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PubMed1994

A novel approach to express a heterologous gene on Kluyveromyces lactis linear killer plasmids: expression of the bacterial aph gene from a cytoplasmic promoter fragment without in-phase fusion to the plasmid open reading frame.

Using the cytoplasmically localized killer plasmids pGKL1 and pGKL2 of Kluyveromyces lactis a new linear hybrid plasmid (pWKL1) was constructed. It consists of pGKL1 into which, in addition to the previously developed cytoplasmically expressible LEU2* selection marker, a phosphotransferase encoding bacterial antibiotic resistance gene has been integrated. In the hybrid plasmid pWKL1 this gene was preceded by a putative transcriptional signal from pGKL2, i.e., the upstream conserved sequence of ORF5 (UCS5). All foreign genes, so far integrated and expressed in linear plasmids, required in addition to a cytoplasmic promoter (UCS) an in phase fusion to the corresponding open reading frame. In this study the UCS5, not containing the translational start of ORF5, and the aph coding region were intentionally not combined in phase, in order to check whether expression can occur under these conditions. Kluyveromyces lactis transformants carrying pWKL1 were highly resistant against the antibiotic geneticine (G418) and exhibited elevated levels of APH activity. Expression of the aph gene was due to the presence of the UCS5 containing fragment (110 bp). Thus, an in phase fusion was not required for expression. This is the first report that, concomitant with a selectable marker gene, foreign DNA can be integrated in a linear plasmid via homologous recombination and more importantly, that in phase fusions are not required generally for expression of heterologous genes in linear plasmids.

Base Sequence↗

PubMed1992

Viral culture and p24 antigenemia of human immunodeficiency virus (HIV)-infected individuals correlated with antibody profiles determined with recombinant polypeptides of all HIV-1 open-reading frames.

The association between viral activity and antibody profiles was investigated in 202 individuals infected by the human immunodeficiency virus (HIV) grouped according to their Walter Reed clinical stage. Each study group was subdivided into subjects positive or negative for markers of active viral replication: presence of serum p24 antigen and viral culture. In Western blots using recombinant antigens, sera of HIV-positive individuals with positive viral markers had a significantly lower antibody reactivity to several viral proteins than did individuals without viral markers. Noticeably, proteins of the gag (p24, p17) and env (gp120, COOH-terminal part of gp41) open-reading frames revealed a decreased reactivity. The antibody response to the regulatory proteins revealed no or poor association with viral activity in the host. The results suggest that seroreactivity is mainly influenced by factors reflecting the viral activity of an HIV-infected individual, while the clinical stage of the patient is less important. Especially, reductions in antibodies against gp120 and p17 were useful markers associated with increased viral activity.

Adult↗

PubMed2000

The open reading frame 5A of foxtail mosaic virus is expressed in vivo and is dispensable for systemic infection.

Infectious transcripts were successfully derived from full-length cDNA clones of foxtail mosaic potexvirus (FoMV). Full-length clones were constructed by RT-PCR whereby 5' and 3' genomic segments of 2.7 and 3.4 kb, respectively, were ligated into Bluescript II KS. The in vitro RNA transcripts were infectious to moncotyledonous (barley) and dicotyledonous (Chenopodium amaranticolor) plant species. Individual mutation studies on clones of each of the five major ORFs confirmed predicted gene function for the polymerase, TGB (triple gene block), and coat protein (CP) genes. Protoplast studies on expression of a unique open reading frame, ORF 5A, which initiates 143 nts upstream of the CP before it "reads through" the CP, revealed that the 5A protein was produced in vivo. Mutation analysis of the 5A ORF indicated, however, that it was not required for either replication or for productive infection of plants. However, the nucleic acid sequences encoding the extended CP segment were shown to be important for CP expression. Additional mutations in 5A had no effect on FoMV replication in protoplasts but rendered the virus noninfectious to plants. A correlation with diminished CP production from both mutant clones implies that synthesis of subgenomic CP mRNA was compromised, and this limited systemic infection.

3' Untranslated Regions↗

PubMed1995

The tendency of lentiviral open reading frames to become A-rich: constraints imposed by viral genome organization and cellular tRNA availability.

Human immunodeficiency virus type 1 (HIV-1) and other lentiviridae demonstrate a strong preference for the A-nucleotide, which can account for up to 40% of the viral RNA genome. The biological mechanism responsible for this nucleotide bias is currently unknown. The increased A-content of these viral genomes corresponds to the typical use of synonymous codons by all members of the lentiviral family (HIV, SIV, BIV, FIV, CAEV, EIAV, visna) and the human spuma retrovirus, but not by other retroviruses like the human T-cell leukemia viruses HTLV-1 and HTLV-II. In this article, we analyzed A-bias for all codon groups in all open reading frames of several lentiviruses. The extent of lentiviral codon bias could be related to host cellular translation. By calculating codon bias indices (CBIs), we were able to demonstrate an inverse correlation between the extent of codon bias and the rate of translation of individual reading frames in these viruses. Specifically, the shift toward A-rich codons is more pronounced in pol than in gag lentiviral genes. Since it is known that Gag synthesis exceeds Pol synthesis by a factor of 20 due to infrequent ribosomal frame-shifting during translation of the gap-pol mRNA molecule, we propose that the aminoacyl-tRNA availability in the host cell restricts the lentiviral preference for A-rich codons. In addition, less A-nucleotides were found in regions of the viral genome encoding multiple functions; e.g., overlapping reading frames (tat-rev-env) or in genes that overlap regulatory sequences (nef-LTR region).(ABSTRACT TRUNCATED AT 250 WORDS)

Adenine↗

PubMed1990

The two open reading frames of the 22K mRNA of human respiratory syncytial virus: sequence comparison of antigenic subgroups A and B and expression in vitro.

The sequence of the 22K mRNA of strain 18537 of antigenic subgroup B of human respiratory syncytial virus (RSV) was determined by sequencing cloned cDNAs of intracellular mRNA. Comparison with the corresponding sequence of the A2 strain of subgroup A showed that there is 78% nucleotide sequence identity overall, that the amino acid sequence of the 22K protein is 92% identical between subgroups and that the 22K mRNA of both subgroups contains a second, internal, overlapping open reading frame (ORF) whose length, nucleotide sequence and potential translational start and stop sites were highly conserved and whose predicted product has 62% amino acid identity between subgroups. Sequence analysis of 36 cDNAs of intracellular 22K mRNA of strain A2 did not detect nucleotide insertions or deletions in the region of overlap between the two ORFs, indicating that the majority of intracellular 22K mRNA is a faithful copy containing the two distinct ORFs. Translation in vitro of mRNAs transcribed from engineered cDNAs showed that an mRNA which contained only the second, internal ORF directed the synthesis of a previously unidentified polypeptide of the predicted size, whereas mRNA representing the complete gene directed the synthesis of both the 22K protein and the product of the internal ORF. This latter species was synthesized in vitro as a discrete, separate protein rather than as a fusion protein. It is not yet known whether this protein is synthesized in RSV-infected cells.

Amino Acid Sequence↗

PubMed1996

Isolation and characterization of Marek's disease virus (MDV) cDNAs from a MDV-transformed lymphoblastoid cell line: identification of an open reading frame antisense to the MDV Eco-Q protein (Meq).

Two Marek's disease virus (MDV) cDNAs of 852 and 1168 bp, which map to the right end of the BamHI-I2 fragment of the MDV genome, were isolated from a cDNA library derived from the MDV transformed lymphoblastoid cell line MKT-1. These cDNAs hybridized to relatively abundant leftward mRNA transcripts in MKT-1 cells and cells lytically infected with MDV. The transcriptional initiation site for these transcripts was located in the adjacent BamHI-Q2 fragment, as determined by RNase protection and primer extension assays. A computer search for the presence of leftward open reading frames (ORFs) revealed two ORFs encoding 135- and 195-amino-acid polypeptides. A polyclonal antibody raised against a protein sequence in the N-terminus of the latter ORF detected a 23-kDa protein in the nuclear fraction of MDV-transformed lymphoblastoid cells. Furthermore, this ORF was antisense to part of the MDV Eco-Q protein (Meq) sequence.

Animals↗

PubMed1997

Establishment of a monkey kidney epithelial cell line with the BARF1 open reading frame from Epstein-Barr virus.

We previously reported that the BARF1 (BamH1-A right frame 1) gene product from Epstein-Barr Virus (EBV) may have oncogenic properties since injection into new-born rats of transfected cell lines resulted in the development of BARF1 expressing tumors, which were aggressive in the case of murine fibroblasts and transient in that of human B lymphocytes. As EBV has been associated with nasopharyngeal carcinoma (NPC) and evidence of BARF1 transcription in this cancer was emerging from our biopsy analyses, we examined the effects of BARF1 transfection into primate primary epithelial cells. The expression of the BARF1 open reading frame in primary monkey kidney epithelial cells led us to the establishment of continuously dividing lines. The BARF1 transfectants showed the major characteristics of immortalized cells: morphological change, short cell doubling time, ability to divide at low cell density and continuous growth over 50 passages. Injection of BARF1 transfectants into nude mice did not induce any tumor. Established subclones were shown to be epithelial cells expressing known keratins as well as the BARF1 coded mRNA and protein. This is the first report indicating that expression of the BARF1 gene product in primary epithelial cells may contribute to the establishment of cell lines.

Animals↗

PubMed2003

Virions of Pariacoto virus contain a minor protein translated from the second AUG codon of the capsid protein open reading frame.

Virions of the alphanodavirus Pariacoto virus (PaV) have T=3 icosahedral symmetry and are assembled from multiple copies of a precursor protein that is cleaved into two mature capsid proteins after assembly. The crystal structure of PaV shows that the N-terminal approximately 30 amino acid residues of the subunits surrounding the 5-fold axes interact extensively with icosahedrally ordered regions of the encapsidated positive-sense genomic RNAs. We found that wild-type PaV particles also contain a minor capsid protein that is truncated by 24 residues at its N terminus. Reverse genetic experiments showed that translation of this protein initiated at the second AUG of the capsid protein open reading frame. When either the longer or shorter version of the capsid protein was expressed independently of the other, it assembled into virus particles and underwent maturational cleavage. Virions that lacked the shorter capsid protein retained infectivity for cultured insect cells and Galleria mellonella larvae.

Animals↗

PubMed1991

Identification and nucleotide sequence analysis of an open reading frame involved in high-frequency conversion of turbid to clear plaque mutants of filamentous phage Cf1t.

Clear plaque mutants (Cf1c) isolated from the temperate filamentous phage Cf1t occurred at a frequency of approximately 10(-3). The pahge yield from Cf1c-infected cells was higher than that from Cf1t-infected cells. Results of spot complementation tests implied that the turbid plaque phenotype is dominant. DNA fragment substitution studies indicated that a NcoI/KpnI fragment of 591 bp was responsible for the determination of plaque turbidity. Sequence data from four Cf1c isolates revealed base pair alterations and a deletion located in the upstream region of an open reading frame (ORFII) which might encode a 18.2-kDa protein. When the ORFII in Cf1t was disrupted by a frameshift mutation, this recombinant phage formed clear plaques. These observations suggest that ORFII may participate in the formation of turbid plaques. ORFII does not show significant homology with the sequence of f1 gpII, gpV, or other known phage proteins.

Amino Acid Sequence↗

PubMed1998

Human T-cell leukemia virus type 1 reverse transcriptase (RT) originates from the pro and pol open reading frames and requires the presence of RT-RNase H (RH) and RT-RH-integrase proteins for its activity.

The first description of an active form of a recombinant human T-cell leukemia virus type 1 (HTLV-1) reverse transcriptase (RT) and subsequent predictions of its amino acid sequence and quaternary structure are reported here. By using amino acid alignment methods, the NH2 and COOH termini of the RT, RNase H (RH), and integrase (IN) domains of the Pol polyprotein were determined. The HTLV-1 RT seems to be unique since its NH2 terminus is probably encoded by the pro open reading frame (ORF) fused downstream, via a transframe peptide, to the polypeptide encoded by the pol ORF. The HTLV-1 Pol amino acid sequence was revealed to be highly similar to that of Rous sarcoma virus (RSV), particularly at the RT-RH hinge region. These two domains remain linked for RSV; this may also be the case for HTLV-1. In light of these results, RT, RT-RH, and RT-RH-IN genes were constructed and introduced into His-tagged protein expression vectors. The corresponding proteins were synthesized in vitro, and the DNA polymerase activities of different protein combinations were tested. Solely the RT-RH-RT-RH-IN combination was found to have a significant activity level. Velocity sedimentation analysis suggested that the HTLV-1 RT-RH and RT-RH-IN monomers are likely associated in an oligomeric structure, probably of the alpha3/beta type.

Amino Acid Sequence↗

PubMed1999

A stable hairpin preceded by a short open reading frame promotes nonlinear ribosome migration on a synthetic mRNA leader.

The regulation of cauliflower mosaic virus (CaMV) pregenomic 35S RNA translation occurs via nonlinear ribosome migration (ribosome shunt) and is mediated by an elongated hairpin structure in the leader. The replacement of the viral leader by a series of short, low-energy stems in either orientation supports efficient ribosomal shunting, showing that the stem per se, and not its sequence, is recognized by the translation machinery. The requirement for cis-acting sequences from the unstructured terminal regions of the viral leader was analyzed: the 5'-terminal polypyrimidine stretch and the short upstream open reading frame (uORF) A stimulate translation, whereas the 3'-flanking region seems not to be essential. Based on these results, an artificial leader was designed with a stable stem flanked by unstructured sequences derived from parts of the 5'- and 3'-proximal regions of the CaMV 35S RNA leader. This artificial leader is shunt-competent in translation assays in vivo and in vitro, indicating that a low-energy stem, broadly used as a device to successfully interfere with ribosome scanning, can efficiently support translation, if preceded by a short uORF. The synthetic 140-nt leader can functionally replace the CaMV 35S RNA 600-nt leader, thus implicating the universal role that nonlinear ribosome scanning could play in translation initiation in eukaryotes.

5' Untranslated Regions↗

PubMed2005

The varicella-zoster virus-mediated delayed host shutoff: open reading frame 17 has no major function, whereas immediate-early 63 protein represses heterologous gene expression.

We reported that varicella-zoster virus (VZV) causes a delayed host shutoff during its replicative cycle. VZV open reading frame 17 (ORF17) is the homologue of the herpes simplex virus (HSV) UL41 gene encoding the virion host shutoff (vhs) protein which is responsible for the shutoff effect observed in HSV-infected cells. In the present study, we demonstrated that ORF17 is expressed as a late protein during the VZV replicative cycle in different infected permissive cell lines which showed a delayed shutoff of cellular RNA. A cell line with stable expression of VZV ORF17 was infected with VZV. In these cells, VZV replication and delayed host shutoff remained unchanged when compared to normal infected cells. ORF17 was not capable of repressing the expression of the beta-gal reporter gene under the control of the human cytomegalovirus immediate-early gene promoter or to inhibit the expression of a CAT reporter gene under the control of the human GAPDH promoter, indicating that ORF17 has no major function in the VZV-mediated delayed host shutoff. To determine whether other viral factors are involved in the host shutoff, a series of cotransfection assays was performed. We found that the immediate-early 63 protein (IE63) was able to downregulate the expression of reporter genes under the control of the two heterologous promoters, indicating that this viral factor can be involved in the VZV-mediated delayed host shutoff. Other factors can be also implicated to modulate the repressing action of IE63 to achieve a precise balance between the viral and cellular gene expression.

Animals↗

PubMed1984

Nucleotide sequence of a 1.1 kb fragment of the pea chloroplast genome containing three tRNA genes, one of which is located within an open reading frame of 91 codons.

The nucleotide sequence of a 1082 bp fragment from the pea (Pisum sativum) chloroplast genome is presented. This fragment contains genes for tRNAGlu, tRNATyr and tRNAAsp as well as an open reading frame (ORF) of 91 codons on one strand and two ORFs of 52 and 59 codons on the complementary strand. The tRNAAsp gene is located entirely within the ORF of 91 codons. The first 366 bp of the fragment correspond to 376 bp at one end of a recently published (1) sequence from the broad bean (Vicia faba) chloroplast genome. These regions contain the tRNAGlu and tRNATyr genes, which are identical and separated by 60 bp in both species. These two genes are probably cotranscribed. The intergenic regions in the corresponding segments from the two species are, except for a 10 bp deletion in the pea sequence, 94% homologous.

Base Composition↗

PubMed1988

Cell lines containing varicella-zoster virus open reading frame 62 and expressing the "IE" 175 protein complement ICP4 mutants of herpes simplex virus type 1.

Vero cells were cotransfected with pSV2neo and a recombinant plasmid containing the varicella-zoster virus (VZV) open reading frame 62 (ORF62). Three neomycin-resistant cell lines were isolated and shown to complement two different ICP4 mutants (tsB21 and d120) of herpes simplex virus (HSV) type 1 (HSV-1). VZV-specific RNA could not be detected in these cell lines, but following infection with tsB21, a 4.3-kilobase VZV transcript was detected. This RNA increased in quantity when cells were infected in the presence of cycloheximide. A VZV-specific protein of 175 kilodaltons was detected in extracts of all three cell lines following infection with wild-type HSV-1 but not in uninfected cells. That VZV RNA and protein were detected only in HSV-1 infected cells suggests that a component of the HSV virion activates the expression of VZV ORF62. The increase in RNA expression seen in the presence of cycloheximide indicates that the protein encoded by VZV ORF62, "IE"175, may be autoregulatory. These data provide further evidence that VZV "IE"175 is the functional analog of the HSV ICP4.

Animals↗

PubMed2000

Kaposi's sarcoma-associated herpesvirus open reading frame 50/Rta protein activates the entire viral lytic cycle in the HH-B2 primary effusion lymphoma cell line.

Rta, the gene product of Kaposi's sarcoma-associated herpesvirus (KSHV) encoded mainly in open reading frame 50 (ORF50), is capable of activating expression of viral lytic cycle genes. What was not demonstrated in previous studies was whether KSHV Rta was competent to initiate the entire viral lytic life cycle including lytic viral DNA replication, late-gene expression with appropriate kinetics, and virus release. In HH-B2, a newly established primary effusion lymphoma (PEL) cell line, KSHV ORF50 behaved as an immediate-early gene and autostimulated its own expression. Expression of late genes, ORF65, and K8.1 induced by KSHV Rta was eliminated by phosphonoacetic acid, an inhibitor of viral DNA polymerase. Transfection of KSHV Rta increased the production of encapsidated DNase-resistant viral DNA from HH-B2 cells. Thus, introduction of an ORF50 expression plasmid is sufficient to drive the lytic cycle to completion in cultured PEL cells.

DNA, Viral↗

PubMed1994

Predicting internal exons by oligonucleotide composition and discriminant analysis of spliceable open reading frames.

A new method which predicts internal exon sequences in human DNA has been developed. The method is based on a splice site prediction algorithm that uses the linear discriminant function to combine information about significant triplet frequencies of various functional parts of splice site regions and preferences of oligonucleotides in protein coding and intron regions. The accuracy of our splice site recognition function is 97% for donor splice sites and 96% for acceptor splice sites. For exon prediction, we combine in a discriminant function the characteristics describing the 5'-intron region, donor splice site, coding region, acceptor splice site and 3'-intron region for each open reading frame flanked by GT and AG base pairs. The accuracy of precise internal exon recognition on a test set of 451 exon and 246693 pseudoexon sequences is 77% with a specificity of 79%. The recognition quality computed at the level of individual nucleotides is 89% for exon sequences and 98% for intron sequences. This corresponds to a correlation coefficient for exon prediction of 0.87. The precision of this approach is better than other methods and has been tested on a larger data set. We have also developed a means for predicting exon-exon junctions in cDNA sequences, which can be useful for selecting optimal PCR primers.

Algorithms↗

PubMed2000

Diverse splicing mechanisms fuse the evolutionarily conserved bicistronic MOCS1A and MOCS1B open reading frames.

Molybdenum is an essential cofactor in many enzymes, but must first be complexed by molybdopterin, whose synthesis requires four enzymatic activities. The first two enzymes of this pathway are encoded by the MOCS1 locus in humans. We describe here a remarkably well-conserved novel mRNA splicing phenomenon that produces both an apparently bicistronic MOCS1AM-OCS1B transcript, as well as a distinct class of monocistronic transcript. The latter are created by a variety of splicing mechanisms (alternative splice donors, alternative splice acceptors, and exon-skipping) to bypass the normal termination nonsense codon of MOCS1A resulting in fusion of the MOCS1A and MOCS1B open reading frames. Therefore, these "no-nonsense" transcripts encode a single bifunctional protein embodying both MOCS1A and MOCS1B activities. This coexpression profile was observed in vertebrates (human, mouse, cow, rabbit, opossum, and chicken) and invertebrates (fruit fly and nematode) spanning at least 700 million years of evolution. Our phylogenetic data also provide evidence that the bicistronic form of MOCS1 mRNA is likely to only produce MOCS1A protein and, combined with Northern analyses, suggests that MOCS1B is translated only as a fusion with MOCS1A. Taken together, the data presented here demonstrate a very highly conserved and physiologically relevant dynamic splicing scheme that profoundly influences the protein-coding potential of the MOCS1 locus.

Alternative Splicing↗

PubMed2005

Open reading frames provide a rich pool of potential natural antisense transcripts in fungal genomes.

Natural antisense transcripts are reported from all kingdoms of life and several recent reports of genomewide screens indicate that they are widely distributed. These transcripts seem to be involved in various biological functions and may govern the expression of their respective sense partner. Very little, however, is known about the degree of evolutionary conservation of antisense transcripts. Furthermore, none of the earlier analyses has studied whether antisense relationships are solely dual or involved in more complex relationships. Here we present a systematic screen for cis- and trans-located antisense transcripts based on open reading frames (ORFs) from five fungal species. The relative number of ORFs involved in antisense relationships varies greatly between the five species. In addition, other significant differences are found between the species, such as the mean length of the antisense region. The majority of trans-located antisense transcripts is found to be involved in complex relationships, resulting in highly connected networks. The analysis of the degree of evolutionary conservation of antisense transcripts shows that most antisense transcripts have no ortholog in any other species. An annotation of antisense transcripts based on Gene Ontology directs to common terms and shows that proteins of genes involved in antisense relationships preferentially localize to the nucleus with common functions in the regulation or maintenance of nucleic acids.

Evolution, Molecular↗