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Results for “regulatory evolution”

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At least 397 records · Page 22Linked to original sources

PubMed2001

N-formyl-methionyl-leucyl-phenylalanine inhibits both gamma interferon- and interleukin-10-induced expression of FcgammaRI on human monocytes.

Three different classes of receptors for the Fc portion of immunoglobulin G (FcgammaRs), FcgammaRI, FcgammaRII, and FcgammaRIII, have been identified on human leukocytes. One of them, FcgammaRI, is a high-affinity receptor capable of induction of functions that include phagocytosis, respiratory burst, antibody-dependent cell-mediated cytotoxicity (ADCC), and secretion of cytokines. This receptor is expressed on mononuclear phagocytes, and this expression is regulated by cytokines and hormones such as gamma interferon (IFN-gamma), IFN-beta, interleukin-10 (IL-10), and glucocorticoids. We have recently demonstrated that the chemotactic peptide N-formyl-methionyl-leucyl-phenylalanine (FMLP) is capable of inducing a time-dependent downregulation of both FcgammaRIIIB and FcgammaRII in human neutrophils, altering FcgammaR-dependent functions. Considering the biological relevance of the regulation of FcgammaRI, we investigated the effect of FMLP on the overexpression of FcgammaRI induced by both IFN-gamma and IL-10 on human monocytes. We demonstrate that FMLP significantly abrogated IFN-gamma- and IL-10-induced FcgammaRI expression, although its basal level of expression was not altered. However, other IFN-gamma-mediated effects such as the overexpression of the major histocompatibility complex class II antigens and the enhancement of lipopolysaccharide-induced secretion of tumor necrosis factor alpha were not affected by FMLP treatment. The formyl peptide completely inhibited the IFN-gamma- and IL-10-induced enhancement of ADCC and phagocytosis carried out by adherent cells. The inhibitory effect of FMLP on FcgammaRI upregulation could exert an important regulatory effect during the evolution of bacterial infections.

Adult↗

PubMed1987

Expression of the Aplysia californica rho gene in Escherichia coli: purification and characterization of its encoded p21 product.

A new family of highly conserved genes, designated rho, has recently been isolated and characterized (P. Madaule and R. Axel, Cell 41:31-40, 1985). These genes have been found in Saccharomyces cerevisiae, Drosophila melanogaster, rats, and humans, and their 21,000-dalton products are highly homologous. The rho p21 protein shares 35% amino acid homology with the Harvey ras p21 protein and on this basis has been proposed to be a G protein. We expressed the Aplysia californica rho gene in Escherichia coli and purified its p21 protein to more than 90% purity. The availability of the rho protein in high quantities made it possible to establish its high affinity for guanine nucleotides. The rho p21 protein had nucleotide-binding properties similar to those of the ras p21 protein. However, a comparison of these proteins revealed some important differences regarding their specificities and affinities. Finally, the rho p21 protein had GTPase activity almost identical to that of a normal ras p21 protein, the rates being 0.106 and 0.105 mol/min per mol of p21, respectively. Thus, the results suggest that the degree of homology found between the ras and rho genes products most likely is related to the conservation of sequences relevant to their ability to bind and hydrolyze guanine nucleotides. The fact that the rho p21 protein binds and hydrolyzes GTP strongly suggests that it is a G protein with a potential regulatory function conserved in evolution.

Animals↗

PubMed2006

Clinical trials bureaucracy: unintended consequences of well-intentioned policy.

BACKGROUND: As randomized controlled trials have become the 'gold standard' for medical research, a complex regulatory structure for the conduct of clinical trials has emerged. However, this structure has not been adequately assessed to ensure that regulations governing human subjects research actually produce the desired effects. PURPOSE: Our purpose is to identify some of the major shortcomings in the current regulatory system of human clinical trials oversight, and to propose some potential solutions to these problems. METHODS: We discuss the evolution of the current US regulatory environment and its application in the context of several widely-used drug therapies. RESULTS: Despite numerous randomized controlled trials, performed within a structure of extensive documentation and data collection, serious shortcomings in a number of pharmaceutical therapies were not detected until after the drugs were approved and widely adopted by clinicians. CONCLUSION: The current system of regulatory bureaucracy in clinical trials has led to an extremely expensive research paradigm that, in spite of complex systems of oversight and exhaustive data collection, cannot be shown to adequately ensure the integrity of the research process and the protection of human research subjects. Some parts of the system, including Research Ethics Review Boards, may not be well-suited to carrying out their core mission of overseeing research conduct, and other aspects of clinical trials regulatory structure, such as monitoring/auditing review and adverse event reporting, may constitute a waste of money and resources. Misdirected data collection and adverse events reporting divert valuable resources and hamper development of large, simple clinical trials powered to definitively answer important research questions. Careful scrutiny of the utility of current or proposed regulatory schemes is required to ensure the integrity of human subjects research and to enhance the effectiveness of research dollars.

Adverse Drug Reaction Reporting Systems↗

PubMed1999

Complex modular cis-acting elements regulate expression of the cardiac specifying homeobox gene Csx/Nkx2.5.

The murine homeobox gene Csx/Nkx2.5 is an evolutionarily highly conserved gene related to the Drosophila tinman gene, which specifies cardiac and visceral mesoderm. Since Csx/Nkx2.5 plays an essential role in heart development, studying its regulation is essential for the better understanding of molecular mechanisms of cardiogenesis and the pathogenesis of congenital heart disease in humans. In this study, we characterized the murine Csx/Nkx2.5 gene and identified two novel untranslated exons, 1a, and 1b, resulting in three different Csx/Nkx2.5 transcripts. To examine the tissue-specific transcriptional regulation in vivo, we analyzed a total of 23 kb of Csx/Nkx2.5 upstream and downstream sequences by generating transgenic embryos carrying lacZ reporter constructs containing various lengths of flanking sequence. With 14 kb of 5' flanking sequence, lacZ expression was observed in the cardiac crescent at E7.5, and in the outflow tract, the interatrial groove, the atrioventricular canal and right and left ventricles, as well as in pharyngeal floor, thyroid primordia, and stomach at E10.5. In adult animals, lacZ expression of the transgene was limited to the atrioventricular junction and the subendocardium of the ventricular septum. Reducing the size of flanking sequence to 3.3 kb of intron 2 restricted lacZ expression to the outflow tract and the basal part of the right ventricle in E10.5 embryos. In contrast, the addition of 6 kb of 3' flanking sequence caused strong expression of the reporter gene in the entire right ventricle. Interestingly, Csx/Nkx2. 5 seems to be negatively regulated by its own gene product, because when lacZ was "knocked-in" to replace the entire coding exons, lacZ expression was much higher in the heart of homozygous embryos than that in the heterozygote. These results indicate that the transcriptional regulatory elements of Csx/Nkx 2.5 seems unexpectedly highly modular, and is temporally regulated in a dynamic manner by different enhancer regions. Since Csx/Nkx2.5-like genes are expressed in all species having a heart, their complex modular organization with multiple enhancers probably reflects progressive addition of regulatory elements during the evolution from a simple heart tube to a complex four-chambered organ.

Alternative Splicing↗

PubMed2001

A comparative genomics approach to prediction of new members of regulons.

Identifying the complete transcriptional regulatory network for an organism is a major challenge. For each regulatory protein, we want to know all the genes it regulates, that is, its regulon. Examples of known binding sites can be used to estimate the binding specificity of the protein and to predict other binding sites. However, binding site predictions can be unreliable because determining the true specificity of the protein is difficult because of the considerable variability of binding sites. Because regulatory systems tend to be conserved through evolution, we can use comparisons between species to increase the reliability of binding site predictions. In this article, an approach is presented to evaluate the computational predictions of regulatory sites. We combine the prediction of transcription units having orthologous genes with the prediction of transcription factor binding sites based on probabilistic models. We augment the sets of genes in Escherichia coli that are expected to be regulated by two transcription factors, the cAMP receptor protein and the fumarate and nitrate reduction regulatory protein, through a comparison with the Haemophilus influenzae genome. At the same time, we learned more about the regulatory networks of H. influenzae, a species with much less experimental knowledge than E. coli. By studying orthologous genes subject to regulation by the same transcription factor, we also gained understanding of the evolution of the entire regulatory systems.

Amino Acid Sequence↗

PubMedDate not supplied

Integrated phylogeny of the primate brain, with special reference to humans and their diseases.

Fossil, comparative anatomic and ontogenic data suggest that several systems of functionally and anatomically related brain regions underwent selective expansion or differentiation during primate evolution, according to the principle of 'integrated phylogeny'. This process was closely tied to expansion of the neocortex, particularly of its association areas. System I regions include the association neocortices as well as the nucleus basalis of Meynert, the entorhinal cortex, and subdivisions of the septum, hippocampal formation and amygdaloid complex. This system undergoes degeneration in Alzheimer's and Pick's diseases and Down syndrome. System II includes segregated circuits involving parts of the frontal cortex, basal ganglia, thalamus, and substantia nigra, and can become defective in obsessive-compulsive disorder, Huntington's and Parkinson's diseases. Certain nuclei in the mesencephalon and brainstem, which co-evolved with System I and II regions, also demonstrate pathology in diseases affecting these systems. Integrated phylogeny of each of these systems during primate evolution likely was promoted by regulatory mutations, gene duplications or chromosomal rearrangements. Thus, understanding the genetic basis of integrated phylogeny of systems of brain regions during primate evolution may elucidate the pathogenesis of the human diseases which affect these regions.

Animals↗

PubMed2006

High regulatory gene use in sea urchin embryogenesis: Implications for bilaterian development and evolution.

A global scan of transcription factor usage in the sea urchin embryo was carried out in the context of the Strongylocentrotus purpuratus genome sequencing project, and results from six individual studies are here considered. Transcript prevalence data were obtained for over 280 regulatory genes encoding sequence-specific transcription factors of every known family, but excluding genes encoding zinc finger proteins. This is a statistically inclusive proxy for the total "regulome" of the sea urchin genome. Close to 80% of the regulome is expressed at significant levels by the late gastrula stage. Most regulatory genes must be used repeatedly for different functions as development progresses. An evolutionary implication is that animal complexity at the stage when the regulome first evolved was far simpler than even the last common bilaterian ancestor, and is thus of deep antiquity.

Animals↗

PubMed2006

Two or four bristles: functional evolution of an enhancer of scute in Drosophilidae.

Changes in cis-regulatory sequences are proposed to underlie much of morphological evolution. Yet, little is known about how such modifications translate into phenotypic differences. To address this problem, we focus on the dorsocentral bristles of Drosophilidae. In Drosophila melanogaster, development of these bristles depends on a cis-regulatory element, the dorsocentral enhancer, to activate scute in a cluster of cells from which two bristles on the posterior scutum arise. A few species however, such as D. quadrilineata, bear anterior dorsocentral bristles as well as posterior ones, a derived feature. This correlates with an anterior expansion of the scute expression domain. Here, we show that the D. quadrilineata enhancer has evolved, and is now active in more anterior regions. When used to rescue scute expression in transgenic D. melanogaster, the D. quadrilineata enhancer is able to induce anterior bristles. Importantly, these properties are not displayed by homologous enhancers from control species bearing only two posterior bristles. We also provide evidence that upstream regulation of the enhancer, by the GATA transcription factor Pannier, has been evolutionarily conserved. This work illustrates how, in the context of a conserved trans-regulatory landscape, evolutionary tinkering of pre-existing enhancers can modify gene expression patterns and contribute to morphological diversification.

Animals↗

PubMed1995

The evolution of national nutrition policy.

Domestic regulatory efforts in the area of nutrition historically have focused on achieving and sustaining the highest possible level of food safety and availability. More recently, the linkages between certain dietary practices and the risk of chronic, degenerative diseases have also become a significant focus of public policy. In order to promote good nutrition practices, the Food and Drug Administration (FDA) now requires a detailed and informative Nutrition Facts food label on virtually all food packages. Other public policies promoted by the FDA and others include increasing public knowledge of the relationship between diet and health; promoting unified food and nutrition policies among all government agencies; educating the American consumer about sound dietary practices; and encouraging the development of technologies that may result in more healthful, more abundant, and more affordable foods.

Agriculture↗

PubMed2005

Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution.

We have sequenced the genome of a second Drosophila species, Drosophila pseudoobscura, and compared this to the genome sequence of Drosophila melanogaster, a primary model organism. Throughout evolution the vast majority of Drosophila genes have remained on the same chromosome arm, but within each arm gene order has been extensively reshuffled, leading to a minimum of 921 syntenic blocks shared between the species. A repetitive sequence is found in the D. pseudoobscura genome at many junctions between adjacent syntenic blocks. Analysis of this novel repetitive element family suggests that recombination between offset elements may have given rise to many paracentric inversions, thereby contributing to the shuffling of gene order in the D. pseudoobscura lineage. Based on sequence similarity and synteny, 10,516 putative orthologs have been identified as a core gene set conserved over 25-55 million years (Myr) since the pseudoobscura/melanogaster divergence. Genes expressed in the testes had higher amino acid sequence divergence than the genome-wide average, consistent with the rapid evolution of sex-specific proteins. Cis-regulatory sequences are more conserved than random and nearby sequences between the species--but the difference is slight, suggesting that the evolution of cis-regulatory elements is flexible. Overall, a pattern of repeat-mediated chromosomal rearrangement, and high coadaptation of both male genes and cis-regulatory sequences emerges as important themes of genome divergence between these species of Drosophila.

Animals↗

PubMed2004

Bapx1 regulates patterning in the middle ear: altered regulatory role in the transition from the proximal jaw during vertebrate evolution.

The middle ear apparatus is composed of three endochondrial ossicles (the stapes, incus and malleus) and two membranous bones, the tympanic ring and the gonium, which act as structural components to anchor the ossicles to the skull. Except for the stapes, these skeletal elements are unique to mammals and are derived from the first and second branchial arches. We show that, in combination with goosecoid (Gsc), the Bapx1 gene defines the structural components of the murine middle ear. During embryogenesis, Bapx1 is expressed in a discrete domain within the mandibular component of the first branchial arch and later in the primordia of middle ear-associated bones, the gonium and tympanic ring. Consistent with the expression pattern of Bapx1, mouse embryos deficient for Bapx1 lack a gonium and display hypoplasia of the anterior end of the tympanic ring. At E10.5, expression of Bapx1 partially overlaps that of Gsc and although Gsc is required for development of the entire tympanic ring, the role of Bapx1 is restricted to the specification of the gonium and the anterior tympanic ring. Thus, simple overlapping expression of these two genes appears to account for the patterning of the elements that compose the structural components of the middle ear and suggests that they act in concert. In addition, Bapx1 is expressed both within and surrounding the incus and the malleus. Examination of the malleus shows that the width, but not the length, of this ossicle is decreased in the mutant mice. In non-mammalian jawed vertebrates, the bones homologous to the mammalian middle ear ossicles compose the proximal jaw bones that form the jaw articulation (primary jaw joint). In fish, Bapx1 is responsible for the formation of the joint between the quadrate and articular (homologues of the malleus and incus, respectively) enabling an evolutionary comparison of the role of a regulatory gene in the transition of the proximal jawbones to middle ear ossicles. Contrary to expectations, murine Bapx1 does not affect the articulation of the malleus and incus. We show that this change in role of Bapx1 following the transition to the mammalian ossicle configuration is not due to a change in expression pattern but results from an inability to regulate Gdf5 and Gdf6, two genes predicted to be essential in joint formation.

Animals↗

PubMed2005

An alien promoter capture as a primary step of the evolution of testes-expressed repeats in the Drosophila melanogaster genome.

Fertility of Drosophila melanogaster males is impaired due to the disruption of the silencing of the X-linked, testis-expressed, repeated Stellate (Ste) genes. Ste silencing is mediated by symmetric transcription of the paralogous Y-linked repeats and exerted by an RNA interference (RNAi) mechanism. Here we present a scenario for the origin of the Ste genes and their suppressors. The primary intermediate of their evolution emerged as a result of the acquisition of a preformed alien, testis-specific promoter. This intermediate is identified as a chimeric gene containing coding region of an autosomal gene for testis-specific protein kinase CK2. The 5' region of the chimera has been acquired from a member of a family of testis-expressed X-linked genes of unknown function. We propose that the evolution and amplification of the novel chimeric gene have led to the overproduction of the regulatory CK2 subunit in testes. The evolution of the Y-linked descendants of the primary intermediate resulted in the RNAi-mediated suppression of excessive expression of the X-linked paralogs. The newly detected "dead family" of cognate repeats on the Y chromosome has contributed to the evolution of Ste and its suppressors via gene conversion. Our results show that RNAi silencing, considered as a defense against viruses and transposable elements, may be involved in the evolution of eukaryotic genomes.

Animals↗

PubMed2005

Transposition of Regulatory Elements by P-Element-Mediated Rearrangements in Drosophila melanogaster.

Previously we described highly unstable mutations in the yellow locus, induced by the chimeric element and consisting of sequences from a distally located 1A unique genomic region, flanked by identical copies of an internally deleted 1.2-kb P element. Here we show that a sequence, which is part of the yellow 1A region, can be transmitted to the AS-C by successive inversion and reinversion generated by yellow- and AS-C-located P elements. The chimeric element contains a regulatory element from the 1A region that specifically blocks yellow wing and body enhancers and simultaneously stimulates yellow expression in bristles. These results suggest that P-element-generated chimeric elements may play a certain role in rapid changes of regulatory regions of genes during evolution.

Alleles↗

PubMed2000

Mutational analysis of Escherichia coli PepA, a multifunctional DNA-binding aminopeptidase.

Escherichia coli PepA is a hexameric aminopeptidase that is also endowed with a DNA-binding activity that functions in transcription control and plasmid dimer resolution. To gain further insight into the functioning of PepA, mutants were selected on the basis of reduced repressibility of a genomic carA-lacZ fusion and studied for the various cellular processes requiring PepA, i.e. repression of the carAB operon, autoregulation, resolution of ColE1 multimers, and peptide proteolysis. The methylation status of the carAB control region was analysed in several pepA mutants and purified proteins were assayed in vitro for car operator DNA binding. This study provides a critical test of predictions advanced on the basis of the structural analysis of PepA and demonstrates the importance for DNA binding of several secondary structural elements in the N-terminal domain and near the very C terminus. By analysis of single amino acid substitutions, we could distinguish the mode of PepA action in car regulation from its action in plasmid resolution. We demonstrate that mere binding of PepA to the car control region is not sufficient to explain its role in pyrimidine-specific regulation; protein-protein interactions appear to play an important role in transcriptional repression. The multifunctional character of PepA and of an increasing number of transcriptional regulators that combine catalytic and regulatory properties, of which several participate in the metabolism of arginine and of the pyrimidines, suggests that enzymes and DNA (RNA) binding proteins fulfilling an essential primeval function may have been recruited in evolution to fulfil an additional regulatory task.

Adenine↗

PubMed2002

The evolution of engrailed genes after duplication and speciation events.

Members of the engrailed class encode transcription factors involved in major steps of metazoan development. Few developmental regulatory genes have been studied in such a wide range of animals. Furthermore duplications of an ancestral engrailed gene independently generated multiple engrailed paralogues in several organisms. This offers the opportunity to reconstruct the evolution of the engrailed family and to study the processes involved in the functional diversification following speciation or duplication events. The ancestral function of engrailedis very likely involved in neurogenesis. Recent studies in Drosophila and mice have shown its crucial role in neuronal connectivity and neuromuscular targeting. engrailed was probably recruited very early for a role in segmentation through intercalary evolution. Several new functions were acquired later on in specific phyla. Some duplication events have been followed by the loss of one paralogue, whereas others have led to the functional diversification of the paralogues. The Duplication-Degenerescence-Complementation model recently proposed by Force et al. seems to be the main process involved in functional diversification after duplication events. This does not exclude acquisition of new functions for one or both paralogues after duplication. The acquisition of such new functions principally involves the evolution of cis-regulatory sequences, but evolution of the coding sequence has also been revealed. However, in all engrailed duplications studied, even in ancient chromosomal duplications, the paralogues have kept redundant functions. In fact, selection seems to maintain a certain redundancy between engrailed paralogues.

Animals↗

PubMed2006

Evolution of kallikrein-related peptidases in mammals and identification of a genetic locus encoding potential regulatory inhibitors.

The human kallikrein locus on chromosome 19 consists of 15 genes encoding serine proteases. Here we review studies on their evolution, which demonstrate that there are several taxon-unique KLK1 paralogs in mouse, rat and horse, but not in primates and many other mammals. Furthermore, the duplication yielding KLK2 and prostate-specific antigen (KLK3) appears to be specific to primates, but a functional progenitor to KLK2 is expressed in the dog prostate. The linkage to a locus of possible regulatory protease inhibitors on chromosome 20 is discussed, as is the potential role of the kallikrein locus in innate immunity.

Animals↗

PubMed2006

Linking floral symmetry genes to breeding system evolution.

Understanding the genetic basis of ecologically important traits is a major focus of evolutionary research. Recent advances in molecular genetic techniques should significantly increase our understanding of how regulatory genes function. By contrast, our understanding of the broader macro-evolutionary implications of developmental gene function lags behind. Here we review published data on the floral symmetry gene network (FSGN), and conduct phylogenetic analyses that provide evidence of a link between floral symmetry and breeding systems in angiosperms via dichogamy. Our results suggest that known genes in the FSGN and those yet to be described underlie this association. We posit that the integration of floral symmetry and the roles of other regulatory genes in plant breeding system evolution will provide new insights about macro-evolutionary patterns and processes in flowering plants.

Biological Evolution↗

PubMedDate not supplied

Sequence and evolution of the FruR protein of Salmonella typhimurium: a pleiotropic transcriptional regulatory protein possessing both activator and repressor functions which is homologous to the periplasmic ribose-binding protein.

The repressor of the fructose (fru) operon of Salmonella typhimurium (FruR) has been implicated in the transcriptional regulation of dozens of genes concerned with central metabolic pathways of carbon utilization. We here report the nucleotide sequence of the gene encoding FruR and analyse both its operator-promoter region and its deduced amino acyl sequence. The FruR protein was overexpressed and was shown to have a molecular weight of about 36 kDa in agreement with the molecular weight deduced from the gene sequence. Sequence analyses revealed that FruR is homologous to 9 distinct bacterial DNA-binding proteins, most of which recognize sugar inducers and all of which possess helix-turn-helix motifs within their N-terminal regions and exhibit sequence identity throughout most of their lengths. FruR is also homologous to the periplasmic ribose-binding protein which serves as a constituent of the ribose transport/chemoreception system. The ribose-binding protein is in turn homologous to binding proteins specific for arabinose and galactose. The periplasmic binding proteins, the structures of some of which have been elucidated in three dimensions, lack the N-terminal helix-turn-helix region, but instead possess N-terminal hydrophobic signal sequences which target them to the periplasm. A phylogenetic tree for the more closely related proteins of this superfamily was constructed, and a signature motif was identified which should facilitate future detection of additional transcriptional regulatory proteins belonging to this family.

Base Sequence↗