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PubMed2004

cDNA cloning, genomic structure, chromosomal mapping, and expression analysis of parotid secretory protein in pig.

A novel cDNA has been isolated from pig parotid glands by 3' and 5' rapid amplification of cDNA ends and designated parotid secretory protein (PSP). The open reading frame of this cDNA covers 714 bases, encoding 238 amino acids, which show 56% identity with human PSP at the level of the primary protein structure. The PSP genomic sequence comprises eight exons and seven introns, is approximately 22 kb in size, determined by sequencing, and maps to pig chromosome 17q21-q23. RT-PCR, dot blot, and Northern blot analyses demonstrated that PSP is strongly expressed in parotid glands, but is not present in heart, liver, lung, kidney, muscle, or stomach. A search for functionally significant protein motifs revealed consensus sequences for casein kinase II phosphorylation and N-myristoylation. We observed a unique amino acid sequence pattern consisting of the residues Leu-X(6)-Leu-X(6)-Leu-X(7)-Leu-X(6)-Leu-X(6)-Leu near the amino-terminal portion of the protein, which is similar to the leucine zipper.

Amino Acid Sequence↗
PubMed1999

The human CILP gene: exon/intron organization and chromosomal mapping.

The human cDNA for cartilage intermediate layer protein (CILP) codes for a larger precursor protein that consists of CILP and a homologue to porcine Nucleotide pyrophosphohydrolase (NTPPHase) [Lorenzo et al. 1998a. J. Biol. Chem. 273, 23469-23475]. The human gene has now been isolated and characterized. Southern blot analysis indicated a single copy of the CILP gene in the human genome. The gene spans approximately 15.3 kbp of genomic DNA, and is organized in nine exons. The 5' flanking region contains a putative promoter region with a TATA-like box localized from -29 to -23 bp upstream of the transcription start site. Analysis of the putative promoter region revealed potentially cis-regulatory eukaryotic elements such as GATA-1, MyoD, MZF1, and CdxA. The protein coding region begins in exon 2 with the putative signal peptide. CILP is encoded from exon 3 to exon 9. In addition, exon 9 also codes for the entire NTPPHase homologue and contains the 3' untranslated region of the gene. All the introns follow the 'gt-ag' rule, except the last intron, intron 8, that belongs to the minor class of pre-mRNA introns that contain 'at-ac' at their 5' and 3' ends, respectively. The CILP gene was mapped to human chromosome 15q22.

Base Sequence↗
PubMed1993

cDNA cloning, chromosomal mapping, and functional characterization of the human peroxisome proliferator activated receptor.

The human peroxisome proliferator activated receptor (hPPAR) was cloned from a human liver cDNA library. The cDNA exhibited 85% and 91% DNA and deduced amino acid sequence identity with mouse PPAR (mPPAR), respectively. The hPPAR gene was mapped on human chromosome 22 slightly telomeric to a linkage group of six genes and genetic markers that are located in the general region 22q12-q13.1. Cotransfection assays of mouse Hepa 1 cells were used to roughly compare the ability of hPPAR- and mPPAR-expressed cDNAs to trans-activate the acyl CoA oxidase (ACO) PPAR response element located 5' upstream to the minimal thymidine kinase promoter driving the expression of the chloramphenicol acetyl transferase (CAT) reporter gene. Both receptors elicited a response with the prototypical peroxisome proliferators nafenopin, clofibrate, and WY-14,643. Moreover, using cotransfection assays in which the CAT reporter plasmid contained the CYP4 A6 gene response element rather than the ACO element, it was shown that hPPAR is capable of very efficiently trans-activating a second PPAR response element. These results indicate that the PPAR is present in humans in a form that is functional and can trans-activate response elements derived from two different genes, the rat ACO and the rabbit CYP4A6.

Acyl-CoA Oxidase↗
PubMed1986

Human prion protein cDNA: molecular cloning, chromosomal mapping, and biological implications.

A human complementary DNA whose protein product is considered to be the major component of scrapie-associated fibrils in Creutzfeldt-Jakob disease, kuru, and Gerstmann-Straussler syndrome has been identified and characterized. The extensive homology of this gene sequence to the hamster PrP 27- to 30-kilodalton prion protein complementary DNA clone, and its existence as a single copy in the human genome, leads to the conclusion that this is the human prion gene. This human prion gene has been mapped to human chromosome 20, negating a direct link between the prion protein and Down's syndrome or the amyloid of Alzheimer's disease.

Amino Acid Sequence↗
PubMed1999

cDNA cloning, characterization, and chromosome mapping of UBE2E3 (alias UbcH9), encoding an N-terminally extended human ubiquitin-conjugating enzyme.

A cDNA encoding a third member of human class III ubiquitin-conjugating enzymes (E2s), UBE2E3, was cloned from a human gastric adenocarcinoma cDNA library. The deduced 207-amino acid protein shares over 94% amino acid identity with the UBC domains of class III E2s, UbcH6, UBE2E2, UbcM2, UbcM3, and UbcD2. But the N-terminal extension exhibited little homology among these, except for UbcM2, which showed 100% identity, and which is thought to be a mouse counterpart. Northern hybridization analysis exhibited a strong 1.9-kb band of UBE2E3 in skeletal muscle. Recombinant fusion protein of GST-UBE2E3 was found to form a thioester bond with ubiquitin (Ub) in an E1-dependent manner, demonstrating that the cDNA encodes a functional E2. In addition, a UBE2E3 mutant of cysteine-145 to serine failed in UBE2E3-Ub complex formation, indicating that the cysteine is essential for E2 function. Using FISH and PCR analysis of radiation hybrid and somatic cell hybrid panels the UBE2E3 gene was mapped to human chromosome 2q32.1 and showed strong linkage to SHGC-8506 (LOD = 11.52) between D2S1302 and D2S364.

Amino Acid Sequence↗
PubMed1997

cDNA cloning, expression and chromosome mapping of the human STAT4 gene: both STAT4 and STAT1 genes are mapped to 2q32.2-->q32.3.

Studies of transcriptional activation by interferons and a variety of cytokines have led to the identification of a family of proteins that serve as signal transducers and activators of transcription (STAT). STAT4 is phosphorylated following interleukin (IL)-12 stimulation and is essential for IL-12 signal transduction. The human STAT4 cDNA was cloned, and both STAT4 and STAT1 genes were mapped to human chromosome bands 2q32.2-->q32.3 by fluorescence in situ hybridization. These results suggest that STAT4 and STAT1 may have arisen via a tandem gene duplication. However, human STAT1 is expressed ubiquitously, whereas human STAT4 is expressed in several tissues including spleen, heart, brain, peripheral blood cells, and testis.

Base Sequence↗
PubMed1983

[Use of transformation for the chromosome mapping of Pseudomonas pseudomallei].

The mapping of the chromosome sections in P. pseudomallei, responsible for the synthesis of histidine, has been carried out with the use of two- and three-factor crossing. Two new groups of marker linkage have been found: his 522 with ilv 658 and his 37 with asp 37 glu 37. The linkage of some of the existing histidine mutations with locus his 37 has been revealed and the relative position of the markers in this linkage group has been shown.

Chromosome Mapping↗
PubMed1994

Cloning and chromosomal mapping of the human nonfunctional gene for L-gulono-gamma-lactone oxidase, the enzyme for L-ascorbic acid biosynthesis missing in man.

Man is among the exceptional higher animals that are unable to synthesize L-ascorbic acid because of their deficiency in L-gulono-gamma-lactone oxidase, the enzyme catalyzing the terminal step in L-ascorbic acid biosynthesis. In the present study, we isolated a segment of the nonfunctional L-gulono-gamma-lactone oxidase gene from a human genomic library, and mapped it on chromosome 8p21.1 by spot blot hybridization using flow-sorted human chromosomes and fluorescence in situ hybridization. Sequencing analysis indicated that the isolated segment represented a 3'-part of the gene, where the regions corresponding to exons VII, IX, X, and XII of the rat L-gulono-gamma-lactone oxidase gene remain with probable deletion of the regions corresponding to exons VIII and XI. In the identified exon regions were found various anomalous nucleotide changes, such as deletion and insertion of nucleotide(s) and nonconformance to the GT/AG rule at intron/exon boundaries. When the conceptual amino acid sequences deduced from the four exon sequences were compared with the corresponding rat sequences, there were a large number of nonconservative substitutions and also two stop codons. These findings indicate that the human nonfunctional L-gulono-gamma-lactone oxidase gene has accumulated a large number of mutations without selective pressure since it ceased to function during evolution.

Amino Acid Sequence↗
PubMed2000

Gene structure and chromosomal mapping of human epithelial calcium channel.

The epithelial Ca(2+) channel, ECaC, represents the rate-limiting step of vitamin D(3)-regulated Ca(2+) (re)absorption in kidney and intestine, and provides, therefore, a new candidate gene for Ca(2+)-related disorders. To supply the basis for direct mutation analysis, we report here the structure of the human ECaC gene (ECAC1(2)). It consists of 16 exons spanning 25 kb with introns ranging from 98 to 8500 bp. The 5'-flanking region of ECAC1 contains four putative vitamin D(3)-responsive elements. At positions -92 and -13 transcription initiation sites were identified, but the former lacks the canonical TATA or CAAT boxes. ECAC1 was mapped to chromosome 7q35 by fluorescent in situ hybridization, reassigning a previous radiation hybrid mapping to 7q31.1-2. The gene of a recently identified rat intestine homologue of ECaC, named Ca(2+) transporter 1, was found juxtaposed to the ECaC gene, indicating that both genes are the products of evolutionary local gene duplication.

Amino Acid Sequence↗
PubMed2007

Chromosome maps of legumes.

Legumes are of immense importance as food and feed, and for sustainable agriculture, due to their ability to fix nitrogen. Here, the chromosome maps of the legumes soybean (Glycine max), Lotus (Lotus japonicus), and red clover (Trifolium pratense) are reviewed. These species have relatively small chromosomes and therefore are difficult to exploit for chromosome studies. Nevertheless, the identification of individual chromosomes became feasible, and chromosome maps have been developed applying image analysis and fluorescence in-situ hybridization. For Lotus japonicus, e.g. detailed chromosome maps have been developed using the information of genetic linkage maps. Future prospects of further legume chromosome mapping for breeding and genetic purposes are discussed.

Chromosome Mapping↗
PubMed1999

Molecular cloning, chromosome mapping and characterization of the mouse CRTH2 gene, a putative member of the leukocyte chemoattractant receptor family.

We have cloned the mouse CRTH2 (chemoattractant receptor-homologous molecule expressed on TH2 cells) gene encoding a putative leukocyte chemoattractant receptor, of which human homologue is expressed selectively in Th2 but not in Th1 clones among T cell clones. The deduced amino-acid sequence of mouse CRTH2 bears 77% identity with its human homologue. Phylogenetic analysis suggested that both mouse and human CRTH2 are closely related to the N-formyl peptide receptor and the C5a receptor among leukocyte chemoattractant receptors. The mouse CRTH2 gene was mapped on chromosome 19c with FISH, where no other genes for leukocyte chemoattractant receptors are mapped. RT-PCR analysis revealed that mouse CRTH2 mRNA is expressed in various cell lineages, including both hematopoietic and non-hematopoietic cell lines. Expression was also observed in liver, lung, kidney, brain, heart, thymus, and spleen. These results suggest that mouse CRTH2 functions in a variety of cells, making the effects of CRTH2 pleiotropic.

Amino Acid Sequence↗
PubMed2000

Comparative chromosome map of the laboratory mouse and Chinese hamster defined by reciprocal chromosome painting.

Cross-species reciprocal chromosome painting was used to determine homologous chromosomal regions between the laboratory mouse and Chinese hamster. When mouse chromosome-specific paints were hybridized to Chinese hamster chromosomes, paints specific for mouse chromosomes 3, 4, 9, 14, 18, 19 and X each painted a single chromosomal region, whilst other mouse paints delineated multiple discrete chromosomal regions. The mouse Y paint produced non-specific signals on Chinese hamster chromosomes. Nineteen mouse autosome paints identified a total of 47 homologous chromosome regions in the genome of the Chinese hamster. Hybridization of Chinese hamster paints to mouse chromosomes not only confirmed the above results, but also identified which of the chromosomal regions of these two species were homologous. In total, 10 Chinese hamster autosomal paints detected 38 homologous autosomal segments in the mouse genome. A comparative chromosome map was established based on these reciprocal chromosome painting patterns. This map forms the basis for exchanging gene mapping information between the species and for studying genome evolution.

Animals↗
PubMed2003

Molecular cloning, genomic organization, chromosomal mapping and subcellular localization of mouse PAP7: a PBR and PKA-RIalpha associated protein.

A mouse protein that interacts with the peripheral-type benzodiazepine receptor (PBR) and the cAMP-dependent protein kinase A (PKA) regulatory subunit RIalpha (PKA-RIalpha), named PBR and PKA associated protein 7 (PAP7) was identified and shown to be involved in hormone-induced steroid biosynthesis in testicular Leydig cells. In the present study, mouse PAP7 cDNA was extended by 5'-rapid amplification of cDNA ends; and a 3432 bp sequence, encoding a 525-amino-acid protein with a calculated molecular weight of 60 kDa, was re-assembled. Mouse and human PAP7 share an 85% amino acid identity and contain a conserved acyl-CoA-binding protein/diazepam binding inhibitor (ACBP/DBI) motif. ACBP/DBI has been identified as the endogenous PBR ligand able to stimulate mitochondrial steroid formation in all steroidogenic cells. The full-length mouse PAP7 gene was cloned and assembled by screening a BAC clone, polymerase chain reaction and searching the mouse genome database. The gene is approximately 29 kb in length and includes eight exons and seven introns. Although it is shorter than the human PAP7 gene, all exons are conserved between the mouse and human. The mouse PAP7 gene was mapped to chromosome 1H3-5 by fluorescence in situ hybridization in agreement with in silico search of the mouse genome database that mapped the PAP7 cDNA sequence to the 1H4 area. Immunofluorescence confocal microscopy demonstrated that PAP7 is mainly localized in the trans-Golgi apparatus and mitochondria in mouse tumor Leydig cells, in agreement with its proposed function in targeting the PKA isoenzyme to organelles rich in PBR, i.e. mitochondria, where phosphorylation of specific protein substrates mediates the hormone-induced steroid formation.

Adaptor Proteins, Signal Transducing↗
PubMed2000

Identification, chromosomal mapping, and partial characterization of mouse InsI6: a new member of the insulin family.

A new member of the mouse insulin family, InsI6, was identified from mouse expressed sequence tags through the use of bioinformatics. A full length cDNA was sequenced and predicts a protein of 191 amino acids. The protein contains a signal peptide and has A and B peptides as well as a connecting peptide consistent with the contention that it is a member of the insulin family. Northern analysis demonstrates that the primary site of expression is the testis, but message is also found in the kidney, small bowel, heart, brain and thymus. The gene was mapped to mouse chromosome 19 by radiation hybrid mapping. The chromosomal location and primary structure of this protein suggest a functional relationship to relaxin and relaxin-related proteins.

Amino Acid Sequence↗
PubMed1999

Characterization and chromosomal mapping of a mouse ortholog of the late-infantile ceroid-lipofuscinosis gene CLN2.

Late-infantile ceroid-lipofuscinosis (CLN2) is an autosomal recessively inherited, neurodegenerative disease in humans. The CLN2 locus has been mapped to Chromosome (Chr) 11p15, and its sequence and genomic organization have recently been reported. In the present study, the cDNA sequence, exon/intron organization, and chromosomal localization of a mouse ortholog of the CLN2 gene are described. The mouse cDNA contains an open reading frame that predicts a protein product of 562 amino acids. The mouse and human coding regions are 86% and 88% identical at the nucleic acid and amino acid levels, respectively. One less codon appears in the mouse cDNA when compared with the human ortholog. The mouse gene (Cln2) spans more than 6 kb and consists of 13 exons separated by introns ranging in size from 111 to 1259 bp. Length polymorphism in an (AC)(n) microsatellite in intron 3 of the mouse Cln2 gene was used to perform segregation analysis with The Jackson Laboratory DNA Panel Mapping Resource. On the basis of this analysis, the Cln2 gene was localized to a region of mouse Chr 7 that corresponds to human Chr 11p15. Characterization of the mouse Cln2 gene will facilitate generation of a mouse model for late-infantile ceroid-lipofuscinosis by gene targeting and identification of functionally important regions of the Cln2 protein.

Amino Acid Sequence↗
PubMed2002

Integration of common bean ( Phaseolus vulgaris L.) linkage and chromosomal maps.

Fluorescent in situ hybridisation of pooled, closely linked RFLP markers was used to integrate the genetic linkage map and the mitotic chromosome map of the common bean. Pooled RFLP probes showed clear and reproducible signals and allowed the assignment of all linkage groups to the chromosomes of two Phaseolus vulgaris cultivars, Saxa and Calima. Low extension values for signals originating from clustered RFLPs suggest that these clones are physically close to each other and that clusters in the genetic map are not a result of suppression of recombination due to the occurrence of chromosome rearrangements. For linkage group K, clustering of markers could be associated with proximity to centromeres. High variation in the number of 45S rDNA loci was observed among cultivars, suggesting that these terminal sites are highly recombinogenic in common bean.

DNA, Ribosomal↗