Horizontal Gene Transfer from Bacteria Has Enabled the Plant-Parasitic Nematode Globodera pallida to Feed on Host-Derived Sucrose
The evolution of plant-parasitic nematodes (PPN) is unusual in that these organisms have acquired a range of genes from bacteria via horizontal gene transfer (HGT). The proteins encoded by most of these genes are involved in metabolism of various components of the plant cell wall during invasion of the host. Recent genome sequencing projects for PPN have shown that Glycosyl Hydrolase Family 32 (GH32) sequences are present in several PPN species. These sequences are absent from almost all other animals. Here, we show that the GH32 sequences from an economically important cyst nematode species, Globodera pallida are function...
Source: Molecular Biology and Evolution - May 15, 2016 Category: Molecular Biology Authors: Danchin, E. G. J., Guzeeva, E. A., Mantelin, S., Berepiki, A., Jones, J. T. Tags: Discoveries Source Type: research
Combinatorial Genetic Modeling of pfcrt-Mediated Drug Resistance Evolution in Plasmodium falciparum
The emergence of drug resistance continuously threatens global control of infectious diseases, including malaria caused by the protozoan parasite Plasmodium falciparum. A critical parasite determinant is the P. falciparum chloroquine resistance transporter (PfCRT), the primary mediator of chloroquine (CQ) resistance (CQR), and a pleiotropic modulator of susceptibility to several first-line artemisinin-based combination therapy partner drugs. Aside from the validated CQR molecular marker K76T, P. falciparum parasites have acquired at least three additional pfcrt mutations, whose contributions to resistance and fitness have ...
Source: Molecular Biology and Evolution - May 15, 2016 Category: Molecular Biology Authors: Gabryszewski, S. J., Modchang, C., Musset, L., Chookajorn, T., Fidock, D. A. Tags: Discoveries Source Type: research
Large-Effect Beneficial Synonymous Mutations Mediate Rapid and Parallel Adaptation in a Bacterium
This study shows that synonymous mutations can be fixed through strong positive selection, but the mechanism for their benefit varies depending on the local sequence context. (Source: Molecular Biology and Evolution)
Source: Molecular Biology and Evolution - May 15, 2016 Category: Molecular Biology Authors: Agashe, D., Sane, M., Phalnikar, K., Diwan, G. D., Habibullah, A., Martinez-Gomez, N. C., Sahasrabuddhe, V., Polachek, W., Wang, J., Chubiz, L. M., Marx, C. J. Tags: Discoveries Source Type: research
Tracing the Archaeal Origins of Eukaryotic Membrane-Trafficking System Building Blocks
In contrast to prokaryotes, eukaryotic cells are characterized by a complex set of internal membrane-bound compartments. A subset of these, and the protein machineries that move material between them, define the membrane-trafficking system (MTS), the emergence of which represents a landmark in eukaryotic evolution. Unlike mitochondria and plastids, MTS organelles have autogenous origins. Much of the MTS machinery is composed of building blocks, including small GTPase, coiled-coil, beta-propeller + alpha-solenoid, and longin domains. Despite the identification of prokaryotic proteins containing these domains, only few repre...
Source: Molecular Biology and Evolution - May 15, 2016 Category: Molecular Biology Authors: Klinger, C. M., Spang, A., Dacks, J. B., Ettema, T. J. G. Tags: Discoveries Source Type: research
Life History Traits, Protein Evolution, and the Nearly Neutral Theory in Amniotes
We report a strong effect of species body mass, longevity, and age of sexual maturity on genome-wide patterns of polymorphism and divergence across the major groups of amniotes, in agreement with the nearly neutral theory. Our results indicate that the rate of protein evolution in amniotes is determined in the first place by the efficiency of purifying selection against deleterious mutations—and this is true of both radical and conservative amino acid changes. Interestingly, the among-species distribution of dN/dS in birds did not follow this general trend: dN/dS was not higher in large, long-lived than in small, sho...
Source: Molecular Biology and Evolution - May 15, 2016 Category: Molecular Biology Authors: Figuet, E., Nabholz, B., Bonneau, M., Mas Carrio, E., Nadachowska-Brzyska, K., Ellegren, H., Galtier, N. Tags: Discoveries Source Type: research
Expression Divergence Is Correlated with Sequence Evolution but Not Positive Selection in Conifers
The evolutionary and genomic determinants of sequence evolution in conifers are poorly understood, and previous studies have found only limited evidence for positive selection. Using RNAseq data, we compared gene expression profiles to patterns of divergence and polymorphism in 44 seedlings of lodgepole pine (Pinus contorta) and 39 seedlings of interior spruce (Picea glauca x engelmannii) to elucidate the evolutionary forces that shape their genomes and their plastic responses to abiotic stress. We found that rapidly diverging genes tend to have greater expression divergence, lower expression levels, reduced levels of syno...
Source: Molecular Biology and Evolution - May 15, 2016 Category: Molecular Biology Authors: Hodgins, K. A., Yeaman, S., Nurkowski, K. A., Rieseberg, L. H., Aitken, S. N. Tags: Discoveries Source Type: research
Evolutionary Dynamics of Floral Homeotic Transcription Factor Protein-Protein Interactions
Protein–protein interactions (PPIs) have widely acknowledged roles in the regulation of development, but few studies have addressed the timing and mechanism of shifting PPIs over evolutionary history. The B-class MADS-box transcription factors, PISTILLATA (PI) and APETALA3 (AP3) are key regulators of floral development. PI-like (PIL) and AP3-like (AP3L) proteins from a number of plants, including Arabidopsis thaliana (Arabidopsis) and the grass Zea mays (maize), bind DNA as obligate heterodimers. However, a PIL protein from the grass relative Joinvillea can bind DNA as a homodimer. To ascertain whether Joinvillea PIL...
Source: Molecular Biology and Evolution - May 15, 2016 Category: Molecular Biology Authors: Bartlett, M., Thompson, B., Brabazon, H., Del Gizzi, R., Zhang, T., Whipple, C. Tags: Discoveries Source Type: research
Decreased Transcription Factor Binding Levels Nearby Primate Pseudogenes Suggest Regulatory Degeneration
Characteristics of pseudogene degeneration at the coding level are well-known, such as a shift toward neutral rates of nonsynonymous substitutions and gain of frameshift mutations. In contrast, degeneration of pseudogene transcriptional regulation is not well understood. Here, we test two predictions of regulatory degeneration along a pseudogenized lineage: 1) Decreased transcription factor (TF) binding and 2) accelerated evolution in putative cis-regulatory regions.
We find evidence for decreased TF binding levels nearby two primate pseudogenes compared with functional liver genes. However, the majority of TF-bound sequen...
Source: Molecular Biology and Evolution - May 15, 2016 Category: Molecular Biology Authors: Douglas, G. M., Wilson, M. D., Moses, A. M. Tags: Discoveries Source Type: research
Compensating the Fitness Costs of Synonymous Mutations
Synonymous mutations do not change the sequence of the polypeptide but they may still influence fitness. We investigated in Salmonella enterica how four synonymous mutations in the rpsT gene (encoding ribosomal protein S20) reduce fitness (i.e., growth rate) and the mechanisms by which this cost can be genetically compensated. The reduced growth rates of the synonymous mutants were correlated with reduced levels of the rpsT transcript and S20 protein. In an adaptive evolution experiment, these fitness impairments could be compensated by mutations that either caused up-regulation of S20 through increased gene dosage (due to...
Source: Molecular Biology and Evolution - May 15, 2016 Category: Molecular Biology Authors: Knöppel, A., Näsvall, J., Andersson, D. I. Tags: Discoveries Source Type: research
Ginkgo and Welwitschia Mitogenomes Reveal Extreme Contrasts in Gymnosperm Mitochondrial Evolution
Mitochondrial genomes (mitogenomes) of flowering plants are well known for their extreme diversity in size, structure, gene content, and rates of sequence evolution and recombination. In contrast, little is known about mitogenomic diversity and evolution within gymnosperms. Only a single complete genome sequence is available, from the cycad Cycas taitungensis, while limited information is available for the one draft sequence, from Norway spruce (Picea abies). To examine mitogenomic evolution in gymnosperms, we generated complete genome sequences for the ginkgo tree (Ginkgo biloba) and a gnetophyte (Welwitschia mirabilis). ...
Source: Molecular Biology and Evolution - May 15, 2016 Category: Molecular Biology Authors: Guo, W., Grewe, F., Fan, W., Young, G. J., Knoop, V., Palmer, J. D., Mower, J. P. Tags: Discoveries Source Type: research
Recent Selection Changes in Human Genes under Long-Term Balancing Selection
Balancing selection is an important evolutionary force that maintains genetic and phenotypic diversity in populations. Most studies in humans have focused on long-standing balancing selection, which persists over long periods of time and is generally shared across populations. But balanced polymorphisms can also promote fast adaptation, especially when the environment changes. To better understand the role of previously balanced alleles in novel adaptations, we analyzed in detail four loci as case examples of this mechanism. These loci show hallmark signatures of long-term balancing selection in African populations, but no...
Source: Molecular Biology and Evolution - May 15, 2016 Category: Molecular Biology Authors: de Filippo, C., Key, F. M., Ghirotto, S., Benazzo, A., Meneu, J. R., Weihmann, A., NISC Comparative Sequence Program, Parra, G., Green, E. D., Andres, A. M. Tags: Discoveries Source Type: research
Mechanisms Underlying Adaptation to Life in Hydrogen Sulfide-Rich Environments
Hydrogen sulfide (H2S) is a potent toxicant interfering with oxidative phosphorylation in mitochondria and creating extreme environmental conditions in aquatic ecosystems. The mechanistic basis of adaptation to perpetual exposure to H2S remains poorly understood. We investigated evolutionarily independent lineages of livebearing fishes that have colonized and adapted to springs rich in H2S and compared their genome-wide gene expression patterns with closely related lineages from adjacent, nonsulfidic streams. Significant differences in gene expression were uncovered between all sulfidic and nonsulfidic population pairs. Va...
Source: Molecular Biology and Evolution - May 15, 2016 Category: Molecular Biology Authors: Kelley, J. L., Arias-Rodriguez, L., Patacsil Martin, D., Yee, M.-C., Bustamante, C. D., Tobler, M. Tags: Discoveries Source Type: research
Purifying Selection on Exonic Splice Enhancers in Intronless Genes
Exonic splice enhancers (ESEs) are short nucleotide motifs, enriched near exon ends, that enhance the recognition of the splice site and thus promote splicing. Are intronless genes under selection to avoid these motifs so as not to attract the splicing machinery to an mRNA that should not be spliced, thereby preventing the production of an aberrant transcript? Consistent with this possibility, we find that ESEs in putative recent retrocopies are at a higher density and evolving faster than those in other intronless genes, suggesting that they are being lost. Moreover, intronless genes are less dense in putative ESEs than i...
Source: Molecular Biology and Evolution - May 15, 2016 Category: Molecular Biology Authors: Savisaar, R., Hurst, L. D. Tags: Discoveries Source Type: research
R2d2 Drives Selfish Sweeps in the House Mouse
A selective sweep is the result of strong positive selection driving newly occurring or standing genetic variants to fixation, and can dramatically alter the pattern and distribution of allelic diversity in a population. Population-level sequencing data have enabled discoveries of selective sweeps associated with genes involved in recent adaptations in many species. In contrast, much debate but little evidence addresses whether "selfish" genes are capable of fixation—thereby leaving signatures identical to classical selective sweeps—despite being neutral or deleterious to organismal fitness. We previously descr...
Source: Molecular Biology and Evolution - May 15, 2016 Category: Molecular Biology Authors: Didion, J. P., Morgan, A. P., Yadgary, L., Bell, T. A., McMullan, R. C., Ortiz de Solorzano, L., Britton-Davidian, J., Bult, C. J., Campbell, K. J., Castiglia, R., Ching, Y.-H., Chunco, A. J., Crowley, J. J., Chesler, E. J., Förster, D. W., French Tags: Fast Track Source Type: research
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Source: Molecular Biology and Evolution - May 15, 2016 Category: Molecular Biology Tags: Cover / standing material Source Type: research
