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At least 793 records · Page 44Linked to original sources
PubMed2006

Novel calcium-binding GTPase (AtCBG) involved in ABA-mediated salt stress signaling in Arabidopsis.

We have identified a novel Ca(2+)-signal sensing GTPase (643 amino acid residues with an estimated molecular mass of 79 kDa) from the Arabidopsis genome database. This protein contains a RHO-like GTPase domain at the N-terminus (15-184 amino acids) and two calcium-binding EF-hand motifs (199-227 and 319-347 amino acids, respectively). It has the capability to bind calcium and hydrolyze GTP; in addition, its GTPase activity is regulated by changes in Ca(2+) concentration. The expression of this gene was induced by ABA and salt stresses, and specific knock-out mutants were highly sensitive to ABA and salt treatments. These findings suggest that this protein is a novel ABA- and salt stress-related Ca(2+) signal transducer.

Abscisic Acid↗
PubMed2003

Three sweet receptor genes are clustered in human chromosome 1.

A search of the human genome database led us to identify three human candidate taste receptors, hT1R1, hT1R2, and hT1R3, which contain seven transmembrane domains. All three genes map to a small region of Chromosome (Chr) 1. This region is syntenous to the distal end of Chr 4 in mouse, which contains the Sac (saccharin preference) locus that is involved in detecting sweet tastants. A genetic marker, DVL1, which is linked to the Sac locus, is within 1700 bp of human T1R3. Recently, the murine T1Rs and its human ortholog have been independently identified in combination as sweet and umami receptors near the Sac locus. All three hT1Rs genes are expressed selectively in human taste receptor cells in the fungiform papillae, consistent with their role in taste perception.

Alleles↗
PubMed2003

Isolation and characterization of the mouse ubiquitin-specific protease Usp15.

We have characterized the mouse ortholog of the human ubiquitin-specific protease USP15. Mouse Usp15 consists of 981 amino acids with a predicted molecular mass of 112 kDa, contains the highly conserved Cys and His boxes present in all members of the UBP family of deubiquitinating enzymes, and is 98% identical/99% similar to human USP15. Usp15 shares 59.5% identity/75.5% sequence similarity with the mouse Unp(Usp4) oncoprotein. Recombinant Usp15 demonstrated ubiquitin-specific protease activity against engineered linear fusions of ubiquitin to glutathione S-transferase. Usp15 can also cleave the ubiquitin-proline bond, as can USP15 and Usp4. Alignment of mouse and human Usp15 and Usp4 protein sequences suggested that Usp15/USP15 may be alternately spliced in a manner analogous to Usp4. Sequence analysis of RT-PCR products from several human and mouse cell lines and tissues revealed alternate splicing in all cells studied. Northern blot analysis of both mouse and human Usp15 revealed two differently sized mRNAs in all tissues examined, owing to alternate polyadenylation sites spaced by 1.5 kb. Chromosomal mapping by interspecific backcross analysis localized the Usp15 gene to the distal region of mouse Chromosome (Chr) 10. This region is syntenic with human Chr 12q24, the location of human USP15, and a different location to Unp(Usp4) (Chr 9). Identification of the mouse Usp15 gene (>69.5 kb) and human USP15 gene (145 kb) sequences in genome databases reveals that both are composed of 22 exons with identical splice sites, and both have an exon/intron structure identical to the mouse Usp4 gene, including the alternately spliced exon. Phylogenetic studies suggest that a sequence currently identified as a chicken Usp4 ortholog is in fact a USP15 ortholog, while bona-fide chicken, cow, and rat Usp4 orthologs can be identified in EST databases.

Amino Acid Sequence↗
PubMed2006

High resolution mapping of chromosomal regions controlling resistance to gastrointestinal nematode infections in an advanced intercross line of mice.

Fine mapping of quantitative trait loci (QTL) associated with resistance to the gastrointestinal parasite Heligmosomoides polygyrus was achieved on F(6)/F(7) offspring (1076 mice) from resistant (SWR) and susceptible (CBA) mouse strains by selective genotyping (top and bottom 20% selected on total worm count in week 6). Fecal egg counts were recorded at weeks 2, 4, and 6, and the average was also analyzed. Blood packed cell volume in weeks 3 and 6 and five immunological traits (mucosal mast cell protease 1, granuloma score, IgG1 against adult worm, IgG1, and IgE to L4 antigen) were also recorded. On Chromosome 1 single-trait analyses identified a QTL with effects on eight traits located at about 24 cM on the F(2) mouse genome database (MGD) linkage map, with a 95% confidence interval (CI) of 20-32 cM established from a multitrait analysis. On Chromosome 17 a QTL with effects on nine traits was located at about 18 cM on the MGD map (CI 17.9-18.4 cM). Strong candidate genes for the QTL position on Chromosome 1 include genes known to be involved in regulating immune responses and on Chromosome 17 genes within the MHC, notably the Class II molecules and tumor necrosis factor.

Animals↗
PubMed2006

The rat prolactin gene family locus: species-specific gene family expansion.

In the rat there is a large family of paralogous genes related to prolactin (PRL). Members of the PRL family are expressed in cell- and temporal-specific patterns in the anterior pituitary, uterus, and placenta. An overriding feature of the PRL family is its association with pregnancy. In this investigation, we used information derived from the public rat genome database as a tool for identifying new members of the rat PRL family. The entire rat PRL gene family locus spans approximately 1.7 megabases (Mb) on Chromosome 17. Genes possessed either 5- or 6-exon organization patterns. We provide information on three newly identified genes orthologous to previously identified members of the mouse PRL gene family [placental lactogen-Ialpha (PL-Ialpha), PL-Ibeta, and proliferin (PLF)] and a new member of the PRL family, termed PRL-like protein-P (PLP-P). Information is also presented on the existence of multiple PLP-M transcripts, which are generated by alternative splicing. Expansion of the PRL family has occurred independently in rodents versus the cow and does not exist in the human and dog. Elucidation of the rat PRL gene family locus provides tools for studying the genetics and biology of the rat PRL family and new insights into species-specific gene family expansion.

Amino Acid Sequence↗
PubMed2000

Whiskers amiss, a new vibrissae and hair mutation near the Krt1 cluster on mouse chromosome 11.

Whiskers amiss (wam) is a new spontaneous recessive mutation in the SELH/Bc strain of mice that causes a phenotype of askew, sometimes kinked or curled, breakable whiskers and disheveled-appearing body hair, apparently owing to disoriented guard hairs. Heterozygotes on three genetic backgrounds are indistinguishable from normal. Using informative SSLPs in the F2 generation after crosses to two normal strains, we have mapped wam to the region of the type I keratin cluster on Chromosome (Chr) 11, within an approximately 6-cM segment according to the current Mouse Genome Database (MGD) map position of flanking SSLPs. Although several other hair mutations also map to the Krt1 region (Re, Rim3, Bdai, Bsk), none has a hair and whisker phenotype similar to that of wam, and, because all are transmitted as dominants, interpretable complementation tests could not be done. Scabbing and tissue loss occur on the rims of the pinnae and tail tip in some aging wam homozygotes, suggesting that wam may be an animal model of a genetic ectodermal disorder. The SELH/Bc strain background appears to have an unusually high rate of spontaneous mutation; wam is the sixth mutation to be described.

Animals↗
PubMed2000

Localization of the mouse kidney disease (kd) gene to a YAC/BAC contig on Chromosome 10.

Mice that are homozygous for the kidney disease (kd) gene on Chromosome (Chr) 10 spontaneously develop a progressive and fatal interstitial nephritis. The disease phenotype is similar to that of the human disease, juvenile nephronophthisis. Using a backcross and intercross breeding strategy and analysis of over 900 resultant progeny, this genetic locus has now been mapped to a minimal co-segregating region of approximately two megabases between D10Mit 193 and D10Mit 38. The location assigned to kd by this study is over 3 cM from the current Mouse Genome Database location. The entire interval has been cloned in yeast artificial chromosome (YAC) and bacterial artificial chromosome (BAC) clones. Recombinant analysis has permitted assignment of 13 Mit microsatellite markers to positions near or within the region. Two new markers have been identified by using single-strand conformation polymorphism (SSCP) analysis of sequenced BAC ends. Several BAC end sequences align with human BAC clones from Chr 6q2 that contain NR2E1. Snx3, and Ros1. Three murine genes, CD24a, fyn, and ColX reported to map in or near the kd region as defined by this study have been evaluated. Though not definitely excluded, they appear to be unlikely candidates.

Animals↗
PubMed1996

Genetic composition of the recombinant congenic strains.

For the study of biological phenomena influenced by multiple genes in mice, the Recombinant Congenic Strains (RCS) have been developed. An RCS series comprises approximately 20 homozygous strains, each of which contains on average 87.5% genes of a common background strain and 12.5% of a common donor strain. In an RCS series, non-linked genes involved in the control of a multigenic trait become distributed into different recombinant congenic strains. In this way a multigenic trait is transformed into a series of single gene traits in which each gene can be studied individually. For the ability to use the strength of the recombinant congenic strains system to its full extent, a thorough genetic characterization is indispensable. We have typed the CcS/Dem and OcB/Dem series for 611 and 550 markers, respectively. This results in a genetic characterization sufficient to detect most donor strain genes. In addition, we report the genetic characterization of the HcB/Dem and HcB(N4)/Dem series. Strains of the latter series contain on average 6.25% of the donor strain genome. Both series have been typed for 130 markers. All the typing data have been deposited in the Mouse Genome Database at The Jackson Laboratory.

Animals↗
PubMed2000

Highly informative Y-chromosomal haplotypes by the addition of three new STRs DYS437, DYS438 and DYS439.

The Y chromosome STRs DYS437, DYS438 and DYS439 were selected from publicly available genome databases and used to analyse an Italian population sample. A tetraplex PCR reaction including the highly informative DYS385 locus, was set up and used for the analysis of 131 male samples to determine allele frequencies and STR diversity values. The number of different haplotypes and the haplotype diversity value found from the analysis of the STRs included in the tetraplex reaction were very similar to those found from the analysis of the basic set of 7 Y-STRs (DYS19, DYS389I/II, DYS390, DYS391, DYS392 and DYS393) previously carried out on the same population sample. By combining the allelic states of the 11 Y-chromosomal STRs we could construct highly informative haplotypes that allowed the discrimination of 93.8% (120 out of 128) of the samples tested. This approach represents a very powerful tool for individual identification and paternity testing in forensic medicine.

DNA Fingerprinting↗
PubMed2002

Overexpression of the Arabidopsis thaliana MinE1 bacterial division inhibitor homologue gene alters chloroplast size and morphology in transgenic Arabidopsis and tobacco plants.

Higher-plant chloroplast division requires some of the same genes that are involved in prokaryotic cell division. These include the FtsZ and MinD proteins. Other genes that might be involved in higher-plant chloroplast division have yet to be characterized. The Arabidopsis thaliana (L.) Heynh. MinE ( AtMinE1) gene was identified in the genomic database, isolated by reverse transcription-polymerase chain reaction and constitutively expressed in tobacco ( Nicotiana tabacum L.) and Arabidopsis plants in both the sense and antisense orientation. Confocal and electron-microscopic analysis of the sense-overexpressing AtMinE1 transgenic tobacco and Arabidopsis plants revealed that the chloroplasts were abnormal in size and shape compared to wild-type Arabidopsis and tobacco chloroplasts. Our results, based on the overexpression of the AtMinE1 gene in tobacco and Arabidopsis, confirm that the AtMinE1 gene is involved in plant chloroplast division.

Amino Acid Sequence↗
PubMed2004

Identification of a Golgi-localised GRIP domain protein from Arabidopsis thaliana.

A family of Golgi-localised molecules was recently described in animals and fungi possessing extensive coiled regions and a short (approximately 40 residues) conserved C-terminal domain, called the GRIP domain, which is responsible for their location to this organelle. Using the model plant Arabidopsis thaliana, we identified a gene (AtGRIP) encoding a putative GRIP protein. We demonstrated that the C-terminal domain from AtGRIP functions as a Golgi-targeting sequence in plant cells. Localisation studies in living cells expressing the AtGRIP fused to a DsRed2 fluorescent probe, showed extensive co-location with the Golgi marker alpha-mannosidase I in transformed tobacco protoplasts. GRIP-like sequences were also found in genomic databases of rice, maize, wheat and alfalfa, suggesting that this domain may be a useful Golgi marker for immunolocalisation studies. Despite low sequence identity amongst GRIP domains, the plant GRIP sequence was able to target to the Golgi of mammalian cells. Taken together, these data indicate that GRIP domain proteins might be implicated in a targeting mechanism that is conserved amongst eukaryotes.

Amino Acid Sequence↗
PubMed2006

Evolution of teleostean hatching enzyme genes and their paralogous genes.

We isolated genes for hatching enzymes and their paralogs having two cysteine residues at their N-terminal regions in addition to four cysteines conserved in all the astacin family proteases. Genes for such six-cysteine-containing astacin proteases (C6AST) were searched out in the medaka genome database. Five genes for MC6AST1 to 5 were found in addition to embryo-specific hatching enzyme genes. RT-PCR and whole-mount in situ hybridization evidenced that MC6AST1 was expressed in embryos and epidermis of almost all adult tissues examined, while MC6AST2 and 3 were in mesenterium, intestine, and testis. MC6AST4 and 5 were specifically expressed in jaw. In addition, we cloned C6AST cDNA homologs from zebrafish, ayu, and fugu. The MC6AST1 to 5 genes were classified into three groups in the phylogenetic positions, and the expression patterns and hatching enzymes were clearly discriminated from other C6ASTs. Analysis of the exon-intron structures clarified that genes for hatching enzymes MHCE and MAHCE were intron-less, while other MC6AST genes were basically the same as the gene for another hatching enzyme MLCE. In the basal Teleost, the C6AST genes having the ancestral exon-intron structure (nine exon/eight intron structure) first appeared by duplication and chromosomal translocation. Thereafter, maintaining such ancestral exon-intron structure, the LCE gene was newly diversified in Euteleostei, and the MC6AST1 to 5 gene orthologs were duplicated and diversified independently in respective fish lineages. The HCE gene lost all introns in Euteleostei, whereas in the lineage to zebrafish, it was translocated from chromosome to chromosome and lost some of its introns.

Amino Acid Sequence↗
PubMed2001

Cloning and characterization of a novel zinc finger protein (MDZF) that is associated with monocytic differentiation of acute promyelocytic leukemia cells.

AIM: To study the characteristics of a novel zinc finger protein designated as monocytic differentiation-associated zinc finger protein (MDZF) and its role in the differentiation of leukemia cells. METHODS: The mRNA expression of MDZF in tissues and cells was analyzed by Northern blot and RT-PCR. Polyclonal antibodies against the N terminus of MDZF were used to analyze protein expression in hematopoietic cell lines and subcellular location of MDZF in promyelocytic NB4 cells. The NB4 cells treated with TPA or ATRA at different intervals were harvested and then the expression level of MDZF protein was determined by Western blot. RESULT: A full-length cDNA was successfully identified from a human monocyte-derived dendritic cell cDNA library which encodes 610 amino acids with eight C2H2 zinc finger motifs and one POZ domain. It was located on chromosome 3 according to the genome database. This novel zinc finger protein was designated as MDZF. One transcript isoform of MDZF was also cloned by RT-PCR. Northern blot showed that MDZF mRNA was restrictedly expressed in heart, skeleton muscle, kidney, liver, and placenta. MDZF protein was expressed in all hematopoietic cell lines examined. Immunoblotting and confocal analysis indicated a dominant cytoplasmic location of MDZF in NB4 cells. Furthermore, after NB4 cells were treated with TPA for 48 h and differentiated into monocytes, MDZF expression increased fivefold in the NB4 cells, but no effect was observed in NB4 cells treated with ATRA. CONCLUSION: A novel zinc finger protein MDZF was cloned. MDZF is upregulated in monocytic, but not granulocytic, differentiation of NB4 acute promyelocytic leukemia cells. MDZF may be a candidate regulator of monocytic differentiation.

Amino Acid Sequence↗
PubMed2003

Molecular cloning and characterization of an SRCAP chromatin remodeling homologue in Toxoplasma gondii.

We have identified and mapped a gene in Toxoplasma gondii that encodes a homologue of SRCAP (Snf2-related CBP activator protein), a member of the SNF/SWI family of chromatin remodeling factors. The genomic locus (TgSRCAP) is present as a single copy and contains 16 introns. The predicted cDNA contains an open reading frame of 8,775 bp and encodes a protein of 2,924 amino acids. We have identified additional SRCAP-like sequences in Apicomplexa for comparison by screening genomic databases. An analysis of SRCAP homologues between species reveals signature features that may be indicative of SRCAP members. Expression of mRNA encoding TgSRCAP is upregulated when tachyzoite (invasive form) parasites are induced to differentiate into bradyzoites (encysted form) in vitro. Recombinant TgSRCAP protein is functionally equivalent to the human homologue, being capable of increasing transcription mediated by CREB.

Adenosine Triphosphatases↗
PubMed2002

The upr-1 gene encodes a catalytic subunit of the DNA polymerase zeta which is involved in damage-induced mutagenesis in Neurospora crassa.

The upr-1 mutant was one of the first mutagen-sensitive mutants to be isolated in Neurospora crassa. However, the function of the upr-1 gene has not yet been elucidated, although some genetic and biochemical data have been accumulated. In order to clone the upr-1 gene, we performed a chromosome walk from the mat locus, the closest genetic marker to upr-1 for which a molecular probe was available, towards the centromere, and a chromosomal contig of about 300-400 kb was constructed. Some of these clones complemented the temperature sensitivity of the un-16 mutation, which is located between mat and upr-1. The un-16 gene was sequenced, and localized in the MIPS Neurospora crassa genome database. We then searched the regions flanking un-16 for homologs of known DNA repair genes, and found a gene homologous to the REV3 gene of budding yeast. The phenotype of the upr-1 mutant is similar to that of the yeast rev3 mutant. An ncrev3 mutant carrying mutations in the N. crassa REV3 homolog was constructed using the RIP (repeat-induced point mutation) process. The spectrum of mutagen sensitivity of the ncrev3 mutant was similar to that of the upr-1 mutant. Complementation tests between the upr-1 and ncrev3 mutations indicated that the upr-1 gene is in fact identical to the ncrev3 gene. To clarify the role of the upr-1 gene in DNA repair, the frequency of MMS and 4NQO-induced mutations was assayed using the ad-8 reversion test. The upr-1 mutant was about 10 times less sensitive to both chemicals than the wild type. The expression level of the upr-1 gene is increased on exposure to UV irradiation in the uvs-2 and mus-8 mutants, which belong to postreplication repair group, as well as in the wild type. All these results suggest that the product of the upr-1 gene functions in damage-induced mutagenesis and DNA translesion synthesis in N. crassa.

Catalytic Domain↗
PubMed2003

An Arabidopsis homologue of bacterial RecA that complements an E. coli recA deletion is targeted to plant mitochondria.

Homologous recombination results in the exchange and rearrangement of DNA, and thus generates genetic variation in living organisms. RecA is known to function in all bacteria as the central enzyme catalyzing strand transfer and has functional homologues in eukaryotes. Most of our knowledge of homologous recombination in eukaryotes is limited to processes in the nucleus. The mitochondrial genomes of higher plants contain repeated sequences that are known to undergo frequent rearrangements and recombination events. However, very little is known about the proteins involved or the biochemical mechanisms of DNA recombination in plant mitochondria. We provide here the first report of an Arabidopsis thaliana homologue of Escherichia coli RecA that is targeted to mitochondria. The mt recA gene has a putative mitochondrial presequence identified from the A. thaliana genome database. This nuclear gene encodes a predicted product that shows highest sequence homology to chloroplast RecA and RecA proteins from proteobacteria. When fused to the GFP coding sequence, the predicted presequence was able to target the fusion protein to isolated mitochondria but not to chloroplasts. The mitochondrion-specific localization of the mt recA gene product was confirmed by Western analysis using polyclonal antibodies raised against a synthetic peptide from a unique region of the mature mtRecA. The Arabidopsis mt recA gene partially complemented a recA deletion in E. coli, enhancing survival after exposure to DNA-damaging agents. These results suggest a possible role for mt recA in homologous recombination and/or repair in Arabidopsis mitochondria.

Amino Acid Sequence↗
PubMed2005

Characterisation of the Aspergillus niger dapB gene, which encodes a novel fungal type IV dipeptidyl aminopeptidase.

We have cloned the Aspergillus niger dapB gene. Analysis of its nucleotide sequence and the corresponding protein sequence indicates that the gene encodes a type IV dipeptidyl aminopeptidase (DPP IV). Based upon its deduced sequence we predict the presence of a transmembrane domain in the protein. Furthermore, dapB-overexpressing transformants display an increase in intracellular DPP IV activity. This is the first reported characterisation of a dipeptidyl aminopeptidase with a transmembrane domain from a filamentous fungus. Using the dapB sequence as a query, we were able to identify 14 DPP IV-encoding genes, and 12 additional DPPIV proteases in public genomic databases. Phylogenetic analysis reveals that in yeasts there are two clades of genes that encode DPP IV proteases with a transmembrane domain. In this study we demonstrate that, as in yeasts, two classes of DPP IV-encoding genes exist in filamentous fungi. However, only one of these codes for DPP IV proteases with a transmembrane domain. The second type present in filamentous fungi encodes extracellular DPP IV proteases. The dapB gene belongs to the first cluster. We propose that DapB plays a role in the proteolytic maturation of enzymes produced by A. niger.

Aspergillus niger↗
PubMed1997

Gene activation at a distance and telomeric silencing are not affected by yeast histone H1.

Until recently, it was believed that the budding yeast Saccharomyces cerevisiae has no histone H1 gene. However, a search of the yeast genome database revealed a possible H1 homologue of 258 amino acids, termed yeast histone H1 (HHO1). The protein shows 36% identity to the human H1 core domain over a stretch of 93 amino acids. Unlike other H1 proteins, Hho1p has a second possible core domain which shows 43% identity to the first core domain. Since vertebrate H1 histone had been implied in gene repression as well as gene activation at a distance, we tested the effect of deleting the yeast H1-like gene on remote activation of a modified GAL1 promoter, which contains a synthetic GAL4 binding site close to the TATA box, and the natural UASG, consisting of four GAL4 binding sites. Different spacing up to 1.8 kb between the proximal binding site and the distal UASG enhancer revealed no differences in gene activation between wild-type and knockout strains. Overexpression of a heterologous histone H1 from sea urchin showed an overall inhibition of gene activation by the GAL1 promoter, whereas overexpression of the yeast histone H1 had no effect. Also, the expression of A1, ALPHA2 or SUC2 genes, all of which are known to be responsive to an altered chromatin structure, was unchanged in HHO1 knockout or HHO1-overexpressing strains when compared to wild-type cells. We also considered the possibility that HHO1 was involved in forming the heterochromatin at telomeres. On testing for telomeric silencing of a URA reporter gene introduced 1.3 kb away from the chromosomal end, we again observed no differences between wild-type and knockout strains. Thus, the yeast histone H1-like gene appears to have no role in gene activation at a distance or in silencing under the conditions tested. It remains to be seen whether the yeast H1 histone is a gene-specific regulator rather than a general chromatin-associated protein.

Animals↗