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At least 1,495 records · Page 83Linked to original sources

PubMed1996

Molecular cloning and expression of mouse procalcitonin.

The nucleotide sequence for mouse calcitonin was determined from a cDNA obtained using a polymerase chain reaction (PCR) based method, the rapid amplification of cDNA ends (RACE)-PCR. Primers designed from highly conserved regions in the coding sequences of known rat and human calcitonin cDNAs were used to amplify calcitonin cDNA as 5'-end and 3'-end fragments from mouse thyroid RNA. The obtained cDNA is 850 bp in length most probably representing the entire mouse calcitonin mRNA. It contains an open reading frame coding for a 136 amino acid protein with a calculated M(r) of 15,143. Comparison of the deduced amino acid sequences of preprocalcitonin of mice with other species revealed highest homologies to the rat (93%) and human (77%) sequences. A recombinant form of mouse precalcitonin (rmPCT) of approximately 17 kDa was expressed as a fusion peptide in E.coli transformed with a PCR-cloned expression construct.

Amino Acid Sequence↗

PubMed1997

A new inward rectifier potassium channel gene (KCNJ15) localized on chromosome 21 in the Down syndrome chromosome region 1 (DCR1).

The Down syndrome chromosome region-1 (DCR1) on subband q22.2 of chromosome 21 is thought to contain genes contributing to many features of the trisomy 21 phenotype, including dysmorphic features, hypotonia, and psychomotor delay. Isolation, mapping, and sequencing of trapped exons and captured cDNAs from cosmids of this region have revealed the presence of a gene (KCNJ15) encoding a potassium (K+) channel belonging to the family of inward rectifier K+ (Kir) channels. The amino acid sequence deduced from the 1125-bp open reading frame indicates that this gene is a member of the Kir4 subfamily; it has been named Kir4.2. It is expressed in kidney and lung during human development and in several adult tissues including kidney and brain. After Kir3.2 (GIRK2), Kir4.2 is the second K+ channel gene of this type described within the DCR1.

Adult↗

PubMed1997

Identification of plasmids in the genus Marinococcus and complete nucleotide sequence of plasmid pPL1 from Marinococcus halophilus.

Several plasmids were detected in the Gram-positive halophilic eubacterium Marinococcus halophilus and in the related strain M52. The complete nucleotide sequence (3874 bp) of one of these plasmids, pPL1, was determined. Four major open reading frames were identified. Whereas orf3 and orf4 showed no sequence similarities to known proteins, rep displayed a high sequence similarity to replication proteins of rolling circle plasmids. Upstream of this ORF, a sequence resembling the double-strand origin was detected. A region probably constituting the single-strand origin was identified. The ORF mob showed sequence similarity with Mob proteins of rolling circle plasmids. The observed characteristics suggest that pPL1 replicates according to the rolling circle mechanism.

Amino Acid Sequence↗

PubMed2000

Nucleotide sequence and analysis of plasmid pMD136 from Pediococcus pentosaceus FBB61 (ATCC43200) involved in pediocin A production.

The complete sequence of the 19515-bp plasmid pMD136 from Pediococcus pentosaceus FBB61 (ATCC43200) has been determined. This plasmid is involved in Pediocin A production, a bacteriocin active against a wide range of gram-positive bacteria. It appears to replicate via a theta mechanism, with structures closely related to those of many lactococcal plasmids. Genes homologous to mobilization functions are also present, which are similar in sequence and arrangement to mobA, mobB, and mobC of some staphylococcal plasmids, although the last one contains a deletion in its central part. The region involved in bacteriocin activity has been limited to a 9.4-kb fragment, containing 10 open reading frames organized in a single operon. Since Pediocin A has a molecular weight of about 80 kDa (Piva and Headon, Microbiology, 140, 697-702, 1994), and a gene long enough to encode it is not present in pMD136, it is proposed that genes residing on the plasmid are responsible for the regulation of bacteriocinogenic activity. Gene arrangement and sequence homologies suggest the presence of a two-component-like regulatory mechanism.

Amino Acid Sequence↗

PubMed1993

IL-2 independent growth and cytotoxicity of herpesvirus saimiri-infected human CD8 cells and involvement of two open reading frame sequences of the virus.

Herpesvirus saimiri is a primate tumor virus and induces acute T cell lymphomas and leukemias in New World monkeys and rabbits. We show in this report that infection of human peripheral white blood cells with a group C strain 484-77 results in selective expansion of CD8 lymphocytes with strong cytotoxic activity and these cells do not require interleukin-2 (IL-2) for growth. Infected cell cultures, termed herpesvirus-activated killer (HAK) cells, have been continuously maintained for several months in tissue culture and these HAK cells contain multiple copies of stable circular viral episomes. The growth and cytotoxicity of HAK cells was found independent of IL-2. Analysis of deletion mutant infected cells suggests that at least two open reading frame sequences of a bicistronic mRNA encoded by the viral genome is involved in controlling IL-2 independence. This model could facilitate studies on growth regulation of human cytotoxic T cells that are important effector cells in immune responses against infectious diseases and cancer and should help us to elucidate the mechanism of transformation by H. saimiri oncogenes.

Base Sequence↗

PubMed1995

Unclassified poxvirus: characterization and physical mapping of Cotia virus DNA and location of a sequence capable of encoding a thymidine kinase.

DNA from Cotia virus, an unclassified poxvirus, was mapped by overlapping fragment analysis using the restriction endonucleases HindIII, PstI, BamHI, XhoI, SalI, and SmaI. The linear genome was 177 kbp in length and possessed inverted terminal repeats and cross-links. A Cotia virus thymidine kinase (TK) gene was detected and mapped to about 74 kbp from the left end of the genome using degenerate oligonucleotide probes. Nucleotide sequencing of the TK gene revealed an open reading frame (ORF) that encoded a peptide of 178 amino acids. An A/T-rich sequence, TAA AAA TGA ATA AATA, and a transcription termination signal, TTTTTGT, were revealed upstream and just downstream of the ORF, respectively, consistent with the characteristic features of an early poxvirus gene. Cotia virus resembles swinepox virus based on the restriction profiles generated by endonucleases and shares amino acid sequence similarity with orthopox, leporipox, Yaba, and fowlpox viruses.

Amino Acid Sequence↗

PubMed2000

Identification of a novel RNA splicing pattern as a basis of restricted cell tropism of erythrovirus B19.

Prior studies on the transcription of erythrovirus B19 have identified a short leader sequence associated with all spliced viral transcripts. While some variability has been observed in the acceptor for this first intron, studies to date in both permissive and nonpermissive cell types have reported a unique splice donor site. In the semipermissive MB-02 cell line, we have found that splicing of this first intron proceeds almost exclusively via a cryptic CT donor downstream of the previously reported GT donor at nucleotide 406. The resulting messages for the viral structural proteins and 11-kDa protein are thereby made bicistronic, with the first expressible polypeptide being a 34 amino acid fusion of the NS-1 and 7.5-kDa proteins. The presence of an upstream open-reading frame on these messages is likely to block effective translation of the downstream structural protein products. We propose this as a significant mechanism in determining B19's tropism on the basis of host cell splicing machinery, and present evidence in support of this model. Additionally, this is the first report of usage of a noncanonical splice donor in B19, and to our knowledge the first report of a CT-AG splice in any system.

Alternative Splicing↗

PubMed1993

DNA sequence and transcript analysis of transposon MuA2, a regulator of Mutator transposable element activity in maize.

The 4942 bp DNA sequence of Zea mays transposon MuA2 was determined. Previous evidence indicated MuA2 controls activity of the Mu1 transposon located in the mutable allele a1-mum2. MuA2 contains two large, ATG-initiated open reading frames (ORFs) of 612 and 232 codons, respectively, located on opposite strands. MuA2 produces two transcripts, each containing one of these ORFs. Four different tandem direct repeat sequences are located downstream of the 612 codon ORF. The restriction map of MuA2 is identical to that of transposon MuR1, which also is known to regulate mutability of a1-mum2. Furthermore, except for a single nucleotide, MuA2 is identical to the Mutator element Mu9.

Amino Acid Sequence↗

PubMed1994

The evolutionary origin of the 35 kb circular DNA of Plasmodium falciparum: new evidence supports a possible rhodophyte ancestry.

In common with other Apicomplexan parasites, Plasmodium falciparum carries two extrachromosomal DNAs, one of which, the 6 kb element, is undoubtedly mitochondrial. The second, generally referred to as the 35 kb circle, is of unknown provenance, but the nature and organization of its genetic content makes a mitochondrial association unlikely and the molecule has features reminiscent of plastid genomes. We now report the occurrence on the circle of an open reading frame specifying a predicted 470 amino acid protein that shares more than 50% identity with a gene currently known only on the plastome of red algae. This high degree of conservation confirms the 35 kb circle's plastid ancestry, and we speculate that it may have originated from the rhodoplast of an ancient red algal endosymbiont in the progenitor of the Apicomplexa.

Amino Acid Sequence↗

PubMed1991

The Adh genomic region of Drosophila ambigua: evolutionary trends in different species.

The study of individual genes is essential to a comprehensive understanding of genome evolution. The wealth of information on alcohol dehydrogenase (Adh) in Drosophila makes this gene particularly suitable for such analysis. We have characterized more than 4 kb of the genomic Adh region in Drosophila ambigua and compared this region to Drosophila mauritiana and Drosophila pseudoobscura. The presence of two genes, Adh and 3'ORF (open reading frame), has been confirmed and some of their essential features have been inferred from primary structural analysis. Inter- and intraspecific comparisons have led us to support that both genes may have diverged from an ancient precursor. They appear to be evolving independently, and show a species-specific pattern. The Adh in the obscura group species lacks amino acids three and four when compared to the species of the melanogaster group and has accumulated most of its amino acid replacements in the third exon. Neither characteristic is observed when any other group species are compared, which suggests that these may be particular features of the evolution of the obscura group. The 3'ORF is highly conserved among the three species analyzed, although variability in the length of the third exon and the nucleotide substitution rate, which is much higher than in Adh, are worth noting. According to our data, both mutation/fixation rates and the distribution of mutations vary over time, which makes it difficult to predict the evolutionary dynamics of specific genome regions.

Alcohol Dehydrogenase↗

PubMed2003

Nucleotide sequence and genome organization of Cucurbit yellow stunting disorder virus RNA1.

The complete nucleotide sequence of Cucurbit yellow stunting disorder virus (CYSDV) RNA1, a member of the Crinivirus genus in the Closteroviridae, was determined. CYSDV RNA1 is 9126 nucleotides long and contains two overlapping open reading frames (ORFs) that encode the replication module, consisting of the putative papain-like cysteine proteinase, methyl transferase, helicase, and polymerase domains, a small 5 kDa hydrophobic protein and two further downstream ORFs potentially encoding proteins respectively 25 and 22 kDa in size. The genomic position and homology of the four domains comprising the replication module appear to be similar for all sequenced criniviruses but there is divergence in the downstream ORFs, in terms of number, size, position and sequence homology.

Base Sequence↗

PubMed1991

Regulation of plaque size and host range by a vaccinia virus gene related to complement system proteins.

A vaccinia virus variant, LC16m8, and its parental Lister (Elstree) strain (LO) were employed to identify the viral gene(s) responsible for plaque size and host range: the large-plaque-forming LO strain but not the small-plaque-forming LC16m8 strain can actively proliferate in Vero (YTV) cells. Previously, we suggested that some particular gene(s) present in the HindIII D fragment of LO DNA was responsible for these biological activities. In the present experiment, the mapping of the putative gene was done by introducing various subfragments of the HindIII D fragment of LO DNA into the gene of LC16m8 strain and screening of the resultant virus variants for the capability of forming large plaques or of proliferating well in Vero cells. The results indicated that an open reading frame (called ps/hr gene) in LO HindIII D fragment was responsible for either plaque size or host range. This gene encoded a polypeptide of 317 amino acids related to the regulators of complement activation (RCA) gene family of mammals. Thus, the present genetic analysis provided direct evidence for a previously unrecognized function of RCA-related proteins encoded by the virus.

Amino Acid Sequence↗

PubMed1991

Cloning and sequence analysis of membrane-bound alkaline phosphatase cDNA of the silkworm, Bombyx mori.

The nucleotide sequence (1974 bp) of cDNA coding for membrane-bound alkaline phosphatases (m-ALP) of Bombyx mori was isolated. The cDNA clone contained an open reading frame encoding a polypeptide (547 amino acids), which contains a hydrophobic signal peptide of 36 amino acids and the mature protein of 511 amino acids (Mr = 56,163). We found a highly hydrophobic domain presumed to be a membrane anchoring region at the C-terminus. Comparing analysis between Bombyx m-ALP and mammalian and Escherichia coli ALPs suggested an evolutionary relationship of sharing a common ancestral gene.

Alkaline Phosphatase↗

PubMed1993

Molecular cloning and characterization of cDNA encoding mouse hepatocyte growth factor.

A cDNA encoding mouse hepatocyte growth factor (HGF) has been cloned and completely sequenced by use of reverse transcriptase-polymerase chain reaction (RT-PCR) and subsequent cloning. Sequence analysis reveals that mouse HGF, similar to its human and rat counterparts, consists of 728 amino acids, and both the alpha- and beta-chains are encoded in a single open reading frame. Strong homology exists in the primary structure of HGF among the three species of mouse, rat and human (more than 90%), especially in Kringle 1 of the alpha chain which is assumed to be an essential domain for binding of HGF to its receptor, c-MET, a proto-oncogene product. Our results suggest the existence of evolutionary pressure to conserve the distinct structure, and presumably the biological functions, of HGF.

Amino Acid Sequence↗

PubMed1990

Cloning, sequencing and chromosomal assignment of a gene from Saccharomyces cerevisiae which is negatively regulated by glucose and positively by lipids.

We report the molecular cloning, nucleotide (nt) sequence and chromosomal assignment of the Saccharomyces cerevisiae gene GLP1. This gene encoded a 15-kDa protein that was synthesized at a low level during growth on glucose and was induced ninefold upon glucose deprivation. When glucose withdrawal was accompanied by the addition of fatty acids the induction was enhanced an additional two- to threefold. The GLP1 gene product was identified as a soluble protein and purified using a combination of gel permeation and ion exchange chromatography. Using oligodeoxyribonucleotides as hybridization probes we have isolated the GLP1 gene and sequenced the single, long open reading frame which is 351 nt in length and is not interrupted by introns. The GLP1 gene directed the transcription of a 700-nt mRNA in response to glucose deprivation. The accumulation of the mRNA was further enhanced twofold by the addition of oleate. We have localized the GLP1 gene to S. cerevisiae chromosome VI.

Amino Acid Sequence↗

PubMed2001

Molecular cloning and characterization of a novel low temperature-induced gene, blti2, from barley (Hordeum vulgare L.).

The Suppression Subtractive Hybridization (SSH) was used to isolate large numbers of low temperature-induced genes from the cold-treated winter barley (Hordeum vulgare L. cv. Dongbori). One hundred and sixty blti (barley low temperature-induced) cDNA clones were obtained. Northern blot analyses showed that several blti clones were differentially expressed by treatment of low temperature, NaCl, dehydration and ABA. One of the clones, blti2, was induced from 3 to 72 h after cold treatment while its transcript was detected only at 12 h after ABA treatment, indicating that the expression of blti2 by low temperature was regulated by an ABA-independent pathway. The full-length cDNA sequences were 944 nucleotides long and the open reading frame consisted of 492 nucleotides encoding 164 amino acids. Nucleotide sequences showed no sequence homology with the previously reported low temperature-responsive (LTR) barley genes, and the deduced amino acid sequences revealed that the blti2 contains three membrane-spanning regions. These results suggest that blti2 is a novel transmembrane protein induced by low temperature.

Amino Acid Sequence↗

PubMed2004

A previously unidentified MECP2 open reading frame defines a new protein isoform relevant to Rett syndrome.

Rett syndrome is caused by mutations in the gene MECP2 in approximately 80% of affected individuals. We describe a previously unknown MeCP2 isoform. Mutations unique to this isoform and the absence, until now, of identified mutations specific to the previously recognized protein indicate an important role for the newly discovered molecule in the pathogenesis of Rett syndrome.

Base Sequence↗

PubMed2000

The Arabidopsis AtEPR1 extensin-like gene is specifically expressed in endosperm during seed germination.

Screening of 10 000 Arabidopsis transgenic lines carrying a gene-trap (GUS) construct has been undertaken to identify markers of seed germination. One of these lines showed GUS activity restricted to the endosperm, at the micropylar end of the germinating seed. The genomic DNA flanking the T-DNA insert was cloned by walking PCR and the insertion was shown to be located 70 bp upstream of a 2285 bp open reading frame (AtEPR1) sharing strong similarities with extensins. The AtEPR1 open reading frame consists of 40 proline-rich repeats and is expressed in both wild-type and mutant lines. The expression of the AtEPR1 gene appears to be under positive control of gibberellic acid, but is not downregulated by abscisic acid during seed germination. No expression was detected in organs other than endosperm during seed germination. The putative role of AtEPR1 is discussed in the light of its specific expression in relation to seed germination.

Amino Acid Sequence↗