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At least 1,387 records · Page 77Linked to original sources
PubMed2002

Association of familial and sporadic rheumatoid arthritis with a single corticotropin-releasing hormone genomic region (8q12.3) haplotype.

OBJECTIVE: Rheumatoid arthritis (RA) is a common disabling autoimmune disease with a complex genetic component. We have previously described linkage of a region of chromosome 8q12.3 with RA and association of the microsatellite marker CRHRA1 with RA in 295 affected sibling-pair families. In the current study we aimed to physically link the RA-associated marker with the corticotropin-releasing hormone (CRH) candidate gene, and to examine the genomic region for additional short tandem repeat (STR) genetic markers in order to clarify the association with RA. METHODS: We examined the association of 2 STR markers with disease in the original 295 multicase families and in a cohort of 131 simplex families to refine our understanding of this genetic region in disease susceptibility in sporadic and familial RA. Genomic library screening and sequencing were used to generate physical sequences in the CRH genomic region. Bioinformatic analysis of the sequence flanking the CRH structural gene was used to screen for additional STRs and other genetic features. Genotyping was carried out using a standard fluorescence approach. Estimations of haplotype frequencies were performed to assess linkage disequilibrium. The transmission disequilibrium test was performed using TRANSMIT. RESULTS: Physical cloning and sequencing analyses identified the genomic region linking the CRHRA1 marker and the CRH structural locus. Moreover, we identified a further STR, CRHRA2, which was in strong linkage disequilibrium with CRHRA1 (P = 4.0 x 10(-14)). A haplotype, CRHRA1*10;CRHRA2*14, was preferentially carried by unaffected parents at a frequency of 8.6% compared with the expected frequency of 3.1%. This haplotype was overtransmitted in the multiply affected families (P = 0.0077) and, similarly, in the simplex families (P = 0.024). Combined analysis of both family cohorts confirmed significant evidence for linkage (P = 4.9 x 10(-4)) and association (P = 5.5 x 10(-3)) for this haplotype with RA. CONCLUSION: In demonstrating significant linkage disequilibrium between these 2 markers, we have refined the disease-associated region to a single haplotype and confirmed the significance of this region in our understanding of the genetics of RA.

Arthritis, Rheumatoid↗
PubMed1994

Cloning of genomic loci and chromosomal localization of the human PCTAIRE-1 and -3 protein kinase genes.

Recent studies on the molecular mechanisms controlling the mammalian cell cycle have disclosed a large family of cdc2-related serine/threonine kinases. Among this gene family, the PCTAIRE protein kinases comprise a distinct subfamily of unknown cellular function. To analyze the genomic structure and chromosomal location of the PCTAIRE-1 and -3 genes, we isolated human cosmid clones for each gene by screening a human genomic library with murine PCTAIRE cDNA probes. Overlapping clones encompassing approximately 60 kb of genomic DNA were obtained for both PCTAIRE-1 and -3. These clones were confirmed to encode authentic PCTAIRE genes by the detection of exon-intron structures and the coincidence of the nucleotide sequence of exons to that of the published human cDNAs. Using these cosmid clones as probes for FISH analyses, the chromosomal loci for PCTAIRE-1 and PCTAIRE-3 were assigned to bands Xp11 and 1q31-q32, respectively.

Animals↗
PubMed2002

Identification and evolutionary analysis of putative cytoplasmic mcpA-like protein in a bacterial strain living in symbiosis with a mycorrhizal fungus.

In this paper we report the identification and characterization of a DNA region containing putative mcpA-like gene coding for a Methyl Accepting Chemotaxis Protein (MCP) and belonging to a Burkholderia endosymbiont of the arbuscular mycorrhizal fungus Gigaspora margarita. A genomic library of total DNA extracted from the fungal spores, representative of the bacterial genome, was used to investigate the prokaryotic genome. PCR experiments with primers designed on the Burkholderia mcpA-like gene and Southern blot analysis demonstrate that they actually belong to the genome of G. margarita endosymbiont. The expression of the mcpA-like gene in the fungal spores was demonstrated by RT-PCR experiments. The detailed comparative analysis of the bacterial MCPs available in databases allowed to draw a possible evolutionary pathway leading to the present-day mcpA genes. Accordingly, the ancestor of the mcpA-like genes was the result of a domain shuffling event involving two ancestral mini-genes encoding a PAS-PAC and a MA domains, respectively, followed by the elongation of the PAS-PAC moiety. The following evolutionary divergence involved not only point mutations, but also larger rearrangements (insertions and deletions) at the 3' end of the gene.

Amino Acid Sequence↗
PubMed1992

Sequence of a novel chicken genomic DNA fragment that hybridizes to the murine Hox-3.1 homeobox.

A chicken genomic library was screened for novel homeobox-like elements. We describe a chicken genomic DNA fragment which hybridizes to the murine Hox-3.1 homeobox. The fragment is a single-copy sequence which seems to be transcribed without spacial or temporal restrictions. The sequence presented here is not representative of anything yet in the databases; however, it contains a very probable open reading frame which would encode a peptide slightly homologous to the Hox-3.1 protein.

Amino Acid Sequence↗
PubMed1994

The adenine phosphoribosyltransferase-encoding gene of Arabidopsis thaliana.

The apt gene, coding for adenine phosphoribosyltransferase (APRT), has been isolated from the plant Arabidopsis thaliana. Data from both Southern analysis and characterization of apt clones isolated from a genomic library is consistent with the occurrence of one apt within the A. thaliana genome. Comparison of the nucleotide sequence of the apt gene with its corresponding cDNA indicates that the gene contains five introns, whereas all other apt isolated to date have fewer introns (four in mammals, two in Drosophila). The locations of the introns within the plant apt coding region are not consistent with the placement of introns in the previously isolated apt of murines, human and Drosophila species. In agreement with its expression pattern in vivo, the upstream region of this plant apt is able to express the beta-glucuronidase-encoding gene (gus) in an apparently constitutive manner in transgenic A. thaliana plants. The apt promoter region is notable for its lack of conventional promoter elements such as TATA, CCAAT or G+C-rich sequence elements.

Adenine Phosphoribosyltransferase↗
PubMed1996

Structure and characterization of the gene encoding a mouse kappa3-related opioid receptor.

A genomic clone comprising the entire cDNA sequence encoding a mouse kappa3-related opioid receptor (KOR-3) was isolated by screening a mouse genomic library with a radiolabeled mouse KOR-3 cDNA probe. Sequence analysis of the genomic clone indicates that the KOR-3 gene contains five exons separated by four introns. The transcription start point (tsp) of KOR-3 was mapped by primer extension analysis of RNAs synthesized either in vivo or in vitro. A TATA-box and several potential regulatory elements, including five GRE sites, four NF-E1 binding sites and one MRE site, are present in the 2 kb of 5'-flanking region. A putative poly(A) signal (AATAAA) is found in the 3'-flanking region.

Amino Acid Sequence↗
PubMed2003

Molecular characterization of a ribosome-associated Hsp70-homologous gene from Rhizopus nigricans.

A ribosome-associated Hsp70-homologous gene (Rnssb-1) was isolated from the genomic library of the filamentous zygomycete fungus Rhizopus nigricans. The nucleotide sequence of a genomic clone encoded the N-terminal part of a protein with high similarity to the yeast SSB ribosome-associated chaperones. The missing 3' end of the gene was obtained by 3' RACE. The Northern blot analysis showed that the Rnssb-1 gene is constitutively expressed and is not induced upon heat shock at 37 degrees C. The primary structure analyses revealed that the coding region of the Rnssb-1 gene is interrupted by at least four introns. Their splicing was not inhibited by exposure of the organism to heat shock as proven by RT-PCR. A Southern blot analysis of R. nigricans genomic DNA confirmed the presence of two additional gene copies of ribosome-associated Hsp70 genes in the fungal genome.

Base Sequence↗
PubMed1997

Isolation and expression of a mouse CB1 cannabinoid receptor gene. Comparison of binding properties with those of native CB1 receptors in mouse brain and N18TG2 neuroblastoma cells.

The predominant animal model in which the pharmacology of cannabinoids is studied is the mouse. Nonetheless, the structure and functional expression of the mouse cannabinoid receptor (CB1) gene have not been reported. We have cloned and expressed the gene for the mouse CB1 receptor and compared its properties with those of native mouse CB1 receptors in brain and N18TG2 neuroblastoma cells. The mouse CB1 gene was isolated from a mouse 129 strain genomic library. Sequence analysis of a 6-kb BamHI fragment of the mouse CB1 genomic clone indicates 95% nucleic acid identity between mouse and rat (99.5% amino acid identity) and 90% nucleic acid identity (97% amino acid identity) between mouse and human. Examination of the 5' untranslated sequence of the mouse CB1 genomic clone revealed a splice junction site approximately 60 bp upstream from the translation start site, indicating the possibility of splice variants of the CB1 receptors. The coding region of the mouse CB1 receptor was stably expressed in 293 cells, and binding by [3H]SR 141716A and [3H]CP-55,940 was determined. The Bmax and Kd values obtained with [3H]SR 141716A (921 +/- 58 fmol/mg and 0.73 +/- 0.13 nM, respectively) were similar to those of native mouse CB1 receptors in brain (Bmax of 1.81 +/- 0.44 pmol/mg, Kd of 0.16 +/- 0.01 nM) and N18TG2 cells (Bmax of 197 +/- 29 fmol/mg, Kd of 0.182 +/- 0.08 nM). The mouse CB1 receptor genomic clone will be a useful tool for studying the function and regulation of the CB1 receptor in mice.

Animals↗
PubMed1997

A phosphate-starvation inducible beta-glucosidase gene (psr3.2) isolated from Arabidopsis thaliana is a member of a distinct subfamily of the BGA family.

We have previously isolated a phosphate starvation-response (psr) cDNA clone, psr3.1, from Brassica nigra which encodes a beta-glucosidase. Southern blots of Arabidopsis thaliana genomic DNA probed with the psr3.1 cDNA indicated that this gene exists as a single locus. A genomic library of A. thaliana was screened at high stringency to isolate the corresponding genomic clone. The resultant clone was coined psr3.2 because of its sequence divergence from isolated psr3.1 cDNA clones. Northern blotting with probes derived from the coding region of the genomic clone showed that this gene is expressed at high levels in P(i)-starved roots and the enhancement occurred within two days of growth in medium lacking P(i). The expression of this gene is repressed by heat shock and anaerobic conditions, and it is not significantly induced by high salinity, or by nitrogen or sulfur deprivation. Sequence analysis of the genomic clone revealed the existence of 13 exons interrupted by 12 AT-rich introns and it possessed a high homology with the B. nigra psr3.1 as well as various other beta-glucosidase genes from other species. Sequence similarity and divergence percentages between the deduced amino acid sequences of the psr3 clones and other beta-glycosidases suggests that they should be included along with two other Brassicaceae genes in a distinct subfamily of the BGA glycosidase gene family. The presence of an endoplasmic reticulum retention signal at the carboxy terminus indicates the likely cellular location of PSR3.2. The possible metabolic and regulatory roles of this enzyme during the P(i)-starvation response are discussed.

Amino Acid Sequence↗
PubMed2003

Cloning and characterization of mouse IL-22 binding protein.

Interleukin-22 (IL-22), a member of IL-10 family, plays some important roles in immune response through activation of the STAT 3 signal transduction pathway. Two types of IL-22-binding receptor have been discovered, a membrane-bound receptor and a soluble receptor, both encoded by different genes. IL-22 may be involved in inflammatory processes specifically regulated by soluble receptors. By screening a mouse genomic library for a human IL-22 binding protein homologue, we identified the mouse genomic clone of IL-22 binding protein. Its coding sequence was verified and isolated by RT-PCR. The gene encodes a protein of 230 amino acids that share 67.1% amino-acid sequence identity with human IL-22 binding protein. We designated this receptor 'mouse IL-22 binding protein' (mIL-22BP). mIL-22BP could be upregulated by LPS stimulation in mouse monocytes. mIL-22BP binds to mouse and human IL-22 and neutralizes STAT3 activation induced by both cytokines in human and rat hepatoma cell lines. Treating B cells with mouse IL-22 induces production of reactive oxygen species, which mIL-22BP blocks.

Amino Acid Sequence↗
PubMed1986

Structure of the human Ia-associated invariant (gamma)-chain gene: identification of 5' sequences shared with major histocompatibility complex class II genes.

The human gene encoding the Ia-associated gamma (or invariant) chain was isolated by screening a genomic library in phage lambda with cDNA probes. The frequency of positive clones in the library, the overlapping restriction maps of the cloned fragments, and the patterns of genomic hybridization suggested that the gamma-chain gene exists as a single copy per haploid genome. The gene consists of 8 exons, spanning approximately 12 kilobases of DNA. All exon sequences were in an open reading frame, contained appropriate splice junction sequences, and encompassed the entire sequence of full-length gamma-chain mRNA, suggesting that the gene we isolated is most likely functional. Furthermore, "CAAT"-type and "TATA"-type promoter sequences were found at the expected positions upstream from the proposed cap site. The organization of the gamma-chain gene has none of the distinctive features of the immunoglobulin superfamily of genes, of which Ia alpha and beta chains are members. Therefore, the evolutionary origins, and perhaps the functions, of the Ia gamma chains are distinct from those of the other two Ia subunits alpha and beta. Despite the unrelatedness of these genes, consensus sequences found approximately 150 base pairs upstream from all the Ia alpha- and beta-chain genes sequenced to date were also found in analogous positions in the gamma-chain gene, suggesting a possible role in the coregulation of expression of these genes.

Base Sequence↗
PubMed1988

Sequences of the bovine and yeast ADP-ribosylation factor and comparison to other GTP-binding proteins.

The ADP-ribosylation factor (ARF) is a 21-kDa GTP-binding protein that serves as the cofactor in the cholera toxin-catalyzed activation of the stimulatory guanine nucleotide-binding protein of adenylate cyclase (Gs). An oligonucleotide probe based on the partial amino acid sequence was used to clone ARF from a bovine adrenal chromaffin cDNA library. The yeast (Saccharomyces cerevisiae) ARF gene was then cloned from a YCp50 genomic library by cross-species hybridization by using the coding region of the bovine gene. RNA gel blots of poly(A)+ RNA indicate that only one ARF message size (900 and 2000 base pairs) is present in yeast and cows, respectively. Comparison of the cDNA-derived amino acid sequences of ARF to other GTP-binding proteins reveals a structural relationship between ARF and the ras family of proteins. A slightly better structural relationship is detected when ARF is compared to the alpha subunits of the trimeric GTP-binding proteins, including Gs alpha. All of the biochemical characteristics of the purified ARF, including the lack of GTPase activity and the posttranslational myristoylation, are consistent with the derived sequences. Comparison of the ARF sequences to that of the chicken processed pseudogene (CPS-1), previously reported as a ras homologue, reveals that CPS-1 is actually an ARF-derived gene. These results demonstrate that ARF is a GTP-binding protein with structural features of both the ras and the trimeric GTP-binding protein families.

ADP-Ribosylation Factors↗
PubMed1995

Cloning and functional expression of a human Y4 subtype receptor for pancreatic polypeptide, neuropeptide Y, and peptide YY.

The pancreatic polypeptide family includes pancreatic polypeptide (PP), neuropeptide Y (NPY), and peptide YY (PYY). Members of the PP family regulate numerous physiological processes, including appetite, gastrointestinal transit, anxiety, and blood pressure. Of the multiple Y-type receptors proposed for PP family members, only the Y1 subtype has been cloned previously. We now report the cloning of an additional Y-type receptor, designated Y4, by homology screening of a human placental genomic library with transmembrane (TM) probes derived from the rat Y1 gene. The Y4 genomic clone encodes a predicted protein of 375 amino acids that is most homologous to Y1 receptors from human, rat, and mouse (42% overall; 55% in TM). 125I-PYY binding to transiently expressed Y4 receptors was saturable (pKd = 9.89) and displaceable by human PP family derivatives: PP (pKi = 10.25) approximately PP2-36 (pKi = 10.06) > PYY (pKi = 9.06) approximately [Leu31,Pro34]NPY (pKi = 8.95) > NPY (pKi = 8.68) > PP13-36 (pKi = 7.13) > PP31-36 (pKi = 6.46) > PP31-36 free acid (pKi < 5). Human PP decreased [cAMP] and increased intracellular [Ca2+] in Y4-transfected LMTK- cells. Y4 mRNA was detected by reverse transcriptase-polymerase chain reaction in human brain, coronary artery, and ileum, suggesting potential roles for Y4 receptors in central nervous system, cardiovascular, and gastrointestinal function.

Amino Acid Sequence↗
PubMed2004

Multiplication of an ancestral gene encoding secreted fungalysin preceded species differentiation in the dermatophytes Trichophyton and Microsporum.

Dermatophytes are human and animal pathogenic fungi which cause cutaneous infections and grow exclusively in the stratum corneum, nails and hair. In a culture medium containing soy proteins as sole nitrogen source a substantial proteolytic activity was secreted by Trichophyton rubrum, Trichophyton mentagrophytes and Microsporum canis. This proteolytic activity was 55-75 % inhibited by o-phenanthroline, attesting that metalloproteases were secreted by all three species. Using a consensus probe constructed on previously characterized genes encoding metalloproteases (MEP) of the M36 fungalysin family in Aspergillus fumigatus, Aspergillus oryzae and M. canis, a five-member MEP family was isolated from genomic libraries of T. rubrum, T. mentagrophytes and M. canis. A phylogenetic analysis of genomic and protein sequences revealed a robust tree consisting of five main clades, each of them including a MEP sequence type from each dermatophyte species. Each MEP type was remarkably conserved across species (72-97 % amino acid sequence identity). The tree topology clearly indicated that the multiplication of MEP genes in dermatophytes occurred prior to species divergence. In culture medium containing soy proteins as a sole nitrogen source secreted Meps accounted for 19-36 % of total secreted protein extracts; characterization of protein bands by proteolysis and mass spectrometry revealed that the three dermatophyte species secreted two Meps (Mep3 and Mep4) encoded by orthologous genes.

Aspergillus↗
PubMed1993

Isolation and characterization of Listeria monocytogenes-specific nucleotide sequences.

Subtracter probe hybridization was used to screen a partial genomic library of a clinical isolate of Listeria monocytogenes. Three clones that hybridized with genomic DNA from 174 strains of L. monocytogenes but not with genomic DNA from 32 strains representing other Listeria spp. were recovered. These data establish the utility of subtracter probe hybridization for recovering L. monocytogenes-specific sequences.

Base Sequence↗
PubMed2001

Secreted aspartic proteinase family of Candida tropicalis.

Medically important yeasts of the genus Candida secrete aspartic proteinases (Saps), which are of particular interest as virulence factors. Like Candida albicans, Candida tropicalis secretes in vitro one dominant Sap (Sapt1p) in a medium containing bovine serum albumin (BSA) as the sole source of nitrogen. Using the gene SAPT1 as a probe and under low-stringency hybridization conditions, three new closely related gene sequences, SAPT2 to SAPT4, encoding secreted proteinases were cloned from a C. tropicalis lambdaEMBL3 genomic library. All bands identified by Southern blotting of EcoRI-digested C. tropicalis genomic DNA with SAPT1 could be assigned to a specific SAP gene. Therefore, the SAPT gene family of C. tropicalis is likely to contain only four members. Interestingly, the SAPT2 and SAPT3 gene products, Sapt2p and Sapt3p, which have not yet been detected in C. tropicalis cultures in vitro, were produced as active recombinant enzymes with the methylotrophic yeast Pichia pastoris as an expression system. As expected, reverse transcriptase PCR experiments revealed a strong SAPT1 signal with RNA extracted from cells grown in BSA medium. However, a weak signal was obtained with all other SAPT genes under several conditions tested, showing that these SAPT genes could be expressed at a basic level. Together, these experiments suggest that the gene products Sapt2p, Sapt3p, and Sapt4p could be produced under conditions yet to be described in vitro or during infection.

Amino Acid Sequence↗
PubMed1986

Molecular cloning of genetic determinants for inhibition of fungal growth by a fluorescent pseudomonad.

Pseudomonas fluorescens HV37a inhibits growth of the fungus Pythium ultimum in vitro. Optimal inhibition is observed on potato dextrose agar, a rich medium. Mutations eliminating fungal inhibition were obtained after mutagenesis with N-methyl-N'-nitro-N-nitrosoguanidine. Mutants were classified by cosynthesis and three groups were distinguished, indicating that a minimum of three genes are required for fungal inhibition. Cosmids that contain wild-type alleles of the genes were identified in an HV37a genomic library by complementation of the respective mutants. This analysis indicated that three distinct genomic regions were required for fungal inhibition. The cosmids containing these loci were mapped by transposon insertion mutagenesis. Two of the cosmids were found to contain at least two genes each. Therefore, at least five genes in HV37a function as determinants of fungal inhibition.

Alleles↗
PubMed2004

Maize DNA-sequencing strategies and genome organization.

A large amount of repetitive DNA complicates the assembly of the maize genome sequence. Genome-filtration techniques, such as methylation-filtration and high-CoT separation, enrich gene sequences in genomic libraries. These methods may provide a low-cost alternative to whole-genome sequencing for maize and other complex genomes.

DNA, Plant↗