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PubMed1993

Evolution of a regulatory gene family: HOM/HOX genes.

With the increasing accumulation of data on the presence of the HOM/HOX class of homeobox genes in the animal kingdom, and with new comparative analyses of these data, strong evolutionary conservation is apparent. It is clear that HOM/HOX genes and their roles in pattern formation were established early during the evolution of major phyla. The functional indications that this system is utilized in quite diverged organisms attest to the fundamental roles of homeobox genes in organismal development.

Animals↗
PubMed2005

Evolution of transcription regulatory genes is linked to niche specialization in the bacterial pathogen Streptococcus pyogenes.

Streptococcus pyogenes is a highly prevalent bacterial pathogen, most often giving rise to superficial infections at the throat or skin of its human host. Three genotype-defined subpopulations of strains exhibiting strong tropisms for either the throat or skin (specialists) or having no obvious tissue site preference (generalists) are recognized. Since the microenvironments at the throat and skin are distinct, the signal transduction pathways leading to the control of gene expression may also differ for throat versus skin strains of S. pyogenes. Two loci (mga and rofA/nra) encoding global regulators of virulence gene expression are positioned 300 kb apart on the genome; each contains alleles forming two major sequence clusters of approximately 25 to 30% divergence that are under balancing selection. Strong linkage disequilibrium is observed between sequence clusters of the transcription regulatory loci and the subpopulations of throat and skin specialists, against a background of high recombination rates among housekeeping genes. A taxonomically distinct commensal species (Streptococcus dysgalactiae subspecies equisimilus) shares highly homologous rof alleles. The findings provide strong support for a mechanism underlying niche specialization that involves orthologous replacement of regulatory genes following interspecies horizontal transfer, although the directionality of gene exchange remains unknown.

Bacterial Proteins↗
PubMed2006

Independent evolution of competence regulatory cascades in streptococci?

Natural genetic transformation is a mechanism of horizontal gene transfer that is widely distributed in bacteria and requires assembly of a DNA uptake machinery. Transformable bacteria use fundamentally the same machine, which in most species is assembled only in cells that are developing competence. Competence regulation usually differs between unrelated species. Here, we examine whether related streptococci use the same competence regulatory cascade. Phylogenetic analyses of streptococcal genome sequences reveal the existence of two paralogous two-component regulatory systems, either of which might control competence. This suggests the distribution of streptococci into two groups that use competence regulatory cascades that have at least partly evolved independently. Comparison of data obtained with two transformable streptococci, Streptococcus pneumoniae and Streptococcus mutans, provides support to this suggestion.

DNA, Bacterial↗
PubMed1992

Transgenic animal studies on the evolution of genetic regulatory circuitries.

The ability to transfer genes from one species to another provides a powerful method to study genetic regulatory differences between species in a homogeneous genetic background. A survey of several transgenic animal experiments indicates that the vast majority of regulatory differences observed between species are due to differences in the cis-acting elements associated with the genes under study. A corollary is that in almost all cases the host species provides the necessary regulatory proteins for expression of the transgenes in specific tissues in which the endogenous homolog is not expressed. Although the details of the cis-acting differences are unknown for most cases, it appears that these differences may consist of the acquisition or loss of unique elements or subtle variation of conserved elements. It is unknown whether much of this variation is directly related to adaptive evolution. The identification of the promoter/enhancer elements responsible for these differences is an important first step in examining the functional significance of this variation.

Animals↗
PubMed2004

Interspecies comparison of neuroglobin, cytoglobin and myoglobin: sequence evolution and candidate regulatory elements.

Neuroglobin and cytoglobin are two novel members of the vertebrate globin family. Their physiological role is poorly understood, although both proteins bind oxygen reversibly and may be involved in cellular oxygen homeostasis. Here we investigate the selective constraints on coding and non-coding sequences of the neuroglobin and cytoglobin genes in human, mouse, rat and fish. Neuroglobin and cytoglobin are highly conserved, displaying very low levels of non-synonymous nucleotide substitutions. An oxygen supply function predicts distinct modes of gene regulation, involving hypoxia-responsive transcription factors. To detect conserved candidate regulatory elements, we compared the neuroglobin and cytoglobin genes in mammals and fish. The myoglobin gene was included to test if it also contains hypoxia-responsive regulatory elements. Long conserved non-coding sequences, indicative of gene-regulatory elements, were found in the cytoglobin and myoglobin, but not in the neuroglobin gene. Sequence comparison and experimental data allowed us to delimit upstream regions of the neuroglobin and cytoglobin genes that contain the putative promoters, defining candidate regulatory regions for functional tests. The neuroglobin and the myoglobin genes both lack conserved hypoxia-responsive elements (HREs) for transcriptional activation, but contain conserved hypoxia-inducible mRNA stabilization signals in their 3' untranslated regions. The cytoglobin gene, in contrast, harbors both conserved HREs and mRNA stabilization sites, strongly suggestive of an oxygen-dependent regulation.

Animals↗
PubMed2005

Direct regulation of knot gene expression by Ultrabithorax and the evolution of cis-regulatory elements in Drosophila.

The regulation of development by Hox proteins is important in the evolution of animal morphology, but how the regulatory sequences of Hox-regulated target genes function and evolve is unclear. To understand the regulatory organization and evolution of a Hox target gene, we have identified a wing-specific cis-regulatory element controlling the knot gene, which is expressed in the developing Drosophila wing but not the haltere. This regulatory element contains a single binding site that is crucial for activation by the transcription factor Cubitus interruptus (Ci), and a cluster of binding sites for repression by the Hox protein Ultrabithorax (UBX). The negative and positive control regions are physically separable, demonstrating that UBX does not repress by competing for occupancy of Ci-binding sites. Although knot expression is conserved among Drosophila species, this cluster of UBX binding sites is not. We isolated the knot wing cis-regulatory element from D. pseudoobscura, which contains a cluster of UBX-binding sites that is not homologous to the functionally defined D. melanogaster cluster. It is, however, homologous to a second D. melanogaster region containing a cluster of UBX sites that can also function as a repressor element. Thus, the knot regulatory region in D. melanogaster has two apparently functionally redundant blocks of sequences for repression by UBX, both of which are widely separated from activator sequences. This redundancy suggests that the complete evolutionary unit of regulatory control is larger than the minimal experimentally defined control element. The span of regulatory sequences upon which selection acts may, in general, be more expansive and less modular than functional studies of these elements have previously indicated.

Animals↗
PubMed1995

Origin of bilaterian body plans: evolution of developmental regulatory mechanisms.

An argument is proposed to explain the origin of large metazoans, based on the regulatory processes that underlie the morphogenetic organization of pattern in modern animals. Genetic regulatory systems similar to those used in modern, indirectly developing marine invertebrates are considered to indicate the Precambrian regulatory platform on which were erected innovations that underlie the development of macroscopic body plans. Those systems are genetic regulatory programs that produce groups of unspecified "set-aside cells" and hierarchical regulatory programs that initially define regions of morphogenetic space in terms of domains of transcription factor expression. These ideas affect interpretation of the development of arthropods and chordates as well as interpretation of the role of the genes of the homeotic complex in embryogenesis.

Animals↗
PubMed1997

Forced evolution of a regulatory RNA helix in the HIV-1 genome.

The 5'and 3'end of the HIV-1 RNA genome forms a repeat (R) element that encodes a double stem-loop structure (the TAR and polyA hairpins). Phylogenetic analysis of the polyA hairpin in different human and simian immunodeficiency viruses suggests that the thermodynamic stability of the helix is fine-tuned. We demonstrated previously that mutant HIV-1 genomes with a stabilized or destabilized hairpin are severely replication-impaired. In this study, we found that the mutant with a destabilized polyA hairpin structure is conditionally defective. Whereas reduced replication is measured in infections at the regular temperature (37 degrees C), this mutant is more fit than the wild-type virus at reduced temperature (33 degrees C). This observation of a temperature-dependent replication defect underscores that the stability of this RNA structure is critical for function. An extensive analysis of revertant viruses was performed to further improve the understanding of the critical sequence and structural features of the element under scrutiny. The virus mutants with a stabilized or destabilized hairpin were used as a starting point in multiple, independent selections for revertant viruses with compensatory mutations. Both mutants reverted to hairpins with wild-type stability along various pathways by acquisition of compensatory mutations. We identified 19 different revertant HIV-1 forms with improved replication characteristics, providing a first look at some of the peaks in the total sequence landscape that are compatible with virus replication. These experiments also highlight some general principles of RNA structure building.

Base Sequence↗
PubMed2026

Diversity and evolution of chromatin regulatory states across eukaryotes.

Histone post-translational modifications (hPTMs) are key regulators of chromatin states, influencing gene expression, epigenetic memory and transposable element repression across eukaryotic genomes. While many hPTMs are evolutionarily conserved, the extent to which the chromatin states they define are similarly preserved remains unclear. Here we developed a combinatorial indexing chromatin immunoprecipitation followed by sequencing method to simultaneously profile specific hPTMs across diverse eukaryotic lineages, including amoebozoans, rhizarians, discobans and cryptomonads. Our analyses revealed highly conserved euchromatin states at active gene promoters and gene bodies. In contrast, we observed diverse configurations of repressive heterochromatin states associated with silenced genes and transposable elements, characterized by various combinations of hPTMs such as H3K9me3, H3K27me3 and/or different H3K79 methylations. These findings suggest that, while core hPTMs are ancient and broadly conserved, their functional readout has diversified throughout eukaryotic evolution, shaping lineage-specific chromatin landscapes.

Histones↗
PubMed1994

Leeway and constraints in the forced evolution of a regulatory RNA helix.

The start of the coat protein gene of RNA phage MS2 adopts a well-defined hairpin structure of 12 bp (including one mismatch) in which the start codon occupies the loop position. An earlier expression study using partial MS2 cDNA clones had indicated that the stability of this hairpin is important for gene expression. For every -1.4 kcal/mol increase in stability a 10-fold reduction in coat protein was obtained. Destabilizations beyond the wild-type value did not affect expression. These results suggested that the hairpin was tuned in the sense that it has the highest stability still compatible with maximal ribosome loading. Employing an infectious MS2 cDNA clone, we have now tested the prediction that the delta G 0 of the coat protein initiator helix is set at a precise value. We have introduced stabilizing and destabilizing mutations into this hairpin in the intact phage and monitored their evolution to viable species. By compensatory mutations, both types of mutants quickly revert along various pathways to wild-type stability, but not to wild-type sequence. As a rule the second-site mutations do not change the encoded amino acids or the Shine-Dalgarno sequence. The return of too strong hairpins to wild-type stability can be understood from the need to produce adequate supplies of coat protein. The return of unstable hairpins to wild-type stability is not self-evident and is presently not understood. The revertants provide an evolutionary landscape of slightly suboptimal phages, that were stable at least for the duration of the experiment (approximately 20 infection cycles).(ABSTRACT TRUNCATED AT 250 WORDS)

Base Composition↗
PubMed2001

Rapid evolution of cis-regulatory sequences via local point mutations.

Although the evolution of protein-coding sequences within genomes is well understood, the same cannot be said of the cis-regulatory regions that control transcription. Yet, changes in gene expression are likely to constitute an important component of phenotypic evolution. We simulated the evolution of new transcription factor binding sites via local point mutations. The results indicate that new binding sites appear and become fixed within populations on microevolutionary timescales under an assumption of neutral evolution. Even combinations of two new binding sites evolve very quickly. We predict that local point mutations continually generate considerable genetic variation that is capable of altering gene expression.

Animals↗
PubMed2002

Evolution of a polymorphic regulatory element in interferon-gamma through transposition and mutation.

Mammalian transposable elements have intrinsic regulatory elements that can activate neighboring genes, and it is speculated that they can also carry extrinsic transactivating DNA sequences to new genomic locations. We have identified a polymorphic segment of the human interferon-gamma promoter region where two adjacent binding sites for NF-kappaB and NFAT originated from the insertion of an Alu element approximately 22-34 MYA. Both binding sites lie outside the Alu consensus sequence but within the boundaries of the insertion, suggesting that this segment of DNA was comobilized when the Alu element moved from another part of the genome. Sequence comparisons and examination of DNA-protein interactions across nine different primate species indicate that the inserted sequence contained the intact NFAT binding site, whereas the ability to bind NF-kappaB evolved through a series of mutations after the insertion. These observations are consistent with the notion that retropseudogenes can comobilize intact regulatory sequences to new locations and thereby influence the evolution of gene regulatory networks; however, the extent to which such events have shaped the evolution of gene regulation remains unknown.

Alu Elements↗
PubMed2005

Modelling the evolution of genetic regulatory networks.

An evolutionary model of genetic regulatory networks is developed, based on a model of network encoding and dynamics called the Artificial Genome (AG). This model derives a number of specific genes and their interactions from a string of (initially random) bases in an idealized manner analogous to that employed by natural DNA. The gene expression dynamics are determined by updating the gene network as if it were a simple Boolean network. The generic behaviour of the AG model is investigated in detail. In particular, we explore the characteristic network topologies generated by the model, their dynamical behaviours, and the typical variance of network connectivities and network structures. These properties are demonstrated to agree with a probabilistic analysis of the model, and the typical network structures generated by the model are shown to lie between those of random networks and scale-free networks in terms of their degree distribution. Evolutionary processes are simulated using a genetic algorithm, with selection acting on a range of properties from gene number and degree of connectivity through periodic behaviour to specific patterns of gene expression. The evolvability of increasingly complex patterns of gene expression is examined in detail. When a degree of redundancy is introduced, the average number of generations required to evolve given targets is reduced, but limits on evolution of complex gene expression patterns remain. In addition, cyclic gene expression patterns with periods that are multiples of shorter expression patterns are shown to be inherently easier to evolve than others. Constraints imposed by the template-matching nature of the AG model generate similar biases towards such expression patterns in networks in initial populations, in addition to the somewhat scale-free nature of these networks. The significance of these results on current understanding of biological evolution is discussed.

Algorithms↗
PubMed2000

Origin and evolution of the regulatory gene male-specific lethal-3.

Dosage compensation in Drosophila is mediated by genes known as "male-specific lethals" (msls). Several msls, including male-specific lethal-3 (msl-3), encode proteins of unknown function. We cloned the Drosophila virilis msl-3 gene. Using the information provided by the sequences of the Drosophila melanogaster and D. virilis genes, we found that sequences of other species can be aligned along their entire lengths with msl-3. Among them, there are genes in yeasts (the Schizosaccharomyces pombe Alp13 gene, as well as a putative Alp13 homolog, found in Saccharomyces cerevisae) and in mammals (MRG15 and MSL3L1 and their relatives) plus uncharacterized sequences of the nematode Caenorhabditis elegans and the plants Arabidopsis thaliana, Lycopersicon esculentum, and Zea mays. A second Drosophila gene of this family has also been found. It is thus likely that msl-3-like genes are present in all eukaryotes. Phylogenetic analyses suggest that msl-3 is orthologous to the mammalian MSL3L1 genes, while the second Drosophila melanogaster gene (which we have called Dm MRG15) is orthologous to mammalian MRG15. These analyses also suggest that the msl-3/MRG15 duplication occurred after the fungus/animal split, while an independent duplication occurred in plants. The proteins encoded by these genes have similar structures, including a putative chromodomain close to their N-terminal end and a putative leucine zipper at their C-terminus. The possible functional roles of these proteins are discussed.

Amino Acid Sequence↗
PubMed2001

Expression and function of Xenopus laevis p75(NTR) suggest evolution of developmental regulatory mechanisms.

Neurotrophins signal through two different classes of receptors, members of the trk family of receptor tyrosine kinases, and p75 neurotrophin receptor (p75(NTR)), a member of the tumor necrosis factor receptor family. While neurotrophin binding to trks results in, among other things, increased cell survival, p75(NTR) has enigmatically been implicated in promoting both survival and cell death. Which of these two signals p75(NTR) imparts depends on the specific cellular context. Xenopus laevis is an excellent system in which to study p75(NTR) function in vivo because of its amenability to experimental manipulation. We therefore cloned partial cDNAs of two p75(NTR) genes from Xenopus, which we have termed p75(NTR)a and p75(NTR)b. We then cloned two different cDNAs, both of which encompass the full coding region of p75(NTR)a. Early in development both p75(NTR)a and p75(NTR)b are expressed in developing cranial ganglia and presumptive spinal sensory neurons, similar to what is observed in other species. Later, p75(NTR)a expression largely continues to parallel p75(NTR) expression in other species. However, Xenopus p75(NTR)a is additionally expressed in the neuroepithelium of the anterior telencephalon, all layers of the retina including the photoreceptor layer, and functioning axial skeletal muscle. Finally, misexpression of full length p75(NTR) and each of two truncated mutants in developing retina reveal that p75(NTR) probably signals for cell survival in this system. This result contrasts with the reported role of p75(NTR) in developing retinae of other species, and the possible implications of this difference are discussed.

Amino Acid Sequence↗
PubMed1986

Evolution of the regulatory isozymes of 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase present in the Escherichia coli genealogy.

The evolutionary history of isozymes for 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase has been constructed in a phylogenetic cluster of procaryotes (superfamily B) that includes Escherichia coli. Members of superfamily B that have been positioned on a phylogenetic tree by oligonucleotide cataloging possess one or more of four distinct isozymes of DAHP synthase. DAHP synthase-0 is insensitive to feedback inhibition, while DAHP synthase-Tyr, DAHP synthase-Trp, and DAHP synthase-Phe are sensitive to feedback inhibition by L-tyrosine, L-tryptophan, and L-phenylalanine, respectively. The evolutionary history of this isozyme family can be deduced within superfamily B by using a cladistic methodology of maximum parsimony (R. A. Jensen, Mol. Biol. Evol. 2:92-108, 1985). DAHP synthase-0 was found in Acinetobacter species and in Oceanospirillum minutulum, organisms that also possess DAHP synthase-Tyr. These two isozymes were apparently present in a common ancestor that predated the evolutionary divergence of contemporary superfamily B sublineages. DAHP synthase-0 is postulated to have been the evolutionary forerunner of DAHP synthase-Trp. The newly evolved DAHP synthase-Trp is postulated to have possessed sensitivity to feedback inhibition by chorismate as well as by L-tryptophan, chorismate sensitivity having been retained in rRNA group I pseudomonads (minor sensitivity), group V pseudomonads (very sensitive), and Lysobacter enzymogenes (ultrasensitive). Organisms constituting the enteric lineage of the phylogenetic tree (including a cluster of four Oceanospirillum species) have all lost the chorismate sensitivity of DAHP synthase-Trp. The absence of DAHP synthase-Phe in the Oceanospirillum cluster of organisms supports the previous conclusion that DAHP synthase-Phe evolved recently within superfamily B, being present only Escherichia coli and its close relatives.

3-Deoxy-7-Phosphoheptulonate Synthase↗
PubMedDate not supplied

Evolving beyond perfection: an investigation of the effects of long-term evolution on fractal gene regulatory networks.

This paper continues a theme of exploring algorithms based on principles of biological development for tasks such as pattern generation, machine learning and robot control. Previous work has investigated the use of genes expressed as fractal proteins to enable greater evolvability of gene regulatory networks (GRNs). Here, the evolution of such GRNs is investigated further to determine whether evolution exhibits natural tendencies towards efficiency and graceful degradation of developmental programs. Experiments where "perfect" GRNs are evolved for a further thousand generations without the addition of any further selection pressure, confirm this hypothesis. After further evolution, the perfect GRNs operate in a more efficient manner (using fewer proteins) and show an improved ability to function correctly with missing genes. When the algorithm is applied to applications (e.g. robot control) this equates to efficient and fault-tolerant controllers.

Algorithms↗