Is Mutation Random or Targeted?: No Evidence for Hypermutability in Snail Toxin Genes
Ever since Luria and Delbruck, the notion that mutation is random with respect to fitness has been foundational to modern biology. However, various studies have claimed striking exceptions to this rule. One influential case involves toxin-encoding genes in snails of the genus Conus, termed conotoxins, a large gene family that undergoes rapid diversification of their protein-coding sequences by positive selection. Previous reconstructions of the sequence evolution of conotoxin genes claimed striking patterns: (1) elevated synonymous change, interpreted as being due to targeted "hypermutation" in this region; (2) elevated tr...
Source: Molecular Biology and Evolution - September 15, 2016 Category: Molecular Biology Authors: Roy, S. W. Tags: Discoveries Source Type: research
On the Potential Origins of the High Stability of Reconstructed Ancestral Proteins
Ancestral reconstruction provides instrumental insights regarding the biochemical and biophysical characteristics of past proteins. A striking observation relates to the remarkably high thermostability of reconstructed ancestors. The latter has been linked to high environmental temperatures in the Precambrian era, the era relating to most reconstructed proteins. We found that inferred ancestors of the serum paraoxonase (PON) enzyme family, including the mammalian ancestor, exhibit dramatically increased thermostabilities compared with the extant, human enzyme (up to 30 °C higher melting temperature). However, the envir...
Source: Molecular Biology and Evolution - September 15, 2016 Category: Molecular Biology Authors: Trudeau, D. L., Kaltenbach, M., Tawfik, D. S. Tags: Discoveries Source Type: research
lolal Is an Evolutionarily New Epigenetic Regulator of dpp Transcription during Dorsal-Ventral Axis Formation
Secreted ligands in the Dpp/BMP family drive dorsal–ventral (D/V) axis formation in all Bilaterian species. However, maternal factors regulating Dpp/BMP transcription in this process are largely unknown. We identified the BTB domain protein longitudinals lacking-like (lolal) as a modifier of decapentaplegic (dpp) mutations. We show that Lolal is evolutionarily related to the Trithorax group of chromatin regulators and that lolal interacts genetically with the epigenetic factor Trithorax-like during Dpp D/V signaling. Maternally driven LolalHA is found in oocytes and translocates to zygotic nuclei prior to the point a...
Source: Molecular Biology and Evolution - September 15, 2016 Category: Molecular Biology Authors: Quijano, J. C., Wisotzkey, R. G., Tran, N. L., Huang, Y., Stinchfield, M. J., Haerry, T. E., Shimmi, O., Newfeld, S. J. Tags: Discoveries Source Type: research
No Evidence That Nitrogen Limitation Influences the Elemental Composition of Isopod Transcriptomes and Proteomes
In this study, we used 13 surface and subterranean isopod species pairs that face strongly contrasted N limitations, either in terms of quantity or quality. We combined in situ nutrient quantification and transcriptome sequencing to test if N limitation selected for N-savings through changes in the expression and composition of the transcriptome and proteome. No evidence of N-savings was found in the total N-budget of transcriptomes or proteomes or in the average protein N-cost. Nevertheless, subterranean species evolving in N-depleted habitats displayed lower N-usage at their third codon positions. To test if this converg...
Source: Molecular Biology and Evolution - September 15, 2016 Category: Molecular Biology Authors: Francois, C. M., Duret, L., Simon, L., Mermillod-Blondin, F., Malard, F., Konecny-Dupre, L., Planel, R., Penel, S., Douady, C. J., Lefebure, T. Tags: Discoveries Source Type: research
High Similarity between Distantly Related Species of a Plant SINE Family Is Consistent with a Scenario of Vertical Transmission without Horizontal Transfers
Many transposable element (TE) families show surprisingly high levels of similarity between distantly related species. This high similarity, coupled with a "patchy" phylogenetic distribution, has often been attributed to frequent horizontal transfers of TEs between species, even though the mechanistic basis tends to be speculative. Here, we studied the evolution of the Au SINE (Short INterspersed Element) family, in which high similarity between distantly related plant species has been reported. We were able to identify several copies present in orthologous regions of various species, including species that diverged ~90 Ma...
Source: Molecular Biology and Evolution - September 15, 2016 Category: Molecular Biology Authors: Fawcett, J. A., Innan, H. Tags: Discoveries Source Type: research
Whole-Genome Sequencing of Native Sheep Provides Insights into Rapid Adaptations to Extreme Environments
This study offers novel insights into rapid genomic adaptations to extreme environments in sheep and other animals, and provides a valuable resource for future research on livestock breeding in response to climate change. (Source: Molecular Biology and Evolution)
Source: Molecular Biology and Evolution - September 15, 2016 Category: Molecular Biology Authors: Yang, J., Li, W.-R., Lv, F.-H., He, S.-G., Tian, S.-L., Peng, W.-F., Sun, Y.-W., Zhao, Y.-X., Tu, X.-L., Zhang, M., Xie, X.-L., Wang, Y.-T., Li, J.-Q., Liu, Y.-G., Shen, Z.-Q., Wang, F., Liu, G.-J., Lu, H.-F., Kantanen, J., Han, J.-L., Li, M.-H., Liu, M.- Tags: Discoveries Source Type: research
Genome-Wide Identification of Regulatory Sequences Undergoing Accelerated Evolution in the Human Genome
In this study, we used DNase I hypersensitive sites (DHSs) to annotate putative regulatory sequences in the human genome, and conducted a genome-wide analysis of the effects of accelerated evolution on regulatory sequences. Working under the assumption that local ancient repeat elements of DHSs are under neutral evolution, we discovered that ~0.44% of DHSs are under accelerated evolution (ace-DHSs). We found that ace-DHSs tend to be more active than background DHSs, and are strongly associated with epigenetic marks of active transcription. The target genes of ace-DHSs are significantly enriched in neuron-related functions,...
Source: Molecular Biology and Evolution - September 15, 2016 Category: Molecular Biology Authors: Dong, X., Wang, X., Zhang, F., Tian, W. Tags: Discoveries Source Type: research
Excess of Deleterious Mutations around HLA Genes Reveals Evolutionary Cost of Balancing Selection
Deleterious mutations are expected to evolve under negative selection and are usually purged from the population. However, deleterious alleles segregate in the human population and some disease-associated variants are maintained at considerable frequencies. Here, we test the hypothesis that balancing selection may counteract purifying selection in neighboring regions and thus maintain deleterious variants at higher frequency than expected from their detrimental fitness effect. We first show in realistic simulations that balancing selection reduces the density of polymorphic sites surrounding a locus under balancing selecti...
Source: Molecular Biology and Evolution - September 15, 2016 Category: Molecular Biology Authors: Lenz, T. L., Spirin, V., Jordan, D. M., Sunyaev, S. R. Tags: Discoveries Source Type: research
Genome-Wide Survey of Gut Fungi (Harpellales) Reveals the First Horizontally Transferred Ubiquitin Gene from a Mosquito Host
Harpellales, an early-diverging fungal lineage, is associated with the digestive tracts of aquatic arthropod hosts. Concurrent with the production and annotation of the first four Harpellales genomes, we discovered that Zancudomyces culisetae, one of the most widely distributed Harpellales species, encodes an insect-like polyubiquitin chain. Ubiquitin and ubiquitin-like proteins are universally involved in protein degradation and regulation of immune response in eukaryotic organisms. Phylogenetic analyses inferred that this polyubiquitin variant has a mosquito origin. In addition, its amino acid composition, animal-like se...
Source: Molecular Biology and Evolution - September 15, 2016 Category: Molecular Biology Authors: Wang, Y., White, M. M., Kvist, S., Moncalvo, J.-M. Tags: Discoveries Source Type: research
Functional and Evolutionary Characterization of a Gene Transfer Agents Multilocus "Genome"
Gene transfer agents (GTAs) are phage-like particles that can package and transfer a random piece of the producing cell’s genome, but are unable to transfer all the genes required for their own production. As such, GTAs represent an evolutionary conundrum: are they selfish genetic elements propagating through an unknown mechanism, defective viruses, or viral structures "repurposed" by cells for gene exchange, as their name implies? In Rhodobacter capsulatus, production of the R. capsulatus GTA (RcGTA) particles is associated with a cluster of genes resembling a small prophage. Utilizing transcriptomic, genetic and bi...
Source: Molecular Biology and Evolution - September 15, 2016 Category: Molecular Biology Authors: Hynes, A. P., Shakya, M., Mercer, R. G., Grüll, M. P., Bown, L., Davidson, F., Steffen, E., Matchem, H., Peach, M. E., Berger, T., Grebe, K., Zhaxybayeva, O., Lang, A. S. Tags: Discoveries Source Type: research
Links between Transcription, Environmental Adaptation and Gene Variability in Escherichia coli: Correlations between Gene Expression and Gene Variability Reflect Growth Efficiencies
Gene expression is known to be the principle factor explaining how fast genes evolve. Highly transcribed genes evolve slowly because any negative impact caused by a particular mutation is magnified by protein abundance. However, gene expression is a phenotype that depends both on the environment and on the strains or species. We studied this phenotypic plasticity by analyzing the transcriptome profiles of four Escherichia coli strains grown in three different culture media, and explored how expression variability was linked to gene allelic diversity. Genes whose expression changed according to the media and not to the stra...
Source: Molecular Biology and Evolution - September 15, 2016 Category: Molecular Biology Authors: Feugeas, J.-P., Tourret, J., Launay, A., Bouvet, O., Hoede, C., Denamur, E., Tenaillon, O. Tags: Discoveries Source Type: research
Functional Conservation and Divergence of daf-22 Paralogs in Pristionchus pacificus Dauer Development
Small-molecule signaling in nematode dauer formation has emerged as a major model to study chemical communication in development and evolution. Developmental arrest as nonfeeding and stress-resistant dauer larvae represents the major survival and dispersal strategy. Detailed studies in Caenorhabditis elegans and Pristionchus pacificus revealed that small-molecule communication changes rapidly in evolution resulting in extreme structural diversity of small-molecule compounds. In C. elegans, a blend of ascarosides constitutes the dauer pheromone, whereas the P. pacificus dauer pheromone includes additional paratosides and in...
Source: Molecular Biology and Evolution - September 15, 2016 Category: Molecular Biology Authors: Markov, G. V., Meyer, J. M., Panda, O., Artyukhin, A. B., Claassen, M., Witte, H., Schroeder, F. C., Sommer, R. J. Tags: Discoveries Source Type: research
Rice Varieties in Archaic East Asia: Reduction of Its Diversity from Past to Present Times
The Asian cultivated rice, Oryza sativa, is one of the most important crops feeding more than a third of global population. In spite of the studies for several decades, the origin and domestication history of rice varietal groups, japonica and indica, have not been fully unveiled. Genetic information of ancient rice remains is essential for direct and exclusive insight into the domestication history of rice. We performed ancient DNA analysis of 950- to 2,800-year-old rice remains excavated from Japan and Korea. We found the presence of both japonica- and indica-type varieties in the Yayoi period and the middle ages of Japa...
Source: Molecular Biology and Evolution - September 15, 2016 Category: Molecular Biology Authors: Kumagai, M., Kanehara, M., Shoda, S., Fujita, S., Onuki, S., Ueda, S., Wang, L. Tags: Fastrack Source Type: research
Visual Pigments, Ocular Filters and the Evolution of Snake Vision
Much of what is known about the molecular evolution of vertebrate vision comes from studies of mammals, birds and fish. Reptiles (especially snakes) have barely been sampled in previous studies despite their exceptional diversity of retinal photoreceptor complements. Here, we analyze opsin gene sequences and ocular media transmission for up to 69 species to investigate snake visual evolution. Most snakes express three visual opsin genes (rh1, sws1, and lws). These opsin genes (especially rh1 and sws1) have undergone much evolutionary change, including modifications of amino acid residues at sites of known importance for sp...
Source: Molecular Biology and Evolution - September 15, 2016 Category: Molecular Biology Authors: Simoes, B. F., Sampaio, F. L., Douglas, R. H., Kodandaramaiah, U., Casewell, N. R., Harrison, R. A., Hart, N. S., Partridge, J. C., Hunt, D. M., Gower, D. J. Tags: Fastrack Source Type: research
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Source: Molecular Biology and Evolution - September 15, 2016 Category: Molecular Biology Tags: Cover / standing material Source Type: research
