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PubMed1999

The R27080 glycoprotein is abundantly secreted from human cytomegalovirus-infected fibroblasts.

A 45 kDa glycoprotein was purified from the culture media of human cytomegalovirus (HCMV)-infected fibroblasts. N-terminal sequencing revealed that the protein, R27080, is the translation product of the R27080 open reading frame of HCMV. R27080 is highly glycosylated and contains no cysteine or methionine residues. Proteolytic cleavage of R27080 by a furin-like enzyme was analysed in transfected COS-7 cells. R27080 is the first identified viral protein secreted from HCMV-infected cells.

Amino Acid Sequence↗

PubMed1998

Human endogenous retrovirus K homologous sequences and their coding capacity in Old World primates.

The coding capacity for retroviral Gag and Env proteins has been maintained in human endogenous retroviruses of the HERV-K family. HERV-K homologous sequences have been found in all Old World primates. Here, we examined Old World primate species for the presence of full-length HERV-K gag and env genes and the presence of gag and env open reading frames as determined by the protein truncation test. Full-length HERV-K env genes were found in DNAs of all Old World primate species, whereas open reading frames for Env protein were found solely in human, chimpanzee, and gorilla DNAs. The mutational event leading to two HERV-K types was found to have occurred after the separation of hominids from lower Old World primates and before the expansion of hominids. Full-length HERV-K gag genes in hominids displayed a 96-bp deletion compared to those in lower Old World primates. The ancient gag variant has not been maintained during hominid evolution. Open reading frames for HERV-K Gag have been found in all Old World primates except chimpanzees. Our study of the HERV-K family during Old World primate evolution contributes to the understanding of their possible biological functions in the host genomes.

Animals↗

PubMed1995

Molecular cloning and nucleotide sequence of purine nucleoside phosphorylase and uridine phosphorylase genes from Klebsiella sp.

Klebsiella sp. LF 1202 was isolated as a bacterium that can assimilate adenosine as a sole source of carbon and nitrogen [F. Ling et al., Agric. Biol. Chem., 55, 573-575 (1991)] from a soil sample. Both the purine nucleoside phosphorylase (PNPase) and uridine phosphorylase (UPase) of this bacterium were induced simultaneously when the bacterium was cultured in a medium containing adenosine or uridine as a sole source of carbon and nitrogen. This induction profile is different from that of Escherichia coli. Here we cloned and sequenced the gene corresponding to each enzyme. The open reading frame (ORF) of the PNPase gene consisted of 717 bp that encoded a polypeptide of 239 amino acids with a molecular weight of 26,198. The ORF of the UPase gene consisted of 834 bp that encoded a polypeptide of 278 amino acids with a molecular weight of 28,912.

Amino Acid Sequence↗

PubMed1997

Localization of an open reading frame with homology to human aspartoacylase upstream from psbA in the prokaryote Prochlorococcus marinus CCMP 1375.

An open reading frame encoding a polypeptide with significant homology (about 28% identity and 16% similarity) to human aspartoacylase (ASPA) was identified in the genome of Prochlorococcus marinus CCMP 1375, an oxyphototrophic bacterium. Sequence alignments show that, in particular, the regions previously suggested to form the catalytic core of human ASPA are evolutionarily conserved and nearly identical to that found in the Prochlorococcus putative ASPA. A glutamate at position 273 is located central to the strongly conserved INEAAY motif and corresponds to a glutamate-285 in human ASPA. A point mutation at this site, resulting in a Glu285Ala missense mutation, was identified previously as the molecular basis for Canavan disease, a form of leukodystrophy. The data provide new insights about conserved and hence functionally important domains of ASPA. The detection of this gene in an unicellular prokaryote demonstrates that this enzymatic activity is more widespread than expected previously. Furthermore, bacteria may be used as simple model organisms to study different forms of ASPA.

Amidohydrolases↗

PubMed1995

Nucleotide sequence and expression of UDP-glucose dehydrogenase gene required for the synthesis of xanthan gum in Xanthomonas campestris.

Xanthomonas campestris pv. campestris, producing large amounts of exopolysaccharide xanthan gum, has a mucoid phenotype. Strain SD7 was a non-mucoid mutant deficient in UDP-glucose dehydrogenase. A DNA fragment able to complement the mutation of SD7 was cloned from the parental wild-type strain Xc11. Sequence analysis of the region required for the complementation revealed an open reading frame which could encode a polypeptide of 445 amino acids with a calculated molecular weight of 48,432, a size similar to that of the product produced by maxicell. The amino acid sequence had significant homology to that of the GDP-mannose dehydrogenase from Pseudomonas aeruginosa.

Amino Acid Sequence↗

PubMed1993

IS231V and W from Bacillus thuringiensis subsp. israelensis, two distant members of the IS231 family of insertion sequences.

IS231 constitutes a family of related insertion sequences (IS) from Bacillus thuringiensis. Two new IS231-related elements, IS231V and IS231W, have been isolated from the 72-MDa plasmid of B. thuringiensis subsp. israelensis. These closely related 1964-bp IS are delimited by 22-bp imperfect inverted repeats strongly similar to those of the other iso-IS231. Although the other known IS231 harbor a single long open reading frame (ORF), IS231V and W display two slightly overlapping ORF on the same DNA strand. They show about 50% identity with the transposase of the other iso-IS231. A frameshifting model is proposed for the synthesis of a fusion product which would constitute their active transposase.

Amino Acid Sequence↗

PubMed1994

On the evolution of arginases and related enzymes.

Sequence analysis of the arginase/agmatine ureohydrolase family, important enzymes in arginine/agmatine metabolism and the urea cycle, reveals the similarity of arginases to formiminoglutamate hydrolase (hutG) in Klebsiella aerogenes and to a previously unidentified open reading frame adjacent to the HMf locus of the archaebacterium Methanothermus fervidus. The gene structure and distribution of these homologous proteins across primary kingdoms suggest that this family is another example of a primordial enzyme possibly present in the universal common ancestor and that can be used as phylogenetic marker.

Amino Acid Sequence↗

PubMed1991

Structural and functional analysis of the rcsA gene from Erwinia stewartii.

RcsA is a positive regulator of genes for extracellular polysaccharide biosynthesis in the Enterobacteriaceae. The nucleotide sequence of the rcsA gene from Erwinia stewartii was determined and compared to rcsA sequences from E. amylovora, Escherichia coli, and Klebsiella pneumoniae. Three highly conserved regions of the gene were identified. The C-terminal end of the open reading frame (ORF) shared significant amino acid homology to the LuxR class of bacterial activator proteins. Insertion and deletion mutagenesis of the 5' non-coding region indicated that maximal expression of rcsA was dependent upon cis-acting regulatory sequences located more than 300 bp upstream of the translational start site.

Amino Acid Sequence↗

PubMed1991

Identification of the infectious laryngotracheitis virus glycoprotein gB gene by the polymerase chain reaction.

The infectious laryngotracheitis virus (ILTV) homologue of the herpes simplex virus type 1 (HSV-1) glycoprotein B (gB) gene was identified by PCR amplification of genomic ILTV DNA. A 488-bp amplified DNA fragment was used to identify and clone two adjacent PstI fragments from genomic ILTV DNA. Sequence analysis of the region surrounding the amplified fragment identified a 2619-bp open reading frame that has 39% homology with both the nucleotide and amino-acid sequences of the HSV-1 gB gene. Northern blot analysis using a portion of the open reading frame as a probe identified a 2.7-kb RNA transcript in ILTV-infected chicken embryo liver cells. Analysis of the predicted amino acid sequence of the ILTV protein indicated that it shares structural features with the gB glycoproteins of other herpesviruses.

Amino Acid Sequence↗

PubMed1990

Red algal plasmids.

Five of 21 red algal genera were found to contain circular dsDNA plasmids, typically of two or more sizes per species. Clones of the two plasmids (GL4.4 and GL3.5 kbp), characterizing all isolates of Gracilariopsis lemaneiformis, do not cross-hybridize with each other, with the nuclear, plastid or mitochondrial genomes of G. lemaneiformis, or with any DNA genomes of the other red algae examined. Clones of both plasmids hybridized with discrete bands on Northern blots of total RNA and poly(A)+ RNA. Sequencing of the G. lemaneiformis 3.5 kbp plasmid revealed two potential open reading frames which, when used to probe Northern blots, confirmed the presence of specific transcripts. These autonomously replicating plasmids are present in high copy number per cell and in constant proportion to each other. Their constancy suggests a function of significance to the species. Red algal plasmids may provide useful vectors for transforming economically important red algal species.

Amino Acid Sequence↗

PubMed1996

The Magnaporthe grisea DNA fingerprinting probe MGR586 contains the 3' end of an inverted repeat transposon.

The Magnaporthe grisea repeat (MGR) sequence MGR586 has been widely used for population studies of the rice blast fungus, and has enabled classification of the fungal population into hundreds of genetic lineages. While studying the distribution of MGR586 sequences in strains of M. grisea, we discovered that the plasmid probe pCB586 contains a significant amount of single-copy DNA. To define precisely the boundary of the repetitive DNA in pCB586, this plasmid and four cosmid clones containing MGR586 were sequenced. Only 740 bp of one end of the 2.6-bp insert in the pCB586 plasmid was common to all clones. DNA sequence analysis of cosmid DNA revealed that all the cosmids contained common sequences beyond the cloning site in pCB586, indicating that the repetitive DNA in the fingerprinting clone is part of a larger element. The entire repetitive element was sequenced and found to resemble an inverted repeat transposon. This putative transposon is 1.86 kb in length and has perfect terminal repeats of 42 bp, which themselves contain direct repeats of 16 bp. The internal region of the transposon possesses one open reading frame which shows similarity at the peptide level to the Pot2 transposon from M. grisea and Fot1 from Fusarium oxysporum. Hybridization studies using the entire element as a probe revealed that some strains of M. grisea, whose DNA hybridized to the pCB586 probe, entirely lacked MGR586 transposon sequences.

Amino Acid Sequence↗

PubMed1998

Isolation and mapping of a novel human kidney- and liver-specific gene homologous to the bacterial acetyltransferases.

Using the differential display method to detect tissue-specific genes, we isolated a novel human gene, designated TSC501, that is expressed in kidney and liver. The cDNA contained an open reading frame of 681 nucleotides encoding 227 amino acids. The predicted product showed homologies in amino acid sequence to three different bacterial acetyltransferases, enzymes that are involved in drug resistance. Radiation hybrid mapping localized this gene to human chromosome bands 2p12-p13.1.

Acetyltransferases↗

PubMed1993

Cloning and sequencing of a full length cDNA encoding ovine lipoprotein lipase.

A cDNA clone encoding lipoprotein lipase has been isolated from an ovine adipocyte library. Sequencing of this clone has revealed a single open reading frame encoding a 450 amino acid protein. Comparison with known LPL sequences from other species shows a high degree of conservation in the sequence of the protein and in the 5' untranslated region of the DNA sequence.

Adipose Tissue↗

PubMed1995

Analysis of the halobacterial plasmid pHK2 minimal replicon.

The pMDS series of cloning vectors developed for use in halophilic archaea have utilized a 10.5-kb plasmid, pHK2, from Haloferax sp. Aa2.2. The minimal replicon of pHK2 has now been determined (3359 bp) and completely sequenced. No significant sequence similarity was found between the pHK2 subfragment and plasmid pHV2 from the closely related H. volcanii. However, a long open reading frame (ORF), named rep, was identified which encodes a putative protein with approx. 30% sequence identity to ORFs within plasmids pGRB1, pHGN1 and pHSB1 from Halobacterium sp. All these putative Rep proteins contain sequence motifs conserved in bacterial plasmids and phage genomes known to replicate via a rolling-circle mechanism.

Amino Acid Sequence↗

PubMed2002

Determination of the complete genomic sequence and analysis of the gene products of the virus of Spring Viremia of Carp, a fish rhabdovirus.

The complete genome of spring viremia of carp virus (SVCV) was cloned and the sequence of 11019 nucleotides was determined. It contains five open reading frames (ORF's) encoding for the nucleoprotein N; phosphoprotein P; matrix protein M; glycoprotein G; and the viral RNA dependent RNA polymerase L. Genes are organised in the order typical for rhabdoviruses: 3'-N-P-M-G-L-5'. The short leader and trailer regions of SVCV exhibit inverse complementarity and are similar to the respective 3' and 5' ends of the genome of vesicular stomatitis virus. To verify the predicted open reading frames proteins were expressed in bacteria and analysed with a polyclonal anti-SVCV serum. Furthermore, monospecific antisera against the distinct viral proteins were generated. Comparison of genome and protein confirm the assignment of SVCV to the genus Vesiculovirus.

3' Untranslated Regions↗

PubMed1997

Nucleotide sequence of a putative periplasmic Mn superoxide dismutase from Acinetobacter calcoaceticus ADP1.

We determined 5.8 kilobases of nucleotide sequence upstream of the rubredoxin encoding rubA gene of Acinetobacter calcoaceticus (Ac) ADP1. Sequence analysis revealed four open reading frames named cysD', cobQ, sodA and lysS, coding for proteins with high similarity to known sulfate adenylate transferases (partial), cobyric acid synthases, superoxide dismutases (Sod) and lysyl tRNA synthetases, respectively. Out of a large number of bacterial Sod sequences SodA of Ac ADP1 is the first member of the Fe/Mn Sod family apparently located in the periplasmic space.

Acinetobacter calcoaceticus↗

PubMed2002

Size and complexity of the nuclear genome of the ectomycorrhizal fungus Paxillus involutus.

The basidiomycete Paxillus involutus is forming ectomycorrhizal symbiosis with a broad range of forest trees. Reassociation kinetics on P. involutus nuclear DNA indicated a haploid genome size of 23 Mb including 11% of repetitive DNA. A similar genome size (20 Mb) was estimated by genomic reconstruction analysis using three single copy genes. To assess the gene density in the P. involutus genome, a cosmid containing a 33-kb fragment of genomic DNA was sequenced and used to identify putative open reading frames (ORFs). Twelve potential ORFs were predicted, eight displayed significant sequence similarities to known proteins found in other organisms and notably, several homologues to the Podospora anserina vegetative incompatibility protein (HetE1) were found. By extrapolation, we estimate the total number of genes in the P. involutus haploid genome to approximately 7700.

Amino Acid Sequence↗

PubMed2003

Genome-wide analysis of iron-dependent growth reveals a novel yeast gene required for vacuolar acidification.

We conducted a genome-wide screen in the budding yeast Saccharomyces cerevisiae of 4,792 homozygous diploid deletions to identify genes that function in iron metabolism. Strains unable to grow on iron-restricted medium contained deletions of genes that encode the structural components of the high affinity iron transport system (FET3, FTR1), the iron-sensing transcription factor AFT1 or genes required for the assembly of the transport system. We also identified genes that were not previously known to play a role in iron metabolism. Deletion of the gene CWH36 resulted in a severe growth defect on iron-limited medium, as well as increased sensitivity to Congo red and calcofluor white. Iron transport studies demonstrated that Deltacwh36 cells have an inability to copper load apoFet3p. Furthermore, Deltacwh36 cells demonstrated additional phenotypes including distorted vacuole morphology and altered kinetics of FM4-64 trafficking. We show that Deltacwh36 cells have a defect in vacuolar acidification through the use of the pH-sensitive dye LysoSensor Green DND-189. In Deltacwh36 cells, the vacuolar H+-ATPase is not assembled and there are reduced levels of at least one subunit of the V0 complex. The open reading frame responsible for the Deltacwh36 phenotypes is YCL005W-A. This gene contains two introns, has homologues in other Saccharomyces strains, and shows weak homology to a component of the vacuolar H+-ATPase found in organisms as diverse as insect and cow.

Amino Acid Sequence↗