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 19 recordsLinked to original sources
PubMed2000

Evidence for translational repression of the SOCS-1 major open reading frame by an upstream open reading frame.

The suppressor of cytokine signalling 1 protein (SOCS-1) belongs to a novel family of cytokine inducible factors which function as inhibitors of the JAK/STAT pathway. While SOCS-1 previously has been described as a single-exon gene, here we present evidence for an additional 5' exon, separated by a 509 bp intron from exon 2. Exon 1 and part of exon 2 contain an open reading frame of 115 nt, ending one nucleotide upstream of the major reading frame. Using SOCS-1-promoter/luciferase constructs, we investigated which sequences are involved in the regulation of SOCS-1 expression. Serial promoter deletion clones indicate the localization and functionality of SP1, interferon-stimulated responsive elements (ISRE), and interferon-gamma-activated sites (GAS) promoter elements in the SOCS-1 5' flanking region. We present evidence that the upstream open reading frame (uORF) represses the translation of the downstream major open reading frame (mORF). Mutating the start codon of the uORF relieves this repression. Our data indicate that expression of the SOCS-1 protein is repressed on translational level by a mechanism, which bears similarities to that postulated for genes like retinoic acid receptor beta2 (RARbeta2), S-adenosylmethionine-decarboxylase (AdoMetDC), Bcl-2, and others.

5' Untranslated Regions↗
PubMed2000

Human herpesvirus 8 open reading frame 26 and open reading frame 65 sequences from multiple myeloma patients: a shared pattern not found in Kaposi's sarcoma or primary effusion lymphoma.

Human herpesvirus 8 (HHV-8), also known as Kaposi's sarcoma-associated herpesvirus, has been implicated in the pathogenesis of Kaposi's sarcoma (KS), primary effusion lymphoma (PEL), multicentric Castleman's disease, and recently multiple myeloma (MM). DNA sequence analyses of HHV-8 suggest that multiple HHV-8 strains exist. We extracted DNA from 24 patients with MM and 3 patients with monoclonal gammopathy of undetermined significance and compared HHV-8 open reading frames (ORFs) 26 and 65 sequences with those derived from patients with KS, PEL, and two HHV-8-positive PEL cell lines KS-1 and BC-1. ORF26 sequence data suggest that MM patients are consistently carriers of HHV-8 strain subtype C3. All MM patients also consistently revealed either a single bp deletion or substitution at position 112197 in ORF65. This unique alteration is not present in patients with KS or PEL or in PEL cell lines. It occurs in the portion of ORF65 that is known to be responsible for a serological response to HHV-8.

Amino Acid Sequence↗
PubMed2004

A mutation in the latency-related gene of bovine herpesvirus 1 inhibits protein expression from open reading frame 2 and an adjacent reading frame during productive infection.

The latency-related (LR) gene of bovine herpesvirus 1 (BHV-1) is abundantly expressed during latency. A mutant BHV-1 strain that contains three stop codons at the 5' terminus of the LR gene (LR mutant) does not reactivate from latency. This study demonstrates that the LR mutant does not express open reading frame 2 or an adjacent reading frame that lacks an initiating ATG (reading frame C). Since the LR mutant and wild-type BHV-1 express similar levels of LR RNA, we conclude that LR protein expression plays an important role in regulating the latency reactivation cycle in cattle.

Animals↗
PubMed1994

The complete sequence of a 33 kb fragment on the right arm of chromosome II from Saccharomyces cerevisiae reveals 16 open reading frames, including ten new open reading frames, five previously identified genes and a homologue of the SCO1 gene.

We report here the sequence of a 33,117 bp DNA fragment located approximately 30 kb from the centromere on the right arm of Saccharomyces cerevisiae chromosome II. We have detected 16 open reading frames (ORFs) longer than 450 bp, provisionally called YBR0301 to YBR0322, covering 70.4% of the entire sequence. The ORFs YBR0301, YBR0302, YBR0303, YBR0305 and YBR0315 correspond to previously sequenced S. cerevisiae genes GAL10, GAL1, FUR4, CAL1 and L2B, respectively. Translation products of two other ORFs, YBR0308 and YBR0312 exhibit similarity to previously known S. cerevisiae proteins: the mitochondrially associated protein SCO1 and the protein kinase YKR2. The predicted protein product of the ORF YBR0321 shows a 41.6% identity score with the Escherichia coli pyroxamine 5'-phosphate oxidase. The nine other ORFs show no significant homology to known proteins.

Amino Acid Sequence↗
PubMed1982

Open reading frame cloning: identification, cloning, and expression of open reading frame DNA.

A plasmid was constructed that facilitates the cloning and expression of open reading frame DNA. A DNA fragment containing a bacterial promoter and the amino terminus of the cI gene of bacteriophage lambda was fused to an amino-terminally deleted version of the lacZ gene. An appropriate cloning site was inserted between these two fragments such that a frameshift mutation was introduced upstream of the lacZ-encoding DNA. This cloning vehicle produces a relatively low level of beta-galactosidase activity when introduced into Escherichia coli. The insertion of foreign DNA at the cloning site can reverse the frameshift mutation and generate plasmids that produce a relatively high level of beta-galactosidase activity. A large fraction of these plasmids produce a fusion protein that has a portion of the lambda cI protein at the amino terminus, the foreign protein segment in the middle, and the lacZ polypeptide at the carboxyl terminus. The production of a high level of beta-galactosidase and a large fusion polypeptide guarantees the cloning of a DNA fragment with at least one open reading frame that traverses the entirety of the fragment. Hence, the method can identify, clone, and express (as part of a larger fusion polypeptide) open reading frame DNA from among a large collection of DNA fragments.

Base Sequence↗
PubMed1994

RNA editing of a conserved reading frame in plant mitochondria increases its similarity to two overlapping reading frames in Escherichia coli.

An open reading frame (orfx) in mitochondria of the higher plants Oenothera berteriana and Arabidopsis thaliana is homologous to orf244 in the mitochondrial genome of Marchantia polymorpha. Homologous sequences are also present in carrot, potato and sugar beet. Profile analysis revealed similarity to two overlapping reading frames in the Escherichia coli genome. Potential translation initiation at conserved ATA (isoleucine) and TTG (leucine) codons is discussed. Transcripts of the open reading frame are altered by RNA editing in Arabidopsis and Oenothera downstream of these codons, suggesting this to be the functionally important region.

Amino Acid Sequence↗
PubMed2004

A second-generation system for unbiased reading frame selection.

Reading frame selection of nucleic acids has important implications for protein engineering and genomics. Current methods are limited because selection of the gene of interest inevitably depends on the solubility of its translated product. Here we report the construction of the pInSALect vector, which provides strict reading frame selection without concomitant selection for protein solubility or folding. This plasmid incorporates the cis-splicing VMA intein sequence from Saccharomyces cerevisiae to facilitate the post-translational self-excision of the protein of interest, thereby eliminating potential aggregation problems. Results from two libraries of chimeric glycinamide ribonucleotide formyltransferases confirm the superior performance of pInSALect over existing reading frame selection systems.

Animals↗
PubMed2005

The hepatitis C virus alternate reading frame (ARF) and its family of novel products: the alternate reading frame protein/F-protein, the double-frameshift protein, and others.

The hepatitis C virus (HCV) has an alternate reading frame (ARF) that overlaps the core protein gene. The overlapping reading frame distinguishes HCV from all of its known viral relatives, with the possible exception of GB virus B (GBV-B). The ARF is expressed during natural HCV infections and stimulates specific immune responses. Like several essential genes in other viruses (e.g., the human immunodeficiency virus polymerase) the ARF lacks an in-frame AUG start codon, suggesting that its expression involves unusual translation-level events. In vitro studies indicate that ribosomal frameshifting may be one of several processes that can lead to translation of the ARF. Frameshifting yields chimeric proteins that have segments encoded in the core gene covalently attached to amino acids encoded in the ARF. A consistent nomenclature for the ARF's protein products has yet to be established. We propose that all proteins that contain amino acids encoded in the + 1 ARF be called alternate reading frame proteins (ARFPs) and that specific ARFPs, such as the ARFP/F-protein, the double-frameshift protein, and the short form of core + 1, be designated as follows: ARFP/F (ARFP/F-protein), ARFP/DF (double-frameshift), and ARFP/S (short form of core + 1). The roles of ARFPs in the HCV life cycle are not yet known. There is a significant possibility that ARFPs may be responsible for some of the effects attributed to the core protein, given that most studies seeking to define the function of the core protein have employed materials likely to contain a combination of the core protein and ARFPs. The observed effects of the core protein include the induction of liver cancer, transformation of cells, and alterations of immune responses. This article reviews the discovery of ARF, describes the RNA structural elements involved in core/ARF gene expression, discusses possible functions of ARFPs, and considers the potential usefulness of ARFPs in vaccines. The HCV ARF is the focus of a new and rapidly expanding area of research, and the results of many ongoing studies are currently available in abstract form only. The preliminary nature of investigations that have not yet been reviewed by peers is noted in the text.

Animals↗
PubMed1991

The promoter, transcriptional unit, and coding sequence of herpes simplex virus 1 family 35 proteins are contained within and in frame with the UL26 open reading frame.

The herpes simplex virus 1 (HSV-1) genome specifies an abundant capsid protein which in denaturing gels forms multiple bands designated family 35 proteins (D.K. Braun, B. Roizman, and L. Pereira, J. Virol. 49:142-153, 1984). Nucleotide-sequencing studies have assigned the coding sequences of these proteins to the open reading frame UL26 (D.J. McGeoch, M.A. Dalrymple, A.J. Davidson, A. Dolan, M.C. Frame, D. McNab, L.J. Perry, J.E. Scott, and P. Taylor, J. Gen. Virol. 69:1531-1574, 1988). IN studies reported here, a series of plasmid constructs containing deletions or insertions of an alpha 4 promoter or of a sequence encoding a cytomegalovirus epitope reacting with a mouse monoclonal antibody revealed the following: the open reading frame previously designated UL26 encodes two proteins which share amino acid sequences, and each coding domain is contained in its own transcriptional unit that terminates at a common, unique poly(A) site. On the basis of the transcription initiation site (+1), it was predicted that the UL26 open reading frame encodes a protein of 635 amino acids, and a protein with an apparent molecular weight of approximately 75,000 has been identified. The second transcriptional unit, designated UL26.5, predicted to specify a protein of 329 amino acids, encodes the family 35 proteins; it is transcribed by an mRNA which initiates at approximately nucleotide +1000 of the UL26 transcription initiation site and is translated from the methionine initiation codon located at position +1099 of the UL26 transcriptional unit. The DNA fragment comprising the sequences downstream of the HpaI cleavage site (+832 of UL26) contains both the promoter and the coding sequence of family 35 proteins and is both competent and efficient in expressing the proteins in transfected cells superinfected with HSV-1 or HSV-2.

Animals↗
PubMed1989

How 'hidden' reading frames are expressed.

Secondary reading frames, 'hidden' under other reading frames, are used for coordinated expression of proteins in several eukaryotic viruses. In some genes, ribosomal frameshifting and initiation or reinitiation of protein synthesis on internal AUG codons are translational mechanisms allowing access to such 'hidden' reading frames. In others, secondary reading frames are translated from alternatively spliced or edited mRNAs.

RNA, Ribosomal↗
PubMed1988

Deletions/insertions, short inverted repeats, sequences resembling att-lambda, and frame shift mutated open reading frames are involved in chloroplast DNA differences in the genus Oenothera subsection Munzia.

A restriction fragment length mutation has been mapped in the large single copy region of the chloroplast DNA from two Munzi-Oenothera species. Fragments containing the deletion/insertion were cloned, further analysed by additional restriction enzymes, and sequenced. A deleted/inserted 136 bp sequence was identified upstream of the 5' end of a tRNA-Leu (UAA) gene and presumably is located in the spacer between this gene and a tRNA-Thr (UGU) gene. The endpoints of the 136 bp sequence are covered by short inverted repeats. Complementary inverted repeats are present in the middle of the deleted/inserted sequence. The repeats are part of sequences resembling the lambda chromosomal attachment site (att-lambda) which is essential for site specific recombination in the lambda/Escherichia coli system. Possible interactions of the repeats during the deletion/insertion process are discussed. The spacer also contains a 1 bp deletion/insertion within an open reading frame (ORF). Due to this frame shift mutation the ORF sizes are quite different between the two Oenothera species.

Amino Acid Sequence↗
PubMedDate not supplied

Editing of rps3/rpl16 transcripts creates a premature truncation of the rpl16 open reading frame.

Overlapping open reading frames corresponding to maize mitochondrial genes rps3 and rpl16 have been found in Petunia mitochondrial DNA. The DNA region associated with these two genes is part of the Petunia mitochondrial recombination repeat and is iterated three times. Analysis of transcripts from these genes shows that there is RNA editing of the coding regions and that one of the editing sites detected in the open reading frame overlap creates a premature stop codon in the rpl16 sequence. No transcripts were detected that were unedited at this site. Thus, in Petunia editing of rpl16 appears to render this gene nonfunctional.

Amino Acid Sequence↗
PubMed1996

Simple procedure for creation of in-frame deletion mutations throughout an open reading frame.

A general method is presented for randomly mutagenizing open reading frames (ORF) to generate in-frame deletions and insertions. The protocol requires expression of the ORF of interest as a hybrid ORF-beta-galactosidase fusion protein. This allows colorimetric screening for beta-galactosidase activity during subsequent mutagenesis steps. Consequently, proteins with no suitable phenotypic selection or screening properties can be readily screened for mutations that disrupt and subsequently restore the reading frame of the hybrid protein. In addition, this system provides gene expression for subsequent biochemical analysis of the mutant proteins. The bovine papillomavirus type 1 (BPV-1) EI ORF has been mutagenized using this method as an example.

Base Sequence↗
PubMed2007

Initiation at the third in-frame AUG codon of open reading frame 3 of the hepatitis E virus is essential for viral infectivity in vivo.

To determine the initiation strategy of the hepatitis E virus (HEV) open reading frame 3 (ORF3), we constructed five HEV mutants with desired mutations in the ORF1 and ORF2 junction region and tested their levels of in vivo infectivity in pigs. A mutant with a C-terminally truncated ORF3 is noninfectious in pigs, indicating that an intact ORF3 is required for in vivo infectivity. Mutations with substitutions in the first in-frame AUG in the junction region or with the same T insertion at the corresponding position of HEV genotype 4 did not affect the virus infectivity or rescue, although mutations with combinations of the two affected virus recovery efficiency, and a single mutation at the third in-frame AUG completely abolished virus infectivity in vivo, indicating that the third in-frame AUG in the junction region is required for virus infection and is likely the authentic initiation site for ORF3. A conserved double stem-loop RNA structure, which may be important for HEV replication, was identified in the junction region. This represents the first report of using a unique homologous pig model system to study the molecular mechanism of HEV replication and to systematically and definitively identify the authentic ORF3 initiation site.

Animals↗
PubMed2006

Functionality of unspliced XBP1 is required to explain evolution of overlapping reading frames.

Eukaryotic genes with overlapping reading frames exemplify some of the most striking biological phenomena. Transcript of one such gene, the gene encoding X-box protein (XBP1), has evolved a mechanism for "on-demand" switching of translation between two overlapping reading frames. Despite the existence of this elaborate system, only one reading frame was believed to be functional. Here, we show that XBP1 evolves in a fashion that is only consistent with functionality of both reading frames. Our study provides a novel evolutionary framework for the analysis of loci with overlapping reading frames, which can be used for identification and analyses of novel dual-coding genes.

Animals↗
PubMed1994

Characterization of the bovine herpesvirus 1 homolog of the herpes simplex virus 1 UL24 open reading frame.

An open reading frame (ORF) of 293 codons which partially overlaps the bovine herpesvirus 1 (BHV1) thymidine kinase (tk) ORF in a head-to-head orientation has been identified by nucleotide sequence analysis. The predicted amino acid sequence of this ORF exhibits an overall identity of 38.1% with that of the herpes simplex virus type 1 (HSV1) UL24 ORF as well as an 80.7% identity with the 57-amino-acid consensus sequence found in the UL24-like ORFs of eight herpesviruses (Jacobson et al., J. Virol, 49, 947-959, 1989). We have therefore designated this BHV1 ORF as the homolog of the HSV1 UL24 ORF with which it also shares a common position and orientation relative to the tk ORF. The BHV1 UL24-like ORF is contained within a 5.2-kb RNA transcript initiating within the tk ORF and is the largest in a group of four 3'-coterminal transcripts. This transcript pattern closely resembles that observed in HSV1-infected cells where five transcripts, the two largest of which contain the UL24 ORF, appear to be 3'-coterminal. In contrast to HSV1 mutants with lesions in the UL24 ORF, a BHV1 deletion mutant which failed to produce detectable levels of the 5.2-kb transcript grew nearly as well as wild-type virus.

Amino Acid Sequence↗
PubMed1990

Identification and characterization of the herpes simplex virus type 1 protein encoded by the UL37 open reading frame.

The UL37 open reading frame of the herpes simplex virus type 1 (HSV-1) DNA genome is located between map units 0.527 and 0.552. We have identified and characterized the UL37 protein product in HSV-1-infected cells. The presence of the UL37 protein was detected by using a polyclonal rabbit antiserum directed against an in vitro-translated product derived from an in vitro-transcribed UL37 mRNA. The UL37 open reading frame encodes for a protein with an apparent molecular mass of 120 kDa in HSV-1-infected cells; the protein's mass was assigned on the basis of its migration in sodium dodecyl sulfate-polyacrylamide gels. The UL37 protein is not present at detectable levels in purified HSV-1 virions, suggesting that it is not a structural protein. Analysis of time course experiments and experiments using DNA synthesis inhibitors demonstrated that the UL37 protein is expressed prior to the onset of viral DNA synthesis, reaching maximum levels late in infection, classifying it as a gamma 1 gene. Elution of HSV-1-infected cell proteins from single-stranded DNA agarose columns by using a linear KCl gradient demonstrated that the UL37 protein elutes from this matrix at a salt concentration similar to that observed for ICP8, the major HSV-1 DNA-binding protein. In addition, computer-assisted analysis revealed a potential ATP-binding domain in the predicted UL37 amino acid sequence. On the basis of the kinetics of appearance and DNA-binding properties, we hypothesize that UL37 represents a newly recognized HSV-1 DNA-binding protein that may be involved in late events in viral replication.

Animals↗
PubMed1996

The promoter and transcriptional unit of a novel herpes simplex virus 1 alpha gene are contained in, and encode a protein in frame with, the open reading frame of the alpha 22 gene.

The herpes simplex virus type 1 genome encodes a set of genes (alpha genes) expressed in the absence of de novo viral protein synthesis. Earlier studies have shown that the product of the alpha 22 gene, a member of this set, is nucleotidylylated by casein kinase II and phosphorylated by viral protein kinases encoded by UL13 and US3. Mutants lacking the carboxyl-terminal domain starting with amino acid 200 exhibit reduced capacity to replicate in primary human cell strains or in cells of rodent derivation and also exhibit reduced expression of a subset of gamma or late genes. We report that the domain of the alpha 22 gene is transcribed by two 3'-coterminal mRNAs. The longer transcript reported encodes the 420-amino-acid alpha 22 protein, whereas the shorter transcript reported here encodes a protein containing the carboxyl-terminal 273 amino acids of the alpha 22 protein. The shorter gene is designated US1.5. The US1.5 mRNA is synthesized in cells infected and maintained in the presence of cycloheximide and under other conditions which restrict viral gene expression to alpha genes. In-frame insertion of linkers encoding 18, 21, or 22 amino acids after codon 200 or 240 of the alpha 22 protein did not affect the known functions or phenotype associated with the wild-type alpha 22 gene or its product. Earlier studies have placed the nucleotidylylated sequences in the amino-terminal portion of the protein. The results of these studies indicate that the US1.5 gene encodes the functions associated with replication in human primary or rodent cells and optimal expression of alpha 0 and gamma genes. This finding brings the number of genes known to map in the unique short region of the herpes simplex virus type 1 DNA to 14 and the total number of different genes to 78.

Amino Acid Sequence↗