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PubMed2000

Isolation and characterization of cDNAs encoding ribosome inactivating protein from Dianthus sinensis L.

To isolate a ribosome inactivating protein (RIP) gene, six plant species were surveyed for antiviral activity. Crude proteins extracted from these plants were tested for the antiviral activity against tobacco mosaic virus (TMV) in Nicotiana glutinosa. All the plants, Spinacia oleracea, Amaranthus lividus, Dianthus superbus, Dianthus sinensis and Celosia cristata, with an exception of Oenanthe stolonifera, presented 70-90% inhibition of viral infectivity. In an attempt to search for the RIP gene from D. sinensis, partial cDNA was obtained by polymerase chain reaction (PCR) of the poly(A)+ RNA from D. sinensis leaves. DNA gel blot analysis showed that D. sinensis has multi-copy RIP genes. The expression of RIP gene was investigated in the flower, leaf, root and stem of D. sinensis, and was found to be most abundant in the leaf. Using the partial cDNA as a probe, seven full-length cDNAs were isolated from a library prepared from D. sinensis leaves. They were divided into three groups on the basis of their nucleotide sequence homology. The three representative clones, cDsRIP1, cDsRIP2 and cDsRIP3 were completely sequenced. They all had an open reading frame of 882 bp. The cDsRIP2 showed 79% homology with dianthin 30 and saporin genes; 59% with PAP and Mirabilis antiviral protein MAP genes. From the analysis of deduced amino acid sequences, it was predicted that D. sinensis RIP cDNAs might have a putative signal peptide of 23 amino acid residues at their N-terminus. When the cDNA was expressed in E. coli, the bacteria was unable to grow upon IPTG induction, suggesting that expression of the gene renders toxicity to E. coli cells.

Amino Acid Sequence↗

PubMed2000

Cloning and Expression of an Elongation Factor-1alpha in Sea Bream (Sparus aurata) Larvae and Adult Tissue.

A clone encoding the polypeptide elongation factor EF-1alpha was isolated from a complementary DNA library prepared from sea bream (Spartus aurata) larvae 1 to 10 days after hatching. The deduced amino acid sequence is between 82% and 95% similar to EF-1alpha in other animal species. EF-1alpha messenger RNA is present at low abundance in sea bream embryos prior to gastrulation, but at around 15 hours postfertilization, there is a 10-fold increase in transcript levels. This increase presumably reflects midblastula transition in this species. In adult sea bream, EF-1alpha appeared to have a relatively uniform distribution across all the tissues analyzed.

Journal Article↗

PubMed2005

A microarray-based comparative analysis of gene expression profiles during grain development in transgenic and wild type wheat.

Global, comparative gene expression analysis is potentially a very powerful tool in the safety assessment of transgenic plants since it allows for the detection of differences in gene expression patterns between a transgenic line and the mother variety. In the present study, we compared the gene expression profile in developing seeds of wild type wheat and wheat transformed for endosperm-specific expression of an Aspergillus fumigatus phytase. High-level expression of the phytase gene was ensured by codon modification towards the prevalent codon usage of wheat genes and by using the wheat 1DX5HMW glutenin promoter for driving transgene expression. A 9K wheat unigene cDNA microarray was produced from cDNA libraries prepared mainly from developing wheat seed. The arrays were hybridised to flourescently labelled cDNA prepared from developing seeds of the transgenic wheat line and the mother variety, Bobwhite, at three developmental stages. Comparisons and statistical analyses of the gene expression profiles of the transgenic line vs. that of the mother line revealed only slight differences at the three developmental stages. In the few cases where differential expression was indicated by the statistical analysis it was primarily genes that were strongly expressed over a shorter interval of seed development such as genes encoding storage proteins. Accordingly, we interpret these differences in gene expression levels to result from minor asynchrony in seed development between the transgenic line and the mother line. In support of this, real time PCR validation of results from selected genes at the late developmental stage could not confirm differential expression of these genes. We conclude that the expression of the codon-modified A. fumigatus phytase gene in the wheat seed had no significant effects on the overall gene expression patterns in the developing seed.

6-Phytase↗

PubMed1995

An increase in expression of the lipocalin 24p3 is found in mouse uterus coincident with birth.

OBJECTIVE: To provide novel insights into the molecular events associated with parturition, a differential screen was made of a mouse uterine complementary deoxyribonucleic acid library to identify selectively expressed genes in late pregnancy. STUDY DESIGN: A differential hybridization was used to screen a mouse complementary deoxyribonucleic acid library prepared from late pregnancy uterus. A 1 kb clone was isolated that was subsequently identified as 24p3, a member of the lipocalin family. By use of radiolabeled complementary deoxyribonucleic acid probes prepared from this clone Northern hybridizations were conducted against total ribonucleic acid purified from mouse uterus collected during late pregnancy and the first week after birth and a variety of other mouse tissues to determine whether this gene is selectively expressed in the uterus coincident with parturition. RESULTS: Low levels of message for the 24p3 gene could be detected in uterine ribonucleic acid, but there was a massive increase in the level of message for this gene on the days surrounding birth. Northern hybridizations conducted against additional tissues collected from both pregnant and nonpregnant mice did not detect message to a similar degree as found in the uterus. CONCLUSIONS: The uterus constitutes a major site of expression of this gene, particularly near birth. The expression of this gene coincident with birth suggests a potential physiologic role of the neutrophil with the induction of labor.

Acute-Phase Proteins↗

PubMed1990

cDNA and deduced amino acid sequences of a dog hepatic cytochrome P450IIB responsible for the metabolism of 2,2',4,4',5,5'-hexachlorobiphenyl.

The nucleotide sequence of a cDNA that codes for the major phenobarbital (PB)-inducible male beagle dog hepatic cytochrome P450 has been determined. Using a rabbit P450IIB cDNA probe (R. Gasser, M. Negishi, and R. M. Philpot, 1988, Mol. Pharmacol, 32, 22-30), a cDNA clone with a 2.6-kilobase pair insert was isolated from a lambda gt11 library prepared from hepatic mRNA from a PB-treated dog. The cloned insert was sequenced and found to contain an open reading frame coding for a polypeptide of 494 amino acids (Mr 56,183). The encoded protein can be assigned to the P450IIB subfamily on the basis of homology to cytochromes P450 from other species. The deduced amino acid sequence is 79% identical to that reported for rabbit P450 BO (P450IIB4) and 75% identical to that for rat P450b (P450IIB1). The sequence identity decreases to less than 52% when the dog sequence is compared with other P450II subfamilies. The deduced NH2-terminal 30 amino acids encoded by the dog cDNA are identical to those determined by sequence analysis of purified dog cytochrome P450 PBD-2, and the amino acid composition concurs with that determined for the PBD-2 protein (D. B. Duignan, I. G. Sipes, T. B. Leonard, and J. R. Halpert, 1987, Arch. Biochem. Biophys. 255, 290-303). Northern blots revealed two mRNA species of approximately 1.9 and 2.9 kilobases in length, which hybridized to the coding region of the dog P450IIB cDNA. The level of total hybridizable mRNA was increased approximately sixfold in livers from PB-treated dogs compared with that in untreated animals. This increase correlates well with the reported nearly sixfold increase in the level of PBD-2 protein and the fivefold increase in the rate of hepatic metabolism of 2,2',4,4',5,5'-hexachlorobiphenyl following PB treatment. The two mRNA species may result from the use of different polyadenylation signals located in the 3'-noncoding region or from transcription of more than one gene for PBD-2. Southern blot analysis indicated that the dog P450IIB subfamily contains at least two closely related genes.

Amino Acid Sequence↗

PubMed1991

Complete amino acid sequence of the type III isozyme of rat hexokinase, deduced from the cloned cDNA.

Clones containing cDNA coding for the Type III isozyme of rat hexokinase (ATP:D-hexose 6-phosphotransferase, EC 2.7.1.1) were isolated from a library prepared in lambda gt10 with rat liver mRNA. Three clones were characterized. Their composite sequence includes the entire coding region for Type III hexokinase, 3' untranslated sequence extending into the polyadenylated region, and 80 bp of 5' untranslated sequence. Extensive similarity in sequence of N- and C-terminal halves of the enzyme, previously seen with the Type I isozyme, is consistent with the view that these 100-kDa mammalian hexokinases are the evolutionary result of duplication and fusion of a gene coding for an ancestral hexokinase having a molecular weight of approximately 50 kDa. Extensive similarities are seen between sequences of the Type I and III isozymes, and those reported for mammalian glucokinase (also called Type IV hexokinase) and for the hexokinase and glucokinase of yeast. Residues thought to be involved in catalytic function are highly conserved in all of these enzymes. Based on a quantitative comparison of sequence similarities, it is concluded that the 50-kDa mammalian glucokinase is more closely related to the 100-kDa mammalian enzymes than it is to the 50-kDa enzymes from yeast. One interpretation of this might be that the mammalian glucokinase arose by resplitting of the gene coding for the 100-kDa mammalian hexokinases.

Amino Acid Sequence↗

PubMed1994

Isolation of Tn917 insertional mutants of Bacillus subtilis that are resistant to the protonophore carbonyl cyanide m-chlorophenylhydrazone.

Tn917 transposition libraries prepared from Bacillus subtilis were screened for mutants that had insertions in the chromosome resulting in resistance to the protonophore carbonylcyanide m-chlorophenylhydrazone (CCCP). Five such strains were characterized. Three of these were found to have distinct insertion sites that resulted in changes in fatty acid composition of the membrane lipids. The lipid changes were qualitatively similar to changes observed earlier in CCCP-resistant strains of B. subtilis that had been isolated after chemical mutagenesis. However, the extent of the changes was more modest, correlating with a lower level of protonophore-resistance. One of these mutants was disrupted in a gene homologous to the Escherichia coli rho gene, as reported earlier (Quirk et al. (1993) J. Bacteriol. 175, 647-654), one was disrupted in a new member of the two-component signalling systems, and the third was disrupted in a new gene of unknown function that apparently forms an operon with transporter genes. The other two CCCP-resistant mutants were disrupted in genes that are likely to encode membrane transporters; the disruption of these genes may have reduced the transmembrane ion leaks during growth, thus conferring modest protonophore-resistance. In one of these strains, the disrupted gene is part of an apparent operon that is a homologue of iron uptake operons from other prokaryotes.

Amino Acid Sequence↗

PubMed1983

The majority of cDNA clones with strong positive signals for the interferon-induction-specific sequences resemble mitochondrial ribosomal RNA genes.

A complementary DNA library prepared from the 12S polyadenylated RNAs extracted from interferon-induced KG-1 cells, a human myeloblast cell line, was screened for the presence of induction-specific sequences. Clones that exhibited strong positive signals were separated by hybridization criteria into nine classes. Clones from classes I through IV consisted of about 78% of the total and unexpectedly were found to resemble human mitochondrial ribosomal RNA genes.

Base Sequence↗

PubMed1984

Cloning and sequence analysis of cDNA for human prealbumin.

A cDNA coding for human prealbumin has been cloned from a cDNA library prepared from human liver. The DNA sequence codes for a polypeptide which consists of 147 amino acids including a whole human prealbumin sequence and a putative signal sequence. The elucidation of this prealbumin cDNA sequence is expected to facilitate a prenatal diagnosis of familial amyloidotic polyneuropathy.

Amino Acid Sequence↗

PubMed1986

The complete nucleotide sequence of canine brain B creatine kinase mRNA: homology in the coding and 3' noncoding regions among species.

To define the structure of canine B creatine kinase, clones were isolated from a library prepared from dog brain mRNA and constructed in the vector lambda gt11. The entire coding portion, the complete 3' nontranslated region, and 43 bp of the 5' noncoding region are reported. Comparison of the predicted amino acid sequence of canine B creatine kinase with the sequence of canine M creatine kinase shows 81% identity. When compared to cDNAS encoding B creatine kinase isolated form other species unusual and striking nucleotide sequence identity in the 3' noncoding region is present. Moreover, two B creatine kinase clones (BCK2 and BCK38) demonstrate microheterogeneity within the 3' nontranslated region indicating variable processing of B creatine kinase pre-mRNA or the existence of multiple genes encoding canine B creatine kinase.

Amino Acid Sequence↗

PubMed1987

Cloning and sequence analysis of bovine beta-casein cDNA.

A bovine beta-casein cDNA clone was isolated from a cDNA library prepared from mammary gland mRNA. Sequence analysis revealed 25 nucleotides (nt) of the 5' noncoding region, 672 nt of the complete sequence coding and a 3' region of approximately 500 nt. When the nucleotide sequence of bovine beta-casein cDNA is compared to rat beta-casein cDNA (5), a high degree of homology is observed in the first 100 nt corresponding to the signal peptide of the pre-beta-caseins.

Animals↗

PubMed1987

cDNA cloning of IL-1 alpha and IL-1 beta from mRNA of U937 cell line.

Clones of cDNAs encoding growth inhibitory factors for human melanoma cell line A375 were isolated from cDNA library prepared by using mRNA derived from human histiocytic lymphoma cell line U937 induced with PMA and further stimulated with LPS. Cloning was achieved using Okayama-Berg cDNA expression vector system that permits expression of the inserted cDNA segments in mammalian cells. By assaying the transfected COS-1 cells supernatants and cell extracts, we isolated two distinct cDNA clones encoding growth inhibitory factors. It was determined by the nucleotide sequences of the inserts, the cDNAs corresponded to IL-1 alpha and -1 beta. Our results indicate U937 cells can be induced to produce both interleukin-1s.

Amino Acid Sequence↗

PubMed1987

Genetic characterization of an Escherichia coli mutant deficient in organophosphonate biodegradation.

An E. coli mutant deficient in organophosphonate biodegradation has been complemented with a cosmid library prepared from a BamHI partial digest of wild-type E. coli W3110. Mutant E. coli SL724, when transformed with cosmid pSL163 and plasmid pSL263, regained the ability to exploit ethylphosphonate as a sole source of phosphorus during growth. In route to complementation, the Tn5 insert of SL724 was subcloned and restriction enzyme mapped. Complementing pSL163 and pSL263 were also characterized via restriction enzyme digests.

Cosmids↗

PubMed1987

Molecular cloning of cDNA for rat liver lipoate acetyltransferase. A component of pyruvate dehydrogenase complex.

One cDNA clone for lipoate acetyltransferase, a component enzyme of pyruvate dehydrogenase complex, was isolated from a rat liver cDNA library prepared in the phage expression vector lambda gt11 using immunological screening with affinity purified anti-lipoate acetyltransferase antibody. It was identified tha cDNA insert in this clone codes for lipoate acetyltransferase by immunoblotting of lysogen carrying the isolated clone. Lipoate acetyltransferase antigenic polypeptide in fusion protein was about 11,000 daltons, agreeing with the size of cDNA insert to be 300 base pairs.

Acetyltransferases↗

PubMed1989

35 kDa fragment of h-caldesmon conserves two consensus sequences of the tropomyosin-binding domain in troponin T.

Using a tropomyosin-coupled affinity column, we have demonstrated a direct association between the chymotryptic 35 kDa fragment of h-caldesmon, which is located at the C-terminal of the parent molecule, and gizzard tropomyosin. We have subsequently determined the nucleotide sequence of cDNA clones encoding the 35 kDa fragment from the cDNA library prepared from chick embryo gizzards, and have deduced the amino acid sequence. Calculating from the predicted sequence, the 35 kDa fragment is composed of 306 amino acid residues. In agreement with the tropomyosin-binding ability, the 35 kDa fragment conserves two consensus sequences of the tropomyosin-binding domain in troponin T. These results suggest that the 35 kDa fragment of h-caldesmon, at least in part, has a common property to the striated muscle troponin T.

Amino Acid Sequence↗

PubMed1989

Isolation and characterization of a molecular cDNA clone of a human mRNA from interferon-treated cells encoding nucleolar protein B23, numatrin.

A cDNA clone encoding human nucleolar phosphoprotein B23, numatrin, was isolated from a library prepared with mRNA from human U cells. The complete nucleotide sequence was determined; it revealed a single open reading frame of 294 amino acids that included four in-frame AUG codons as potential sites of translation initiation. Comparison of the human B23 nucleotide sequence with the rat and mouse B23 sequences revealed 91% homology (hum:rat, and hum:mus) in the coding region; the predicted B23 proteins displayed 94% amino acid identity. Northern gel blot analysis revealed a single B23 mRNA species of approximately 1.5 kb. The level of B23 mRNA in U cells was not detectably altered by treatment with either alpha or gamma interferon. Southern gel blot analysis revealed polymorphism within the human B23 gene structure, and suggested the presence of multiple B23 genes and/or extensive splicing of B23 RNA transcripts.

Amino Acid Sequence↗

PubMed1989

cDNA-cloning, sequencing and expression in glucocorticoid-stimulated quiescent Swiss 3T3 fibroblasts of mouse lipocortin I.

We isolated and sequenced mouse lipocortin I cDNA clones from a lambda gt10 cDNA library prepared from Swiss 3T3 mRNA. The homology with human lipocortin I at the amino acid level is 86%. When confluent layers of Swiss 3T3 cells were stimulated with 10% fetal calf serum, expression of lipocortin I was strongly stimulated. In parallel, DNA synthesis was induced with a peak at 24 hours after glucocorticoid treatment indicating induction of cell proliferation. In the absence of serum glucocorticoid treatment provoked neither induction of DNA synthesis nor expression of lipocortin I. We conclude that serum contains an unidentified factor, which acts synergistically with glucocorticoids on cell proliferation and lipocortin I expression.

5,8,11,14-Eicosatetraynoic Acid↗

PubMed1991

Organization of the mouse acid beta-galactosidase gene.

Overlapping murine genomic DNA fragments containing the entire cDNA sequence were isolated from a cosmid library prepared from the DBA/2J strain of mice. The gene is more than 80-kb long, consisting of 16 exons. All of the exon-intron boundaries have been defined. The organization of the gene is highly conserved between the murine and human genes at least for the several exons and introns for which information for the human gene is available [Morreau et al., J. Biol. Chem. 264:20655, 1989]. Primer extension and RNase protection experiments indicated the presence of three potential transcription initiation sites, which are preceded by GC-rich SP1 binding sites but without typical TATA or CAT boxes, as is often the case for genes coding for housekeeping proteins. Compared to the cDNA sequence from C57BL/6J mouse, there were five nucleotide polymorphisms in the protein-coding region, two of which resulted in altered amino acids.

Animals↗