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At least 253 records · Page 14Linked to original sources
PubMed1989

Structure of the gene for human plasminogen activator inhibitor-2. The nearest mammalian homologue of chicken ovalbumin.

Plasminogen activator inhibitor-2 (PAI-2) can regulate the formation of plasmin by inhibiting urokinase and tissue plasminogen activator. PAI-2 is induced in monocytes and endothelium by inflammatory mediators, and it is made in the placenta during pregnancy. PAI-2 is a member of the serine protease inhibitor gene family, and it is particularly similar to chicken ovalbumin. Like ovalbumin, PAI-2 is secreted without cleavage of a signal peptide. To determine the structure of the PAI-2 gene, two bacteriophage lambda human genomic DNA libraries were screened with PAI-2 cDNA probes. Characterization of three positive clones shows that the human PAI-2 gene spans 16.5 kilobases and has eight exons. The 5'-untranslated sequence of the PAI-2 mRNA is 77 base pairs in length as suggested by primer extension and S1 nuclease mapping. The eukaryotic consensus sequence TATAAAA is found 22 base pairs 5' of the proposed cap site. The PAI-2 gene is on chromosome 18q21-23 as determined by hybridization to flow-sorted chromosomes and by in situ hybridization. There appear to be two common PAI-2 alleles that differ by six nucleotides in exons 1, 4, and 8. The structure of the PAI-2 gene is quite different from that of PAI-1 although these two inhibitors have common target protease specificity. In contrast, the structure of the PAI-2 gene is very similar to that of the chicken ovalbumin gene. When protein sequences are aligned to obtain maximal identity, six of the seven intron positions in the PAI-2 gene are identical to those in the chicken ovalbumin gene. We conclude that PAI-2 is the closest mammalian homologue of avian ovalbumin.

Amino Acid Sequence↗
PubMed1991

Sequence of three members and expression of a new major subfamily of glutelin genes from rice.

Three members have been isolated of an additional glutelin gene subfamily, named subfamily B, consisting of about five members per haploid rice genome. Restriction fragment length polymorphism analysis showed major differences between Japonica and Indica lines, indicating the divergence of the subfamily since the split between the two varieties. While corresponding exons of the subfamily B showed 80 to 88% nucleotide sequence homology, those exons were only 60-65% homologous to those of the glutelin A subfamily, distinguishing them from the subfamily A. Intron position and derived polypeptide structure, in addition to the nucleotide sequence, confirm the subfamily B members as glutelins. Analysis of RNA from seeds of different stages of development showed that the subfamily B members were expressed at the same time as those of subfamily A, demonstrating coordinated regulation of the two subfamilies.

Amino Acid Sequence↗
PubMed1997

Genomic organization and evolution of alternative exons in a Drosophila calcium channel gene.

The genomic organization of a gene coding for an alpha 1 subunit of a voltage-gated calcium channel of Drosophila melanogaster (Dmca IA) was determined. Thirty-four exons, distributed over 45 kb of genomic sequence, have been identified and mapped, including exons in three regions involved in alternative splicing and new sites potentially involved in RNA editing. The comparison of the intron/exon boundaries of this channel with a mammalian counterpart shows that the genomic structure of these two genes has remained fairly similar during evolution, with more than half of the Drosophila intron positions being perfectly conserved compared to the human channel. Phylogenetic analysis of the mutually exclusive alternative exons revealed that they have diverged considerably. It is suggested that this divergence, rather than reflecting evolutionary age, is the likely result of accelerated rates of evolution following duplication.

Amino Acid Sequence↗
PubMed2003

Genomic comparison of P-type ATPase ion pumps in Arabidopsis and rice.

Members of the P-type ATPase ion pump superfamily are found in all three branches of life. Forty-six P-type ATPase genes were identified in Arabidopsis, the largest number yet identified in any organism. The recent completion of two draft sequences of the rice (Oryza sativa) genome allows for comparison of the full complement of P-type ATPases in two different plant species. Here, we identify a similar number (43) in rice, despite the rice genome being more than three times the size of Arabidopsis. The similarly large families suggest that both dicots and monocots have evolved with a large preexisting repertoire of P-type ATPases. Both Arabidopsis and rice have representative members in all five major subfamilies of P-type ATPases: heavy-metal ATPases (P1B), Ca2+-ATPases (endoplasmic reticulum-type Ca2+-ATPase and autoinhibited Ca2+-ATPase, P2A and P2B), H+-ATPases (autoinhibited H+-ATPase, P3A), putative aminophospholipid ATPases (ALA, P4), and a branch with unknown specificity (P5). The close pairing of similar isoforms in rice and Arabidopsis suggests potential orthologous relationships for all 43 rice P-type ATPases. A phylogenetic comparison of protein sequences and intron positions indicates that the common angiosperm ancestor had at least 23 P-type ATPases. Although little is known about unique and common features of related pumps, clear differences between some members of the calcium pumps indicate that evolutionarily conserved clusters may distinguish pumps with either different subcellular locations or biochemical functions.

Adenosine Triphosphatases↗
PubMed1998

Characterization and chromosome location of the gene GSTZ1 encoding the human Zeta class glutathione transferase and maleylacetoacetate isomerase.

The Zeta class of cytosolic glutathione-S-transferases (GSTs) has recently been identified and spans a range of species from plants to humans. The cDNA and protein of a human member of this class have been previously characterised in our laboratory. This cDNA has also been described as maleylacetoacetate isomerase (MAAI), an enzyme of the phenylalanine catabolism pathway (Fernandez-Canon and Penalva, 1998). The present study has determined the structure and chromosome location of the gene encoding human GSTZ1/MAAI. The gene spans approximately 10.9 kb and is composed of 9 exons. Three intron positions of GSTZ1 were precisely conserved compared to the carnation and Caenorhabditis elegans Zeta GST genes. Fluorescent in situ hybridization mapped the gene to a single locus on chromosome 14q24.3, which is in agreement with an independent localization between the Genethon markers D14S263 and D14S67. The coding region of the gene differed from the GSTZ1 cDNA at two nucleotide positions in exon 3, resulting in Lys-32-->Glu and Arg-42--> Gly substitutions. This gene structure information will allow analysis of the polymorphism in genomic DNA samples, and enables further investigations into genetic defects in this step of the phenylalanine catabolism pathway.

Amino Acid Sequence↗
PubMed1988

Isolation and analysis of the mouse opsin gene.

We have identified three overlapping 5'-truncated mouse opsin cDNA clones by immunologically screening a lambda gt11 retina expression library. Using one of the cDNA clones as a probe, we isolated a 5 kb genomic fragment that encompassed the complete coding sequence for mouse opsin. The coding region for opsin was interrupted by four introns positioned precisely as those previously described for other mammalian opsins. In contrast to the single major opsin mRNA in the bovine and human retina, Northern analysis of mouse retina RNA demonstrated the presence of at least five distinct species of polyadenylated opsin mRNAs. Their sizes ranged from 1.7 kb to 5.1 kb.

Amino Acid Sequence↗
PubMed2005

Isolation and sequence analysis of P450 genes from a pyrethroid resistant colony of the major malaria vector Anopheles funestus.

Pyrethroid resistance has been demonstrated in populations of Anopheles funestus from South Africa and southern Mozambique. Resistance is associated with elevated P450 monooxygenase enzymes. In this study, degenerate primers based on conserved regions of Anopheles gambiae P450 CYP4, 6 and 9 families were used to amplify genomic and cDNA templates from A. funestus. A total of 12 CYP4, 12 CYP6 and 7 CYP9 partial genes have been isolated and sequenced. BLAST results revealed that A. funestus P450s generally have a high sequence identity to A. gambiae with above 75% identity at the amino acid level. The exception is CYP9J14. The A. gambiae P450 showing highest identity to CYP9J14 exhibits only 55% identity suggesting that CYP9J14 may have arisen from a recent duplication event. Molecular phylogenetic analysis based on amino acid sequences also supported this hypothesis. Intron positions, but not size, were highly conserved between the two species. The high level of orthology that exists in the P450 gene families of these two species may facilitate the prediction of individual P450 protein function.

Amino Acid Sequence↗
PubMed2001

Identification, mapping, and phylogenetic analysis of three novel chicken CC chemokines.

We have identified three novel chicken CC chemokine genes among cDNA clones derived from lipopolysaccharide-stimulated cells of the chicken macrophage cell line HD11. Two of these chemokines show DNA sequence homology to the mammalian genes SCYA20 (MIP-3alpha) and SCYA5 (RANTES), while the third shows similar levels of homology to several mammalian CC chemokines. Sequencing of genomic DNA showed that all three chicken chemokines possess the three-exon structure and conserved intron positions typical of mammalian CC chemokines. Genetic mapping of the three chicken chemokines locates them in three chromosomal regions which correspond to regions containing homologous chemokines in humans. Phylogenetic analysis of the currently known chicken and human chemokines suggests that individual chicken and human chemokines derive from common ancestral genes in patterns that reflect their genomic positions, indicating that the diversity of chemokine genes pre-dated avian-mammalian divergence. Since the function of the chemokines is principally to act as intermediates between stimulated cells and specific subsets of responding immune cells, this suggests that the complex organization of the immune system and diversity of responding cells were largely in place at that time.

Animals↗
PubMed1999

pADPRT-2: a novel mammalian polymerizing(ADP-ribosyl)transferase gene related to truncated pADPRT homologues in plants and Caenorhabditis elegans.

Until recently, poly(ADP-ribosyl)ation was supposed to be confined only to polymerizing(ADP-ribosyl)transferase/(ADP-ribose)polymerase (E.C. 2.4.2.30). Here, we present novel polymerizing(ADP-ribosyl)transferase homologues from mouse and man that lack all of the N-terminal DNA binding and BRCA1 C-terminus domains and will be designated polymerizing(ADP-ribosyl)transferase-2 as distinguished from the classical polymerizing(ADP-ribosyl)transferase (polymerizing(ADP-ribosyl)transferase-1). The murine polymerizing(ADP-ribosyl)transferase-2 gene shares three identical intron positions with its Caenorhabditis elegans (EMBL nucleotide sequence database Z47075) and one with the Arabidopsis thaliana homologue ('APP', GenBank database AF069298). Expression of the murine polymerizing(ADP-ribosyl)transferase-2 gene was elevated in spleen, thymus and testis and the corresponding poly(ADP-ribosyl)ation activity might account for most of the residual poly(ADP-ribosyl)ation observed in polymerizing(ADP-ribosyl)transferase-1(-/-) mice.

Amino Acid Sequence↗
PubMed2004

Calcium sensors and their interacting protein kinases: genomics of the Arabidopsis and rice CBL-CIPK signaling networks.

Calcium signals mediate a multitude of plant responses to external stimuli and regulate a wide range of physiological processes. Calcium-binding proteins, like calcineurin B-like (CBL) proteins, represent important relays in plant calcium signaling. These proteins form a complex network with their target kinases being the CBL-interacting protein kinases (CIPKs). Here, we present a comparative genomics analysis of the full complement of CBLs and CIPKs in Arabidopsis and rice (Oryza sativa). We confirm the expression and transcript composition of the 10 CBLs and 25 CIPKs encoded in the Arabidopsis genome. Our identification of 10 CBLs and 30 CIPKs from rice indicates a similar complexity of this signaling network in both species. An analysis of the genomic evolution suggests that the extant number of gene family members largely results from segmental duplications. A phylogenetic comparison of protein sequences and intron positions indicates an early diversification of separate branches within both gene families. These branches may represent proteins with different functions. Protein interaction analyses and expression studies of closely related family members suggest that even recently duplicated representatives may fulfill different functions. This work provides a basis for a defined further functional dissection of this important plant-specific signaling system.

Amino Acid Sequence↗
PubMed2000

Tomato contains homologues of Arabidopsis cryptochromes 1 and 2.

Cryptochromes are blue light photoreceptors found in both plants and animals. They probably evolved from photolyases, which are blue/UV-light-absorbing photoreceptors involved in DNA repair. In seed plants, two different cryptochrome (CRY) genes have been found in Arabidopsis and one in Sinapis, while three genes have been found in the fern Adiantum. We report the characterisation of tomato CRY genes CRY1 and CRY2. They map to chromosomes 4 and 9, respectively, show relatively constitutive expression and encode proteins of 679 and 635 amino acids, respectively. These proteins show higher similarity to their Arabidopsis counterparts than to each other, suggesting that duplication between CRY1 and CRY2 is an ancient event in the evolution of seed plants. The seed plant cryptochromes form a group distinct from the fern cryptochromes, implying that only one gene was present in the common ancestor between these two groups of plants. Most intron positions in CRY genes from plants and ferns are highly conserved. Tomato cryl and cry2 proteins carry C-terminal domains 210 and 160 amino acids long, respectively. Several conserved motifs are found in these domains, some of which are common to both types of cryptochromes, while others are cryptochrome-type-specific.

Amino Acid Sequence↗
PubMed1994

Mapping of the beta 2 subunit gene (GABRB2) to microdissected human chromosome 5q34-q35 defines a gene cluster for the most abundant GABAA receptor isoform.

The gamma-aminobutyric acid receptor (GABAAR) is a multisubunit Cl- channel that mediates most fast inhibitory synaptic transmission in the central nervous system. Molecular evolution has given rise to many genetic variants of GABAAR subunits, including alpha 1-6, beta 1-4, gamma 1-4, delta, and rho 1-2, suggesting that an enormous number of combinations of subunits are possible. Here we report that the beta 2 gene is located on chromosome 5q34-q35, defining a cluster comprising alpha 1, beta 2, and gamma 2 genes that together code for the most abundant GABAAR isoform. The fact that intron position is conserved in the beta 1-3 genes, taken together with the observation that chromosomes 4 and 15 also contain distinct alpha-beta-gamma gene clusters, strongly suggests that an ancestral alpha-beta-gamma cluster was duplicated and translocated to at least two different chromosomes. This organization of GABAAR gene clusters may have been preserved as linkage provides a mechanism for facilitating coordinate gene expression.

Amino Acid Sequence↗
PubMed1993

Organization of a rainbow trout estrogen receptor gene.

The complete coding region of the estrogen receptor gene was isolated from a rainbow trout genomic library. This gene is divided into ten exons spanning at least 30 kb of genomic DNA. With two exceptions, intron positions are identical to those of the human estrogen receptor gene. The 5' end of the gene, including 1.7 kb of the promoter region, was sequenced. This region exhibits several putative regulatory elements. Localization of a potential estrogen responsive element to the first exon suggests that this gene is autoregulated. This 5' end region was also shown to be able to drive the expression of a CAT reporter gene in Xenopus laevis oocytes.

Amino Acid Sequence↗
PubMed2004

Phylogenetic origin of LI-cadherin revealed by protein and gene structure analysis.

The intestine specific LI-cadherin differs in its overall structure from classical and desmosomal cadherins by the presence of seven instead of five cadherin repeats and a short cytoplasmic domain. Despite the low sequence similarity, a comparative protein structure analysis revealed that LI-cadherin may have originated from a five-repeat predecessor cadherin by a duplication of the first two aminoterminal repeats. To test this hypothesis, we cloned the murine LI-cadherin gene and compared its structure to that of other cadherins. The intron-exon organization, including the intron positions and phases, is perfectly conserved between repeats 3-7 of LI-cadherin and 1-5 of classical cadherins. Moreover, the genomic structure of the repeats 1-2 and 3-4 is identical for LI-cadherin and highly similar to that of the repeats 1-2 of classical cadherins. These findings strengthen our assumption that LI-cadherin originated from an ancestral cadherin with five domains by a partial gene duplication event.

Amino Acid Sequence↗
PubMed1989

The genomic nucleotide sequences of two differentially expressed actin-coding genes from the sea star Pisaster ochraceus.

The genomic sequences of two differentially expressed actin genes from the sea star Pisaster ochraceus are reported. The cytoplasmic actin gene (Cy) is expressed in eggs and early development. The muscle actin gene (M) is expressed in tube feet and testes. Both genes contain an 1125-nucleotide coding region interrupted by three introns at codons 41, 121 and 204. Gene M contains two additional introns at codons 150 and 267. The intron position at codon 150, although present in higher vertebrate actins, has not been reported in actin genes from invertebrates. The M gene coding region has 89.5% nucleotide homology to the Cy gene, and differs from the Cy actin gene in 13 of 375 amino acids (aa), 11 of which are found in the C-terminal half of the gene. The C-terminal half of the M gene contains a significant number of muscle isotype codons. Even though there is only 1 aa change in the first 150 codons, there have been limited substitutions at many four-fold degenerate sites which may indicate selection pressure upon the secondary structure of the mRNA and/or a biased codon usage. Variant CCAAT, TATA, and poly(A)-addition signals have been identified in the 5' and 3' flanking regions. The presence of 5' and 3' splice junction sequences in the 5' flanking region of the Cy gene suggests the potential for an intron there.

Actins↗
PubMed1989

Transcriptional and posttranscriptional regulation contributes to the sex-regulated expression of two sequence-related genes at the janus locus of Drosophila melanogaster.

We investigated the structure and developmental pattern of expression of two genes clustered at the janus locus, located at 99D.3R. Data obtained from genomic and cDNA sequencing and from a combination of S1 mapping and primer extension experiments indicated a very unusual organization of this locus, which appeared to be composed of two partially overlapping genes, designated janA and janB. These two genes were found to be transcribed in the same direction. janA encoded one minor and two major transcripts. The 5' end of the janB mRNA mapped within the 3' untranslated region of the janA transcribed sequence. The overlapping region was 118 bases long. Similarities observed between these two genes with respect to both peptidic sequence and intron position strongly suggested that this locus originated from the duplication of an ancestral transcription unit. However, each of the resulting genes has acquired its own specificity of expression linked to sex determination. The janB transcript was detected only in males, and its expression at the adult stage was restricted to germ line cells. The janA gene displayed a much more complex expression; one of the major mRNAs was found in both sexes and at all stages, whereas the two other janA transcripts were expressed only in males.

Amino Acid Sequence↗
PubMed1991

Macronuclear and micronuclear configurations of a gene encoding the protein synthesis elongation factor EF 1 alpha in Stylonychia lemnae.

The micronuclear and macronuclear configurations of a gene encoding the protein synthesis elongation factor EF 1 alpha in the hypotrich ciliate Stylonychia lemnae were compared. The two sequences are generally colinear. The coding sequence of the micronuclear gene is, however, interrupted by a 64 bp insert flanked by a 2 bp direct repeat in a gene region which is moderately conserved among EF 1 alpha genes of different organisms. The insertion site is distinct from known intron positions in eukaryotic EF 1 alpha genes. The insert sequence shows inverted repeats at its ends and thus exhibits typical features of an internal eliminated sequence (IES). Comparison with other such sequences in the related organism Oyxtricha nova shows that the IES falls into a new group of such elements. The macronuclear gene exhibits a strikingly limited codon usage, which cannot be simply explained by the overall base composition of the DNA but probably also relates to the very high copy number of the macronuclear gene and the putative high amount of the gene product.

Amino Acid Sequence↗
PubMed1998

Structure of the human CD94 C-type lectin gene.

The genomic structure of the human CD94 gene was obtained by analyzing genomic clones obtained from two different libraries. The CD94 gene contains six exons separated by five introns. The carbohydrate-recognition domain (CRD) is encoded by three exons, and the conservation of intron positions within the CRD indicated that CD94 is closely related to group V of C-type lectins. Primer extension and S1 nuclease protection assays showed that initiation of transcription in the CD94 gene is heterogeneous, but restricted to a 60 base pair region around the major initiation site enclosed within a putative initiator element (TTA+1TTCA). The study of the promoter region of CD94 may help to understand the selective expression of this C-type lectin glycoprotein on NK cells and subsets of cytotoxic T cells.

Antigens, CD↗