Divergent MLS1 Promoters Lie on a Fitness Plateau for Gene Expression
Qualitative patterns of gene activation and repression are often conserved despite an abundance of quantitative variation in expression levels within and between species. A major challenge to interpreting patterns of expression divergence is knowing which changes in gene expression affect fitness. To characterize the fitness effects of gene expression divergence, we placed orthologous promoters from eight yeast species upstream of malate synthase (MLS1) in Saccharomyces cerevisiae. As expected, we found these promoters varied in their expression level under activated and repressed conditions as well as in their dynamic res...
Source: Molecular Biology and Evolution - April 20, 2016 Category: Molecular Biology Authors: Bergen, A. C., Olsen, G. M., Fay, J. C. Tags: Discoveries Source Type: research
Indispensability of Horizontally Transferred Genes and Its Impact on Bacterial Genome Streamlining
Why are certain bacterial genomes so small and compact? The adaptive genome streamlining hypothesis posits that selection acts to reduce genome size because of the metabolic burden of replicating DNA. To reveal the impact of genome streamlining on cellular traits, we reduced the Escherichia coli genome by up to 20% by deleting regions which have been repeatedly subjects of horizontal transfer in nature. Unexpectedly, horizontally transferred genes not only confer utilization of specific nutrients and elevate tolerance to stresses, but also allow efficient usage of resources to build new cells, and hence influence fitness i...
Source: Molecular Biology and Evolution - April 20, 2016 Category: Molecular Biology Authors: Karcagi, I., Draskovits, G., Umenhoffer, K., Fekete, G., Kovacs, K., Mehi, O., Baliko, G., Szappanos, B., Györfy, Z., Feher, T., Bogos, B., Blattner, F. R., Pal, C., Posfai, G., Papp, B. Tags: Discoveries Source Type: research
Evaluating Phylostratigraphic Evidence for Widespread De Novo Gene Birth in Genome Evolution
The source of genetic novelty is an area of wide interest and intense investigation. Although gene duplication is conventionally thought to dominate the production of new genes, this view was recently challenged by a proposal of widespread de novo gene origination in eukaryotic evolution. Specifically, distributions of various gene properties such as coding sequence length, expression level, codon usage, and probability of being subject to purifying selection among groups of genes with different estimated ages were reported to support a model in which new protein-coding proto-genes arise from noncoding DNA and gradually in...
Source: Molecular Biology and Evolution - April 20, 2016 Category: Molecular Biology Authors: Moyers, B. A., Zhang, J. Tags: Discoveries Source Type: research
Human Lineage-Specific Transcriptional Regulation through GA-Binding Protein Transcription Factor Alpha (GABPa)
A substantial fraction of phenotypic differences between closely related species are likely caused by differences in gene regulation. While this has already been postulated over 30 years ago, only few examples of evolutionary changes in gene regulation have been verified. Here, we identified and investigated binding sites of the transcription factor GA-binding protein alpha (GABPa) aiming to discover cis-regulatory adaptations on the human lineage. By performing chromatin immunoprecipitation-sequencing experiments in a human cell line, we found 11,619 putative GABPa binding sites. Through sequence comparisons of the human ...
Source: Molecular Biology and Evolution - April 20, 2016 Category: Molecular Biology Authors: Perdomo-Sabogal, A., Nowick, K., Piccini, I., Sudbrak, R., Lehrach, H., Yaspo, M.-L., Warnatz, H.-J., Querfurth, R. Tags: Discoveries Source Type: research
Proteins with Highly Evolvable Domain Architectures Are Nonessential but Highly Retained
The functions of proteins are usually determined by domains, and the sequential order in which domains are connected to make up a protein chain is known as the domain architecture. Here, we constructed evolutionary networks of protein domain architectures in species from three major life lineages (bacteria, fungi, and metazoans) by connecting any two architectures between which an evolutionary event could be inferred by a model that assumes maximum parsimony. We found that proteins with domain architectures with a higher level of evolvability, indicated by a greater number of connections in the evolutionary network, are pr...
Source: Molecular Biology and Evolution - April 20, 2016 Category: Molecular Biology Authors: Hsu, C.-H., Chiang, A. W. T., Hwang, M.-J., Liao, B.-Y. Tags: Discoveries Source Type: research
267 Spanish Exomes Reveal Population-Specific Differences in Disease-Related Genetic Variation
Recent results from large-scale genomic projects suggest that allele frequencies, which are highly relevant for medical purposes, differ considerably across different populations. The need for a detailed catalog of local variability motivated the whole-exome sequencing of 267 unrelated individuals, representative of the healthy Spanish population. Like in other studies, a considerable number of rare variants were found (almost one-third of the described variants). There were also relevant differences in allelic frequencies in polymorphic variants, including ~10,000 polymorphisms private to the Spanish population. The allel...
Source: Molecular Biology and Evolution - April 20, 2016 Category: Molecular Biology Authors: Dopazo, J., Amadoz, A., Bleda, M., Garcia-Alonso, L., Aleman, A., Garcia-Garcia, F., Rodriguez, J. A., Daub, J. T., Muntane, G., Rueda, A., Vela-Boza, A., Lopez-Domingo, F. J., Florido, J. P., Arce, P., Ruiz-Ferrer, M., Mendez-Vidal, C., Arnold, T. E., Sp Tags: Discoveries Source Type: research
Environmental Correlation Analysis for Genes Associated with Protection against Malaria
Genome-wide searches for loci involved in human resistance to malaria are currently being conducted on a large scale in Africa using case-control studies. Here, we explore the utility of an alternative approach—"environmental correlation analysis, ECA," which tests for clines in allele frequencies across a gradient of an environmental selection pressure—to identify genes that have historically protected against death from malaria. We collected genotype data from 12,425 newborns on 57 candidate malaria resistance loci and 9,756 single nucleotide polymorphisms (SNPs) selected at random from across the genome, and...
Source: Molecular Biology and Evolution - April 20, 2016 Category: Molecular Biology Authors: Mackinnon, M. J., Ndila, C., Uyoga, S., Macharia, A., Snow, R. W., Band, G., Rautanen, A., Rockett, K. A., Kwiatkowski, D. P., Williams, T. N. Tags: Discoveries Source Type: research
A Genetic Mechanism for Convergent Skin Lightening during Recent Human Evolution
Skin lightening among Eurasians is thought to have been a convergence occurring independently in Europe and East Asia as an adaptation to high latitude environments. Among Europeans, several genes responsible for such lightening have been found, but the information available for East Asians is much more limited. Here, a genome-wide comparison between dark-skinned Africans and Austro-Asiatic speaking aborigines and light-skinned northern Han Chinese identified the pigmentation gene OCA2, showing unusually deep allelic divergence between these groups. An amino acid substitution (His615Arg) of OCA2 prevalent in most East Asia...
Source: Molecular Biology and Evolution - April 20, 2016 Category: Molecular Biology Authors: Yang, Z., Zhong, H., Chen, J., Zhang, X., Zhang, H., Luo, X., Xu, S., Chen, H., Lu, D., Han, Y., Li, J., Fu, L., Qi, X., Peng, Y., Xiang, K., Lin, Q., Guo, Y., Li, M., Cao, X., Zhang, Y., Liao, S., Peng, Y., Zhang, L., Guo, X., Dong, S., Liang, F., Wang, Tags: Discoveries Source Type: research
Adaptive Genetic Robustness of Escherichia coli Metabolic Fluxes
Genetic robustness refers to phenotypic invariance in the face of mutation and is a common characteristic of life, but its evolutionary origin is highly controversial. Genetic robustness could be an intrinsic property of biological systems, a result of direct natural selection, or a byproduct of selection for environmental robustness. To differentiate among these hypotheses, we analyze the metabolic network of Escherichia coli and comparable functional random networks. Treating the flux of each reaction as a trait and computationally predicting trait values upon mutations or environmental shifts, we discover that 1) geneti...
Source: Molecular Biology and Evolution - April 20, 2016 Category: Molecular Biology Authors: Ho, W.-C., Zhang, J. Tags: Discoveries Source Type: research
Post-embryonic Hourglass Patterns Mark Ontogenetic Transitions in Plant Development
The historic developmental hourglass concept depicts the convergence of animal embryos to a common form during the phylotypic period. Recently, it has been shown that a transcriptomic hourglass is associated with this morphological pattern, consistent with the idea of underlying selective constraints due to intense molecular interactions during body plan establishment. Although plants do not exhibit a morphological hourglass during embryogenesis, a transcriptomic hourglass has nevertheless been identified in the model plant Arabidopsis thaliana. Here, we investigated whether plant hourglass patterns are also found postembr...
Source: Molecular Biology and Evolution - April 20, 2016 Category: Molecular Biology Authors: Drost, H.-G., Bellstädt, J., O'Maoileidigh, D. S., Silva, A. T., Gabel, A., Weinholdt, C., Ryan, P. T., Dekkers, B. J. W., Bentsink, L., Hilhorst, H. W. M., Ligterink, W., Wellmer, F., Grosse, I., Quint, M. Tags: Fast Track Source Type: research
The Diversity and Molecular Evolution of B-Cell Receptors during Infection
B-cell receptors (BCRs) are membrane-bound immunoglobulins that recognize and bind foreign proteins (antigens). BCRs are formed through random somatic changes of germline DNA, creating a vast repertoire of unique sequences that enable individuals to recognize a diverse range of antigens. After encountering antigen for the first time, BCRs undergo a process of affinity maturation, whereby cycles of rapid somatic mutation and selection lead to improved antigen binding. This constitutes an accelerated evolutionary process that takes place over days or weeks. Next-generation sequencing of the gene regions that determine BCR bi...
Source: Molecular Biology and Evolution - April 20, 2016 Category: Molecular Biology Authors: Hoehn, K. B., Fowler, A., Lunter, G., Pybus, O. G. Tags: Fast Track Source Type: research
Contrasting Frequencies and Effects of cis- and trans-Regulatory Mutations Affecting Gene Expression
Heritable differences in gene expression are caused by mutations in DNA sequences encoding cis-regulatory elements and trans-regulatory factors. These two classes of regulatory change differ in their relative contributions to expression differences in natural populations because of the combined effects of mutation and natural selection. Here, we investigate how new mutations create the regulatory variation upon which natural selection acts by quantifying the frequencies and effects of hundreds of new cis- and trans-acting mutations altering activity of the TDH3 promoter in the yeast Saccharomyces cerevisiae in the absence ...
Source: Molecular Biology and Evolution - April 20, 2016 Category: Molecular Biology Authors: Metzger, B. P. H., Duveau, F., Yuan, D. C., Tryban, S., Yang, B., Wittkopp, P. J. Tags: Fast Track Source Type: research
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Source: Molecular Biology and Evolution - April 20, 2016 Category: Molecular Biology Tags: Cover / standing material Source Type: research
