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At least 883 records · Page 49Linked to original sources
PubMed1993

Primary structure of three distinct isoabrins determined by cDNA sequencing. Conservation and significance.

A family of toxic proteins, the isoabrins, which possess N-glycosylase activity toward eukaryotic 28 S r-RNA, may have potential use in cancer chemotherapy. By polymerase chain reaction techniques, cDNA clones of three isoabrins, carrying A and B-chain sequences, were isolated and their nucleotide sequences were determined. The isoabrins consist of an A-chain comprised of 250 of 251 amino acids, followed by a 10 amino acid linker and a B-chain of 267 amino acids. There is substantial conservation in the B-chain of the three isoabrins, with less than six amino acid substitutions, whereas as many as 46 amino acid substitutions occur in the A-chains. Based on the relationships between the biological activities and the putative amino acid sequences of the isoabrins, three isoabrins, abrin-a, -b and -d, could be identified and the potential epitope of immunological response of these isoabrins could be assigned.

Abrin↗
PubMed1995

Vitamin D dependent rickets type II and normal vitamin D receptor cDNA sequence. A cluster in a rural area of Cauca, Colombia, with more than 200 affected children.

Vitamin D dependent rickets type II is an autosomal recessive disease caused by the vitamin D defective receptor. More than 200 patients with different types of lower limb deformities were detected in a rural area of the Cauca department in the southwest part of Colombia. Patients were well nourished and in good physical condition in spite of their deformities. None of them presented alopecia, myopathy, seizures or aminoaciduria. Serum analysis showed significantly lower serum calcium as compared to normal relatives, though in the normal low range, normal phosphorus, high alkaline phosphatase, normal 25-hydroxyvitamin D3 and high 1,25-dihydroxyvitamin D3, indicating target organ resistance. The cDNA analysis showed normal nucleotide sequence. We suggest that our patients represent a distinct form of receptor-positive resistance to vitamin D. This report is the first extensive study on this class of patients.

Adult↗
PubMed1990

Identification by molecular cloning of two cDNA sequences from the plant Brassica napus which are very similar to mammalian protein phosphatases-1 and -2A.

Two clones encoding protein phosphatase (PP) catalytic subunits have been isolated from a Brassica napus cDNA library screened with rabbit muscle PP1 alpha and PP2A alpha cDNAs. The deduced protein sequences are very similar to those of mammalian PP1 alpha and PP2A alpha (72% and 79% overall identity, respectively) indicating that they are the plant homologues of PP1 alpha and PP2A alpha. This high degree of similarity provides a molecular explanation for the remarkable conservation of the catalytic and regulatory properties between animal and plant protein phosphatases and supports the concept that PP1 and PP2A may be the most highly conserved of known enzymes.

Amino Acid Sequence↗
PubMed2002

cDNA sequences and mRNA levels of two hexamerin storage proteins PinSP1 and PinSP2 from the Indianmeal moth, Plodia interpunctella.

In insects, storage proteins or hexamerins accumulate apparently to serve as sources of amino acids during metamorphosis and reproduction. Two storage protein-like cDNAs obtained from a cDNA library prepared from fourth instar larvae of the Indianmeal moth (Plodia interpunctella) were cloned and sequenced. The first clone, PinSP1, contained 2431 nucleotides with a 2295 nucleotide open reading frame (ORF) encoding a protein with 765 amino acid residues. The second cDNA, PinSP2, consisted of 2336 nucleotides with a 2250-nucleotide ORF encoding a protein with 750 amino acid residues. PinSP1 and PinSP2 shared 59% nucleotide sequence identity and 44% deduced amino acid sequence identity. A 17-amino acid signal peptide and a molecular mass of 90.4 kDa were predicted for the PinSP1 protein, whereas a 15-amino acid signal peptide and a mass of 88 kDa were predicted for PinSP2. Both proteins contained conserved insect larval storage protein signature sequence patterns and were 60-70% identical to other lepidopteran larval storage proteins. Expression of mRNA for both larval storage proteins was determined using the quantitative reverse transcription polymerase chain reaction method. Only very low levels were present in the second instar, but both mRNAs dramatically increased during the third instar, peaked in the fourth instar, decreased dramatically late in the same instar and pupal stages, and were undetectable during the adult stage. Males and females exhibited similar mRNA expression levels for both storage proteins during the pupal and adult stages. The results support the hypothesis that P. interpunctella, a species that does not feed after the larval stage, accumulates these two storage proteins as reserves during larval development for subsequent use in the pupal and adult stages.

Amino Acid Sequence↗
PubMed1991

Analysis of the cDNA sequence encoding MHC-A beta in tubular epithelium from mouse kidney.

Class II gene products of the major histocompatibility complex (MHC) are not expressed usually in abundance on normal epithelium. The cell surface visibility of such proteins for the immune system is thought to be limited protectively in order to minimize inflammation consequent to the recognition of self-antigens in parenchymal structures by T lymphocytes. In the current experiments we investigated whether the previously recognized sparseness of A beta on the surface of tubular epithelial cells might be accounted for by a protein coding difference deduced from the primary structure of its transcript compared with sequence from lymphoid cells that normally express A beta in generous amounts. We demonstrate, however, using clones obtained from a cDNA library prepared from tubular epithelium harvested from H-2s (A beta/alpha+; E beta/alpha-) mice susceptible to autoimmune interstitial nephritis, that the nucleotide sequence encoding the class II A beta chain in cells from both compartments is essentially identical. Our findings suggest that there is no primary structural aberrancy in the coding region of parenchymal A beta that would contribute to its low expression. The protective tolerance afforded by reduced numbers of class II molecules in normal tissues is, therefore, more likely the result of repressive regulatory processes.

Animals↗
PubMed1989

Cloning of cDNA Sequences Encoding the Calcium-Binding Protein, Calmodulin, from Barley (Hordeum vulgare L.).

Full- and partial-length cDNAs encoding calmodulin mRNA have been cloned and sequenced from barley (Hordeum vulgare L.). Barley leaf mRNA, size-fractionated in sucrose density gradients, was used to synthesize double-stranded cDNA. The cDNA was cloned in lambdagt10 and screened with a synthetic, 14-nucleotide oligonucleotide probe, which was designed using the predicted coding sequences of the carboxy termini of spinach and wheat calmodulin proteins. The primary structure of barley calmodulin, predicted from DNA sequencing experiments, consists of 148 amino acids and differs from that of wheat calmodulin in only three positions. In two of the three positions, the amino acid changes are conservative, while the third change consists of an apparent deletion/insertion. The overall nucleotide sequence similarity between the amino acid coding regions of barley and vertebrate calmodulin mRNAs is approximately 77%. However, a region encoding 11 amino acids of the second Ca(2+)-binding domain is very highly conserved at the nucleotide level compared with the rest of the coding sequences (94% sequence identity between barley and chicken calmodulin mRNAs). Genomic Southern blots reveal that barley calmodulin is encoded by a single copy gene. This gene is expressed as a single size class of mRNA in all tissues of 7-day-old barley seedlings. In addition, these analyses indicate that a barley calmodulin cDNA coding region subclone is suitable as a probe for isolating calmodulin genes from other plants.

Journal Article↗
PubMed1994

Molecular cloning of a novel luteinizing-hormone/human-chorionic-gonadotropin-receptor cDNA. Identification of a long 3' untranslated region and cDNA sequence of the major transcript in rat ovary.

The biological action of luteinizing hormone/human chorionic gonadotropin (lutropin/choriogonadotropin) in the ovary is mediated by interaction with its specific receptor. Lutropin/choriogonadotropin-receptor hnRNA is processed into multiple mRNAs. However, nucleotide sequences for many of the transcripts, including the major form (6.7 kb), have yet to be determined. In an attempt to identify a cDNA encoding the major transcript, we have isolated a 3.5-kb cDNA clone from a rat ovary cDNA library. The 3.5-kb cDNA recognized only two (6.7 kb, 4.4 kb) of the three (6.7, 4.4, 2.6 kb) ovarian lutropin/choriogonadotropin-receptor transcripts when used as a probe. The first 732 nucleotides of the newly identified 3.5-kb cDNA showed 98% identity to the 3' untranslated region (3' UTR) of the previously cloned cDNA corresponding to the 4.4-kb transcript. Southern blot analysis indicated that the 3.5-kb cDNA and the C-terminal domain of the lutropin/choriogonadotropin-receptor originate from the same gene. Oligonucleotide-directed cleavage of the 6.7-kb lutropin/choriogonadotropin-receptor mRNA by RNase H revealed that the newly identified 3.5-kb cDNA is a 3' extension of the 4.4-kb transcript. We propose that the nucleotide sequence of the 6.7-kb lutropin/choriogonadotropin-receptor transcript, the major form found in rat ovary, contains a long 3' UTR, which has not been previously identified.

Animals↗
PubMed1996

cDNA sequence analysis and expression of the expression of the ribosomal protein S24 during oogenesis and embryonic development of the sea urchin Paracentrotus lividus.

A gene for the Paracentrotus lividus ribosomal protein S24, called P1-S24, has been isolated and sequenced. Ribosomal protein P1-S24 consists 130 amino acids and has a molecular weight of 14869 Da. Sequence analysis shows a high percentage (90%) identity with the corresponding gene of Strongylocentrotus purpuratus. Hybridization of the cDNA to digested sperm DNA suggests that P1-S24 is represented in no more than two copies. Studies of the temporal expression of P1-S24 gene indicate a good correlation between this and the expression of the rRNA genes both during oogenesis and embryonic development.

Amino Acid Sequence↗
PubMed1998

Complete cDNA sequence of the Ki-ras proto-oncogene in the liver of wild English sole (Pleuronectes vetulus) and mutation analysis of hepatic neoplasms and other toxicopathic liver lesions.

A complete copy of Ki-ras b cDNA from English sole (Pleuronectes vetulus), a benthic marine flatfish, was cloned and sequenced. The percent identity between the predicted amino acid sequence of English sole and human Ki-ras b was 97%, whereas the percent identity between the English sole gene and rainbow trout or Rivulus Ki-ras b was 98%. Areas of amino-acid sequence conservation included codons 12, 13, and 61, the positions in which mutations are observed in ras cellular oncogenes in other species. The 5' untranslated region (UTR), consisting of 217 nt, was not highly GC rich but contained four ATG start codons upstream of the major open reading frame. The 3' UTR, containing 26 nt, was AU rich. Analysis of Ki-ras mutations was performed on a variety of necrotic, preneoplastic, and neoplastic lesions in livers from 13 English sole collected from contaminated waterways in Puget Sound, WA. Despite reports of Ki-ras mutations in hepatic tumors from other fish, no mutations in codons 12, 13, or 61 were found in hepatic lesions from English sole by direct DNA sequencing of polymerase chain reaction-amplified genomic DNA. Although mutations could exist at levels below the detection limits of this analysis, the results suggest that Ki-ras has a role in liver carcinogenesis that varies according to the fish species or carcinogen. Furthermore, future studies of the etiology of chemically induced cancer in feral English sole should consider mutations in other cancer-related genes, such a5p53, Ha-ras, and N-ras.

Amino Acid Sequence↗
PubMed2005

Gene structure of the ciliate Sterkiella histriomuscorum based on a combined analysis of DNA and cDNA sequences from 21 macronuclear chromosomes.

Macronuclear deoxyribonucleic acid (DNA) in hypotrichous ciliates consists of a set of linear molecules ranging in size from 0.5 to several tens of kilobases and typically carrying a single gene. Each minichromosome is present at a ploidy of >or=1,000 per macronucleus. These molecules are known as gene-sized molecules. Multigene molecules are also present, but are still poorly described. In analyzing the encystment-excystment cycle of Sterkiella histriomuscorum, we have characterized a set of 21 macronuclear molecules both at the DNA and complementary DNA (cDNA) levels. On a total of 23 validated coding sequences, we mapped the 5' and 3' untranslated regions for a subset of 10 and 18 transcripts, respectively. A combination of DNA and cDNA data allows us to precisely determine several structural features of macronuclear chromosomes, such as the organization of multigene molecules, an intron content higher than expected, and a conserved sequence surrounding the initiation transcription site. It also reveals one coding sequence containing a transcribed 10-bp element that displays the characteristic features of internal eliminated sequences (IES). Its presence in a fraction of the minichromosomes carrying this gene raises the possibility of an incomplete IES excision process during the development of the S. histriomuscorum macronucleus.

3' Untranslated Regions↗
PubMed2005

Cloning of full-length cDNA sequence of a novel candidate gene related to mouse cleft palate.

OBJECTIVE: Cloning and screening a novel candidate gene related to developing mouse cleft palate. METHODS: The differentially expressed genes were cloned by modified PCR-based subtractive hybridization. After identification using reverse dot blotting, positive clones were sequenced and analyzed for homology in GenBank databases. RESULTS: Four novel express sequence tags were obtained, one of which spanning 809 bp was the full-length of the novel gene cDNA identified by Northern hybridization. CONCLUSION: A novel candidate gene related to mouse cleft palate was cloned.

Adaptor Proteins, Signal Transducing↗
PubMed1992

cDNA sequence of the small subunit of the hamster ribonucleotide reductase.

Ribonucleotide reductase activity is markedly elevated in cell lines selected for resistance to hydroxyurea, a cytotoxic drug known specifically to inhibit ribonucleotide reductase. From a cDNA library constructed from a highly hydroxyurea-resistant hamster lung cell line, 600H in which the activity is elevated more than 80-fold, we have isolated a full length cDNA for the small subunit of the reductase. The cDNA is 3.48 kb long with an open reading frame of 1158 nucleotides and a long 3' flanking region of 2169 nucleotides from the termination codon. The derived polypeptide sequence is closely similar to the small subunit of the mouse, differing from it in 20 amino acid positions. Most of these replacements occur in the N-terminal segment of the protein. The hamster subunit does not contain 4 amino acid residues found in the mouse small subunit near the C-terminal end. RNA blots probed with the cDNA show two poly(A)+ RNA species which are elevated in hydroxyurea-resistant cells.

Amino Acid Sequence↗
PubMed2002

cDNA sequence and tissue expression of Fugu rubripes prion protein-like: a candidate for the teleost orthologue of tetrapod PrPs.

We report the isolation and characterization of a cDNA coding for Fugu rubripes prion protein (PrP)-like of 180 amino acids which includes the PrP-conserved hydrophobic region homologous to that of Xenopus PrP. In addition to the hydrophobic region, Fugu PrP-like has several features common to PrPs, such as a signal sequence, a basic nature (pI 9.7) and a single intron in the 5' untranslated region. A possible glycosyl phosphatidylinositol (GPI) anchor site also exists in PrP-like. In expression analysis, PrP-like mRNA was detected in retina, skin, and brain, all of which express PrP mRNA in mammals. In a genome fragment clone (T002589, 31945 bp) sequenced by the Fugu Genomics Project, PrP-like located between KIAA0168 and SLC231A homologues. In human chromosome 20p13, PrP, Doppel, KIAA0168, and SLC231A align in this order. The close gene arrangement between the Fugu and human genomes suggests that Fugu PrP-like is a real orthologue of human PrP. However, Fugu PrP-like does not possess tandem repeats or a region with two glycosylation sites and a disulphide bridge. We do not declare that the cloned Fugu PrP-like represents fish PrP due to structural inconsistency, but believe that it will offer new insights into the evolution of PrPs from fish to tetrapods.

Amino Acid Sequence↗
PubMed1987

Characterization of cDNA sequences corresponding to three distinct HMG-1 mRNA species in line CHO Chinese hamster cells and cell cycle expression of the HMG-1 gene.

We have isolated cDNA clones encoding the high mobility group (HMG) protein HMG-1 in line CHO Chinese hamster cells. The cDNA clones correspond to the three HMG-1 mRNA species detected on Northern blots. Three different polyadenylation sites are found to be used. The three mRNA species of sizes 1.05, 1.45 and 2.45 kb are generated by differential polyadenylation at sites 115 nucleotides, 513 nucleotides and 1515 nucleotides downstream from the stop codon. A perfectly conserved putative poly(A) signal AAUAAA is present upstream of only one of the three poly(A) sites. Two homologous but imperfect sequences exist upstream from the other two poly(A) sites. All three HMG-1 mRNA species maintain significant levels throughout the M, G1 and S phases of the cell cycle and the rate of large HMG protein (HMG-1 and HMG-2) synthesis increases approximately two-fold from G1 to S phase.

Amino Acid Sequence↗
PubMed1990

Full-length DQ beta cDNA sequences of HLA-DR2/DQw1 subtypes: genetic interactions between two DQ beta loci generate human class II HLA diversity.

Two-dimensional gel electrophoresis of DQ molecules from three different Dw subtypes (Dw2, Dw12, and Dw21/FJO) of the HLA-DR2/DQw1 haplotype reveals that one alpha beta heterodimer of DQ molecule is expressed by each subtype and the DQ beta chain is electrophoretically variable among the three DR2/DQw1 subtypes. We have constructed cDNA libraries from the same homozygous typing cells used in the two-dimensional polyacrylamide gel electrophoresis analyses (HTC VYT for Dw2, HTC DHO for Dw12, and HTC FJO for Dw21/FJO) and isolated DQ beta cDNA clones with full-length coding sequences for each subtype. The deduced amino acid sequences show that the DQ beta chains of these three DR2/DQw1 subtypes are highly polymorphic and confirm their electrophoretic heterogeneity: for a mature protein of 229 amino acids, they differ with each other by 10-17 amino acids in the first domain and by 3-7 residues in the C-terminal sequence. Comparison among the available DQ beta sequences representing the four major DQ specificities (DQw1, DQw2, DQw3, and DQw4) in the DQ subregion as defined by serologic method suggests that (1) DR2,Dw2,DQw1 and DR3,DQw2 haplotypes probably interact with each other to generate the DQw3 and DQw4 beta alleles and (2) an evolutionary scheme may be proposed to relate the various beta alleles of the four major DQ specificities.

Alleles↗
PubMed1988

Chicken riboflavin-binding protein. cDNA sequence and homology with milk folate-binding protein.

The Rd gene is expressed in the livers and oviducts of laying hens and codes for the riboflavin-binding protein (RfBP) of egg yolk and egg white. A lambda gt11 cDNA library derived from chicken oviduct poly(A)+ RNA was screened with polyclonal rabbit antiserum to chicken RfBP. Positive clones were isolated and rescreened with a mixed oligonucleotide probe corresponding to residues 20-25 of the mature protein. The largest cDNA clone (969 base pairs) was subcloned into plasmid pIBI21, and the nucleotide sequence was determined by the dideoxynucleotide method. This clone contained the entire coding region for RfBP. The published amino acid sequence of the mature protein was confirmed. In addition, the following 17-residue signal peptide was deduced: Met-Leu-Arg-Phe-Ala-Ile-Thr-Leu-Phe-Ala-Val-Ile-Thr-Ser-Ser-Thr-Cys. Unexpectedly, the nucleotide sequence codes for 2 adjacent arginine residues at the carboxyl terminus that are not observed in the mature protein. The amino acid sequence of RfBP is homologous with bovine milk folate-binding protein. Eight of the nine pairs of cysteines involved in disulfide bonds in RfBP are conserved in folate-binding protein, as are all of the tryptophan residues. Sequence identity between homologous regions of these two vitamin-binding proteins is more than 30%.

Amino Acid Sequence↗
PubMed1993

Multiple cDNA sequences of bovine tracheal lysozyme.

The principal role of lysozyme is to prevent bacterial invasion at body surfaces. We are interested in how lysozyme is regulated at the surface of the respiratory tract, where the serous gland cell is regarded as the primary cellular source of this enzyme. Since the cow genome contains at least 10 lysozyme-like genes, our objective was to determine which of them are expressed in the cow tracheal gland serous cell. By screening tracheal cDNA libraries with a probe constructed from the cDNA encoding stomach lysozyme 2, we obtained 3 lysozyme cDNAs: 5a (1023 base pairs (bp)), 7a (1060 bp), and 14d (1249 bp). cDNA 7a corresponds to a previously reported gene (showing sequence identity to the stomach 2 lysozyme gene), whereas cDNAs 5a and 14d correspond to lysozyme genes not previously reported. Northern blot analysis of cow tracheal RNA showed lysozyme mRNAs of three distinct lengths. Based on hybridization with probes specific for each cDNA, we determined that the longest transcript corresponded to cDNA 5a, the shortest to 7a, and the intermediate-length transcript to 14d. Cultured cow tracheal gland serous cell RNA, reverse transcribed and amplified by the polymerase chain reaction with primers common to all three cDNAs, yielded a product that hybridized to oligonucleotide probes specific for all three cDNAs but most strongly to that for 5a. These results indicate that multiple lysozyme mRNAs are expressed in the cow trachea and that the lysozyme encoded by cDNA 5a is the major form expressed in the tracheal gland serous cell. This serous cell lysozyme is predicted to differ importantly in structure from both 7a and 14d lysozymes, with an arginine:lysine ratio almost 10-fold higher. The sequence differences may underlie functional differences, including variable resistance to proteolysis and variable affinity for large polyanions (e.g. mucins) found in the respiratory tract lumen.

Amino Acid Sequence↗
PubMed1990

The cDNA sequences encoding two components of the polymeric fraction of the intracellular hemoglobin of Glycera dibranchiata.

The intracellular hemoglobin of the polychaete Glycera dibranchiata consists of several components, some of which self-associate into a "polymeric" fraction. The cDNA library constructed from the poly(A+) mRNA of Glycera erythrocytes (Simons, P. C., and Satterlee, J. D. (1989) Biochemistry 28, 8525-8530) was screened with two oligodeoxynucleotide probes corresponding to the amino acid sequences MEEKVP and AMNSKV. Each of the two probes identified a full-length positive insert; these were sequenced using the dideoxynucleotide chain termination method. One clone was 630 bases long and contained 36 bases of 5'-untranslated RNA, a reading frame of 441 bases coding for the 147 amino acids of globin P2 including the residues MEEKVP, and a 3'-untranslated region of 153 bases. The other clone was 540 bases long and contained 24 bases of 5'-untranslated RNA, an open reading frame of 441 bases coding for globin P3 including the residues AMNSKV, and a 3'-untranslated region of 75 bases. The inferred amino acid sequences of the two globins were in agreement with the partial amino acid sequences obtained by chemical methods. The P2 and P3 globin sequences, together with the previously determined P1 sequence of a complete insert and partial sequences P4, P5, and P6 obtained from partial inserts (Zafar, R. S., Chow, L. H., Stern, M. S., Vinogradov, S. N., and Walz, D. A. (1990) Biochim. Biophys. Acta, in press) suggest that there are at least six components in the polymeric fraction of Glycera hemoglobin, which is in agreement with the results of polyacrylamide gel electrophoresis in Tris/glycine buffer, pH 8.3, 6 M urea. Nothern and dot blot analyses of Glycera erythrocyte poly(A+) mRNA using the foregoing two cDNA probes clearly demonstrated the presence of mature messages encoding both types of globins. Comparison of the polymeric sequences P1, P2, and P3 with the "monomeric" globins M-II and M-IV using the alignment and templates of Bashford et al. (Bashford, D., Chothia, C., and Lesk, A. M. (1987) J. Mol. Biol. 196, 199-216) showed that all five globins have identical residues at 39 positions. At 44 positions, the three polymeric globins share identical residues that differ from the identical residues at the corresponding locations in the monomeric sequences M-II and M-IV including position E7, where the latter have leucine instead of the distal histidine. At 15 positions, there occurs an alteration from polar to nonpolar or from a small nonpolar to a larger nonpolar residue in going from the monomeric to the polymeric globins.(ABSTRACT TRUNCATED AT 400 WORDS)

Amino Acid Sequence↗