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PubMedDate not supplied

Avian Helios and evolution of the Ikaros family.

Abstract Helios (Znfn1a2) is an Ikaros-related lymphoid regulatory protein with possible involvement in T-cell development and function as well as in the early events of haematopoietic stem cell differentiation. To evaluate the role of Helios in avian haemato/lymphopoiesis, we have characterized the avian Helios gene. In contrast to studies in mouse and human, we have found that the highly conserved avian Helios encodes a novel exon and three isoforms. Furthermore, the avian Helios expression precedes Ikaros in the ontogeny, being present already on the first day of embryonic development. Additionally, expression in the bursa of Fabricius, germinal centres and B-cell lines suggests a role for Helios also in the B-cell lineage. Phylogenetic studies of the Ikaros family along with data on paralogous chromosome segments in the human genome connect the expansion of the Ikaros family and thus possibly the emergence of the adaptive immune system with the putative second round of genome duplications and indicate that the Ikaros gene family is linked with the Hox gene clusters.

Amino Acid Sequence↗
PubMed2004

Transgenic study of parallelism in plant morphological evolution.

Developmental constraint is indicated when one finds that similar genetic mechanisms are responsible for independent origins of the same derived phenotype. We studied three independent origins of rosette flowering within the mustard family and attempted to evaluate the extent to which the same mechanisms were involved in each transition from the ancestral phenotype, inflorescence flowering. We used transformation to move a candidate gene, LFY, and its cis-regulatory sequences from rosette-flowering species into an inflorescence-flowering recipient, Arabidopsis thaliana, in place of its endogenous LFY gene. The transgenic phenotypes of experimental and control lines (containing an A. thaliana LFY transgene) and the expression driven by the cis-regulatory sequences show that changes at the LFY locus might have contributed to the evolution of rosette flowering in two of the three lineages. In the third case, changes upstream of LFY are implicated. Our data suggest that changes in a single developmental regulatory program were involved in multiple origins of the same derived trait but that the specific genetic changes were different in each case.

Arabidopsis Proteins↗
PubMed2006

Conservation of upstream regulators of scute on the notum of cyclorraphous Diptera.

Bristles on the notum of many cyclorraphous flies are arranged into species-specific stereotyped patterns. Differences in the spatial expression of the proneural gene scute correlate with the positions of bristles in those species looked at so far. However, the examination of a number of genes encoding trans-regulatory factors, such as pannier, stripe, u-shaped, caupolican and wingless, indicates that they are expressed in conserved domains on the prospective notum. This suggests that the function of a trans-regulatory network of genes is relatively unchanged in derived Diptera, and that many differences are likely to be due to changes in cis-regulatory sequences of scute. In contrast, in Anopheles gambiae, a basal species with no stereotyped bristle pattern, the expression patterns of pannier and wingless are not conserved, and expression of AgASH, the Anopheles proneural gene, does not correlate in a similar manner with the bristle pattern. We discuss the possibility that independently acting cis-regulatory sequences at the scute locus may have arisen in the lineage giving rise to cyclorraphous flies.

Animals↗
PubMed2003

Who came first--larvae or adults? origins of bilaterian metazoan larvae.

There is a classic controversy in zoology over whether the common ancestor of living bilaterian phyla was a benthic animal with a bilaterian body plan, or was a pelagic larva-like animal similar to what we see today in the primary larvae of indirect-developing bilaterians. We examine the current larva-like adult hypothesis, and present an alternate model for the evolution of complex life histories by intercalation of larval features into the ontogeny of an ancestral direct-developing bilaterian. This gradual accumulation of larval features results in a developmental regulatory program that produces a larva distinct in body plan from the adult. The evolution of a rapid and complete metamorphosis is made possible by the convergent evolution of set aside cells in the final stages of the emergence of indirect developing larval forms. Although convergences abound either hypothesis for the evolution of developmental pathways and life histories, the bilaterian first hypothesis is consistent with all stages of evolution of a complex life history being selectively advantageous, with the rapid evolution of larval forms, and with the frequent co-option of genes from the adult phase of the life cycle prevalent in the evolution of embryos and larvae.

Animals↗
PubMed2002

Extensive domain shuffling in transcription regulators of DNA viruses and implications for the origin of fungal APSES transcription factors.

BACKGROUND: Viral DNA-binding proteins have served as good models to study the biochemistry of transcription regulation and chromatin dynamics. Computational analysis of viral DNA-binding regulatory proteins and identification of their previously undetected homologs encoded by cellular genomes might lead to a better understanding of their function and evolution in both viral and cellular systems. RESULTS: The phyletic range and the conserved DNA-binding domains of the viral regulatory proteins of the poxvirus D6R/N1R and baculoviral Bro protein families have not been previously defined. Using computational analysis, we show that the amino-terminal module of the D6R/N1R proteins defines a novel, conserved DNA-binding domain (the KilA-N domain) that is found in a wide range of proteins of large bacterial and eukaryotic DNA viruses. The KilA-N domain is suggested to be homologous to the fungal DNA-binding APSES domain. We provide evidence for the KilA-N and APSES domains sharing a common fold with the nucleic acid-binding modules of the LAGLIDADG nucleases and the amino-terminal domains of the tRNA endonuclease. The amino-terminal module of the Bro proteins is another, distinct DNA-binding domain (the Bro-N domain) that is present in proteins whose domain architectures parallel those of the KilA-N domain-containing proteins. A detailed analysis of the KilA-N and Bro-N domains and the associated domains points to extensive domain shuffling and lineage-specific gene family expansion within DNA virus genomes. CONCLUSIONS: We define a large class of novel viral DNA-binding proteins and their cellular homologs and identify their domain architectures. On the basis of phyletic pattern analysis we present evidence for a probable viral origin of the fungus-specific cell-cycle regulatory transcription factors containing the APSES DNA-binding domain. We also demonstrate the extensive role of lineage-specific gene expansion and domain shuffling, within a limited set of approximately 24 domains, in the generation of the diversity of virus-specific regulatory proteins.

Amino Acid Sequence↗
PubMed2005

Structure, expression, and transcriptional regulation of the Strongylocentrotus franciscanus spec gene family encoding intracellular calcium-binding proteins.

The mechanisms by which gene expression patterns emerge during evolution are poorly understood. The sea urchin spec genes offer a useful means to investigate evolutionary mechanisms. Genes of the spec family from Strongylocentrotus purpuratus and Lytechinus pictus have identical patterns of aboral ectoderm-specific expression but exhibit species-specific differences in copy number, genomic structure, temporal expression, and cis-regulatory architecture. Here, we identify spec genes from a phylogenetic intermediate, Strongylocentrotus franciscanus, to gain insight into the evolution of the spec gene family and its transcriptional regulation. We identified two spec genes in the S. franciscanus genome, sfspec1a and sfspec1b, that were orthologous to spec1 from S. purpuratus. sfspec1b transcripts began to accumulate at the blastula stage and became progressively more abundant; this was reminiscent of spec expression in L. pictus but different from that in S. purpuratus. As expected, sfspec1b expression was restricted to aboral ectoderm cells. The six-exon structure of the sfspec1b genomic locus was identical to that of the S. purpuratus spec genes and was bounded by two repeat-spacer-repeat (RSR) repetitive sequence elements, which are conserved features of S. purpuratus spec genes and function as transcriptional enhancers. The enhancer activity of the sfspec1b RSRs was comparable to that of their S. purpuratus counterparts, although the placement and orientation of crucial cis-regulatory elements within the RSRs differed. We discovered a spec gene in S. franciscanus that was only distantly related to other spec genes but was highly conserved in S. purpuratus. Unexpectedly, this gene was expressed exclusively in endoderm lineages. Our results show that the evolution of spec cis-regulatory elements is highly dynamic and that substantial alterations can occur when maintaining or grossly modifying gene expression patterns.

Amino Acid Sequence↗
PubMed2003

Transcriptional regulation and the evolution of development.

A growing body of evidence suggests that changes in transcriptional regulation form an important part of the genetic basis for the evolution of development. At a microevolutionary level, all the necessary conditions are present: populations harbor abundant genetic variation for differences in transcription profiles, a substantial fraction of these variants can influence organismal phenotype, and some variants have fitness consequences and are subject to natural selection. At a macroevolutionary level, the evidence is less direct but strongly suggestive: specific differences in anatomy and gene expression are often correlated, while comparisons of transcription profiles among distantly related taxa point to extensive evolutionary changes in regulatory gene networks. Understanding how transcriptional regulatory systems evolve, and what contributions these changes have made to the evolution of phenotype, represents a major challenge for Evo-Devo.

Animals↗
PubMed2006

Divergence from a dedicated cellular suicide mechanism: exploring the evolution of cell death.

The developmental cell death in the nematode C. elegans is controlled by a simple and dedicated genetic program. This genetic program is evolutionarily conserved in higher organisms, including mammals. However, although mammalian homologs of C. elegans cell death gene products continue to regulate apoptosis, they are no longer dedicated regulators of cell death. On the other hand, multiple cellular noncell death-related mechanisms have been recruited to regulate cell death under different conditions. Such evidence suggests that evolution has led to an extensive integration of mammalian apoptosis machinery with multiple cellular physiological processes.

Animals↗
PubMed2005

The transcriptional consequences of mutation and natural selection in Caenorhabditis elegans.

The evolutionary importance of gene-expression divergence is unclear: some studies suggest that it is an important mechanism for evolution by natural selection, whereas others claim that most between-species regulatory changes are neutral or nearly neutral. We examined global transcriptional divergence patterns in a set of Caenorhabditis elegans mutation-accumulation lines and natural isolate lines to provide insights into the evolutionary importance of transcriptional variation and to discriminate between the forces of mutation and natural selection in shaping the evolution of gene expression. We detected the effects of selection on transcriptional divergence patterns and characterized them with respect to coexpressed gene sets, chromosomal clustering of expression changes and functional gene categories. We directly compared observed transcriptional variation patterns in the mutation-accumulation and natural isolate lines to a neutral model of transcriptome evolution to show that strong stabilizing selection dominates the evolution of transcriptional change for thousands of C. elegans expressed sequences.

Animals↗
PubMed1999

Patterns of evolutionary rate variation among genes of the anthocyanin biosynthetic pathway.

The anthocyanin biosynthetic pathway is responsible for the production of anthocyanin pigments in plant tissues and shares a number of enzymes with other biochemical pathways. The six core structural genes of this pathway have been cloned and characterized in two taxonomically diverse plant species (maize and snapdragon). We have recently cloned these genes for a third species, the common morning glory, Ipomoea purpurea. This additional information provides an opportunity to examine patterns of evolution among genes within a single biochemical pathway. We report here that upstream genes in the anthocyanin pathway have evolved substantially more slowly than downstream genes and suggest that this difference in evolutionary rates may be explained by upstream genes being more constrained because they participate in several different biochemical pathways. In addition, regulatory genes associated with the anthocyanin pathway tend to evolve more rapidly than the structural genes they regulate, suggesting that adaptive evolution of flower color may be mediated more by regulatory than by structural genes. Finally, for individual anthocyanin genes, we found an absence of rate heterogeneity among three major angiosperm lineages. This rate constancy contrasts with an accelerated rate of evolution of three CHS-like genes in the Ipomoea lineage, indicating that these three genes have diverged without coordinated adjustment by other pathway genes.

Acyltransferases↗
PubMedDate not supplied

Absence of endogenous interleukin-10 enhances the evolution of acute lung injury.

Interleukin-10 (IL-10) exerts a wide spectrum of regulatory activities in the immune and inflammatory response. The aim of this study was to investigate the role of endogenous IL-10 on the modulation of the inflammatory response in mice subjected to carrageenan-induced lung injury. When compared to carrageenan-treated IL-10 wild-type (WT) mice, carrageenan-treated IL-10 knock-out mice (IL-10KO) mice experienced a higher rate of pleural exudation, and polymorphonuclear cell migration. Exudate levels of the pro-inflammatory cytokines tumour necrosis factor, interleukin-1beta and interleukin-6 were also greatly enhanced in IL-10KO mice in comparison to wild-type mice. Lung myeloperoxidase (MPO) activity was significantly reduced in IL-10WT mice when compared to IL-10KO mice-treated with carrageenan. The degree of oxidative and nitrosative damage was significantly higher in IL-10KO mice than in wild-type littermates, as indicated by elevated malondialdehyde levels and formation of nitrotyrosine and poly (ADP-ribose) synthetase (PARS). Staining of lung tissue sections obtained from carrageenan-treated IL-10WT with an anti-COX-2 antibody showed a positive staining of the inflamed tissue. Furthermore, expression of inducible nitric oxide synthase (iNOS) was found mainly in the macrophages of the inflamed lungs from carrageenan-treated IL-10WT mice. The intensity and degree of the staining for COX-2 and iNOS were markedly enhanced in tissue sections obtained from carrageenan-treated IL-10KO mice. Most notably, the degree of lung injury caused by carrageenan was also enhanced in IL-10KO mice. Taken together, our results clearly demonstrate that endogenous IL-10 exerts an anti-inflammatory role during acute inflammation and tissue damage associated with carrageenan-induced pleurisy, possibly by regulating neutrophil recruitment, and the subsequent cytokine and oxidant generation.

Acute Disease↗
PubMed1995

Interleukin-1 and its inhibitors: a biologic and therapeutic model for the role of growth regulatory factors in leukemias.

Production of growth factors may provide a mechanism for disease evolution in some leukemias. Interleukin-1 is a plelotropic cytokine with the ability to synergize with other growth factors as well as to stimulate their production and release. Autocrine and/or paracrine secretion of interleukin-1 has been implicated in the pathogenesis of both chronic and acute myelogenous leukemia. Recently, a series of both specific and nonspecific IL-1 inhibitory molecules have been identified. These include IL-1 receptor antagonist, soluble IL-1 receptors, IL-1-converting enzyme inhibitor, IL-4, IL-10 and IL-1-antisense. Early experiments demonstrating the ability of some of these molecules to inhibit acute and chronic myelogenous leukemia growth suggest that clinical trials of these compounds may provide a novel management approach in these malignancies. Here we review the potential biologic and therapeutic role of IL-1 and its inhibitors in the myeloid leukemias.

Animals↗
PubMed2000

Maintenance of functional equivalence during paralogous Hox gene evolution.

Biological diversity is driven mainly by gene duplication followed by mutation and selection. This divergence in either regulatory or protein-coding sequences can result in quite different biological functions for even closely related genes. This concept is exemplified by the mammalian Hox gene complex, a group of 39 genes which are located on 4 linkage groups, dispersed on 4 chromosomes. The evolution of this complex began with amplification in cis of a primordial Hox gene to produce 13 members, followed by duplications in trans of much of the entire unit. As a consequence, Hox genes that occupy the same relative position along the 5' to 3' chromosomal coordinate (trans-paralogous genes) share more similarity in sequence and expression pattern than do adjacent Hox genes on the same chromosome. Studies in mice indicate that although individual family members may have unique biological roles, they also share overlapping functions with their paralogues. Here we show that the proteins encoded by the paralogous genes, Hoxa3 and Hoxd3, can carry out identical biological functions, and that the different roles attributed to these genes are the result of quantitative modulations in gene expression.

Alleles↗
PubMed1997

Trans gene regulation in adaptive evolution: a genetic algorithm model.

This is a continuation of earlier studies on the evolution of infinite populations of haploid genotypes within a genetic algorithm framework. We had previously explored the evolutionary consequences of the existence of indeterminate-"plastic"-loci, where a plastic locus had a finite probability in each generation of functioning (being switched "on") or not functioning (being switched "off"). The relative probabilities of the two outcomes were assigned on a stochastic basis. The present paper examines what happens when the transition probabilities are biased by the presence of regulatory genes. We find that under certain conditions regulatory genes can improve the adaptation of the population and speed up the rate of evolution (on occasion at the cost of lowering the degree of adaptation). Also, the existence of regulatory loci potentiates selection in favour of plasticity. There is a synergistic effect of regulatory genes on plastic alleles: the frequency of such alleles increases when regulatory loci are present. Thus, phenotypic selection alone can be a potentiating factor in a favour of better adaptation.

Adaptation, Physiological↗
PubMed2005

Bacterial genome size reduction by experimental evolution.

Bacterial evolution toward endosymbiosis with eukaryotic cells is associated with extensive bacterial genome reduction and loss of metabolic and regulatory capabilities. Here we examined the rate and process of genome reduction in the bacterium Salmonella enterica by a serial passage experimental evolution procedure. The initial rate of DNA loss was estimated to be 0.05 bp per chromosome per generation for a WT bacterium and approximately 50-fold higher for a mutS mutant defective in methyl-directed DNA mismatch repair. The endpoints were identified for seven chromosomal deletions isolated during serial passage and in two separate genetic selections. Deletions ranged in size from 1 to 202 kb, and most of them were not associated with DNA repeats, indicating that they were formed via RecA-independent recombination events. These results suggest that extensive genome reduction can occur on a short evolutionary time scale and that RecA-dependent homologous recombination only plays a limited role in this process of jettisoning superfluous DNA.

Base Pair Mismatch↗
PubMed2006

Bioinformatics of alternative splicing and its regulation.

The sequencing of the human genome and ensuing wave of data generation have brought new light upon the extent and importance of alternative splicing as an RNA regulatory mechanism. Alternative splicing could potentially explain the complexity of protein repertoire during evolution, and defects in the splicing mechanism are responsible for diseases as complex as cancer. Among the challenges that rise in light of these discoveries are cataloguing splice variation in the human and other eukaryotic genomes, and identifying and characterizing the splicing regulatory elements that control their expression. Bioinformatics efforts tackling these two questions are just at the beginning. This article is a survey of these methods.

Alternative Splicing↗