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At least 181 records · Page 10Linked to original sources

Functional mutants of the sequence-specific transcription factor p53 and implications for master genes of diversity.

There are many sources of genetic diversity, ranging from programmed mutagenesis in antibody genes to random mutagenesis during species evolution or development of cancer. We propose that mutations in DNA sequence-specific transcription factors that target response elements (REs) in many genes can also provide for rapid and broad phenotypic diversity, if the mutations lead to altered binding affinities at individual REs. To test this concept, we examined the in vivo transactivation capacity of wild-type human and murine p53 and 25 partial function mutants. The p53s were expressed in yeast from a rheostatable promoter, and the transactivation capacities toward >15 promoter REs upstream of a reporter gene were measured. Surprisingly, there was wide variation in transactivation by the mutant p53s toward the various REs. This is the first study to address directly the impact of mutations in a sequence-specific transcription factor on transactivation from a wide array of REs. We propose a master gene hypothesis for phenotypic diversity where the master gene is a single transcriptional activator (or repressor) that regulates many genes through different REs. Mutations of the master gene can lead to a variety of simultaneous changes in both the selection of targets and the extent of transcriptional modulation at the individual targets, resulting in a vast number of potential phenotypes that can be created with minimal mutational changes without altering existing protein-protein interactions.

Amino Acid Substitution↗

The increasing complexity of the Snail gene superfamily in metazoan evolution.

The Snail family of zinc-finger transcription factors is involved not only in the development of vertebrate and invertebrate embryos, but also in tumour progression. Following the identification of eight new members, we have analysed the evolutionary history of these genes and found that they constitute a superfamily that groups two independent families, Snail and Scratch. We propose that the duplication of an ancestral gene at the time of the metazoan radiation (1000-500 Myr ago) gave rise to Snail and Scratch, and that independent duplications in protostomes and deuterostomes led to the present situation. We discuss the implications of the distinct duplication events on the acquisition of new functions.

Animals↗

Genetics, development and plant evolution.

The recent mapping of quantitative trait loci in plants indicates that traits are often controlled by relatively few genes, some of which have large effects. Developmental genetics has shown that plant development is often regulated by transcription factors that activate developmental programs in response to internal or environmental signals. These transcription factors are good candidates for the major genes that govern morphological evolution in plants.

Anthocyanins↗

[FOXP2: from the specific disorder to the molecular biology of language. II. Implications for the ontogenesis and phylogenesis of language].

INTRODUCTION: Cloning FOXP2, the first gene linked to a hereditary variant of specific language impairment (SLI), has allowed researchers to conduct more precise studies into the nature and developmental path of the molecular bases governing the organisation and functioning of the neuron centres responsible for language processing. DEVELOPMENT: The FOXP2 gene codes for a transcriptional repressor that regulates the proliferation and/or migration of certain neuronal populations in the basal ganglia, cortex, cerebellum and thalamus, and presumably plays a part in the organisation and/or functioning of the fronto-thalamic-striatal system. Moreover, the analysis of the developmental history of the gene suggests that the transcriptional factor FOXP2, although it is quite old, has undergone certain modifications in its secondary structure and has acquired a potential site for phosphorylation for protein kinase C during the recent developmental history of the human species. CONCLUSIONS: The evidence discussed in this article allows us to suggest FOXP2 plays a significant role in the ontogenetic and phylogenetic development of language. On the one hand, it seems to validate certain general models of linguistic processing that call for a more important role of the subcortical structures (above all for the basal ganglia) in that processing. On the other hand, it seems to suggest that the modifications undergone by FOXP2 would have also allowed certain regions (such as Broca's area) to be recruited for language, either by facilitating the appearance of syntax and/or verbal working memory or by transferring control of articulation to those regions, thereby laying down the foundations for the appearance of spoken language.

Brain↗

The ancestral role of COE genes may have been in chemoreception: evidence from the development of the sea anemone, Nematostella vectensis (Phylum Cnidaria; Class Anthozoa).

An orthologue of the COE family of helix-loop-helix transcription factors was recovered from the anthozoan Nematostella vectensis (Cnidaria). NvCOE has high sequence similarity to vertebrate and invertebrate orthologues in all three major functional domains of the protein. In situ hybridization studies show early expression through the cleavage period but transcripts are down regulated at gastrulation while remaining expressed at high levels only in the apical tuft of cilia at the aboral end of the planula larva. It is likely that one of the ancestral roles of the COE family of genes may have been in the development of chemosensory neurons.

Animals↗

Myc/Max/Mad in invertebrates: the evolution of the Max network.

The Myc proto-oncogenes, their binding partner Max and their antagonists from the Mad family of transcriptional repressors have been extensively analysed in vertebrates. However, members of this network are found in all animals examined so far. Several recent studies have addressed the physiological function of these proteins in invertebrate model organisms, in particular Drosophila melanogaster. This review describes the structure of invertebrate Myc/Max/Mad genes and it discusses their regulation and physiological functions, with special emphasis on their essential role in the control of cellular growth and proliferation.

Amino Acid Sequence↗

AmphiFoxE4, an amphioxus winged helix/forkhead gene encoding a protein closely related to vertebrate thyroid transcription factor-2: expression during pharyngeal development.

The full-length sequence and developmental expression of amphioxus AmphiFoxE4 are described. Transcripts of the gene are first detected in the pharyngeal endoderm, where the club-shaped gland is forming and subsequently in the definitive gland itself. AmphiFoxE4 is closely related to vertebrate genes encoding the thyroid-specific transcription factor-2 (TTF2), which plays an early developmental role in the morphogenesis of the thyroid gland and a later role in hormone-mediated control of thyroid function. In amphioxus, AmphiFoxE4 expression is not thyroid specific because the club-shaped gland, the only structure expressing the gene, is not homologous to the vertebrate thyroid; instead, the thyroid homologue of amphioxus is a specialized region of the pharyngeal endoderm called the endostyle. We propose that (a) the pharynx of an amphioxus-like ancestor of the vertebrates included a club-shaped gland that expressed FoxE4 as well as an endostyle that did not, and (b) the club-shaped gland soon disappeared in the vertebrate line of descent but (c) not before there was a homeogenetic transfer of FoxE4 expression from the club-shaped gland to the nearby endostyle. Such a transfer could have provided part of the genetic program enabling the endostyle to separate from the pharyngeal endoderm and migrate away as the rudiment of the thyroid gland.

Amino Acid Sequence↗

Hox genes and the evolution of diverse body plans.

Homeobox genes encode transcription factors that carry out diverse roles during development. They are widely distributed among eukaryotes, but appear to have undergone an extensive radiation in the earliest metazoa, to generate a range of homeobox subclasses now shared between diverse metazoan phyla. The Hox genes comprise one of these subfamilies, defined as much by conserved chromosomal organization and expression as by sequence characteristics. These Hox genes act as markers of position along the antero-posterior axis of the body in nematodes, arthropods, chordates, and by implication, most other triploblastic phyla. In the arthropods this role is visualized most clearly in the control of segment identity. Exactly how Hox genes control the structure of segments is not yet understood, but their differential deployment between segments provides a model for the basis of segment diversity. Within the arthropods, distantly related taxonomic groups with very different body plans (insects, crustaceans) may share the same set of Hox genes. The expression of these Hox genes provides a new character to define the homology of different body regions. Comparisons of Hox gene deployment between insects and a branchiopod crustacean suggest a novel model for the derivation of the insect body plan.

Animals↗

Evolutionary conservation of redundancy between a diverged pair of forkhead transcription factor homologues.

The Caenorhabditis elegans gene pes-1 encodes a transcription factor of the forkhead family and is expressed in specific cells of the early embryo. Despite these observations suggesting pes-1 to have an important regulatory role in embryogenesis, inactivation of pes-1 caused no apparent phenotype. This lack of phenotype is a consequence of genetic redundancy. Whereas a weak, transitory effect was observed upon disruption of just T14G12.4 (renamed fkh-2) gene function, simultaneous disruption of the activity of both fkh-2 and pes-1 resulted in a penetrant lethal phenotype. Sequence comparison suggests these two forkhead genes are not closely related and the functional association of fkh-2 and pes-1 was only explored because of the similarity of their expression patterns. Conservation of the fkh-2/pes-1 genetic redundancy between C. elegans and the related species C. briggsae was demonstrated. Interestingly the redundancy in C. briggsae is not as complete as in C. elegans and this could be explained by alterations of pes-1 specific to the C. briggsae ancestry. With overlapping function retained on an evolutionary time-scale, genetic redundancy may be extensive and expression pattern data could, as here, have a crucial role in characterization of developmental processes.

Amino Acid Sequence↗

Genetic redundancy in endoderm specification within the genus Caenorhabditis.

Specification of the endoderm precursor, the E cell, in Caenorhabditis elegans requires a genomic region called the Endoderm Determining Region (EDR). We showed previously that end-1, a gene within the EDR encoding a GATA-type transcription factor, restores endoderm specification to embryos deleted for the EDR and obtained evidence for genetic redundancy in this process. Here, we report molecular identification of end-3, a nearby paralog of end-1 in the EDR, and show that end-1 and end-3 together define the endoderm-specifying properties of the EDR. Both genes are expressed in the early E lineage and each is individually sufficient to specify endodermal fate in the E cell and in non-endodermal precursors when ectopically expressed. The loss of function of both end genes, but not either one alone, eliminates endoderm in nearly all embryos and results in conversion of E into a C-like mesectodermal precursor, similar to deletions of the EDR. While two putative end-1 null mutants display no overt phenotype, a missense mutation that alters a residue in the zinc finger domain of END-3 results in misspecification of E in approximately 9% of mutant embryos. We report that the EDR in C. briggsae, which is estimated to have diverged from C. elegans approximately 50--120 myr ago, contains three end-like genes, resulting from both the ancient duplication that produced end-1 and end-3 in C. elegans, and a more recent duplication of end-3 in the lineage specific to C. briggsae. Transgenes containing the C. briggsae end homologs show E lineage-specific expression and function in C. elegans, demonstrating their functional conservation. Moreover, RNAi experiments indicate that the C. briggsae end genes also function redundantly to specify endoderm. We propose that duplicated end genes have been maintained over long periods of evolution, owing in part to their synergistic function.

Alleles↗

Phylogenetic profiling of protein interaction networks in eukaryotic transcription factors reveals focal proteins being ancestral to hubs.

The combination of genomic, proteomic and other data, enables to reconstruct the evolution of complex cellular units thus transcending the more reductionistic view of traditional molecular phylogeny. However, most models which try to investigate the evolution of protein interaction networks so far are based on the analysis of their global statistical properties, such as their scale-free behaviour. We have investigated phylogenies of three families of ancient eukaryotic transcription factors for which fairly reliable interaction data are available. For all three families, bZIP, bHLH and NR (nuclear receptors), we find that homo-dimerising proteins were probably the ancestors and that series of single gene duplications, in combination with domain-rearrangements, were the main driving force in establishing the basic network architecture. However, the overall scaling behaviour does not always precisely confer to some theoretical models on network evolution. In conclusion, new models which reflect the biological details of molecular evolution, need to be developed.

Basic-Leucine Zipper Transcription Factors↗

Isolation of the mouse (MFH-1) and human (FKHL 14) mesenchyme fork head-1 genes reveals conservation of their gene and protein structures.

The very recently found evolutionarily conserved DNA-binding domain of 100 amino acids, termed the fork head domain, emerged from a sequence comparison of the rat hepatocyte transcription factor HNF-3 alpha and the homeotic gene fork head of Drosophila. We previously isolated a new member of this family, the mesenchyme fork head-1 (MFH-1) gene, which is expressed in developing mesenchyme. Here we describe the isolation of the mouse (MFH-1) and human (FKHL14) chromosomal MFH-1 genes and the determination of the gene and protein structures of MFH-1. We found that the MFH-1 gene has no introns and that the identity of the amino acid sequences of mouse and human MFH-1 proteins is 94%. We also investigated the transcriptional activity of the mouse and human MFH-1 proteins and found that both proteins act as positive transactivators.

Amino Acid Sequence↗

Genomic inventory and expression of Sox and Fox genes in the cnidarian Nematostella vectensis.

The Sox and Forkhead (Fox) gene families are comprised of transcription factors that play important roles in a variety of developmental processes, including germ layer specification, gastrulation, cell fate determination, and morphogenesis. Both the Sox and Fox gene families are divided into subgroups based on the amino acid sequence of their respective DNA-binding domains, the high-mobility group (HMG) box (Sox genes) or Forkhead domain (Fox genes). Utilizing the draft genome sequence of the cnidarian Nematostella vectensis, we examined the genomic complement of Sox and Fox genes in this organism to gain insight into the nature of these gene families in a basal metazoan. We identified 14 Sox genes and 15 Fox genes in Nematostella and conducted a Bayesian phylogenetic analysis comparing HMG box and Forkhead domain sequences from Nematostella with diverse taxa. We found that the majority of bilaterian Sox groups have clear Nematostella orthologs, while only a minority of Fox groups are represented, suggesting that the evolutionary pressures driving the diversification of these gene families may be distinct from one another. In addition, we examined the expression of a subset of these genes during development in Nematostella and found that some of these genes are expressed in patterns consistent with roles in germ layer specification and the regulation of cellular behaviors important for gastrulation. The diversity of expression patterns among members of these gene families in Nematostella reinforces the notion that despite their relatively simple morphology, cnidarians possess much of the molecular complexity observed in bilaterian taxa.

Amino Acid Sequence↗

Transient expression of a winged-helix protein, MNF-beta, during myogenesis.

A novel winged-helix transcription factor, MNF-beta, is expressed coincidentally with cell cycle withdrawal and differentiation of skeletal myogenic cells. MNF-beta is closely related to the myocyte nuclear factor (MNF) protein previously described (now termed MNF-alpha), but expression of the two isoforms is differentially regulated, and they exhibit distinctive functional properties with respect to DNA binding in vitro and transcriptional regulatory activity in transient-transfection assays. A DNA sequence motif binding MNF-beta with high affinity was selected from a library of random oligonucleotides and was found to be similar to but distinct from the cognate binding site for HNF-3beta, a more distantly related winged-helix protein. The temporal pattern of MNF-beta expression and the presence of MNF binding motifs within conserved promoter elements of several genes that modulate cell cycle progression support a working hypothesis that MNF proteins may modulate proliferation of myogenic precursor cells during development and muscle regeneration.

Amino Acid Sequence↗

Regulation of the chicken lysozyme locus in transgenic mice.

The chicken lysozyme locus is transcriptionally activated during macrophage differentiation. Each cis-regulatory element has its unique activation stage during cell differentiation, whereby maximal transcriptional activity of the gene is only observed when all cis-elements are active. The complete chicken lysozyme locus is expressed position independently and at a high level in macrophages of transgenic mice. For correct transgene regulation, the cooperation of all cis-regulatory elements is required. These cis-regulatory elements specify the mode of regulation and we observe the same expression pattern of the transgene in the mouse and the endogenous gene in chicken macrophages. This indicates that the transcription factors responsible for chicken lysozyme regulation are highly conserved in evolution. The endogenous mouse lysozyme gene is regulated differently. The chromatin of the lysozyme locus is highly structured in the transcriptionally active, as well as in the inactive state. The transcriptional activation of the lysozyme locus is accompanied by extensive chromatin rearrangements, which are disturbed when one essential cis-regulatory element is deleted and the transgenes are subjects to genomic position effects. Based on these results, we propose that a distinct chromatin architecture of a gene locus is required for its correct activation.

Animals↗

Regulation of the Lim-1 gene is mediated through conserved FAST-1/FoxH1 sites in the first intron.

The Lim-1 gene encodes a LIM-homeodomain transcription factor that is highly conserved among vertebrates and is required for successful gastrulation and head formation. The expression of this gene in the mesoderm of the gastrula is known to require an activin/nodal signal. Earlier studies have shown that the Xenopus Lim-1 (Xlim-1) gene contains an activin response element (ARE) in its first intron, which cooperates with an activin-unresponsive upstream promoter in the regulation of the gene. Here, we show that the Xlim-1 ARE contains a cluster of FAST-1/FoxH1 and Smad4 recognition sites; such sites have been shown to mediate activin/nodal responses in other genes. By using reporter constructs with mutated FAST-1/FoxH1 sites and FAST-1/FoxH1 protein chimeras, we show that the regulation of Xlim-1 by activin depends on FAST-1/FoxH1 function. Comparative studies on the zebrafish lim1 gene indicate the presence of FoxH1 sites in the first intron of this gene and provide evidence for the requirement for FoxH1 function in its regulation. These results illuminate the conserved nature of the transcriptional regulation of the Lim-1 gene in different vertebrate animals.

Activins↗

Novel PAX6 binding sites in the human genome and the role of repetitive elements in the evolution of gene regulation.

Pax6 is a critical transcription factor in the development of the eye, pancreas, and central nervous system. It is composed of two DNA-binding domains, the paired domain (PD), which has two helix-turn-helix (HTH) motifs, and the homeodomain (HD), made up from another HTH motif. Each HTH motif can bind to DNA separately or in combination with the others. We identified three novel binding sites that are specific for the PD and HD domains of human PAX6 from single-copy human genomic DNA libraries using cyclic amplification of protein binding sequences (CAPBS) and electrophoretic mobility shift assays (EMSAs). One of the binding sites was found within sequences of repetitive Alu elements. However, most of the Alu sequences were unable to bind to PAX6 because of a small number of mismatches (mostly in CpG dinucleotide hot spots) in the consensus Alu sequences. PAX6 binding Alu elements are found primarily in old and intermediate-aged Alu subfamilies. These data along with our previously identified B1-type Pax6 binding site showed that evolutionarily conserved Pax6 has target sites that are disparate in primates and rodents. This difference indicates that human and mouse Pax6-regulated gene networks may have evolved through these lineage-specific repeat elements.

Alu Elements↗

Functional characterization of evolutionarily conserved DNA regions in forkhead box f1 gene locus.

The Forkhead Box f1 (Foxf1) transcription factor (previously known as HFH-8 or Freac-1) is expressed in the septum transversum and splanchnic (visceral) mesoderm and is required for proper development of gut-derived organs. Sequence comparisons of mouse and human Foxf1 genes have revealed highly conserved DNA sequences located within the -5.3-kb Foxf1 promoter region and the 400-nucleotide regulatory element located 1 kb 3' to the Foxf1 gene (3'RE). To examine their transcriptional activity during mouse embryonic development, we generated transgenic mice in which the expression of the beta-galactosidase transgene was controlled by the -2.7-kb Foxf1 promoter region, the -5.3-kb Foxf1 promoter region, or the -5.3-kb Foxf1 promoter region fused to the 3'RE. The -5.3-kb Foxf1 promoter sequences induced appropriate transgene expression in the midgut and developing intestine, whereas the -2.7-kb Foxf1 promoter region was transcriptionally inactive. Addition of 3'RE to the -5.3-kb Foxf1 promoter restored proper transgene expression in the foregut, liver, and lung mesenchyme and prevented ectopic transgene expression in the developing nervous system. Cotransfection studies demonstrated that FoxA2 protein bound to the 3'RE region (+4506/+4529 bp) and was sufficient to inhibit expression of the -5.3-kb Foxf1 promoter. Furthermore, C/EBPbeta and HNF-6 proteins bound to the 3'RE region (+4647/+4694 bp) and provided synergistic transcriptional activation of the -5.3-kb Foxf1 promoter in cotransfection assays. These studies demonstrated that the conserved Foxf1 3'RE region is essential for proper tissue-specific regulation of the Foxf1 promoter region during mouse embryogenesis.

Animals↗