Evolutionary rate depends on number of protein-protein interactions independently of gene expression level: response.
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Evolution, Molecular↗
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Phylogenetic analysis and developmental expression of thymosin-beta4 gene in amphioxus.
Thymosin-beta4 is a highly conserved actin-binding protein that plays an important role in multiple early developmental events and functions in keeping the adult life in vertebrates. Here a cDNA for a thymosin-beta4 gene was isolated from the amphioxus, Branchiostoma belcheri. A molecular phylogenetic tree constructed from the deduced amino acid sequence of the isolated cDNA indicates that this gene belongs to the thymosin-beta4 subfamily, but it is split at the base of the vertebrate gene clade in evolution. In situ hybridization reveals that the expression is detected in the locations homologous to orthologous genes expressing regions of vertebrate embryos and adults, such as the neural plate, neural tube, paraxial mesoderm, differentiating somites, pharynx and gut, midgut diverticulus, blood vessels and body spaces. These results are interpreted to mean that thymosin-beta4 genes might play a conserved role in the patterning of chordate embryos and functions in adults.
Amino Acid Sequence↗
[The neuronal zootype].
We present an hypothesis, derived from the zootype concept of Slack, Holland and Graham. The main point of this hypothesis is to postulate that the primordial function of the zootype genes is to design an appropriate neuronal network in bilaterian animals, by controlling the genes involved in the specificity of the axon pathways. This would be the primary function of the zootype genes in development and their primitive function in evolution. The hypothesis is discussed in view of the current knowledge on the Hox genes, their evolution, their genomic organisation, their expression and their targets.
Animals↗
Beyond the Hox: how widespread is homeobox gene clustering?
The arrangement of Hox genes into physical clusters is fundamental to the patterning of animal body plans, through the phenomenon of colinearity. Other homeobox genes are often described as dispersed, implying they are not arranged into clusters. Contrary to this view, however, two clusters of non-Hox homeobox genes have been reported: the amphioxus ParaHox gene cluster and the Drosophila 93D/E cluster (referred to here as the NKL cluster). Here I examine the antiquity of these gene clusters, their conservation and their pattern of evolution in vertebrate genomes. I argue that the ParaHox gene cluster arose early in animal evolution, and duplicated in vertebrates to give the four clusters in human and mouse genomes. The NKL cluster is also ancient, and also duplicated to yield four descendent clusters in mammalian genomes. The NKL and Hox gene clusters were originally chromosomal neighbours, within an ancient and extensive array of at least 30 related homeobox genes. There is no necessary relationship between clustering and colinearity, although it is argued that the ParaHox gene cluster does show modified spatial colinearity. A novel hypothesis for the evolution of ParaHox gene expression in deuterostomes is presented.
Amphibians↗
Development of decompensated dilated cardiomyopathy is associated with decreased gene expression and activity of the milrinone-sensitive cAMP phosphodiesterase PDE3A.
BACKGROUND: Phosphodiesterase III (PDE3) inhibitors are inotropic agents used to treat congestive heart failure (CHF) and are less effective in patients with severe CHF. Little is known about relative changes in PDE3 activity or gene expression during the evolution of cardiomyopathy. METHODS AND RESULTS: In the present study, we evaluated temporal changes in PDE3A gene expression before and after pacing-induced CHF in nine mongrel dogs. Three weeks of left ventricular (LV) pacing produced LV end-diastolic pressures of 15+/-1.7 mm Hg, whereas overt CHF at 4 to 5 weeks was associated with LV end-diastolic pressures of 24+/-1.7 mm Hg; prepacing values were 6.6+/-0.6 mm Hg. Total RNA isolated from LV tissues was analyzed on Northern blots; 10 unpaced normal hearts served as tissue controls. Signals for PDE3A mRNAs (7, 8, and 10 kb) or PDE4D (7.6 kb) were normalized against glyceraldehyde-3-phosphate dehydrogenase (GAPDH) or ribosomal 18S RNA. Before the onset of CHF, PDE3A/GAPDH ratios were not different between the control and 3-week paced groups. In contrast, all PDE3A/GAPDH ratios were selectively reduced by 52%, and PDE3A/18S was reduced by 70% (P<.05) in CHF; PDE4D/GAPDH (or 18S) was unchanged. LV tissues from four control and four CHF dogs were also processed to isolate cytosolic and microsomal membrane protein for cAMP PDE3 activity assays. CHF was associated with a significant 54% reduction (P<.05) in microsomal but not cytosolic PDE3 activity. CONCLUSIONS: Selective downregulation of PDE3A may account in part for the ineffectiveness of milrinone in the treatment of severe CHF.
3',5'-Cyclic-AMP Phosphodiesterases↗
Rapid evolution of mammalian X-linked testis-expressed homeobox genes.
Homeobox genes encode transcription factors that function in various developmental processes and are usually evolutionarily conserved in their sequences. However, two X-chromosome-linked testis-expressed homeobox genes, one from rodents and the other from fruit flies, are known to evolve rapidly under positive Darwinian selection. Here we report yet another case, from primates. TGIFLX is an X-linked homeobox gene that originated by retroposition of the autosomal gene TGIF2, most likely in a common ancestor of rodents and primates. While TGIF2 is ubiquitously expressed, TGIFLX is exclusively expressed in adult testis. A comparison of the TGIFLX sequences among 16 anthropoid primates revealed a significantly higher rate of nonsynonymous nucleotide substitution (d(N)) than synonymous substitution (d(S)), strongly suggesting the action of positive selection. Although the high d(N)/d(S) ratio is most evident outside the homeobox, the homeobox has a d(N)/d(S) of approximately 0.89 and includes two codons that are likely under selection. Furthermore, the rate of radical amino acid substitutions that alter amino acid charge is significantly greater than that of conservative substitutions, suggesting that the selection promotes diversity of the protein charge profile. More interestingly, an analysis of 64 orthologous homeobox genes from humans and mice shows substantially higher rates of amino acid substitution in X-linked testis-expressed genes than in other genes. These results suggest a general pattern of rapid evolution of mammalian X-linked testis-expressed homeobox genes. Although the physiological function of and the exact selective agent on TGIFLX and other rapidly evolving homeobox genes are unclear, the common expression pattern of these transcription factor genes led us to conjecture that the selection is related to one or more aspects of male reproduction and may contribute to speciation.
Amino Acid Sequence↗
[Retroviral regulators of gene expression in the human genome as possible factors for its evolution].
Human endogenous viruses, including their possible role in evolution, are reviewed.
Biological Evolution↗
Chordate evolution in a new light.
Gene expression studies in embryos often provide insights into evolutionary relationships across phyla. In this issue of Cell, Lowe et al. examine the patterning of the bilaterian nervous system by studying gene expression in a hemichordate, the acorn worm. Although these animals have an unstructured nervous system, they show surprisingly conserved gene expression domains, shedding new light on the evolution of the central nervous system and the phylogenetic placement of chordates.
Animals↗
The evolution of arthropod segmentation: insights from comparisons of gene expression patterns.
The comparison of gene expression patterns in a number of insect and crustacean species has led to some insight into the evolution of arthropod patterning mechanisms. These studies have revealed the fundamental nature of the parasegment in a number of organisms, shown that segments can be generated sequentially at the molecular level, and suggested that pair-rule pre-patterning might not be shared by all insects.
Animals↗
Decoupled evolution of coding region and mRNA expression patterns after gene duplication: implications for the neutralist-selectionist debate.
The neutralist perspective on molecular evolution maintains that the vast majority of mutations affecting gene function are neutral or deleterious. After a gene duplication where both genes are retained, it predicts that original and duplicate genes diverge at clock-like rates. This prediction is usually tested for coding sequences, but can also be applied to another important aspect of gene function, the genes' expression pattern. Moreover, if both sequence and expression pattern diverge at clock-like rates, a correlation between divergence in sequence and divergence in expression patterns is expected. Duplicate gene pairs with more highly diverged sequences should also show more highly diverged expression patterns. This prediction is tested for a large sample of duplicated genes in the yeast Saccharomyces cerevisiae, using both genome sequence and microarray expression data. Only a weak correlation is observed, suggesting that coding sequence and mRNA expression patterns of duplicate gene pairs evolve independently and at vastly different rates. Implications of this finding for the neutralist-selectionist debate are discussed.
Biological Evolution↗
Crustacean appendage evolution associated with changes in Hox gene expression.
Homeotic (Hox) genes specify the differential identity of segments along the body axis of insects. Changes in the segmental organization of arthropod bodies may therefore be driven by changes in the function of Hox genes, but so far this has been difficult to demonstrate. We show here that changes in the expression pattern of the Hox genes Ubx and AbdA in different crustaceans correlate well with the modification of their anterior thoracic limbs into feeding appendages (maxillipeds). Our observations provide direct evidence that major morphological changes in arthropod body plans are associated with changes in Hox gene regulation. They suggest that homeotic changes may play a role in the normal process of adaptive evolutionary change.
Animals↗
Amphioxus and lamprey AP-2 genes: implications for neural crest evolution and migration patterns.
The neural crest is a uniquely vertebrate cell type present in the most basal vertebrates, but not in cephalochordates. We have studied differences in regulation of the neural crest marker AP-2 across two evolutionary transitions: invertebrate to vertebrate, and agnathan to gnathostome. Isolation and comparison of amphioxus, lamprey and axolotl AP-2 reveals its extensive expansion in the vertebrate dorsal neural tube and pharyngeal arches, implying co-option of AP-2 genes by neural crest cells early in vertebrate evolution. Expression in non-neural ectoderm is a conserved feature in amphioxus and vertebrates, suggesting an ancient role for AP-2 genes in this tissue. There is also common expression in subsets of ventrolateral neurons in the anterior neural tube, consistent with a primitive role in brain development. Comparison of AP-2 expression in axolotl and lamprey suggests an elaboration of cranial neural crest patterning in gnathostomes. However, migration of AP-2-expressing neural crest cells medial to the pharyngeal arch mesoderm appears to be a primitive feature retained in all vertebrates. Because AP-2 has essential roles in cranial neural crest differentiation and proliferation, the co-option of AP-2 by neural crest cells in the vertebrate lineage was a potentially crucial event in vertebrate evolution.
Ambystoma↗
Repression and loss of gene expression outpaces activation and gain in recently duplicated fly genes.
Evolutionists widely acknowledge that regulatory genetic changes are of paramount importance for morphological and genomic evolution. Nevertheless, mechanistic complexity and a paucity of data from nonmodel organisms have prevented testing and quantifying universal hypotheses about the macroevolution of gene regulatory mechanisms. Here, we use a phylogenetic approach to provide a quantitative demonstration of a previously hypothesized trend, whereby the evolutionary rate of repression or loss of gene expression regions is significantly higher than the rate of activation or gain. Such a trend is expected based on case studies in regulatory evolution and under models of molecular evolution where duplicated genes lose duplicated expression patterns in a complementary fashion. The trend is important because repression of gene expression is a hypothesized mechanism for the origin of evolutionarily novel morphologies through specialization.
Animals↗
Evolution of steroid-inducible RP2 mRNA expression in the mouse kidney.
We have examined the structure and expression of mRNAs encoded by the androgen-inducible RP2 gene in the kidneys of nine mouse species within the genus Mus. There is considerable interspecies variation in the lengths of the major RP2 transcripts; some of this variation is due to the presence or absence of a B1 repetitive element in the 3'-untranslated region of the gene. In addition, the extent of RP2 mRNA induction by testosterone differs among the species. Two species show 10-20-fold induction, while others display a reduced response or none at all. Analysis of an interspecific hybrid indicates that the inducibility phenotype is inherited in an additive fashion. A correlation between RP2 inducibility and the time of formation of lineages within the Mus genus suggests that induction evolved in a stepwise fashion, with the acquisition of a modest hormonal response being followed by the appearance of a greater response. The interspecies variations in RP2 mRNA structure and regulation provide a useful model for the identification and study of genetic elements that elicit evolutionary alterations in steroid-modulated gene expression.
Animals↗
Chicken orthologues of mammalian imprinted genes are clustered on macrochromosomes and replicate asynchronously.
In the chicken genome, most orthologues of mouse imprinted genes are clustered on macrochromosomes. Only a few orthologues are located in the microchromosome complement. Macrochromosomal and, to a lesser extent, microchromosomal regions containing imprinted gene orthologues exhibit asynchronous DNA replication. We conclude that highly conserved arrays of imprinted gene orthologues were selected during vertebrate evolution, long before these genes were recruited for parent-specific gene expression by genomic imprinting mechanisms. Evidently, the macrochromosome complement provides a better chromatin environment for the establishment of asynchronous DNA replication and imprinted gene expression later in evolution than microchromosomes.
Animals↗
The role of RNA interference in heterochromatic silencing.
Soon after its discovery 75 years ago, heterochromatin, a dense chromosomal material, was found to silence genes. But its importance in regulating gene expression was controversial. Long thought to be inert, heterochromatin is now known to give rise to small RNAs, which, by means of RNA interference, direct the modification of proteins and DNA in heterochromatic repeats and transposable elements. Heterochromatin has thus emerged as a key factor in epigenetic regulation of gene expression, chromosome behaviour and evolution.
Animals↗
The remarkable evolutionary history of the human amylase genes.
Analysis of the structures of the human amylase genes has demonstrated that this multigene family contains at least five tandem gene copies, closely related in sequence but with distinct tissue specific expression. The structures of the genes demonstrate that the human salivary amylase gene was derived from a preexisting pancreatic amylase gene. Insertion of a retrovirus upstream of the amylase gene is responsible for the alteration in tissue specificity. A parotid specific enhancer has been identified within the retrovirus by expression studies in transgenic mice. The independent origin of salivary amylase in rodents and primates suggests that there has been strong evolutionary selection for amylase in saliva. The amylase genes demonstrate a novel mechanism for evolution of new patterns of tissue specific gene expression.
Amylases↗
Comparative analysis of regulatory transcription factors in Schizosaccharomyces pombe and budding yeasts.
Regulatory transcription factors (rTFs), which bind specific DNA sequences in the regulatory regions of genes and subsequently activate or repress transcription, play a central role in programming genomic expression. The number of rTFs in a species might therefore reflect its functional complexity. For simple organisms like yeast, a relatively small number of rTFs might be expected that is fairly constant between yeast species. We show that the budding yeast, Saccharomyces cerevisiae, contains 201 rTfs, which is one of the largest rTF numbers found in yeast species for which genome sequences are available. This is a much higher number than the 129 rTFs found in the fission yeast, Schizosaccharomyces pombe, which is currently the yeast with the lowest number of rTFs. Comparative analysis of several different budding yeast species shows that most of the 'extra' rTFs found in S. cerevisiae were probably acquired as a result of a whole genome duplication (WGD) event that occurred in an ancestor of a subset of budding yeast species. However, we also show that budding yeast species that have not been affected by the WGD contain a greater number of rTFs than S. pombe (mean = 145). Thus, two or more mechanisms have led to the 60% increase in rTFs in S. cerevisiae compared to S. pombe. This difference may correlate with a more extensive functional divergence in budding yeasts compared to fission yeasts. The relatively small number of rTFs in S. pombe make this organism an attractive model for global studies of mechanisms that programme gene expression.
Evolution, Molecular↗