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PubMedDate not supplied

[Various aspects of evolution of Alu repeats in mammals].

A complex study on various evolutionary peculiarities of the mammalia dispersed Alu repeats (Alu repeats of primates and B1 of rodents) has been carried out by phylogenetic analysis. A phylogenetic tree, containing the 7SL RNA genes and the Alu repeats of primates and rodents has been constructed. It has been shown that the branch of the phyletic line leading to the Alu repeats of primates and B1 of rodents from the 7SL RNA genes occurred after the divergence of the 7SL RNA genes of amphibia and mammalia, but before the divergence of the 7SL RNA genes of primates and rodents (250.10 years ago). A statistically reliable slowing down in the evolutionary rates of one of two monomers for the human Alu repeats has been proved. It may be caused by the functional load of the corresponding monomer in connection with the presence of a definit regulatory site in it.

Animals↗

PubMedDate not supplied

Dissociation of expression patterns of homeodomain transcription factors in the evolution of developmental mode in the sea urchins Heliocidaris tuberculata and H. erythrogramma.

The direct-developing sea urchin species Heliocidaris erythrogramma has a radically modified ontogeny. Along with gains of novel features, its entire ectoderm has been reorganized, resulting in the apparent absence of a differentiated oral ectoderm, a major module present in the pluteus of indirect-developing species, such as H. tuberculata. The restoration of an obvious oral ectoderm in H. erythrogrammaxH. tuberculata hybrids, indicates the action of dominant regulatory factors from the H. tuberculata genome. We sought candidate regulatory genes based on the prediction that they should include genes that govern development of the oral ectoderm in the pluteus, but play different roles in H. erythrogramma. Such genes may have a large effect in the evolution of development. Goosecoid (Gsc), Msx, and the sea urchin Abd-B-like gene (Hox11/13b) are present and expressed in both species and the hybrid embryos. Both Gsc and Msx are oral ectoderm specific in H. tuberculata, and show novel and distinct expression patterns in H. erythrogramma. Gsc assumes a novel ectodermal pattern and Msx shifts to a novel and largely mesodermal pattern. Both Gsc and Msx show a restoration of oral ectoderm expression in hybrids. Hox11/13b is not expressed in oral ectoderm in H. tuberculata, but is conserved in posterior spatial expression among H. tuberculata, H. erythrogramma and hybrids, serving as a control. Competitive RT-PCR shows that Gsc, Msx, and Hox11/13b are under different quantitative and temporal controls in the Heliocidaris species and the hybrids. The implications for the involvement of these genes in the rapid evolution of a direct developing larva are discussed.

Animals↗

PubMed1980

Dosage compensation of X-linked heat-shock puffs in Drosophila pseudoobscura.

Four major puffs are inducible by heat shock in the larval salivary gland chromosomes of D. pseudoobscura. Two of these puffs are present at 23 and 39-40 on the right arm of the X chromosome and two are present at 53 and 58 on chromosome 2. By means of in situ hybridization, residual homologies were demonstrated between the puffs at 23 in D. pseudoobscura and at 63 C in D. melanogaster, and between the two chromosome 2 puffs of D. pseudoobscura and 87A and 87C of D. melanogaster. RNA synthesis was monitored as a function of 3H-uridine incorporation in the major heat-induced puffs of D. pseudoobscura and was found to be equivalent in males and females indicating dosage compensation of the two X-linked loci. The evoluation of the regulatory controls of these genes is discussed.

Animals↗

PubMed2002

Conservation of gene co-regulation in prokaryotes and eukaryotes.

Genes that are part of the same operon in prokaryotes, or have the same expression pattern in eukaryotes, are transcriptionally co-regulated. If genes are consistently co-regulated across distantly related organisms, the genes have closely associated functions. It has been shown previously that such genes have a strong tendency to belong to the same protein complex in prokaryotes, and we show by an analysis of the sequences and their expression in the yeast Saccharomyces cerevisiae and the worm Caenorhabditis elegans that this is also true for eukaryotes. Our analysis reveals that the number of conserved co-regulated genes is small in eukaryotes, as has been shown previously in prokaryotes, indicating that there are extensive variations in the gene regulatory network across organisms.

Animals↗

PubMed2002

Genetic polymorphism of the major regulatory element HS-40 upstream of the human alpha-globin gene cluster.

The highly conserved 350-bp major regulatory element HS-40 (or alphaMRE) upstream of the human alpha-globin gene cluster is involved in the regulation of alpha-globin gene expression. The study of alphaMRE differences between human populations and the evolution of alphaMRE sequences in mammals may lead to a better understanding of the function and importance of this element in the regulation of expression of the downstream alpha-cluster. Denaturing gradient gel electrophoresis was used to determine the sequence heterogeneity of the alphaMRE region in 276 unrelated individuals, representing seven different populations. Furthermore, we analysed the alpha major regulatory elements of chimpanzee, orang-utan and rhesus monkeys and compared them with the equivalent human and murine sequences. Six different alphaMRE haplotypes (labelled A to F) were found in humans. Haplotype frequencies between the seven populations showed a gradual shift to a higher haplotype A distribution from west to east, being the highest in Indonesians. The African sample shows the largest divergence in haplotypes. Five out of six different haplotypes were present, three of which were exclusively found in Africans. The high prevalence of the haplotype A in humans, together with the conservation of this haplotype in apes, suggests that it is the ancestral one. The alphaMRE fragment appears to be a highly polymorphic marker, which could be used in combination with the regular markers in the alpha-cluster to extend the haplotype and to follow segregation of alpha-thalassaemia genes in population studies more accurately.

Animals↗

PubMed2006

Flower-like terminal structures in racemose inflorescences: a tool in morphogenetic and evolutionary research.

Terminal flower-like structures (TFLS) occur in many angiosperms that possess indeterminate inflorescences such as spikes, racemes, or spadices. We describe and review TFLS in early-divergent angiosperms, especially the magnoliid order Piperales and the monocot order Alismatales, in which floral interpretation is controversial. Essentially similar TFLS occur in a wide range of taxa. Among magnoliids, they occur in some Piperales (Saururaceae and a few Piperaceae), but are absent from Chloranthaceae. Among monocots, they occur in some early-divergent families such as Acoraceae, Aponogetonaceae, Juncaginaceae, Potamogetonaceae, and Ruppiaceae. Similar TFLS with obscure organ identity are recorded in mutants of Arabidopsis. TFLS can often be interpreted as pseudanthia (close aggregations of reduced flowers), but in some cases the entire terminal pseudanthium is very similar to a true flower. In some cases, elaborated TFLS could therefore have given rise to what are normally termed 'true' (i.e. euanthial) flowers. Data presented here on terminal pseudanthia in Potamogeton and Ruppia support a pseudanthial evolutionary origin of reproductive units in the alismatid families Zannichelliaceae and Cymodoceaceae. Furthermore, in some alismatid species, either the entire inflorescence apex or an individual primordium at or near the inflorescence tip can be transformed into a filamentous or tubular (or intermediate) structure. A tubular structure enclosing stamens and carpels is described in Piper. This indicates that pseudanthium formation can provoke morphological novelties, perhaps due to new patterns of overlap between expression zones of regulatory genes and/or new spatial constraints.

Alismatales↗

PubMed1988

Does heterochromatin variation potentiate speciation? A study in Nesokia.

An increasing incidence of sex-chromosome variation in constitutive heterochromatin, including individuals with mosaic genotypes, has been observed in a single natural population of Nesokia indica, the Indian mole rat. Variations in the heterochromatic areas of the X chromosome are largely due to deletions at R-band-positive regions corresponding to folate-sensitive fragile sites. All individuals with either a pre- or post-zygotic loss or gain of sex-chromosome heterochromatin have so far proved to be infertile. Whether such F1 sterility is due to abnormal gonadal development, gametic incompetence, or other factors is not clear. More important is the indication that the constitutive heterochromatin of this species may contain coding DNA sequences with putative regulatory functions.

Animals↗

PubMed1996

The evolution of chromosomal sex determination and dosage compensation.

In many species, sex is determined by a system based on X and Y chromosomes, the latter having lost much of their genetic activity. Y chromosomes have evolved independently many times, and the associated change in gene dosage in the heterogametic (XY) sex is often compensated for by regulatory mechanisms which ensure equal amounts of gene products of X-linked loci in males and females. There have recently been substantial advances in our knowledge of the molecular biology and genetics of sex chromosomes and dosage compensation, and in our understanding of the population genetic processes which are involved in their evolution.

Animals↗

PubMed1995

Structure and evolution of CyI cytoplasmic actin-encoding genes in the indirect- and direct-developing sea urchins Heliocidaris tuberculata and Heliocidaris erythrogramma.

The CyI cytoplasmic actin-encoding genes of Heliocidaris erythrogramma (He), a direct-developing sea urchin, and H. tuberculata, an indirect developer, were isolated and compared to the homologous CyI gene of another indirect developer, Strongylocentrotus purpuratus. Comparisons show that despite the differences in development, the actin gene structures and sequences are highly similar. The coding and 3' untranslated regions are conserved. The 5' He regulatory region has an inserted repeat element, but is otherwise similar to its homologues in the arrangement of presumptive transcription control elements.

Actins↗

PubMedDate not supplied

The effect of molecular inhibition on evolutionary learning: studies in the hypernetwork architecture.

The hypernetwork architecture is a biologically inspired learning model based on abstract molecules and molecular interactions that exhibits functional and organizational correlation with biological systems. Hypernetwork organisms were trained, by molecular evolution, to solve N-input parity tasks. We found that learning improves when molecules exhibit inhibitory sites, allowing molecular inhibition and opening the possibility of forming negative feedback regulatory pathways. Optimal learning is achieved when at least 20% of the molecules in each cell have inhibitory sites. Intra-cellular as well as inter-cellular molecular inhibitions play an important role in the information processing of hypernetwork organisms, by maintaining a balance of the molecular cascade reactions. Similar mechanisms inside neurons are considered important for memory.

Algorithms↗

PubMed2005

Identification and categorization of horizontally transferred genes in prokaryotic genomes.

Horizontal gene transfer (HGT), a process through which genomes acquire genetic materials from distantly related organisms, is believed to be one of the major forces in prokaryotic genome evolution. However, systematic investigation is still scarce to clarify two basic issues about HGT: (1) what types of genes are transferred; and (2) what influence HGT events over the organization and evolution of biological pathways. Genome-scale investigations of these two issues will advance the systematical understanding of HGT in the context of prokaryotic genome evolution. Having investigated 82 genomes, we constructed an HGT database across broad evolutionary timescales. We identified four function categories containing a high proportion of horizontally transferred genes: cell envelope, energy metabolism, regulatory functions, and transport/binding proteins. Such biased function distribution indicates that HGT is not completely random; instead, it is under high selective pressure, required by function restraints in organisms. Furthermore, we mapped the transferred genes onto the connectivity structure map of organism-specific pathways listed in Kyoto Encyclopedia of Genes and Genomes (KEGG). Our results suggest that recruitment of transferred genes into pathways is also selectively constrained because of the tuned interaction between original pathway members. Pathway organization structures still conserve well through evolution even with the recruitment of horizontally transferred genes. Interestingly, in pathways whose organization were significantly affected by HGT events, the operon-like arrangement of transferred genes was found to be prevalent. Such results suggest that operon plays an essential and directional role in the integration of alien genes into pathways.

Bacterial Proteins↗

PubMed2005

Ancient and recent positive selection transformed opioid cis-regulation in humans.

Changes in the cis-regulation of neural genes likely contributed to the evolution of our species' unique attributes, but evidence of a role for natural selection has been lacking. We found that positive natural selection altered the cis-regulation of human prodynorphin, the precursor molecule for a suite of endogenous opioids and neuropeptides with critical roles in regulating perception, behavior, and memory. Independent lines of phylogenetic and population genetic evidence support a history of selective sweeps driving the evolution of the human prodynorphin promoter. In experimental assays of chimpanzee-human hybrid promoters, the selected sequence increases transcriptional inducibility. The evidence for a change in the response of the brain's natural opioids to inductive stimuli points to potential human-specific characteristics favored during evolution. In addition, the pattern of linked nucleotide and microsatellite variation among and within modern human populations suggests that recent selection, subsequent to the fixation of the human-specific mutations and the peopling of the globe, has favored different prodynorphin cis-regulatory alleles in different parts of the world.

Alleles↗

PubMed1997

Reproductive isolation and morphogenetic evolution in Drosophila analyzed by breakage of ethological barriers.

This article reports the breaking of ethological barriers through the constitution of soma-germ line chimeras between species of the melanogaster subgroup of Drosophila, which are ethologically isolated. Female Drosophila yakuba and D. teissieri germ cells in a D. melanogaster ovary produced functional oocytes that, when fertilized by D. melanogaster sperm, gave rise to sterile yakuba-melanogaster and teissieri-melanogaster male and female hybrids. However, the erecta-melanogaster and orena-melanogaster hybrids were lethal, since female D. erecta and D. orena germ cells in a D. melanogaster ovary failed to form oocytes with the capacity to develop normally. This failure appears to be caused by an altered interaction between the melanogaster soma and the erecta and orena germ lines. Germ cells of D. teissieri and D. orena in a D. melanogaster testis produced motile sperm that was not stored in D. melanogaster females. This might be due to incompatibility between the teissieri and orena sperm and the melanogaster seminal fluid. A morphological analysis of the terminalia of yakuba-melanogaster and teissieri-melanogaster hybrids was performed. The effect on the terminalia of teissieri-melanogaster hybrids of a mutation in doublesex, a regulatory gene that controls the development of the terminalia, was also investigated.

Animals↗

PubMed2002

[Molecular evolution of tandem heterochromatic repeats in connection with their function in the genome of Drosophila melanogaster].

Molecular evolution and divergence of paralogous tandem heterochromatic repeats Stellate and Su(Ste) located on the X and Y chromosomes, respectively, are discussed. These repeats appear to emerge as a result of amplification of a unique autosomal euchromatic gene encoding the regulatory beta-subunit of the CK2 protein kinase. The autosomal gene and the clusters of heterochromatic repeats are transcribed in testes. A high level of the Stellate expression leads to partial male sterility and disturbed meiosis. The Stellate expression and its adverse effects are suppressed by homologous Su(Ste) repeats. In genome evolution, the open reading frames (ORF) of Stellate and Su(Ste) putative ancestor were maintained by translational selection. Then the coding Su(Ste) function had been damaged and switched to a new one related to antisense Su(Ste) transcription and suppression of the Stellate genes. Symmetrical (sense and antisense) Su(Ste) transcription causes the formation of a double-strand RNA, which by interference (selective switching off the homologous gene expression) suppresses the Stellate genes. The biological significance and the driving forces of evolution of the species-specific balanced interaction of Stellate and Su(Ste) repeats remain mysterious.

Amino Acid Sequence↗

PubMed1972