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At least 991 records · Page 55Linked to original sources

PubMed1994

Molecular cloning and structural analysis of the rabbit gastrin/CCKB receptor gene.

Gastrin and cholecystokinin exert a variety of physiological actions in the central nervous system and digestive tract that are mediated through one or more receptors exhibiting similar affinity for the two peptides. We isolated genomic clones encoding the rabbit gastrin/CCKB receptor by screening a rabbit EMBL phage library with a cDNA probe based on the nucleotide sequence of the human gastrin/CCKB receptor. The gene contained a putative 1356-bp open reading frame consisting of five exons interrupted by 4 introns and encoded a protein of 452 amino acids. The putative protein-coding region of the gene exhibits 93 to 97% amino acid similarity with corresponding cDNAs previously identified in human, canine and rodent brain or gastric tissues.

Alternative Splicing↗

PubMed2000

Full-length nucleotide sequence of a simian TT virus isolate obtained from a chimpanzee: evidence for a new TT virus-like species.

Recently, we identified TT virus (TTV) isolates from nonhuman primates and named them simian TTV (s-TTV). To characterize the genomic structure of these isolates in more detail, the full-length nucleotide sequence of the s-TTV isolate (designated s-TTV CH65-1), recovered from a chimpanzee born in West Africa, was amplified by nested PCR with inverted primers deduced from the untranslated region of s-TTV DNA. CH65-1 was composed of 3899 nucleotides (nt) and had two open reading frames (ORF) spanning 2295 nt (ORF1) and 402 nt (ORF2). The sequence had only 52.3% similarity to the prototype TA278 human isolate. Phylogenetic analysis demonstrated that CH65-1 was distinct from the human TTV isolates. These results suggested that s-TTV may represent a new TTV-like viral species or genus.

Animals↗

PubMed1992

Structure and expression of the barley lipid transfer protein gene Ltp1.

We have characterized a gene (Ltp1) encoding a barley lipid transfer protein. Northern blot analysis showed that Ltp1 mRNA accumulates specifically in the aleurone layer of developing and germinating seeds. Southern blot analysis indicated that LTP1 protein is encoded by a single gene in barley. Sequence analysis of Ltp1 showed that it contains an open reading frame of 351 bp interrupted by a single intron of 133 bp. Transient expression assays indicated that 702 bp of the 5' upstream region of Ltp1 is sufficient to direct aleurone-specific expression during late seed development and early germination.

Amino Acid Sequence↗

PubMed2002

Complete nucleotide sequence of the genomic RNA of Aconitum latent virus (genus Carlavirus) isolated from Delphinium sp..

We determined the complete nucleotide sequence of Aconitum latent virus (AcLV-D) isolated from Delphinium sp. The genomic RNA of AcLV-D is 8,657 nucleotides in length, excluding the poly (A) tail. Based on computer analysis, six open reading frames (ORFs) were identified as for other carlaviruses. Although each ORF differs from those of previously reported carlaviruses, the coat protein of AcLV and Potato virus M (PVM) shows a high level of identity. The results suggest that AcLV is a distinct carlavirus species but closely related to PVM.

Amino Acid Sequence↗

PubMed1992

Molecular analysis of a gene from Bacteroides fragilis involved in metronidazole resistance in Escherichia coli.

The region of Bacteroides fragilis DNA on the recombinant plasmid pMT100 responsible for conferring metronidazole resistance in Escherichia coli strains was characterized. An open reading frame (ORF1) of 195 bp encoded a protein of 64 amino acids with a predicted M(r) of 7.3 kDa. Deletion analysis indicated that ORF1 conferred the metronidazole resistance phenotype and encoded a protein with an apparent M(r) of approximately 8-10 kDa.

Amino Acid Sequence↗

PubMed1993

Nucleotide sequence of the Chinese hamster Na+/H+ exchanger NHE1.

We have cloned and sequenced the cDNA coding for the Chinese hamster Na+/H+ antiporter expressed in the CCL39 fibroblast cell line. This cDNA contains an open reading frame encoding a protein of 822 amino acids which is homologous to the human NHE1 isoform. Sequence comparison studies show that the first cytoplasmic loop of the transporter is completely different between the two species indicating that the conservation of this domain is not required for the function of the antiporter.

Amino Acid Sequence↗

PubMed1996

Sequence of a gene encoding a putative primary sigma factor from Borrelia burgdorferi strain B31.

Utilizing a polymerase chain reaction-based approach, the gene (rpoD) encoding the primary sigma factor from Borrelia burgdorferi strain B31 was cloned and sequenced. Nucleotide sequence analysis revealed an open reading frame (ORF) of 1632 bp (543 amino acids (aa), 63.7 kDa). Comparison with Escherichia coli sigma 70 and Bacillus subtilis sigma 43 showed a high degree of similarity in the aa sequences, especially for the regions that are known to be required for promoter recognition and core binding.

Amino Acid Sequence↗

PubMed1999

Cloning and sequence analysis of the gene encoding Methylophilus methylotrophus cytochrome c", a unique protein with a perpendicular orientation of the histidinyl ligands.

Cytochrome c" from Methylophilus methylotrophus is an unusual monohaem protein that undergoes a major redox-linked spin-state transition: one of the two axial histidines bound to the iron in the oxidised form is detached upon reduction and a proton is taken up. A 3.5-kb DNA fragment, containing the gene encoding cytochrome c" (cycA), has been cloned and sequenced. The cytochrome c" gene codes for a pre-protein with a typical prokaryotic 20-residue signal sequence, suggesting that the protein is synthesised as a precursor which is processed during its secretion into the periplasm. The C-terminus of cytochrome c" has homology with the corresponding region of an oxygen-binding haem protein (SHP) from phototrophically grown Rhodobacter sphaeroides. SHP is similar in size and in the location of its haem-binding site. Immediately downstream from cytochrome c" a second open reading frame (ORF) codes for a 23-kDa protein with similarity to the cytochrome b-type subunit of Ni-Fe hydrogenase. The possibility of coordinated expression of cycA and this ORF is discussed.

Amino Acid Sequence↗

PubMed2003

A pentatricopeptide repeat-containing gene that promotes the processing of aberrant atp6 RNA of cytoplasmic male-sterile rice.

A fertility restorer gene (Rf-1) of [ms-bo] cytoplasmic male sterility (CMS) in rice has been reported to be responsible for the processing of RNA of aberrant atp6 of mitochondria. We have carried out map-based cloning of the Rf-1 gene and found that a 4.7-kb genomic fragment of a restorer line promoted the processing of aberrant atp6 RNA when introduced into a CMS line. The genomic fragment contained a single open reading frame encoding 18 repeats of the 35 amino acid pentatricopeptide repeat (PPR) motif. The cloned PPR gene is a possible candidate of Rf-1. A non-restoring genotype was identified to have deletions within the coding region.

Adenosine Triphosphatases↗

PubMed1991

Yeast ribosomal proteins: XII. YS11 of Saccharomyces cerevisiae is a homologue to E. coli S4 according to the gene analysis.

We isolated and sequenced a gene, YS11A, encoding ribosomal protein YS11 of Saccharomyces cerevisiae. YS11A is one of two functional copies of the YS11 gene, located on chromosome XVI and transcribed in a lower amount than the other copy which is located on chromosome II. The disruption of YS11A has no effect on the growth of yeast. The 5'-flanking region contains a similar sequence to consensus UASrpg and the T-rich region. The open reading frame is interrupted with an intron located near the 5'-end. The predicted amino acid sequence reveals that yeast YS11 is a homologue to E. coli S4, one of the ram proteins, three chloroplast S4s and others out of the ribosomal protein sequences currently available.

Amino Acid Sequence↗

PubMed1992

The nucleotide sequence of red clover mottle virus bottom component RNA.

The complete nucleotide sequence of the bottom component RNA (B RNA) of red clover mottle virus strain S has been determined. The sequence consists of 6033 nucleotides and contains a single long open reading frame sufficient to encode a protein of M(r) 210,258. The proteolytic processing sites within this protein have been deduced by comparison of its sequence with that of the B RNA-encoded protein of cowpea mosaic virus. Comparison of the amino acid sequences of the individual proteins confirms that the two viruses have a similar genome organization.

Amino Acid Sequence↗

PubMed2003

A new virus infecting Myzus persicae has a genome organization similar to the species of the genus Densovirus.

The genomic sequence of a new icosahedral DNA virus infecting Myzus persicae has been determined. Analysis of 5499 nt of the viral genome revealed five open reading frames (ORFs) evenly distributed in the 5' half of both DNA strands. Three ORFs (ORF1-3) share the same strand, while two other ORFs (ORF4 and ORF5) are detected in the complementary sequence. The overall genomic organization is similar to that of species from the genus DENSOVIRUS: ORFs 1-3 most likely encode the non-structural proteins, since their putative products contain conserved replication motifs, NTP-binding domains and helicase domains similar to those found in the NS-1 protein of parvoviruses. The deduced amino acid sequences from ORFs 4 and 5 show sequence similarities with the structural proteins of the members of the genus DENSOVIRUS: These data indicate that this virus is a new species of the genus Densovirus in the family PARVOVIRIDAE: The virus was tentatively named Myzus persicae densovirus.

Amino Acid Sequence↗

PubMed1994

Cloning and sequence analysis of the gene encoding Lactococcus lactis malolactic enzyme: relationships with malic enzymes.

Malolactic enzyme is the key enzyme in the degradation of L-malic acid by lactic acid bacteria. Using degenerated primers designed from the first 20 N-terminal amino acid sequence of lactococcal malolactic enzyme, a 60-bp DNA fragment containing part of the mleS gene was amplified from Lactococcus lactis in a polymerase chain reaction. This specific probe was used to isolate two contiguous fragments covering the gene as a whole. The 1.9-kb region sequenced contains an open reading frame of 1623 bp, coding a putative protein of 540 amino acids. The deduced amino acid sequence reveals that lactococcal putative protein (Mlep) is highly homologous to the malic enzyme of other organisms. Expression of the mleS gene in Escherichia coli results in malolactic activity.

Amino Acid Sequence↗

PubMed1996

Identification and sequencing of a novel insertion sequence, IS1471, in Burkholderia cepacia strain 2a.

A novel insertion sequence (IS), IS1471, has been identified which is inserted into IS element IS1071 possessed by plasmid pIJB1 in Burkholderia cepacia strain 2a. Nucleotide sequencing has revealed that IS1471 is 1112 bp in length and is flanked by 22/21-bp imperfect inverted repeats with a 3-bp duplication of the target sequence IS1471 contains a single open reading frame encoding a putative polypeptide of 345 amino acids with molecular mass of 39406 Da. Searches of DNA and protein sequence databases did not result in the detection of any homologous IS elements, suggesting that IS1471 is novel and may not belong to any known IS groups.

Amino Acid Sequence↗

PubMed1995

Genetic structure of the dnaA region of the cyanobacterium Synechocystis sp. strain PCC6803.

We have cloned and sequenced the dnaA region of Synechocystis sp. strain PCC6803, a bacterium with a light-dependent cell cycle. The dnaA gene product, DnaA, is the central factor for replication initiation in bacteria. The deduced amino acid sequence of the protein encoded by the cyanobacterial dnaA gene is 45% identical to DnaA of Bacillus subtilis and fits very well into the homology pattern of the known eubacterial DnaA proteins. The genetic environment of the Synechocystis sp. strain PCC6803 dnaA gene is completely different from the one in other eubacteria. An open reading frame of unknown function, orf134, was detected upstream of dnaA. The purT gene homolog encoding the glycinamide ribonucleotide transformylase T starts about 200 bp away from this open reading frame in the opposite direction. Downstream of the dnaA gene we detected the start of the psbDC operon, which codes for the photosystem II reaction center proteins D2 and CP43 that are involved in the positioning of chlorophyll a.

Acyltransferases↗

PubMed1996

Amino acid substitutions in membrane-spanning domains of Hol1, a member of the major facilitator superfamily of transporters, confer nonselective cation uptake in Saccharomyces cerevisiae.

Selection for the ability of Saccharomyces cerevisiae cells to take up histidinol, the biosynthetic precursor to histidine, results in dominant mutations at HOL1. The DNA sequence of HOL1 was determined, and it predicts a 65-kDa protein related to the major facilitator family (drug resistance subfamily) of putative transport proteins. Two classes of mutations were obtained: (i) those that altered the coding region of HOL1, conferring the ability to take up histidinol; and (ii) cis-acting mutations (selected in a mutant HOL1-1 background) that increased expression of the Hol1 protein. The ability to transport histidinol and other cations was conferred by single amino acid substitutions at any of three sites located within putative membrane-spanning domains of the transporter. These mutations resulted in the conversion of a small hydrophobic amino acid codon to a phenylalanine codon. Selection for spontaneous mutations that increase histidinol uptake by such HOL1 mutants resulted in mutations that abolish the putative start codon of a six-codon open reading frame located approximately 171 nucleotides downstream of the transcription initiation site and 213 nucleotides upstream of the coding region of HOL1. This single small upstream open reading frame (uORF) confers translational repression upon HOL1; genetic disruption of the putative start codon of the uORF results in a 5- to 10-fold increase in steady-state amounts of Hol1 protein without significantly affecting the level of HOL1 mRNA expression.

Alleles↗

PubMed1998

Identification of a linked set of genes in Serpulina hyodysenteriae (B204) predicted to encode closely related 39-kilodalton extracytoplasmic proteins.

A tandem pair of nearly identical genes from Serpulina hyodysenteriae (B204) were cloned and sequenced. The full open reading frame of one gene and the partial open reading frame of the neighboring gene appear to encode secreted proteins which are homologous to, yet distinct from, the 39-kDa extracytoplasmic protein purified from the membrane fraction of S. hyodysenteriae. We have designated these newly identified genes vspA and vspB (for variable surface protein).

Amino Acid Sequence↗

PubMed2005

Constituents of SH1, a novel lipid-containing virus infecting the halophilic euryarchaeon Haloarcula hispanica.

Recent studies have indicated that a number of bacterial and eukaryotic viruses that share a common architectural principle are related, leading to the proposal of an early common ancestor. A prediction of this model would be the discovery of similar viruses that infect archaeal hosts. Our main interest lies in icosahedral double-stranded DNA (dsDNA) viruses with an internal membrane, and we now extend our studies to include viruses infecting archaeal hosts. While the number of sequenced archaeal viruses is increasing, very little sequence similarity has been detected between bacterial and eukaryotic viruses. In this investigation we rigorously show that SH1, an icosahedral dsDNA virus infecting Haloarcula hispanica, possesses lipid structural components that are selectively acquired from the host pool. We also determined the sequence of the 31-kb SH1 genome and positively identified genes for 11 structural proteins, with putative identification of three additional proteins. The SH1 genome is unique and, except for a few open reading frames, shows no detectable similarity to other published sequences, but the overall structure of the SH1 virion and its linear genome with inverted terminal repeats is reminiscent of lipid-containing dsDNA bacteriophages like PRD1.

Amino Acid Sequence↗