Biomedical subjects

David M Irwin

Publications and source records attributed to David M Irwin.

11 recordsLinked to original sources

PubMed2006

In silico identification and Bayesian phylogenetic analysis of multiple new mammalian kallikrein gene families.

Kallikrein gene families have been identified previously in genomes of the human, the mouse, and the rat, and individual kallikrein-like genes have been found in many more species. This study presents the in silico identification of kallikrein gene families in the recently sequenced genomes of four additional mammalian species, the chimpanzee, the dog, the pig, and the opossum. Phylogenies were constructed with gene sequences from all seven mammalian families, using Bayesian analysis, which clarified the evolutionary relationships between these genes. Individual gene sequences, as well as concatenated constructs of multiple sequences, were used. Fifteen kallikrein genes were located in the chimpanzee (Pan troglodytes) genome, while only 14 were identified in the canine (Canis familiaris) genome as no orthologue to human KLK3 was found. Thirteen genes were identified from the pig (Sus scrofa) genome, which lacked homologues to KLK2 and KLK3, and 11 genes, orthologous to human KLK5 through KLK15, were found in the opossum (Monodelphis domestica) genome. No kallikrein genes were identified from the available genome sequences of the chicken (Gallus gallus) or African clawed frog (Xenopus tropicalis). Within the family of kallikreins several subfamilies were suggested by phylogenetic analysis. One consisted of KLK4, KLK5, and KLK14; another of KLK9, KLK11, and KLK15; a third of KLK10 and KLK12; a fourth of KLK6 and KLK13; and finally one of KLK8 and the classical kallikreins (KLK1, KLK2, and KLK3).

Animals↗

PubMed2006

Cloning of stanniocalcin (STC) cDNAs of divergent teleost species: Monomeric STC supports monophyly of the ancient teleosts, the osteoglossomorphs.

Molecular cloning of teleost stanniocalcin (STC) cDNAs was undertaken in two species of order Osteoglossiformes of subdivision Osteoglossomorpha and one species of each of orders Cypriniformes and Perciformes within the subdivision Euteleostei. The elephantnose (Gnathonemus petersii) and the butterflyfish (Pantadon buchholzi) are basal teleosts in different osteoglossiforme suborders yet their 218 amino acid (aa) mature hormones, from prehormones of 249 and 251aa, respectively, have only 10 cysteine residues. A substitution for cysteine at the intermonomeric disulfide linkage site, implies that their STCs exist as monomeric peptides, as is the case with STC from another osteoglossormorph, arawana [Amemiya, Y., Marra, L.E., Reyhani, N., Youson, J.H., 2002. Stanniocalcin from an ancient teleost: a monomeric form of the hormone and a possible extracorpuscular distribution. Mol. Cell. Endocrinol. 188, 141-150]. The STC cDNA of the generalized teleost and cyprinid, the white sucker (Catostomus commersoni), encodes a prehormone of 249aa with a signal peptide of 31aa and a mature protein of 218aa that possesses 11 cysteine residues. The latter feature is consistent with a previous analysis that white sucker mature STC is a glycosylated, homodimeric peptide [Amemiya, Y., Marra, L.E., Reyhani, N., Youson, J.H., 2002. Stanniocalcin from an ancient teleost: a monomeric form of the hormone and a possible extracorpuscular distribution. Mol. Cell. Endocrinol. 188, 141-150]. An open reading frame of the STC cDNA of the derived teleost and perciforme, the smallmouth bass (Micropterus dolomieui), encodes a prehormone of 255aa with a signal peptide of 33aa and a mature protein of 222aa. The position of the 11 cysteines in smallmouth bass STC suggests that it exists as a homodimeric peptide. A phylogenetic analysis, using the new STC-1 amino acid sequences and those in the gene data base provided strong support for monophyly of the Osteoglossomorpha and indicated, with positioning of white sucker and smallmouth bass, that this molecule has some utility as a taxonomic marker. This analysis also suggested that two STC-1 gene sequences exist in multiple fish genomes, and that they may be a product of the fish-specific genome duplication. The mutation in the osteoglossomorph STC likely occurred after the appearance of the first teleosts and before movement of the tectonic plates.

Amino Acid Sequence↗

PubMed2005

Intron 1 sequences are required for pancreatic expression of the human proglucagon gene.

The mammalian proglucagon gene is expressed in pancreatic islet A-cells, intestinal L-cells, and select neurons of the brain, where posttranslational processing results in the liberation of a unique profile of peptides. Despite the importance of proglucagon-derived peptides in human biology, little is known about the regulation of the human gene, as the rat gene has been the preferred model for understanding the regulation of proglucagon gene expression. Previously, we have shown that although the immediate promoter region of the rat proglucagon gene is sufficient for expression in pancreatic islet cells, the homologous human proglucagon promoter sequences are not sufficient. We have now used a comparative genomic approach to identify noncoding sequences near the human proglucagon gene that are conserved among mammals, and thus potentially are regulatory sequences. Our alignments identified three evolutionarily conserved noncoding regions (ECR), one is the immediate promoter region (ECR1), the second is about 5 kb 5' to the mRNA start site (ECR2), and the third is near the 3' end of the first intron (ECR3). Our in vitro transient transfection assays with reporter gene constructs that include the human ECR3 support expression in rodent islet cell lines. Complementary studies with transgenic mice possessing a reporter gene regulated by a human proglucagon gene promoter-intron 1 (including ECR3) sequences express the reporter gene in the pancreas, as well as the intestine and selected neurons. These studies suggest that conserved sequences within intron 1 of the human proglucagon gene are important for expression in the pancreas.

Animals↗

PubMed2005

Structure and expression of the chicken proglucagon gene.

The rat and human proglucagon gene immediate promoter regions have differing transcriptional activities in islet cell lines. It is unclear upon which lineage the expression changes have occurred, or which base changes and transcription factors explain the changes in promoter activity. We have studied the expression of the chicken proglucagon gene to better understand changes in mammalian proglucagon gene promoter activity. The chicken proglucagon gene is composed of seven exons, and contains an additional exon that contains much of intervening peptide 1 that has not been seen in any other proglucagon gene. Despite very limited sequence identity between chicken and rat proglucagon promoters, the chicken proglucagon promoter supports reporter gene expression in rodent glucagon-expressing cell lines. These results suggest that the immediate proglucagon promoter region likely has retained ability to be expressed in islet cells, but a few changes to this sequence on the human lineage have extinguished expression of the immediate promoter region. Our work also demonstrate that in contrast to the conserved human proglucagon promoter region which has lost promoter activity that significant changes in proglucagon promoter sequence can occur yet retain expression potential.

Animals↗

PubMed2004

A second insulin gene in fish genomes.

The recent characterization of diverse vertebrate genomes has revealed the importance of gene duplication in vertebrate evolution. Evidence suggests that a genome duplication event occurred on the lineage leading to teleost fish-species that are often used to understand human biology. The existence of a genome duplication event complicates the use of fish as a model for human diseases as there are often two fish homologues for a single copy human gene. Often the second homologue has not been recognized. Our searches of the near complete zebrafish and fugu fish genomes indicate that both species have two insulin genes. Phylogenetic analysis indicates that the two genes are likely the product of the fish-specific genome duplication. The maintenance of two insulin genes within the fish suggests that the two genes have different functions. Thus the well-characterized insulin genes in some fish species may not be complete homologues of the human insulin gene.

Amino Acid Sequence↗

PubMed2004

Fish proglucagon genes have differing coding potential.

Regulation of tissue-specific hormone production involves transcription, post-translational and physiological regulation. The proglucagon gene has been an ideal molecule for understanding many aspects of regulation of hormone production. Gene duplications often allow the evolution of new gene function, and the proglucagon gene has been duplicated on the lineage leading to teleost fish, while most other vertebrates have only a single proglucagon gene. The recent characterization of near complete pufferfish and zebrafish genomes allowed us to determine the structure of the duplicated genes. We searched the pufferfish and zebrafish genomes for proglucagon-like sequences. Our searches identified two proglucagon-like genes in both the pufferfish and zebrafish genomes. In pufferfish the proglucagon-like genes are surrounded by genes that are similar to genes that flank the proglucagon gene in mammalian genomes, indicating that gene order near the proglucagon gene has been maintained since the fish-mammal divergence approximately 450 million years ago. Characterization of the duplicated fish proglucagon genes indicates that one of the two genes is predicted to encode glucagon, GLP-1 and GLP-2. In contrast, the second proglucagon gene is predicted to encode only glucagon and GLP-1, but not GLP-2. Thus the two fish proglucagon genes have different coding potential, and, therefore likely differ in function. Regulation of gene expression potentially has a role in the regulation of production of proglucagon derived peptides in fish.

Amino Acid Sequence↗

PubMed2004

Evolution of cow nonstomach lysozyme genes.

Expansion of the lysozyme gene family is associated with the evolution of the ruminant lifestyle in ruminant artiodactyls such as the cow. Gene duplications allowed recombination between stomach lysozyme genes that may have assisted in the evolution of an enzyme adapted to survive and function in the stomach environment. Despite amplification of lysozyme genes, cow tears, milk, and blood are considered to be lysozyme deficient. Here we have identified 2 new cow lysozyme cDNA sequences and show that at least 4 different lysozymes are expressed in cows in nonstomach tissues and probably function as antibacterial defence enzymes. These 4 lysozyme genes are in addition to the 4 digestive lysozyme genes expressed in the stomach, yielding a number of expressed lysozyme genes in the cow larger than that found in most nonlysozyme-deficient mammals. In contrast to expectations, evidence for recombination between stomach and nonstomach lysozyme genes was found. Recombination, through concerted evolution, may have allowed some lysozymes to acquire the ability to survive in occasional acidic environments.

Amino Acid Sequence↗

PubMed2003

Molecular evolution of vertebrate goose-type lysozyme genes.

We have found that mammalian genomes contain two lysozyme g genes. To better understand the function of the lysozyme g genes we have examined the evolution of this small gene family. The lysozyme g gene structure has been largely conserved during vertebrate evolution, except at the 5' end of the gene, which varies in number of exons. The expression pattern of the lysozyme g gene varies between species. The fish lysozyme g sequences, unlike bird and mammalian lysozyme g sequences, do not predict a signal peptide, suggesting that the encoded proteins are not secreted. The fish sequences also do not conserve cysteine residues that generate disulfide bridges in the secreted bird enzymes, supporting the hypothesis that the fish enzymes have an intracellular function. The signal peptide found in bird and mammalian lysozyme g genes may have been acquired as an exon in the ancestor of birds and mammals, or, alternatively, an exon encoding the signal peptide has been lost in fish. Both explanations account for the change in gene structure between fish and tetrapods. The mammalian lysozyme g sequences were found to have evolved at an accelerated rate, and to have not perfectly conserved the known active site catalytic triad of the bird enzymes. This observation suggests that the mammalian enzymes may have altered their biological function, as well.

Amino Acid Sequence↗

PubMed2003

Aberrant regulation of human intestinal proglucagon gene expression in the NCI-H716 cell line.

Despite interest in understanding glucagon-like peptide-1 (GLP-1) production, the factors important for GLP-1 biosynthesis remain poorly understood. We examined control of human proglucagon gene expression in NCI-H716 cells, a cell line that secretes GLP-1 in a regulated manner. Insulin, phorbol myristate acetate, or forskolin, known regulators of rodent proglucagon gene expression, had no effect, whereas sodium butyrate decreased levels of NCI-H716 proglucagon mRNA transcripts. The inhibitory effect of sodium butyrate was mimicked by trichostatin A but was not detected with sodium acetate or isobutyrate. The actions of butyrate were not diminished by the ERK1/2 inhibitor PD98059, p38 inhibitor SB203580, or soluble guanylate cyclase inhibitor LY83583 or following treatment of cells with KT5823, a selective inhibitor of cGMP-dependent protein kinase. NCI-H716 cells expressed multiple proglucagon gene transcription factors including isl-1, pax-6, pax-2, cdx-2/3, pax-4, hepatocyte nuclear factor (HNF)-3 alpha, HNF-3beta, HNF-3 gamma, and Nkx2.2. Nevertheless, the butyrate-dependent inhibition of proglucagon gene expression was not associated with coordinate changes in transcription factor expression and both the human and rat transfected proglucagon promoters were transcriptionally inactive in NCI-H716 cells. Hence, NCI-H716 cells may not be a physiologically optimal model for studies of human enteroendocrine proglucagon gene transcription.

Adenocarcinoma↗

PubMed2002

Ancient duplications of the human proglucagon gene.

The human proglucagon gene (GCG) is encoded within a finished 576-kb DNA sequence generated by the Human Genome Project. GCG is flanked by 18 kb and 65 kb of DNA, 5' and 3', respectively, that do not encode genes. The genomic sequence that includes GCG was found to have a long history of gene duplication events. Some members of the glucagon-like family of genes, GCG on chromosome 2 and GIP on chromosome 17, may be products of ancient genome duplications on the early vertebrate lineage. A large genomic tandem duplication event that included DPP4-like and GCG genes occurred before the amphibian-mammal divergence, but one of the duplicated copies of GCG has been lost on the human lineage. Recently, a processed pseudogene of the X-chromosome-linked gene TIMM8A was inserted downstream of GCG. Some ancient duplicates of GCG may retain physiological functions in other vertebrates.

Animals↗

PubMed2002

Human glucagon gene promoter sequences regulating tissue-specific versus nutrient-regulated gene expression.

The glucagon-like peptides (GLPs) are synthesized and secreted in a nutrient-dependent manner in rodents; however, the factors regulating human GLP-1 and GLP-2 biosynthesis remain unclear. To understand how nutrients regulate human proglucagon gene expression, we studied the expression of a human proglucagon promoter-growth hormone (GH) transgene in 1.6 human glucagon-GH transgenic mice. Fasting-refeeding significantly decreased and increased the levels of circulating mouse insulin and transgene-derived hGH (P < 0.05 fasting vs. refeeding) and decreased and upregulated, respectively, the levels of endogenous mouse proglucagon RNA in the ileum but not in the jejunum or colon. High-fiber feeding significantly increased the levels of glucose-stimulated circulating hGH and upregulated levels of mouse intestinal proglucagon gene expression in the jejunum, ileum, and colon (P < 0.05, 0 vs. 30% fiber diet). In contrast, neither fasting-refeeding nor a high-fiber diet upregulated the expression of the human proglucagon promoter-hGH transgene. These findings demonstrate that human proglucagon gene regulatory sequences specifying tissue-specific expression in gut endocrine cells are not sufficient for recognition of energy-derived signals regulating murine glucagon gene expression in enteroendocrine cells in vivo.

Animal Nutritional Physiological Phenomena↗