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Results for “regulatory evolution”

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PubMed2005

Quail-duck chimeras reveal spatiotemporal plasticity in molecular and histogenic programs of cranial feather development.

The avian feather complex represents a vivid example of how a developmental module composed of highly integrated molecular and histogenic programs can become rapidly elaborated during the course of evolution. Mechanisms that facilitate this evolutionary diversification may involve the maintenance of plasticity in developmental processes that underlie feather morphogenesis. Feathers arise as discrete buds of mesenchyme and epithelium, which are two embryonic tissues that respectively form dermis and epidermis of the integument. Epithelial-mesenchymal signaling interactions generate feather buds that are neatly arrayed in space and time. The dermis provides spatiotemporal patterning information to the epidermis but precise cellular and molecular mechanisms for generating species-specific differences in feather pattern remain obscure. In the present study, we exploit the quail-duck chimeric system to test the extent to which the dermis regulates the expression of genes required for feather development. Quail and duck have distinct feather patterns and divergent growth rates, and we exchange pre-migratory neural crest cells destined to form the craniofacial dermis between them. We find that donor dermis induces host epidermis to form feather buds according to the spatial pattern and timetable of the donor species by altering the expression of members and targets of the Bone Morphogenetic Protein, Sonic Hedgehog and Delta/Notch pathways. Overall, we demonstrate that there is a great deal of spatiotemporal plasticity inherent in the molecular and histogenic programs of feather development, a property that may have played a generative and regulatory role throughout the evolution of birds.

Animals↗

PubMed1976

The myeloproliferative disorders. Correlation between clinical evolution and alterations of granulopoiesis.

Patients with myeloproliferative disorders were prospectively studied by in vitro agar-gel marrow culture technics to evaluate factors involved in the evolution of abnormal granulopoiesis. Marrow granulocytic colony-forming capacity was determined in 78 patients with chronic myeloid leukemia, subacute myeloid leukemia, preleukemia, Di Guglielmo's syndrome, polycythemia vera or essential thrombocythemia. A wide range of marrow colony-forming capacity values was noted early in disease courses; however, in 26 of 33 patients decreased colony-forming capacity was associated with disease transformation into acute myeloid leukemia or other clinically aggressive stages. An increased proportion of abnormally light buoyant density (less than 1.062 g/cm3) colony-forming cells was present in the marrow and peripheral blood of 15 of 16 patients with chronic myeloid leukemia, subacute myeloid leukemia, preleukemia or essential thrombocythemia; in seven of eight patients with greater than 35 per cent abnormally light colony-forming cells their disease subsequently underwent transformation. Elevated levels of urinary colony-stimulating factor output were noted in 17 of 31 patients, and in 10 of 12 patients whose disease subsequently underwent acute transformation within 10 months of study. In six of seven patients who simultaneously had an increased urinary output of colony-stimulating factor and low colony-forming capacity in marrow, transformation occurred within 10 months. These findings indicate that progressive abnormalities of both marrow clonal growth patterns and levels of possible humoral regulatory substances develop during evolution of these diseases. In contrast, patients with idiopathic sideroblastic ineffective erythropoiesis had normal values for marrow colony-forming capacity, proportion of light density colony-forming cells and urinary colony-stimulating factor output, and in none has their disease transformed into acute myeloid leukemia. These in vitro studies appear useful for clinical staging, evaluating prognosis and categorizing patients with myeloproliferative disorders.

Adolescent↗

PubMed2001

Solitary human endogenous retroviruses-K LTRs retain transcriptional activity in vivo, the mode of which is different in different cell types.

Solitary long terminal repeats (LTRs) of human endogenous retroviruses (HERVs), tens of thousands of which are spread all over the genome, contain a variety of potential transcription regulatory elements. Information on transcriptional behavior of individual solitary LTRs, however, is limited. We studied the transcriptional activity of several individual HERV-K LTRs in a variety of tissues and cell lines. The RT-PCR technique targeted at specific amplification of the U3 or U5 regions of individual LTRs together with their unique genomic flanks was used to estimate the content of each region in the transcripts. An unequal abundance of the U3 and U5 regions of the transcripts of the same LTR in different cells and tumors was observed. Each LTR is transcribed differently in different cells or tissues, and transcriptional behavior of different LTRs was different in the same cell line or tissue. The transcriptional status of LTRs varies in response to mitogenic and stress factors and in tumor tissues compared to normal counterparts. The LTRs thus seem to be the subjects of specific transcription regulation. The data obtained indicate that an appreciable fraction of the LTRs retained regulatory potential throughout millions of years of evolution and thus may contribute to the overall transcription regulatory network.

Endogenous Retroviruses↗

PubMed2002

Comparative endocrinology of the insulin-like growth factor-binding protein.

Emerging early in chordate evolution, the IGF-regulatory axis diverged from an insulin-like predecessor into a vertebrate regulatory system specializing in cell growth activation and allied anabolic functions. Essential to the divergence of the IGF and insulin systems was an early presence of soluble IGF-binding proteins (IGFBPs), which bind IGF peptides at much higher affinity than that of the insulin receptor but at comparable affinities to that of the IGF receptor. IGFBPs have no homology with IGF receptors. Instead, IGFBPs are a derived group of proteins within a superfamily of cysteine-rich growth factors, whose members are found throughout the animal taxa. While blocking IGF actions through the insulin receptor is a fundamental role, IGFBPs evolved within the vertebrate line into centralized, 'integrators' of the endocrine growth-regulatory apparatus. IGFBPs have substantial influences on the distribution and bioavailability of IGF peptides in the cellular and physiological environments, but they have a variety of other properties. The six principal mammalian IGFBPs exhibit an array of specialized properties that appear to be derived from a complex evolutionary history (including cell membrane association, interaction with proteins that post-translationally modify them, direct IGF-independent effects on cells, and others) and they are regulated by a diversity of 'outside' factors (e.g. other hormones, metabolic status, stress). Thus, IGFBPs are multifunctional integrators having diverse physiological 'agendas'. Much less is known about IGFBPs and their properties in the other vertebrate taxa. Increasingly, however, it is being recognized that they play equally important endocrine roles, in both conserved and non-conserved ways, when compared with those currently defined in mammals. This review highlights selected 'comparative aspects' in current IGFBP research, in an attempt to view this essential group of endocrine regulators from a wider, biological perspective.

Animals↗

PubMed1987

Towards a general theory of adaptive walks on rugged landscapes.

Adaptive evolution, to a large extent, is a complex combinatorial optimization process. In this article we take beginning steps towards developing a general theory of adaptive "walks" via fitter variants in such optimization processes. We introduce the basic idea of a space of entities, each a 1-mutant neighbor of many other entities in the space, and the idea of a fitness ascribed to each entity. Adaptive walks proceed from an initial entity, via fitter neighbors, to locally or globally optimal entities that are fitter than their neighbors. We develop a general theory for the number of local optima, lengths of adaptive walks, and the number of alternative local optima accessible from any given initial entity, for the baseline case of an uncorrelated fitness landscape. Most fitness landscapes are correlated, however. Therefore we develop parts of a universal theory of adaptation on correlated landscapes by adaptive processes that have sufficient numbers of mutations per individual to "jump beyond" the correlation lengths in the underlying landscape. In addition, we explore the statistical character of adaptive walks in two independent complex combinatorial optimization problems, that of evolving a specific cell type in model genetic networks, and that of finding good solutions to the traveling salesman problem. Surprisingly, both show similar statistical features, encouraging the hope that a general theory for adaptive walks on correlated and uncorrelated landscapes can be found. In the final section we explore two limits to the efficacy of selection. The first is new, and surprising: for a wide class of systems, as the complexity of the entities under selection increases, the local optima that are attainable fall progressively closer to the mean properties of the underlying space of entities. This may imply that complex biological systems, such as genetic regulatory systems, are "close" to the mean properties of the ensemble of genomic regulatory systems explored by evolution. The second limit shows that with increasing complexity and a fixed mutation rate, selection often becomes unable to pull an adapting population to those local optima to which connected adaptive walks via fitter variants exist. These beginning steps in theory development are applied to maturation of the immune response, and to the problem of radiation and stasis. Despite the limitations of the adaptive landscape metaphor, we believe that further development along the lines begun here will prove useful.

Adaptation, Biological↗

PubMed1990

Phosphorylation of rat liver inorganic pyrophosphatase by ATP in the absence and in the presence of protein kinase.

Cytoplasmic inorganic pyrophosphatase of rat liver can be phosphorylated by cAMP-dependent protein kinase on a serine residue with a concomitant increase in enzymic activity. Phosphorylation is also observed in the absence of protein kinase, but in this case much higher concentrations of ATP are required and the stability characteristics of the phosphoenzyme resemble those of an acyl phosphate. Kinase-free phosphorylation of the animal inorganic pyrophosphatase, unlike that of microbial pyrophosphatases, does not activate the enzyme. Pyrophosphatase may thus provide a new example of an enzyme whose evolution involves convergence of regulatory phosphorylation mechanisms.

Adenosine Triphosphate↗

PubMed1989

Expression of engrailed proteins in arthropods, annelids, and chordates.

engrailed is a homeobox gene that has an important role in Drosophila segmentation. Genes homologous to engrailed have been identified in several other organisms. Here we describe a monoclonal antibody that recognizes a conserved epitope in the homeodomain of engrailed proteins of a number of different arthropods, annelids, and chordates; we use this antibody to isolate the grasshopper engrailed gene. In Drosophila embryos, the antibody reveals engrailed protein in the posterior portion of each segment during segmentation, and in a segmentally reiterated subset of neuronal cells during neurogenesis. Other arthropods, including grasshopper and two crustaceans, have similar patterns of engrailed expression. However, these patterns of expression are not shared by the annelids or chordates we examined. Our results provide the most comprehensive view that has been obtained of how expression patterns of a regulatory gene vary during evolution. On the basis of these patterns, we suggest that engrailed is a gene whose ancestral function was in neurogenesis and whose function was co-opted during the evolution of segmentation in the arthropods, but not in the annelids and chordates.

Amino Acid Sequence↗

PubMed2005

Molecular characterization of new members of the Hevea brasiliensis hevein multigene family and analysis of their promoter region in rice.

The cloning of hevein genes from Hevea brasiliensis was undertaken with the objective to isolate useful promoters to drive transgene expression in genetically engineered rubber tree. Four different full length genes were cloned by library screening and a fifth, a partial gene, by adaptor-anchored PCR. Sequence alignment revealed that hevein genes, although highly conserved in their transcribed region, diverged in two groups, with major differences in their promoter region, suggesting a more rapid evolution of the upstream regulatory functions of the genes than the downstream functions of their protein products. The promoter regions from two hevein genes representative of each group were isolated and analyzed in rice. Although both were functional, only the longest promoter sequence (PHev2.1) conferred a high level of expression to the transgene in various tissues of this heterologous host. It was in addition up-regulated by mechanical wounding and fungal infection in leaves. A number of potential cis-regulatory elements were identified in silico and are discussed in view of the expression profiles observed in rice.

Base Sequence↗

PubMed2006

Cooperation of sonic hedgehog enhancers in midline expression.

In zebrafish, as in other vertebrates, the secreted signalling molecule Sonic hedgehog (Shh) is expressed in organiser regions such as the embryonic midline and the zona limitans intrathalamica (zli). To investigate the regulatory mechanisms underlying the pattern of shh expression, we carried out a systematic analysis of the intronic regulatory sequences of zebrafish shh using stable transgenesis. Deletion analysis identified the modules responsible for expression in the embryonic shield, the hypothalamus and the zli and confirmed the activities of previously identified notochord and floor plate enhancers. We detected a strong synergism between regulatory regions. The degree of synergy varied over time in the hypothalamus suggesting different mechanisms for initiation and maintenance of expression. Our data show that the pattern of shh expression in the embryonic central nervous system involves an intricate crosstalk of at least 4 different regulatory regions. When compared to the enhancer activities of the mouse Shh gene, we observed a remarkable divergence of function of structurally conserved enhancer sequences. The activating region ar-C (61% identical to SFPE2 in mouse Shh), for example, mediates floor plate expression in the mouse embryo while it directs expression in the forebrain and the notochord and only weakly in the floor plate in the zebrafish embryo. This raises doubts on the predictive power of phylogenetic footprinting and indicates a stunning divergence of function of structurally conserved regulatory modules during vertebrate evolution.

Animals↗

PubMed2000

Genomic exploration of the hemiascomycetous yeasts: 21. Comparative functional classification of genes.

We explored the biological diversity of hemiascomycetous yeasts using a set of 22000 newly identified genes in 13 species through BLASTX searches. Genes without clear homologue in Saccharomyces cerevisiae appeared to be conserved in several species, suggesting that they were recently lost by S. cerevisiae. They often identified well-known species-specific traits. Cases of gene acquisition through horizontal transfer appeared to occur very rarely if at all. All identified genes were ascribed to functional classes. Functional classes were differently represented among species. Species classification by functional clustering roughly paralleled rDNA phylogeny. Unequal distribution of rapidly evolving, ascomycete-specific, genes among species and functions was shown to contribute strongly to this clustering. A few cases of gene family amplification were documented, but no general correlation could be observed between functional differentiation of yeast species and variations of gene family sizes. Yeast biological diversity seems thus to result from limited species-specific gene losses or duplications, and for a large part from rapid evolution of genes and regulatory factors dedicated to specific functions.

Ascomycota↗

PubMed1998

Learning and homeostasis: drug addiction and the McCollough effect.

The contribution of conditioned responses (CRs) to homeostasis may be seen by examining seemingly disparate phenomena of color vision (aftereffects and chromatic adaptation) and drug addiction (withdrawal symptoms and tolerance). Color aftereffects may be elicited by nonchromatic stimuli previously paired with color (the McCollough effect, [ME]). Similarly, pharmacological aftereffects may be elicited by nonpharmacological stimuli previously paired with a drug (withdrawal symptoms). The authors summarize evidence indicating that both the ME and withdrawal symptoms are CRs. The chromatic CR is expressed as chromatic adaptation in the presence of color, and the ME in the absence of color. The pharmacological CR is expressed as pharmacological adaptation (tolerance) in the presence of the drug, and withdrawal symptoms in the absence of the drug. Both drug withdrawal symptoms and the ME are manifestations of the contribution of conditioning to normal homeostatic regulation. The authors discuss the implications of this conclusion for understanding regulatory processes and the evolution of behavioral mechanisms.

Color Perception↗

PubMed1981

Integration, transcription, and control of a Drosophila heat shock gene in mouse cells.

Mouse L cells were transformed with a cloned 3.6-kilobase (kb) segment of Drosophila melanogaster DNA carrying the 2.25-kb transcribed sequence for the Drosophila 70,000-dalton heat shock protein (hsp70) and 1.1 kb and 0.2 kb of 5' and 3' flanking DNA, respectively. Heat shock of one of three such transformed cell lines containing multiple copies of the intact Drosophila segment induced the abundant accumulation of transcripts of the Drosophila gene, with correct or nearly correct 5' and 3' termini. This provides evidence, in accord with earlier indications, that diverse eukaryotes, including vertebrates, have heat shock systems similar to that studied extensively in Drosophila. Our results suggest that the signals for heat shock transcription and the chromosomal sites with which they interact have been highly conserved in evolution and that the regulatory sequences controlling transcription of the gene for hsp70 lie within the 3.6-kb Drosophila segment.

Animals↗

PubMed2003

History of regulation of assisted reproductive technology (ART) in the USA: a work in progress.

The advent of human assisted reproductive technology (ART) has engendered much legal and ethical debate. This article examines the evolution of regulation in ART in the USA and discusses the impetus for, and repercussions of, the Human Fertilisation and Embryology Authority in the UK. Key differences in government legislation between the UK and USA have driven the evolution of a distinct regulatory body that oversees ART in the USA. The National Advisory Board on Ethics in Reproduction (NABER) serves as an unofficial advisory body that addresses ethical issues in reproduction. The Society for Assisted Reproductive Technology (SART) maintains a registry that collects, reports and verifies data for individual ART clinics. Clinic-specific success rates are readily available through annual reports published through a collaboration of SART, the American Society of Reproductive Medicine (ASRM), the Center for Disease Control (CDC), and the National Infertility Association (RESOLVE). The ASRM has assumed a strong advisory role in addressing ethical issues and practice guidelines in assisted reproduction. Thus, although there is no central body to regulate ART in the USA, basic legislation, standards and guidelines that drive the provision of these services do exist in the USA.

Female↗

PubMed2003

Breaking cellular symmetry along planar axes in Drosophila and vertebrates.

In many organs, epithelial cells are polarized not only along the apicobasal axis, but also along a second axis within a plane. Acquisition of the latter polarity, known as planar cell polarity (PCP) or tissue polarity, is crucial for specialized cellular functions. Genetic programming of PCP has been most thoroughly studied in Drosophila, which has allowed identification of a number of regulatory molecules that are evolutionally conserved. One group of the regulators is responsible for interpreting a hypothetical polarity cue and directing local cytoskeletal reorganization. This group includes a seven-pass transmembrane cadherin known as Flamingo (also known as Starry night), other receptors, and downstream components; and many of those molecules are redistributed to restricted subcellular compartments. Recent studies on a trio of cell-surface molecules challenge a previous hypothesis about the identity of the polarity cue and prompt a novel hypothesis about a global input. Studies on vertebrate systems support the notion that the molecular mechanisms demonstrated in Drosophila are applicable to at least two classes of polarized behaviors of vertebrate cells: sensory hair morphogenesis in the inner ear epithelium, and convergent extension movements during gastrulation.

Animals↗

PubMed2025

Redundant and Singular Regulatory Elements Underlie the Rapidly Evolving Pigmentation of Drosophila.

A major hurdle in understanding the molecular changes responsible for metazoan diversity is the characterization of cis-regulatory elements (CREs) for gene regulatory networks (GRNs). CRE changes are suspected to be commonplace in trait evolution, since such changes circumvent the deleterious effects of pleiotropy. A growing list of genes, though, is known to be regulated by redundant CREs. Such redundant CRE architectures complicate the characterization of GRN evolution, as they compound the effort to characterize each locus, and raise the questions of how and whether genes with redundant architectures evolve expression. Here, we used the evolution of sexually dimorphic abdomen pigmentation of Drosophila (D.) melanogaster as a model to study the function and evolution of CREs. Numerous sequences were evaluated that were previously predicted as potential abdomen CREs. Most of these predictions were validated, including two, four, and ten that, respectively, reside in the homothorax, grainy head, and Eip74EF transcription factor loci. The homothorax CREs were found to be partially redundant for this gene's pigmentation function, and pupal-stage Homothorax expression and the CRE activities were conserved among Drosophila species with the derived dimorphic and ancestral monomorphic phenotypes. Similarly, the Eip74EF CREs were conserved in the monomorphic D. willistoni. Thus, this gene's extensive CRE spatiotemporal redundancy has been conserved for over 30 million years, predating the dimorphic trait. Pigmentation evolution has been connected elsewhere to changes in nonredundant CREs. When these traits evolve, GRN changes may be biased towards the genes with singular nonredundant CREs, while the expression of redundantly regulated genes remains conserved.

Animals↗

PubMed2025

Genotype by Environment Interactions in Gene Regulation Underlie the Response to Soil Drying in the Model Grass Brachypodium distachyon.

Gene expression is a quantitative trait under the control of genetic and environmental factors and their interaction, so-called genotype and environment (G × E). Understanding the mechanisms driving G × E is fundamental for ensuring stable crop performance across environments and for predicting the response of natural populations to climate change. Gene expression is regulated through complex molecular networks, yet the interactions between genotype and environment in gene regulation are rarely considered, particularly at the genome scale. Current frameworks and experimental designs often lack power to explicitly test network rewiring or to systematically compare regulatory networks. Here, we leverage a highly replicated RNA-sequencing dataset to model genome-scale gene expression variation between two natural accessions of the model grass Brachypodium distachyon and their response to soil drying. We first identified genotypic, environmental, and G × E effects on physiological, metabolic, and gene expression traits. We identify patterns of conservation-or variation-in gene coexpression networks and link these coexpression features to physiological traits. We further develop predictions of gene-gene interactions using causal inference and screen for interactions specific to-or with higher affinity in-a single genotype, treatment, or their interaction, G × E. Our analyses identify variation in candidate gene regulatory networks that may shape the evolution of environmental response in B. distachyon. We highlight the environmentally dependent regulatory control of several metabolic traits shown previously to play a role in drought acclimation. The framework presented here provides a scalable approach for more complex comparisons, particularly with the growing availability of large datasets from technologies such as single-cell transcriptomics.

Brachypodium↗

PubMed2002

Protein kinases and protein phosphatases in prokaryotes: a genomic perspective.

For many years, the regulation of protein structure and function by phosphorylation and dephosphorylation was considered a relatively recent invention that arose independently in each phylogenetic domain. Over time, however, incidents of apparent domain trespass involving the presence of 'eukaryotic' protein kinases or protein phosphatases in prokaryotic organisms were reported with increasing frequency. Today, genomics has provided the means to examine the phylogenetic distribution of 'eukaryotic' protein kinases and protein phosphatases in a comprehensive and systematic manner. The results of these genome searches challenge previous conceptions concerning the origins and evolution of this versatile regulatory mechanism.

Phosphoprotein Phosphatases↗

PubMed2001

Birth of two chimeric genes in the Hominidae lineage.

How genes with newly characterized functions originate remains a fundamental question. PMCHL1 and PMCHL2, two chimeric genes derived from the melanin-concentrating hormone (MCH) gene, offer an opportunity to examine such an issue in the human lineage. Detailed structural, expression, and phylogenetic analysis showed that the PMCHL1 gene was created near 25 million years ago (Ma) by a complex mechanism of exon shuffling through retrotransposition of an antisense MCH messenger RNA coupled to de novo creation of splice sites. PMCHL2 arose 5 to 10 Ma by an event of duplication involving a large chromosomal region encompassing the PMCHL1 locus. The RNA expression patterns of those chimeric genes suggest that they have been submitted to strong regulatory constraints during primate evolution.

Animals↗