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PubMed2002

Cloning and gene expression of a cDNA for the chicken follicle-stimulating hormone (FSH)-beta-subunit.

Follicle-stimulating hormone (FSH) is a member of pituitary glycoprotein hormones that are composed of two dissimilar subunits, alpha and beta. Very little information is available regarding the nucleotide and amino acid sequence of FSH-beta in avian species. For better understanding of the phylogenic diversity and evolution of FSH molecule, we have isolated and sequenced the complete complementary DNA (cDNA) encoding chicken FSH-beta precursor molecule by reverse transcription-polymerase chain reaction (RT-PCR) and rapid amplification of cDNA end (RACE) methods. The cloned chicken FSH-beta cDNA consists of 2457-bp nucleotides, including 44-bp nucleotides of the 5'-untranslated region (UTR), 396 bp of the open reading frame, and an extraordinarily long 3'-UTR of 2001-bp nucleotides followed by a poly(A)((16)) tail. It encodes a 131-amino-acid precursor molecule of FSH-beta-subunit with a signal peptide of 20 amino acids followed by a mature protein of 111 amino acids. Twelve cysteine residues, forming six disulfide bonds within beta-subunit and two putative asparagine-linked glycosylation sites, are also conserved in the chicken FSH-beta-subunit. Four proline residues, presumably responsible for changing the backbone direction of protein structure, are conserved in chicken FSH-beta-subunit as well. The nucleotide sequence of chicken FSH-beta cDNA shows high homology with quail FSH-beta cDNA, 97% homology in the open reading frame, and 85% homology in the 3'-UTR. The deduced amino acid sequence of chicken FSH-beta-subunit shows a remarkable similarity to other avian FSH-beta-subunits, 98% homology with quail, and 93% homology with ostrich, whereas a lower similarity (66 to 70%) is noted when compared with mammalian FSH-beta-subunits. By contrast, when comparing with the beta-subunits of chicken luteinizing hormone and thyroid-stimulating hormone, the homologies are as low as 37 and 40%, respectively. FSH-beta mRNA was only expressed in pituitary gland out of various tissues examined and can be up-regulated by gonadotropin-releasing hormone in pituitary tissue culture as estimated by real-time quantitative PCR.

3' Untranslated Regions↗

PubMed1993

Mapping of aldose reductase gene sequences to human chromosomes 1, 3, 7, 9, 11, and 13.

Aldose reductase (alditol:NAD(P)+ 1-oxidoreductase; EC 1.1.1.21) (AR) catalyzes the reduction of several aldehydes, including that of glucose, to the corresponding sugar alcohol. Using a complementary DNA clone encoding human AR, we mapped the gene sequences to human chromosomes 1, 3, 7, 9, 11, 13, 14, and 18 by somatic cell hybridization. By in situ hybridization analysis, sequences were localized to human chromosomes 1q32-q42, 3p12, 7q31-q35, 9q22, 11p14-p15, and 13q14-q21. As a putative functional AR gene has been mapped to chromosome 7 and a putative pseudogene to chromosome 3, the sequences on the other seven chromosomes may represent other active genes, non-aldose reductase homologous sequences, or pseudogenes.

Aldehyde Reductase↗

PubMed1994

Isolation and characterization of transcribed sequences from a chromosome 16 hn-cDNA library and the physical mapping of genes and transcribed sequences using a high-resolution somatic cell panel of human chromosome 16.

A hn-cDNA (heteronuclear complementary DNA) library was constructed from a mouse/human somatic cell hybrid, CY18, which contains chromosome 16 as the only human chromosome. Hexamer primers constructed from consensus 5' intron splice sequences were used to generate cDNA from the immature unspliced mRNA. The resulting cDNA library was screened with a total human DNA probe to identify potential human clones. Rescreening was necessary, and use of a mouse-derived clone with homology to 7SL RNA proved successful in eliminating the majority of mouse clones. Thirteen clones had open reading frames, and of those, five showed homology to human sequences in GenBank. Two clones had homology to random partially sequenced cDNAs, one clone was likely to be a GRP78 pseudogene, one clone mapped the PHKG2 gene to 16p11.2-16p12.1, and one clone had homology to human S13 ribosomal protein. All clones except the latter were mapped to a high-resolution somatic cell panel. Although isolation of human chromosome 16 genes from this library was successful, it was apparent that cDNA synthesis was initiated at sites other than intron splice sites, presumably by mispairing of the hexamers.

Animals↗

PubMed1994

Chromosomal localization of murine ryanodine receptor genes RYR1, RYR2, and RYR3 by in situ hybridization.

In situ hybridization experiments were performed using complementary DNA probes to determine the location on murine chromosomes of the three genes of the ryanodine receptor/Ca2+ channel family: RYR1, RYR2, and RYR3. The skeletal ryanodine receptor, or type 1 (Ryr1), maps to bands 7A2-7A3; the cardiac ryanodine receptor, or type 2 (Ryr2), to 13A1-13A2; and type 3 (Ryr3) to 2E5-2F3.

Animals↗

PubMed1996

Sequence of human hexokinase III cDNA and assignment of the human hexokinase III gene (HK3) to chromosome band 5q35.2 by fluorescence in situ hybridization.

Complementary DNA clones encoding human hexokinase III were isolated from a liver cDNA library. There was 84.7% identity between the amino acid sequences of human and rat hexokinase III. RNA blotting showed the presence of hexokinase III mRNA in liver and lung. Fluorescence in situ hybridization localized the human hexokinase III gene (HK3) to chromosome 5, band q35.2.

Amino Acid Sequence↗

PubMed1998

Characterization of an aFGF gene expression vector with therapeutic potential.

BACKGROUND: Topical application of growth factors to wounds has proven to be suboptimal in achieving epithelial growth and accelerating healing. We propose transfection of fibroblasts with a gene for acidic fibroblast growth factor (aFGF) which will allow continuous, local delivery of the growth factor to wounds, ulcerative lesions, or healing tissues. METHODS: We utilized a pMEXneo vector containing the human aFGF gene with a secretory signal sequence from the hst/KS3 gene to obtain continuous secretion of therapeutic doses of aFGF. NIH 3T3 fibroblasts were transfected using a liposomal transfection reagent and grown in selective media. RESULTS: Dot blot hybridization with labeled complementary DNA probes revealed the presence of plasmid DNA in transfected but not wild type fibroblasts. Intracellular concentrations of aFGF remained low in transfected cells; however, the media contained high levels (32 +/- 7 nM) of aFGF as measured by ELISA. Concentrations of aFGF capable of stimulating cell proliferation were maintained for several weeks. CONCLUSIONS: The aFGF cDNA was transcribed and translated into a functional polypeptide that is secreted from NIH 3T3 cells at physiologically significant concentrations. Stable transfection with a eukaryotic vector which induces secretion of aFGF at levels promoting cell growth holds promise for clinical application in wounds or healing tissue. Transfection could be achieved by topical or endoscopic injection of this type of vector.

3T3 Cells↗

PubMed1996

Cloning of cDNA encoding rat spermatidal protein TP2 and expression in Escherichia coli.

Rat spermatidal protein TP2 is a basic nuclear protein containing two atoms of zinc bound per molecule. We report here cloning of complementary DNA encoding rat TP2 by the RT-PCR method. The nucleotide sequence of cloned TP2 cDNA differs at a few positions from the sequence already reported in the literature. We have cloned rat TP2 cDNA into the expression vector pTrc 99A. Upon induction with 1 mM IPTG, there was a low level of expression of TP2 which could be recovered in the soluble form. Recombinant TP2 was purified from the soluble form. Recombinant TP2 was purified from the soluble extract of E. coli using nickel-agarose and heparin-agarose chromatography and was shown to be identical to native rat TP2 as revealed by immunoblotting with anti-rat TP2 antibodies and radioactive 65Zn-blotting.

Amino Acid Sequence↗

PubMed1999

Cloning, expression, and purification of cytidine deaminase from Arabidopsis thaliana.

The complementary DNA (cDNA) coding for Arabidopsis thaliana cytidine deaminase 1 (AT-CDA1) was obtained from the amplified A. thaliana cDNA expression library, provided by R. W. Davis (Stanford University, CA). AT-CDA1 cDNA was subcloned into the expression vector pTrc99-A and the protein, expressed in Escherichia coli following induction with isopropyl 1-thio-beta-d-galactopyranoside, showed high cytidine deaminase activity. The nucleotide sequence showed a 903-bp open reading frame encoding a polypeptide of 301 amino acids with a calculated molecular mass of 32,582. The deduced amino acid sequence of AT-CDA1 showed no transit peptide for targeting to the chloroplast or mitochondria indicating that this form of cytidine deaminase is probably expressed in the cytosol. The recombinant AT-CDA1 was purified to homogeneity by a heat treatment followed by an ion-exchange chromatography. The final enzyme preparation was >98% pure as judged by SDS-PAGE and showed a specific activity of 74 U/mg. The molecular mass of AT-CDA1 estimated by gel filtration was 63 kDa, indicating, in contrast to the other eukaryotic CDAs, that the enzyme is a dimer composed of two identical subunits. Inductively coupled plasma-optical emission spectroscopy analysis indicated that the enzyme contains 1 mol of zinc atom per mole of subunit. The kinetic properties of AT-CDA1 both toward the natural substrates and with analogs indicated that the catalytic mechanism of the plant enzyme is probably very similar to that of the human the E. coli enzymes.

Amino Acid Sequence↗

PubMed1994

Evidence that the alpha a gene of barley stripe mosaic virus encodes determinants of pathogenicity to oat (Avena sativa).

Complementary DNA clones from which infectious RNA can be transcribed were used to map the genetic determinants for oat (Avena sativa L.) pathogenicity of barley stripe mosaic virus (BSMV). Pseudorecombinant analysis of BSMV strains ND18 (nonpathogenic to oat) and CV42 (pathogenic to oat) indicated that the ability to systemically infect oat mapped to RNA alpha. A homologous recombinant of ND18 (18 alpha TKTKIN), possessing nucleotides 2218 to 2454 from CV42 RNA alpha, induced symptoms on oat similar to those generated by wild-type CV42. Six amino acids encoded by the alpha a gene differ between ND18 (PQSQTK) and CV42 (TKTKIN) in this region. Fine structure recombinants that encoded subsets of the six amino acid changes either were slow in their infection phenotype (18 alpha TKTK and 18 alpha TQSQIN) relative to recombinant 18 alpha TKTKIN or were not infectious (18 alpha KTKIN and 18 alpha KTK) to inoculated oat plants. Neither coat protein antigen nor viral RNA was detected in inoculated plants that did not display symptoms. All recombinants infected isolated oat protoplasts, however, as determined by Northern and Western blots of extracts from inoculated oat protoplasts. The accumulation of viral genomic RNAs in protoplasts among the recombinants tested was similar, except for that of recombinant 18 alpha TKTK which was reduced by 30%. The data support an earlier suggestion (Y. Zheng, and M. C. Edwards, 1990, J. Gen. Virol. 71, 1865-1868) that resistance of oat to BSMV strain ND18 is due to restricted virus movement in planta and provide evidence that the alpha a protein itself may be involved in the movement of BSMV in the infected plant.

Amino Acid Sequence↗

PubMed1997

Identification of sites that act together to direct dimerization of human foamy virus RNA in vitro.

Retroviral particles contain two molecules of genomic RNA, which are noncovalently linked near their 5' ends in a region called the dimer linkage structure (DLS). By using complementary DNA oligonucleotides and deletion mutants to impair RNA dimerization of the human foamy virus (HFV), three sites, designated SI, SII, and SIII, were found within a 159-nucleotide RNA fragment of HFV that are involved in dimerization in vitro. SI overlaps the primer-binding site; and SII contains the palindromic sequence, UCCCUAGGGA, the disruption of which impairs dimer formation; and SIII extends into the gag gene. The first two sites are highly conserved in the other primate foamy viruses, SFV-1, SFV-3, and SFVcpz, whereas the third appears to be shared only by HFV and SFVcpz. RNA of HFV and SFV-3 could form heterodimers, indicating that both viruses dimerize by similar mechanisms. On testing thermal stability, dimers of the 159-nucleotide fragment dissociated between 40 and 70 degrees, with half of the dimers dissociating at 55 degrees. Since the splice donor site of HFV is located at position 51 of viral RNA, the DLS is part of the genomic RNA exclusively.

Binding Sites↗

PubMed2002

Expression of a full-length hepatitis C virus cDNA up-regulates the expression of CC chemokines MCP-1 and RANTES.

We had previously reported the cloning of the complete genome of an isolate of hepatitis C virus (HCV), HCV-S1, of genotype 1b. We have constructed a full-length complementary DNA (cDNA) clone of HCV-S1 using nine overlapping cDNA clones that encompassed its entire genome. HCV core, E1, E2, NS-3, -4B, -5A, and -5B proteins were detected in 293T cells by immunoblot analyses when expression of the full-length HCV-S1 was driven under a CMV promoter. Expression of full-length HCV-S1 led to induction of the CC chemokines RANTES and MCP-1 at both the mRNA and the protein levels in HeLa, Huh7, and HepG2 cells. Reporter gene assays showed that a minimal MCP-1 promoter construct containing 128 nucleotides upstream of its translational start site was sufficient for optimal HCV-mediated activation. HCV induced AP-1 binding activities to this region, as determined from electrophoretic mobility shift assays and supershifts with anti-AP-1 antibodies. Transfection of full-length HCV-S1 up-regulated both AP-1 binding activities as well as c-jun transcripts. A minimal promoter construct containing 181 nucleotides upstream of the RANTES translational start site was sufficient for maximal HCV-mediated induction. Gel mobility shift and supershift assays showed that HCV induced NF-kappaB and other unknown binding activities to the A/B-site within this region. In HeLa cells, HCV core and NS5A could separately augment promoter activities of both MCP-1 and RANTES. In Huh7 cells, only NS5A produced a similar effect, while rather surprisingly, HCV core induced a dramatic reduction in promoter activities of these two genes. This study provides the first direct evidence for the induction of CC chemokines in HCV infection and draws attention to their roles in affecting the progress and outcome of HCV-associated liver diseases.

Chemokine CCL2↗

PubMed2025

RNA Sequencing Protocols for Short-Read Sequencing.

RNA sequencing (RNA-seq) methodologies allow the discovery of novel variants and transcripts. These comprise three general steps: (1) capture of RNA species of interest, (2) conversion of RNA to complementary DNA (cDNA), and (3) modification of cDNA to fit the sequencing platform. Here we describe four different library preparation protocols for short-read sequencing: cDNA synthesis with poly(A) selection, library preparation with ribosomal depletion, and cDNA synthesis with SMART® (Switching Mechanism at 5' end of RNA Template) technology for low and Pico inputs.

Gene Library↗

PubMed1995

Increased transcript levels of a methionine synthase during adhesion-induced activation of Chlamydomonas reinhardtii gametes.

Chlamydomonas gametes of opposite mating types interact through flagellar adhesion molecules called agglutinins leading to a signal transduction cascade that induces cell wall loss and activation of mating structures along with other cellular responses that ultimately result in zygote formation. To identify molecules involved in these complex cellular events, we have employed subtractive and differential hybridization with cDNA from mt+ gametes activated for fertilization and non-signaling, vegetative (non-gametic) cells. We identified 55 cDNA clones whose transcripts were regulated in activated gametes. Here we report the molecular cloning and characterization of the complementary DNA (cDNA) for one clone whose transcripts in activated gametes were several-fold higher than in normal gametes. Regulation of the transcript was not related simply to protein synthesis because it was not increased in cells synthesizing new cell wall proteins. The cDNA contained a single open reading frame (ORF) of 815 amino acids encoding a polypeptide of calculated relative mass of 87 kDa. Database search analysis and sequence alignment indicated that the deduced amino acid sequence exhibited 42% identity and 62% similarity to a class of prokaryotic methyl transferases (5-methyltetrahydrofolate-homocysteine methyl transferase; EC 2.1.1.14) known to be involved in the terminal step of de novo biosynthesis of methionine. This enzyme catalyzes transfer of a methyl group from 5-methyltetrahydrofolate to homocysteine resulting in methionine formation. Affinity-purified polyclonal antibodies raised against a bacterially produced GST-fusion protein identified a 85 kDa soluble protein in Chlamydomonas gametes. Southern blot hybridization indicated that the enzyme is encoded by a single-copy gene. The evidence presented in this paper raises the possibility that, in addition to its participation in de novo biosynthesis and regeneration of methionine, Chlamydomonas methionine synthase may play a role in adhesion-induced events during fertilization.

5-Methyltetrahydrofolate-Homocysteine S-Methyltran↗

PubMed1995

Cold stability of pyruvate, orthophosphate dikinase of Flaveria brownii.

The nucleotide sequences of the complementary DNA of pyruvate, Pi dikinase (PPDK) from Flaveria bidentis, a C4 plant which possesses a cold-sensitive form of PPDK, and Flaveria brownii, a 'C4-like' plant which possesses a cold-tolerant form of PPDK, were determined. PPDK was isolated from the leaves of both Flaveria species and purified and the N-terminal amino acid sequences characterised. Together with a maize PPDK cDNA, cDNA inserts which code for the mature form of PPDK of F. bidentis and of F. brownii were expressed in bacteria and the cold sensitivity of the expressed PPDK studied. The cold sensitivity of the PPDK expressed in bacteria mimics the cold sensitivity of PPDK found in vivo in all three plant species. This study indicates that the cold sensitivity of plant PPDK is controlled by the primary structure of the enzyme.

Amino Acid Sequence↗

PubMed1995

Sodium channel functioning based on an octagonal structure model.

The complete amino acid sequence of a sodium channel from squid Loligo bleekeri has been deduced by cloning and sequence analysis of the complementary DNA. A unique feature of the squid sodium channel is the 1,522 residue sequence, approximately three-fourths of those of the rat sodium channels I, II and III. On the basis of the sequence, and in comparison with those of vertebrate sodium channels, we have proposed a tertiary structure model of the sodium channel where the transmembrane segments are octagonally aligned and the four linkers of S5-6 between segments S5 and S6 play a crucial role in the activation gate, voltage sensor and ion selective pore, which can slide, depending on membrane potentials, along inner walls consisting of alternating segments S2 and S4. The proposed octagonal structure model is contrasted with that of Noda et al. (Nature 320; 188-192, 1986). The octagonal structure model can explain the gating of activation and inactivation, and ion selectivity, as well as the action mechanism of both tetrodotoxin (TTX) and alpha-scorpion toxin (ScTX), and can be applied not only to the sodium channel, but also to the calcium channel, potassium channel and cGMP-gated channel.

Amino Acid Sequence↗

PubMed1994

Cloning and expression of the A2a adenosine receptor from guinea pig brain.

A full-length complementary DNA (cDNA) clone encoding the guinea pig brain A2 adenosine receptor has been isolated by polymerase chain reaction (PCR) and low-stringency-hybridization screening of a guinea pig brain cDNA library. This cDNA contains a long open reading frame encoding a 409-amino acid-residue protein which is highly homologous to the A2 adenosine receptors previously cloned from other species. Hydrophobicity analysis of the deduced protein sequence reveals seven hydrophobic regions, characteristic of a member of the G-protein-coupled receptor superfamily. Radioligand binding assay and functional (GTPase and cAMP) assays of the receptor, transiently expressed in mammalian cells, demonstrate typical characteristics of the A2 type adenosine receptor. The messenger RNA (mRNA) of this A2 receptor is found in the brain, heart, kidney and spleen. Receptor autoradiography with [3H]CGS21680, a specific A2 agonist, and in situ hybridization with A2 cRNA probe in guinea pig brain indicate that the receptor is expressed exclusively in the caudate nucleus. The pharmacological profile and anatomical distribution of this receptor indicate that it is of the A2a subtype. This work represents the first cloning of an A2a receptor in a rodent species, offers a complete pharmacological characterization of the receptor and provides an anatomical comparison between binding profile and gene expression of the receptor.

Amino Acid Sequence↗

PubMed1994

The complete nucleotide sequences of the coat protein cistron and the 3' non-coding region of a newly-identified potyvirus infecting sweetpotato, as compared to those of sweetpotato feathery mottle virus.

Complementary DNA representing 728 nucleotides of the 3' end of the genomic RNA of sweetpotato virus G (SPV-G) a newly-identified potyvirus infecting sweetpotato, was cloned and sequenced. This sequence was combined with that previously determined for the 5' terminal part of the coat protein cistron of the virus. The whole sequence contained a single open reading frame (ORF) of 1065 nucleotide, with the capacity to encode a coat protein of 355 amino acids, significantly larger than that of other potyviruses. The ORF was followed by an untranslated region of 222 nucleotides and a poly (A) tail. The coat protein of SPV-G was only distantly related to that of known potyviruses, with the exception of sweetpotato feathery mottle virus (SPFMV). Indeed, sequence identity in the C-terminal three quarters of the coat protein (more than 80%) and in the 3' untranslated region (more than 70%) indicate that SPV-G should be considered as closely related to, though distinct from SPFMV. This subset relationship is similar to that previously reported for members of the bean yellow mosaic virus subgroup or the bean common mosaic virus subgroup.

Amino Acid Sequence↗

PubMed1996

Molecular evidence that the whitefly-transmitted sweetpotato mild mottle virus belongs to a distinct genus of the Potyviridae.

Complementary DNA representing 2 108 nucleotides at the 3' end of the genomic RNA of the whitefly-transmitted sweetpotato mild mottle virus (SPMMV) was cloned after PCR. Sequence analysis revealed an open reading frame of 1 797 nucleotides which codes for a protein of 599 amino acids, followed by a 3' non-coding region of 311 nucleotides. Alignment of the deduced amino acid sequence with corresponding sequences of other members of the Potyviridae demonstrated that part of the presumptive RNA-dependent RNA polymerase and the coat protein coding regions of SPMMV are found at the 3' end of its genome, in that order. Alignment of the amino acid sequence of the core of SPMMV coat protein with those of selected members of the Potyviridae showed limited identity, thus demonstrating--with phylogenetic analysis--that SPMMV belongs to a distinct genus of the family Potyviridae.

Amino Acid Sequence↗