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At least 739 records · Page 41Linked to original sources
PubMed1995

A 43.5 kb segment of yeast chromosome XIV, which contains MFA2, MEP2, CAP/SRV2, NAM9, FKB1/FPR1/RBP1, MOM22 and CPT1, predicts an adenosine deaminase gene and 14 new open reading frames.

A 43,481 bp fragment from the left arm of chromosome XIV of Saccharomyces cerevisiae was sequenced. A gene for tRNA(phe) and 23 non-overlapping open reading frames (ORFs) were identified, seven of which correspond to known yeast genes: MFA2, MEP2, CAP/SRV2, NAM9, FKB1/FPR1/RBP1, MOM22 and CPT1. One ORF may correspond to the yet unidentified yeast adenosine deaminase gene. Among the 15 other ORFs, four exhibit known signatures, which include a protein tyrosine phosphatase, a cytoskeleton-associated protein and two ATP-binding proteins, four have similarities with putative proteins of yeast or proteins from other organisms and seven exibit no significant similarity with amino acid sequences described in data banks. One ORF is identical to yeast expressed sequence tags (EST) and therefore corresponds to an expressed gene. Six ORFs present similarities to human dbESTs, thus identifying motifs conserved during evolution. Nine ORFs are putative transmembrane proteins. In addition, one overlapping and three antisense ORFs, which are not likely to be functional, were detected.

Adenosine Deaminase↗
PubMed2003

Aldo-keto reductases as modulators of stress response.

Human aldose reductase (AKR1B1) has been implicated as a factor in the pathogenesis of diabetic complications. However, little is known about the physiological role of this enzyme or of related aldo-keto reductases in human tissues. In mammalian systems, a gene knock out approach is often employed as an experimental strategy to probe for gene function. However, in the murine system, phenotypic characterization of an aldose reductase (AKR1B3) knock out is likely to be complicated due to functional compensation by redundant AKRs including AKRs 1A (aldehyde reductase), 1B7 (FR-1) and 1B8 (MVDP). As an alternate strategy, we are examining the budding yeast Saccharomyces cerevisiae as a model system for a functional genomics study of AKRs. A distinct advantage of this system centers on the ability to readily ablate multiple targeted genes in a single strain. In addition to providing insights into functional redundancy, this system allows us to use a genetic approach to study possible effector pathways associated with one or more individual genes. Yeast open reading frames (ORFs) encoding AKRs with functional similarity to human aldose reductase (AKR1B1) were identified by BLAST analysis and were functionally validated by studies of recombinant proteins. By ablating three of the yeast AKR genes most functionally similar to AKR1B1, we have created a unique strain of S. cerevisiae that shows enhanced sensitivity to stress. Ongoing studies with oligonucleotide arrays show that the triple null strain has an altered transcription profile consistent with an enhanced stress response in comparison with the parental strain. These data indicate that AKR-null strains may provide new insights into signaling mechanisms involving this family of proteins.

Alcohol Oxidoreductases↗
PubMed1999

Identification and molecular analysis of rough-colony-specific outer membrane proteins of Actinobacillus actinomycetemcomitans.

Actinobacillus actinomycetemcomitans, a gram-negative bacterium isolated from the human mouth, has been implicated in the pathogenesis of early-onset periodontitis. Primary isolates cultured from subgingival plaque exhibit an adherent, rough colony phenotype which spontaneously converts to a nonadherent, smooth phenotype upon in vitro subculture. The rough colony variant produces abundant fimbriae and autoaggregates, while the smooth colony variant is planktonic and produces scant fimbriae. To begin to understand the significance of colony variation in biofilm formation by A. actinomycetemcomitans, outer membrane protein profiles of four isogenic rough and smooth colony variants were compared by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Two proteins with relative molecular masses of 43 and 20 kDa were expressed by the rough colony variants exclusively. Expression of these proteins was not found to be dependent on growth phase, oxygen tension, or type of complex medium. N-terminal amino acid sequences of these proteins obtained by Edman degradation were compared with sequences from the University of Oklahoma A. actinomycetemcomitans genome database. Two contiguous open reading frames (ORFs) encoding proteins having sequence homology with these proteins were identified. The 43-kDa protein (RcpA [rough colony protein A]) was similar to precursor protein D of the general secretion pathway of gram-negative bacilli, while the 20-kDa protein (RcpB [rough colony protein B]) appeared to be unique. The genes encoding these proteins have been cloned from A. actinomycetemcomitans 283 and sequenced. A BLASTX (gapped BLAST) search of the surrounding ORFs revealed homology with other fimbria-related proteins. These data suggest that the genes encoding the 43-kDa (rcpA) and 20-kDa (rcpB) proteins may be functionally related to each other and to genes that may encode fimbria-associated proteins.

Aggregatibacter actinomycetemcomitans↗
PubMed2000

The Legionella pneumophila iraAB locus is required for iron assimilation, intracellular infection, and virulence.

Legionella pneumophila, a facultative intracellular parasite of human alveolar macrophages and protozoa, causes Legionnaires' disease. Using mini-Tn10 mutagenesis, we previously isolated a L. pneumophila mutant that was hypersensitive to iron chelators. This mutant, NU216, and its allelic equivalent, NU216R, were also defective for intracellular infection, particularly in iron-deficient host cells. To determine whether NU216R was attenuated for virulence, we assessed its ability to cause disease in guinea pigs following intratracheal inoculation. NU216R-infected animals yielded 1,000-fold fewer bacteria from their lungs and spleen compared to wild-type-130b-infected animals that had received a 50-fold-lower dose. Moreover, NU216R-infected animals subsequently cleared the bacteria from these sites. While infection with 130b resulted in high fever, weight loss, and ruffled fur, inoculation with NU216R did not elicit any signs of disease. DNA sequence analysis revealed that the transposon insertion in NU216R lies in the first open reading frame of a two-gene operon. This open reading frame (iraA) encodes a 272-amino-acid protein that shows sequence similarity to methyltransferases. The second open reading frame (iraB) encodes a 501-amino-acid protein that is highly similar to di- and tripeptide transporters from both prokaryotes and eukaryotes. Southern hybridization analyses determined that the iraAB locus was largely limited to strains of L. pneumophila, the most pathogenic of the Legionella species. A newly derived mutant containing a targeted disruption of iraB showed reduced ability to grow under iron-depleted extracellular conditions, but it did not have an infectivity defect in the macrophage-like U937 cells. These data suggest that iraA is critical for virulence of L. pneumophila while iraB is involved in a novel method of iron acquisition which may utilize iron-loaded peptides.

Amino Acid Sequence↗
PubMed2004

Health-related quality of life outcomes following elective open or endovascular AAA repair: a randomized controlled trial.

PURPOSE: To assess health-related quality of life outcomes after endovascular versus open abdominal aortic aneurysm repair. METHODS: Participants were randomly assigned to receive either endovascular or open abdominal aortic aneurysm (AAA) surgery according to a rate of 3 endovascular patients to 1 with open repair. Data on patient characteristics, operative aspects, and procedural and device-related complications were compiled at a single center. Health-related quality of life was assessed before treatment and 1 and 3 months following operation using the Medical Outcomes Study Short-Form 36-item Health Survey (SF-36) and the EuroQol questionnaire. RESULTS: Between 1996 and 1999, 57 patients (54 men; mean age 69 years, range 52-82) underwent endovascular and 19 patients (16 men; mean age 68 years, range 52-81) underwent open AAA repairs. Preoperatively, comparable scores were recorded in both treatment groups. One month after operation, patients of both groups scored significantly lower on the SF-36 domains of Role Limitations due to physical problems and Pain compared to preoperative scores. Three months after operation, both groups had scores in all domains comparable to preoperative levels of functioning. There was a significant benefit for the endovascular group 1 month after operation in the SF-36 domains of Physical Functioning, Role Limitations due to physical problems, Vitality, and Pain; their score on the EuroQol Usual Activities item was also significantly better. After 3 months, there were no longer differences between groups. CONCLUSIONS: Short-term health-related quality of life benefits were found after endovascular repair compared with standard open surgery.

Aged↗
PubMed1998

Genomic organization of the human C3a receptor.

The human C3a receptor (C3aR) mediates the activation of cells by the potent proinflammatory chemoattractant C3a, an anaphylatoxin, generated in the early phase of an inflammatory reaction by proteolytic cleavage of the complement component C3. To understand the molecular mechanisms that regulate C3aR gene expression, we initiated studies to determine its genomic and mRNA organization. We now report the following novel findings: (1) The C3aR is a single-copy gene as shown by Southern hybridization of human genomic DNA. (2) Using PCR amplification of DNA from monochromosomal somatic cell hybrid and radiation hybrid panels, the C3aR locus was mapped to chromosome 12p13. (3) Genomic DNA clones encompassing the C3aR locus were isolated from a human genomic DNA library and characterized by restriction mapping, Southern blotting, PCR analysis and DNA sequencing. Comparison of the genomic with the known cDNA sequences revealed a single 6-kb intron sequence located 1 1 bp upstream of the ATG initiation codon. The open reading frame and the complete 3' untranslated region are encoded on a single exon.

Base Sequence↗
PubMed1993

Mapping a putative pyruvoyl decarboxylase active site to human cytomegalovirus open reading frame UL77.

Human cytomegalovirus is present as an apparently innocuous infection among a large proportion of the adult population that causes serious disease when congenitally transferred (1). Human cytomegalovirus disease may become life threatening when found as an infection of immunocompromised transplant and AIDS patients (1,2). We now map a putative pyruvoyl decarboxylase enzyme prosthetic group, known to be essential to the active site of this class of enzymes, to Human cytomegalovirus open reading frame UL77. The significance of finding a putative pyruvoyl decarboxylase enzyme prosthetic group among human cytomegalovirus open reading frame codons is p = 0.001. The UL77 polypeptide was aligned with human, yeast and bacterial S-AdoMet decarboxylase enzymes. Alignment of UL77 and S-AdoMet decarboxylase enzymes indicates that UL77 may contain a similar activity.

Adenosylmethionine Decarboxylase↗
PubMed1990

Nucleotide sequence of the E2-peplomer protein gene and partial nucleotide sequence of the upstream polymerase gene of transmissible gas gastroenteritis virus (Miller strain).

The E2-peplomer protein gene of the virulent Miller strain of transmissible gastroenteritis virus (TGEV) was sequenced from cDNA clones and compared to the E2 gene sequence of the avirulent Purdue strain. Sequence comparisons indicate that most amino acid differences occur in the N-terminal half of the E2-peplomer which represents the most exposed region of the protein. In addition, analysis of an incompletely sequenced open reading frame (ORF) to the immediate 5' side of the E2 gene indicates extensive sequence homology with the infectious bronchitis virus (IBV) F2 gene which is thought to encode a RNA polymerase.

Amino Acid Sequence↗
PubMed1991

The isolation and characterisation of plant sequences homologous to human hypervariable minisatellites.

We have isolated DNA probes, homologous to the human hypervariable minisatellite sequence 33.15, from the genome of rice (Oryza sativa). These probes are capable of producing a multilocus rice DNA fingerprint. The rice sequence has a tandem repeating structure based on a 12 bp GC-rich repeat which shows homology to its human counterpart. This probe detects up to 30 loci which are at a number of unlinked chromosomal sites. The GC-rich sequence is invariably associated with an open reading frame (ORF) of unknown function. The ORF is probably a member of a small multigene family.

Amino Acid Sequence↗
PubMed1998

Complete nucleotide sequence analysis of a Western Pacific dengue-1 virus strain.

We have determined the complete nucleotide sequence and the deduced amino acid polypeptide sequence of the genome of a dengue-1 (DEN-1) virus strain isolated from a patient on Nauru in the Western Pacific in 1974 (West Pac 74). The complete genome is 10,735 nucleotides in length and contains a single long open reading frame of 10,176 nucleotides encoding a polyprotein of 3392 amino acids. When compared to DEN-1 Singapore S275/90, the nucleotide and amino acid sequence homology are 94% and 97.8%, respectively.

Amino Acid Sequence↗
PubMed2000

The genome sequence of the thermoacidophilic scavenger Thermoplasma acidophilum.

Thermoplasma acidophilum is a thermoacidophilic archaeon that thrives at 59 degrees C and pH 2, which was isolated from self-heating coal refuse piles and solfatara fields. Species of the genus Thermoplasma do not possess a rigid cell wall, but are only delimited by a plasma membrane. Many macromolecular assemblies from Thermoplasma, primarily proteases and chaperones, have been pivotal in elucidating the structure and function of their more complex eukaryotic homologues. Our interest in protein folding and degradation led us to seek a more complete representation of the proteins involved in these pathways by determining the genome sequence of the organism. Here we have sequenced the 1,564,905-base-pair genome in just 7,855 sequencing reactions by using a new strategy. The 1,509 open reading frames identify Thermoplasma as a typical euryarchaeon with a substantial complement of bacteria-related genes; however, evidence indicates that there has been much lateral gene transfer between Thermoplasma and Sulfolobus solfataricus, a phylogenetically distant crenarchaeon inhabiting the same environment. At least 252 open reading frames, including a complete protein degradation pathway and various transport proteins, resemble Sulfolobus proteins most closely.

Archaeal Proteins↗
PubMed1997

Isolation of a novel human gene from the Down syndrome critical region of chromosome 21q22.2.

Down syndrome is the most common birth defect, and is caused by trisomy 21. We identified a novel gene in the so-called Down syndrome critical region by means of computer-aided exon prediction and subsequent cDNA cloning. The gene, designated as DCRA (Down syndrome Critical Region gene A), consists of eight exons of 3,252 bp in total and encodes a large open reading frame of 297 amino acid residues. The open reading frame shows significant homology to Hbeta58, a mouse gene essential for embryogenesis, PEP8, a yeast homologue of Hbeta58, and an expressed sequence tag of Arabidopsis thariana, suggesting that DCRA has some important function that has been conserved during the course of evolution. DCRA is expressed in most tissues examined, including fetal and adult brain, heart, lung, liver, and kidney. The cDNA of the DCRA mouse homologue, Dcra, was also cloned. It is 2,157 bp long and has an open reading frame of 297 amino acid residues, which shows 92% identity to human DCRA. Dcra is expressed in all the embryo and adult tissues examined.

Adult↗
PubMed1996

Two additional 5' exons in the human Vigilin gene distinguish it from the chicken gene and provide the structural basis for differential routes of gene expression.

Vigilin, a 150-kDa protein, contains 14 tandemly arranged domains, each consisting of a KH RNA-binding motif and a spacer region. Here, we report on the physical structure of the human Vigilin gene with 29 exons, thereby outnumbering the chicken gene by two additional 5' exons. These additional exons, 1A and 1B, are alternatively though concurrently spliced to exon 1C which is homologous to the first exon in the chicken gene. None of the additional human exons code for an amino-terminal extension of Vigilin, due to in-frame stop codons. Structural features of exon 1A, however, would allow the translation of a 13-amino-acid peptide from an upstream open reading frame preceding the vigilin open reading frame. We suggest that exons 1A and 1B have been gained during evolution, allowing alternative routes of expression control of the human Vigilin gene.

Alternative Splicing↗
PubMed1994

Nucleotide sequence and structural organization of Yersinia pestis insertion sequence IS100.

Insertion sequence IS100 was localized on a 9.5-kb plasmid of Yersinia pestis and was shown to be specific for Y. pestis and serotype I strains of Y. pseudotuberculosis. The nucleotide sequence of IS100 isolated from this plasmid was determined. The element, which was flanked by 5-bp direct repeats, contained 1953 bp including imperfect inverted terminal repeats of 52 and 61 bp long (43 bp were identical). Two open reading frames encoding potential polypeptides of 340 and 252 amino acids were identified on one DNA strand. Nucleotide sequence as well as deduced polypeptide sequences of IS100 were homologous to those of IS21, IS232 and IS640.

Base Sequence↗
PubMed1995

Functional cloning of the dihydropteroate synthase gene of Staphylococcus haemolyticus.

A 1,7-kilobase fragment of the Staphylococcus haemolyticus chromosome containing the dihydropteroate synthase gene has been cloned by complementation in a temperature-sensitive mutant of Escherichia coli. The gene, designated folP, predicts a gene product of 29613 Da which shares significant amino acid sequence identity with other known bacterial dihydropteroate synthases. Analysis of the DNA sequence upstream and downstream of folP identified two further, incomplete open reading frames, one of which shows predicted amino acid sequence similarity to a second bacterial folic acid synthesis enzyme, dihydroneopterin aldolase.

Aldehyde-Lyases↗
PubMed1999

The F420H2-dehydrogenase from Methanolobus tindarius: cloning of the ffd operon and expression of the genes in Escherichia coli.

The membrane-bound F420H2-dehydrogenase from the methylotrophic methanogen Methanolobus tindarius oxidizes reduced coenzyme F420 and feeds the electrons into an energy-conserving electron transport chain. Based on the N-terminal amino acid sequence of the 40-kDa subunit of F420H2-dehydrogenase the corresponding gene ffdB was detected in chromosomal DNA of M. tindarius. Sequence analysis, primer extension, and RT-PCR experiments indicated that ffdB is part of an operon harboring three additional open reading frames (ffdA, ffdC, ffdD). The corresponding mRNA transcript and transcription start sites were determined. All four genes could be heterologously expressed in Escherichia coli.

Amino Acid Sequence↗
PubMed1993

Menaquinone (vitamin K2) biosynthesis: cloning, nucleotide sequence, and expression of the menC gene from Escherichia coli.

The benzenoid aromatic compound o-succinylbenzoic acid is formed by dehydration of the prearomatic compound 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylic acid by the enzyme o-succinylbenzoate synthase, encoded by the menC gene. A 1.3-kb PstI-PvuII fragment was found to complement the menC mutation. The complete nucleotide sequence of this fragment revealed a single open reading frame of 954 bp capable of encoding a 35-kDa protein. A consensus sequence for a ribosomal binding site but no promoter consensus sequences were found. However, the first base of the initiating codon of this open reading frame overlaps the upstream menB gene termination codon, suggesting an operon-like organization for these genes. Consistent with this suggestion, the menB promoter can initiate transcription of the menC gene.

Amino Acid Sequence↗