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At least 973 records · Page 54Linked to original sources

PubMed2001

Duck hepatitis B virus expresses a regulatory HBx-like protein from a hidden open reading frame.

Duck hepatitis B viruses (DHBV), unlike mammalian hepadnaviruses, are thought to lack X genes, which encode transcription-regulatory proteins believed to contribute to the development of hepatocellular carcinoma. A lack of association of chronic DHBV infection with hepatocellular carcinoma development supports this belief. Here, we demonstrate that DHBV genomes have a hidden open reading frame from which a transcription-regulatory protein, designated DHBx, is expressed both in vitro and in vivo. We show that DHBx enhances neither viral protein expression, intracellular DNA synthesis, nor virion production when assayed in the full-length genome context in LMH cells. However, similar to mammalian hepadnavirus X proteins, DHBx activates cellular and viral promoters via the Raf-mitogen-activated protein kinase signaling pathway and localizes primarily in the cytoplasm. The functional similarities as well as the weak sequence homologies of DHBx and the X proteins of mammalian hepadnaviruses strongly suggest a common ancestry of ortho- and avihepadnavirus X genes. In addition, our data disclose similar intracellular localization and transcription regulatory functions of the corresponding proteins, raise new questions as to their presumed role in hepatocarcinogenesis, and imply unique opportunities for deciphering of their still-enigmatic in vivo functions.

Amino Acid Sequence↗

PubMed1997

Transformation system for a wastewater treatment yeast, Hansenula fabianii J640: isolation of the orotidine-5'-phosphate decarboxylase gene (URA3) and uracil auxotrophic mutants.

A transformation system for Hansenula fabianii J640, a commonly used wastewater treatment yeast, was constructed. As a host cell, a uracil auxotrophic mutant designated as H. fabianii J640 u-1, which was confirmed to have a mutation at the locus of the gene for orotidine-5'-phosphate (OMP) decarboxylase (URA3), was obtained by positive selection using 5-fluoroorotic acid. A plasmid named pHFura3, which includes a 795-bp open-reading frame of the OMP decarboxylase H. fabianii, was obtained by complementation of the Escherichia coli pyrF mutant, pHFura3 could transform H. fabianii J640 u-1 by a non-homologous and frequently multicopy integration into the host genomic DNA.

Amino Acid Sequence↗

PubMed2000

Full-length sequence of a Canadian porcine reproductive and respiratory syndrome virus (PRRSV) isolate.

Presently, one of the most economically important pathogens affecting swine is the porcine reproductive and respiratory syndrome virus (PRRSV). This virus is prevalent in herds throughout the world and continues to pose a significant threat as newer and more virulent disease phenotypes emerge. In this report we describe the full-length nucleotide sequence of a Canadian PRRSV isolate, designated PA8. A consecutive sequence of 15,411 nucleotides was obtained from a set of overlapping cDNA clones. In order to determine the extent of genetic variation among isolates recovered from swine in Canada and the US, as well as to understand the molecular mechanisms governing the evolution of PRRSV, the full-length sequence of PA8 was compared with that of two US isolates, VR2332 and 16244B. The genomic sequence of PA8 shared 98.2% and 99.2% identity with 16244B and VR2332, respectively. The untranslated regions (UTR) at the 5' and 3' ends of the genome were very well conserved. Notable exceptions include an eight nucleotide difference at the 5' end of the 5' UTR of VR2332 relative to PA8 and 16244B and a two nucleotide difference in the 3' UTR of PA8 relative to VR2332 and 16244B. In contrast to PA8 and VR2332, 16244B possessed two nucleotide differences within the RNA pseudoknot structure of the ribosomal frameshift region between open reading frame (ORF)1a and ORF1b. Amino acid differences were distributed throughout the genome, however they appeared to be most extensive in Nsp1beta and ORF5 of the nonstructural and structural coding regions, respectively, suggesting that the evolutionary pressure to conserve these viral genes is somewhat lower.

3' Untranslated Regions↗

PubMed1991

Complete cDNA and gene sequence of the developmentally regulated arylphorin of Calliphora vicina and its homology to insect hemolymph proteins and arthropod hemocyanins.

Two cDNA libraries were prepared from poly(A)+ RNA isolated from fat bodies of last instar larvae of the blowfly Calliphora vicina. The libraries were probed with a genomic clone containing the coding sequence for an arylphorin subunit. Two cDNA clones as well as the genomic clone were mapped and their nucleotide sequences were determined. This revealed the presence of an open reading frame corresponding to a polypeptide with 759 amino acid residues. The deduced primary structure of Calliphora arylphorin and hemolymph proteins of other insect species and arthropod hemocyanine show nearly 30% identity. Highly conserved regions could be also identified.

Adipose Tissue↗

PubMed1990

Gene expression in cells infected with gammaherpesvirus saimiri: properties of transcripts from two immediate-early genes.

During productive infections of cells with the gammaherpesvirus, herpesvirus saimiri (HVS), a polyadenylated RNA of 2.2-2.4 kb accumulates to form a large fraction of virus-specified RNA. This transcript is from the virus thymidylate synthase (TS) gene and its synthesis, like that of late mRNAs encoding the virus structural proteins, is sensitive to an inhibitor of virus DNA synthesis (phosphonoacetic acid, PAA). Transcription which is insensitive to PAA occurs from many parts of the HVS genome, including the EcoRI-D, EcoRI-E, EcoRI-I, and HindIII-G fragments. A 1.6-kb RNA from EcoRI-I/E and a 1.3-kb RNA from HindIII-G accumulate in HVS-infected cells incubated in the continuous presence of cycloheximide, and thus represent immediate-early (IE) class transcripts. The 1.3-kb message from HindIII-G is the predominant stable RNA under these conditions; accumulation of the 1.6-kb transcript from EcoRI-I/E (which encodes the previously characterized 52-kDa IE phosphoprotein) is markedly more dependent on the multiplicity of infection. The sequence of a 2.5-kbp region of the HindIII-G fragment has been determined and a single major open reading frame is present within the boundaries of the 1.3-kb IE RNA. Comparison of the amino acid sequence of the encoded protein (IE-G) with current databases of protein sequences failed to demonstrate significant similarities with herpesvirus proteins, but did detect a significant similarity with a region of the protein specified by an open reading frame in the LTR of mouse mammary tumor virus. The function of the IE gene in HindIII-G and the basis for the distinctive multiplicity dependence of IE transcription from the 52-kDa gene remain to be established.

Amino Acid Sequence↗

PubMed1994

Sequences of ccpA and two downstream Bacillus megaterium genes with homology to the motAB operon from Bacillus subtilis.

A regulatory gene with 69% nucleotide sequence identity to the Bacillus subtilis ccpA was cloned from Bacillus megaterium by complementation of a mutant relieved of catabolite repression. Sequencing of the gene and its adjacent regions revealed two additional open reading frames (ORFs) downstream from ccpA. These three genes are presumably in one operon. ORF1 and ORF2 show homology to two genes downstream from ccpA in B. subtilis, as well as to the B. subtilis motA and motB genes, respectively.

Amino Acid Sequence↗

PubMed1995

A gene encoding gamma-adaptin is required for apical extension growth in Ustilago maydis.

The nucleotide (nt) sequence of an Ustilago maydis (Um) gene that complemented a partially osmotic-remedial temperature-sensitive (or-ts) mutant defective in apical extension growth has been determined. It contained a continuous open reading frame (OFR) predicted to encode a protein of 853 amino acids (aa). The deduced aa sequence was homologous to gamma-adaptin, a component of clathrin-coated vesicles derived from the Golgi.

Adaptor Protein Complex gamma Subunits↗

PubMed1992

The complete DNA sequence of yeast chromosome III.

The entire DNA sequence of chromosome III of the yeast Saccharomyces cerevisiae has been determined. This is the first complete sequence analysis of an entire chromosome from any organism. The 315-kilobase sequence reveals 182 open reading frames for proteins longer than 100 amino acids, of which 37 correspond to known genes and 29 more show some similarity to sequences in databases. Of 55 new open reading frames analysed by gene disruption, three are essential genes; of 42 non-essential genes that were tested, 14 show some discernible effect on phenotype and the remaining 28 have no overt function.

Base Sequence↗

PubMed1991

Sequencing and expression of the rne gene of Escherichia coli.

RNase E is a major endonucleolytic RNA processing enzyme in Escherichia coli. We have sequenced a 3.2 kb EcoRI-BamHI fragment encoding the rne gene, and identified its reading frame. Upstream from the gene, there are appropriate consensus sequences for a putative promoter and a ribosome binding site. We have translated this gene using a T7 RNA polymerase/promoter system. We determined 25 amino acids from the N-terminal of the translated product and they are in full agreement with the DNA sequence. The translated product of the rne gene migrates in SDS containing polyacrylamide gels as a 110,000 Da polypeptide, but the open reading frame found in the sequenced DNA indicates a much smaller protein. The entity that migrates as a 110,000 Da contains RNA, which could account, at least partially, for the migration of the rne gene product in SDS containing polyacrylamide gels.

Amino Acid Sequence↗

PubMed1993

Nucleotide sequence of beet cryptic virus 3 dsRNA2 which encodes a putative RNA-dependent RNA polymerase.

The nucleotide sequence of a DNA copy of beet cryptic virus 3 double-stranded RNA2 was determined, and one strand was found to contain a single long open reading frame of 1431 nucleotides which encoded a putative polypeptide containing 478 amino acid residues with an M(r) of 54.9K. This polypeptide contained conserved amino acid sequence motifs found in the genes that encode putative RNA-dependent RNA polymerases of other RNA viruses.

Amino Acid Sequence↗

PubMed2002

Isolation and genetic characterization of a novel filamentous bacteriophage, a deleted form of phage f237, from a pandemic Vibrio parahaemolyticus O4:K68 strain.

We isolated a filamentous bacteriophage, VfO4K68, from the pandemic Vibrio parahaemolyticus strain belonging to 04:K68 serovar. The VfO4K68 DNA lacked a 1,893-bp fragment present in that of the distinctive region of f237, a filamentous phage isolated from a pandemic 03:K6 strain (Nasu, H. et al., J. Clin. Microbiol., 38, 2156-2161, 2000). The deletion resulted in the formation of a novel open reading frame (ORF) that possesses homology to the ORF 27 of ETA phage and staphylococcal enterotoxin E (SEE) of Staphylococcus aureus. VfO4K68 was able to infect the recipient 03:K6 serovar strains. These results suggest that VfO4K68 might act as a genetic transmitter and play some roles in the pandemic V. parahaemolyticus infection.

Amino Acid Sequence↗

PubMed1995

Translation of the open reading frame encoded by comS, a gene of the srf operon, is necessary for the development of genetic competence, but not surfactin biosynthesis, in Bacillus subtilis.

A small open reading frame, comS of the srf operon, is the site of mutations that impair competence development in Bacillus subtilis. comS open reading frame translation was required for competence, as was confirmed by the suppression of a comS amber mutation [comS(Am)] by the nonsense suppressor sup-3. comS(Am), when introduced into the srf operon, eliminated late competence gene expression but had no significant effect on surfactin production.

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↗

PubMed1996

Sequencing of a 9.2 kb telomeric fragment from the right arm of Saccharomyces cerevisiae chromosome XIV.

We report the complete sequence of a 9.2 kb fragment next to and including the right telomere of Saccharomyces cerevisiae chromosome XIV. Four open reading frames (ORFs) longer than 100 amino acids were observed in the sequenced segment. One ORF (378 codons) does not show any significant homology with proteins in the databases and corresponds to a putative new gene. Two ORFs are almost identical to the known YCR007/YKL219 and PAU1-like hypothetical protein families already identified on several S. cerevisiae chromosomes. These ORFs, whose function is unknown, are generally associated with sub-telomeric regions of chromosomes. The fourth one shows significant identities with bacterial mannitol dehydrogenases. It could be a yeast gene implicated in the metabolism of mannitol (or a related substrate). The sequence has been deposited in the EMBL data library under Accession Number X86790.

Amino Acid Sequence↗

PubMed1999

Evidence for nonlinear capacitance in biomembrane channel system.

The electrophysiological properties of voltage-dependent anion channels from mitochondrial membrane have been studied in a bilayer membrane system. It was observed that the probability of opening of the membrane channel depends on externally applied voltage and the plot is a bell-shaped curve symmetric around probability axis. A scheme of conformational energy levels under varying externally applied voltage was formulated. Assuming that the probability follows Boltzmann distribution, we arrive at an expression of change in energy containing a separate term identical to the energy of a capacitor. This fact indicates the possibility of existence of an added capacitance due to the channel protein. Further it was shown that the aforesaid channel capacitor could be a function of voltage leading to nonlinearity. We have offered a general method of calculating nonlinear capacitance from the experimental data on opening probability of a membrane channel. In case of voltage-dependent anion channel the voltage dependence of the capacitor has a power 0.786. The results have been interpreted in view of the structural organization of the channel protein in the membrane. Our hypothesis is that the phenomenon of capacitor behaviour is a general one for membrane channels.

Animals↗

PubMed1993

Autogenous transcriptional activation of a thiostrepton-induced gene in Streptomyces lividans.

Although the antibiotic thiostrepton is best known as an inhibitor of protein synthesis, it also, at extremely low concentrations (< 10(-9) M), induces the expression of a regulon of unknown function in certain Streptomyces species. Here, we report the purification of a Streptomyces lividans thiostrepton-induced transcriptional activator protein, TipAL, whose N-terminus is similar to a family of eubacterial regulatory proteins represented by MerR. TipAL was first purified from induced cultures of S.lividans as a factor which bound to and activated transcription from its own promoter. The tipAL gene was overexpressed in Escherichia coli and TipAL protein purified in a single step using a thiostrepton affinity column. Thiostrepton enhanced binding of TipAL to the promoter and catalysed specific transcription in vitro. TipAS, a second gene product of the same open reading frame consisting of the C-terminal domain of TipAL, is apparently translated using its own in-frame initiation site. Since it is produced in large molar excess relative to TipAL after induction and also binds thiostrepton, it may competitively modulate transcriptional activation.

Amino Acid Sequence↗

PubMed1992

DNA sequencing and analysis of a 24.7 kb segment encompassing centromere CEN11 of Saccharomyces cerevisiae reveals nine previously unknown open reading frames.

A 24.7 kb segment of the cosmid clone pUKG047 containing a Sau3AI-partial fragment from the centromere region of Saccharomyces cerevisiae chromosome XI was sequenced and analysed. A mixed strategy of directed methods including exonuclease III nested deletion, restriction fragment subcloning and oligonucleotide-directed sequences was carried out. Exclusive use was made of the Applied Biosystems Taq DyeDeoxy Terminator Cycle technology and a laser-based AB1373A sequencing system for reactions, gel electrophoresis and automated reading. A total of 12 open reading frames (ORFs) was found. Nine new ORFs (YK102 to YK110) were identified, three of which (YK102, YK107, YK108) showed homologies to proteins of known function from other organisms. In addition, sequence analysis revealed three recently functionally characterized genes (MET14, VPS/SPO15, PAP1), which could be joined to the earlier published CEN11 region.

Amino Acid Sequence↗

PubMed1994

Molecular cloning, tissue expression of human xanthine dehydrogenase.

Xanthine dehydrogenase (XDH, EC 1.1.1.204) is a molybdenum iron-sulphur flavin hydroxylase which oxidizes a variety of purines, pterins and other heterogenic nitrogen compounds, serving as a rate-limiting enzyme in nucleic acid degradation. In this work, we have isolated and sequenced cDNA clones of human liver XDH. The obtained cDNA covers 4577 bases of human liver XDH mRNA with a 63 bp 5'-end untranslated region and a 515 bp 3'-end untranslated region. A termination codon TGA and a polyadenylation signal AATAAA were identified. An open reading frame encodes 1333 amino acid residues. The assignment of the N-terminal was confirmed by directly sequencing that region of purified human milk XDH. Northern blot analysis shows that the human XDH gene is widely expressed in human tissues.

Amino Acid Sequence↗