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PubMed1998

Evolution by nearly-neutral mutations.

Genetic systems are complex and interact at various levels; among amino acids or nucleotide sites, among gene products, and among regulatory regions and proteins. Patterns of synonymous and nonsynonymous substitutions of mammalian genes indicate that nonsynonymous substitutions are nearly neutral, coming from interactions among amino acids. As an interactive system, the NK model of Kauffman was analysed. This model assumes that each amino acid makes a fitness contribution that depends upon the amino acid and upon K other amino acids among the N that make the protein. Through simulations, it was found that there are numerous nearly-neutral mutations in this model, and that evolution is rapid in small populations and slow in large ones. The system moves on the rugged fitness landscape by mutation, random genetic drift and selection. Small populations have more chance to attain novel genetic systems than large ones because of larger effects of random drift, but the chance of extinction becomes greater.

Animals↗

PubMed1999

The golden decade of molecular floral development (1990-1999): A cheerful obituary

Cloning of genes involved in the specification of floral meristem and organ identity and in the transition to flowering in some model plants such as Arabidopsis, Antirrhinum, and Petunia during the last decade represents an unprecedented step forward towards an understanding of floral development. Most of these genes belong to conserved and widespread gene families encoding transcription factors, such as the MADS-box genes, FLO-like, and AP2-like genes. Current work on the molecular genetic basis of floral development still focuses on a deeper understanding of the classical model systems, which are all higher eudicots. However, in order to apply the current knowledge about floral developmental genetics to plant breeding and evolutionary biology, flowering plant diversity is now also seriously taken into account. In the next decade, developmental control genes will be studied less and less individually, but rather as components of complex gene regulatory networks. The necessary technology is currently being developed. Learning to understand the origin and evolution of these gene networks will also help to clarify the origin and diversification of flowers, one of the most "abominable" and long-standing mysteries of botany. Copyright 1999 Wiley-Liss, Inc.

Journal Article↗

PubMed1987

The molecular genetics of C1 utilizing microorganisms. An overview.

The availability of recombinant DNA techniques has enabled the successful genetic analysis and manipulation of a range of C1 utilizing microorganisms. It has resulted in the identification of genes of interest on both plasmids and the chromosome; enabled the linkage of chromosomal genes to be determined; established the function and regulatory patterns of genes essential for utilization of C1 compounds and provided information on the evolution of methanogenic bacteria.

Bacteria↗

PubMed2006

An evolutionarily conserved 16-kDa thioredoxin-related protein is an antioxidant which regulates the NF-kappaB signaling pathway.

Thioredoxin (TRX) is generally a 12-kDa protein-disulfide reductase. Here, we report the discovery of a 16-kDa thioredoxin-related protein designated Cr-TRP16, from a "living fossil," the horseshoe crab (Carcinoscorpius rotundicauda). Cr-TRP16 contains an atypical WCPPC catalytic motif and possesses the classical thiodisulfide reductase activity, as indicated by the insulin reduction assay. Furthermore, Cr-TRP16 can function as an antioxidant and protect against DNA nicking by reactive oxygen species. Overexpression of Cr-TRP16 regulated the transcription of NF-kappaB-dependent genes probably by enhancing NF-kappaB DNA-binding activity, suggesting possible roles for Cr-TRP16 in modulating the NF-kappaB signaling pathway. In vivo, the antioxidant pyrrolidine dithiocarbamate suppressed the expression of NF-kappaB-regulated genes such as IkappaB and inducible nitric oxide synthase. This further supports the notion that oxidative stress is also a regulatory factor of the NF-kappaB signaling pathway, a phenomenon which has been entrenched for several hundred million years. Furthermore, we demonstrated that the 16-kDa thioredoxins are evolutionarily conserved from Caenorhabditis elegans to human. Interestingly, thioredoxin-like 6, a human homologue of Cr-TRP16, could also enhance NF-kappaB DNA-binding activity, suggesting that the regulatory role of the 16-kDa thioredoxins on NF-kappaB is well conserved through evolution.

Amino Acid Sequence↗

PubMed2006

Type I interferon [corrected] gene induction by the interferon regulatory factor family of transcription factors.

Induction of type I interferons (IFNs) by viruses and other pathogens is crucial for innate immunity, and it is mediated by the activation of pattern-recognition receptors, such as Toll-like receptors and cytosolic receptors such as RIG-I and MDA5. The type I IFN induction is primarily controlled at the gene transcriptional level, wherein a family of transcription factors, interferon regulatory factors (IRFs), plays central roles. Here, we summarize the recent studies on IRFs, providing a paradigm of how genes are ingeniously regulated during immune responses. We also consider some evolutional aspects on the IFN-IRF system.

Animals↗

PubMed2004

Statistical analysis of the spatial distribution of operons in the transcriptional regulation network of Escherichia coli.

We have performed a statistical analysis of the spatial distribution of operons along the DNA in the transcriptional regulation network of Escherichia coli. The analysis reveals that pairs of operons that regulate each other and those that are co-regulated tend to lie much closer to one another than would be expected for a random network. Moreover, these pairs of operons tend to be transcribed in diverging directions. This spatial arrangement of operons allows the upstream regulatory domains to overlap and interfere with each other and our analysis also demonstrates the statistical significance of this motif of overlapping operons. Overlapping operons afford additional regulatory control, such as the correlated or anticorrelated expression of operons. We show by a mean-field analysis of a feed-forward loop that overlapping operons can drastically enhance the performance of gene regulatory networks. Our results suggest that regulatory control can provide a selective pressure that drives operons together in the course of evolution.

DNA, Bacterial↗

PubMed2000

Intermediate filament proteins in echinoderm coelomocytes.

The presence and organization of intermediate filament (IF) proteins in petaloid coelomocytes from two species of echinoderms, the sea urchin Strongylocentrotus droehachiensis and the sea cucumber Cucumaria frondosa, were studied. Two monoclonal antibodies (IFA and Ah6) and one polyclonal antibody (W3-1) that together recognize invertebrate as well as vertebrate IF proteins were used to probe coelomocytes by immunofluorescence and immunoblotting methods. All three antibodies cross-reacted with a single Mr 68,000 sea urchin lamin, as well as two putative lamin isoforms of approximately Mr 70,000 and 68,000 in sea cucumber coelomocytes. Both IFA and Ah6 labeled granular material in the cytoplasm of sea urchin coelomocytes; by contrast, IFA labeling revealed a striking network of reticular material irregularly arrayed within the central regions of the sea cucumber coelomocyte cytoplasm. In addition, foci of Ah6-positive material were present in coelomocyte nuclei from both species. Comparison of immunoblotting patterns among whole cell and isolated nuclear preparations suggest that the cytoplasmic IF-like material is composed of Mr 46,000 and 58,000 polypeptides, while Mr 215,000 and 185,000 proteins are candidates for the immunoreactive nuclear foci. Further study of the functions of these non-filamentous arrays of IF proteins may furnish valuable insights into the evolution of IF function within vertebrate cells, particularly with respect to certain cytoplasmic and nuclear regulatory functions with which IF proteins have been speculated to be involved.

Amino Acid Sequence↗

PubMed2002

Glycoxidized low-density lipoprotein downregulates endothelial nitricoxide synthase in human coronary cells.

OBJECTIVES: We examined the hypothesis that low-density lipoprotein (LDL) that is both oxidized and glycosylated potently downregulates the expression of endothelial nitric oxide synthase III (NOSIII) in human coronary endothelial cells. BACKGROUND: Diabetes mellitus is accompanied by both oxidation and glycosylation of LDL, but the potential interaction of these processes or the pathophysiologic effects of these modified lipoproteins on arteries are poorly understood. METHODS: Low-density lipoprotein was glycoxidized in vitro, and Western and Northern blot analyses were used to investigate NOSIII expression in human coronary endothelial cells. Nitric oxide (NO) bioactivity was represented by both basal and bradykinin-stimulated cellular cyclic guanosine monophosphate accumulation and L-citrulline conversion from L-arginine. Nuclear run-on experiments were performed to study the transcription rate of nascent NOSIII messenger ribonucleic acid (mRNA). RESULTS: Data showed a significant decrease in NOSIII expression after 24-h treatment with glycosylated low-density lipoprotein (glycLDL) and oxidized low-density lipoprotein (oxLDL). Accordingly, we observed a significant dose-dependent reduction in NO bioactivity (p < 0.05 to p < 0.001 vs. untreated cells, native low density lipoprotein [nLDL], glycLDL, and oxLDL). Glyc-oxLDL did not reduce the half-life of NOSIII mRNA or significantly enhance L-citrulline conversion. Nuclear run-on experiments showed that high doses of glyc-oxLDL can reduce the transcription rate of nascent NOSIII mRNA (densitometric analysis revealed a reduction of 25% [p < 0.05 vs. untreated cells, nLDL, and glycLDL] after treatment of cells with 300 microg/ml glyc-oxLDL). The effects of glyc-oxLDL are not related to the higher levels of oxidative compounds in comparison to those of oxLDL. CONCLUSIONS: These results indicate that glyc-oxLDL, per se, may influence signal transduction pathways involving NO-mediated regulatory signals and NOSIII activity in human endothelial cells. This phenomenon can adversely influence the evolution of clinical vascular complications, coronary heart disease, and atherogenesis in diabetic patients.

Blotting, Northern↗

PubMed2004

Reduce your pelvis in 10000 years or less.

While the avid dieter obsesses about reduction of different body parts, permanent reduction of many structures seems to be achieved relatively effortlessly (though much more slowly) throughout evolution. In a recent article in Nature, Shapiro et al. examine one such example, the genetic basis of pelvic reduction in the threespine stickleback fish (2004). They conclude that a regulatory mutation in the Pitx1 gene is responsible for the pelvic reduction.

Animals↗

PubMed2001

Mesophyll-specific, light and metabolic regulation of the C4 PPCZm1 promoter in transgenic maize.

To play an essential role in C4 photosynthesis, the maize C4 phosphoenolpyruvate carboxylase gene (PPCZm1) acquired many new expression features, such as leaf specificity, mesophyll specificity, light inducibility and high activity, that distinguish the unique C4 PPC from numerous non-C4 PPC genes in maize. We present here the first investigation of the developmental, cell-specific, light and metabolic regulation of the homologous C4 PPCZm1 promoter in stable transgenic maize plants. We demonstrate that the 1.7 kb of the 5'-flanking region of the PPCZm1 gene is sufficient to direct the C4-specific expression patterns of beta-glucuronidase (GUS) activity, as a reporter, in stable transformed maize plants. In light-grown shoots, GUS expression was strongest in all developing and mature mesophyll cells in the leaf, collar and sheath. GUS activity was also detected in mesophyll cells in the outer husks of ear shoots and in the outer glumes of staminate spikelets. We did not observe histological localization of GUS activity in light- or dark-grown callus, roots, silk, developing or mature kernels, the shoot apex, prop roots, or pollen. In addition, we used the stable expressing transformants to conduct and quantify physiological induction studies. Our results indicate that the expression of the C4 PPCZm1-GUS fusion gene is mesophyll-specific and influenced by development, light, glucose, acetate and chloroplast biogenesis in transgenic maize plants. These studies suggest that the adoption of DNA regulatory elements for C4-specific gene expression is a crucial step in C4 gene evolution.

Acetates↗

PubMed1985

Gene expression and cAMP.

By comparing the 5'-flanking region of the porcine gene for the urokinase form of plasminogen activator with those of other cAMP-regulated genes, we identify a 29-nucleotide sequence that is tentatively proposed as the cAMP-regulatory unit. Homologous sequences are present (i) in the cAMP-regulated rat tyrosine aminotransferase, prolactin, and phosphoenolpyruvate carboxykinase genes and (ii) 5' to the transcription initiation sites of cAMP-regulated Escherichia coli genes. From this we conclude that the expression of cAMP-responsive genes in higher eukaryotes may be controlled, as in E. coli, by proteins that form complexes with cAMP and then show sequence-specific DNA-binding properties. The complex formed by cAMP and the regulatory subunit of the type II mammalian protein kinase might be one candidate for this function. Based on several homologies we suggest that this subunit may have retained both the DNA-binding specificity and transcription-regulating properties in addition to the nucleotide-binding domains of the bacterial cAMP-binding protein. If this were so, dissociation of protein kinase by cAMP would activate two processes: (i) protein phosphorylation by the catalytic subunit and (ii) transcription regulation by the regulatory subunit.

Animals↗

PubMed1993

Localization of sequences controlling the spatial, temporal, and sex-specific expression of the esterase 6 locus in Drosophila melanogaster adults.

The esterase 6 gene (Est-6) of Drosophila melanogaster is expressed in a variety of tissues that differ between larval and adult stages and among related species. Variability in the level of expression of this locus among different species and strains and its species- and tissue-specific patterns of expression make it a useful system for studying the evolution of gene regulation in Drosophila. We have begun to determine the location of the regulatory regions of Est-6 by constructing deletion mutants of the 5' regions of the gene and transforming them back into flies. Deletion mutants of the putative 5' promoter regions of Est-6 were fused to the bacterial beta-galactosidase gene (lacZ) and assayed for their ability to direct tissue-specific expression in transformed D. melanogaster adults. We have identified four independently acting Est-6 regulatory regions that direct the expression of lacZ in (i) the ejaculatory duct; (ii) the adult salivary glands; (iii) the respiratory system, prefrons, antennae, and maxillary palps; and (iv) the ejaculatory bulb and prefrons. We also found a region near the start of transcription that directed expression of Est-6 in the cardia or proventriculus in some transformed lines.

Animals↗

PubMed2004

Spectral Repeat Finder (SRF): identification of repetitive sequences using Fourier transformation.

MOTIVATION: Repetitive DNA sequences, besides having a variety of regulatory functions, are one of the principal causes of genomic instability. Understanding their origin and evolution is of fundamental importance for genome studies. The identification of repeats and their units helps in deducing the intra-genomic dynamics as an important feature of comparative genomics. A major difficulty in identification of repeats arises from the fact that the repeat units can be either exact or imperfect, in tandem or dispersed, and of unspecified length. RESULTS: The Spectral Repeat Finder program circumvents these problems by using a discrete Fourier transformation to identify significant periodicities present in a sequence. The specific regions of the sequence that contribute to a given periodicity are located through a sliding window analysis, and an exact search method is then used to find the repetitive units. Efficient and complete detection of repeats is provided together with interactive and detailed visualization of the spectral analysis of input sequence. We demonstrate the utility of our method with various examples that contain previously unannotated repeats. A Web server has been developed for convenient access to the automated program. AVAILABILITY: The Web server is available at http://www.imtech.res.in/raghava/srf and http://www2.imtech.res.in/raghava/srf

Algorithms↗

PubMed1994

Effects of the maleless mutation on X and autosomal gene expression in Drosophila melanogaster.

The mutational effect of the maleless (mle) gene in Drosophila has been reexamined. Earlier work had suggested that mle along with other male-lethal genes was responsible for hypertranscription of the X chromosome in males to bring about dosage compensation. Prompted by studies on dosage sensitive regulatory genes, we tested for effects of mlets on the phenotypes of 16 X or autosomal mutations in adult escapers of lethality. In third instar larvae, prior to the major lethal phase of mle, we examined activities of 6 X or autosomally encoded enzymes, steady state mRNA levels of 15 X-linked or autosomal genes and transcripts from two large genomic segments derived from either the X or from chromosome 2 and present in yeast artificial chromosomes. In contrast to the previously hypothesized role, we detected pronounced effects of mle on the expression of both X-linked and autosomal loci such that a large proportion of the tested genes were increased in expression, while only two X-linked loci were reduced. The most prevalent consequence was an increase of autosomal gene expression, which can explain previously observed reduced X:autosome transcription ratios. These observations suggest that if mle plays a role in the discrimination of the X and the autosomes, it may do so by modification of the effects of dosage sensitive regulatory genes.

Animals↗

PubMed2000

The genetics of phenotypic plasticity. IX. Genetic architecture, temperature, and sex differences in Drosophila melanogaster.

We examined the genetic architecture of plasticity of thorax and wing length in response to temperature in Drosophila melanogaster. Reaction norms as a function of growth temperature were analyzed in 20 isofemale lines in a natural population collected from Grande Ferrade near Bordeaux (southern France) in two different years. We found evidence for a complex genetic architecture underlying the reaction norms and differences between males and females. Reaction norms were negative quadratics. Genetic correlations were moderately high between traits within environments. Among characteristic values, the magnitudes of genetic correlations varied among traits and sexes. We hypothesized that genetic correlations among environments would decrease as temperatures became more different. This expectation was upheld for only one trait, female thorax length. For males for both traits, the correlations were large for both very similar and very different temperatures. These correlations may constrain the evolution of the shape of the reaction norms. Whether the extent of independence implies specific regulatory genes or only a specific allelic regulation of trait genes can not be decided from our results.

Animals↗

PubMed1996

Recoding: dynamic reprogramming of translation.

A minority of genes in probably all organisms rely on "recoding" for translation of their mRNAs. In these cases, the rules for decoding are temporarily altered through the action of specific signals built into the mRNA sequences. Three classes are described. 1. Frameshifting at a particular site allows expression of a protein from an mRNA with overlapping open reading frames, often giving two protein products from one mRNA. 2. The meanings of code words are altered: specific stop codons can be redirected to encode selenocysteine, tryptophan, or glutamine. 3. Ribosomes can translate over coding gaps in mRNA. These novel mechanisms expand the repertoire of the genetic code and are at the heart of several regulatory schemes.

Animals↗

PubMed1998

Functional coupling of neurotransmitters with second messengers during cleavage divisions: facts and hypotheses.

Current data on the role of classical neurotransmitters as multiple and multifunctional regulators of early embryogenesis are reviewed. It is shown that these developmental regulators are coupled with second messengers. Peculiarities of this prenervous coupling emphasized and are used as the basis for discussing the problem of the evolutionary origin of cell regulatory systems.

Animals↗

PubMed2003

[Are acute toxicity testing and the three Rs rule reconcilable? Example of the lethal dose 50 determination].

Toxicity assessment and demonstration of innocuousness of chemical compounds have been part of the research studies conducted in the fields of pharmacy, agriculture and chemical industry for years. Acute systemic toxicity studies are an important element of the safety evaluation. They remain compulsory for regulatory purposes and important for the public opinion that does not accept the risk anymore. Evolutions of the ethics in animal experiments foster a necessary reduction of the number of animals involved in this type of experiments, following the well-known principle of the three Rs rule of Russell and Burch (1959) (Reduction, refinement and replacement). These two views seem in contradiction. Using the example of acute toxicity testing and focusing on the now very criticized parameter lethal dose 50, we will present approaches, including statistical ones, that a toxicologist can use, when free to choose, to keep on conducting the indispensable in vivo studies while abiding by ethical recommendations.

Animal Testing Alternatives↗