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Results for “regulatory evolution”

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PubMed2005

Compensatory cis-trans evolution and the dysregulation of gene expression in interspecific hybrids of Drosophila.

Hybrids between species are often characterized by novel gene-expression patterns. A recent study on allele-specific gene expression in hybrids between species of Drosophila revealed cases in which cis- and trans-regulatory elements within species had coevolved in such a way that changes in cis-regulatory elements are compensated by changes in trans-regulatory elements. We hypothesized that such coevolution should often lead to gene misexpression in the hybrid. To test this hypothesis, we estimated allele-specific expression and overall expression levels for 31 genes in D. melanogaster, D. simulans, and their F1 hybrid. We found that 13 genes with cis-trans compensatory evolution are in fact misexpressed in the hybrid. These represent candidate genes whose dysregulation might be the consequence of coevolution of cis- and trans-regulatory elements within species. Using a mathematical model for the regulation of gene expression, we explored the conditions under which cis-trans compensatory evolution can lead to misexpression in interspecific hybrids.

Alleles↗

PubMed2005

Regulatory gene expressions in the ascidian ventral sensory vesicle: evolutionary relationships with the vertebrate hypothalamus.

In extant chordates, the overall patterning along the anteroposterior and dorsoventral axes of the neural tube is remarkably conserved. It has thus been proposed that four domains corresponding to the vertebrate presumptive forebrain, midbrain-hindbrain transition, hindbrain, and spinal cord were already present in the common chordate ancestor. To obtain insights on the evolution of the patterning of the anterior neural tube, we performed a study aimed at characterizing the expression of regulatory genes in the sensory vesicle of Ciona intestinalis, the anteriormost part of the central nervous system (CNS) related to the vertebrate forebrain, at tailbud stages. Selected genes encoded primarily for homologues of transcription factors involved in vertebrate forebrain patterning. Seven of these genes were expressed in the ventral sensory vesicle. A prominent feature of these ascidian genes is their restricted and complementary domains of expression at tailbud stages. These patterning markers thus refine the map of the developing sensory vesicle. Furthermore, they allow us to propose that a large part of the ventral and lateral sensory vesicle consists in a patterning domain corresponding to the vertebrate presumptive hypothalamus.

Animals↗

PubMed2005

The mediator of RNA polymerase II.

Mediator (TRAP/ARC/PC2) is a large (22-28 subunit) protein complex that binds RNA polymerase II and controls transcription from class II genes. The evolutionarily conserved core of Mediator is found in all eukaryotes. It binds RNA polymerase II and is probably critical for basal transcription but it also mediates activation and repression of transcription. During evolution the complex has acquired additional species-specific subunits. These serve as an interface for regulatory factors and support specific signalling pathways. Recent mechanistic studies are consistent with the hypothesis that Mediator marks genes for binding by RNA polymerase II whereupon it subsequently activates the preinitiation complex. It is further likely that Mediator coordinates the recruitment of chromatin-modifying cofactor activities.

Animals↗

PubMed1996

Chromosomal integration dependent induction of junB by growth factors requires multiple flanking evolutionarily conserved sequences.

The junB locus contains nine flanking evolutionarily conserved sequences (FECS) that share 72% to 91% sequence identity between human and mouse. These FECS encompass the same regions of flanking DNA necessary for maximal mitogenic induction of junB. Most of the cis elements reported to date that affect junB regulation also reside within FECS. These observations suggest that the persistence of FECS through evolution reflects a necessary role in junB transcriptional regulation. In this report, we identify specific regulatory cis elements within junB FECS II and III and provide a quantitative analysis of the contribution made by these sequences to junB induction. These cis elements include a Serum Response Element (SRE), two Ets sites previously unrecognized as contributing to junB expression, and two novel Ets-linked motifs (ELMs). In general, mutating any single element significantly impairs junB induction. Moreover, the same mutations alter the structure of junB 5' flanking DNA within chromatin. Collectively, these results suggest that multiple proteins bound within FECS confederate to form a functional promoter complex, the activity of which is dependent upon a specific chromatin architecture.

Animals↗

PubMed2001

The evolution of bacterial LuxI and LuxR quorum sensing regulators.

Quorum sensing is a widespread form of bacterial communication in which individual cells produce and respond to specific N-acyl homoserine lactone signal metabolites. The different autoinducer synthases that generate these signals and the receptor/activator proteins that mediate the cell's response to them constitute evolutionarily conserved families of regulatory proteins known as the LuxI and LuxR families, respectively. We have performed a phylogenetic analysis of 76 individual LuxI and LuxR homologues present in diverse members of the Gram-negative Proteobacteria. The results were consistent with an early origin for these regulators during the evolution of the Proteobacteria, with functional pairs of luxI and luxR genes possibly coevolving as regulatory cassettes. In many cases, specific LuxI and LuxR family members appeared to have been inherited horizontally. In particular, those species containing multiple LuxI and/or LuxR homologues usually appeared to have obtained each individual homologue or functional pair of homologues from an independent source. Because multiple homologues interact to form regulatory cascades, this finding suggests that hierarchical signalling pathways can potentially evolve by the sequential integration of pre-existing regulatory circuits acquired from diverse sources.

Bacterial Proteins↗

PubMed2004

Cell cycle genes in ovarian cancer: steps toward earlier diagnosis and novel therapies.

Human malignant tumors are characterized by abnormal proliferation resulting from alterations in cell cycle-regulatory mechanisms. The regulatory pathways controlling cell cycle phases include several oncogenes and tumor suppressor genes that display a range of abnormalities with potential usefulness as markers of evolution or treatment response in ovarian cancer. This review summarizes the current knowledge about these aberrations in malignant tumors of the ovary. We sought to divide cell cycle-regulatory genes into four subgroups on the basis of their predominant role in a specific phase or during the transition between two phases of the cell cycle.

Cell Cycle↗

PubMed1990

Duplication and divergence of the amino-terminal coding region of the complement receptor 1 (CR1) gene. An example of concerted (horizontal) evolution within a gene.

Human C3b/C4b receptor or complement receptor type one (CR1) is one of a family of receptor and regulatory glycoproteins that are encoded at a single genetic region (1q32) and are composed largely of a tandemly repeated motif (short consensus repeat or SCR) of approximately 60 amino acids. In addition, CR1 features an internal homology of seven SCRs in length, known as a long homologous repeat, that is reiterated four times, in the major polymorphic size variant, from SCR-1 to SCR-28, and may be reiterated three, five, and six times in other polymorphic forms. In the course of studying CR1, we detected sequences closely related to CR1 on several overlapping genomic clones. We have characterized a 40-kilobase CR1-like genomic region containing 10 potential exons that are 95% homologous to the amino-terminal coding portion of CR1. This region appears to be a partial duplication of CR1 and may encode a related gene. A comparison of CR1 and CR1-like sequences suggests that unequal crossing-over and concerted evolution have occurred within the most precisely reiterated subregion of CR1. Similar mechanisms have been important in the evolution of tandemly repeated genes and could provide the means for generation of the CR1 polymorphic size variants.

Amino Acid Sequence↗

PubMed1995

Constraints on intron evolution in the gene encoding the myosin alkali light chain in Drosophila.

Interspecific comparisons of intron sequences reveal conserved blocks of invariant nucleotides and several other departures from the strictly neutral model of molecular evolution. To distinguish the past action of evolutionary forces in introns known to have regulatory information, we examined nucleotide sequence variation at 991 sites in a random sample of 16 Drosophila melanogaster alleles of the gene encoding the myosin alkali light chain (Mlc1). The Mlc1 gene of D. melanogaster encodes two MLC1 isoforms via developmentally regulated alternative pre-mRNA splicing. Analyses of these data reveal that introns 4 and 5, which flank the alternatively spliced exon 5, have reduced levels of both intraspecific polymorphism and interspecific divergence relative to intron 3. No polymorphism was observed in any of the exons examined in D. melanogaster. A genealogical analysis clearly demonstrates the occurrence of intragenic recombination in the ancestral history of Mlc1. Recombination events are estimated to be 13 times more likely than mutation events over the span of the sequenced region. Although there is little evidence for pairwise linkage disequilibrium in the Mlc1 region, higher order disequilibrium does seem to be present in the 5' half of the portion of the gene that was examined. Predictions of the folding free energy of the pre-mRNA reveal that sampled alleles have a significantly higher (less stable) free energy than do randomly permuted sequences. These results are consistent with the hypothesis that introns surrounding an alternatively spliced exon are subjected to additional constraints, perhaps due to specific aspects of secondary structure required for appropriate splicing of the pre-mRNA molecule.

Alternative Splicing↗

PubMed1987

Regulatory mutations that allow the growth of Escherichia coli on butanol as carbon source.

Starting with adhC mutants of Escherichia coli in which alcohol dehydrogenase (ADH) and acetaldehyde CoA dehydrogenase (ACDH) are expressed constitutively at high levels, we selected mutants with still higher levels of both enzymes. Selection for growth on ethanol in the presence of inhibitors of ADH gave several mutants that had from 2- to 10-fold increases in the levels of both enzymes. These mutations were found to map far from the adhC locus at around 90 min. Such adhR mutants were unable to grow on acetate or ethanol in certain media unless supplemented with extra manganese. This growth disability was suppressed by secondary mutations, one of which, aceX, increased sensitivity to several toxic metals and may perhaps derepress Mn transport. When the adhR mutation expressing the highest ADH and ACDH levels was present together with fadR and atoC mutations (allowing efficient catabolism of acetoacetyl-CoA) and with an aceX mutation, the resulting strains became capable of using n-butanol as sole carbon and energy source. The use of butanol by E. coli illustrates the artificial evolution of a new catabolic pathway, in this case by the selection of four successive regulatory mutations (fadR, adhC, atoC, and adhR) together with the poorly defined aceX mutation. Each stage in the acquisition of this novel pathway confers the ability to use a new growth substrate: decanoic acid (fadR), ethanol (adhC), butyric acid (atoC), and butanol (adhR, when present with aceX).

1-Butanol↗

PubMed1991

Structural and functional conservation of synaptotagmin (p65) in Drosophila and humans.

Synaptotagmin (p65) is an abundant synaptic vesicle protein that contains two copies of a sequence that is homologous to the regulatory region of protein kinase C. Full length cDNAs encoding human and Drosophila synaptotagmins were characterized to study its structural and functional conservation in evolution. The deduced amino acid sequences for human and rat synaptotagmins show 97% identity, whereas Drosophila and rat synaptotagmins are only 57% identical but exhibit a selective conservation of the two internal repeats that are homologous to the regulatory region of protein kinase C (78% invariant residues in all three species). The two internal repeats of synaptotagmin are only slightly more homologous to each other than to protein kinase C, and the differences between the repeats are conserved in evolution, suggesting that they might not be functionally equivalent. The cytoplasmic domains of human and Drosophila synaptotagmins produced as recombinant proteins in Escherichia coli specifically bound phosphatidylserine similar to rat synaptotagmin. They also hemagglutinated trypsinized erythrocytes at nanomolar concentrations. Hemagglutination was inhibited both by negatively charged phospholipids and by a recombinant fragment from rat synaptotagmin that contained only a single copy of the two internal repeats. Together these results demonstrate that synaptotagmin is highly conserved in evolution compatible with a function in the trafficking of synaptic vesicles at the active zone. The similarity of the phospholipid binding properties of the cytoplasmic domains of rat, human, and Drosophila synaptotagmins and the selective conservation of the sequences that are homologous to protein kinase C suggest that these are instrumental in phospholipid binding. The human gene for synaptotagmin was mapped by Southern blot analysis of DNA from somatic cell hybrids to chromosome 12 region cen-q21, and the Drosophila gene by in situ hybridization to 23B.

Amino Acid Sequence↗

PubMed2005

Maize genetics: the treasure of the Sierra Madre.

Massive morphological changes occurred during the domestication of maize from wild teosinte. Some of the most important shifts are due to altered expression patterns of major regulatory genes.

Biological Evolution↗

PubMed2005

Camels and zebrafish, viruses and cancer: a microRNA update.

MicroRNAs (miRNAs) form an extensive class of RNA molecules that regulate gene expression at post-transcriptional level. In recent years, much progress has been made in dissection of biogenesis and functions of miRNAs. There are at least several hundred miRNA genes in the human genome, and the emerging evidence suggests that miRNAs are broadly implicated in gene regulation. Here, we review some recent advances, and particularly we discuss how comparative genomics helps to identify novel miRNA genes, how studies in zebrafish reveal roles of miRNAs in morphogenesis, how changes in miRNA expression patterns are connected with cancer and how host-virus coevolution exploits miRNA regulatory pathways.

Animals↗

PubMed2005

Circuit topology and the evolution of robustness in two-gene circadian oscillators.

Many parameters driving the behavior of biochemical circuits vary extensively and are thus not fine-tuned. Therefore, the topology of such circuits (the who-interacts-with-whom) is key to understanding their central properties. I here explore several hundred different topologies of a simple biochemical model of circadian oscillations to ask two questions: Do different circuits differ dramatically in their robustness to parameter change? If so, can a process of gradual molecular evolution find highly robust topologies when starting from less robust topologies? I find that the distribution of robustness among different circuit topologies is highly skewed: Most show low robustness, whereas very few topologies are highly robust. To address the second evolutionary question, I define a topology graph, each of whose nodes corresponds to one circuit topology that shows circadian oscillations. Two nodes in this graph are connected if they differ by only one regulatory interaction within the circuit. For the circadian oscillator I study, most topologies are connected in this graph, making evolutionary transitions from low to high robustness easy. A similar approach has been used to study the evolution of robustness in biological macromolecules, with similar results. This suggests that the same principles govern the evolution of robustness on different levels of biological organization. The regulatory interlocking of several oscillating gene products in biological circadian oscillators may exist because it provides robustness.

Biological Clocks↗

PubMed2004

Regulation of allergy and autoimmunity in helminth infection.

Parasitic infections are a major theme in the "hygiene hypothesis", as allergies and autoimmune diseases are less prevalent in countries with higher burdens of helminths and other parasitic organisms. Helminths"-the grouping of multicellular worm parasites including nematodes, cestodes and trematodes-tend to establish long-lived, chronic infections indicating successful down-modulation of the host immune system. In this review, we describe the intricate immunology of host-helminth interactions and how parasites manipulate immune responses to enhance their survival. In so doing, they often minimise immunopathology and, it is suggested, reduce host susceptibility to, and severity of allergic and autoimmune diseases. Studies on helminth-infected communities and individuals support the hypothesis that an immuno-regulatory network promoted by parasites extends its influence to limiting allergies. Experimental models are now probing more deeply into the area of immune modulation by helminths, and we discuss the likely mechanisms by which helminths could be establishing a strongly regulatory environment. Understanding and harnessing the modulatory capacity of helminths may uncover novel therapeutic interventions, mimicking and exploiting their evolution for our benefit. Parasitic infections are a major theme in the "hygiene hypothesis", as allergies and autoimmune diseases are less prevalent in countries with higher burdens of helminths and other parasitic organisms. Helminths"-the grouping of multicellular worm parasites including nematodes, cestodes and trematodes-tend to establish long-lived, chronic infections indicating successful down-modulation of the host immune system. In this review, we describe the intricate immunology of host-helminth interactions and how parasites manipulate immune responses to enhance their survival. In so doing, they often minimise immunopathology and, it is suggested, reduce host susceptibility to, and severity of allergic and autoimmune diseases. Studies on helminth-infected communities and individuals support the hypothesis that an immuno-regulatory network promoted by parasites extends its influence to limiting allergies. Experimental models are now probing more deeply into the area of immune modulation by helminths, and we discuss the likely mechanisms by which helminths could be establishing a strongly regulatory environment. Understanding and harnessing the modulatory capacity of helminths may uncover novel therapeutic interventions, mimicking and exploiting their evolution for our benefit.

Animals↗

PubMed1996

Polyclonal antisera elicited bý lysozymes: insights into antigenic structure and evolution.

Polyclonal antisera elicited by evolutionary variants of bird lysozymes c played a major role in the development of the multideterminant-regulatory model to describe the antigenic structure of globular proteins and in the demonstration that there is a strong correlation between immunological differences and amino acid sequence differences. This chapter reviews the evidence and calculations used to show, for lysozyme c and several other proteins, the essentially the entire surface of globular proteins is antigenic, that nearly all evolutionary substitutions affect immunological cross-reactivity, and that there is empirical and theoretical support for the use of immunological distances to infer genealogical relationships and establish approximate evolutionary time scales. In addition this chapter discusses several examples of the use of polyclonal antisera to lysozymes c and g to gain insights into molecular and organismal evolution and the regulation of gene expression.

Animals↗

PubMed1996

Gen(om)e duplications in the evolution of early vertebrates.

Phylogenetic analyses and sequence surveys of developmental regulator gene families indicate that two large-scale gene duplications, most likely genome duplications, occurred in ancestors of vertebrates. Relaxed constraints allowed duplicated and thus redundant genes to diverge in a two stage mechanism. Neutral changes dominated at first but then positively selected regulatory changes evolved the novel and increasingly complex vertebrate developmental program.

Animals↗

PubMed1980

Experiments in microbial evolution: new enzymes, new metabolic activities.

Biological evolution has resulted in a richness and diversity of species. Among microorganisms this is most evident in the wealth and diversity of biochemical transformations. Evidence for evolutionary relationships may be obtained from comparative studies, but with microorganisms it is also possible to follow evolution in action. Microbial populations adapt rapidly to changes in the environment and the evolution of new metabolic activities can be observed in laboratory experiments. The enzymes of many catabolic pathways are synthesized in response to the presence of inducing substrates. New catabolic activities may be acquired by mutations in regulatory genes resulting in alterations in the specificity of induction, or in enzyme synthesis in the absence of inducer. Mutations in structural genes may given rise to enzymes with altered substrate specificities. In bacteria, catabolic genes may be carried on plasmids and the exchange of plasmids among bacterial populations increases the evolutionary potential. Experiments in microbial evolution have produced strains with novel catabolic activities involving regulatory or structural gene mutations, gene duplications and plasmid exchange. Enzymes studied in this way include amidase, ribitol dehydrogenase, evolved beta-galactosidase, and enzymes of the catabolic pathways for pentoses and pentitols and haloaromatic compounds.

Amidohydrolases↗

PubMed1998

A vertebrate model of extreme physiological regulation.

Investigation of vertebrate regulatory biology is restricted by the modest response amplitudes in mammalian model species that derive from a lifestyle of frequent small meals. By contrast, ambush-hunting snakes eat huge meals after long intervals. In juvenile pythons during feeding, there are large and rapid increases in metabolism and secretion, in the activation of enzymes and transporter proteins, and in tissue growth. These responses enable an economic hypothesis concerning the evolution of regulation to be tested. Combined with other experimental advantages, these features recommend juvenile pythons as the equivalent of a squid axon in vertebrate regulatory biology.

Animals↗