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At least 541 records · Page 30Linked to original sources
PubMed1997

The nucleotide sequence of a 39 kb segment of yeast chromosome IV: 12 new open reading frames, nine known genes and one genes for Gly-tRNA.

The complete nucleotide sequence of a 39,090 bp segment from the left arm of yeast chromosome IV was determined. Twenty-one open reading frames (ORFs) longer than 100 amino acids and a Gly-tRNA gene were discovered. Nine of the 21 ORFs (D0892, D1022, D1037, D1045, D1057, D1204, D1209, D1214, D1219) correspond to the previously sequenced Saccharomyces cerevisiae genes for the NAD-dependent glutamate dehydrogenase (GDH), the secretory component (SHR3), the GABA transport protein (UGA4), the high mobility group-like protein (NHP2), the hydroxymethylbilane synthase (HEM3), the methylated DNA protein-cysteine S-methyltransferase (MGT1), a putative sugar transport protein, the Shm1 protein (SHM1) and the anti-silencing protein (ASF2). The inferred amino acid sequences of 11 ORFs show significant similarity with known proteins from various organisms, whereas the remaining ORF does not share any similarity with known proteins.

Chromosome Mapping↗
PubMed2000

Kaposi's sarcoma-associated herpesvirus (human herpesvirus-8) open reading frame 36 protein is a serine protein kinase.

Kaposi's sarcoma-associated herpesvirus (KSHV) is a gammaherpesvirus that is implicated in the pathogenesis of Kaposi's sarcoma. The nucleotide sequence of the KSHV open reading frame (ORF) 36 predicts a polypeptide with significant sequence homology to known protein kinases. In this paper, we show that KSHV ORF36 mRNA is expressed during lytic growth and that ORF36 protein is localized in the nucleus. To determine whether the KSHV ORF36 protein is a protein kinase, we expressed it as a glutathione S-transferase (GST) fusion protein (GST-ORF36). Affinity-purified preparations of the GST-ORF36 fusion protein revealed that the protein is autophosphorylated. Mutation of lysine-108 to glutamine dramatically decreased the protein kinase activity of the purified protein, supporting the hypothesis that the protein kinase activity is inherent to the ORF36 protein. Phosphoamino acid analysis showed that the KSHV ORF36 fusion protein is phosphorylated on a serine residue, implying that KSHV ORF36 encodes a serine protein kinase.

Amino Acid Sequence↗
PubMed1993

Detection of a protein encoded by the vaccinia virus C7L open reading frame and study of its effect on virus multiplication in different cell lines.

Vaccinia virus encodes several proteins, the activity of which is essential for multiplication in different cell types. Both the C7L and K1L open reading frames (ORFs) have been characterized as viral determinants for multiplication in human cells. To confirm and extend these findings we inserted the C7L ORF into the genome of a mutant virus unable to multiply in human cells and showed that this virus recovered its ability to replicate. Deletion of C7L from a wild-type viral genome did not adversely affect virus multiplication in human cells but it did reduce replication in hamster Dede cells. When both C7L and K1L were deleted from the vaccinia virus genome only poor or no viral yields were obtained from various human cell lines. Recombinant viruses were also constructed to facilitate the study of C7L protein synthesis during infection. One virus in which the lacZ ORF was fused downstream and in-frame with the C7L ORF enabled us to characterize the C7L protein as an early gene product. Another recombinant virus was constructed so that the carboxy terminus of the C7L ORF product contained an additional 28 amino acids from the carboxy terminus of K1L. Tagging of C7L in this way allowed us to detect the fusion protein by immunoprecipitation with antibodies against the K1L protein. Furthermore, the hybrid protein retained its biological properties. The recombinant viruses constructed in this work should be useful for studies of the molecular basis of the activity of viral host range proteins.

Animals↗
PubMed1993

The 1,629-nucleotide open reading frame located downstream of the Autographa californica nuclear polyhedrosis virus polyhedrin gene encodes a nucleocapsid-associated phosphoprotein.

A 78-kDa protein was produced in bacteria from a clone of the 1,629-nucleotide open reading frame located immediately downstream from the polyhedrin gene of Autographa californica nuclear polyhedrosis virus. The identity of this protein was confirmed by its reactivity with peptide antiserum and amino terminal peptide sequencing after purification from transformed bacteria. The polypeptide was used to produce polyclonal antisera in rabbits. Immunoblot analysis of insect cells infected with the baculovirus indicated that two related proteins with molecular masses of 78 and 83 kDa were synthesized late in infection. Biochemical fractionation studies indicated that both of these proteins were present in purified nucleocapsids from budded and occluded virus preparations. Immunoprecipitation of 32P-labeled proteins and treatment of purified nucleocapsids with alkaline phosphatase demonstrated that the 83-kDa protein was a phosphorylated derivative of the 78-kDa protein. Furthermore, immunoelectron microscopy revealed that the proteins were localized to regions of nucleocapsid assembly within the infected cell and appeared to be associated with the end structures of mature nucleocapsids.

Animals↗
PubMed1996

Human adenovirus type 9 E4 open reading frame 1 encodes a cytoplasmic transforming protein capable of increasing the oncogenicity of CREF cells.

The induction of estrogen-dependent rat mammary tumors by human adenovirus type 9 (Ad9) requires the Ad9 E4 open reading frame 1 (9ORF1) protein, which alone can transform that rat embryo fibroblast cell line CREF in vitro. In the present study, independent pools of both 9ORF1-expressing and control CREF cells were generated by selection with G418 and compared with respect to transformed properties. Indirect immunofluorescence analyses revealed that more than 99% of the cells that made up the 9ORF1-transfected pools expressed 9ORF1 protein and, together with confocal laser scanning microscopy, indicated that this E4 protein was located predominantly within the cytoplasm of cells. With regard to transformation, cells of the 9ORF1-expressing pools differed from those of control pools by forming foci, displaying morphological alterations, growing more efficiently in soft agar, and reaching higher saturation densities. Following injection into immunocompetent syngeneic rats, the 9ORF1-expressing pool cells exhibited greatly enhanced oncogenicity compared with control pool cells. These results show that 9ORF1 protein (i) localizes predominantly within the cytoplasm, (ii) confers multiple general transformed characteristics to CREF cells in vitro, and (iii) increases the tumorigenic properties of these cells in vivo.

Adenovirus E4 Proteins↗
PubMed1995

DNA sequence analysis of a 35 kb segment from Saccharomyces cerevisiae chromosome VII reveals 19 open reading frames including RAD54, ACE1/CUP2, PMR1, RCK1, AMS1 and CAL1/CDC43.

We present DNA sequence data from a 35,364 bp region on the left arm of chromosome VII of Saccharomyces cerevisiae. This region contains 19 open reading frames (ORFs). ORF G1821 corresponds to the RAD54 gene involved in repair and recombination (Emery et al., 1991). G1810 is identical to the ACE1 gene sequenced by Szczypka and Thiele (1989), required for copper-inducible transcription of the CUP1 gene. The first 693 bp on the minus strand represent part of the 3' non-coding region from the P-type ATPase gene PMR1, previously sequenced by Rudolph et al. (1989), which is identical to the SSC1 gene (Smith et al., 1988). G1845 corresponds to the RCK1 protein kinase gene from S. cerevisiae (Dahlkvist and Sunnerhagen, 1994). G1861 is almost identical to the alpha-mannosidase gene AMS1 reported by Yoshihisa and Anraku (1989) and G1864 has 100% identity with the yeast CAL1 gene (Ohya et al., 1989)/CDC43 gene (Johnson et al., 1990) which is involved in control of cell polarity. This region also contains a gene specifying a Leu-tRNA precursor and a remnant of a tau element. ORF G1880 shows some similarity to the S. cerevisiae SNF2, STH1 and NPS1 genes and to the human ERCC1 gene. A 93 bp region shows similarity to yeast EST sequenced by Burns et al. (1994). None of the remaining ORFs has similarity to any sequence within the databases screened.

Amino Acid Sequence↗
PubMed1992

A repetitive DNA element, associated with telomeric sequences in Drosophila melanogaster, contains open reading frames.

He-T sequences are a complex repetitive family of DNA sequences in Drosophila that are associated with telomeric regions, pericentromeric heterochromatin, and the Y chromosome. A component of the He-T family containing open reading frames (ORFs) is described. These ORF-containing elements within the He-T family are designated T-elements, since hybridization in situ with the polytene salivary gland chromosomes results in detectable signal exclusively at the chromosome tips. One T-element that has been sequenced includes ORFs of 1,428 and 1,614 bp. The ORFs are overlapping but one nucleotide out of frame with respect to each other. The longer ORF contains cysteine-histidine motifs strongly resembling nucleic acid binding domains of gag-like proteins, and the overall organization of the T-element ORFs is reminiscent of LINE elements. The T-elements are transcribed and appear to be conserved in Drosophila species related to D. melanogaster. The results suggest that T-elements may play a role in the structure and/or function of telomeres.

Amino Acid Sequence↗
PubMed2002

Felis domesticus papillomavirus, isolated from a skin lesion, is related to canine oral papillomavirus and contains a 1.3 kb non-coding region between the E2 and L2 open reading frames.

We have characterized the complete genome (8300 bp) of an isolate of Felis domesticus papillomavirus (FdPV) from a domestic cat with cutaneous papillomatosis. A BLAST homology search using the nucleotide sequence of the L1 open reading frame demonstrated that the FdPV genome was most closely related to canine oral papillomavirus (COPV). A 384 bp non-coding region (NCR) was found between the end of L1 and the beginning of E6, and a 1.3 kbp NCR was located between the end of E2 and the beginning of L2. Phylogenetic analysis placed FdPV in the E3 clade with COPV. Both viruses contain the atypical second NCR, which has no homology with sequences in existing databases.

Animals↗
PubMed1995

Analysis of a 32.8 kb segment of yeast chromosome IV reveals 21 open reading frames, including TPS2, PPH3, RAD55, SED1, PDC2, AFR1, SSS1, SLU7 and a tRNA for arginine.

We report the nucleotide sequence of a 32.8 kb DNA segment from the right arm of Saccharomyces cerevisiae chromosome IV. The sequence contains 20 open reading frames (ORFs) longer than 300 bp as well as the 240 bp gene coding for the essential SSS1 secretory protein. Nine ORFs previously totally or partially sequenced (TPS2, PPH3, RAD55, SED1, PDC2, AFR1, SSS1, SLU7 and D4478) are presented, as well as the transmembrane protein D4405, the leucine zipper containing D4495 and a new tRNA for arginine. D4456 and D4461 are separated by a single in-frame stop codon only. The other five ORFs show no particular features or significant homology.

Amino Acid Sequence↗
PubMed1996

The sequence of a 30 kb fragment on the left arm of chromosome XV from Saccharomyces cerevisiae reveals 15 open reading frames, five of which correspond to previously identified genes.

We report the sequence of a 30,469 bp long DNA fragment on the left arm of chromosome XV of Saccharomyces cerevisiae. The fragment contains 15 open reading frames (ORFs) of at least 300 bp. Five previously sequenced yeast genes, PHO80, TIR2, SLG1, the gene encoding the subtilisin-like protease III precursor and the gene coding for ATP-dependent permease, are found among these ORFs. By DNA sequence comparison, two ORFs identified previously reported expressed sequence tags from yeast. Of the proteins encoded by the remaining eight ORFs, six show similarities to proteins from different organisms and two lack detectable similarity with any amino acid sequence described in public data banks.

Chromosomes, Fungal↗
PubMed2006

Posttranscriptional regulation by the upstream open reading frame of the phosphoethanolamine N-methyltransferase gene.

Phosphoethanolamine N-methyltransferase (PEAMT) is involved in choline biosynthesis in plants. The 5' untranslated region (UTR) of several PEAMT genes was found to contain an upstream open reading frame (uORF). We generated transgenic Arabidopsis calli that expressed a chimeric gene constructed by fusing the 5' UTR of the Arabidopsis PEAMT gene (AtNMT1) upstream of the beta-glucuronidase gene. The AtNMT1 uORF was found to be involved in declining levels of the chimeric gene mRNA and repression of downstream beta-glucuronidase gene translation in the calli when the cells were treated with choline. Further, we discuss the role of the uORF.

5' Untranslated Regions↗
PubMed1994

In vivo characterisation of a translational enhancer upstream from the coat protein open reading frame of potato virus S.

The 101 nucleotide region upstream from the ATG of the potato virus S (PVS) coat protein gene was isolated and the effect of this region on the translation of a downstream open reading frame analysed in vivo. Translation was monitored using the reporter genes B-glucuronidase (GUS) and luciferase (LUC). Translational enhancement was assayed transiently using DNA microprojectile bombardment into both leaf and pollen tissue and also by polyethylene glycol mediated transfection of tobacco protoplasts. In both cases the presence of this region resulted in a 2-3 fold increase in translation when compared to reporter expression with synthetic leader and authentic plant leader constructs. Tobacco plants stability transformed with this PVS 101 nucleotide region and downstream GUS gene gave 4 times the level of translation over synthetic leader GUS control plants.

Base Sequence↗
PubMed1998

Forced evolution reveals the importance of short open reading frame A and secondary structure in the cauliflower mosaic virus 35S RNA leader.

Cauliflower mosaic virus pregenomic 35S RNA begins with a long leader sequence containing an extensive secondary structure and up to nine short open reading frames (sORFs), 2 to 35 codons in length. To test whether any of these sORFs are required for virus viability, their start codons were mutated either individually or in various combinations. The resulting viral mutants were tested for infectivity on mechanically inoculated turnip plants. Viable mutants were passaged several times, and the stability of the introduced mutations was analyzed by PCR amplification and sequencing. Mutations at the 5'-proximal sORF A and in the center of the leader resulted in delayed symptom development and in the appearance of revertants. In the central leader region, the predicted secondary structure, rather than the sORF organization, was restored, while true reversions or second-site substitutions in response to mutations of sORF A restored this sORF. Involvement of sORF A and secondary structure of the leader in the virus replication cycle, and especially in translation of the 35S RNA via ribosome shunting, is discussed.

Base Sequence↗
PubMed1994

A novel explanation for the existence of open reading frames on latency-associated transcripts of alphaherpesviruses.

Recent studies indicate that alphaherpesviruses express latency associated transcripts (LATs) from the antisense strand of immediate early (IE) genes of the viral genome. It has been discussed that LATs containing extended open reading frames (ORFs) might be translated into protein products. We found that a salient feature of some herpesvirus DNAs is a high GC preference at the third codon positions. As a consequence, the probability of a stop codon arising at two of the six frames of the DNA strand is very low. The regions missing stop codons frequently start with ATG, resulting in extended ORFs. Therefore, the presence of a gene-long ORF does not necessarily mean that it is relevant to real translation.

Alphaherpesvirinae↗
PubMed1992

The putative E5 open reading frame of cottontail rabbit papillomavirus is dispensable for papilloma formation in domestic rabbits.

In the cottontail rabbit papillomavirus (CRPV)-rabbit system, recombinant CRPV DNA can induce papillomas. This investigation was undertaken to evaluate whether the E5 open reading frame (ORF) of CRPV is required for papilloma formation. The CRPV genome we utilized, CRPV-WA, was sequenced in the E5 region and was found to contain one deletion, two insertions, and one transition mutation compared with CRPV-KS, the CRPV genome that has been fully sequenced. Despite these differences, an intact E5 ORF is preserved, supporting the notion that this gene may serve a biological function. One frameshift and two in-frame mutations were constructed in the small region of the 5' end of the E5 ORF that follows the E2 stop codon and precedes the L2 ORF. Several hundred rabbit skin sites were inoculated with each DNA preparation with a jet injector to test the ability of three CRPV E5 mutant DNAs to induce papillomas. In vivo results showed that each of the mutants induced papillomas, and biochemical analysis demonstrated that the E5 mutations present in DNA inocula were retained in the papillomas. The frequency of papilloma formation, however, was generally lower with each of the CRPV E5 mutants than with wild-type CRPV DNA, particularly so for the E5 frameshift mutant, suggesting that although the recognized E5 ORF is not required in domestic rabbits for the induction of papillomas by CRPV DNA, it may facilitate their formation.

Amino Acid Sequence↗
PubMedDate not supplied

[Potential open reading frames within 5'-untranslated regions of eukaryotic mRNAs].

It is known that 5'-untranslated sequences of eukaryotic mRNA often contain AUG triplets, which may serve as the sites of translation initiation. It is thought that these leader open reading frames can fulfil the regulatory functions and encode functionally active proteins. However, they have been incompletely characterized. The article deals with the context organization of leader reading frames of eukaryotic mRNAs. It has been shown that their characteristics correlate with the position relative to the protein-encoding sequence, which may be associated with the efficiency of initiation of translation.

5' Untranslated Regions↗
PubMed2000

Open reading frame 2 of porcine circovirus type 2 encodes a major capsid protein.

Porcine circovirus 2 (PCV2), a single-stranded DNA virus associated with post-weaning multisystemic wasting syndrome of swine, has two potential open reading frames, ORF1 and ORF2, greater than 600 nucleotides in length. ORF1 is predicted to encode a replication-associated protein (Rep) essential for replication of viral DNA, while ORF2 contains a conserved basic amino acid sequence at the N terminus resembling that of the major structural protein of chicken anaemia virus. Thus far, the structural protein(s) of PCV2 have not been identified. In this study, a viral structural protein of 30 kDa was identified in purified PCV2 particles. ORF2 of PCV2 was cloned into a baculovirus expression vector and the gene product was expressed in insect cells. The expressed ORF2 gene product had a molecular mass of 30 kDa, similar to that detected in purified virus particles. The recombinant ORF2 protein self-assembled to form capsid-like particles when viewed by electron microscopy. Antibodies against the ORF2 protein were detected in samples of sera obtained from pigs as early as 3 weeks after experimental infection with PCV2. These results show that the major structural protein of PCV2 is encoded by ORF2 and has a molecular mass of 30 kDa.

Animals↗
PubMed2003

Open reading frame 122 of Helicoverpa armigera single nucleocapsid nucleopolyhedrovirus encodes a novel structural protein of occlusion-derived virions.

Helicoverpa armigera single nucleocapsid nucleopolyhedrovirus (HaSNPV) and its closely related variant H. zea SNPV (HzSNPV) contain 20 open reading frames (ORFs) unique among baculoviruses. In this report, the function of HaSNPV ORF 122 (Ha122) is investigated. Ha122 was transcribed as a polyadenylated transcript from 8 h post-infection in infected H. armigera insect cells. 5'RACE analysis indicated that Ha122 transcription starts predominantly in the consensus major late transcription initiation motif DTAAG, around 47 nt upstream of the putative translation start codon, with a minor start at position -89. Using 3'RACE, the transcription stop site mapped 27 nt downstream of the putative translation stop codon. By Western blot analysis using a chicken-derived polyclonal antibody, the product of Ha122 was found in infected cells to be a 21 kDa protein, close to the theoretical size of 21.6 kDa. The Ha122 protein, when fused to green fluorescent protein, was observed in the nuclei of H. armigera cells but only in conjunction with wild-type HaSNPV infection. The 21 kDa protein was located specifically in the nucleocapsid of occlusion-derived virions (ODVs) and not in that of budded virus. The available data suggest that Ha122 is a functional ORF of HaSNPV and HzSNPV and that the 21 kDa protein is a novel specific component of baculovirus ODVs.

Amino Acid Sequence↗