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PubMed1998

Genomic structure and chromosome location of the murine PDE1B phosphodiesterase gene.

Cyclic nucleotide phosphodiesterases (PDEs) catalyze the hydrolysis of cAMP and cGMP, thereby participating in regulation of the intracellular concentrations of these second messengers. The PDE1 family is defined by regulation of activity by calcium and calmodulin. We have cloned and characterized the mouse PDE1B gene, which encodes the 63-kDa calcium/calmodulin-dependent PDE (CaM-PDE), an isozyme that is expressed in the CNS in the olfactory tract, dentate gyrus, and striatum and may participate in learning, memory, and regulation of phosphorylation of DARPP-32 in dopaminergic neurons. We screened an I-129/SvJ mouse genomic library and identified exons 2-13 of the PDE1B gene that span 8.4 kb of genomic DNA. Exons range from 67 to 205 nucleotides and introns from 91 to 2250 nucleotides in length. Exon 1 was not present in the 3 kb of genomic DNA 5' to exon 2 in our clones. The mouse PDE1B gene shares many similar or identical exon boundaries as well as considerable sequence identity with the rat PDE4B and PDE4D genes and the Drosophila dunce cAMP-specific PDE gene dnc, suggesting that these genes all arose from a common ancestor. Using fluorescence in situ hybridization, we localized the PDE1B gene to the distal tip of mouse Chromosome (Chr) 15.

3',5'-Cyclic-AMP Phosphodiesterases↗
PubMed1999

Genomic structure and chromosomal localization of the mouse gene Punc.

The mouse gene Punc encodes a member of the immunoglobulin superfamily of cell surface proteins. It is highly expressed in the developing embryo in nervous system and limb buds. At mid-gestation, however, expression levels of Punc decrease sharply. To allow investigation of such a regulatory mechanism, the genomic locus encompassing the Punc gene was cloned, characterized, and mapped. Fluorescent in situ hybridization was used to determine the chromosomal location of the Punc gene of mouse and human. Mouse Punc maps to Chromosome (Chr) 9 in the region D-E1, whereas the human PUNC gene is localized to Chr 15 at 15q22.3-23, a region known to be syntenic to mouse 9D-E1. The human PUNC gene therefore maps close to a genetic locus that is linked to Bardet-Biedl Syndrome, an autosomal recessive human disorder. Confirmation for the location of human PUNC was obtained through sequence relationships between mouse Punc cDNA, human PUNC cDNA, genomic sequence upstream of the murine Punc gene, and human STS markers that had been previously mapped on Chr 15. The STS sequence WI-14920 is in fact derived from the 3'-untranslated region of the human PUNC gene. WI-14920 had been placed at 228cR from the top of the Chr 15 linkage group, which provided positional information for the human PUNC gene at high resolution. Thus, this study identifies PUNC as the gene corresponding to a previously anonymous marker and serves as a basis to investigate its role in genetic disorders.

Amino Acid Sequence↗
PubMed2025

The dynamic centromere.

Centromeres are fundamental chromosomal structures that ensure accurate chromosome segregation during cell division. Despite their conserved and essential role in maintaining genomic stability, centromeres are subject to rapid evolutionary change. At the heart of centromere identity is the histone H3 variant CENP-A, an epigenetic mark that defines and propagates active centromeres and is essential for their function. Recent evidence supports a rapid evolution of centromere DNA sequences but also suggests a certain degree of flexibility in CENP-A deposition and propagation. The phenomenon of centromere drift, recently observed in humans, highlights how the dynamic repositioning of CENP-A and associated epigenetic environment over time maintains a regulated equilibrium, ensuring centromere function despite positional variation. Understanding these processes is crucial for unraveling centromere dynamics and their broader implications for genome stability and evolution.

Centromere↗
PubMed1996

Structure of chromosomal DNA coding for Pseudomonas putida S-1 salicylate hydroxylase.

A gene coding for the salicylate hydroxylase has been isolated from chromosomal DNA of Pseudomonas putida S-1 and sequenced. The DNA fragment contained an open reading frame of 1266 bp encoding a polypeptide of 421 amino acid residues. The predicted amino acid sequence of the protein gave a good agreement with the sequences determined with the peptides isolated from the enzyme but methionine residue in the amino terminal was deleted in the N-terminal sequence of the enzyme protein. The nucleotide and amino acid sequences of the salicylate hydroxylase shared several common characteristics with those of the enzyme encoded on the plasmid DNA of P. putida PpG7; homology of nucleotide sequence is 58% and that of amino acid sequence is 56%. We could find two large conserved regions of the amino acid sequence at or near FAD- and NADH-binding regions. The FAD-binding site locates on the amino terminal and a lysine residue, functioning as an NADH-binding site (K. Suzuki, M. Mizuguchi, T. Gomi, and E. Itagaki, 1995, J. Biochem. 117,579-585), locates as Lys163.

Amino Acid Sequence↗
PubMed1990

The mouse keratin 19-encoding gene: sequence, structure and chromosomal assignment.

Keratin 19 (K19) is synthesized mainly in embryonic and adult simple epithelia, but has also been found in stratified epithelia as well. K19 is the smallest known keratin and is remarkable in that, contrary to all other keratins, it does not have a designated partner for the formation of filaments, implying that regulation of its expression is different from other keratin-encoding genes. As a first step in elucidating the mechanisms by which the K19 gene is regulated in relatively undifferentiated embryonic and in terminally differentiated adult tissues, a series of overlapping clones containing the complete mouse K19 gene was isolated from a mouse genomic library and characterized. The nucleotide (nt) sequence extends over 5119 nt and includes six exons. A region of 303 nt upstream from the transcription start point (tsp) was also sequenced. Comparison with the human and bovine K19 genes revealed the existence of homologies in both the coding and noncoding regions. The putative promoter region of the mouse K19 gene is highly homologous to the corresponding sequences of the human and bovine K19 genes. It contains an ATA box, a CAAT box and two potential Sp1-binding sites. Significant homologies were also found between the sequences of the introns of the mouse, human and bovine genes: this was particularly evident in introns 2, 3, 4 and 5. Intron 1, which showed the greatest degree of divergence, was found to contain many repetitive elements. Finally, it is shown that the mouse K19 gene cosegregates with the type-I keratin-encoding gene locus (Krt-1) on chromosome 11.

Amino Acid Sequence↗
PubMed1992

Structure and chromosomal localization of the gene encoding barley seed peroxidase BP 2A.

A clone, lambda Prx6.1, coding for a barley seed peroxidase (BP; EC 1.11.1.7), was isolated from a genomic library using a cDNA coding for the barley seed peroxidase, BP 1, as a probe. The nucleotide sequence coded for a BP showing 73% amino acid (aa) sequence identity with BP 1 and less than 50% similarity with other sequenced plant peroxidases. The aa composition is 92% identical to that determined for BP 2 purified from mature barley grains, and therefore the gene product is named BP 2A. The alignment suggests that the coding region is interrupted by a 76-bp intron having the consensuses GT and AG, at the 5' and 3' ends, respectively. Alignment with BP 1 suggests that BP 2A has a leader peptide of 36 aa and the mature protein is 319 aa. Alanine and leucine account for 50% of the residues of the leader peptide. Of the codons used 90% have a C or G in the third position. The promoter shows a putative abscisic acid-response element, 5'-GTACGTGTC, 115 bp upstream from the start codon. The BP 2A-encoding gene was RFLP-mapped on barley chromosome 3, and we suggest for this peroxidase locus the name Prx6.

Amino Acid Sequence↗
PubMed1994

Structure and chromosomal localization of CYP6A1, a cytochrome P450-encoding gene from the house fly.

We determined the sequence of a cytochrome P450-encoding gene, CYP6A1, in an insecticide-resistant strain (Rutgers) and in insecticide-susceptible strains (aabys and sbo) of the house fly Musca domestica. The deduced amino acid (aa) sequence of CYP6A1 is 98% identical between Rutgers and aabys, and it is identical between Rutgers and sbo. Differences in aa sequence occur in regions that are not thought to participate in the active site. CYP6A1 has a single intron, 60 bp in length. It does not occur in a position homologous to intron sites in genes of the related CYP3 family or other vertebrate P450 families. We mapped the transcription start point (tsp), TATA box and barbie box [Shaw and Fulco, J. Biol. Chem. 269 (1993) 2997-3004] of this phenobarbital-inducible gene. Although overexpression of CYP6A1 in strain Rutgers is controlled by a locus on chromosome II [Cariño et al., Insect Biochem. Mol. Biol. 24 (1994) 411-418], we have localized CYP6A1 to chromosome V, thus showing that a trans-acting factor controls the overexpression of the gene in the Rutgers strain.

Amino Acid Sequence↗
PubMed1996

Structure and chromosomal location of the mouse medium-chain acyl-CoA dehydrogenase-encoding gene and its promoter.

Medium-chain acyl-coenzyme A dehydrogenase (MCAD; mouse gene Acadm; human gene ACADM) catalyzes the initial step of fatty acid beta-oxidation in mitochondria. Inherited MCAD deficiency is an autosomal recessive disorder that occurs at high frequency in humans and is associated with considerable morbidity and mortality. We have cloned and characterized mouse Acadm which spans approximately 25 kb and contains 12 exons. The promoter region does not contain TATA or CAAT boxes and is G + C-rich (60%) within 200 bp of the cap site. A CpG island extends from 5' of the transcription start point into intron 1. The 5' regulatory region and a portion of intron 1 contain several Sp1 consensus sites and three regions containing hexamer DNA sequences that match the binding consensus for steroid/thyroid nuclear receptors. These putative nuclear receptor response elements (NRRE) share DNA sequence homology and electrophoretic mobility shift characteristics with known NRRE in the human ACADM promoter [Carter et al., J. Biol. Chem. 268 (1993) 13805-13810]. We have mapped mouse Acadm to the distal end of chromosome 3. Sequences previously localized to chromosome 8 are shown to be a pseudogene, and an additional pseudogene was identified on chromosome 11.

Acyl-CoA Dehydrogenase↗
PubMed1990

Structure and chromosome localization of the human eosinophil-derived neurotoxin and eosinophil cationic protein genes: evidence for intronless coding sequences in the ribonuclease gene superfamily.

Human genomic DNAs for the eosinophil granule proteins, eosinophil-derived neurotoxin (EDN) and eosinophil cationic protein (ECP), were isolated from genomic libraries. Alignment of EDN (RNS2) and ECP (RNS3) gene sequences demonstrated remarkable nucleotide similarities in noncoding sequences, introns, and flanking regions, as well as in the previously known coding regions. Detailed examination of the 5'-noncoding regions yielded putative TATA and CAAT boxes, as well as similarities to promoter motifs from unrelated genes. A single intron of 230 bases was found in the 5' untranslated region and we suggest that a single intron in this region and an intronless coding region are features common to many members of the RNase gene superfamily. The RNS2 and RNS3 genes were localized to the q24-q31 region of human chromosome 14. It is likely that these two genes arose as a consequence of a gene duplication event that took place approximately 25-40 million years ago and that a subset of anthropoid primates possess both of these genes or closely related genes.

Animals↗
PubMed1991

On the structure and chromosome location of the 72- and 92-kDa human type IV collagenase genes.

The 72- and 92-kDa type IV collagenases are members of a group of secreted zinc metalloproteases. Two members of this family, collagenase and stromelysin, have previously been localized to the long arm of chromosome 11. Here we assign both of the two type IV collagenase genes to human chromosome 16. By sequencing, the 72-kDa gene is shown to consist of 13 exons, 3 more than have been reported for the other members of this gene family. The extra exons encode the amino acids of the fibronectin-like domain which has so far been found in only the 72- and 92-kDa type IV collagenase. The evolutionary relationship among the members of this gene family is discussed.

Amino Acid Sequence↗
PubMed2005

Protein arginine methyltransferase 6 specifically methylates the nonhistone chromatin protein HMGA1a.

The HMGA family proteins HMGA1a and HMGA1b are nuclear nonhistone species implicated in a wide range of cellular processes including inducible gene transcription, modulation of chromosome structure through nucleosome and chromosome remodeling, and neoplastic transformation. HMGA proteins are highly modified, and changes in their phosphorylation states have been correlated with the phase of the cell cycle and changes in their transcriptional activity. HMGA1a is also methylated in the first DNA-binding AT-hook at Arg25 and other sites, although the enzyme or enzymes responsible have not been identified. We demonstrate here that a GST fusion of protein arginine methyltransferase 6 (PRMT6) specifically methylates full-length recombinant HMGA1a protein in vitro. Although GST fusions of PRMT1 and PRMT3 were also capable of methylating the full-length HMGA1a polypeptide, they recognize its proteolytic degradation products much better. GST fusions of PRMT4 or PRMT7 were unable to methylate the full-length protein or its degradation products. We conclude that PRMT6 is a good candidate for the endogenous enzyme responsible for HGMA1a methylation.

HMGA1a Protein↗
PubMed2003

Structure and chromosomal localization of the gene for crotamine, a toxin from the South American rattlesnake, Crotalus durissus terrificus.

Crotamine is a 42 amino acid-long basic polypeptide, one of the major components of the South American rattlesnake, Crotalus durissus terrificus, venom. The mRNA has about 340 nucleotides and codifies a pre-crotamine, including the signal peptide, the mature crotamine, and a final lysine. In this report, we describe the crotamine gene with 1.8 kb organized into three exons separated by a long phase-1 (900 bp) and a short phase-2 (140 bp) introns. Exon 1 includes the 5'-untranslated region and codifies the first 19 amino acids of the signal peptide. Exon 2 codifies 42 amino acids, three belonging to the signal peptide and 39 to the mature crotamine. Exon 3 codifies the last three amino acids of the mature toxin and the terminal lysine. The crotamine gene was mapped by in situ hybridization to the end of the long arm of chromosome 2, the intensity of signals differing between the two homologues. This may reflect a difference in gene copy numbers between chromosomes, a possible explanation for the variable amounts of crotamine found in the venom.

Animals↗
PubMed1991

Structure and chromosome assignment of human S100 alpha and beta subunit genes.

The human S-100 alpha and beta subunit genes were isolated from human genomic DNA library. The restriction endonuclease mapping and DNA sequencing analysis revealed that both subunit genes consisted of three exons and two introns. Two Ca2(+)-binding domains were independently encoded by exon 2 and exon 3. Spot-blot hybridization analysis with flow-sorted chromosomes showed that human alpha and beta subunit genes were assigned to chromosome 1 and chromosome 21, respectively.

Amino Acid Sequence↗