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PubMed2002

Cloning of bovine CD69.

CD69 is rapidly inducible on various hematopoietic cells upon stimulation and is detectable as an early activation antigen. Although CD69 is well characterized in human and mouse, no information is available on bovine CD69. We report here that, bovine CD69 was cloned from a cDNA expression library prepared from activated peripheral blood lymphocytes. The full-length cDNA contained an 80bp 5' untranslated region, followed by a 600bp coding region and AU-rich motifs in a 3' untranslated region (GenBank accession number AF272828). Comparison of the bovine CD69 coding sequence reveals 69.4 and 78.2% nucleotide sequence identities with mouse and human CD69, respectively. The predicted amino acid sequence of bovine CD69 shares 56.3 and 62.3% sequence identity when compared with mouse and human CD69, respectively. Bovine CD69 has the highly conserved amino acid sequences found in the C-type lectin family, suggesting that the conserved residues may be important for conformation and binding to the, as yet unidentified ligand. In addition, the cytoplasmic tail of bovine CD69 has two casein kinase-2 (CK-2) phosphorylation sites. These data suggest that bovine CD69 plays an important role in the activation of lymphocytes.

Amino Acid Sequence↗

PubMed1992

Growth-regulated expression of rhoG, a new member of the ras homolog gene family.

Cellular transition from the resting state to DNA synthesis involves master switches genes encoding transcriptional factors (e.g., fos, jun, and egr genes), whose targets remain to be fully characterized. To isolate coding sequences specifically accumulated in late G1, a differential screening was performed on a cDNA library prepared from hamster lung fibroblasts stimulated for 5 h with serum. One of the positive clones which displayed a sevenfold induction, turned out to code for a protein sharing homology to Ras-like products. Cloning and sequence analysis of the human homolog revealed that this putative new small GTPase, referred to as rhoG, is more closely related to the rac, CDC42, and TC10 members of the rho (ras homolog) gene family and might have diverged very early during evolution. rhoG mRNA accumulates in proportion to the mitogenic strength of various purified growth factors used for the stimulation, as a consequence of transcriptional activation. G1-specific RNA accumulation is impaired upon addition of antimitogenic cyclic AMP and is enhanced when protein synthesis is inhibited, mainly as a result of RNA stabilization. rhoG mRNA expression is observed in a wide variety of human organs but reaches a particularly high level in lung and placental tissues.

Amino Acid Sequence↗

PubMed2000

Suppression subtractive hybridization identifies genes expressed in oviduct during mouse preimplantation period.

Fertilization and development of mouse embryos occur in the ampullae of oviduct. Various growth factors and embryotrophic factors produced by the oviductal cells have been demonstrated to enhance embryo development in vitro. As a step towards understanding the genetic changes of mouse oviduct during mouse embryos preimplantation period, we adopted suppression subtractive hybridization (SSH) to establish four subtracted cDNA libraries to identify (1) oviduct-expressing genes, and (2) genes that may support embryo development in vivo. Using this method, we isolated 82, 88, 99, and 109 clones from four mouse libraries prepared from 0 (day 0), 24 (day 1), 48 (day 2), and 72 h (day 3) post-human chorionic gonadotropin (hCG) treated mice. Reverse dot-blot analysis confirmed that 25 (day 0), 24 (day 1), 40 (day 2), and 29 (day 3) clones were highly expressed in mouse oviduct when compared to other tissues. DNA sequence analysis identified genes encoding mouse oviduct-specific glycoprotein (MOGP), actin-binding protein 280, and several viral genes. Northern analysis confirmed that the genes were mainly expressed in oviduct, with some viral genes also expressed in uterus. About 9% of these oviduct expressing clones (11/118) were novel. We further demonstrated that one of the novel clones ODEG0-17 was expressed in the oviduct during early embryo preimplantation period and rarely in other tissues by RT-PCR. Our results show that SSH is a powerful method applicable to identifying tissue-specific transcripts on fertilization and development.

Animals↗

PubMed1995

Analysis of randomly isolated cDNAs from developing endosperm of rice (Oryza sativa L.): evaluation of expressed sequence tags, and expression levels of mRNAs.

Using a cDNA library prepared from poly(A)+ RNA from 10-day-old rice endosperm, partial nucleotide sequences of randomly isolated clones were analyzed. A total of 153 (30.6%) out of 500 cDNA clones showed high amino acid identity to previously identified genes. There was significant redundancy in cDNAs encoding prolamine and glutelin. About 21.0% of the cDNA clones were found to code for seed storage protein genes. Consequently, 37 independent genes were identified. Using cDNA clones encoding glutelin, prolamine, seed allergen, alpha-1,4-glucan branching enzyme, glycine-rich RNA binding protein, metallothionein, non-specific lipid-transfer protein and ubiquitin conjugating enzyme the accumulation of mRNA during rice seed development was compared. Genes associated with seed storage protein and starch biosynthesis were expressed according to expected developmental stages. Glycine-rich RNA binding protein genes as well as metallothionein-like protein genes were highly expressed in developing seeds, but low in leaves of whole plants.

Blotting, Northern↗

PubMed1991

Preferential expression of c-kit protooncogene transcripts in small cell lung cancer.

As an initial step to understand rapid growth of small cell lung cancer (SCLC), a complementary DNA library prepared from a SCLC cell line was screened with viral oncogene probes encoding protein-tyrosine kinases, which are known to play an important role in regulation of cell growth. Fifteen clones hybridizing with v-fms probe were isolated, and, by partial sequence analysis, four of them were identified to be c-kit protooncogenes. Northern blot study demonstrated that most of the SCLC tumors and cell lines expressed c-kit transcripts, while non-SCLC tumors and cell lines did not. Neither amplification nor rearrangement of the c-kit gene was demonstrated in SCLC cell lines by Southern blot analysis, however. Our results suggested that c-kit expression in SCLC reflects the unique biological nature of the tumor cells different from non-SCLC and further suggested that the c-kit product may participate in autocrine or paracrine stimulation of SCLC growth.

Base Sequence↗

PubMed1994

Preparation of a subtractive cDNA library enriched in cDNAs which expressed at a high level in cultured senescent human fibroblasts.

Subtracted cDNA library was prepared by subtracting [cDNA from young growing SV40-transformed human fibroblasts] from [cDNA from growing SV40-transformed fibroblasts in extended lifespan]. Isolated cDNA clones which expressed at high level in life-extended transformed cells also expressed at high level in normal senescent fibroblasts but did at low level in growing and growth-arrested young cells. Neither fibronectin nor procollagen cDNA was isolated. This cDNA library is useful for isolation of senescent-specific cDNA species which express at high level in normal senescent cells but at low level in growing and growth-arrested young cells, avoiding growth-arrest-specific cDNAs.

Animals↗

PubMed2000

Cloning and characterization of glyoxalase I from soybean.

Glyoxalase I and glutathione transferase (GST) are two glutathione-dependent enzymes which are enhanced in plants during cell division and in response to diverse stress treatments. In soybean, a further connection between these two enzymes has been suggested by a clone (Accession No. X68819) resembling a GST being described as a glyoxalase I. To characterize glyoxalase I in soybean, GmGlyox I resembling the dimeric enzyme from animals has been cloned from a cDNA library prepared from soybean suspension cultures. When expressed in Escherichia coli, GmGlyox I was found to be a 38-kDa dimer composed of 21-kDa subunits and unlike the enzyme from mammals showed activity in the absence of metal ions. GmGlyox I was active toward the hemithioacetal adducts formed by reacting methylglyoxal, or phenylglyoxal, with glutathione, homoglutathione, or gamma-glutamylcysteine, showing no preference for homoglutathione adducts over glutathione adducts, even though homoglutathione is the dominant thiol in soybean. When the clone X68819 was expressed in E. coli, the respective recombinant enzyme was active as a GST rather than a glyoxalase and was termed GmGST 3. GmGST 3 was active as a homodimer (45 kDa) composed of 26-kDa subunits and showed a preference for glutathione over homoglutathione when conjugating 1-chloro-2,4-dinitrobenzene. Both enzymes are associated with cell division in soybean cultures, but GmGST 3 (0.4% total protein) was 40 times more abundant than GmGlyox I (0.01%).

Amino Acid Sequence↗

PubMedDate not supplied

Patterns of gene expression in the developing adult sea urchin central nervous system reveal multiple domains and deep-seated neural pentamery.

The adult sea urchin central nervous system (CNS) is composed of five radial nerve cords connected to a circular nerve ring. Although much is known about the molecular mechanisms underlying the development and function of the nervous systems of many invertebrate and vertebrate species, virtually nothing is known about these processes in echinoderms. We have isolated a set of clones from a size-selected cDNA library prepared from the nervous system of the sea urchin Heliocidaris erythrogramma for use as probes. A total of 117 expressed sequence clones were used to search the GenBank database. Identified messages include genes that encode signaling proteins, cytoskeletal elements, cell surface proteins and receptors, cell proliferation and differentiation factors, transport and channel proteins, and a RNA DEAD box helicase. Expression was analyzed by RNA gel blot hybridization to document expression through development. Many of the genes have apparently neural limited expression and function, but some have been co-opted into new roles, notably associated with exocytotic events at fertilization. Localization of gene expression by whole-mount in situ hybridization shows that the morphologically simple sea urchin radial CNS exhibits complex organization into localized transcriptional domains. The transcription patterns reflect the morphological pentamery of the echinoderm CNS and provide no indication of an underlying functional bilateral symmetry in the CNS.

Amino Acid Sequence↗

PubMed1983

Chicken calmodulin genes. A species comparison of cDNA sequences and isolation of a genomic clone.

A cDNA library, prepared from poly(A+) mRNA isolated from chicken brain, was screened for calmodulin sequences using the cloned full length structural gene from Electrophorus electricus as probe (Lagacé, L., Chandra, T., Woo, S.L.C., and Means, A.R. (1983) J. Biol. Chem. 258, 1684-1688). Fifteen positive signals were detected among 4500 recombinant clones from which two overlapping clones (pCB12 and pCB15) were selected for subsequent DNA sequencing. The combined unique sequences of the two cDNA clones yielded 1395 base pairs and contained the entire coding region for calmodulin, 94 base pairs of the 5'-nontranslated region, and the entire 3'-nontranslated region of 857 base pairs. The derived amino acid sequence of chicken calmodulin is identical with that of the bovine or human protein. Compared to the eel, there is a single conservative amino acid substitution at position 74 which is occupied by Arg in the chicken and Lys in the eel. The overall nucleotide homology between the amino acid coding regions of chicken and eel calmodulin mRNA is 79%. However, the 5'- and 3'-nontranslated regions of the chicken and eel mRNA for calmodulin are highly diverged with sequence homologies of 21 and 29%, respectively. The cDNA clones were used as probes to determine the size and distribution of calmodulin mRNA in a variety of chicken tissues. In all tissues examined, two species of mRNA for calmodulin were detected at 1600 and 1900 nucleotides. Both mRNAs occurred in the cytoplasm with an abundance ratio of 4:1 for the 1600 and 1900 species, respectively. The two mRNAs appear to result from differential processing of transcripts from a single calmodulin gene. Screening of a chicken genomic phage library using pCB12 as a probe yielded a single positive designated CL-1 which contains a DNA insert of 13.5 kilobase pairs. Partial sequencing of CL-1 has confirmed the presence of sequences which code for calmodulin. A comparison of the restriction maps of CL-1 and pCB12 and pCB15 indicates that CL-1 contains at least 3 intervening sequences.

Amino Acid Sequence↗

PubMed1991

Characterization of a member of the immunoglobulin gene superfamily that possibly represents an additional class of growth factor receptor.

We have screened cDNA libraries prepared from embryonic chicken tissues to isolate additional genes encoding growth factor receptors. Nucleotide sequencing of a cDNA encoding a gene, which we have termed klg, revealed it to represent an additional member of the immunoglobulin gene superfamily, which also possesses extensive sequence similarity to the protein-tyrosine kinase growth factor receptor genes. The klg gene was shown to encode a 140-kDa glycoprotein. However, the sequence of the tyrosine kinase domain is unusual in that the aspartate residue located within the highly conserved Asp-Phe-Gly triplet is replaced by an alanine residue. The presence of this aspartate has previously been found to be essential for tyrosine kinase activity. Consistent with the replacement of this aspartate, we were unable to detect any evidence of an associated kinase activity with the klg-encoded protein. These observations raise the possibility that the klg gene product represents a newly discovered class of receptor that plays a role in signal attenuation rather than signal propagation.

Amino Acid Sequence↗

PubMed2001

Molecular characterization of a troponin I-like protein from the hard tick Haemaphysalis longicornis.

A cDNA expression library prepared from mRNA of Haemaphysalis longicornis (H. longicornis) was screened with a H. longicornis-infested rabbit serum. A cDNA encoding 27/30kDa proteins was cloned and designated P27/30 gene. The predicted amino acid sequence of the P27/30 gene shows a rather high homology (58% amino acid identities and 11% amino acid similarity) with Drosophila melanogaster troponin I clone E2. H. longicornis P27/30 possesses amino acid sequence of actin-binding domains of troponin I at the amino acid residues 128-148, suggesting that H. longicornis P27/30 is a troponin I-like protein. By immunoblot analysis, mouse anti-recombinant P27/30 serum reacted with major constituent protein bands in extracts of adult ticks, and also immunoreacted with muscle, cuticle, gut, and salivary gland in H. longicornis ticks. Moreover, immunohistochemistry using the anti-P27/30 serum showed a strong reactivity in muscle, suggesting that native P27/30 is expressed abundantly in that tissue.

Amino Acid Sequence↗

PubMed1999

Molecular cloning and sequencing of cDNAs encoding homologues of human Ku70 and Ku80 autoantigen from Xenopus and their expression in various Xenopus tissues.

We isolated cDNA clones encoding Ku70 and Ku80 homologues of Xenopus laevis from a cDNA library prepared from Xenopus oocytes. The nucleotide sequences of these Ku70 and Ku80 homologues have coding sequences of 1833 bp and a 611 aa protein, and 2178 bp and a 726 aa protein, respectively. The amino acid sequences deduced from the open reading frame of the Ku70 and Ku80 cDNA clones were highly homologous to those from Ku genes previously isolated, such as human (ca. 65% and ca. 62% identity, respectively) and mouse (ca. 65% and ca. 60%), and show a certain degree of homology to Drosophila (ca. 27% with Ku70), Caenorhabditis elegans (ca. 20% with Ku80) and Saccharomyces cerevisiae (ca. 23% and ca. 19%). Our detailed comparison of the predicted amino acid sequences among these species revealed the highly conserved octa-peptide LPFXXDIR common to both Xenopus Ku70 and Ku80 homologues in the region showing the high homology throughout the species tested. A Northern analysis using specific cDNA probes showed that Ku poly(A)+ mRNAs are expressed at high levels in Xenopus adult oocyte and testis.

Amino Acid Sequence↗

PubMed1998

cDNA cloning and expression analysis of genes encoding GSH synthesis in roots of the heavy-metal accumulator Brassica juncea L.: evidence for Cd-induction of a putative mitochondrial gamma-glutamylcysteine synthetase isoform.

In roots of Brassica juncea L. cadmium (Cd) exposure (25 microM) induces a massive formation of phytochelatins (PCs), which is accompanied by an only moderate decrease (-20%) of the putative PC precursor glutathione (GSH). As PC formation in roots could be the result of local GSH de novo synthesis and/or depend on GSH import from the shoot, we have analyzed the expression of the enzymes involved in GSH synthesis in the root, namely OAS(thiol)lyase (OAS-TL; catalysing the last step in Cys biosynthesis), gamma-glutamylcysteine synthetase (gamma-ECS), and glutathione synthetase (GSHS). cDNA clones were isolated from a cDNA library prepared from heavy metal exposed roots. Protein sequences from cDNA clones encoding OAS-TL, gamma-ECS, and GSHS, all exhibited putative mitochondrial targeting sequences, however, for OAS-TL also two putative cytosolic isoforms were isolated. Furthermore, we have cloned several metallothionein cDNAs of the MT2 group. Northern blot analysis with coding region probes revealed that in roots of Cd-exposed plants transcript amounts for OAS-TL and GSHS were only moderately increased, whereas gamma-ECS mRNA showed a stronger increase. Expression analysis with 3'-UTR probes indicated that among the putative mitochondrial OAS-TL, gamma-ECS and GSHS isoforms only gamma-ECS was up-regulated in response to Cd exposure. Conversely, transcripts for MT2 appeared to be slightly reduced. The results indicate that in roots Cd-induced PC synthesis correlates with a moderate increase of expression of genes involved in GSH synthesis, the change for gamma-ECS being most pronounced.

Amino Acid Sequence↗

PubMed2006

A multifunctional hybrid glycosyl hydrolase discovered in an uncultured microbial consortium from ruminant gut.

A unique multifunctional glycosyl hydrolase was discovered by screening an environmental DNA library prepared from a microbial consortium collected from cow rumen. The protein consists of two adjacent catalytic domains. Sequence analysis predicted that one domain conforms to glycosyl hydrolase family 5 and the other to family 26. The enzyme is active on several different beta-linked substrates and possesses mannanase, xylanase, and glucanase activities. Site-directed mutagenesis studies on the catalytic residues confirmed the presence of two functionally independent catalytic domains. Using site-specific mutations, it was shown that one catalytic site hydrolyzes beta-1,4-linked mannan substrates, while the second catalytic site hydrolyzes beta-1,4-linked xylan and beta-1,4-linked glucan substrates. Polysaccharide Analysis using Carbohydrate gel Electrophoresis (PACE) also confirmed that the enzyme has discrete domains for binding and hydrolysis of glucan- and mannan-linked polysaccharides. Such multifunctional enzymes have many potential industrial applications in plant processing, including biomass saccharification, animal feed nutritional enhancement, textile, and pulp and paper processing.

Animals↗

PubMed1997

Molecular characterization and cytological mapping of a non-repetitive DNA sequence region from the W chromosome of chicken and its use as a universal probe for sexing carinatae birds.

A non-repetitive genomic DNA region of about 25 kb was cloned from the W chromosome of chicken using a genomic library prepared from a single W chromosome of the chicken. This region was mapped by fluorescence in situ hybridization (FISH) with mitotic and lampbrush chromosomes to a position between the major EcoRI family and the pericentromeric Xhol family on the W chromosome. A 0.6-kb EcoRI fragment (EE0.6) subcloned from this region consists of a sequence that can be obtained by the exon-trapping procedure and flanking sequences. Sequences, which are closely similar to that of EE0.6, are widely conserved on the W chromosomes of Carinatae birds, as revealed by Southern blot hybridization to HindIII-digested female and male genomic DNAs from 18 species of birds belonging to eight different taxonomic orders. The female sex of those birds can be determined by the presence of an unambiguous female-specific band. For many species of birds, the female sex can also be determined by polymerase chain reaction (PCR) using a set of primers from the flanking sequences in the chicken EE0.6.

Animals↗

PubMed2004

Upregulation of the mitochondrial phosphate carrier during freezing in the wood frog Rana sylvatica: potential roles of transporters in freeze tolerance.

Screening of a cDNA library prepared from liver of the freeze-tolerant wood frog (Rana sylvatica) identified a freeze-responsive clone containing a 1370-nt sequence with an open reading frame of 360 amino acids. Sequence analysis revealed 84-86% identity with the mammalian inorganic phosphate carrier (PiC) that spans the inner mitochondrial membrane. Northern blot analysis showed that pic transcript levels increased over a time course of freezing, reaching 60-fold upregulation after 24-h frozen. Transcript levels were also assessed under freezing-related stresses with results showing a strong increase in pic transcript levels in response to dehydration (elevated 9.0-fold in 40% dehydrated frogs) but not under anoxia. Western blotting revealed elevated PiC protein over a time course of freeze-thaw whereas other mitochondrial carriers (dicarboxylate carrier, oxoglutarate transporter) of the same family were not affected by freezing. This modulation of PiC protein levels may play a role in mitochondrial ionic and/or osmotic balance during freeze-induced cell volume reduction.

Acclimatization↗

PubMed1990

Cloning and expression of N-acetylglucosaminyltransferase I, the medial Golgi transferase that initiates complex N-linked carbohydrate formation.

This laboratory has previously identified a human gene encoding N-acetylglucosaminyltransferase I (GlcNAc-TI; EC 2.4.1.101) by complementation of the glycosylation defect in the Lec1 Chinese hamster ovary (CHO) cell mutant. A phage lambda library prepared from genomic DNA of a tertiary Lec1 transfectant (3 degrees T) has now been used to obtain clones encoding an active GlcNAc-TI enzyme. A small genomic DNA fragment [approximately 4.6 kilobases (kb)], isolated from an Alupositive lambda clone, conferred human GlcNAc-TI activity upon transfection into Lec1 cells. An approximately 1.3-kb probe generated from this DNA fragment detected unique but distinct DNA fragments in human and CHO genomic DNA. The probe also hybridized to a poly(A)+ RNA of approximately 2.7 kb in human and CHO cells and allowed the isolation of a full-length cDNA encoding human GlcNAc-TI activity. The overall features of the cDNA and deduced protein sequence (445 amino acids) are typical of other Golgi transferases that are type II transmembrane proteins. Northern blot analysis with the same probe showed that Lec1 mutant cells also possessed an approximately 2.7-kb poly(A)+ RNA, indicating that the lec1 mutation is a point mutation.

Amino Acid Sequence↗

PubMed1992

A second gene for the African green monkey poliovirus receptor that has no putative N-glycosylation site in the functional N-terminal immunoglobulin-like domain.

Using cDNA of the human poliovirus receptor (PVR) as a probe, two types of cDNA clones of the monkey homologs were isolated from a cDNA library prepared from an African green monkey kidney cell line. Either type of cDNA clone rendered mouse L cells permissive for poliovirus infection. Homologies of the amino acid sequences deduced from these cDNA sequences with that of human PVR were 90.2 and 86.4%, respectively. These two monkey PVRs were found to be encoded in two different loci of the genome. Evolutionary analysis suggested that duplication of the PVR gene in the monkey genome had occurred after the species differentiation between humans and monkeys. The NH2-terminal immunoglobulin-like domain, domain 1, of the second monkey PVR, which lacks a putative N-glycosylation site, mediated poliovirus infection. In addition, a human PVR mutant without N-glycosylation sites in domain 1 also promoted viral infection. These results suggest that domain 1 of the monkey receptor also harbors the binding site for poliovirus and that sugar moieties possibly attached to this domain of human PVR are dispensable for the virus-receptor interaction.

Amino Acid Sequence↗