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PubMedDate not supplied

Nucleotide sequence, chromosome localization, and evolutionary conservation of a serine hydroxymethyltransferase-processed pseudogene.

The nucleotide sequence and chromosomal localization of a human pseudogene is reported. Sequence data suggest that this pseudogene was derived via reverse transcription from the gene encoding the cytosolic isoform of the enzyme serine hydroxymethyltransferase. In addition, a heteroduplex analysis of this pseudogene among several species of nonhuman primate indicates a relatively high degree of sequence conservation.

Animals↗
PubMed1984

Autoantibody activity against evolutionary conserved juxtanuclearly arranged antigen in mice with tumors induced by a progressor Moloney sarcoma virus transformant.

Adult STU mice with tumors induced by a progressor Moloney sarcoma virus transformant developed serum antibodies against juxtanuclearly arranged structures (JNS). 14 days after tumor cell transplantation the antibody activity against JNS could be observed. During repeated tumor transfers anti-JNS development always accompanied tumor proliferation. In indirect immunofluorescence microscopy JNS were recognized by these antibodies not only in cultured cells of murine origin (normal as well as transformed cells), but also in cells of other mammalian species (rat, bat, hamster, dog, goat, cattle, horse) and even in cells of members of two further vertebrate classes: avian embryo fibroblasts and a fish-derived cell line. In the various cell lines tested, the morphology of the JNS differed, but they were always arranged close to the nucleus. The distinct perinuclear and juxtanuclear position is indicative for the Golgi region; the staining pattern after osmium impregnation and immunoelectron microscopy supported the localization of the recognized structures in this cellular compartment. Drugs like monensin or colcemid, which are known to influence Golgi morphology and function, altered the staining pattern of the antibodies drastically. The widespread occurrence of this antigenic determinant(s) in cultured cells from different species suggests that this Golgi component is highly conserved in evolution. According to immunoprecipitation studies four proteins with apparent molecular weights of 250,000, 96,000, 53,000, and 38,000 daltons were recognized by these antisera. It remains to be determined, if these molecules are involved in the described serological reaction.

Animals↗
PubMed2002

Evolutionary conservation of otd/Otx2 transcription factor action: a genome-wide microarray analysis in Drosophila.

BACKGROUND: Homeobox genes of the orthodenticle (otd)/Otx family have conserved roles in the embryogenesis of head and brain. Gene replacement experiments show that the Drosophila otd gene and orthologous mammalian Otx genes are functionally equivalent, in that overexpression of either gene in null mutants of Drosophila or mouse can restore defects in cephalic and brain development. This suggests that otd and Otx genes control a comparable subset of downstream target genes in either organism. Here we use quantitative transcript imaging to analyze this equivalence of otd and Otx gene action at a genomic level. RESULTS: Oligonucleotide arrays representing 13,400 annotated Drosophila genes were used to study differential gene expression in flies in which either the Drosophila otd gene or the human Otx2 gene was overexpressed. Two hundred and eighty-seven identified transcripts showed highly significant changes in expression levels in response to otd overexpression, and 682 identified transcripts showed highly significant changes in expression levels in response to Otx2 overexpression. Among these, 93 showed differential expression changes following overexpression of either otd or Otx2, and for 90 of these, comparable changes were observed under both experimental conditions. We postulate that these transcripts are common downstream targets of the fly otd gene and the human Otx2 gene in Drosophila. CONCLUSION: Our experiments indicate that approximately one third of the otd-regulated transcripts also respond to overexpression of the human Otx2 gene in Drosophila. These common otd/Otx2 downstream genes are likely to represent the molecular basis of the functional equivalence of otd and Otx2 gene action in Drosophila.

Animals↗
PubMed2006

Evolutionary conservation of domain-domain interactions.

BACKGROUND: Recently, there has been much interest in relating domain-domain interactions (DDIs) to protein-protein interactions (PPIs) and vice versa, in an attempt to understand the molecular basis of PPIs. RESULTS: Here we map structurally derived DDIs onto the cellular PPI networks of different organisms and demonstrate that there is a catalog of domain pairs that is used to mediate various interactions in the cell. We show that these DDIs occur frequently in protein complexes and that homotypic interactions (of a domain with itself) are abundant. A comparison of the repertoires of DDIs in the networks of Escherichia coli, Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, and Homo sapiens shows that many DDIs are evolutionarily conserved. CONCLUSION: Our results indicate that different organisms use the same 'building blocks' for PPIs, suggesting that the functionality of many domain pairs in mediating protein interactions is maintained in evolution.

Animals↗
PubMed1996

Characterization of the mouse DAX-1 gene reveals evolutionary conservation of a unique amino-terminal motif and widespread expression in mouse tissue.

The human genetic disorder adrenal hypoplasia congenita with hypogonadotropic hypogonadism results from mutations in the recently isolated DAX-1 gene, a member of the nuclear hormone receptor superfamily. To study the role of DAX-1 in adrenal development and activation of the hypothalamic pituitary-gonadal axis, animal model systems will be essential. Here, we report the isolation and characterization of the mouse DAX-1 gene and its tissue-specific pattern of expression. The mouse DAX-1 gene codes for a 472-amino acid protein, with 75% overall nucleotide sequence homology to its human homolog. The 3.5 amino-terminal repeats of a unique motif with probable DNA-binding activity have been conserved between mouse and human, although highest conservation in the DAX-1 peptide exists in the carboxy-terminal ligand-binding domain. The DAX-1 gene remains X-linked in the mouse, consistent with its potential role in sex determination. We have developed a sensitive reverse transcription-PCR assay that detects DAX-1 messenger RNA in the central nervous system, pituitary, lung, heart, spleen, kidney, and thymus in addition to the adrenal and testis DAX-1 expression noted for the human DAX-1 gene. Future studies using mouse models of altered DAX-1 expression will be critical in defining the role of this factor in tissue- and development-specific gene regulation.

Amino Acid Sequence↗
PubMed1997

Characterization of the cholecystokinin and gastrin genes from the bullfrog, Rana catesbeiana: evolutionary conservation of primary and secondary sites of gene expression.

The gastrin and cholecystokinin (CCK) genes, and the complementary DNAs they encode, have been isolated and sequenced from the bullfrog, Rana catesbeiana. The CCK gene promoter region possess the same four well characterized transcriptional control elements as the human CCK gene, namely an E-box, AP-1 binding site, Sp1 site, and TATA box. In contrast, no obvious regulatory motifs are conserved in the gastrin gene. Alignment of the bullfrog preprohormone sequences with other members of the CCK/gastrin peptide family showed that preproCCK has been conserved to a greater degree during evolution than preprogastrin. In mammalian species, gastrin gene expression is typically associated with the antrum, and CCK with the small intestine and brain. However numerous secondary sites of CCK/gastrin gene expression have also been found. RT-PCR showed a high degree of conservation of both primary and secondary sites of CCK/gastrin production between mammals and the bullfrog, with gastrin messenger RNA being detected in the antrum, duodenum, colon, pancreas, brain, and testes, whereas CCK mRNA was observed in the brain, lung, testes, and throughout the length of the small intestine. In situ hybridization using radiolabeled gene specific antisense oligonucleotides uncovered CCK and gastrin messenger RNA in distinct areas of the bullfrog central nervous system and pituitary gland. Notably, the gastrin gene was expressed in the pituitary gland and hypothalamus of the bullfrog, as previously seen in mammals. This highly preserved tissue expression pattern suggests that gastrin plays specific roles in the hypothalamus and pituitary gland that are distinct from those of CCK. Our findings show that in spite of the structural resemblance, bullfrog CCK and gastrin constitute independent neuroendocrine peptide systems.

Amino Acid Sequence↗
PubMed1994

An evolutionary conserved COUP-TF binding element in a neural-specific gene and COUP-TF expression patterns support a major role for COUP-TF in neural development.

The COUP transcription factors (COUP-TF and ARP-1) are the most highly conserved members of the nuclear receptor superfamily throughout evolution. Previous studies indicated that COUP orphan receptors may be involved in early neurogenesis in Drosophila and zebrafish. Here we identified a neural-specific gene, arrestin, whose transcription can be regulated by endogenous COUPs through a DR-7 element (direct repeat with a 7-base pair spacer) located upstream of the transcription start site. Importantly, the COUP binding site of the arrestin gene promoter is conserved among mouse, bovine, and human. However, the mouse element is also capable of responding to retinoic acid while the element in the human gene does not. Expression of COUP-TF correlates with the known expression sites of the arrestin gene in vivo, notably during the differentiation of the retina. We also show that COUP-TF is expressed in a spatio-temporally defined pattern in the murine central nervous system during embryogenesis. It appears that the expression pattern of COUP-TF is unique in certain regions of the developing brain, which would indicate a novel role for COUP-TF and/or ARP-1, distinct from their role in restricting other hormonal signaling pathways. Together our data suggest that COUPs play a crucial role in controlling a subset of neural-specific programs during development.

Animals↗
PubMed2002

Evolutionary conserved sequences are required for the insulation of the vertebrate Hoxd complex in neural cells.

Transcriptional regulation of vertebrate Hox genes involves enhancer sequences located either inside or outside the gene clusters. In the mouse Hoxd complex, for example, series of contiguous genes are coordinately controlled by regulatory sequences located at remote distances. However, in different cellular contexts, Hox genes may have to be insulated from undesirable external regulatory influences to prevent ectopic gene activation, a situation that would likely be detrimental to the developing embryo. We show the presence of an insulator activity, at one extremity of the Hoxd complex, that is composed of at least two distinct DNA elements, one of which is conserved throughout vertebrate species. However, deletion of this element on its own did not detectably affect Hoxd gene expression, unless another DNA fragment located nearby was removed in cis. These results suggest that insulation of this important gene cluster relies, at least in part, upon a sequence-specific mechanism that displays some redundancy.

Animals↗
PubMed2005

Functional analysis of the chicken delta1-crystallin enhancer activity in Drosophila reveals remarkable evolutionary conservation between chicken and fly.

Functional conservation of enhancers among evolutionarily diverged organisms is a powerful way to identify basic regulatory circuits and key developmental regulators. This is especially applicable to Crystallin genes. Despite unexpected heterogeneity and diversity in their DNA sequences, many studies have revealed that most of the Crystallin genes are regulated by a relatively small set of developmentally important transcription factors. The chicken delta1-crystallin is one of the best-characterized Crystallin genes. Its lens-specific regulation is governed by a 30 bp long DC5 fragment present in the third intron of the gene. DC5 contains PAX6 and SOX2 binding sites, and its activity depends on the cooperative binding of these two transcription factors. To test the idea that Pax6 and Sox2, together with the DC5 enhancer, could form a basic regulatory circuit functional in distantly related animals, we introduced the DC5 fragment into Drosophila and studied its activation pattern and regulation. The results show that the DC5 enhancer is not only active in the compound eye but, remarkably, is specifically active in those cells responsible for Crystallin secretion in Drosophila, i.e. the cone cells. However, regulation of the DC5 enhancer is carried out not by Pax6, but by Pax2 (D-Pax2; shaven--FlyBase) in combination with the Sox2 homologue SoxN. Both proteins (D-PAX2 and SOXN) bind cooperatively to the DC5 fragment and activate the enhancer synergistically. As PAX6 and PAX2 proteins derive from the same ancestor, we propose that during evolution Pax6 function in vertebrate lens development was retained by Pax2 in Drosophila.

Animals↗
PubMed1992

Hair follicle differentiation: expression, structure and evolutionary conservation of the hair type II keratin intermediate filament gene family.

During hair follicle development several cell streams are programmed to differentiate from the cell population of the follicle bulb. In the hair cells, a number of keratin gene families are transcriptionally activated. We describe the characterization of the type II keratin intermediate filament (IF) gene family which is expressed early in follicle differentiation. In sheep wool, four type II IF proteins are expressed. One gene has been completely sequenced and the expression of three of the genes examined in detail. The sequenced gene encodes a 55 x 10(3) Mr protein of the type II keratin IF protein family, designated KII-9 in the new nomenclature we have adopted and described in the Introduction. The gene has a similar exon/intron structure to the epidermal type II keratin IF genes. In situ hybridization experiments show that the genes are expressed in the hair cortical cells but not in the cells of the outer root sheath, inner root sheath or medulla. During hair keratinocyte differentiation the type II IF genes are sequentially activated and coexpressed in the same cells. Expression is first detected in cells in the middle of the follicle bulb located near the dermal papilla and, subsequently, two of the genes are transcriptionally activated in the differentiating keratinocytes as they migrate upwards, in the upper part of the bulb. A fourth type II IF gene is activated later. The genes with the same expression pattern are also closely related in sequence and a number of conserved elements are present in the promoters of those genes, including a novel element which is also found in the promoter of a coexpressed type I IF gene and three other hair keratin genes.

Amino Acid Sequence↗
PubMed1995

Evolutionary conservation of a cell fate specification gene: the Hydra achaete-scute homolog has proneural activity in Drosophila.

Members of the Achaete-scute family of basic helix-loop-helix transcription factors are involved in cell fate specification in vertebrates and invertebrates. We have isolated and characterized a cnidarian achaete-scute homolog, CnASH, from Hydra vulgaris, a representative of an evolutionarily ancient branch of metazoans. There is a single achaete-scute gene in Hydra, and the bHLH domain of the predicted gene product shares a high degree of amino acid sequence similarity with those of vertebrate and Drosophila Achaete-scute proteins. In Hydra, CnASH is expressed in a subset of the interstitial cells as well as differentiation intermediates of the nematocyte pathways. In vitro translated CnASH protein can form heterodimers with the Drosophila bHLH protein Daughterless, and these dimers bind to consensus Achaete-scute DNA binding sites in a sequence-specific manner. Ectopic expression of CnASH in wild-type late third instar Drosophila larvae and early pupae leads to the formation of ectopic sensory organs, mimicking the effect of ectopic expression of the endogenous achaete-scute genes. Expression of CnASH in flies that are achaete and scute double mutants gives partial rescue of the mutant phenotype, comparable to the degree of rescue obtained by ectopic expression of the Drosophila genes. These results indicate that the achaete-scute type of bHLH genes for cell fate specification, as well as their mode of action, arose early and have been conserved during metazoan evolution.

Amino Acid Sequence↗
PubMed2002

Development of pigment-cup eyes in the polychaete Platynereis dumerilii and evolutionary conservation of larval eyes in Bilateria.

The role of Pax6 in eye development in insects and vertebrates supports the view that their eyes evolved from simple pigment-cup ocelli present in their last common ancestors (Urbilateria). The cerebral eyes in errant polychaetes represent prototype invertebrate pigment-cup ocelli and thus resemble the presumed ancestral eyes. We have analysed expression of conserved eye specification genes in the early development of larval and adult pigment-cup eyes in Platynereis dumerilii (Polychaeta, Annelida, Lophotrochozoa). Both larval and adult eyes form in close vicinity of the optic anlagen on both sides of the developing brain ganglia. While pax6 is expressed in the larval, but not in the developing, adult eyes, expression of six1/2 from trochophora stages onwards specifically outlines the optic anlagen and thus covers both the developing larval and adult eyes. Using Platynereis rhabdomeric opsin as differentiation marker, we show that the first pair of adult eye photoreceptor cells is detected within bilateral clusters that transitorily express ath, the Platynereis atonal orthologue, thus resembling proneural sensory clusters. Our data indicate that--similar to insects, but different from the vertebrates--polychaete six1/2 expression outlines the entire visual system from early developmental stages onwards and ath-positive clusters generate the first photoreceptor cells to appear. We propose that pax6-, six1/2- and ath-positive larval eyes, as found in today's trochophora, were present already in Urbilateria.

Amino Acid Sequence↗
PubMed2002

Parasegmental organization of the spider embryo implies that the parasegment is an evolutionary conserved entity in arthropod embryogenesis.

Spiders belong to the chelicerates, which is a basal arthropod group. To shed more light on the evolution of the segmentation process, orthologs of the Drosophila segment polarity genes engrailed, wingless/Wnt and cubitus interruptus have been recovered from the spider Cupiennius salei. The spider has two engrailed genes. The expression of Cs-engrailed-1 is reminiscent of engrailed expression in insects and crustaceans, suggesting that this gene is regulated in a similar way. This is different for the second spider engrailed gene, Cs-engrailed-2, which is expressed at the posterior cap of the embryo from which stripes split off, suggesting a different mode of regulation. Nevertheless, the Cs-engrailed-2 stripes eventually define the same border as the Cs-engrailed-1 stripes. The spider wingless/Wnt genes are expressed in different patterns from their orthologs in insects and crustaceans. The Cs-wingless gene is expressed in iterated stripes just anterior to the engrailed stripes, but is not expressed in the most ventral region of the germ band. However, Cs-Wnt5-1 appears to act in this ventral region. Cs-wingless and Cs-Wnt5-1 together seem to perform the role of insect wingless. Although there are differences, the wingless/Wnt-expressing cells and en-expressing cells seem to define an important boundary that is conserved among arthropods. This boundary may match the parasegmental compartment boundary and is even visible morphologically in the spider embryo. An additional piece of evidence for a parasegmental organization comes from the expression domains of the Hox genes that are confined to the boundaries, as molecularly defined by the engrailed and wingless/Wnt genes. Parasegments, therefore, are presumably important functional units and conserved entities in arthropod development and form an ancestral character of arthropods. The lack of by engrailed and wingless/Wnt-defined boundaries in other segmented phyla does not support a common origin of segmentation.

Amino Acid Sequence↗
PubMed2005

Evolutionary conservation of minor U12-type spliceosome between plants and humans.

Splicing of rare, U12-type or AT-AC introns is mediated by a distinct spliceosome that assembles from U11, U12, U4atac, U6atac, and U5 snRNPs. Although in human cells the protein composition of minor and major snRNPs is similar, differences, particularly in U11 and U12 snRNPs, have been recently described. We have identified an Arabidopsis U11 snRNP-specific 35K protein as an interacting partner of an RS-domain-containing cyclophilin. By using a transient expression system in Arabidopsis protoplasts, we show that the 35K protein incorporates into snRNP. Oligo affinity selection and glycerol gradient centrifugation revealed that the Arabidopsis 35K protein is present in monomeric U11 snRNP and in U11/U12-di snRNP. The interaction of the 35K protein with Arabidopsis SR proteins together with its strong sequence similarity to U1-70K suggests that its function in splicing of minor introns is analogous to that of U1-70K. Analysis of Arabidopsis and Oryza sativa genome sequences revealed that all U11/U12-di-snRNP-specific proteins are conserved in dicot and monocot plants. In addition, we have identified an Arabidopsis gene encoding the homolog of U4atac snRNA and a second Arabidopsis gene encoding U6atac snRNA. Secondary structure predictions indicate that the Arabidopsis U4atac is able to form dimeric complexes with both Arabidopsis U6atac snRNAs. As revealed by RNaseA/T1 protection assay, the U4atac snRNA gene is expressed as an ~160-nt RNA, whereas the second U6atac snRNA gene seems to be a pseudogene. Taken together, our data indicate that recognition and splicing of minor, AT-AC introns in plants is highly similar to that in humans.

Amino Acid Motifs↗
PubMed2006

Evolutionary conservation of a functionally important backbone phosphate group critical for aminoacylation of histidine tRNAs.

All histidine tRNA molecules have an extra nucleotide, G-1, at the 5' end of the acceptor stem. In bacteria, archaea, and eukaryotic organelles, G-1 base pairs with C73, while in eukaryotic cytoplasmic tRNAHis, G-1 is opposite A73. Previous studies of Escherichia coli histidyl-tRNA synthetase (HisRS) have demonstrated the importance of the G-1:C73 base pair to tRNAHis identity. Specifically, the 5'-monophosphate of G-1 and the major groove amine of C73 are recognized by E. coli HisRS; these individual atomic groups each contribute approximately 4 kcal/mol to transition state stabilization. In this study, two chemically synthesized 24-nucleotide RNA microhelices, each of which recapitulates the acceptor stem of either E. coli or Saccharomyces cervisiae tRNAHis, were used to facilitate an atomic group "mutagenesis" study of the -1:73 base pair recognition by S. cerevisiae HisRS. Compared with E. coli HisRS, microhelixHis is a much poorer substrate relative to full-length tRNAHis for the yeast enzyme. However, the data presented here suggest that, similar to the E. coli system, the 5' monophosphate of yeast tRNA(His) is critical for aminoacylation by yeast HisRS and contributes approximately 3 kcal/mol to transition state stability. The primary role of the unique -1:73 base pair of yeast tRNAHis appears to be to properly position the critical 5' monophosphate for interaction with the yeast enzyme. Our data also suggest that the eukaryotic HisRS/tRNAHis interaction has coevolved to rely less on specific major groove interactions with base atomic groups than the bacterial system.

Acylation↗
PubMed2005

Evolutionary conservation of 5' upstream sequence of nine genes between human and great apes.

Nucleotide sequences of nine 5' upstream gene regions for human, chimpanzee, gorilla, and orangutan were determined. We estimated nucleotide differences (d) for each region between human and great apes. The overall d was 0.027 (ranged from 0.004 to 0.052). Rates of nucleotide substitution were estimated by using d and divergence times of human, chimpanzee, gorilla, and orangutan. The overall rate of nucleotide substitution between human and other hominoids was estimated to be 0.52-0.85 x 10(-9). This rate in 5' upstream regions was lower than that of synonymous sites, suggesting that 5' upstream regions have evolved under some functional constraints. Because lower rates have been reported for coding sequences in primates compared to rodents, we also estimated the rate (1.17-1.76 x 10(-9)) of nucleotide substitutions for the corresponding 5' upstream regions in rodents (mouse/rat comparison). Thus the primate rate was lower than rodent rate also for the 5' upstream regions.

5' Flanking Region↗