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PubMed1997

The sequence of a 8 kb segment on the right arm of yeast chromosome VII identifies four new open reading frames and the genes for yTAFII145.

We report the sequence of a 8,061 bp fragment of Saccharomyces cerevisiae chromosome VII. Five open reading frames (ORFs) of at least 100 amino acids were identified. Three show similarities to the amino-acid sequence of known gene products. ORF G9374 corresponds to the gene coding for the yTAFII145 protein: a TBP-associated factor whose amino-acid sequence was previously reported (Reese et al., 1994). The remaining ORF does not display similarities to known sequences.

Amino Acid Sequence↗

PubMed1984

A large interspersed repeat found in mouse DNA contains a long open reading frame that evolves as if it encodes a protein.

DNA sequence analysis of a region contained within a large, interspersed repetitive family of mice reveals a long open reading frame. This sequence extends 978 base pairs between two stop codons, creating a reading frame that is open for 326 amino acids. The DNA sequence in this region is conserved between three distantly related Mus species, as well as between mouse and monkey, in a manner that is characteristic of regions undergoing selection for protein function.

Amino Acid Sequence↗

PubMed1986

The adjacent dnaZ and dnaX genes of Escherichia coli are contained within one continuous open reading frame.

The dnaZ and dnaX loci of Escherichia coli have been genetically defined as separate genes, both of which are essential for DNA replication (1). The 2.1 kb region of DNA that complements mutations in both genes has a maximum coding capacity of approximately 80,000 daltons. Two protein products are produced from this region with molecular weights of 77,000 and 52,000 (2,3). We have sequenced a 2.7 kb fragment containing the dnaZ and dnaX genes and determined that it contains only one open reading frame of sufficient length to encode either of these proteins. This open reading frame may encode a protein of 71,147 daltons or of 68,451 daltons depending on which potential translational initiation codon is utilized. There are two transcriptional promoters preceding the gene as well as a ribosome binding site preceding the two potential initiation codons. Both the promoters and ribosome binding sites are predicted to be weak, perhaps contributing to the low expression of these genes.

Base Sequence↗

PubMed1993

Identification of C-terminal amino acid residues of cauliflower mosaic virus open reading frame III protein responsible for its DNA binding activity.

We cloned in Escherichia coli truncated versions of the protein p15 encoded by open reading frame III of cauliflower mosaic virus. We then compared the ability of the wild-type p15 (129 amino acids) and the deleted p15 to bind viral double-stranded DNA genome. Deletions of > 11 amino acids in the C-terminal proline-rich region resulted in loss of DNA binding activity of wild-type p15. Moreover, a point mutation of the proline at position 118 sharply reduced the interaction between the viral protein and DNA. These results suggest that cauliflower mosaic virus p15 belongs to the family of DNA binding proteins having a proline-rich motif involved in interaction with double-stranded DNA.

Amino Acid Sequence↗

PubMed1995

The sequence of a 27 kb segment on the right arm of chromosome VII from Saccharomyces cerevisiae reveals MOL1, NAT2, RPL30B, RSR1, CYS4, PEM1/CHO2, NSR1 genes and ten new open reading frames.

The DNA sequence of a 26,677 bp fragment from the right arm of chromosome VII from Saccharomyces cerevisiae reveals 18 open reading frames (ORFs) longer than 300 bp. Eight ORFs correspond to previously characterized genes. G6620 is the 3' end of the MOL1 gene coding for a polypeptide similar to stress-inducible proteins from Fusarium; G6630 is the NAT2 gene which encodes a methionine N-acetyltransferase; G6635 is the RPL30B gene coding for the ribosomal protein L30; G6658 is RSR1 encoding a ras-related protein; G6667 is CYS4, the gene for cystathionine beta-synthase; G6670 is identical to ORF2 located close to CYS4; G6673 is PEM1/CHO2 encoding a phosphatidylethanolamine methyltransferase; G7001 is the NSR1 gene coding for a nuclear signal recognition protein. G6664 shares significant homology with the ORF YKR076w from chromosome XI. The other nine ORFs show no significant homology to any protein sequence presently available in the public data bases.

Amino Acid Sequence↗

PubMed2001

Transgenic tobacco plants expressing the potato virus X open reading frame 3 gene develop specific resistance and necrotic ring symptoms after infection with the homologous virus.

Tobacco plants were transformed with the open reading frame 3 gene from Potato virus X (PVX) coding for the p12 protein. Although the transgenic plants exhibited a normal morphological aspect, microscopic examination revealed extensive alterations in leaf tissue structure. After being challenged with PVX, the transgenic plants showed resistance to PVX infection and formation of specific leaf symptoms consisting of concentric rings encircled by necrotic borders. These novel symptoms were accompanied by biochemical changes normally associated with the hypersensitive response (HR) and were absent in noninfected transgenic plants or in PVX-infected nontransgenic plants. No equivalent virus resistance was observed after inoculation with Tobacco mosaic virus or Potato virus Y, suggesting the presence of a specific resistance mechanism. Despite development of HR-like symptoms, systemic acquired resistance was not induced in PVX-infected p12 transgenic plants. No evidence of an RNA-mediated resistance mechanism was found.

Capsid↗

PubMed1997

Multiple human endogenous retrovirus (HERV-K) loci with gag open reading frames in the human genome.

Human endogenous retrovirus HERV-K is present in 25-30 copies per haploid human genome. At least one of these loci is capable of producing full-length Gag protein, high amounts of which have been detected in germ cell tumors and derived cell lines. The latter display HERV-K Gag-encoded retroviral particles. Here, we employed the protein truncation test (PTT) in combination with a monochromosomal hybrid mapping panel to identify the human chromosomes harboring HERV-K gag genes with an open reading frame for Gag protein. Eight human chromosomes were found to contain intact HERV-K gag genes. PTT results were corroborated by partial sequencing of subregions from different HERV-K gag genes. The high number of HERV-K Gag open reading frames supports the idea of retroviral sequences retaining a biological benefit in the human genome.

Animals↗

PubMed1988

The positive regulatory function of the 5'-proximal open reading frames in GCN4 mRNA can be mimicked by heterologous, short coding sequences.

Translational control of GCN4 expression in the yeast Saccharomyces cerevisiae is mediated by multiple AUG codons present in the leader of GCN4 mRNA, each of which initiates a short open reading frame of only two or three codons. Upstream AUG codons 3 and 4 are required to repress GCN4 expression in normal growth conditions; AUG codons 1 and 2 are needed to overcome this repression in amino acid starvation conditions. We show that the regulatory function of AUG codons 1 and 2 can be qualitatively mimicked by the AUG codons of two heterologous upstream open reading frames (URFs) containing the initiation regions of the yeast genes PGK and TRP1. These AUG codons inhibit GCN4 expression when present singly in the mRNA leader; however, they stimulate GCN4 expression in derepressing conditions when inserted upstream from AUG codons 3 and 4. This finding supports the idea that AUG codons 1 and 2 function in the control mechanism as translation initiation sites and further suggests that suppression of the inhibitory effects of AUG codons 3 and 4 is a general consequence of the translation of URF 1 and 2 sequences upstream. Several observations suggest that AUG codons 3 and 4 are efficient initiation sites; however, these sequences do not act as positive regulatory elements when placed upstream from URF 1. This result suggests that efficient translation is only one of the important properties of the 5' proximal URFs in GCN4 mRNA. We propose that a second property is the ability to permit reinitiation following termination of translation and that URF 1 is optimized for this regulatory function.

Base Sequence↗

PubMed1996

Sequence analysis of a 13.4 kbp fragment from the left arm of chromosome XV reveals a malate dehydrogenase gene, a putative Ser/Thr protein kinase, the ribosomal L25 gene and four new open reading frames.

A 13421 bp fragment located near the left telomere of chromosome XV (cosmid pEOA461) has been sequenced. Seven non-overlapping open reading frames (ORFs) encoding polypeptides longer than 100 residues have been found (AOB859, AOC184, AOE375, AOX142i, AOE423, AOA476 and AOE433). An additional ORF (AOE131) is found within AOA476. Three of them (AOC184, AOA476 and AOE433) show no remarkable identity with proteins deposited in the data banks. ORF AOB859 is quite similar to a hypothetical yeast protein of similar size located in chromosome VI, particularly within the C-terminal half. AOE375 encodes a new member of the glycogen synthase kinase-3 subfamily of Ser/Thr protein kinases. AOX142i is the gene encoding the previously described ribosomal protein L25. AOE423 codes for a protein virtually identical to the MDH2 malate dehydrogenase isozyme. However, our DNA sequence shows a single one-base insertion upstream of the reported initiating codon. This would produce a larger ORF by extending 46 residues the N-terminus of the protein. The existence of this insertion has been confirmed in three different yeast strains, including FY1679.

Amino Acid Sequence↗

PubMedDate not supplied

[Expression of the third open reading frame of the drosophila MDG4 retrotransposon similar to the retroviral env-genes, occurring through splicing].

The presence of a third long open reading frame (ORF3) is the common feature of a number of Drosophila retrotransposons, including MDG4 (gypsy). Thus, these elements have a strong structural resemblance to the integrated forms of vertebrate retroviruses. To elucidate the mode of expression of ORF3, transcription analysis of MDG4 for several D. melanogaster strains and Schneider 2 cultured cells was carried out. In all cases the analysis revealed the presence of 2-kb subgenomic ORF3 transcripts in the polyadenylated RNA fractions. It was shown by using the cDNA-PCR technique with different sets of primers that these subgenomic 2-kb RNAs are generated through splicing of full-length MDG4 transcripts. In all cases, only one DNA fragment is amplified for each suitable pair of primers, indicating that there is probable no alternative splicing during the ORF3 expression. The primary structure of spliced RNA was determined, and its analysis shows that both MDG4 subfamilies (6K and 7K) are apparently able to encode functionally active translation products of ORF3. The regulation at the level of splicing is supposed to be one of the most important factors controlling the transposition frequency of MDG4.

Alternative Splicing↗

PubMed1993

A novel open reading frame in tobacco mosaic virus genome coding for a putative small, positively charged protein.

From sequence comparisons between the tobramovirus genomes an open reading frame (ORF-X) potentially encoding a small, positively charged protein (33- to 45-amino-acids long) was found to overlap the immediate 3' and 5' sides of the transport protein gene and coat protein gene, respectively. In vitro translation of the monocistronic artificial transcripts generated with T7 RNA polymerase yielded a protein of M(r) 4000 (p4) and an unexpected trypsin-sensitive complex of M(r) 54,000 that was resistant to reduction with 2-mercaptoethanol but could be dissociated by 8 M urea. Assembly of this complex was inhibited completely by site-directed mutagenesis within a conserved, positively charged 5-amino-acid long segment of the ORF-X protein. After centrifugation in low salt buffer the 54-kDa complex remained mostly associated with ribosomes. Apparently this complex represents a specific aggregate of the p4 product of ORF-X with a protein of approximate M(r) 50,000 that is a component of the translation apparatus.

Amino Acid Sequence↗

PubMed1992

Role of the open reading frames of Rous sarcoma virus leader RNA in translation and genome packaging.

The Rous sarcoma virus (RSV) RNA leader sequence carries three open reading frames (uORFs) upstream of the AUG initiator of the gag gene. We studied, in vivo, the role of these uORFs by changing two or three nucleotides of the three AUGs or by deleting the first uORF. Our results show that (i) unlike most previously characterized uORFs, which decrease translation, the first uORF (AUG1) of RSV acts as an enhancer of translation, since absence of the first AUG decreased translation; AUG3 also modulates translation, probably by interfering with scanning ribosomes as described for other upstream ORFs, and mutation of AUG2 had no effect on translation. (ii) Mutation of each of the upstream AUGs lowered the infectivity of progeny virions. (iii) Unexpectedly, mutation of AUG1 and/or AUG3 dramatically reduced RNA packaging by 50-to 100-fold, unlike mutation of AUG2 which did not alter RNA packaging efficiency. Additional mutants in the vicinity of uORF1 and uORF3 were constructed in order to elucidate the mechanism by which uORFs affect RNA packaging: a translation model requiring uORFs 1 and 3, and involving ribosome pausing at AUG 3 is discussed.

Amino Acid Sequence↗

PubMed2002

Memory cytotoxic T cell responses to viral tegument and regulatory proteins encoded by open reading frames 4, 10, 29, and 62 of varicella-zoster virus.

Cytotoxic T cell recognition of tegument and regulatory proteins encoded by open reading frames (ORFs) 4, 10, 29, and 62 of varicella-zoster virus (VZV) was evaluated using limiting dilution conditions to estimate the precursor frequencies of memory T cells specific for these proteins in immune subjects. Responder cell frequencies for ORFs 4, 10, and 62 gene products, which are virion tegument components and function as immediate early viral transactivating proteins, were equivalent. CTLp recognition of VZV proteins made in latently infected cells, which include ORF4 and ORF62 proteins, was not maintained preferentially when compared to ORF10 protein, which has not been shown to be expressed during latency. T cell recognition of ORF29 protein, the major DNA binding protein, which is expressed during replication but not incorporated into the virion tegument, was less common than responses to ORFs 4, 10, and 62 gene products. Older individuals had diminished numbers of memory CTLp that lysed autologous targets expressing IE62 protein; these responses were increased after immunization with live attenuated varicella vaccine to the range observed in younger adults. Adaptive immunity to VZV is characterized by a broad repertoire of memory CTL responses to proteins that comprise the virion tegument and regulate viral gene expression in infected cells.

Adult↗

PubMed1986

Nucleotide sequence of RNA segment 7 of influenza B/Singapore/222/79: maintenance of a second large open reading frame.

The nucleotide sequence of RNA segment 7 of influenza B/Singapore/222/79 has been determined. The deduced amino acid sequence of the M1 protein indicates that it contains 248 amino acids of which 243 are identical in the B/Lee/40 M1 protein. A second overlapping open reading frame with a maximum coding region of 195 amino acids has also been maintained in the 39 years separating the two isolates. The deduced amino acid sequence of the second coding region displays 86% homology with the comparable B/Lee/40 sequence (27 changes). The conservation of the second open reading frame suggests that this region is important in the replicative cycle of influenza B viruses.

Base Sequence↗

PubMed1993

Varicella-zoster virus open reading frame 10 protein, the herpes simplex virus VP16 homolog, transactivates herpesvirus immediate-early gene promoters.

The varicella-zoster virus (VZV) open reading frame 10 (ORF10) protein is the homolog of the herpes simplex virus type 1 (HSV-1) protein VP16. These are two virion tegument proteins that have extensive amino acid sequence identity in their amino-terminal and middle domains. ORF10, however, lacks the acidic carboxy terminus which is critical for transactivation by VP16. Earlier studies showed that VZV ORF10 does not form a tertiary complex with the TAATGARAT regulatory element (where R is a purine) with which HSV-1 VP16 interacts, suggesting that ORF10 may not have transactivating ability. Using transient-expression assays, we show that VZV ORF10 is able to transactivate VZV immediate-early (IE) gene (ORF62) and HSV-1 IE gene (ICP4 and ICP0) promoters. Furthermore, cell lines stably expressing ORF10 complement the HSV-1 mutant in1814, which lacks the transactivating function of VP16, and enhance the de novo synthesis of infectious virus following transfection of HSV-1 virion DNA. These results indicate that ORF10, like its HSV-1 homolog VP16, is a transactivating protein despite the absence of sequences similar to the VP16 carboxy-terminal domain. The transactivating function of the VZV ORF10 tegument protein may be critical for efficient initiation of viral infection.

Amino Acid Sequence↗

PubMed1998

The US5 open reading frame of herpes simplex virus type 1 does encode a glycoprotein (gJ).

Based on sequence analysis, the protein encoded by the US5 open reading frame (ORF) of herpes simplex virus type 1 (HSV-1) was predicted to contain an N-glycosylation site and was given the designation of glycoprotein J (gJ). However, the US5 gene product has not been identified and the identity of gJ as a glycoprotein has not been confirmed. We have cloned and expressed the DNA encoding the complete sequence of the US5 ORF, using a baculovirus expression system. Western blotting, using polyclonal antibody raised against synthetic US5 peptides, revealed two major baculovirus-US5-expressed protein bands with apparent molecular weights of 16-17 and 10 kD. The recombinant US5 was found on the membrane of Spodoptera frugiperda cells and was susceptible to tunicamycin, endoglycosidase H, glycosidase F and partially resistant to endoglycosidase F. Vaccination of mice with baculovirus-expressed US5 did not induce a neutralizing antibody to HSV-1 or provide protection against lethal HSV-1 challenge. However, serum from these vaccinated mice was able to recognize US5 in purified HSV-1 virions by Western blot analyses and on the surface of HSV-1-infected cells by immunofluorescence. These findings establish that US5 does encode a glycoprotein and confirm the appropriateness of naming the US5 gene product gJ.

Amino Acid Sequence↗

PubMed1996

Rice tungro spherical virus: nucleotide sequence of the 3' genomic half and studies on the two small 3' open reading frames.

Rice tungro spherical virus (RTSV) consists of a single-stranded RNA genome of about 12 kilobases that contains one large open reading frame, ORF 1 and two small ORFs 2 and 3 at its 3' end (Shen et al., 1993, Virology 193:621-630); it was suggested that ORF 2 was expressed via a frameshift. To study the genomic information of RTSV and the variation between different RTSV isolates, the 3' half of a Philippine isolate and parts of a Thai and an Indian isolate were cloned and sequenced. Significant sequence differences were found in ORF 2 and in the 3' non-translated region. Additional stop codons have been revealed in the previously described ORF 2 in several independent clones from the three different virus isolates, the most conserved stop codon in the middle of ORF 2 being confirmed by direct RNA sequencing. These results suggest that ORF 2 could only express a peptide of about 5 kDa instead of 12 kDa as proposed earlier. Polyclonal antisera were raised against ORF 2 and 3 proteins as fusions with glutathione-S-transferase. Using these antisera we failed to detect any virus-specific peptides in extracts from infected rice plants and in virus preparations. The nucleotide sequence of the 3' end of our RTSV isolates contains several small ORFs and does not contain a repeat of 256 nucleotides found in the published sequence. These results indicate that RTSV could contain an unusually long 3' non-coding region of 1240 nucleotides in length.

Amino Acid Sequence↗

PubMed2006

Neither the RNA nor the proteins of open reading frames 3a and 3b of the coronavirus infectious bronchitis virus are essential for replication.

Gene 3 of infectious bronchitis virus is tricistronic; open reading frames (ORFs) 3a and 3b encode two small nonstructural (ns) proteins, 3a and 3b, of unknown function, and a third, structural protein E, is encoded by ORF 3c. To determine if either the 3a or the 3b protein is required for replication, we first modified their translation initiation codons to prevent translation of the 3a and 3b proteins from recombinant infectious bronchitis viruses (rIBVs). Replication in primary chick kidney (CK) cells and in chicken embryos was not affected. In chicken tracheal organ cultures (TOCs), the recombinant rIBVs reached titers similar to those of the wild-type virus, but in the case of viruses lacking the 3a protein, the titer declined reproducibly earlier. Translation of the IBV E protein is believed to be initiated by internal entry of ribosomes at a structure formed by the sequences corresponding to ORFs 3a and 3b. To assess the necessity of this mechanism, we deleted most of the sequence representing 3a and 3b to produce a gene in which ORF 3c (E) was adjacent to the gene 3 transcription-associated sequence. Western blot analysis revealed that the recombinant IBV produced fivefold less E protein. Nevertheless, titers produced in CK cells, embryos, and TOCs were similar to those of the wild-type virus, although they declined earlier in TOCs, probably due to the absence of the 3a protein. Thus, neither the tricistronic arrangement of gene 3, the internal initiation of translation of E protein, nor the 3a and 3b proteins are essential for replication per se, suggesting that these proteins are accessory proteins that may have roles in vivo.

Animals↗