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At least 919 records · Page 51Linked to original sources
PubMed1995

Characterization of the superoxide dismutase gene and its upstream region from Methanobacterium thermoautotrophicum Marburg.

A gene (sod) encoding superoxide dismutase (SOD) was isolated from the strictly anaerobic archaeon Methanobacterium thermoautotrophicum Marburg. Its identify was confirmed by functional complementation of an Escherichia coli mutant strain lacking SOD activity and by DNA sequence analysis of a cloned fragment. Upstream of sod, separated by a 5-bp intergenic region, lies the open reading frame orfk which potentially codes for a protein of 209 amino acid residues. The amino acid sequence for this presumptive product had a similarity coefficient of 55.5% to a subunit of the alkyl hydroperoxide reductase (encoded by the ahpC gene) from Salmonella typhimurium.

Amino Acid Sequence↗
PubMed1992

Structural organization of pBC1, a cryptic plasmid from Bacillus coagulans.

The complete nucleotide sequence of the Bacillus coagulans plasmid pBC1 was determined. The sequence revealed an open reading frame encoding a polypeptide of 259 amino acids. This open reading frame shows sequence similarity to genes coding for replication-associated proteins in a group of gram-positive bacterial plasmids known to replicate via single-stranded intermediates. A region required for replication in cis, when the intact replicon is supplied in trans, was identified as well.

Amino Acid Sequence↗
PubMed1996

Thermostable chemotaxis proteins from the hyperthermophilic bacterium Thermotoga maritima.

An expressed sequence tag homologous to cheA was previously isolated by random sequencing of Thermotoga maritima cDNA clones (C. W. Kim, P. Markiewicz, J. J. Lee, C. F. Schierle, and J. H. Miller, J. Mol. Biol. 231: 960-981, 1993). Oligonucleotides complementary to this sequence tag were synthesized and used to identify a clone from a T. maritima lambda library by using PCR. Two partially overlapping restriction fragments were subcloned from the lambda clone and sequenced. The resulting 5,251-bp sequence contained five open reading frames, including cheA, cheW, and cheY. In addition to the chemotaxis genes, the fragment also encodes a putative protein isoaspartyl methyltransferase and an open reading frame of unknown function. Both the cheW and cheY genes were individually cloned into inducible Escherichia coli expression vectors. Upon induction, both proteins were synthesized at high levels. T. maritima CheW and CheY were both soluble and were easily purified from the bulk of the endogenous E. coli protein by heat treatment at 80 degrees C for 10 min. CheY prepared in this way was shown to be active by the demonstration of Mg(2+)-dependent autophosphorylation with [32P]acetyl phosphate. In E. coli, CheW mediates the physical coupling of the receptors to the kinase CheA. The availability of a thermostable homolog of CheW opens the possibility of structural characterization of this small coupling protein, which is among the least well characterized proteins in the bacterial chemotaxis signal transduction pathway.

Amino Acid Sequence↗
PubMed1995

Conservation of an intact human immunodeficiency virus type 1 vif gene in vitro and in vivo.

Replication of vif-negative human immunodeficiency virus type 1 (HIV-1) is attenuated in certain cell lines and highly impaired in peripheral blood lymphocytes in vitro. To determine whether intact vif is positively selected during natural HIV-1 infection and to determine vif sequence variability, we employed PCR amplification, cloning, and sequencing to investigate the vif region of replicating virus in short-term-passage HIV-1 primary isolates from five asymptomatic individuals and from five persons with AIDS. A total of 46 vif clones were obtained and analyzed. Recombinant proviruses were constructed from selected vif clones from one patient and found to be fully infectious. We found that 38 of the 46 clones sequenced carried open vif reading frames and that there was a low degree of heterogeneity of vif genes within isolates from the same individual and among isolates from different donors. The cysteines previously found to be essential for vif protein function were conserved in all clones. A phylogenetic tree constructed from all available vif nucleotide sequences resulted in a virus grouping similar to those of gag and env. Direct sequencing of vif amplified by PCR from uncultured lymphocytes of 15 individuals at various stages of progression toward AIDS demonstrated vif open reading frames in 13 of 15 samples tested. There was no obvious correlation between disease status and the presence of an intact vif within this sample group at the time of sample procurement. The conservation of the vif open reading frame in vitro and in vivo and its limited variability following virus transmission in vitro are consistent with a role for vif in natural HIV-1 infection.

Amino Acid Sequence↗
PubMed1996

Characterization of the products of the U(L)43 gene of herpes simplex virus 1: potential implications for regulation of gene expression by antisense transcription.

The products, RNA or proteins, of the herpes simplex virus 1 open reading frame U(L)43 have not been previously identified. The expression of an open reading frame antisense to U(L)43, U(L)43.5 (P. L. Ward, D. E. Barker, and B. Roizman, J. Virol. 70:2684-2690, 1996), has been reported. We report the existence of a transcript corresponding to the domain of the U(L)43 open reading frame extending approximately 30 bp from the predicted TATA box to the predicted polyadenylation signal. The RNA of the U(L)43 open reading frame accumulates to higher levels in the presence of phosphonoacetic acid, an inhibitor of viral DNA synthesis, than in its absence, whereas the U(L)43.5 transcript accumulates in larger amounts in the absence of phosphonoacetic acid. The open reading frame tagged with a sequence encoding a 20-amino-acid epitope yielded a protein with an apparent Mr of 32,000, i.e., considerably lower than that predicted from the size of the open reading frame. The discovery of a pair of antisense genes expressed during productive infection raises the possibilities that additional antisense genes exist and that the antisense arrangement provides still another mechanism for regulation of gene expression.

Animals↗
PubMed2000

Primary structure of the Herpesvirus ateles genome.

Herpesvirus ateles is an agent indigenous to spider monkeys (Ateles spp.) and causes fulminant lymphomas in various New World primates. Structural and genetic relatedness led to the classification of this virus as a member of the genus Rhadinovirus. It is most closely related to Herpesvirus saimiri. The 108,409-bp light DNA segment of the herpesvirus ateles strain 73 genome has two genes for U-RNA-like transcripts and 73 open reading frames, of which at least 6 show significant homologies to cellular genes (encoding complement control proteins, apoptosis-regulatory proteins, D-type cyclins, interleukin-8 receptors, and enzymes involved in nucleotide metabolism). The left terminal region of the light DNA segment bears the putative rhadinovirus oncogene tio.

Amino Acid Sequence↗
PubMed2002

Sequence analysis of pLBB1, a cryptic plasmid from Lactobacillus delbrueckii subsp. bulgaricus.

The first report of the complete nucleotide sequence of a cryptic plasmid from Lactobacillus delbrueckii subsp. bulgaricus (Lactobacillus bulgaricus) is presented. The plasmid pLBB1 consists of 6127 bp with a GC content of 44.8%. No ssDNA was detected by hybridization experiments, which is consistent with the notion that pLBB1 does not replicate by a rolling circle mechanism. A putative replication region of pLBB1 was cloned and found to be functional in Lactobacillus johnsonii and Lactococcus lactis. Plasmid pLBB1 showed significant DNA sequence identity with plasmid pLL1212 from Lactobacillus delbrueckii subsp. lactis (Lactobacillus lactis) CRL1212 (GenBank accession No. AF109691). Four open reading frames (ORFs) larger than 100 amino acids were identified. ORFA shared similarity with a putative primase-helicase system, and ORFB and ORFC exhibited limited identity with a mobilization protein and a transposase, respectively. Curing experiments did not allowed us to assign a function to the ORFs.

Amino Acid Sequence↗
PubMed1997

Molecular cloning of pea cDNA encoding cycloartenol synthase and its functional expression in yeast.

The cDNA encoding cycloartenol synthase [EC 5.4.99.8] has been isolated from pea seedling by an efficient PCR using sets of degenerate primers based on the highly conserved sequences of the known 2,3-oxidosqualene cyclase cDNAs. The obtained cDNA contains a 2271-bp open reading frame and is encoding a predicted protein of 757 amino acids with high homology (81%) to Arabidopsis thaliana cycloartenol synthase. The PCR-amplified open reading frame (ORF) has been inserted into pYES2, an expression vector in yeast, under the control of galactose-inducible promoter. Significant cycloartenol synthase activity has been found in the homogenate of the yeast transformed with the plasmid containing PCR-amplified ORF.

Amino Acid Sequence↗
PubMed1991

[Design of a species-specific DNA probe based on the pFra plasmid of the plague pathogen].

The recombinant plasmid pBS1 carrying a 2 kb SalGI fragment of Yersinia pestis pFra plasmid was constructed by insertion of the fragment into a vector plasmid pBR327. SalGI-BspRI 400 bp subfragment was recloned into a pBR322 vector plasmid. Open reading frame was found in the fragment by DNA sequencing technique. The subfragment designated F1-probe permits one to identify specifically the Yersinia pestis strains harbouring pFra plasmid, thus, differing them from closely related Yersiniea and other representatives of Enterobacteriaceae family.

Amino Acid Sequence↗
PubMed1995

Identification of a cDNA that encodes a 1-acyl-sn-glycerol-3-phosphate acyltransferase from Limnanthes douglasii.

Two different techniques were used to isolate potential cDNAs for acyl-CoA: 1-acyl-sn-glycerol-3-phosphate acyltransferase (LPA-AT) enzymes from Limnanthes douglasii. Both heterologous screening with the maize pMAT1 clone and in vivo complementation of the Escherichia coli mutant JC201 which is deficient in LPA-AT activity, were carried out. Clones identified by these procedures were different. Homology searches demonstrated that the clone isolated by heterologous probing, pLAT1, encodes a protein which is most similar to the maize (open reading frame in pMAT1) and yeast SLC1 proteins, which are putative LPA-AT sequences. This L. douglasii sequence shows much lower homology to the E. coli LPA-AT protein PlsC, which is the only LPA-AT sequence confirmed by over-expression studies. The clone isolated by complementation, pLAT2, encodes a protein with homology to both SLC1 and PlsC. It was not possible to over-express the complementing protein encoded by pLAT2 but further experimentation on membranes from complemented JC201 demonstrated that they possess a substrate specificity distinctly different from PlsC and similar to Limnanthes sp. microsome specificity. This data strongly supports the contention that pLAT2 is an LPA-AT clone. Northern blot analysis revealed different expression patterns for the two genes in pLAT1 and pLAT2. Transcription of the gene encoding the insert of pLAT2 occurred almost exclusively in developing seed tissue, whilst the cDNA of pLAT1 hybridised to poly(A)+ mRNA from seed, stem and leaf, demonstrating more widespread expression throughout the plant. Southern blot analysis indicated that the cDNA of pLAT2 was transcribed from a single-copy gene while that for pLAT1 was a member of a small gene family.

1-Acylglycerol-3-Phosphate O-Acyltransferase↗
PubMed1996

Genetic variation in open reading frame 2 of field isolates and laboratory strains of equine arteritis virus.

The open reading frame 2 (ORF2) of three laboratory strains, the live attenuated vaccine virus, and 18 field isolates of equine arteritis virus (EAV) from Europe and North America was sequenced. The ORF2 of EAV encodes the Gs protein that is abundantly expressed in infected cells but constitutes less than 2% of the virion protein mass. Variation of ORF2 among the isolates facilitated phylogenetic analysis that largely confirmed results of an earlier study based on sequence divergence of ORF5 of the same isolates of EAV, despite exposure of the proteins encoded by ORF2 (Gs) and ORF5 (GL) to potentially different selective pressures in vivo. The data indicate that the Gs protein is highly conserved between isolates, considerably more so than the GL protein, consistent with an important role of the Gs protein in virus replication.

Amino Acid Sequence↗
PubMed1999

Genetic and biochemical analyses of the tec operon suggest a route for evolution of chlorobenzene degradation genes.

The TecA broad-spectrum chlorobenzene dioxygenase of Burkholderia sp. strain PS12 catalyzes the first step in the mineralization of 1,2,4, 5-tetrachlorobenzene. The catabolic genes were localized on a small plasmid that belongs to the IncPbeta incompatibility group. PCR analysis of the genetic environment of the tec genes indicated high similarity to the transposon-organized catabolic tcb chlorobenzene degradation genes of Pseudomonas sp. strain P51. Sequence analysis of the regions flanking the tecA genes revealed an upstream open reading frame (ORF) with high similarity to the todF 2-hydroxy-6-oxo-2,4-heptadienoate hydrolase gene of Pseudomonas putida F1 and a discontinuous downstream ORF showing high similarity to the todE catechol 2,3-dioxygenase gene of strain F1. Both homologues in strain P51 exist only as deletion remnants. We suggest that different genetic events thus led to inactivation of the perturbing meta-cleavage enzymes in strains P51 and PS12 during the evolution of efficient chlorobenzene degradation pathways. Biochemical characterization of TodF-like protein TlpF and a genetically refunctionalized TodE-like protein, TlpE, produced in Escherichia coli provided data consistent with the proposed relationships.

Amino Acid Sequence↗
PubMed1992

Sequence of a 10.7 kb segment of yeast chromosome XI identifies the APN1 and the BAF1 loci and reveals one tRNA gene and several new open reading frames including homologs to RAD2 and kinases.

We report here the DNA sequence of a segment of chromosome XI of Saccharomyces cerevisiae extending over 10.7 kb. The sequence was determined using a double-strand sequencing strategy adapted from the random-clone strategy. The segment contains seven non-overlapping long open reading frames, YKL500, 505, 510, 513, 516, 518 and 520 and one tRNA gene. YKL505 and YKL513 are two already sequenced genes, the BAF1/ABF1 and the APN1 genes, respectively. YKL510 exhibits a strong homology to the RAD2 protein and YKL516 is presumably a protein kinase.

Amino Acid Sequence↗
PubMed1994

cDNA sequence, gene sequence, and properties of murine pallidin (band 4.2), the protein implicated in the murine pallid mutation.

Band 4.2, which plays an important but poorly understood role in erythrocyte function and survival, is a major component of erythrocyte membranes. Recently, it has been shown that the gene for murine protein band 4.2 colocalizes on chromosome 2 with the murine pallid mutation, which affects the formation or function of intracellular storage granules in melanocytes and platelets and lysosomes in kidney. As a first step in identifying the mutation responsible for the pallid phenotype, we have sequenced the entire normal murine band 4.2 gene. Our results show that the gene for murine band 4.2 is approximately 22 kb in size, with 13 exons and 12 intervening introns. The organization of the mouse band 4.2 gene is identical to that of the human band 4.2 gene and similar to that of the genes for the transglutaminase enzymes, reiterating the membership of protein band 4.2 in the transglutaminase gene superfamily. We also present 3.5 kb of normal murine erythroid band 4.2 cDNA sequence containing an open reading frame of 2073 bp and coding for 691 amino acids. This is the same size as the human erythrocyte protein, with which the murine protein shares a 72% amino acid identity.

Amino Acid Sequence↗
PubMed1991

A PMR2 tandem repeat with a modified C-terminus is located downstream from the KRS1 gene encoding lysyl-tRNA synthetase in Saccharomyces cerevisiae.

The KRS1 gene encodes the cytoplasmic form of Saccharomyces cerevisiae lysyl-tRNA synthetase. The KRS1 locus has been characterized. The lysyl-tRNA synthetase gene is unique in the yeast genome. The gene is located on the right arm of chromosome IV and disruption of the open reading frame leads to lethality. These results contrast with the situation encountered in Escherichia coli where lysyl-tRNA synthetase is coded by two distinct genes, lysS and lysU, and further address the possible biological significance of this gene duplication. The nucleotide sequence of the 3'-flanking region has been established. It encodes a long open reading frame whose nucleotide and amino acid structures are almost identical to PMR2, a cluster of tandemly repeated genes coding for P-type ion pumps. The sequence alterations relative to PMR2 are mainly located at the C-terminus of the protein.

Amino Acid Sequence↗
PubMed1991

Isolation and genetic structure of IS112, an insertion sequence responsible for the inactivation of the SalI restriction-modification system of Streptomyces albus G.

IS112 is a transposable element identified in Streptomyces albus G by its frequent mutagenic insertion into the genes for the SalI restriction-modification system. IS112 is present in several copies in the genome of S. albus G. Homologous sequences were detected in other Streptomyces strains. Sequence analysis revealed that IS112 has a length of 883 bp with a GC content of 67.4%. The copy that was isolated contained imperfect inverted repeats (16/20 match) at its ends and was flanked by a 2 bp duplication at the target site, which was located within the gene (salIR) for the SalI endonuclease. A long open reading frame (ORF) encoding a putative polypeptide of 256-253 amino acids spans almost the entire sequence. Significant homology was detected between this polypeptide and that corresponding to ORFB of IS493, an insertion sequence recently isolated from Streptomyces lividans 66.

Amino Acid Sequence↗
PubMed1996

A naturally occurring 46-amino acid deletion of cytidine monophospho-N-acetylneuraminic acid hydroxylase leads to a change in the intracellular distribution of the protein.

Cytidine monophospho-N-acetylneuraminic acid (CMP-NeuAc) hydroxylase is a key enzyme for the expression of N-glycolylneuraminic acid. The molecular cloning of this enzyme from mouse liver has been described in our previous report (Kawano T, Koyama S, Takematsu H, Kozutsumi Y, Kawasaki H, Kawashima S, Kawasaki T, Suzuki A (1995) J Biol Chem 270: 16458-63). During the cDNA cloning, a cDNA containing a truncated open reading frame (ORF) was isolated. This clone encodes a protein of 531 amino acids which lacks 46 amino acids in the middle of the normal full-length protein. The percentage of this mRNA containing the truncated ORF out of the total population of CMP-NeuAc hydroxylase mRNA in various mouse tissues was about 10-25%. The truncated protein was expressed in COS-1 cells, but did not show any enzymatic activity. The truncated protein was localized to the region which appeared to be the endoplasmic reticulum, whereas the full-length protein with normal enzymatic activity was detected in the cytosol. These data suggest that this naturally occurring 46-amino acid deletion leads to a change in the intracellular distribution of CMP-NeuAc hydroxylase, and a loss in the activity of this enzyme.

Amino Acid Sequence↗