Isolated cDNA Clones Research Articles

The Extracellular Adenosine Deaminase Growth Factor, ADGF/CECR1, Plays a Role in Xenopus Embryogenesis via the Adenosine/P1 Receptor

Adenosine deaminase-related growth factors (ADGF), also known as CECR1 in vertebrates, are a novel family of growth factors with sequence similarity to classical cellular adenosine deaminase. Although genes for ADGF/CECR1 have been identified in both invertebrates as well as vertebrates, their in vivo functions in vertebrates remain unknown. We isolated cDNA clones for two cerc 1s from Xenopus laevis. Both recombinant Xenopus CECR1s exhibited adenosine deaminase and growth factor activity, and the adenosine deaminase activity was found to be indispensable for growth factor activity. The Xenopus cerc 1s are expressed in the somites, pronephros, eyes, cement gland, neural tube, and neural floor plate of the embryos. Knock-down of these two genes using morpholino oligonucleotides caused a reduction in the body size and abnormalities of the body axis in the Xenopus embryos, accompanied by selective changes in the expression of developmental marker genes. Injection of adenosine, agonists for adenosine/P1 receptors, or adenosine deaminase inhibitor into late gastrula archenteron embryos resulted in developmental defects similar to those caused by morpholino oligonucleotide injection. These results show, for the first time, the involvement of CECR1s via the adenosine/P1 receptors in vertebrate embryogenesis via regulation of extracellular adenosine concentrations.

Thyroid hormone receptor expression during metamorphosis of Atlantic halibut ( Hippoglossus hippoglossus)

Flatfish such as the Atlantic halibut ( Hippoglossus hippoglossus) undergo a dramatic metamorphosis that transforms the pelagic, symmetric larva into a benthic, cranially asymmetric juvenile. In common with amphibian metamorphosis, flatfish metamorphosis is under endocrine control with thyroid hormones being particularly important. In this report we confirm that tri-iodothyronine (T 3) levels peak at metamorphic climax during halibut metamorphosis. Moreover, we have isolated cDNA clones of TRα and TRβ genes and confirmed the presence in halibut of two TRα isoforms (representing the products of distinct genes) and two TRβ isoforms (generated from a single gene by alternative splicing). Real-time PCR was used to assess expression of these genes during metamorphosis. TRβ shows the most dramatic expression profile, with a peak occurring during metamorphic climax.

Isolation of cDNA Clones of Genes Differentially Expressed During Somatic Embryogenesis of Pinus roxburghii

Isolation of cDNA Clones of Genes Differentially Expressed During Somatic Embryogenesis of Pinus roxburghii

Molecular Cloning of Two Estrogen Receptors Expressed in the Testis of the Japanese Common Goby, Acanthogobius flavimanus

We isolated cDNA clones of two estrogen receptors (ER1 and ER2) from testis of the Japanese common goby (Acanthogobius flavimanus). The cDNAs of ER1 contained 3,796 nucleotides, including an open reading frame encoding 564 amino acids (Mr: 61.9 kDa); the cDNA for ER2 was 3,274 nucleotides long, with an open reading frame of 567 amino acids (Mr: 63.5 kDa). The deduced aminoacid sequences of ER1 and ER2 each had a characteristic ER structure consisting of five domains (A/B, DNA-binding, D, ligand-binding, and F) and were homologous to ERalpha and ERbeta of other vertebrates. We therefore named ER1 and ER2 as goby ERalpha (gERalpha) and goby ERbeta (gERbeta), respectively. The DNA- and ligand-binding domains in each gER showed high similarity to the corresponding domains of other vertebrates. Analysis of the distribution of gERalpha and gERbeta mRNAs in tissue by reverse transcription-polymerase chain reaction (RT-PCR) analysis revealed that gERalpha was expressed at high levels in brain and testis, and gERbeta was expressed most strongly in testis. In situ hybridization showed that the mRNA of each gER was expressed mainly in the Sertoli cells of goby testis.

The molecular biology of cyanogenesis.

The cyanogenic polymorphism in Trifolium repens L. (white clover) has been used as the basis of a study of the genetic control of cyanogenesis. The Ac locus controls the presence of two cyanoglucosides in white clover. Biochemical characterization of cyanoglucoside biosynthesis in plants containing different Ac alleles has shown that this is a complex locus which affects more than one step in the pathway. A study of the in vivo synthesis and processing of the cyanogenic beta-glucosidase (linamarase) of white clover led to the isolation of cDNA clones for this enzyme. The cloning strategy and structure of the cDNA clones is described. Together with biochemical and genetic data, these clones have been used to characterize the Li locus which controls linamarase activity in white clover. It has been shown that 'null' alleles of the Li locus result in very reduced levels of transcription of homologous mRNA sequences. The use of these cDNA clones to investigate the genomic organization of cyanogenesis genes in both white clover and other cyanogenic species is described, and their use in structural analysis of the cyanogenic beta-glucosidase is discussed.

The Fibrinolytic Activity of a Novel Protease Derived from a Tempeh Producing Fungus,Fusariumsp. BLB

Tempeh is a traditional Indonesian soybean-fermented food produced by filamentous fungi, Rhizopus sp. and Fusarium sp. We isolated and sequenced the genomic gene and a cDNA clone encoding a novel protease (FP) from Fusarium sp. BLB. The genomic gene was 856 bp in length and contained two introns. An isolated cDNA clone encoded a protein of 250 amino acids. The predicted amino acid sequence of FP showed highest homology, of 76%, with that of trypsin from Fusarium oxysporum. The hydrolysis activity of FP toward synthetic peptide was higher than that of any other protease tested, including Nattokinases. Furthermore, the thrombolytic activity of FP was about 2.1-fold higher than that of Nattokinase when the concentration of plasminogen was 24 units/ml. These results suggest that FP is superior to Nattokinases in dissolving fibrin when absorbed into the blood.

Expression and enzyme activity of glutathione reductase is upregulated by Fe-deficiency in graminaceous plants

Glutathione reductase (GR) plays an important role in the response to biotic and abiotic stresses in plants. We studied the expression patterns and enzyme activities of GR in graminaceous plants under Fe-sufficient and Fe-deficient conditions by isolating cDNA clones for chloroplastic GR (HvGR1) and cytosolic GR (HvGR2) from barley. We found that the sequences of GR1 and GR2 were highly conserved in graminaceous plants. Based on their nucleotide sequences, HvGR1 and HvGR2 were predicted to encode polypeptides of 550 and 497 amino acids, respectively. Both proteins showed in vitro GR activity, and the specific activity for HvGR1 was 3-fold that of HvGR2. Northern blot analyses were performed to examine the expression patterns of GR1 and GR2 in rice (Os), wheat (Ta), barley (Hv), and maize (Zm). HvGR1, HvGR2, and TaGR2 were upregulated in response to Fe-deficiency. Moreover, HvGR1 and TaGR1 were mainly expressed in shoot tissues, whereas HvGR2 and TaGR2 were primarily observed in root tissues. The GR activity increased in roots of barley, wheat, and maize and shoot tissues of rice, barley, and maize in response to Fe-deficiency. Furthermore, it appeared that GR was not post-transcriptionally regulated, at least in rice, wheat, and barley. These results suggest that GR may play a role in the Fe-deficiency response in graminaceous plants.

Rat organic solute carrier protein 1 (rOscp1) mediated the transport of organic solutes in Xenopus laevis oocytes: Isolation and pharmacological characterization of rOscp1

Rat organic solute carrier protein 1 (rOscp1) was isolated from a rat testis cDNA library. Isolated rOscp1 cDNA consisted of 1089 base pairs that encoded a 363-amino acid protein, and the amino acid sequence was 88% and 93% identical to that of human OSCP1 (hOSCP1) and mouse Oscp1 (mOscp1), respectively. The message for rOscp1 is highly detected in rat testis. When expressed in X. oocytes, rOscp1 mediated the high affinity transport of p-aminohippurate (PAH) with a K m value of 15.7 ± 1.9 μM, and rOscp1-mediated organic solutes were exhibited in time- and Na +-independent manners. rOscp1 also transported various structurally heterogenous compounds such as testosterone, dehydroepiandrosterone sulfate (DHEA-S), and taurocholate with some differences in substrate specificity compared with hOSCP1. Immunohistochemical analysis revealed that the rOscp1 protein is localized in the basal membrane side of Sertoli cells as observed in mouse testis [Kobayashi et al., 2007; Kobayashi, Y., Tsuchiya, A., Hayashi, T., Kohyama, N., Ohbayashi, M., Yamamoto, T., 2007. Isolation and characterization of polyspecific mouse organic solute carrier protein 1 (mOscp1). Drug Metabolism and Disposition 35 (7), 1239–1245]. Thus, the present results indicate that a newly isolated cDNA clone, rOscp1, is a polyspecific organic solute carrier protein with some differences in substrate specificity compared with human and mouse OSCP1.

Isolation of cDNA clones for genes up-regulated in drought-treated Alternanthera philoxeroides root

Alternanthera philoxeroides is one of the rather few amphibious plants that can normally grow in both water and upland conditions. Adventitious roots of Alternanthera philoxeroides seedlings will grow long, thick, fleshy during drought stress, which are assumed to improve performance of the plant by more efficient storage and extraction of water from deep soil layers. In order to isolate cDNA clones of morphogenesis-related genes from A. philoxeroides roots, the seedlings were treated with drought and the differential display technique was used. By using 18 primer combinations, nineteen putative drought up-regulated gene segments were obtained and one of them was confirmed having been up-regulated by reverse northern blot and subsequently cloned and sequenced. A homologous analysis revealed that it might be a new gene segment. Semi-quantitative RT-PCR analysis showed that the gene was up-regulated by drought and salt stress.

Expression, characterization, and gene knockdown of zebrafish doublecortin-like protein kinase

Doublecortin-like protein kinase (DCLK) is a protein Ser/Thr kinase expressed in brain and believed to play crucial roles in neuronal development. To investigate the biological significance of DCLK, we isolated cDNA clones for zebrafish DCLK (zDCLK) and found that there were five splice variants of the kinase. In this study, the catalytic properties of a major isoform of zDCLK, which we designated as zDCLK1, and of an N-terminal truncated mutant retaining the kinase domain were examined by expressing them in Escherichia coli. Mutational analysis of recombinant zDCLK suggested that the kinase was activated not only by phosphorylation at Thr-576 in the activation loop but also by autophosphorylation at the other site(s) in the catalytic domain. zDCLK significantly phosphorylated protein substrates such as myelin basic protein, histones, and synapsin I. Subcellular localization of zDCLK and its N-terminal deletion mutant implicated that microtubule-association of zDCLK is mediated through N-terminal doublecortin like domain of this enzyme. Western blotting analysis and whole mount in situ hybridization revealed that zDCLK was highly expressed in brain and eyes after 24-h post fertilization. Gene knockdown of zDCLK using morpholino-based antisense oligonucleotides induced significant increase of apoptotic cells in the central nervous systems and resulted in the increase of the morphologically abnormal embryos in a dose-dependent manner. These results suggest that zDCLK may play crucial roles in the central nervous systems during the early stage of embryogenesis.

Characterization and cDNA cloning of aminopeptidase A from the venom of Gloydius blomhoffi brevicaudus

The aminopeptidase activities of snake venoms from Gloydius blomhoffi brevicaudus, Gloydius halys blomhoffii, Trimeresurus flavoviridis, Bothrops jararaca and Crotalus atrox were investigated. Aminopeptidase A (APA), aminopeptidase B and aminopeptidase N activities were present in all snake venoms. The strongest APA activity was found in venom from G. blomhoffi brevicaudus. The susceptibility to metallopeptidase inhibitors and the pH optimum of the partially purified enzyme from G. blomhoffi brevicaudus venom were similar to those of known APAs from mammals. A G. blomhoffi brevicaudus venom gland cDNA library was screened to isolate cDNA clones using probes based on highly conserved amino acid sequences in known APAs. Molecular cloning of APA from G. blomhoffi brevicaudus venom predicted that it was a type II integral membrane protein containing 958 amino acid residues with 17 potential N-linked glycosylation sites. It possessed a His-Glu-Xaa-Xaa-His-(Xaa) 18-Glu zinc binding motif that allowed the classification of this protein as a member of the M1 family of zinc-metallopeptidases, or gluzincins. The deduced amino acid sequence shows approximately 60% sequence identity to mammalian APA sequences. This is the first study to report the primary structure of APA from a reptile.

Isolation of cDNA clones corresponding to genes differentially expressed in pericarp of mume (Prunus mume) in response to ripening, ethylene and wounding signals

Ripening of climacteric fruit is a complex developmental process that includes many changes in gene expression. Some ripening‐regulated genes are responsive to ethylene and/or wounding signals. Wounding increased Pm‐ACS1 expression in Prunus mume (Japanese apricot), but was negatively regulated by ethylene. However, exposure of freshly harvested mature green mume fruit to ethylene induced PmACS1. Fifteen complementary DNA clones corresponding to messenger RNAs differentially expressed in the pericarp of P. mume fruit in response to ripening, ethylene and wounding signals were isolated by differential display. Quantitative real‐time PCR analysis distinctly showed that these genes are differentially regulated. Genes that were upregulated during fruit ripening include Pm15 (cinnamyl‐alcohol dehydrogenase), Pm21 (2‐oxoacid‐dependent dioxygenase), Pm22 (1‐acyl‐sn‐glycerol‐3‐phosphate acyltransferase), Pm27 (unknown function), Pm38 (alcohol dehydrogenase), Pm41 (no homology), Pm52 (no homology), Pm65 (pectate lyase), Pm68 (expansin), Pm69 (serine carboxypeptidase) and Pm94 (alcohol acyltransferase). Expression of most of these genes was also inducible by ethylene and some of them were inducible by wounding. Pm3 (water channel protein, MIP) and Pm8 (unknown function) were downregulated during ripening. Expression of Pm71 (no homology) and Pm74 (NAC family protein) did not increase during ripening or in response to ethylene, but was upregulated in response to wounding. The possible physiological roles of these genes during ripening and in response to ethylene and wounding are discussed.

VCC-1, a novel chemokine, promotes tumor growth

We have identified a novel human gene by transcriptional microarray analysis, which is co-regulated in tumors and angiogenesis model systems with VEGF expression. Isolation of cDNA clones containing the full-length VCC-1 transcript from both human and mouse shows a 119 amino acid protein with a 22 amino acid cleavable signal sequence in both species. Comparison of the protein product of this gene with hidden Markov models of all known proteins shows weak but significant homology with two known chemokines, SCYA17 and SCYA16. Northern analysis of human tissues detects a 1 kb band in lung and skeletal muscle. Murine VCC-1 expression can also be detected in lung as well as thyroid, submaxillary gland, epididymis, and uterus tissues by slot blot analysis. By quantitative real time RT-PCR 71% of breast tumors showed 3- to 24-fold up-regulation of VCC-1. In situ hybridization of breast carcinomas showed strong expression of the gene in both normal and transformed mammary gland ductal epithelial cells. In vitro, human microvascular endothelial cells grown on fibronectin increase VCC-1 expression by almost 100-fold. In addition, in the mouse angioma endothelial cell line PY4.1 the gene was over-expressed by 28-fold 6 h after induction of tube formation while quiescent and proliferating cells showed no change. VCC-1 expression is also increased by VEGF and FGF treatment, about 6- and 5-fold, respectively. Finally, 100% of mice injected with NIH3T3 cells over-expressing VCC-1 develop rapidly progressing tumors within 21 days while no growth is seen in any control mice injected with NIH3T3 cells containing the vector alone. These results strongly suggest that VCC-1 plays a role in angiogenesis and possibly in the development of tumors in some tissue types.

A branched-chain amino acid aminotransferase gene isolated from Hordeum vulgare is differentially regulated by drought stress

Differential display was used to isolate cDNA clones showing differential expression in response to ABA, drought and cold in barley seedling shoots. One drought-regulated cDNA clone (DD12) was further analyzed and found to encode a branched-chain amino acid aminotransferase (HvBCAT-1). A genomic clone was isolated by probing the Morex BAC library with the cDNA clone DD12 and the structure of Hvbcat-1 was elucidated. The coding region is interrupted by six introns and contains a predicted mitochondrial transit peptide. Hvbcat1 was mapped to chromosome 4H. A comparison was made to rice and Arabidopsis genes to identify conserved structural patterns. Complementation of a yeast (Saccharomyces cerevisiae) double knockout strain revealed that HvBCAT-1 can function as the mitochondrial (catabolic) BCATs in vivo. Transcript levels of Hvbcat-1, increased in response to drought stress. As the first enzyme in the branched-chain amino acid (BCAA) catabolic pathway, HvBCAT-1 might have a role in the degradation of BCAA. Degradation of BCAA could serve as a detoxification mechanism that maintains the pool of free branched-chain amino acids at low and non toxic levels, under drought stress conditions.

Transcriptional profiling of summer wheat, grown under different realistic UV-B irradiation regimes

There is limited information on the impact of present-day ultraviolet-B (UV-B) radiation on a reprogramming of gene expression in crops. Summer wheat was cultivated in controlled environmental facilities under simulated realistic climatic conditions. We investigated the effect of different regimes of UV-B radiation on summer wheat (Triticum aestivum L.) cultivars Nandu, Star and Turbo. Until recently, these were most important in Bavaria. Different cultivars of crops often show great differences in their sensitivity towards UV-B radiation. To identify genes that might be involved in UV-B defence mechanisms, we first analyzed selected genes known to be involved in plant defence mechanisms. RNA gel blot analysis of RNA isolated from the flag leaf of 84-day-old plants showed differences in transcript levels among the cultivars. Flag leaves are known to be important for grain development, which was completed at 84 days post-anthesis. Catalase 2 (Cat2) transcripts were elevated by increased UV irradiation in all cultivars with highest levels in cv. Nandu. Pathogenesis-related protein 1 (PR1) transcripts were elevated only in cv. Star. A minor influence on transcripts for phenylalanine ammonia-lyase (PAL) was observed in all three cultivars. This indicates different levels of acclimation to UV-B radiation in the wheat cultivars studied. To analyze these responses in more detail, UV-B-exposed flag leaves of 84-day-old wheat (cv. Nandu) were pooled to isolate cDNAs of induced genes by suppression-subtractive hybridization (SSH). Among the initially isolated cDNA clones, 13 were verified by RNA gel blot analysis showing an up-regulation at elevated levels of UV-B radiation. Functional classification revealed genes encoding proteins associated with protein assembly, chaperonins, programmed cell death and signal transduction. We also studied growth, flowering time, ear development and yield as more typical agricultural parameters. Plant growth of young plants was reduced at increased UV-B radiation. Flowering and ear development were delayed concomitantly, whereas total grain weight was not influenced at any of the UV-B irradiation regimes.

The lift pool method for isolation of cDNA clones from lambda phage libraries

A PCR based strategy was developed to screen a Xenopus oocyte λgt10 cDNA library. The PCR-based lift pool (LP) method follows the same two tiered strategy as conventional screening of phage libraries by filter hybridization. Two rounds of plating, one at high density to detect the clone, and one at low density to purify the clone to homogeneity, are performed. In the first round, lysates from high density plates, termed plate pools (PP), serve as template for PCR. In the second round, phage particles adhering to plaque lifts of low density plates are washed off nitrocellulose filters to create LPs, which are used as template for PCR. The integrity of the plaques on the low-density plates is preserved. Once a positive LP has been identified, plaques on the corresponding plate are screened individually by PCR. Using isoform specific primer pairs for Xenopus myosin 7a and myosin 1d, two lambda clones were isolated. Subsequent DNA sequence analysis confirmed their identities as myosin isoforms (GenBank accession numbers: DQ100353 and AF540952). This method offers a time saving, cost-effective alternative to other hierarchical pooling strategies for the repeated screening by PCR of an arrayed lambda phage library.

The lift pool method for isolation of cDNA clones from lambda phage libraries

The lift pool method for isolation of cDNA clones from lambda phage libraries

Characterization and cDNA cloning of dipeptidyl peptidase IV from the venom of Gloydius blomhoffi brevicaudus

Dipeptidyl peptidase activity was investigated in snake venoms from Gloydius blomhoffi brevicaudus, Gloydius halys blomhoffii, Trimeresurus flavoviridis and Crotalus atrox. The strongest dipeptidyl peptidase IV (DPP IV) activity was found in venom from G. blomhoffi brevicaudus. The substrate specificity, susceptibility to inhibitors, and pH optimum of the partially purified enzyme were similar to those of known DPP IVs from bacteria and eukaryotes. The G. blomhoffi brevicaudus venom gland cDNA library was screened to isolate cDNA clones using probes based on amino acid sequences highly conserved in known DPP IVs. Two cDNA species encoding DPP IV were obtained, and designated as DPP IVa and DPP IVb. This is the first study to report the primary structure of DPP IV from a reptile. The deduced amino acid sequences for DPP IVa and DPP IVb both consist of 751 amino acid residues and are highly homologous to each other. A putative catalytic triad for serine proteases, Ser-616, Asp-694, and His-726, is present. It is of particular interest that the deduced NH 2-terminal sequence associated with the characteristic signal peptide is identical to that determined from the purified DPP IV. This indicates that the signal peptide of snake venom DPP IV is not cleaved off during biosynthesis, unlike those of other snake venom proteins.

Structural components of the synaptonemal complex, SYCP1 and SYCP3, in the medaka fish Oryzias latipes

The synaptonemal complex (SC) is a meiosis-specific structure essential for synapsis of homologous chromosomes. For the first time in any non-mammalian vertebrates, we have isolated cDNA clones encoding two structural components of the SC, SYCP1 and SYCP3, in the medaka, and investigated their protein expression during gametogenesis. As in the case of mammals, medaka SYCP1 and SYCP3 are expressed solely in meiotically dividing cells. In the diplotene stage, SYCP1 is diminished at desynaptic regions of chromosomes and completely lost on the chromosomes at later stages. SYCP3 is localized along the arm and centromeric regions of chromosomes at metaphase I, and its existence on the whole chromosomes persists up to anaphase I, a situation different from that reported in the mouse, in which SYCP3 is confined to the centromeric regions but lost on the arm regions at metaphase I. Thus, the expression patterns of SC components are different in mammals and fish despite the resemblance in morphological structure of the SC, suggesting divergence in the function of the SC in regulation of meiosis-specific chromosomal behavior. Since the antibody against medaka SYCP3 is cross-reactive to other fishes, it should be generally useful for a meiosis-specific marker in fish germ cells.

Molecular cloning and sequence analysis of the β-1,3-glucan synthase catalytic subunit gene from a medicinal fungus, Cordyceps militaris

The entomopathogenic fungus Cordyceps militaris belongs to vegetable wasps and plant worms and is used as herbal medicine, but β-1,3-glucan biosynthesis has been poorly studied in C. militaris. The fungal FKS1 gene encodes an integral membrane protein that is the catalytic subunit of β-1,3-glucan synthase. Here, we isolated cDNA clones encoding a full-length open reading frame of C. militaris FKS1. Cordyceps militaris Fks1 protein is a 1981 amino acid protein that shows significant similarity with other fungal Fks proteins. This study is the first report of molecular cloning of the β-1,3-glucan synthase catalytic subunit gene from vegetable wasps and plant worms.