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At least 1,351 records · Page 75Linked to original sources

PubMed1998

Molecular cloning and functional expression of a protein-serine/threonine phosphatase from the hyperthermophilic archaeon Pyrodictium abyssi TAG11.

An open reading frame coding for a putative protein-serine/threonine phosphatase was identified in the hyperthermophilic archaeon Pyrodictium abyssi TAG11 and named Py-PP1. Py-PP1 was expressed in Escherichia coli, purified from inclusion bodies, and biochemically characterized. The phosphatase gene is part of an operon which may provide, for the first time, insight into a physiological role for archaeal protein phosphatases in vivo.

Amino Acid Sequence↗

PubMed2003

Identification and characterization of a mandelamide hydrolase and an NAD(P)+-dependent benzaldehyde dehydrogenase from Pseudomonas putida ATCC 12633.

The enzymes of the mandelate metabolic pathway permit Pseudomonas putida ATCC 12633 to utilize either or both enantiomers of mandelate as the sole carbon source. The genes encoding the mandelate pathway were found to lie on a single 10.5-kb restriction fragment. Part of that fragment was shown to contain the genes coding for mandelate racemase, mandelate dehydrogenase, and benzoylformate decarboxylase arranged in an operon. Here we report the sequencing of the remainder of the restriction fragment, which revealed three further open reading frames, denoted mdlX, mdlY, and mdlD. All were transcribed in the opposite direction from the genes of the mdlABC operon. Sequence alignments suggested that the open reading frames encoded a regulatory protein (mdlX), a member of the amidase signature family (mdlY), and an NAD(P)(+)-dependent dehydrogenase (mdlD). The mdlY and mdlD genes were isolated and expressed in Escherichia coli, and the purified gene products were characterized as a mandelamide hydrolase and an NAD(P)(+)-dependent benzaldehyde dehydrogenase, respectively.

Aldehyde Oxidoreductases↗

PubMed1998

Nucleotide sequence of a marsupial interleukin-10 cDNA from the Australian brushtail possum (Trichosurus vulpecula).

A cDNA encoding a marsupial interleukin-10 (IL-10), was isolated from Australian brushtail possum alveolar macrophages. The cDNA of 1604 bp had an open reading frame of 522 bp coding for a protein of 174 amino acids. Its deduced amino acid sequence had an identity of 60% with cat, 58% with pig, 56% with human and cow, 52% with mouse and 53% with rat IL-10. The expression of IL-10 was up-regulated in both LPS-stimulated and Mycobacterium bovis-infected possum alveolar macrophages.

Amino Acid Sequence↗

PubMed2002

Identification of human male germ cell-associated kinase, a kinase transcriptionally activated by androgen in prostate cancer cells.

Androgen is involved in both normal development and malignant transformation of prostate cells. The signal transduction pathways associated with these processes are not well understood. Using a novel kinase display approach, we have identified a protein kinase, human male germ cell-associated kinase (hMAK), which is transcriptionally induced by the androgenic hormone 5alpha-dihydrotestosterone (DHT). The kinetics of induction is rapid and dose-dependent, and the induction is not blocked by cycloheximide treatment. Real time reverse transcription-PCR studies demonstrated a 9-fold induction of hMAK by 10 nm DHT at 24 h post-stimulation. The expression levels of hMAK in prostate cancer cell lines are in general higher than those of normal prostate epithelial cells. A reverse transcription-PCR product encompassing the entire hMAK open reading frame was isolated. The results from sequencing analysis showed that the hMAK protein is 623 amino acids in length and contains a kinase catalytic domain at its N terminus, followed by a proline/glutamine-rich domain. The catalytic domain of this kinase contains sequence motifs related to both the cyclin-dependent kinase and the mitogen-activated protein kinase families. When expressed in COS1 cells, hMAK is kinase-active as demonstrated by autophosphorylation and phosphorylation of exogenous substrate and is localized in the nucleus. A 3.7-kilobase pair promoter of the hMAK locus was isolated from a human genomic DNA bacterial artificial chromosome clone and was shown to be activated by DHT. This activation can be blocked by an anti-androgen drug bicalutamide (Casodex), implicating the involvement of androgen receptor in this process. Taken together, these data suggest that hMAK is a protein kinase targeted by androgen that may participate in androgen-mediated signaling in prostate cancer cells.

Amino Acid Sequence↗

PubMed1991

Nucleotide sequence analysis and genomic organization of the NY-RPV isolate of barley yellow dwarf virus.

cDNA clones representing the ssRNA genome of the NY-RPV isolate of barley yellow dwarf luteovirus (BYDV) were sequenced and 5600 nucleotides of the genome were determined. The deduced genome organization has limited similarity to that of another BYDV isolate, Vic-PAV, but is identical to that of beet western yellows (BWYV) and potato leafroll (PLRV) luteoviruses. NY-RPV has six major positive-sense open reading frames (ORFs) and, by comparison with RNA-dependent RNA polymerase and nucleic acid helicase consensus sequence motifs, it is postulated that NY-RPV ORF2 and ORF3 encode the viral replicase, which is expressed by a translational frameshift mechanism. The region of the NY-RPV genome containing the 22K coat protein ORF, the apparently associated internal apparent VPg ORF and the ORF immediately 3'-proximal (ORF6) to the coat protein ORF are organized as reported for other luteoviruses. Evidence is presented showing that ORF6 is expressed by readthrough of the coat protein gene termination codon, and that this protein is associated with the intact virus as a 65K protein. Although NY-RPV infects graminaceous rather than dicotyledonous plants, the taxonomic relationships between BYDV isolates and other luteoviruses deduced from the genome organization and sequence data strongly suggest that NY-RPV is distinct from the PAV-like isolates of BYDV and is more closely related to BWYV and PLRV.

Amino Acid Sequence↗

PubMed2002

The nucleotide sequence of Shiga toxin (Stx) 2e-encoding phage phiP27 is not related to other Stx phage genomes, but the modular genetic structure is conserved.

In this study we determined the complete nucleotide sequence of Shiga toxin 2e-encoding bacteriophage phi P27, isolated from the Shiga toxin-producing Escherichia coli patient isolate 2771/97. phi P27 is integrated as a prophage in the chromosomal yecE gene. This integration generates identity segments of attL and attR sites with lengths of 11 nucleotides. The integrated prophage genome has a size of 42,575 bp. We identified 58 open reading frames (ORFs), each with a length of >150 nucleotides. The deduced proteins of 44 ORFs showed significant homologies to other proteins present in sequence databases, whereas 14 putative proteins did not. For 29 proteins, we could deduce a putative function. Most of these are related to the basic phage propagation cycle. The phi P27 genome represents a mosaic composed of genetic elements which are obviously derived from related and unrelated phages. We identified five short linker sequences of 22 to 151 bp in the phi P27 sequence which have also been detected in a couple of other lambdoid phages. These linkers are located between functional modules in the phage genome and are thought to play a role in genetic recombination. Although the overall DNA sequence of phi P27 is not highly related to other known phages, the data obtained demonstrate a typical lambdoid genome structure.

Bacteriophages↗

PubMed1992

Hepatitis B virus X protein is not central to the viral life cycle in vitro.

The hepatitis B x (HBx) gene is the smallest open reading frame of the hepatitis B virus (HBV) genome. It is conserved among all mammalian hepadnaviruses and is expressed during viral infection. While the HBx protein (pX) has been shown to trans-activate the transcription of a wide range of viral and cellular genes and to induce liver cancer in transgenic mice, the significance of pX for the life cycle of HBV itself has not been elucidated. To assess the function of pX in viral replication and virion export, we designed an X-minus mutant by introduction of a stop codon at the beginning of the HBx gene without affecting the viral polymerase gene product. Transient transfection analyses using different cell lines revealed that this X-minus mutant directs the synthesis of wild-type levels of viral proteins, replicative intermediates, and virion export. These data suggest that the expression of the highly conserved HBx gene is not central for the life cycle of HBV in vitro but may be involved in the pathogenicity of hepadnavirus infection, including liver cancer development.

Base Sequence↗

PubMed1996

Coding sequence-dependent ribosomal arrest at termination of translation.

A remarkably high percentage of proto-oncogene, growth factor, cellular receptor, and viral transcript leaders contain short upstream open reading frames (uORFs), yet the significance and regulatory effects of these uORFs have not been well characterized. In the case of the human cytomegalovirus gpUL4 (gp48) transcript, the second of three uORFs (uORF2) inhibits translation of the downstream cistron by a process that depends on the uORF2 amino acid coding information. To investigate the mechanism underlying this unusual regulatory element, we adapted the toeprinting (or reverse transcriptase extension inhibition) assay for use in detecting positions of ribosomal stalling on gp48 transcripts. Using a cell-free translation system, we demonstrate that ribosomes arrest at the termination codon of uORF2 by a uORF2 coding sequence-dependent mechanism. Further, the sequence requirements for ribosomal stalling are the same as for inhibition of downstream translation. We also provide evidence for ribosomal stalling in vivo, on the natural viral mRNA. These data support the hypothesis that the inhibition of downstream translation results from uORF2 peptide-dependent ribosomal arrest at termination and suggest that translation termination may be a regulatory step in expression of some eukaryotic genes.

Animals↗

PubMed1996

The sequence of a 16,691 bp segment of Saccharomyces cerevisiae chromosome IV identifies the DUN1, PMT1, PMT5, SRP14 and DPR1 genes, and five new open reading frames.

As part of the European BIOTECH programme, the nucleotide sequence of a 16691 bp fragment from the left arm of chromosome IV of Saccharomyces cerevisiae has been deduced. Analysis of the sequence reveals the presence of 13 open reading frames (ORFs) larger than 100 codons. five of these were previously identified as genes DUN1, PMT1, PMT5, SRP14 and DPR1. One putative protein, D2371p, contains an ATP-GTP binding site, and shares homology to the ArsA component of an Escherichia coli arsenical pump. No significant homology to any known protein has been found for the other ORFs. D2378p contains a zinc finger domain.

Amino Acid Sequence↗

PubMed1992

Sequence of the HMR region on chromosome III of Saccharomyces cerevisiae.

A 10,095 base pair DNA fragment from the right arm of chromosome III of Saccharomyces cerevisiae has been sequenced and analysed. It encompasses the silent mating-type locus HMR. Both HMRa1 and HMRa2 genes, as well as their flanking regulatory regions, have been identified. Three new open reading frames longer than 80 amino acid residues were found in this fragment. One of them (YCR137) shows features compatible with a membranous localization and a transporter function. The other two do not show a similarity with any known gene. A new gene coding for tRNA(thr)al (ACU) has been identified. It is located in a region coding for several delta sequences.

Amino Acid Sequence↗

PubMed1995

Sequence of a 9.8 kb segment of yeast chromosome II including the three genes of the MAL3 locus and three unidentified open reading frames.

We report the DNA sequence of a segment located on the right arm of chromosome II from Saccharomyces cerevisiae S288C near the subtelomeric sequences. The sequence was determined using a random cloning strategy followed by an oligonucleotide-directed sequencing. The segment contains four non-overlapping open reading frames (ORFs) YBR297w, YBR298c, YBR299w and YBR301c, and two overlapping ones (YBR300c and YBR300w). Three of them--YBR297w, YBR298c and YBR299w--are the MAL3R (transcriptional regulatory protein), MAL3T (maltose permease) and MAL3S (maltase) genes of the MAL3 locus previously localized. The three other ORFs are unidentified. Another MAL locus (MALl) has been localized on chromosome VII. The Mal- phenotype of strain S288c cannot be explained by telomeric silencing.

Base Sequence↗

PubMed1996

The hermit transposable element of the Australian sheep blowfly, Lucilia cuprina, belongs to the hAT family of transposable elements.

We report the cloning of hermit, a member of the hAT family of transposable elements from the genome of the Australian sheep blowfly, Lucilia cuprina. Hermit is 2716 bp long and is 49% homologous to the autonomous hobo element, HFL1, at the nucleic acid level. Hermit has 15 bp terminal inverted repeats that share 10 bp with the terminal inverted repeats of HFL1. Conceptual translation reveals a 583 residue open reading frame (ORF) that is 64% similar and 42% identical to the HFL1 ORF. However, the sequence of the hermit element contains two frameshifts within the putative ORF, indication that hermit is an inactive element. Analysis of L. cuprina strains from within and outside Australia suggested that hermit is present as a single copy in all the genomes analysed.

Amino Acid Sequence↗

PubMed1995

Molecular cloning and complete nucleotide sequence of carnation Italian ringspot tombusvirus genomic and defective interfering RNAs.

The complete sequences of genomic and defective interfering (DI) RNAs of carnation Italian ringspot tombusvirus (CIRV) were determined. The genome (4760 nt) has an organization identical to that reported for other tombusviruses except that the pre-readthrough domain of the viral replicase encoded by the 5'-proximal open reading frame (ORF) is larger. In particular, the N-terminal region of this protein differs from the corresponding region of the other members of the genus Tombusvirus and Carmovirus. Two DI RNAs were found in infected tissues whose sequences were completely derived from genomic RNA. The smaller molecule (474 nt) is contained completely within the larger molecule (656 nt), which suggests that it is derived from the larger one.

Base Sequence↗

PubMed1999

Nucleotide sequence of coat protein gene of yam mild mosaic virus, isolated in Papua New Guinea.

We determined the 3'-termimus 1353 nucleotides (nts) in length excluding the poly (A) tail of yam mild mosaic potyvirus (YMMV) RNA. The sequence starts within a long open reading frame (ORF) 1209 nts and is followed by untranslated region (3'-UTR) of 144 nts. The coat protein (CP) contains 266 amino acids (aa) with molecular ratio (Mr) of approximately 30 kDa. The CP of YMMV differs substantially from yam mosaic virus (YMV), Japanese yam mosaic virus (JYMV) (57 and 61% of amino acid sequence identity) and other potyvirus species. This result suggests that YMMV should be classified as a new yam potyvirus.

3' Untranslated Regions↗

PubMed1993

Characterization of a tropomyosin cDNA from the hydrozoan Podocoryne carnea.

A cDNA clone from the hydrozoan Podocoryne carnea was characterized. It consists of an open reading frame of 726 nt flanked by a 84 nt 5' and a 307 nt 3' untranslated region. The corresponding gene exists apparently as a single copy. The transcript is ubiquitously expressed in the polyp and the medusa stage. Several features of the predicted peptide sequence indicate a relationship to tropomyosins. At the amino acid level it shares 26-30% identical residues with other invertebrate and vertebrate tropomyosin sequences.

Amino Acid Sequence↗

PubMed1991

Sequence analysis of the homeobox-containing exon of the murine Hox-4.3 homeogene.

A homeobox-containing gene * was detected by Southern analysis of a cosmid spanning a region of the murine HOX-4 complex between Hox-4.4 (Hox-5.2) and Hox-4.2 (Hox-5.1) with a probe derived from the Hox-4.2 homeobox. The sequence of a cross-hybridizing region revealed an open reading frame encoding an Antennapedia (Antp) class homeodomain highly homologous to the products of human HOX4C (Hox-5.4/HOX4E), mouse Hox-3.1 and Hox-2.4. This, together with strong conservation of sequences 3' to the homoebox, indicates that we have cloned the murine Hox-4.3 gene. No other homeobox sequences were detected in this screen suggesting that the HOX-4 complex lacks paralogous genes represented in the equivalent regions of other HOX loci.

Amino Acid Sequence↗

PubMed1993

Isolation and characterization of a gene involved in ethylene biosynthesis from Arabidopsis thaliana.

The ethylene forming enzyme (EFE) is a key factor in ethylene biosynthesis. To understand better the regulation of ethylene biosynthesis in vegetative tissues, we set out to isolate and characterize a complementary DNA (cDNA) encoding the EFE from Arabidopsis thaliana. An A. thaliana cDNA library was screened with pTOM 13, a tomato cDNA coding for the EFE. A cDNA clone (pEAT1) was isolated. The cDNA is 1200 nucleotides (nt) in length and predicts a protein of M(r) 36,663. The insert includes the complete open reading frame of 972 bp and shows strong homology with several reported sequences, both at the nt and amino acid level. In whole seedlings, expression of pEAT1 was enhanced by wounding, ethrel, Fe2+, and 1-amino-cyclopropane-carboxylic acid (ACC) treatments. In contrast, heat shock had no effect on the expression.

Amino Acid Sequence↗

PubMed1994

Cloning, sequence and in vitro transcription/translation analysis of a 3.2-kb EcoRI-HindIII fragment of Leuconostoc oenos bacteriophage L10.

A 3.2-kb EcoRI-HindIII DNA fragment of Leuconostoc oenos bacteriophage L10 was cloned and sequenced. Computer-assisted analysis of the sequence identified eleven possible open reading frames (ORFs) that were all on the same strand. In vitro transcription/translation analysis of the full-length DNA fragment yielded five prominent proteins that were correlated with ORFs by their sizes and expression from deleted clones. Only those ORFs containing recognizable Shine-Dalgarno sequences coded for proteins. Neither the nucleotide sequence, nor deduced amino-acid sequences showed significant homology with other known sequences.

Amino Acid Sequence↗