, the 180-kDa protein is analogous to gag-pol fusion proteins.

Amino Acid Sequence↗
PubMed1995

Construction and genetic analysis of dicistronic polioviruses containing open reading frames for epitopes of human immunodeficiency virus type 1 gp120.

On the basis of previous studies of dicistronic (dc) polioviruses that carried two internal ribosomal entry sites (L. Alexander, H.-H. Lu, and E. Wimmer, Proc. Natl. Acad. Sci. USA 91:1406-1410, 1994; A. Molla, S. K. Jang, A. V. Paul, Q. Reuer, and E. Wimmer, Nature [London] 356:255-257, 1992), we have constructed a variety of dc polioviruses which express foreign genetic elements that were inserted either between two internal ribosomal entry site elements upstream of the poliovirus open reading frame (pPNENPO derivatives) or upstream of the open reading frame for the poliovirus proteinase 2Apro (pDI-E2A derivatives). Surprisingly, the addition of an N-terminal secretory pathway signal sequence to the open reading frame of the inserted foreign sequences (specifying either truncated versions of human immunodeficiency virus type 1 [HIV-1] gp120 or chloramphenicol acetyltransferase) resulted in a null phenotype, whereas removal of the signal sequence led to the production of viable viruses. Constructs that carried a foreign gene with a signal sequence were negative in RNA synthesis, an observation that suggested a very early block in viral replication. The insertion of transmembrane sequences downstream of the leader sequence did not reverse the replication block. Studies of dc polioviruses that encoded the truncated versions of HIV-1 gp120 showed an increase in genetic stability that correlated with a decrease in the size of the insert. A dc construct that contained a minigene encoding the principal neutralization determinant of HIV-1 produced a stable virus that retained the foreign sequence through multiple passages in cultured cells. These data indicate that dc polioviruses have potential as vaccines for the expression of small foreign epitopes.

Amino Acid Sequence↗
PubMed2006

Entries in the Leiden Duchenne muscular dystrophy mutation database: an overview of mutation types and paradoxical cases that confirm the reading-frame rule.

The severe Duchenne and milder Becker muscular dystrophy are both caused by mutations in the DMD gene. This gene codes for dystrophin, a protein important for maintaining the stability of muscle-fiber membranes. In 1988, Monaco and colleagues postulated an explanation for the phenotypic difference between Duchenne and Becker patients in the reading-frame rule: In Duchenne patients, mutations induce a shift in the reading frame leading to prematurely truncated, dysfunctional dystrophins. In Becker patients, in-frame mutations allow the synthesis of internally deleted, but largely functional dystrophins. Currently, over 4700 mutations have been reported in the Leiden DMD mutation database, of which 91% are in agreement with this rule. In this study we provide an update of the mutational variability in the DMD gene, particularly focusing on genotype-phenotype correlations and mutations that appear to be exceptions to the reading-frame rule.

Databases, Genetic↗
PubMed1994

Amplification of selected exons by polymerase chain reaction enables determination of the translational reading frame of dystrophin mRNA resulting from deletion mutations.

Duchenne and Becker muscular dystrophies (DMD and BMD) are severe and mild phenotypes, respectively, of the mutated dystrophin gene. Based on the frameshift theory, an out-of-frame deletion causes DMD, while an in-frame deletion causes BMD. Amplification of deletion-prone exons by polymerase chain reaction (PCR) has been used for the screening of deletion mutations of the dystrophin gene. However, it is difficult to determine the resulting translational reading frame in deleted cases by amplification of the deletion-prone exons. To determine the resulting translational reading frame, we employed a method which selectively amplifies exons affecting the following translational reading frame. Using this method, thirty-three DMD/BMD patients with a deletion mutation in the central region of the dystrophin gene were examined. Twenty-seven of 29 DMD patients had out-of-frame deletions, while only two had in-frame deletions. All four BMD patients had in-frame deletions. Therefore, 93.9% patients fitted the frameshift theory. This method is very useful for clinical diagnosis because of its precision and convenience.

Base Sequence↗
PubMed1999

Nucleotide and peptide sequences of the open reading frame encoding a truncated toxin A gene of Clostridium difficile strain CCUG 20309.

The open reading frame encoding a putative truncated toxin A gene of Clostridium difficile in strain CCUG 20309 (ATCC 8864), a strain that produces toxin B but not toxin A, was sequenced by cycle sequencing method. The coding region contains 2097 base pairs and has a GC content of 26.4%. The deduced polypeptide is 50 kDa and is generally hydrophilic. Although strain CCUG 20309 of C. difficile was reported not to produce toxin A, it is enterotoxic, an inherent property of toxin A in pathogenic strains of C. difficile. It therefore remains to be determined whether a truncated form of toxin A could actually be expressed from the open reading frame by this strain of C. difficile.

Amino Acid Sequence↗
PubMed1994

Inferring genes from open reading frames.

One expects that in DNA without protein coding function, stop codons (which constitute three of the 64 possible codons) should occur frequently in all reading frames, and that a long open reading frame (ORF) can be interpreted as a sign for the existence of a gene. We make a beginning on introducing quantitative measures of confidence into this inference--taking Saccharomyces cerevisiae as a sample case--and show that some common assumptions can reasonably be questioned. In particular we show that statistical support for the biological function of shorter ORFs listed as putative genes in recent papers is in fact very weak. This is an issue of practical as well as theoretical interest, since researching the function of a putative gene is difficult and expensive.

Base Composition↗
PubMed1989

Deletion mutants of herpesvirus saimiri define an open reading frame necessary for transformation.

Analysis of a 5,549-base-pair sequence at the left end of herpesvirus saimiri unique (L-) DNA revealed two open reading frames and genes for five small nuclear U RNAs (herpesvirus saimiri U RNAs). Replication-competent deletion mutants were constructed in order to assess the importance of these genetic features for transformation by this oncogenic herpesvirus. Although not required for replication, one of the open reading frames was found to be required for immortalization of marmoset T lymphocytes into continuously growing cell lines. The protein predicted by this reading frame (STP; saimiri transformation-associated protein) has a highly hydrophobic stretch of 26 amino acids sufficient for a membrane-spanning domain near its carboxy terminus; this domain is immediately preceded by a sequence appropriate for formation of a metal-binding domain (His X2 His X6 Cys X2 Cys, where Xs are other amino acids). One of two poly(A)+ RNAs that could encode STP is bicistronic, while the other has a long 5' untranslated region (approximately 1.5 kilobases). Although some analogies can be drawn between STP and LMP (lymphocyte membrane protein) of Epstein-Barr virus, STP is not related in sequence to LMP.

Amino Acid Sequence↗
PubMed1994

Sequence of a 28.6 kb region of yeast chromosome XI includes the FBA1 and TOA2 genes, an open reading frame (ORF) similar to a translationally controlled tumour protein, one ORF containing motifs also found in plant storage proteins and 13 ORFs with weak or no homology to known proteins.

The complete DNA sequence of cosmid clone pUKG148 comprising 28,600 base pairs was determined from an ordered set of subclones. The sequence contains 22 open reading frames longer than 100 amino acids of which five are entirely covered by other, longer reading frames. YKL054 exhibits 25% homology at the amino acid level to a number of plant storage proteins of the glutenin type, YKL056 is 40% homologous to a translationally controlled mammalian tumour protein, YKL058 (TOA2) is identical to the small subunit of transcription factor TFIIA from yeast and YKL060 is identical to the FBA1 gene also from yeast, already sequenced but not mapped to chromosome XI. The remaining 13 open reading frames show weak or no homology to known genes.

Amino Acid Sequence↗
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↗
PubMed2005

Murine gammaherpesvirus 68 open reading frame 11 encodes a nonessential virion component.

Open reading frame 11 (ORF11) is a conserved gammaherpesvirus gene that remains undefined. We identified the product of murine gammaherpesvirus 68 (MHV-68) ORF11, p43, as a virion component with a predominantly perinuclear distribution in infected cells. MHV-68 lacking p43 grew normally in vitro but showed reduced lytic replication in vivo and a delay in seeding to the spleen. Subsequent latency amplification was normal. Thus, MHV-68 ORF11 encoded a virion component that was important for in vivo lytic replication but dispensable for the establishment of latency.

Animals↗