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PubMed2002

Basic functional analysis of six unknown open reading frames from Saccharomyces cerevisiae: four from chromosome VII and two from chromosome XV.

Six open reading frames (ORFs) of unknown function from Saccharomyces cerevisiae from the left arms of chromosomes VII and XV were disrupted by the short-flanking homology method in the diploid strains FY1679 and CENPK2. In each case, the entire ORF, with the exception of the first nucleotide of the start codon, was eliminated and replaced by the kanMX4 cassette. Correct integration of the disrupting marker was checked by colony PCR of the geneticin (G418)-resistant transformants. Sporulation followed by tetrad dissection of the diploids revealed that none of the ORFs encoded a product essential for the viability of either yeast strain. The neutral effect of these disruptions extended to mating and sporulation, since it was possible to create homozygous diploid disruptants that were capable of sporulation. Basic phenotypic analysis was carried out on all strains by growing them on three different media at three different temperatures and revealed no significant differences between disruptants and the parental strains. A cognate clone and a kanMX4 disruption cassette were created for five of the six ORFs by gap repair with specific long-flanking homology cassettes. For experimental reasons, the cognate clone and disruption cassette corresponding to the sixth ORF (YGL161w) had to be created by PCR.

Chromosomes, Fungal↗

PubMed2006

Identification of transcriptionally active open reading frames within the RD1 genomic segment of Mycobacterium tuberculosis.

OBJECTIVE: To identify transcriptionally active open reading frames (ORFs), predicted by bioinformatics, within RD1 genomic segment of Mycobacterium tuberculosis using reverse transcription-polymerase chain reaction (RT-PCR). MATERIALS AND METHODS: M. tuberculosis H37Rv was grown in Middlebrook 7H9 medium for 8 weeks and total RNA was isolated using standard procedures. The cDNA was synthesized using first-strand cDNA synthesis kit and general primers provided in the kit [pd (N)6, and/or Not I-d(T)18] as well as forward primers specific for each predicted RD1 ORF. Specific forward and reverse primers in PCR were used to amplify ORF-specific cDNA. The amplified products were identified on the basis of size using agarose gel electrophoresis, and their identity was confirmed by DNA sequencing. RESULTS: RT-PCR demonstrated expression of 13 of the 14 bioinformatics-predicted ORFs within RD1 genomic segment of M. tuberculosis. However, cDNA synthesis and PCR amplifications of specific products varied with respect to primer requirement and reaction conditions, respectively. All ORFs of <1.5 kb were amplified in standard RT-PCR, whereas several large-size ORFs (>1.5 kb) required internal primers for amplification in semi-nested RT-PCR. The sequencing of RT-PCR-amplified products of ORFs confirmed their identity. CONCLUSION: Bioinformatics analysis of DNA can accurately predict ORFs within M. tuberculosis-specific genomic regions, and RT-PCR is a suitable technique to confirm their expression in bacteria.

Bacterial Proteins↗

PubMed1990

Open reading frame VIII is not required for viability of cauliflower mosaic virus.

Open reading frame (ORF) VIII of cauliflower mosaic virus (CaMV) was analyzed by site-directed mutagenesis in order to investigate its potential function for the viral life cycle. Removal of either the start or the stop codon of ORF VIII, as well as interruption of ORF VIII by a new stop codon, did not affect infectivity. Unlike certain ORF VII mutants all three ORF VIII mutants are stable. Hence the ORF VIII product is not essential and ORF VIII mutations do not have deleterious polar effects on the expression of the downstream ORF V, which codes for the viral protease/reverse transcriptase.

Codon↗

PubMed1990

Trans-activation of viral tk promoters by proteins encoded by varicella zoster virus open reading frames 61 and 62.

Plasmids containing the varicella zoster virus (VZV) open reading frames (ORFs) 61 and 62 were used in a transient co-transfection assay to test for trans-activation of the VZV and herpes simplex virus type 1 (HSV-1) thymidine kinase (tk) promoters. The trans-activating potential of the polypeptides encoded by these VZV ORFs, designated p51 and p140, was compared to that of their HSV-1 homologs ICP0 and ICP4, respectively. VZV p51 was functionally inactive in this system while p140 appeared to be a much stronger transcriptional activator than ICP4. Co-transfection of plasmids encoding VZV p140 and HSV-1 ICP0 resulted in a synergistic activation of the reporter gene as has been shown for the combination of ICP4 and ICP0.

Herpesvirus 3, Human↗

PubMed2005

Open reading frame yjbI of Bacillus subtilis codes for truncated hemoglobin.

A hypothetical open reading frame from Bacillus subtilis genome, yjbI [NCBI genome database Accession No. ] having homology to many globin and globin-like proteins from different microbial genomes, was selectively amplified from the chromosomal DNA of B. subtilis strain DB104 based on genome sequence database of B. subtilis strain 168. The gene was cloned and over-expressed in Escherichia coli under the transcriptional control of tandem lambda P(L) and P(R) promoters, and the protein was purified to homogeneity. The single-chain monomeric hemoglobin-like protein is stable to the extent of 5.45 kcal/mol at 25 degrees C, binds carbon mono-oxide, and shows optical spectra characteristic of hemoproteins. The protein also exhibits peroxidase-like activity. This is the first report of a truncated bacterial globin endowed with peroxidase-like activity. The activity is enhanced in the presence of urea and guanidine hydrochloride, more so in the presence of the latter. Presumably, only a small portion of the protein is involved in peroxidase activity, which is exposed with increasing concentration of the denaturants.

Amino Acid Sequence↗

PubMed1990

A method for construction of long randomized open reading frames and polypeptides.

A method is presented for construction of randomized open reading frame sequences (ORFs) and gene libraries containing them. The building blocks for the ORFs were 75 bp long DNA fragments generated by cloning sequences from a single synthetic oligonucleotide preparation by bridge mutagenesis. The fragments had the property that, regardless of their orientation in the ligated product, the ORF of the construct was maintained. The heterogeneity of the ORFs resulted from the random ligation of 2000 different DNA fragments. The randomized ORFs were cloned downstream from the lac promoter in a multicopy plasmid in Escherichia coli. To test the method, a library of 10(6) clones was constructed.

Amino Acid Sequence↗

PubMed1990

Analysis of human papillomavirus type 16 open reading frame E7 immortalizing function in rat embryo fibroblast cells.

The E7 open reading frame of human papillomavirus type 16 (HPV-16) encodes a protein that can immortalize primary rat cells, cooperate with the ras oncoprotein to transform low passage rat cells and transform established rodent cells to anchorage independence. The immortalizing and cooperation functions have been investigated using a series of point mutations that introduce single amino acid changes into the E7 protein in two distinct regions. Certain mutations altering amino acids conserved between the E7 protein of genital HPV types, the adenovirus E1a protein and simian virus 40 large T antigen abolished the ability of the E7 protein to immortalize or cooperate with ras in a focus forming assay. Mutations in a consensus sequence for a casein kinase II recognition site, which is also shared by E1a and large T, reduced immortalizing activity, but did not affect the ability to cooperate with ras. Single mutations disrupting cysteine motifs, which form putative zinc-binding sites in the second region, reduced the activity of the E7 protein, whereas double mutants, in which neither of the cysteine motifs remained intact, showed no or very low activity. The activity of the mutants in immortalization and cooperation assays was essentially the same as their transforming activities in NIH 3T3 cells. This indicates that these three functions of E7 map to overlapping domains which cannot be separated by these mutations in the region of E1a/large T homology or the cysteine motifs.

Amino Acid Sequence↗

PubMed1992

Mutagenesis of human papillomavirus types 6 and 16 E7 open reading frames alters the electrophoretic mobility of the expressed proteins.

The E7 open reading frames of human papillomavirus type 6 (HPV-6) and HPV-16 encode proteins consisting of 98 amino acids that are quite similar in sequence yet different in electrophoretic mobility. Moreover, these proteins vary strikingly in oncogenicity. To investigate the molecular basis of the differences in structure and function, site-directed mutagenesis was used to exchange non-conserved amino acid residues between the two proteins. The mutated coding regions were expressed as fusion proteins in Escherichia coli and identified by Western blotting. Comparative analysis of the affinity-purified mutated E7 fusion proteins in polyacrylamide slab mini-gels in the presence of SDS and 2-mercaptoethanol revealed altered electrophoretic mobilities. This analysis suggests that the aspartic acid at residue 4 (Asp 4) contributes to the characteristic aberrant migration of the HPV-16 E7 protein in SDS-polyacrylamide gels.

Amino Acid Sequence↗

PubMed1989

Mutational analysis of the human immunodeficiency virus vpr open reading frame.

Mutations were introduced by recombinant DNA techniques into the vpr open reading frame of an infectious molecular clone of human immunodeficiency virus type 1. The effect of these changes on the replicative and cytopathologic properties of the virus recovered from transfected cells was studied in several human CD4+ lymphocyte cell lines. In all cases, mutant viruses were infectious and cytopathic. However, when a low-input dose was used, mutants grew significantly more slowly than the wild-type virus. The growth kinetics of vpr mutants were distinct from those of vif and vpu mutants.

Cytopathogenic Effect, Viral↗

PubMed2000

Analysis of deletion phenotypes and GFP fusions of 21 novel Saccharomyces cerevisiae open reading frames.

As part of EUROFAN (European Functional Analysis Network), we investigated 21 novel yeast open reading frames (ORFs) by growth and sporulation tests of deletion mutants. Two genes (YNL026w and YNL075w) are essential for mitotic growth and three deletion strains (ynl080c, ynl081c and ynl225c) grew with reduced rates. Two genes (YNL223w and YNL225c) were identified to be required for sporulation. In addition we also performed green fluorescent protein (GFP) tagging for localization studies. GFP labelling indicated the spindle pole body (Ynl225c-GFP) and the nucleus (Ynl075w-GFP) as the sites of action of two proteins. Ynl080c-GFP and Ynl081c-GFP fluorescence was visible in dot-shaped and elongated structures, whereas the Ynl022c-GFP signal was always found as one spot per cell, usually in the vicinity of nuclear DNA. The remaining C-terminal GFP fusions did not produce a clearly identifiable fluorescence signal. For 10 ORFs we constructed 5'-GFP fusions that were expressed from the regulatable GAL1 promoter. In all cases we observed GFP fluorescence upon induction but the localization of the fusion proteins remained difficult to determine. GFP-Ynl020c and GFP-Ynl034w strains grew only poorly on galactose, indicating a toxic effect of the overexpressed fusion proteins. In summary, we obtained a discernible GFP localization pattern in five of 20 strains investigated (25%). A deletion phenotype was observed in seven of 21 (33%) and an overexpression phenotype in two of 10 (20%) cases.

Gene Deletion↗

PubMed1994

The RING finger domain of the varicella-zoster virus open reading frame 61 protein is required for its transregulatory functions.

Varicella-zoster virus (VZV) open reading frame 61 (ORF61) protein transactivates expression of VZV promoters. VZV ORF61 is functionally homologous to herpes simplex virus type 1 (HSV-1)-infected cell protein 0 (ICP0); however, amino acid sequence homology of these two proteins is limited to the RING finger domains, a recently identified sequence motif composed of cysteine and histidine residues, located in their amino-terminal regions. A carboxy-terminal truncation mutant of ICP0 (which retains the RING finger domain) was previously shown to act as a potent transrepressor and as a dominant-negative mutant in the presence of full-length ICP0. We have shown that the corresponding region of ORF61 has similar properties. Amino-terminal truncation mutants of VZV ORF61 and HSV-1 ICP0, which lack the RING finger domain, cannot transactivate VZV promoters; however, fusion of the amino portion of one protein to the carboxy portion of the other restored the transactivating activity of the full-length proteins. To further study the role of the ORF61 RING finger domain, cysteine or histidine residues of this domain were individually replaced with serine or aspargine, respectively. Each of these amino acid substitution mutants in the RING finger abolished the transactivating activity of the full-length ORF61 protein. Each of the substitutions also reduced the transrepressing and dominant-negative properties of a carboxy-terminal truncation mutant of ORF61. These results indicate that the RING finger domain is required for the transregulatory functions of ORF61.

Amino Acids↗

PubMed2000

Herpes simplex virus 1 open reading frames O and P are not necessary for establishment of latent infection in mice.

Open reading frame (ORF) O and ORF P partially overlap and are located antisense to the gamma(1)34.5 gene within the domain transcribed during latency. In wild-type virus-infected cells, ORF O and ORF P are completely repressed during productive infection by ICP4, the major viral transcriptional activator/repressor. In cells infected with a mutant in which ORF P was derepressed there was a significant delay in the appearance of the viral alpha-regulatory proteins ICP0 and ICP22. The ORF O protein binds to and inhibits ICP4 binding to its cognate DNA site in vitro. These characteristics suggested a role for ORF O and ORF P in the establishment of latency. To test this hypothesis, two recombinant viruses were constructed. In the first, R7538(P-/O-), the ORF P initiator methionine codon, which also serves as the initiator methionine codon for ORF O, was replaced and a diagnostic restriction endonuclease was introduced upstream. In the second, R7543(P-/O-)R, the mutations were repaired to restore the wild-type virus sequences. We report the following. (i) The R7538(P-/O-) mutant failed to express ORF O and ORF P proteins but expressed a wild-type gamma(1)34.5 protein. (ii) R7538(P-/O-) yields were similar to that of the wild type following infection of cell culture or following infection of mice by intracerebral or ocular routes. (iii) R7538(P-/O-) virus reactivated from latency following explanation and cocultivation of murine trigeminal ganglia with Vero cells at a frequency similar to that of the wild type, herpes simplex virus 1(F). (iv) The amount of latent R7538(P-/O-) virus as assayed by quantitative PCR is eightfold less than that of the repair virus. The repaired virus could not be differentiated from the wild-type parent in any of the assays done in this study. We conclude that ORF O and ORF P are not essential for the establishment of latency in mice but may play a role in determining the quantity of latent virus maintained in sensory neurons.

Animals↗

PubMed1994

Transcriptional mapping of the varicella-zoster virus regulatory genes encoding open reading frames 4 and 63.

Four of the 68 varicella-zoster virus (VZV) unique open reading frames (ORFs), i.e., ORFs 4, 61, 62, and 63, encode proteins that influence viral transcription and are considered to be positional homologs of herpes simplex virus type 1 (HSV-1) immediate-early (IE) proteins. In order to identify the elements that regulate transcription of VZV ORFs 4 and 63, the encoded mRNAs were mapped in detail. For ORF 4, a major 1.8-kb and a minor 3.0-kb polyadenylated [poly(A)+] RNA were identified, whereas ORF 63-specific probes recognized 1.3- and 1.9-kb poly(A)+ RNAs. Probes specific for sequences adjacent to the ORFs and mapping of the RNA 3' ends indicated that the ORF 4 RNAs were 3' coterminal, whereas the RNAs for ORF 63 represented two different termination sites. S1 nuclease mapping and primer extension analyses indicated a single transcription initiation site for ORF 4 at 38 bp upstream of the ORF start codon. For ORF 63, multiple transcriptional start sites at 87 to 95, 151 to 153, and (tentatively) 238 to 243 bp upstream of the ORF start codon were identified. TATA box motifs at good positional locations were found upstream of all mapped transcription initiation sites. However, no sequences resembling the TAATGARAT motif, which confers IE regulation upon HSV-1 IE genes, were found. The finding of the absence of this motif was supported through analyses of the regulatory sequences of ORFs 4 and 63 in transient transfection assays alongside those of ORFs 61 and 62. Sequences representing the promoters for ORFs 4, 61, and 63 were all stimulated by VZV infection but failed to be stimulated by coexpression with the HSV-1 transactivator Vmw65. In contrast, the promoter for ORF 62, which contains TAATGARAT motifs, was activated by VZV infection and coexpression with Vmw65. These results extend the transcriptional knowledge for VZV and suggest that ORFs 4 and 63 contain regulatory signals different from those of the ORF 62 and HSV-1 IE genes.

Base Sequence↗

PubMed1993

Specific deletions in the hepatitis B virus core open reading frame in patients with chronic active hepatitis B.

The polymerase chain reaction (PCR) and DNA sequencing were used to examine genomic variation in the pre-core/core open reading frame of the hepatitis B virus (HBV) in chronically infected patients. Gel electrophoresis of amplification products showed the presence of shortened forms of the core gene in addition to the full length product. These shortened forms were seen only in patients with chronic active hepatitis (CAH) seropositive for HBeAg and not in patients with chronic persistent hepatitis (CPH) or HBeAg minus CAH. Cloning and DNA sequencing revealed the presence of a number of overlapping deletions within the core gene, the majority being in-frame, which were clustered within aa 81-114 of the core gene product. These deletions were found in patients with CAH from different racial and geographical backgrounds, whereas PCR analysis of the surface and X open reading frames showed no shortened forms suggesting deletions to be specific to the core gene in these patients. Because the product of the core gene--the HBV core antigen--is believed to be the major target for T-cell-mediated liver damage, it seems likely that the products of core genes carrying deletions will alter immune recognition and may be of importance in the progression of inflammatory liver damage.

Base Sequence↗

PubMed1994

LTE1 of Saccharomyces cerevisiae is a 1435 codon open reading frame that has sequence similarities to guanine nucleotide releasing factors.

The DNA sequence of the LTE1 gene on the left arm of chromosome I of Saccharomyces cerevisiae has been determined. The LTE1 open reading frame comprises 4305 bp that can be translated into 1435 amino acid residues. The position of this open reading frame corresponds well to that of a 4.7 kb transcript that has been mapped to this position. The derived amino acid sequence has significant similarities to the amino acid sequence of the guanine nucleotide releasing factor isolated from a rat brain library. The carboxy-terminus of the LTE1 protein also shows similarities to other guanine nucleotide exchange factors of the S. cerevisiae CDC25 family.

Amino Acid Sequence↗

PubMed2003

Expression of non-open reading frames isolated from phage display due to translation reinitiation.

An unusual 38 codon sequence was previously isolated from a random peptide library by binding to growth hormone binding protein in phage display. This sequence, H10, and several variants did not contain open reading frames, but expressed a beta-galactosidase reporter 10-40% as well as control in both the original reading frame from phage display and the frame -1 to it. Inspection of the sequence suggested that expression in the -1 frame resulted from initiation at a downstream ATG in that frame, present in H10 and its variants, subsequently confirmed by site-directed mutagenesis. Unexpectedly, mutagenesis of that out-of-frame downstream ATG also increased expression in the original non-open reading frame by two- to threefold, creating a TTG codon adjacent to an existing in-frame TTG codon, suggesting downstream translational reinitiation at a putative TTG start. We undertook an extensive site-directed mutagenesis approach and report that this hypothesis is almost certainly correct. Features required for this reinitiation include an upstream translation start and a stop that can even be a suppressed amber codon 22 nucleotides further downstream from the restart. Replacing the TTG with ATG increases expression only twofold. Reinitiation occurs in either of two reading frames in this sequence.

Amino Acid Sequence↗

PubMed2006

Nickase and a protein encoded by an open reading frame downstream from the nickase BspD6I gene form a restriction endonuclease complex.

We are the first to have isolated a protein (186 amino acid residues) encoded by the open reading frame adjacent to the end of the BspD6I nickase (N.BspD6I) gene. Cleavage of both DNA strands near the sequence recognized by nickase (5 -GAGTC/5 -GACTC) occurs when this protein is added to the reaction mixture containing N.BspD6I. The protein encoded by the open reading frame and the nickase are suggested to be subunits of heterodimeric restriction endonuclease R.BspD6I.

Amino Acid Sequence↗

PubMed1989

Human antibodies react with an epitope of the human papillomavirus type 6b L1 open reading frame which is distinct from the type-common epitope.

Recombinant proteins encoded by the human papillomavirus type 6b (HPV6b) L1 open reading frame react with sera from patients with condylomata acuminata and also react with rabbit antiserum raised against sodium dodecyl sulfate-disrupted bovine papillomavirus type 1 (BPV1) virions. To map the immunoreactive epitopes, a series of procaryotic expression plasmids was made which contained a nested set of 3' to 5' deletions in the HPV6b L1 open reading frame. The deleted plasmids expressed a set of carboxy to amino terminus truncated fusion proteins. Regions containing the immunoreactive epitopes were mapped by determining which of the deleted fusion proteins retained reactivity with sera in Western immunoblot assays. The coding sequence for a human antibody-reactive linear epitope mapped between HPV6b nucleotide coordinates 7045 and 7087, and the rabbit anti-BPV1-reactive epitope coding sequence mapped between coordinates 6377 and 6454. Synthetic peptides derived from the epitope mapping were reacted with sera in enzyme-linked immunosorbent assay. Human sera reacted with synthetic peptide QSQAITCQKPTPEKEKPDPYK (HPV6b L1 amino acids 417 through 437). Rabbit anti-BPV1 and rabbit antisera raised against HPV16 L1 recombinant proteins reacted with the synthetic peptide DGDMVDTGFGAMNFADLQTNKSDVPIDI (HPV6b L1 amino acids 193 through 220). Human sera which reacted with HPV6b L1 fusion proteins cross-reacted with an HPV11 L1 fusion protein but did not react with fusion proteins encoded by HPV1a, HPV16, or HPV18. Rabbit anti-BPV1 reacted with L1 fusion proteins encoded by all of these HPV types. In contrast to the type-common (rabbit anti-BPV1-reactive) epitope, the human antibody-reactive epitope appears to be relatively HPV type specific.

Amino Acid Sequence↗