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PubMed2006

Evolutionary conservation of neuropeptide expression in the thymus of different species.

Evidence suggests that the immune and neuroendocrine systems cross talk by sharing ligands and receptors. Hormones and neuropeptides produced by the neuroendocrine system often modulate the function of lymphoid organs and immune cells. We have previously reported the intrathymic expression of somatostatin (SOM) in the mouse and that several neuropeptides, most notably calcitonin-gene-related peptide (CGRP), neuropeptide Y (NPY), SOM and substance P (SP), can modulate thymocyte development. However, little is known about the intrathymic expression of these neuropeptides either in the mouse or in other species. Moreover, a comparative analysis of the expression of these molecules would highlight the evolutionary importance of intrathymic neuroendocrine interactions in T-cell development. We have studied the expression of different neuropeptides in the thymus of zebrafish, Xenopus, avians, rodent, porcine, equine and human by immunohistochemistry and reverse transcription-polymerase chain reaction. We found that CGRP, NPY, SOM, SP and vasointestinal polypeptide (VIP) are expressed in the thymus of all species investigated. The thymic location of many of these neuropeptides was conserved and appears to be within the stromal compartments. Interestingly, in the avian thymus the expression of CGRP, SOM and SP appears to change depending on the age of the tissue. These findings suggest that neuropeptides may play an important role in T-cell development and provide further evidence of cross talk between the immune and neuroendocrine systems.

Animals↗
PubMed1997

Gene sequence, localization, and evolutionary conservation of DAZLA, a candidate male sterility gene.

We have isolated the human homologue of the mouse germ cell-specific transcript Tpx2, which we had previously mapped to mouse chromosome 17. Sequence analysis shows that the human gene is part of the DAZ (Deleted in Azoospermia) family, represents the human homologue of the mouse Dazla and Drosophila boule genes, and is termed DAZLA. Like Dazla and boule, DAZLA is single copy and maps to 3p25. This defines a new region of synteny between mouse chromosome 17 and human chromosome 3. Unlike DAZ, which has multiple DAZ repeats, DAZLA encodes a putative RNA-binding protein with a single RNA-binding motif and a single DAZ repeat. DAZLA is more closely related to Dazla in the mouse than to the Y-linked homologue DAZ (88% identity overall with mouse Dazla compared to 76% identity with the human DAZ protein sequence). Southern blot analysis showed that DAZLA is autosomal in all mammals tested and that DAZ has been recently translocated to the Y chromosome, sometime after the divergence of Old World and New World primates. To investigate the evolutionary relatedness of DAZLA and DAZ further, their partial genomic structures were obtained and compared. This revealed that the genomic organization of both genes in the 5' region is highly conserved. DAZLA is a new member of the DAZ family of genes, which is associated with spermatogenesis and male sterility. Familial cases of male infertility in humans show an autosomal recessive mode of inheritance. It is possible that some of these families may carry mutations in the DAZLA gene.

Amino Acid Sequence↗
PubMed1998

The human hypoxia-inducible factor 1alpha gene: HIF1A structure and evolutionary conservation.

The HIF1A gene encodes the HIF-1alpha subunit of hypoxia-inducible factor 1, a transcription factor that is essential for cardiovascular development and systemic O2 homeostasis. HIF1A consists of 15 exons that are interrupted by introns at the same locations as in the mouse Hif1a gene, although sequences mediating alternative splicing and alternative translation initiation events in the mouse are not present in the human gene. Placement of introns differs between HIF1A and EPAS1, which encodes the human HIF-2alpha protein. Transcription of the HIF1A gene was initiated over a 15-nt region downstream of two SP1 sites. A 0.7-kb region of 5' flanking sequences functioned as a strong promoter in transient expression assays. Comparison of 0.8 kb of 5' flanking and 5' untranslated sequences from the HIF1A and Hif1a genes revealed 70% identity. The proximal 300 bp of 5' flanking sequences was 83% identical, including the SP1 sites and transcription initiation sites. These results suggest evolutionary selection for maintenance of HIF1A structure, function, and regulation.

Amino Acid Sequence↗
PubMed1992

Evolutionary conservativeness of electric field in the Cu,Zn superoxide dismutase active site. Evidence for co-ordinated mutation of charged amino acid residues.

Equipotential lines were calculated, using the Poisson-Boltzmann equation, for six Cu,Zn superoxide dismutases with different protein electric charge and various degrees of sequence homology, namely those from ox, pig, sheep, yeast, and the isoenzymes A and B from the amphibian Xenopus laevis. The three-dimensional structures of the porcine and ovine superoxide dismutases were obtained by molecular modelling reconstruction using the structure of the highly homologous bovine enzyme as a template. The three-dimensional structure of the evolutionary distant yeast Cu,Zn superoxide dismutase was recently resolved by us, while computer-modelled structures are available for X. laevis isoenzymes. The six proteins display large differences in the net protein charge and distribution of electrically charged surface residues but the trend of the equipotential lines in the proximity of the active sites was found to be constant in all cases. These results are in line with the very similar catlytic rate constants experimentally measured for the corresponding enzyme activities. This analysis shows that electrostatic guidance for the enzyme-substrate interaction in Cu,Zn superoxide dismutases is related to a spatial distribution of charges, arranged so as to maintain, in the area surrounding the active sites, an identical electrostatic potential distribution, which is conserved in the evolution of this protein family.

Animals↗
PubMed1991

Evolutionary conservation of intron position in a subfamily of genes encoding carbohydrate-recognition domains.

The structure of the gene encoding a chicken liver receptor, the chicken hepatic lectin, which mediates endocytosis of glycoproteins has been established. The coding sequence is divided into six exons separated by five introns. The first three exons correspond to separate functional domains of the receptor polypeptide (cytoplasmic tail, transmembrane sequence, and extracellular neck region), while the final three exons encode the Ca(2+)-dependent carbohydrate-recognition domain. These results, as well as computer-assisted multiple sequence comparisons, establish this receptor as the evolutionary homolog of the mammalian asialoglycoprotein receptors. It is interesting that the chicken receptor falls into a subfamily of proteins along with the mammalian asialoglycoprotein receptors, since the saccharide-binding specificity of the chicken receptor resembles more closely that of a different set of calcium-dependent animal lectins, which includes the mannose-binding proteins. The portions of the genes encoding the carbohydrate-recognition domains of these proteins lack introns. The results suggest that divergence of intron-containing and intron-lacking carbohydrate-recognition domains preceded shuffling events in which other functional domains were associated with the carbohydrate-recognition domains. This was followed by further divergence, generating a variety of saccharide-binding specificities.

Amino Acid Sequence↗
PubMed1992

Structural complexity and evolutionary conservation of the Drosophila homeotic gene proboscipedia.

Mutations of the homeotic gene proboscipedia (pb) of Drosophila cause striking transformations of the adult mouthparts, to legs or antennae. We report here an analysis of the gene structure of pb. Coding sequences across a 34 kb interval yield, by alternative splicing, four identified mRNA forms which differ immediately upstream of the homeobox. As a consequence, the homeodomain is expected to reside in four different contexts in the predicted protein isoforms. Mammalian homologs of pb, human HOX-2H and murine Hox-2.8, were identified based on the similarities of their homeodomains (95% identity) and several other conserved motifs. Examination of a collection of pb mutant alleles with antisera directed against the N-terminal region, the center or the C-terminal region of the protein showed that, surprisingly, several partial loss-of-function pb alleles appear to generate partially functional proteins truncated at their C-termini. This suggests that a significant portion of the protein contributes quantitatively to pb function, but is partially dispensable. Finally, evolutionary considerations suggest that pb may be one of several ancient genes which preceded the process yielding the modern homeotic gene complexes.

Amino Acid Sequence↗
PubMed1985

Amino acid sequence microheterogeneities of basic (type II) cytokeratins of Xenopus laevis epidermis and evolutionary conservativity of helical and non-helical domains.

Three clones coding for carboxy-terminal portions of type II cytokeratins have been isolated from a cDNA library constructed from the epidermis of the frog Xenopus laevis. These clones have been identified by hybridization-selection-translation and Northern blot analysis, and contain sequences complementary to mRNAs of similar size that code for three different polypeptides of the Mr 64,000 group, Ia-c, i.e. the only major type II cytokeratins expressed in this tissue. A comparison of the corresponding nucleotide sequences and the amino acid sequences deduced therefrom shows only minor differences in these polypeptides, most of which occur as isolated point mutations. This indicates that coding sequences of the different type II cytokeratin genes in epidermis of Xenopus are very similar, in contrast to the more extended differences of type II cytokeratin genes expressed in mammalian epidermis, which probably reflects a lower degree of evolutionary divergence of members of this protein family in amphibia. A comparison of the Xenopus sequences with those of mammalian type II cytokeratins reveals the same characteristic features, i.e. an alpha-helical domain ending with the familiar consensus sequence T Y R (X Y) L E G E, followed by a non-helical domain Cl enriched in hydroxyamino acids. Both domains are remarkably conserved in sequence between Xenopus and mammals. The following glycine-rich domain (C2) displays similar oligopeptide repeats (mostly of the type G G G M in the frog keratins), and the terminal C3 domain is characterized by a region exceptionally rich in hydroxyamino acids, which immediately precedes a cluster of basic amino acids at the carboxy terminus. Our results show that the typical features of the domain of type II cytokeratins are already established in amphibia and that these homologies are not restricted to the alpha-helical rod of these proteins but, in principle, extend to the other domains located in the so-called hypervariable tail portion. This suggests that the hypervariable regions are not subject to random variability but contain functionally important domains that have been well conserved during evolution.

Amino Acid Sequence↗
PubMed1989

Human homologue of mouse lymph node homing receptor: evolutionary conservation at tandem cell interaction domains.

A cDNA clone homologous to the mouse lymph node homing receptor core protein (mLHRc) was isolated from a cDNA library derived from stimulated human peripheral blood lymphocytes. Human RNA blot analysis shows a tissue and cell-line distribution of transcript expression generally parallel to that seen in the mouse, with expression confined to lymphoid tissues and some cell lines. Genomic DNA analysis suggests a low-copy gene under high-stringency conditions. The complete nucleotide sequence predicts a mature protein of 334 amino acids, identical in length to mLHRc. The protein shows striking conservation globally between human and mouse sequences. In particular, all three genre of protein interaction domains identified in the mouse--an animal lectin domain, an epidermal growth factor (EGF)-like domain, and two homologous repeat units preserving the motif of complement regulatory proteins (CRP)--are present in the human protein (hLHRc), and maintain the same tandem arrangement. The lectin and EGF-like regions are the most homologous, while the CRP domains are less conserved between species. The two CRP units in hLHRc are distinct from those in mLHRc in that they are homologous to one another rather than identical, suggesting strong pressure for maintenance of two repeats in this molecule. hLHRc is distinct from other kinds of lymphocyte adhesion molecules represented by VLA-4 (integrin) or CD44/gp90Hermes and, together with mLHRc and two other recently described molecules having a similar domain motif, defines a novel class of adhesion molecules exhibiting distinct evolutionary features. We propose that hLHRc likely represents the protein core of the human homologue of mLHRc functionally as well as structurally.

Amino Acid Sequence↗
PubMed1988

Evolutionary conservation of the chromosomal configuration and regulation of amylase genes among eight species of the Drosophila melanogaster species subgroup.

Nuclear DNA was extracted from each of the eight species comprising the Drosophila melanogaster species subgroup. Southern hybridization of this DNA by using a molecular probe specific for the alpha-amylase coding region showed that the duplicated structure of the amylase locus, first found in D. melanogaster, is conserved among all species of the melanogaster subgroup. Evidence is also presented for the concerted evolution of the duplicated genes within each species. In addition, it is shown that the glucose repression of amylase gene expression, which has been extensively studied in D. melanogaster, is not confined to this species but occurs in all eight members of the species subgroup. Thus, both the duplicated gene structure and the glucose repression of Drosophila amylase gene activity are stable over extended periods of evolutionary time.

Amylases↗
PubMed2005

Evolutionary conserved chromosomal segments in the human karyotype are bounded by unstable chromosome bands.

In this paper an ancestral karyotype for primates, defining for the first time the ancestral chromosome morphology and the banding patterns, is proposed, and the ancestral syntenic chromosomal segments are identified in the human karyotype. The chromosomal bands that are boundaries of ancestral segments are identified. We have analyzed from data published in the literature 35 different primate species from 19 genera, using the order Scandentia, as well as other published mammalian species as out-groups, and propose an ancestral chromosome number of 2n = 54 for primates, which includes the following chromosomal forms: 1(a+c(1)), 1(b+c(2)), 2a, 2b, 3/21, 4, 5, 6, 7a, 7b, 8, 9, 10a, 10b, 11, 12a/22a, 12b/22b, 13, 14/15, 16a, 16b, 17, 18, 19a, 19b, 20 and X and Y. From this analysis, we have been able to point out the human chromosome bands more "prone" to breakage during the evolutionary pathways and/or pathology processes. We have observed that 89.09% of the human chromosome bands, which are boundaries for ancestral chromosome segments, contain common fragile sites and/or intrachromosomal telomeric-like sequences. A more in depth analysis of twelve different human chromosomes has allowed us to determine that 62.16% of the chromosomal bands implicated in inversions and 100% involved in fusions/fissions correspond to fragile sites, intrachromosomal telomeric-like sequences and/or bands significantly affected by X irradiation. In addition, 73% of the bands affected in pathological processes are co-localized in bands where fragile sites, intrachromosomal telomeric-like sequences, bands significantly affected by X irradiation and/or evolutionary chromosomal bands have been described. Our data also support the hypothesis that chromosomal breakages detected in pathological processes are not randomly distributed along the chromosomes, but rather concentrate in those important evolutionary chromosome bands which correspond to fragile sites and/or intrachromosomal telomeric-like sequences.

Alouatta↗
PubMed2002

Developmental constraints conserve evolutionary pattern in an osteichthyan dentition.

The lungfish dentition is different from other osteichthyan fish because it has a characteristic and unique pattern of teeth arranged as toothplates. Growth, addition of teeth, and retention as part of a statodont dentition are determined by the initiation pattern. In adult lungfish new teeth are only added laterally to each radial row in the dentition. This is in marked contrast to marginal rows of teeth with regular, alternating replacement in most osteichthyans. We analyze development from fossil hatchling forms of the Late Devonian dipnoan Andreyevichthys and compare with those of Neoceratodus, the Australian lungfish. The specific pattern of development, unique within lungfish, is also present in the transitory, marginal, anterior dentition in both, reflecting a strongly conserved developmental pattern. These marginal teeth form but are then lost in both, so that also this program of development is conserved within lungfish for 360 million years, from the earliest known form.

Animals↗
PubMed1983

Unusual evolutionary conservation and frequent DNA segment exchange in class I genes of the major histocompatibility complex.

From comparisons of homologous DNA sequences for many different genes, it was shown that the silent positions of protein-encoding regions and introns evolve at high and remarkably similar rates for different genes. In addition, both silent positions and introns behave like clocks; they accumulated base substitutions at approximately constant rates with respect to geological time. The rates of evolution were estimated to be 5.5 X 10(-9), 3.7 X 10(-9), and 5.3 X 10(-9) per site per year for silent positions, short introns (less than approximately equal to 300 base pairs), and long introns (more than approximately equal to 500 base pairs), respectively. Contrary to expectation from the evolutionary clocks, DNA sequence comparison between pHLA 12.4 (a cloned HLA sequence) of man and Ld together with other H-2 genes of mouse, the class I genes of the major histocompatibility complex, revealed a surprisingly small amount of base substitution for both the introns and the silent positions; the degree of divergence is only about 60% of that of standard genes in the same species comparison. Furthermore, several segmental homologies have been observed between the class I genes of mouse, suggesting the frequent occurrence of gene conversion or double unequal crossing-over in evolution. Interrelations between the extreme polymorphism of the class I genes, the low evolutionary drift of the introns and the silent positions, and the frequent gene conversion or unequal crossing-over within the mouse genes are discussed.

Animals↗
PubMed1998

Evidence for evolutionary conservation of sex-determining genes.

Most metazoans occur as two sexes. Surprisingly, molecular analyses have hitherto indicated that sex-determining mechanisms differ completely between phyla. Here we present evidence to the contrary. We have isolated the male sexual regulatory gene mab-3 from the nematode Caenorhabditis elegans and found that it is related to the Drosophila melanogaster sexual regulatory gene doublesex (dsx)2. Both genes encode proteins with a DNA-binding motif that we have named the 'DM domain'. Both genes control sex-specific neuroblast differentiation and yolk protein gene transcription; dsx controls other sexually dimorphic features as well. The form of DSX that is found in males can direct male-specific neuroblast differentiation in C. elegans. This structural and functional similarity between phyla suggests a common evolutionary origin of at least some aspects of sexual regulation. We have identified a human gene, DMT1, that encodes a protein with a DM domain and find that DMT1 is expressed only in testis. DMT1 maps to the distal short arm of chromosome 9, a location implicated in human XY sex reversal. Proteins with DM domains may therefore also regulate sexual development in mammals.

Adaptor Proteins, Signal Transducing↗
PubMed1995

Cloning and expression of an evolutionary conserved single-domain angiotensin converting enzyme from Drosophila melanogaster.

Mammalian somatic angiotensin converting enzyme (EC 3.4.15.1, ACE) consists of two highly homologous (N- and C-) domains encoded by a duplicated gene. We have identified an apparent single-domain (67 kDa) insect angiotensin converting enzyme (AnCE) in embryos of Drosophila melanogaster which converts angiotensin I to angiotensin II (Km, 365 microM), removes Phe-Arg from the C terminus of bradykinin (Km, 22 microM), and is inhibited by ACE inhibitors, captopril (IC50 = 1.1 x 10(-9) M) and trandolaprilat (IC50 = 1.6 x 10(-8) M). We also report the cloning and expression of a Drosophila AnCE cDNA which codes for a single-domain 615-amino acid protein with a predicted 17-amino acid signal peptide and regions with high levels of homology to both the N- and C-domains of mammalian somatic ACE, especially around the active site consensus sequence. Northern analysis identified a single 2.1-kilobase mRNA in Drosophila embryos, and Southern analysis of Drosophila genomic DNA indicates that the insect gene is not duplicated. When expressed in COS-7 cells, the AnCE protein is a secreted enzyme, which converts angiotensin I to angiotensin II and is inhibited by captopril (IC50 = 5.6 x 10(-9) M) and trandolaprilat (IC50 = 2 x 10(-8) M). The evolutionary significance of these results is discussed.

Amino Acid Sequence↗
PubMedDate not supplied

Protein promoting vibrations in enzyme catalysis--a conserved evolutionary motif.

A computational method to identify residues important in creating a protein promoting vibration (PPV) in enzymes was previously developed and applied to horse liver alcohol dehydrogenase (HLADH), resulting in the identification of eight important residues. From these residues, we define a sequence motif, the PPV generating sequence, and find it to be unique and general to a larger group of alcohol dehydrogenases from diverse sources, demonstrating that nature has selected for the PPV generating sequence.

Alcohol Dehydrogenase↗
PubMed1980

Evolutionary conservation of linkage groups: additional evidence from murid and cricetid rodents.

In Mus musculus, family Muridae, the glucosephosphate isomerase (Gpi-l), pink-eyed dilution (p), albinism (c), and beta-type globin (Hbb) loci are known to be linked in the order Gpi-l-p-c-Hbb. In Rattus norvegicus, another murid rodent, the p, c, and Hbb loci are known to be linked in the same order and with similar recombination frequencies. In Peromyscus maniculatus, family Cricetidae, it was previously known that p and c are linked and by analogy to Mus musculus that linkage group should be bounded by Gpi-l near p and by a beta-globin locus near c. Linkage has now been established between Gpi-l and the Hbe globin locus in Peromyscus. However, the observed recombination frequency in Peromyscus (16.3%) is significantly lower than in Mus, suggesting that perhaps a chromosomal inversion has occurred during the evolutionary divergence of the two rodent families. Linkage relationships were also tested between the Hbc1, Hbd1, and Hbe1 globin variants. Hbc1 (presumably an alpha-type globin) segregated independently from Hbd1 and Hbe1 (presumably beta-type globins). No recombination was observed between Hbd1 and Hbe1. Those two globin genes may be alleles at a single locus, although circumstantial evidence suggests that they represent tightly linked duplicate loci.

Animals↗
PubMed1993

Identity elements of tRNA(Trp). Identification and evolutionary conservation.

In this study, the varying reactivities of Bacillus subtilis tryptophanyl-tRNA synthetase toward prokaryotic, eukaryotic, and halophile tRNAs were employed to define the potential identity elements on tRNA(Trp). On this basis mutagenesis was performed to obtain, through in vivo heterologous expression in Escherichia coli and in vitro transcription with T7 RNA polymerase, mutant B. subtilis tRNA(Trp) for comparison with the wild-type. These comparisons served to establish G73 and the anticodon as major identity elements, and A1-U72, G5-C68, and A9 as minor identity elements. While the tryptophanyl-tRNA synthetase from B. subtilis and E. coli require G73 to function, replacement of G73 by A73 favors the enzyme from yeast. This change points to the variation of the identity elements for the same amino acid among different organisms. The similarity in these elements between B. subtilis and E. coli tryptophanyl-tRNA synthetase, however, suggests that identity elements on tRNA, like the active centers on enzymes, undergo evolutionary change at slower rates than less essential portions of the macromolecule.

Animals↗
PubMedDate not supplied

Human pro alpha 1(I) collagen gene structure reveals evolutionary conservation of a pattern of introns and exons.

The collagens represent an interesting example of a structurally related but genetically distinct family of proteins. Type I, the most abundant of the vertebrate collagens, comprises two pro alpha 1(I) chains and one pro alpha 2(I) chain, each containing terminal propeptides and a central domain of 338 (Gly, X, Y) repeats. The structure of the chicken pro alpha 2(I) gene shows an intriguing relationship between exon organization and the arrangement of (Gly, X, Y) repeats (see ref. 2 for review). This has led to the suggestion that the collagens evolved from a common ancestral unit of 54 base pairs (bp). Here we present the structure of the entire human pro alpha 1(I) gene and compare this with the chicken pro alpha 2(I). The exon arrangement of the two genes is remarkably similar, although the human pro alpha 1(I) is more compact because of the shorter length of its introns. The data strongly support the notion that the type I genes have evolved from an ancestral multi-exon unit, and that once the gene was translated, a strong evolutionary pressure caused it to maintain this elaborate structure.

Amino Acid Sequence↗