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PubMed1998

Cloning and expression of cDNA for a human Sia alpha 2,3Gal beta 1, 4GlcNA:alpha 2,8-sialyltransferase (hST8Sia III).

The cDNA encoding human Sia-alpha2,3-Gal-beta1,4-GlcNAc-R:alpha2, 8-sialyltransferase, hST8Sia III, was isolated by screening of a human brain cDNA library with polymerase chain reaction-amplified DNA probe generated from the sequence of mouse ST8Sia III (mST8Sia III) and by 5' rapid amplification of cDNA ends of mRNA isolated from human brain tissues. Comparative analysis of the predicted protein-coding region between our cloned hST8Sia III and mST8Sia III showed 92 and 96% identities in the nucleotide and the amino acid sequence, respectively. The soluble hST8Sia III protein expressed in COS-7 showed an extremely high catalytic activity of transferring sialic acid through alpha2,8-linkage to intact fetuin glycoprotein, whereas the transferring activity was completely undetectable toward either alpha2,6-sialylated glycoprotein or desialylated glycoprotein acceptors. Northern analysis of hST8Sia III showed that the transcript corresponding to 11 kb was expressed in both human fetal and adult brain, while the expression of the 5.5-kb transcript was restricted to fetal liver, indicating that the expression of hST8Sia III is developmentally and tissue-specifically regulated.

Amino Acid Sequence↗

PubMed1998

Genetic alterations in the retinoblastoma protein-related p107 gene in human hematologic malignancies.

Genetic alterations in the p107 gene, a close relative of the retinoblastoma tumor suppressor gene, have never been identified in human malignancies. When we searched for such alterations in human hematologic malignancies by Southern blot analysis, 2 of 21 cell lines and 1 of 88 primary disorders had genomic alterations within the gene. Particularly, an altered p107 gene in a diffuse-large B-cell lymphoma cell line, KAL-1, harbored an intragenic deletion of about 15 kbp leading to the expression of an altered p107 mRNA devoid of 819 nucleotides of the coding sequences, which predicts to encode an approximately 87-kDa protein. This cell line was found to express solely a p107 derivative of 84 kDa by immunoblotting analysis. These results suggest that alterations in the p107 gene are probably related to a limited subset of human hematologic malignancies.

Gene Deletion↗

PubMed2000

Molecular cloning and genomic structure of human frizzled-3 at chromosome 8p21.

WNT receptors encoded by the Frizzled genes are implicated in carcinogenesis as well as in embryonic development. Human Frizzled-3 (FZD3) gene, encoding seven-transmembrane receptor with the N-terminal cysteine-rich domain, has been cloned and characterized. Expression of the FZD3 mRNAs was investigated by using three FZD3 specific probes: HF3S1, corresponding to the 5'-UTR and a part of the coding region; HF3S2, corresponding to a part of the coding region; HF3S3, corresponding to the 3'-UTR. HF3S1 and HF3S2 hybridized to the 14.0-, 9.0-, 4.0- and 1.8-kb FZD3 mRNA, while HF3S3 hybridized to the 14.0-, 9.0-, and 4.0-kb FZD3 mRNA. The 14. 0-kb FZD3 mRNA was the major transcript in fetal brain and adult cerebellum, while the 1.8-kb FZD3 mRNA was the major transcript in adult pancreas, and many cancer cell lines examined. The 1.8-kb FZD3 mRNA, alternatively polyadenylated by the internal AATAAA signal in the coding region, is predicted to encode the truncated FZD3 protein lacking the region through the second extracellular loop to the C-terminal tail, and might function as the transmembrane-type antagonist for WNTs. The FZD3 gene consists of 8 exons, and has been mapped to human chromosome 8p21.

Adenosine Monophosphate↗

PubMed2001

Identification and characterization of a novel human testis-specific kinase substrate gene which is downregulated in testicular tumors.

By using the positional candidate gene approach, we identified a novel putative serine/threonine kinase substrate gene that maps to chromosome 19q13.3. Screening of expressed sequence tags and reverse transcription-polymerase chain reaction of total RNA from human tissues allowed us to establish the expression of the gene and delineate its genomic organization (GenBank Accession No. AF200923). This gene (TSKS, for testis-specific kinase substrate) is composed of 11 exons and 10 intervening introns and is likely the human homolog of the mouse testis-specific serine kinase substrate gene. The predicted protein-coding region of the gene is 1779 bp, encoding for a 592-amino-acid polypeptide with a calculated molecular mass of 65.1 kDa. Genomic analysis of the region 19q13.3 placed the TSKS gene close to the known genes IRF3, RRAS, and alpha-Adaptin A. TSKS exhibits high levels of expression exclusively in human testicular tissue. The expression of TSKS is downregulated in cancerous testicular tissue, in comparison to adjacent normal tissue. TSKS expression was very low or undetectable in seminoma, teratocarcinoma, embryonal, and Leydig cell tumors, while high expression was observed in testicular tissue adjacent to tumors which contain premalignant carcinoma in situ. The expression of the TSKS gene was very low in two human embryonal carcinoma cell lines, 2102Ep and NTERA-2. These observations suggest a role of TSKS in testicular physiology, most probably in the process of spermatogenesis or spermiogenesis.

Amino Acid Sequence↗

PubMed1998

Induction of relational schemas: common processes in reasoning and complex learning.

Five experiments were performed to test whether participants induced a coherent representation of the structure of a task, called a relational schema, from specific instances. Properties of a relational schema include: An explicit symbol for a relation, a binding that preserves the truth of a relation, potential for higher-order relations, omnidirectional access, potential for transfer between isomorphs, and ability to predict unseen items in isomorphic problems. However relational schemas are not necessarily coded in abstract form. Predictions from relational schema theory were contrasted with predictions from configural learning and other nonstructural theories in five experiments in which participants were taught a structure comprised of a set of initial-state,operator-->end-state instances. The initial-state,operator pairs were presented and participants had to predict the correct end-state. Induction of a relational schema was achieved efficiently by adult participants as indicated by ability to predict items of a new isomorphic problem. The relational schemas induced showed the omnidirectional access property, there was efficient transfer to isomorphs, and structural coherence had a powerful effect on learning. The "learning to learn" effect traditionally associated with the learning set literature was observed, and the long-standing enigma of learning set acquisition is explained by a model composed of relational schema induction and structure mapping. Performance was better after reversal of operators than after shift to an alternate structure, even though the latter entailed more overlap with previously learned tasks in terms of the number of configural associations that were preserved. An explanation for the reversal shift phenomenon in terms of induction and mapping of a relational schema is proposed. The five experiments provided evidence supporting predictions from relational schema theory, and no evidence was found for configural or nonstructural learning theories.

Adult↗

PubMed1999

A polyketide synthase gene required for biosynthesis of fumonisin mycotoxins in Gibberella fujikuroi mating population A.

Fumonisins are toxins associated with several mycotoxicoses and are produced by the maize pathogen Gibberella fujikuroi mating population A (MP-A). Biochemical analyses indicate that fumonisins are a product of either polyketide or fatty acid biosynthesis. To isolate a putative polyketide synthase (PKS) gene involved in fumonisin biosynthesis, we employed PCR with degenerate PKS primers and a cDNA template prepared from a fumonisin-producing culture of G. fujikuroi. Sequence analysis of the single PCR product and its flanking DNA revealed a gene (FUM5) with a 7.8-kb coding region. The predicted FUM5 translation product was highly similar to bacterial and fungal Type I PKSs. Transformation of a cosmid clone carrying FUM5 into G. fujikuroi enhanced production in three strains and restored wild-type production in a fumonisin nonproducing mutant. Disruption of FUM5 reduced fumonisin production by over 99% in G. fujikuroi MP-A. Together, these results indicate that FUM5 is a PKS gene required for fumonisin biosynthesis.

3-Oxoacyl-(Acyl-Carrier-Protein) Synthase↗

PubMed1994

The mouse insulin-like growth factor II/cation-independent mannose 6-phosphate (IGF-II/MPR) receptor gene: molecular cloning and genomic organization.

The mammalian insulin-like growth factor II/cation-independent mannose 6-phosphate receptor (IGF-II/MPR) is a multifunctional protein that binds both IGF-II and ligands containing a mannose 6-phosphate recognition marker through distinct high-affinity sites. This receptor plays an integral part in lysosomal enzyme transport, has a potential role in growth factor maturation and clearance, and may mediate IGF-II-activated signal transduction through a G-protein-coupled mechanism. Recent studies have shown that production of IGF-II/MPR mRNA and protein begins in the mouse embryo soon after fertilization and have demonstrated that the receptor gene is on mouse chromosome 17 and is maternally imprinted. In this paper, we report the cloning and characterization of the mouse IGF-II/MPR gene. The gene is 93 kb long, is composed of 48 exons, and codes for a predicted protein of 2482 amino acids. The extracellular part of the receptor is encoded by exons 1-46, with each of 15 related repeating motifs being determined by parts of 3-5 exons. A single fibronectin type II-like element is found in exon 39. The transmembrane portion of the receptor also is encoded by exon 46, and the cytoplasmic region by exons 46-48. The positions of exon-intron splice junctions are conserved between several of the repeats in the IGF-II/MPR and the homologous extracellular region of the gene for the other known lysosomal sorting receptor, the cation-dependent mannose 6-phosphate receptor.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗

PubMed1995

Genomic structure, promoter sequence, and induction of expression of the mouse Nramp1 gene in macrophages.

A candidate gene for the mouse chromosome 1 host resistance locus Bcg/Ity/Lsh was recently cloned and designated Nramp (natural resistance-associated macrophage protein). Nramp is part of a small family of at least two genes, Nramp1 and Nramp2. Primer extension and cDNA cloning were used to isolate the complete 5' end of the Nramp1 mRNA. Analysis of genomic cosmid and bacteriophage clones overlapping the complete Nramp1 gene revealed that the gene was composed of 15 exons and spanned 11.5 kb of genomic DNA. Positioning of introns on the coding portion of the mRNA revealed a modular relationship between coding exons and predicted structural domains of the protein, with 8 of the 12 transmembrane (TM) domains encoded by individual exons. Northern blotting analysis indicated that Nramp1 expression was restricted to J774A.1 and RAW 264.7 macrophage lines and was dramatically increased by treatment with interferon-gamma (IFN-gamma) and lipopolysaccharide (LPS). Primer extension and S1 nuclease mapping experiments were used to locate the transcription initiation site of Nramp1 and revealed the presence of one major and several minor initiation sites. Nucleotide sequencing of the corresponding region failed to detect classical TATA and CAAT elements, but identified two putative initiator sequences located near the major initiation site. Consensus sequences for binding of the macrophage and B-cell-specific transcription factor PU.1, as well as several LPS (NF-IL6) and IFN-gamma response elements, were also identified.

Amino Acid Sequence↗

PubMed1997

The NTN2L gene encoding a novel human netrin maps to the autosomal dominant polycystic kidney disease region on chromosome 16p13.3.

The netrins define a family of chemotropic factors that have been shown to play a central role in axon guidance. We identified two exon traps encoding netrin-like sequences during the assembly of a transcriptional map for the genomic interval surrounding the polycystic kidney disease type 1 and tuberous sclerosis type 2 genes. We describe the characterization of a novel human netrin-2-like gene, designated NTN2L, and its transcript. The genomic interval containing the NTN2L gene was sequenced, and the coding region was predicted based on computer analysis. The structure of the NTN2L gene has been confirmed utilizing nested RT-PCR. The NTN2L gene is predicted to encode a 580-amino-acid protein having homology to the chicken and Drosophila netrins and to Caenorhabditis elegans UNC-6. The NTN2L gene has a restricted pattern of expression; its transcript is undetectable by Northern analysis in all tissues examined, but can be recovered from spinal cord RNA by RT-PCR. This report represents the first description and characterization of a human netrin.

Amino Acid Sequence↗

PubMed1998

Nucleotide sequencing analysis of the 146-kilobase segment around the IkBL and MICA genes at the centromeric end of the HLA class I region.

To elucidate the complete gene structure and to identify new genes involved in the development of HLA class I antigen-associated diseases in the class I region of the human major histocompatibility complex on chromosome 6, a YAC clone (745D12) covering the 146-kb segment around the IkBL and MICA loci was isolated from a YAC library constructed from the B-cell line, BOLETH. A physical map of this region was constructed by isolation of overlapping cosmid clones derived from 745D12. Of these, five contiguous cosmids were chosen for DNA sequencing by the shotgun strategy to give a single contig of 146,601 bp from 2.8 kb telomeric of the IkBL gene to exon 6 of MICA. This region was confirmed to contain five known genes, IkBL, BAT1, MICB, P5-1, and HLA-X (class I fragment), from centromere to telomere, and their exon-intron organizations were determined. The 3.8-1 homologue gene (3.8-1-hom) showing 99.7% identity with the 3.8-1 cDNA clone, which was originally isolated using the 3.8-kb EcoRI fragment between the HLA-54/H and the HLA-G genes, was detected between MICA and MICB and was suggested to represent the cognate 3.8-1 genomic sequence from which the cDNA clone was derived. No evidence for the presence of expressed new genes could be obtained in this region by homology and EST searches or coding and exon prediction analyses. One TA microsatellite repeat spanning 2545 bases with as many as 913 repetitions was found on the centromeric side of the MICA gene and was indicated to be a potential hot spot for genetic recombination. The two segments of approximately 35 kb upstream of the MICA and MICB genes showed high sequence homology (about 85%) to each other, suggesting that segmental genome duplication including the MICA and MICB genes must have occurred during the evolution of the human MHC.

Carrier Proteins↗

PubMed2001

The cluster of BTN genes in the extended major histocompatibility complex.

We sequenced the 170-kb cluster of BTN genes in the extended major histocompatibility complex region, 4 Mb telomeric of human leukocyte antigen class I genes, at 6p22.1. The cluster consists of seven genes belonging to the expanding B7/butyrophilin-like group, a subset of the immunoglobulin gene superfamily. The main complex is composed of six genes, from two subfamilies, BTN2 and BTN3, arranged in pairs. This alternating pattern must have evolved by duplications of an original block of two genes, one from each subfamily. The sequences from the two subfamilies share approximately 50% amino acid identity. By analysis of repeat elements within each block, these duplications may be dated to approximately 100 million years ago, at about the time of the branching of the Rodentia and Primate lineages. The single BTN1A1 (butyrophilin) gene was positioned approximately 25 kb centromeric to the cluster. Each gene covers approximately 12 kb and consists of seven (BTN2 subfamily) or nine (BTN3 subfamily) coding exons. The predicted leader sequence, immunoglobulin-like IgV (variable)/IgC (constant) ectodomains, and the predicted transmembrane domain are encoded on separate exons and are separated from a B30.2 domain by a variable number of very short exons, 21 and 27 nucleotides in length. BTN transcripts were detected in all tissues examined. Alternative splicing, involving particularly the carboxyl-terminal B30.2 domain, was a notable feature. Most transcripts of BTN2 subfamily genes contained this domain, whereas BTN3 genes did not. Using immunofluorescence, we showed surface expression of BTN-green fluorescent protein fusions in mammalian cell transfectants.

Alternative Splicing↗

PubMed2000

Heteroclite subgenomic RNAs are produced in porcine reproductive and respiratory syndrome virus infection.

Porcine reproductive and respiratory syndrome virus (PRRSV) was shown to produce atypical subgenomic RNAs that contain open reading frame la nucleotides and are present under a wide variety of culture conditions, including high and low multiplicities of infection, in simian and porcine host cells, and during infection with cell-adapted and wild-type PRIRSV strains. Sequence analysis demonstrated that they are heterogeneous in 5-3' junction sequence and size and may code for different predicted fusion proteins. This is the first report of these novel RNA5 in arteriviruses and we have termed them heteroclite (meaning 'deviating from common forms or rules") subgenomic RNAs. The unique properties of these subgenomic RNAs include (a) apparent association with normal virus infection and stability during serial passage, (b) packaging of heteroclite RNAs into virus-like particles, (c) short, heterogeneous sequences which may mediate the generation of these RNAs, (d) a primary structure which consists of the two genomic termini with one large internal deletion, and (eJ little apparent interference with parental virus replication. These subgenomic RNA5 may be critical to, or a necessary side product of, viral replication. The expression of these novel RNA species support the template-switching model of similarity-assisted RNA recombination. In summary, PRRSV readily undergoes nonhomologous RNA recombination to generate heteroclite sub-genomic RNA5.

3' Untranslated Regions↗

PubMed1990

Systemically wound-responsive genes in poplar trees encode proteins similar to sweet potato sporamins and legume Kunitz trypsin inhibitors.

When the lower leaves of hybrid poplar trees are mechanically wounded, several novel mRNAs accumulate in the unwounded upper leaves (Parsons TJ, Bradshaw HD, Gordon MP: Systemic accumulation of specific mRNAs in response to wounding in poplar trees, Proc Natl Acad Sci USA, in press). A partial cDNA clone corresponding to a transcript from the wound-responsive gene designated win 3 (wound-inducible) has been cloned by differential hybridization to 32P-labelled cDNA from the leaves of wounded trees. Northern blots show a large accumulation of win 3 transcripts in the unwounded leaves of wounded trees. Southern blot analysis of poplar DNA suggests that win 3 is a member of a multigene family. The nucleotide sequences of several win 3 cDNA clones have been determined, indicating that at least three win 3 gene family members are transcribed. A genomic clone of a win 3 gene family member has been isolated and a 1.5 kb Hind III fragment containing the predicted protein-coding and 5' upstream regions has been sequenced. The putative win 3 gene product is similar to the major soluble proteins of sweet potato tubers, sporamin A and sporamin B. Both Win3 and the sporamins share significant amino acid sequence identity with Kunitz-type trypsin inhibitors from legume seeds. The Kunitz family of proteinase inhibitors thus joints three other proteinase inhibitor families which are systemically responsive to wounding.

Amino Acid Sequence↗

PubMed1994

Characterization of a tobacco gene encoding a pollen-specific polygalacturonase.

We report here the isolation and characterization of a gene which is specifically expressed during late pollen development in Nicotiana tabacum L. cv. Havana and which exhibits homology to bacterial, fungal and plant polygalacturonases. This gene is ca. 4.3 kb, from the transcription start-site to the 3' polyadenylation-site sequences. It contains three introns of 620, 706 and 1400 bp and encodes a 1.5 kb message that contains an A-rich 5'-untranslated-leader sequence of 81 bases and a variable-length 3'-untranslated sequence of between 180 and 320 bases. Located within intron 3 is a 414 bp sequence which exhibits 79% homology to a sequence within the endochitinase gene; both sequences share the same internal repeat structure and exhibit features consistent with them being defective transposable elements. The predicted protein sequence coded for by Npg1 shows, in addition to a number of highly conserved cysteines, four conserved domains with the bacterial and fungal polygalacturonase genes. The pollen-specific polygalacturonases as a group can be distinguished from the fruit-ripening polygalacturonases by a number of criteria. It is suggested that these differences reflect the functional differences between plant endo- and exo-polygalacturonases. Npg1 is one of a two-member gene family expressed predominantly in the male gametophyte upon first microspore mitosis. From expression studies of promoter::GUS transgenes it is clear that the -744 bp to +74/+85 bp of Npg1 sequence (with respect to the transcription start site) is sufficient to drive the expression of the GUS reporter gene in a manner that reflects the spatial and temporal expression of Npg1 as determined by dot-blot and northern analysis.

Amino Acid Sequence↗

PubMed1996

Cloning and characterization of PO22, a pollen-expressed gene in alfalfa.

Genomic and cDNA clones have been isolated for a new gene (PO22) expressed in mature pollen of alfalfa. PO22 represents a single- or low-copy gene containing 4 introns, 2 transcriptional start sites, and coding for a predicted protein of 340 amino acids with no signal peptide and a coiled coil structure of 39 amino acids near the carboxyl end. The amino acid sequence of PO22 is 38% identical to that of an early nodule-specific gene (ENOD8), also from alfalfa.

Cloning, Molecular↗

PubMed1992

Characterization of a pollen-specific cDNA clone from Nicotiana tabacum expressed during microgametogenesis and germination.

This report describes the isolation and characterization of a cDNA clone representing a gene specifically expressed in pollen. A cDNA library was constructed against mRNA from mature pollen of Nicotiana tabacum. It was screened differentially against cDNA from mRNA of leaf and of pollen. One clone, NTPc303, was further characterized. On northern blot this clone hybridizes to a transcript 2100 nucleotides in length. NTPc303 is abundant in pollen. Expression of the corresponding gene is restricted to pollen, because no other generative or vegetative tissue contains transcripts hybridizing to NTPc303. Expression of NTP303 is evolutionarily conserved: homologous transcripts are present in pollen from various plant species. The first NTP303 transcripts are detectable on northern blot at the early bi-nucleate stage and accumulate until the pollen has reached maturity. During germination and pollen tube growth in vitro new NTP303 transcripts appear. This transcription has been proved by northern blots as well as by pulse labelling experiments. Nucleotide sequence analysis revealed that NTPc303 has an open reading frame coding for a predicted protein of 62 kDa. This protein shares homology to ascorbate oxidase and other members of the blue copper oxidase family. A possible function for this clone during pollen germination is discussed.

Amino Acid Sequence↗

PubMed1986

The nucleotide sequence of the mercuric resistance operons of plasmid R100 and transposon Tn501: further evidence for mer genes which enhance the activity of the mercuric ion detoxification system.

The DNA sequences of the mercuric resistance determinants of plasmid R100 and transposon Tn501 distal to the gene (merA) coding for mercuric reductase have been determined. These 1.4 kilobase (kb) regions show 79% identity in their nucleotide sequence, and in both sequences two common potential coding sequences have been identified. In R100, the end of the homologous sequence is disrupted by an 11.2 kb segment of DNA which encodes the sulfonamide and streptomycin resistance determinants of Tn21. This insert contains terminal inverted repeat sequences and is flanked by a 5 base pair (bp) direct repeat. The first of the common potential coding sequences is likely to be that of the merD gene. Induction experiments and mercury volatilization studies demonstrate an enhancing but non-essential role for these merA-distal coding sequences in mercury resistance and volatilization. The potential coding sequences have predicted codon usages similar to those found in other Tn501 and R100 mer genes.

Amino Acid Sequence↗

PubMed1987

Primary structure of two nonallelic beta-globin chains from DBA/2 mice.

The amino acid sequences of the beta major and beta minor globin chains from DBA/2 mice have been determined. This information is of interest because DBA/2 mice are the strain of origin for most murine erythroleukemia lines. The primary structure of DBA/2 beta globins agrees completely with that predicted from the coding properties of BALB/c beta globin genes. This identity does not support a rapid evolutionary divergence in inbred mouse strains, at least at these loci in these strains.

Amino Acid Sequence↗