Diverse Spatial, Temporal, and Sexual Expression of Recently Duplicated Androgen-Binding Protein Genes in \u3ci\u3eMus musculus\u3c/i\u3e

Background The genes for salivary androgen-binding protein (ABP) subunits have been evolving rapidly in ancestors of the house mouse Mus musculus, as evidenced both by recent and extensive gene duplication and by high ratios of nonsynonymous to synonymous nucleotide substitution rates. This makes ABP an appropriate model system with which to investigate how recent adaptive evolution of paralogous genes results in functional innovation (neofunctionalization). Results It was our goal to find evidence for the expression of as many of the Abp paralogues in the mouse genome as possible. We observed expression of six Abpa paralogues and five Abpbg paralogues in ten glands and other organs located predominantly in the head and neck (olfactory lobe of the brain, three salivary glands, lacrimal gland, Harderian gland, vomeronasal organ, and major olfactory epithelium). These Abp paralogues differed dramatically in their specific expression in these different glands and in their sexual dimorphism of expression. We also studied the appearance of expression in both late-stage embryos and postnatal animals prior to puberty and found significantly different timing of the onset of expression among the various paralogues. Conclusion The multiple changes in the spatial expression profile of these genes resulting in various combinations of expression in glands and other organs in the head and face of the mouse strongly suggest that neofunctionalization of these genes, driven by adaptive evolution, has occurred following duplication. The extensive diversification in expression of this family of proteins provides two lines of evidence for a pheromonal role for ABP: 1) different patterns of Abpa/Abpbg expression in different glands; and 2) sexual dimorphism in the expression of the paralogues in a subset of those glands. These expression patterns differ dramatically among various glands that are located almost exclusively in the head and neck, where the sensory organs are located. Since mice are nocturnal, it is expected that they will make extensive use of olfactory as opposed to visual cues. The glands expressing Abp paralogues produce secretions (lacrimal and salivary) or detect odors (MOE and VNO) and thus it appears highly likely that ABP proteins play a role in olfactory communication

The early expansion and evolutionary dynamics of POU class genes.

The POU genes represent a diverse class of animal-specific transcription factors that play important roles in neurogenesis, pluripotency, and cell-type specification. Although previous attempts have been made to reconstruct the evolution of the POU class, these studies have been limited by a small number of representative taxa, and a lack of sequences from basally branching organisms. In this study, we performed comparative analyses on available genomes and sequences recovered through "gene fishing" to better resolve the topology of the POU gene tree. We then used ancestral state reconstruction to map the most likely changes in amino acid evolution for the conserved domains. Our work suggests that four of the six POU families evolved before the last common ancestor of living animals-doubling previous estimates-and were followed by extensive clade-specific gene loss. Amino acid changes are distributed unequally across the gene tree, consistent with a neofunctionalization model of protein evolution. We consider our results in the context of early animal evolution, and the role of POU5 genes in maintaining stem cell pluripotency

Tissue-specific silencing of homoeologs in natural populations of the recent allopolyploid Tragopogon mirus

The definitive version is available at www3.interscience.wiley.com http://dx.doi.org/10.1111/j.1469-8137.2010.03205.

Coordinated functional divergence of genes after genome duplication in Arabidopsis thaliana

Gene and genome duplications have been rampant during the evolution of flowering plants. Unlike small-scale gene duplications, whole-genome duplications (WGDs) copy entire pathways or networks, and as such create the unique situation in which such duplicated pathways or networks could evolve novel functionality through the coordinated sub-or neofunctionalization of its constituent genes. Here, we describe a remarkable case of coordinated gene expression divergence following WGDs in Arabidopsis thaliana. We identified a set of 92 homoeologous gene pairs that all show a similar pattern of tissue-specific gene expression divergence following WGD, with one homoeolog showing predominant expression in aerial tissues and the other homoeolog showing biased expression in tip-growth tissues. We provide evidence that this pattern of gene expression divergence seems to involve genes with a role in cell polarity and that likely function in the maintenance of cell wall integrity. Following WGD, many of these duplicated genes evolved separate functions through subfunctionalization in growth/development and stress response. Uncoupling these processes through genome duplications likely provided important adaptations with respect to growth and morphogenesis and defense against biotic and abiotic stress

Characterization of Expression of the KCNE Gene Family in Zebrafish, Danio rerio

The KCNE gene family codes for five transmembrane accessory proteins, minK related peptides or Mirps, involved in the modification of voltage-gated potassium (Kv) channels, K+ selective pores vital in the regulation of membrane potential and repolarization in all organisms. In mammals, all five KCNE gene members are conserved and active in the heart. In the zebrafish Danio rerio, there are no apparent orthologs for KCNE2 or KCNE5, yet they contain Kv channels with homologous structure, function, and Mirp regulatory behavior to other organisms. Sequence analysis of wildtype zebrafish KCNE1, 3 and 4, and rtPCR on RNA from zebrafish tissues to assess adult expression led to the identification of the Mirps in zebrafish and a depiction of their expression patterns. Specifically, zebrafish were phylogenetically identified as homologs to KCNE1 and KCNE4 from other species and KCNE1 and KCNE3 cDNA showed expression in wildtype adult zebrafish heart tissue, implicating that MinK, Mirp2, and Mirp3 play active roles in the regulation of voltage-gated potassium channels in zebrafish, Danio rerio

Comparison of hom(oe)ologous regions containing clusters of duplicated RGAs within Musa species and with rice

Understanding structure and evolution of genomic regions coding for proteins of agronomical interest is an important objective for crop improvement. We compare hom(oe)ologous regions within monocot genomes through BAC annotation. Here, we present putative orthologous and paralogous relationships of a highly duplicated Resistance Gene Analog (RGA) locus within Musa species and between Musa and rice species. (Résumé d'auteur

Why highly expressed proteins evolve slowly

Much recent work has explored molecular and population-genetic constraints on the rate of protein sequence evolution. The best predictor of evolutionary rate is expression level, for reasons which have remained unexplained. Here, we hypothesize that selection to reduce the burden of protein misfolding will favor protein sequences with increased robustness to translational missense errors. Pressure for translational robustness increases with expression level and constrains sequence evolution. Using several sequenced yeast genomes, global expression and protein abundance data, and sets of paralogs traceable to an ancient whole-genome duplication in yeast, we rule out several confounding effects and show that expression level explains roughly half the variation in Saccharomyces cerevisiae protein evolutionary rates. We examine causes for expression's dominant role and find that genome-wide tests favor the translational robustness explanation over existing hypotheses that invoke constraints on function or translational efficiency. Our results suggest that proteins evolve at rates largely unrelated to their functions, and can explain why highly expressed proteins evolve slowly across the tree of life.Comment: 40 pages, 3 figures, with supporting informatio

Gene Duplicability-Connectivity-Complexity across Organisms and a Neutral Evolutionary Explanation

Gene duplication has long been acknowledged by biologists as a major evolutionary force shaping genomic architectures and characteristics across the Tree of Life. Major research has been conducting on elucidating the fate of duplicated genes in a variety of organisms, as well as factors that affect a geneﾒs duplicabilityﾖthat is, the tendency of certain genes to retain more duplicates than others. In particular, two studies have looked at the correlation between gene duplicability and its degree in a protein-protein interaction network in yeast, mouse, and human, and another has looked at the correlation between gene duplicability and its complexity (length, number of domains, etc.) in yeast. In this paper, we extend these studies to six species, and two trends emerge. There is an increase in the duplicability-connectivity correlation that agrees with the increase in the genome size as well as the phylogenetic relationship of the species. Further, the duplicabilitycomplexity correlation seems to be constant across the species. We argue that the observed correlations can be explained by neutral evolutionary forces acting on the genomic regions containing the genes. For the duplicability-connectivity correlation, we show through simulations that an increasing trend can be obtained by adjusting parameters to approximate genomic characteristics of the respective species. Our results call for more research into factors, adaptive and non-adaptive alike, that determine a geneﾒs duplicability

Diversification at Transcription Factor Binding Sites within a Species and the Implications for Environmental Adaptation

PublishedEvolution of new cellular functions can be achieved both by changes in protein coding sequences and by alteration of expression patterns. Variation of expression may lead to changes in cellular function with relatively little change in genomic sequence. We therefore hypothesize that one of the first signals of functional divergence should be evolution of transcription factor–binding sites (TFBSs). This adaptation should be detectable as substantial variation in the TFBSs of alleles. New data sets allow the first analyses of intraspecies variation from large number of whole-genome sequences. Using data from the Saccharomyces Genome Resequencing Project, we have analyzed variation in TFBSs. We find a large degree of variation both between these closely related strains and between pairs of duplicated genes. There is a correlation between changes in promoter regions and changes in coding sequences, indicating a coupling of changes in expression and function. We show that 1) the types genes with diverged promoters vary between strains from different environments and 2) that patterns of divergence in promoters consistent with positive selection are detectable in alleles between strains and on duplicate promoters. This variation is likely to reflect adaptation to each strain's natural environment. We conclude that, even within a species, we detect signs of selection acting on promoter regions that may act to alter expression patterns. These changes may indicate functional innovation in multiple genes and across the whole genome. Change in function could represent adaptation to the environment and be a precursor to speciation.This work was funded by Biotechnology and Biological Sciences Research Council grant BB/F007620/1