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At least 721 records · Page 40Linked to original sources
PubMed1994

The sequence of an 8.8 kb segment on the left arm of chromosome II from Saccharomyces cerevisiae reveals four new open reading frames including homologs of animal DNA polymerase alpha-primases and bacterial GTP cyclohydrolase II.

The DNA sequence of two contiguous 7648 bp and 1194 bp BamHI fragments from the cosmid alpha 1201 located about 60 kb from the centromere on the left arm of chromosome II from Saccharomyces cerevisiae has been determined. Sequence analysis reveals four new open reading frames longer than 300 bp: YBL0415 (309 bp), YBL0416 (4539 bp), YBL0417 (1035 bp) and YBL0414 (2115 bp), which extends into the neighbouring 5.2 kb BamHI fragment. The YBL0414 shows homologies to the mouse 68 kDa and Drosophila melanogaster 76 kDa subunits of the DNA polymerase alpha-primase complex. The YBL0417 is homologous to bacterial GTP cyclohydrolase II (EC 3.5.4.25).

Amino Acid Sequence↗
PubMed2000

Complete nucleotide sequence of a cryptic plasmid from the marine bacterium Vibrio splendidus and identification of open reading frames.

A 2.3-kb replication-proficient fragment was previously obtained from a cryptic plasmid (pPS41) isolated from a marine Vibrio splendidus isolate (P. A. Sobecky, T. J. Mincer, M. C. Chang, A. Toukdarian, and D. R. Helinski, 1998, Appl. Environ. Microbiol. 64, 2822-2830). Analysis of the complete nucleotide sequence of plasmid pPS41 revealed two additional open reading frames (ORFs). Analysis of ORF-1 revealed that its translated product has 125 amino acids with a predicted MW of 16,978 and ORF-2 encodes a putative protein of 151 amino acids with a predicted MW of 19,802. The ORF-2 encoded protein showed 31 to 35% sequence homology to proteins identified to have a role in plasmid mobilization. These proteins are encoded on plasmids found in Escherichia coli and Pasteurella multocida. Plasmid pPS41 could be mobilized by a conjugative plasmid at frequencies of 1 x 10(-2) to 2 x 10(-2).

Amino Acid Sequence↗
PubMed1999

Comparison of genetic variability at multiple loci across the genomes of the major subtypes of Kaposi's sarcoma-associated herpesvirus reveals evidence for recombination and for two distinct types of open reading frame K15 alleles at the right-hand end.

Kaposi's sarcoma (KS)-associated herpesvirus or human herpesvirus 8 (HHV8) DNA is found consistently in nearly all classical, endemic, transplant, and AIDS-associated KS lesions, as well as in several AIDS-associated lymphomas. We have previously sequenced the genes for the highly variable open reading frame K1 (ORF-K1) protein from more than 60 different HHV8 samples and demonstrated that they display up to 30% amino acid variability and cluster into four very distinct evolutionary subgroups (the A, B, C, and D subtypes) that correlate with the major migrationary diasporas of modern humans. Here we have extended this type of analysis to six other loci across the HHV8 genome to further evaluate overall genotype patterns and the potential for chimeric genomes. Comparison of the relatively conserved ORF26, T0.7/K12, and ORF75 gene regions at map positions 0. 35, 0.85, and 0.96 revealed typical ORF-K1-linked subtype patterns, except that between 20 and 30% of the genomes analyzed proved to be either intertypic or intratypic mosaics. In addition, a 2,500-bp region found at the extreme right-hand side of the unique segment in 45 HHV8 genomes proved to be highly diverged from the 3,500-bp sequence found at this position in the other 18 HHV8 genomes examined. Furthermore, these previously uncharacterized "orphan" region sequences proved to encompass multiexon latent-state mRNAs encoding two highly diverged alleles of the novel ORF-K15 protein. The predominant (P) and minor (M) forms of HHV8 ORF-K15 are structurally related integral membrane proteins that have only 33% overall amino acid identity to one another but retain conserved likely tyrosine kinase signaling motifs and may be distant evolutionary relatives of the LMP2 latency protein of Epstein-Barr virus. The M allele of ORF-K15 is also physically linked to a distinctive M subtype of the adjacent ORF75 gene locus, and in some cases, this linkage extends as far back as the T0.7 locus also. Overall, the results suggest that an original recombination event with a related primate virus from an unknown source introduced exogenous right-hand side ORF-K15(M) sequences into an ancient M form of HHV8, followed by eventual acquisition into the subtype C lineage of the modern P-form of the HHV8 genome and subsequent additional, more recent transfers by homologous recombination events into several subtype A and B lineages as well.

Alleles↗
PubMed2003

Five unique open reading frames of infectious laryngotracheitis virus are expressed during infection but are dispensable for virus replication in cell culture.

The chicken alphaherpesvirus infectious laryngotracheitis virus (ILTV) exhibits several unique genetic features including an internal inversion of a conserved part of the unique long genome region. At one end, this inversion is preceded by a cluster of five open reading frames (ORFs) of 335-411 codons, designated ORF A to ORF E, that are not present in any other known herpesvirus genome. In this report we analysed expression of these genes and identified the corresponding viral RNA and protein products. Northern blot analyses showed 3'-coterminal transcripts of ORFs A and B, and monocistronic mRNAs of ORFs C and D. ORF E is part of a 3'-coterminal transcription unit that includes the conserved glycoprotein H and thymidine kinase genes. Monospecific antisera obtained after immunization of rabbits with bacterial fusion proteins allowed detection of the protein products of ORF A (40 kDa), ORF B (34 kDa), ORF C (38 and 30 kDa), ORF D (41 kDa) and ORF E (44 kDa) in ILTV-infected cells. For functional analyses, five virus recombinants possessing deletions within the individual ORFs and concomitant insertions of a reporter gene cassette encoding green fluorescent protein were generated. All virus mutants were replication competent in cell culture, but exhibited reduced virus titres or plaque sizes when compared to wild-type ILTV. These findings indicate that the ILTV-specific ORF A to ORF E genes might be important for virus replication in the natural host organism.

Animals↗
PubMed1993

Translation of the placenta growth factor mRNA is severely affected by a small open reading frame localized in the 5' untranslated region.

The recently identified placenta growth factor gene (PIGF) code for a protein related to the vascular permeability factor (VPF). We present evidence indicating that expressing of this gene could be regulated at the post-transcriptional level. The region upstream to the coding region of PIGF mRNA contains a small open reading frame (ORF), potentially coding for a peptide of 15 amino acids. The translation of different constructs in reticulocyte and wheat germ lysates as well as in COS-1 and CV-1 cells indicates that this short region is a translational inhibitory element since mutations in its two potential initiator codons increase PIGF synthesis in vivo. Using RNAse protection assay, we demonstrate that the PIGF mRNAs obtained from human term placenta and JEG choriocarcinoma cell line have a complete 5' untranslated region and, consequently, also the above mentioned small ORF. Finally, the analysis of a bovine PIGF genomic clone reveals that this small ORF is strongly conserved with respect to both putative peptide sequences and distance from the PIGF coding region.

Amino Acid Sequence↗
PubMed2000

Sinorhizobium fredii USDA257, a cultivar-specific soybean symbiont, carries two copies of y4yA and y4yB, two open reading frames that are located in a region that encodes the type III protein secretion system.

Sinorhizobium fredii USDA257 forms nitrogen-fixing nodules on primitive soybean (Glycine max) cultivar Peking but fails to nodulate the improved cultivar McCall. Cultivar specificity is governed by a plasmid-borne locus, nolXBTUV. By DNA sequence analysis, we have identified two open reading frames, y4yA and y4yB, immediately downstream of nolX. Northern (RNA) blot analysis indicated that the expression of both y4yA and y4yB is inducible by isoflavonoids, and an intact copy of nolX is required. Two copies each of y4yA and y4yB are present in S. fredii USDA257, one on the sym plasmid (y4yAsp and y4yBsp), and the other on the chromosome (y4yAc and y4yBc). The cultivar-nonspecific strain USDA191 lacks y4yAc and y4yBc. Introduction of y4yAc plus y4yBc from USDA257 into USDA191 did not influence the ability of the latter strain to nodulate McCall soybean plants. Unlike nolX, the inactivation of y4yAsp and y4yBsp of USDA257 did not extend the host range of this strain. A double mutant, in which both the plasmid and chromosomal copies of y4yA and y4yB were mutated, had no observable effect on symbiotic ability of USDA257. The y4yAsp and y4yBsp mutants did not influence flavonoid-dependent extracellular protein production. Rhizobium sp. strain NGR234 and S. saheli USDA4893 both contain sequences similar to S. fredii USDA257 y4yAsp and y4yBsp; however, Bradyrhizobium spp., the traditional soybean symbionts, lack these genes.

Amino Acid Sequence↗
PubMed1998

The major open reading frame of the beta2.7 transcript of human cytomegalovirus: in vitro expression of a protein posttranscriptionally regulated by the 5' region.

beta2.7 is the major early transcript produced during human cytomegalovirus infection. This abundantly expressed RNA is polysome associated, but no protein product has ever been detected. In this study, a stable peptide of 24 kDa was produced in vitro from the major open reading frame (ORF), TRL4. Following transient transfection, the intracellular localization was nucleolar and the expression was posttranscriptionally inhibited by the 5' sequence of the transcript, which harbors two short upstream ORFs.

Animals↗
PubMed1999

Human herpesvirus 6 open reading frame U83 encodes a functional chemokine.

Some viruses including herpesviruses have undergone evolution to benefit viral infection and propagation by pirating and modifying host genes such as chemokine genes. Human herpesvirus 6 (HHV-6), acutely or persistently infects mononuclear cells in vitro. DNA sequence analysis of HHV-6 has revealed that the putative protein encoded by an open reading frame (ORF) of the U83 gene in HHV-6 variant B resembled a human chemokine. We have cloned the U83 gene and analyzed the biological function of this gene. The U83 gene contained an ORF encoding a 113-amino-acid peptide, starting at the first methionine and containing a possible signal peptide and the typical cysteine residues characteristic of the chemokines. Reverse transcription-PCR analysis of mRNA and immunofluorescent-antibody testing of infected cells both indicated that the encoded protein was a late protein. The ORF U83 gene fused to the Fc gene was expressed as a fusion protein in COS-7 cells by transfection, and the fusion protein was purified from the supernatant of transfected cells to test its biological function. The purified protein was capable of inducing transient calcium mobilization in THP-1 cells and of chemotactically activating THP-1 cells. These findings suggested that the U83 protein might play an important role in HHV-6 propagation in vivo by activating and trafficking mononuclear cells to sites of viral replication, thus aiding the development of superbly efficient virus production mechanisms.

Amino Acid Sequence↗
PubMed1996

Human cytomegalovirus (HCMV) smallest capsid protein identified as product of short open reading frame located between HCMV UL48 and UL49.

The capsid of cytomegalovirus contains an abundant, low-molecular-weight protein whose coding sequence within the viral genome had not been identified. We have used a combination of biochemical and immunological techniques to demonstrate that this protein, called the smallest capsid protein in human cytomegalovirus, is encoded by a previously unidentified 225-bp open reading frame (ORF) located between ORFs UL48 and UL49. This short ORF, called UL48/49, is the positional homolog of herpes simplex virus ORF UL35 (encoding capsid protein VP26) and shows partial amino acid sequence identity to positional homologs in human herpes viruses 6 and 7.

Amino Acid Sequence↗
PubMed1989

Identification of L2 open reading frame gene products of bovine papillomavirus type 1 using monoclonal antibodies.

Four hybridoma cell lines producing monoclonal antibodies (MAbs) to bovine papillomavirus type 1 (BPV-1) L2 open reading frame (ORF) gene products have been established from mice immunized with a BPV-1 L2-beta-galactosidase fusion protein. Hybridomas were selected and cloned (from over 700 hybridomas) on the basis of specific reactivity of supernatant fluids with BPV-1 L2 epitopes on disrupted BPV-1 particles and L2-beta-galactosidase fusion proteins by ELISA and Western blotting, and with acetone-fixed frozen sections of BPV-1-induced fibropapillomas by immunofluorescence. These MAbs were not reactive with intact BPV-1 particles or BPV-1 L1-beta-galactosidase fusion proteins by ELISA or with beta-galactosidase by ELISA and Western blotting. The four MAbs detected viral structural proteins of Mr 76K, 68K and possibly 55K in purified BPV-1 preparations by Western blotting. Two of the four MAbs were cross-reactive with BPV-2-induced fibropapillomas. These findings suggest that (i) the BPV-1 L2 ORF encodes the minor capsid protein(s), (ii) the gene products of the BPV-1 L2 ORF have Mr values of 76K, 68K and possibly 55K, (iii) minor capsid epitopes are internal to the BPV-1 particle, and (iv) MAbs reactive with genetically engineered truncated BPV-1 L2 ORF gene products can distinguish between BPV-1 and BPV-2 productive infections.

Animals↗
PubMed1997

Transcription of the derepressed open reading frame P of herpes simplex virus 1 precludes the expression of the antisense gamma(1)34.5 gene and may account for the attenuation of the mutant virus.

Open reading frame P (ORF P), located at the 3' terminus of the 8.5-kb DNA sequence transcribed during latency and almost completely antisense to the gamma(1)34.5 gene, is naturally repressed by infected cell protein 4 (ICP4), the major herpes simplex virus 1 regulatory protein. Earlier studies on cells infected with a mutant in which the expression of ORF P is derepressed have shown that (i) the accumulation of the alpha infected cell proteins 0 (ICP0) and 22 (ICP22), the products of spliced mRNAs, is reduced congruent with the binding of ORF P protein to p32, a component of the ASF/SF2 splicing factors, (ii) ORF P protein colocalizes with spliceosomes, (iii) both gamma(1)34.5 mRNA and protein are virtually undetectable, and (iv) the virus is attenuated on intracerebral inoculation in mice. We report the construction and characterization of two recombinant viruses: R7546, in which ORF P transcription was derepressed and the initiator methionine codon was replaced; and R7547, in which both mutations were repaired to the wild-type genotype. The mutations in R7546 do not alter the amino acid sequence of the gamma(1)34.5 gene. We report that (i) the reduction in the accumulation of gamma(1)34.5 mRNA and protein in cells infected with mutant viruses expressing derepressed ORF P genes reflects the effects of antisense transcription of ORF P rather than a function of ORF P protein, (ii) the attenuated phenotype of the viruses carrying derepressed ORF P genes is due largely to the absence of the gamma(1)34.5 protein, and (iii) the reduction in accumulation of ICP0 and ICP22 requires the expression of ORF P protein.

Alternative Splicing↗
PubMed1999

Characterization of Varicella-Zoster virus glycoprotein K (open reading frame 5) and its role in virus growth.

Varicella-zoster virus (VZV) is an alphaherpesvirus that is the causative agent of chickenpox and herpes zoster. VZV open reading frame 5 (ORF5) encodes glycoprotein K (gK), which is conserved among alphaherpesviruses. While VZV gK has not been characterized, and its role in viral replication is unknown, homologs of VZV gK in herpes simplex virus type 1 (HSV-1) and pseudorabies virus (PRV) have been well studied. To identify the VZV ORF5 gene product, we raised a polyclonal antibody against a fusion protein of ORF5 codons 25 to 122 with glutathione S-transferase and used it to study the protein in infected cells. A 40,000-molecular-weight protein was detected in cell-free virus by Western blotting. In immunogold electron microscopic studies, VZV gK was in enveloped virions and was evenly distributed in the cytoplasm in infected cells. To determine the function of VZV gK in virus growth, a series of gK deletion mutants were constructed with VZV cosmid DNA derived from the Oka strain. Full and partial deletions in gK prevented viral replication when the gK mutant cosmids were transfected into melanoma cells. Insertion of the HSV-1 (KOS) gK gene into the endogenous VZV gK site did not compensate for the deletion of VZV gK. The replacement of VZV gK at a nonnative AvrII site in the VZV genome restored the phenotypic characteristics of intact recombinant Oka (rOka) virus. Moreover, gK complementing cells transfected with a full gK deletion mutant exhibited viral plaques indistinguishable from those of rOka. Our results are consistent with the studies of gK proteins of HSV-1 and PRV showing that gK is indispensable for viral replication.

Amino Acid Sequence↗
PubMed2000

Negative and translation termination-dependent positive control of FLI-1 protein synthesis by conserved overlapping 5' upstream open reading frames in Fli-1 mRNA.

The proto-oncogene Fli-1 encodes a transcription factor of the ets family whose overexpression is associated with multiple virally induced leukemias in mouse, inhibits murine and avian erythroid cell differentiation, and induces drastic perturbations of early development in Xenopus. This study demonstrates the surprisingly sophisticated regulation of Fli-1 mRNA translation. We establish that two FLI-1 protein isoforms (of 51 and 48 kDa) detected by Western blotting in vivo are synthesized by alternative translation initiation through the use of two highly conserved in-frame initiation codons, AUG +1 and AUG +100. Furthermore, we show that the synthesis of these two FLI-1 isoforms is regulated by two short overlapping 5' upstream open reading frames (uORF) beginning at two highly conserved upstream initiation codons, AUG -41 and GUG -37, and terminating at two highly conserved stop codons, UGA +35 and UAA +15. The mutational analysis of these two 5' uORF revealed that each of them negatively regulates FLI-1 protein synthesis by precluding cap-dependent scanning to the 48- and 51-kDa AUG codons. Simultaneously, the translation termination of the two 5' uORF appears to enhance 48-kDa protein synthesis, by allowing downstream reinitiation at the 48-kDa AUG codon, and 51-kDa protein synthesis, by allowing scanning ribosomes to pile up and consequently allowing upstream initiation at the 51-kDa AUG codon. To our knowledge, this is the first example of a cellular mRNA displaying overlapping 5' uORF whose translation termination appears to be involved in the positive control of translation initiation at both downstream and upstream initiation codons.

3T3 Cells↗
PubMed2001

Human cytomegalovirus open reading frame TRL11/IRL11 encodes an immunoglobulin G Fc-binding protein.

Several herpesviruses encode Fc receptors that may play a role in preventing antibody-mediated clearance of the virus in vivo. Human cytomegalovirus (HCMV) induces an Fc-binding activity in cells upon infection, but the gene that encodes this Fc-binding protein has not been identified. Here, we demonstrate that the HCMV AD169 open reading frame TRL11 and its identical copy, IRL11, encode a type I membrane glycoprotein that possesses IgG Fc-binding capabilities.

Amino Acid Sequence↗
PubMed1992

The open reading frames in the 3' long terminal repeats of several mouse mammary tumor virus integrants encode V beta 3-specific superantigens.

Mice expressing the minor lymphocyte stimulation antigens, Mls-1a, -2a, or -3a, singly on the B10.BR background have been generated. Mls phenotypes correlate with the integration of mouse mammary tumor viruses (MTV) in the mouse genome. The open reading frames within the 3' long terminal repeats of the integrated MTVs 1, 3, 6, and 13 encode V beta 3-specific superantigens. Sequence data for these viral superantigens is presented, indicating that it is the COOH-terminal portion of the viral superantigen that interacts with the T cell receptor V beta element.

Amino Acid Sequence↗
PubMed2004

Varicella-Zoster virus proteins encoded by open reading frames 14 and 67 are both dispensable for the establishment of latency in a rat model.

A rat model of Varicella-Zoster virus (VZV) provides a system in which to investigate the molecular determinants of viral latency in dorsal root ganglia (DRG). In this study, we determined whether the VZV glycoproteins gC and gI, corresponding to VZV open reading frames (ORFs) 14 and 67, respectively, were required for the establishment of latency in this model. A VZV gI deletion mutant (DeltagI) derived from a recombinant Oka (rOka) cosmid and a gC null mutant obtained from a clinical isolate were inoculated into the footpads of 6-week-old rats, and the presence of viral DNA and eight different VZV RNA transcripts corresponding to the three classes of genes was investigated by in situ RT-PCR amplification and in situ hybridization (ISH) in the DRG at 1 week, 1 month, and 18-24 months after infection. VZV DNA and restricted RNA expression was established with both deletion mutants as well as the parental rOka virus. Both VZV DNA and RNA were detected in neurons and non-neuronal cells. The pattern of viral RNA expression detected with both gC and gI mutants was restricted with transcripts for VZV genes 62 and 63 most frequently expressed 18-24 months after infection. Transcripts for VZV genes 18, 28, and 29 were also detected at these time points but at a slightly lower frequency. Transcripts for the late gene 40 were never detected. We conclude that VZV ORFs 14 and 67 are dispensable for the establishment of a latent infection in this model.

Animals↗
PubMed1999

Systematic identification, classification, and characterization of the open reading frames which encode novel helicase-related proteins in Saccharomyces cerevisiae by gene disruption and Northern analysis.

Helicase-related proteins play important roles in various cellular processes incuding DNA replication, DNA repair, RNA processing and so on. It has been well known that the amino acid sequences of these proteins contain several conserved motifs, and that the open reading frames (ORFs) which encode helicase-related proteins make up several gene families. In this study, we have identified 134 ORFs that encode helicase-like proteins in the Saccharomyces genome, based on similarity with the ORFs of authentic helicase and helicase-related proteins. Multiple alignment of the ORF sequences resulted in the 134 ORFs being classified to 11 clusters. Seven out of 21 previously uncharacterized ORFs (YDL031w, YDL070w, YDL084w, YGL150c, YKL078w, YLR276c, and YMR128w) were identified by systematic gene disruption, to be essential for vegetative growth. Three (YDR332w, YGL064c, and YOL095c) out of the remaining 14 dispensable ORFs exhibited the slow-growth phenotype at 30 degrees C and 37 degrees C. Furthermore, the expression profiles of transcripts from 43 ORFs were examined under seven different growth conditions by Northern analysis and reverse transcription-polymerase chain reaction, indicating that all of the 43 tested ORFs were transcribed. Interestingly, we found that the level of transcript from 34 helicase-like genes was markedly increased by heat shock. This suggests that helicase-like genes may be involved in the biosynthesis of nucleic acids and proteins, and that the genes can be transcriptionally activated by heat shock to compensate for the repressed synthesis of mRNA and protein.

Amino Acid Sequence↗
PubMed1995

Strategy for deletion of complete open reading frames in Saccharomyces cerevisiae.

The classical disruption method for yeast genes is by using in vitro deletion of the gene of interest, or of a part of it, with restriction enzymes. We are now routinely using a strategy that takes advantage of polymerase chain reactions (PCRs) which amplify large pieces of DNA. Since this approach results in a complete, precise deletion of the open reading frame, which is replaced by a unique restriction site, the ligated PCR can be used for the insertion of different markers or for two-step gene disruptions without an inserted marker. As we have now used this strategy for the deletion of more than ten genes we have in this report included some hints based on our experience.

Gene Deletion↗