Comparative genomic aspects of rat, mouse and human MHC class I gene regions

In this review a particular aspect of the genomic structure of the major histocompatibility complex (MHC), the organization of MHC class I regions, will be discussed for the rat in comparison to mouse and human.     

Haptoglobin in Carnivora: a unique molecular structure in bear, cat and dog haptoglobins

Haptoglobin (Hp), a hemoglobin-binding protein in plasma, consists of α and β subunits and has a tetra-chain arrangement (β-α-α-β) connected by disulfide bridges in most mammals so far examined. Dog Hp has been reported to be unique compared with other Hps in respect that (1) the two αβ units are joined by a non-covalent interaction rather than a disulfide bridge and (2) the α chain has an oligosaccharide-binding sequence (Asn-X-Ser/Thr) and is glycosylated. To determine whether the unique structures of dog Hp are common in the Carnivora, we purified Hps from sera of bear and cat, and analyzed their subunit structure and partial amino acid sequences. The analyses by gel filtration and sodium dodecyl sulfate-polyacrylamide gel electrophoresis, under both reducing and non-reducing conditions, revealed that bear and cat Hps have similar subunit arrangements to dog Hp, suggesting the absence of a disulfide bridge between two α chains. This was confirmed by amino acid sequence analysis of the α chains: that is, Cys₁₅ participating in the inter-α chain disulfide bridge was replaced by Val in bear or Leu in cat and dog. Thus, the unique subunit arrangement of Hp reported in dog may be common in the Carnivora. In contrast to dog Hp, however, α chains of bear and cat Hps were found not to have the typical oligosaccharide binding sequence on their α chains and were not glycosylated.     

Scanning electron microscope study of cat and dog enamel structure

Scanning electron microscopy revealed several similarities as well as significant differences in the enamel structure between cat and dog teeth. Three enamel layers were present in both species; a surface rodless (aprismatic) layer, an outer layer of parallel rods (only at some sites), and an inner layer with prominent Hunter-Schreger bands. In the inner layer of both carnivores, the diameter of individual rods varied significantly and frequently their course changed abruptly with respect to neighboring rods. In dog teeth the cross-sectional shape of inner enamel rods was pleomorphic, but hexagonal in outer enamel. In contrast, cat enamel rods were rounded in both inner and outer enamel layers. Hunter-Schreger bands of cats circumscribed the teeth in relatively straight segments, but these bands showed pronounced waviness in dog teeth. In cats and dogs the surface rodless layer was structurally continuous with subjacent interrod enamel and covered all tooth surfaces with the exception of the cervical areas. The data show that the structure of inner and outer enamel layers differ between these two carnivore species and that the enamel structure of the cat was most similar to that described in humans. One principal difference between carnivore and human teeth is that the growth lines of carnivores do not terminate at perikymata on the tooth surface.     

Comparative genomic analysis of two avian (quail and chicken) MHC regions

We mapped two different quail Mhc haplotypes and sequenced one of them (haplotype A) for comparative genomic analysis with a previously sequenced haplotype of the chicken Mhc. The quail haplotype A spans 180 kb of genomic sequence, encoding a total of 41 genes compared with only 19 genes within the 92-kb chicken Mhc. Except for two gene families (B30 and tRNA), both species have the same basic set of gene family members that were previously described in the chicken "minimal essential" Mhc. The two Mhc regions have a similar overall organization but differ markedly in that the quail has an expanded number of duplicated genes with 7 class I, 10 class IIB, 4 NK, 6 lectin, and 8 B-G genes. Comparisons between the quail and chicken Mhc class I and class II gene sequences by phylogenetic analysis showed that they were more closely related within species than between species, suggesting that the quail Mhc genes were duplicated after the separation of these two species from their common ancestor. The proteins encoded by the NK and class I genes are known to interact as ligands and receptors, but unlike in the quail and the chicken, the genes encoding these proteins in mammals are found on different chromosomes. The finding of NK-like genes in the quail Mhc strongly suggests an evolutionary connection between the NK C-type lectin-like superfamily and the Mhc, providing support for future studies on the NK, lectin, class I, and class II interaction in birds.     

Comparative genomic analysis of human and chimpanzee proteases

Proteolytic enzymes are implicated in multiple physiological and pathological processes. The availability of the sequence of the chimpanzee genome has allowed us to determine that the chimpanzee degradome-the repertoire of protease genes from this organism-is composed of at least 559 protease and protease-like genes and is virtually identical to that of human, containing 561 genes. Despite the high degree of conservation between both genomes, we have identified important differences that vary from deletion of whole genes to small insertion/deletion events or single nucleotide changes that lead to the specific gene inactivation in one species, mostly affecting immune system genes. For example, the genes encoding PRSS33/EOS, a macrophage serine protease conserved in most mammals, and GGTLA1 are absent in chimpanzee, while the gene for metalloprotease MMP23A, located in chromosome 1p36, has been specifically duplicated in the human genome together with its neighbor gene CDC2L1. Other differences arise from single nucleotide changes in protease genes, such as NAPSB and CASP12, resulting in the presence of functional genes in chimpanzee and pseudogenes in human. Finally, we have confirmed that the Trypanosoma lytic factor HPR is inactive in chimpanzee, likely contributing to the susceptibility of chimpanzees to T. brucei infection. This study provides the first analysis of the chimpanzee degradome and might contribute to the understanding of the molecular bases underlying variations in host defense mechanisms between human and chimpanzee.     

Osteogenesis imperfecta. Human, dog, cat, fox. Comparative analysis of the ultrastructural aspects

In the present work the authors have observed the ultrastructure of different types of cartilage and connective tissues of four different species of animals affected with osteogenesis imperfecta (man dog cat and young fox. The ultrastructural pictures demonstrate that the morphological aspects of cartilage of different species are often comparable and all cartilage tissues present the following characters: 1) Some lipid droplets inside the cytoplasm. 2) A reduction of the number and diameter of collagen fibrils. 3) A sensible increase of diameter of the alcianophilic bands that are ultrastructural representation of glycosaminoglycans. Some abnormal aspect has been seen on the connective non cartilagineus tissues.     

Nomenclature for factors of the dog major histocompatibility system (DLA), 2000: second report of the ISAG DLA Nomenclature Committee

The International Society for Animal Genetics (ISAG) Dog Leukocyte Antigen (DLA) Nomenclature Committee met during the "Comparative Evolution of the Mammalian major Histocompatibility Complex (MHC)" meeting in Manchester, UK on 10 September 2000. The main points discussed were the naming of class I genes and alleles, and the inclusion of alleles from other canidae.     

Primary structures of dog and cat amyloid A proteins: comparison to human AA

1. The complete amino acid sequences of canine and feline amyloid A (AA) proteins were determined and compared with the sequence of human AA protein. 2. The dog and cat AA proteins were 84% homologous with human AA through residue 69. 3. Between the residues which correspond to 69 and 70 in the human sequence, the dog and cat proteins had an insertion of eight amino acids after which homology with human AA resumed. 4. While human AA commonly ends at position 76, the carboxyl termini of dog and cat AA proteins corresponded to position 86 in the sequence of the precursor protein-serum amyloid A. 5. These results are particularly interesting with respect to evolution of the serum amyloid A gene family.     

Comparative effects of ketoconazole on rat, dog and human testicular steroidogenesis

Ketoconazole is an antifungal azole derivative which also inhibits the cytochrome P-450(17)alpha, catalyzing the conversion of progestins into androgens. The effects of ketoconazole on human, dog and rat testosterone biosynthesis were compared using short term incubations of dispersed testicular cells. The results showed that ketoconazole inhibited androgen biosynthesis at lower concentrations in dispersed human testicular cells (IC50: 0.08 mumol/l) than in canine (IC50: 0.1 mumol/l) and rat cells (IC50 greater than or equal to 0.2 mumol/l). Furthermore, they demonstrated that ketoconazole first inhibited the 17,20-lyase activity and then the 17-hydroxylation in rat and dog cells whereas only the 17-hydroxylation was affected in human cells.     

Genomic divergences among cattle,dog and human estimated from large-scale alignments of genomic sequences

Background

Approximately 11 Mb of finished high quality genomic sequences were sampled from cattle, dog and human to estimate genomic divergences and their regional variation among these lineages.

Results

Optimal three-way multi-species global sequence alignments for 84 cattle clones or loci (each >50 kb of genomic sequence) were constructed using the human and dog genome assemblies as references. Genomic divergences and substitution rates were examined for each clone and for various sequence classes under different functional constraints. Analysis of these alignments revealed that the overall genomic divergences are relatively constant (0.32–0.37 change/site) for pairwise comparisons among cattle, dog and human; however substitution rates vary across genomic regions and among different sequence classes. A neutral mutation rate (2.0–2.2 × 10(-9) change/site/year) was derived from ancestral repetitive sequences, whereas the substitution rate in coding sequences (1.1 × 10(-9) change/site/year) was approximately half of the overall rate (1.9–2.0 × 10(-9) change/site/year). Relative rate tests also indicated that cattle have a significantly faster rate of substitution as compared to dog and that this difference is about 6%.

Conclusion

This analysis provides a large-scale and unbiased assessment of genomic divergences and regional variation of substitution rates among cattle, dog and human. It is expected that these data will serve as a baseline for future mammalian molecular evolution studies.

     

Nomenclature for factors of the dog major histocompatibility system (DLA), 1998: first report of the ISAG DLA Nomenclature Committee

A Nomenclature committee for Factors of the Dog Major Histocompatibility System or Dog Leukocyte Antigen (DLA) has been convened under the auspices of the International Society for Animal Genetics (ISAG) to define a sequence based nomenclature for the genes of the DLA system. The remit of this committee includes: assignment of gene names rules for naming alleles assignment of names to published alleles assignment of names to new alleles rules for acceptance of new alleles DLA Nomenclature Committee, rules for acceptance, DLA genes and alleles, sequence based nomenclature.     

The cloning, genomic structure, localization, and expression of human deoxyribonuclease IIbeta

Acidic endonuclease activity is present in all cells in the body and much of this can be attributed to the previously cloned and ubiquitously expressed deoxyribonuclease II (DNase II). Database analysis revealed the existence of expressed sequence tags and genomic segments coding for a protein with considerable homology to DNase II. This report describes the cloning of this cDNA, which we term deoxyribonuclease IIbeta (DNase IIbeta) and comparison of its expression to that of the originally cloned DNase II (now termed DNase IIalpha). The cDNA encodes a 357 amino acid protein. This protein exhibits extensive homology to DNase IIalpha including an amino-terminal signal peptide and a conserved active site, and has many of the regions of identity that are conserved in homologs in other mammals as well as C. elegans and Drosophila. The gene encoding DNase IIbeta has identical splice sites to DNase IIalpha. Human DNase IIbeta is highly expressed in the salivary gland, and at low levels in trachea, lung, prostate, lymph node, and testis, whereas DNase IIalpha is ubiquitously expressed in all tissues. The expression pattern of human DNase IIbeta suggests that it may function primarily as a secreted enzyme. Human saliva was found to contain DNase IIalpha, but after immunodepletion, considerable acid-active endonuclease remained which we presume is DNase IIbeta. We have localized the gene for human DNase IIbeta to chromosome 1p22.3 adjacent (and in opposing orientation) to the human uricase pseudogene. Interestingly, murine DNase IIbeta is highly expressed in the liver. Uricase is also highly expressed in mouse but not human liver and this may explain the difference in expression patterns between human and mouse DNase IIbeta.     

The human BARX2 gene: genomic structure, chromosomal localization, and single nucleotide polymorphisms

The BARX genes 1 and 2 are Bar class homeobox genes expressed in craniofacial structures during development. In this report, we present the genomic structure, chromosomal localization, and polymorphic markers in BARX2. The gene has four exons, ranging in size from 85 to 1099 bp. BARX2 is localized on human chromosome 11q25, as determined by radiation hybrid mapping. In the mouse, Barx2 is coexpressed with Pitx2 in several tissues. Based on the coexpression, BARX2 was assumed to be a candidate gene for those cases of Rieger syndrome that cannot be associated with mutations of PITX2. Mutations in PITX2 cause some cases of Rieger syndrome, an autosomal dominant disorder affecting eyes, teeth, and umbilicus. DNA from Rieger patients was subjected to single-strand conformation polymorphism screening of the BARX2 coding region. Three single nucleotide polymorphisms were found in a normal population, although no etiologic mutations were detectable in over 100 cases of Rieger syndrome or in individuals with related ocular disorders.     

Cation specificity of propranolol-induced changes in RBC membrane permeability: comparative effects in human, dog and cat erythrocytes

Propranolol, in the presence of calcium, causes marked K efflux from human red blood cells (high K, low Na). The studies reported here indicate this effect of propranolol is specific for K and does not represent a nonspecific permeability increase for intracellular cations to leave the cell. Amphotericin-treated human RBC's (high Na, low K) and dog RBC's (high Na, low K) both gain K and increase in size when incubated in a K-medium containing propranolol and calcium. No effect was noted when cat RBC's (high Na, low K) were similarly treated. Propranolol, independent of added calcium, also inhibited the normally increased Na efflux observed when dog RBC's are suspended in K-medium. These species differences in response to propranolol thus may serve as a focus for elucidating the mechanism by which this drug alters normal membrane physiology. The unique drug effect on Na permeability of canine erythrocytes also may be a useful probe for the study of dog RBC volume regulation.     

Comparative genomic organization of the human and bovine PRNP locus

We sequenced a 208-kb BAC clone spanning the bovine prion protein (PRNP) locus, and compared the genomic structure with that of human. As a result, we determined the precise breakpoint between the two syntenic genomes, located on the 5' UTR of the PRNP gene, and discovered two highly repetitive sequences near the breakpoint. Further analysis demonstrated that the genomic structure of three genes, PRNP, PRND, and RASSF2, within the syntenic region of the bovine genome is highly conserved in order and orientation. The PRNT locus was not found in bovine but is conserved in several primates, including human. Moreover, we confirmed that the bovine RASSF2 is composed of 10 exons, as is the human gene, showing some difference from a previous report. Our findings may provide useful clues for understanding the evolutional process in the PRNP locus and also the mechanism that allows TSE from cattle to infect humans.     

Comparison of protein structure and genomic structure of human, rabbit, and limulus C-reactive proteins: Possible implications for function and evolution

The primary structures of human, rabbit, and Limulus C-reactive proteins (CRPs) have been compared by a computer program. Based on these data, a PAMs matrix (accepted point mutation per 100 residues) was constructed to generate topologies for the three proteins. Five trees with the shortest absolute length were generated, but only one positive tree was found. Using the relatively well-established distance between human and rabbit of 150 million years, we calculate that human and Limulus CRPs diverged at least 500 million years ago. The data indicate that the amino acid sequence indentity between Limulus CRPs and their mammalian counterparts is about 25%, strongly suggesting that human CRP, rabbit CRP, and Limulus CRPs share common ancestral genes. There are two highly conserved regions in the primary structures among the CRPs. Residues 52–67 in Limulus CRP and residues 51–66 in human CRP show identity in 10 of 16 positions, with 3 additional conservative replacements. This region of the molecule is thought to be involved in the binding of phosphorylcholine ligand. Residues 139–153 in Limulus CRP and residues 133–147 in human CRP show identity in 9 of 15 positions, with 5 additional conservative replacements. The biological function of this stretch of amino acid sequence is thought to be associated with the CA²⁺ binding of the CRPs.This article was presented during the proceedings of the International Conference on Macromolecular Structure and Function, held at the National Defence Medical College, Tokorozawa, Japan, December 1985.