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Evolution at two levels of gene expression in yeast  [PDF]
Carlo G. Artieri,Hunter B. Fraser
Quantitative Biology , 2013,
Abstract: Despite the greater functional importance of protein levels, our knowledge of gene expression evolution is based almost entirely on studies of mRNA levels. In contrast, our understanding of how translational regulation evolves has lagged far behind. Here we have applied ribosome profiling - which measures both global mRNA levels and their translation rates - to two species of Saccharomyces yeast and their interspecific hybrid in order to assess the relative contributions of changes in mRNA abundance and translation to regulatory evolution. We report that both cis and trans-acting regulatory divergence in translation are abundant, affecting at least 35% of genes. The majority of translational divergence acts to buffer changes in mRNA abundance, suggesting a widespread role for stabilizing selection acting across regulatory levels. Nevertheless, we observe evidence of lineage-specific selection acting on a number of yeast functional modules, including instances of reinforcing selection acting at both levels of regulation. Finally, we also uncover multiple instances of stop-codon readthrough that are conserved between species. Our analysis reveals the under-appreciated complexity of post-transcriptional regulatory divergence and indicates that partitioning the search for the locus of selection into the binary categories of 'coding' vs. 'regulatory' may overlook a significant source of selection, acting at multiple regulatory levels along the path from genotype to phenotype.
Rates of evolution in stress-related genes are associated with habitat preference in two Cardamine lineages
Lino Ometto, Mingai Li, Luisa Bresadola, Claudio Varotto
BMC Evolutionary Biology , 2012, DOI: 10.1186/1471-2148-12-7
Abstract: High-throughput sequencing was used to obtain gene sequences from C. resedifolia and C. impatiens. Using the available A. thaliana gene sequences and annotation, we identified nearly 3,000 triplets of putative orthologues, including genes involved in cold response, photosynthesis or in general stress responses. By comparing estimated rates of molecular substitution, codon usage, and gene expression in these species with those of Arabidopsis, we were able to evaluate the role of positive and relaxed selection in driving the evolution of Cardamine genes. Our analyses revealed a statistically significant higher rate of molecular substitution in C. resedifolia than in C. impatiens, compatible with more efficient positive selection in the former. Conversely, the genome-wide level of selective pressure is compatible with more relaxed selection in C. impatiens. Moreover, levels of selective pressure were heterogeneous between functional classes and between species, with cold responsive genes evolving particularly fast in C. resedifolia, but not in C. impatiens.Overall, our comparative genomic analyses revealed that differences in effective population size might contribute to the differences in the rate of protein evolution and in the levels of selective pressure between the C. impatiens and C. resedifolia lineages. The within-species analyses also revealed evolutionary patterns associated with habitat preference of two Cardamine species. We conclude that the selective pressures associated with the habitats typical of C. resedifolia may have caused the rapid evolution of genes involved in cold response.Organisms adapt to different habitats through natural selection, which favors the fixation of alleles that increase the fitness of the individual that bears them. However, it is quite difficult to identify the locus/loci targeted by selection. One reason is that the number of loci involved in a particular adaptation and their phenotypic effects vary depending on the genetic a
Chromosomal Redistribution of Male-Biased Genes in Mammalian Evolution with Two Bursts of Gene Gain on the X Chromosome  [PDF]
Yong E. Zhang,Maria D. Vibranovski,Patrick Landback,Gabriel A. B. Marais,Manyuan Long
PLOS Biology , 2012, DOI: 10.1371/journal.pbio.1000494
Abstract: Mammalian X chromosomes evolved under various mechanisms including sexual antagonism, the faster-X process, and meiotic sex chromosome inactivation (MSCI). These forces may contribute to nonrandom chromosomal distribution of sex-biased genes. In order to understand the evolution of gene content on the X chromosome and autosome under these forces, we dated human and mouse protein-coding genes and miRNA genes on the vertebrate phylogenetic tree. We found that the X chromosome recently acquired a burst of young male-biased genes, which is consistent with fixation of recessive male-beneficial alleles by sexual antagonism. For genes originating earlier, however, this pattern diminishes and finally reverses with an overrepresentation of the oldest male-biased genes on autosomes. MSCI contributes to this dynamic since it silences X-linked old genes but not X-linked young genes. This demasculinization process seems to be associated with feminization of the X chromosome with more X-linked old genes expressed in ovaries. Moreover, we detected another burst of gene originations after the split of eutherian mammals and opossum, and these genes were quickly incorporated into transcriptional networks of multiple tissues. Preexisting X-linked genes also show significantly higher protein-level evolution during this period compared to autosomal genes, suggesting positive selection accompanied the early evolution of mammalian X chromosomes. These two findings cast new light on the evolutionary history of the mammalian X chromosome in terms of gene gain, sequence, and expressional evolution.
Chromosomal Redistribution of Male-Biased Genes in Mammalian Evolution with Two Bursts of Gene Gain on the X Chromosome  [PDF]
Yong E. Zhang,Maria D. Vibranovski,Patrick Landback,Gabriel A. B. Marais,Manyuan Long
PLOS Biology , 2010, DOI: 10.1371/journal.pbio.1000494
Abstract: Mammalian X chromosomes evolved under various mechanisms including sexual antagonism, the faster-X process, and meiotic sex chromosome inactivation (MSCI). These forces may contribute to nonrandom chromosomal distribution of sex-biased genes. In order to understand the evolution of gene content on the X chromosome and autosome under these forces, we dated human and mouse protein-coding genes and miRNA genes on the vertebrate phylogenetic tree. We found that the X chromosome recently acquired a burst of young male-biased genes, which is consistent with fixation of recessive male-beneficial alleles by sexual antagonism. For genes originating earlier, however, this pattern diminishes and finally reverses with an overrepresentation of the oldest male-biased genes on autosomes. MSCI contributes to this dynamic since it silences X-linked old genes but not X-linked young genes. This demasculinization process seems to be associated with feminization of the X chromosome with more X-linked old genes expressed in ovaries. Moreover, we detected another burst of gene originations after the split of eutherian mammals and opossum, and these genes were quickly incorporated into transcriptional networks of multiple tissues. Preexisting X-linked genes also show significantly higher protein-level evolution during this period compared to autosomal genes, suggesting positive selection accompanied the early evolution of mammalian X chromosomes. These two findings cast new light on the evolutionary history of the mammalian X chromosome in terms of gene gain, sequence, and expressional evolution.
Molecular evolution of sex-biased genes in the Drosophila ananassae subgroup
Sonja Grath, John F Baines, John Parsch
BMC Evolutionary Biology , 2009, DOI: 10.1186/1471-2148-9-291
Abstract: Sex-biased expression is generally conserved between D. melanogaster and D. ananassae, with the majority of genes exhibiting the same bias in the two species. However, about one-third of the genes have either gained or lost sex-biased expression in one of the species and a small proportion of genes (~4%) have changed bias from one sex to the other. The male-biased genes of D. ananassae show evidence of positive selection acting at the protein level. However, the signal of adaptive protein evolution for male-biased genes is not as strong in D. ananassae as it is in D. melanogaster and is limited to genes with conserved male-biased expression in both species. Within D. ananassae, a significant signal of adaptive evolution is also detected for female-biased and unbiased genes.Our findings extend previous observations of widespread adaptive protein evolution to an independent Drosophila lineage, the D. ananassae subgroup. However, the rate of adaptive evolution is not greater for male-biased genes than for female-biased or unbiased genes, which suggests that there are differences in sex-biased gene evolution between the two lineages.Sex-biased genes, i.e. those that differ in expression level between males and females, may be subject to differing selective constraints depending on the sex in which they are expressed or they may experience conflicting selective pressures in males and females (reviewed in [1]). Previous studies of Drosophila melanogaster have shown that male-biased genes, especially those expressed in reproductive tissues, consistently exhibit high levels of adaptive protein evolution [2,3]. Genome-wide comparisons of the ratio of the nonsynonymous substitution rate to the synonymous substitution rate (dN/dS) also indicate that male-biased genes are more functionally divergent between closely-related Drosophila species and are less likely to have identifiable orthologs between distantly-related species than genes with female-biased or unbiased expression
Expression levels of candidate genes for intramuscular fat deposition in two Banna mini-pig inbred lines divergently selected for fatness traits
Zhao, Su-Mei;Li, Wei-Zhen;Pan, Hong-Bin;Huang, Ying;Yang, Ming-Hua;Wei, Hong-Jiang;Gao, Shi-Zheng;
Genetics and Molecular Biology , 2012, DOI: 10.1590/S1415-47572012005000079
Abstract: intramuscular fat (imf) content plays an important role in meat quality. many genes involved in lipid and energy metabolism were identified as candidate genes for imf deposition, since genetic polymorphisms within these genes were associated with imf content. however, there is less information on the expression levels of these genes in the muscle tissue. this study aimed at investigating the expression levels of sterol regulating element binding protein-1c (srebp-1c), diacylglycerol acyltransferase (dgat-1), heart-fatty acids binding protein (h-fabp), leptin receptor (lepr) and melanocortin 4 receptor (mc4r) genes and proteins in two divergent banna mini-pig inbred lines (bmil). a similar growth performance was found in both the fat and the lean bmil. the fat meat and imf content in the fat bmil were significantly higher than in the lean bmil, but the lean meat content was lower. the serum triacylglycerol (tag) and free fatty acid (ffa) contents were significantly higher in the fat than in the lean bmil. the expression levels of srebp-1c, dgat-1 and h-fabp genes and proteins in fat bmil were increased compared to the lean bmil. however, the expression levels of lepr and mc4r genes and proteins were lower.
Antioxidant Machinery Differs between Melanic and Light Nestlings of Two Polymorphic Raptors  [PDF]
Ismael Galván,Laura Gangoso,Juan M. Grande,Juan J. Negro,Airam Rodríguez,Jordi Figuerola,Carlos Alonso-Alvarez
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0013369
Abstract: Colour polymorphism results from the expression of multiallelic genes generating phenotypes with very distinctive colourations. Most colour polymorphisms are due to differences in the type or amount of melanins present in each morph, which also differ in several behavioural, morphometric and physiological attributes. Melanin-based colour morphs could also differ in the levels of glutathione (GSH), a key intracellular antioxidant, because of the role of this molecule in melanogenesis. As GSH inhibits the synthesis of eumelanin (i.e. the darkest melanin form), individuals of darker morphs are expected to have lower GSH levels than those of lighter morphs. We tested this prediction in nestlings of two polymorphic raptors, the booted eagle Hieraaetus pennatus and the Eleonora's falcon Falco eleonorae, both of which occur in two morphs differing in the extent of eumelanic plumage. As expected, melanic booted eagle nestlings had lower blood GSH levels than light morph eagle nestlings. In the Eleonora's falcon, however, melanic nestlings only had lower GSH levels after controlling for the levels of other antioxidants. We also found that melanic female eagle nestlings had higher levels of antioxidants other than GSH and were in better body condition than light female eagle nestlings. These findings suggest an adaptive response of melanic nestlings to compensate for reduced GSH levels. Nevertheless, these associations were not found in falcons, indicating species-specific particularities in antioxidant machinery. Our results are consistent with previous work revealing the importance of GSH on the expression of melanic characters that show continuous variation, and suggest that this pathway also applies to discrete colour morphs. We suggest that the need to maintain low GSH levels for eumelanogenesis in dark morph individuals may represent a physiological constraint that helps regulate the evolution and maintenance of polymorphisms.
Evidence of association between Nucleosome Occupancy and the Evolution of Transcription Factor Binding Sites in Yeast
Krishna BS Swamy, Wen-Yi Chu, Chun-Yi Wang, Huai-Kuang Tsai, Daryi Wang
BMC Evolutionary Biology , 2011, DOI: 10.1186/1471-2148-11-150
Abstract: We compared the transcription factor binding site frequency in nucleosome occupied regions and nucleosome depleted regions in promoters of old (orthologs among Saccharomycetaceae) and young (Saccharomyces specific) genes; and in duplicate gene pairs. We demonstrated that nucleosome occupied regions accommodate greater binding site variations than nucleosome depleted regions in young genes and in duplicate genes. This finding was confirmed by measuring the difference in evolutionary rates of binding sites in sensu stricto yeasts at nucleosome occupied regions and nucleosome depleted regions. The binding sites at nucleosome occupied regions exhibited a consistently higher evolution rate than those at nucleosome depleted regions, corroborating the difference in the selection constraints at the two regions. Finally, through site-directed mutagenesis experiment, we found that binding site gain or loss events at nucleosome depleted regions may cause more expression differences than those in nucleosome occupied regions.Our study indicates the existence of different selection constraint on binding sites at nucleosome occupied regions than at the nucleosome depleted regions. We found that the binding sites have a different rate of evolution at nucleosome occupied and depleted regions. Finally, using transcription factor binding site-directed mutagenesis experiment, we confirmed the difference in the impact of binding site changes on expression at these regions. Thus, our work demonstrates the importance of composite analysis of chromatin and transcriptional evolution.The chromatin of eukaryotic genomes is compacted into several levels. Nucleosomes, which form the lowest level of compaction, are made up of ~147 bp of DNA wrapped around a histone protein complex and interspersed by ~50 bp of exposed linker DNA. In recent years, the occupancy of nucleosome positions in yeasts has been investigated by using different approaches (such as tiling arrays and parallel sequencing), wh
Parallel Evolution and Horizontal Gene Transfer of the pst Operon in Firmicutes from Oligotrophic Environments  [PDF]
Alejandra Moreno-Letelier,Gabriela Olmedo,Luis E. Eguiarte,Leon Martinez-Castilla,Valeria Souza
International Journal of Evolutionary Biology , 2011, DOI: 10.4061/2011/781642
Abstract: The high affinity phosphate transport system (pst) is crucial for phosphate uptake in oligotrophic environments. Cuatro Cienegas Basin (CCB) has extremely low P levels and its endemic Bacillus are closely related to oligotrophic marine Firmicutes. Thus, we expected the pst operon of CCB to share the same evolutionary history and protein similarity to marine Firmicutes. Orthologs of the pst operon were searched in 55 genomes of Firmicutes and 13 outgroups. Phylogenetic reconstructions were performed for the pst operon and 14 concatenated housekeeping genes using maximum likelihood methods. Conserved domains and 3D structures of the phosphate-binding protein (PstS) were also analyzed. The pst operon of Firmicutes shows two highly divergent clades with no correlation to the type of habitat nor a phylogenetic congruence, suggesting horizontal gene transfer. Despite sequence divergence, the PstS protein had a similar 3D structure, which could be due to parallel evolution after horizontal gene transfer events. 1. Introduction Phosphorus is an essential nutrient for multiple processes such as the synthesis of DNA, RNA, ATP, and many other pathways involving phosphorylation [1]. However, it is not an abundant element on the planet and can only be obtained form organic detritus or from tectonics and volcanism [2, 3], so, its availability is a limiting factor for all life forms. As growth rate and primary productivity are highly dependent on phosphorus [4–6], bacteria have different mechanisms for the uptake and storage of phosphates to be able to cope with this limitation [1, 7–9]. Some of the genes involved in phosphorus metabolism belong to the pho regulon that is induced by phosphorus starvation by a two-component regulatory system in several bacteria such as Escherichia coli, Bacillus subtilis, and Cyanobacteria [8, 10–13]. The pho regulon is comprised of 20 or so genes that include phosphatases, phosphate transport systems, and other enzymes used to assimilate phosphorus form other sources such as phosphonates [8]. Even though the pho regulon is found in both Eubacteria and Archaea, the number and identity of the genes are highly variable and not always congruent with the 16S rRNA gene phylogeny of the organisms [11, 14]. It is also to be expected that the genes involved in phosphate uptake and metabolism would be under strong selection. Among the genes of the pho regulon, the high affinity phosphate transport system (pst) is thought to be responsible for phosphate uptake under nutrient stress [8, 10]. Pst is a typical ABC transport system encoded in 4 to 6
Evolution of trappin genes in mammals
Akira Kato, Alejandro P Rooney, Yutaka Furutani, Shigehisa Hirose
BMC Evolutionary Biology , 2010, DOI: 10.1186/1471-2148-10-31
Abstract: The database analyses revealed that: 1) duplicated trappin multigenes were found recently in the nine-banded armadillo; 2) duplicated two trappin genes had been found in the Afrotherian species (elephant, tenrec, and hyrax) since ancient days; 3) a single trappin-2 gene was found in various eutherians species; and 4) no typical trappin gene has been found in chicken, zebra finch, and opossum. Bayesian analysis estimated the date of the duplication of trappin genes in the Afrotheria, guinea pig, armadillo, cow, and pig to be 244, 35, 11, 13, and 3 million-years ago, respectively. The coding regions of trappin multigenes of almadillo, bovine, and pig evolved much faster than the noncoding exons, introns, and the flanking regions, showing that these genes have undergone accelerated evolution, and positive Darwinian selection was observed in pig-specific trappin paralogs.These results suggest that trappin is an eutherian-specific molecule and eutherian genomes have the potential to form trappin multigenes.Trappins are a family of small secretory proteins that possess an N-terminal transglutaminase-substrate (TGS) domain and a C-terminal whey acidic protein (WAP) domain [1]. The TGS domain consists of repeats of six semi-conserved amino acids, KGQDPV, that act as anchoring regions. In this case, the lysine or glutamine residues of these regions are cross-linked with extracellular-matrix proteins by the action of transglutaminases, which helps trappin molecules to become concentrated at the site of action [2-4]. In contrast, the WAP domain is a four-disulfide core region and is defined by eight conserved cysteine residues. The WAP domain of trappin shows anti-proteolytic [4-6] and antimicrobial [7-9] activities that allow it to act as an innate immune defense molecule. In fact, trappin-2 displays antibacterial activities against Gram-positive and Gram-negative bacteria [7-9]; it also has antifungal activity [9], and the antimicrobial activity is independent of its antipro
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