Evolution of P2A and P5A ATPases:ancient gene duplications and the red algal connection to green plants revisited

In a search for slowly evolving nuclear genes that may cast light on the deep evolution of plants, we carried out phylogenetic analyses of two well-characterized subfamilies of P-type pumps (P2A and P5A ATPases) from representative branches of the eukaryotic tree of life. Both P-type ATPase genes were duplicated very early in eukaryotic evolution and before the divergence of the present eukaryotic supergroups. Synapomorphies identified in the sequences provide evidence that green plants and red algae are more distantly related than are green plants and eukaryotic supergroups in which secondary or tertiary plastids are common, such as several groups belonging to the clade that includes Stramenopiles, Alveolata, Rhizaria, Cryptophyta and Haptophyta (SAR). We propose that red algae branched off soon after the first photosynthesizing eukaryote had acquired a primary plastid, while in another lineage that led to SAR, the primary plastid was lost but, in some cases, regained as a secondary or tertiary plastid

Neofunctionalization of mitochondrial proteins and incorporation into signaling networks in plants

Because of their symbiotic origin, many mitochondrial proteins are well conserved across eukaryotic kingdoms. It is however less obvious how specific lineages have obtained novel nuclear-encoded mitochondrial proteins. Here, we report a case of mitochondrial neofunctionalization in plants. Phylogenetic analysis of genes containing the Domain of Unknown Function 295 (DUF295) revealed that the domain likely originated in Angiosperms. The C-terminal DUF295 domain is usually accompanied by an N-terminal F-box domain, involved in ubiquitin ligation via binding with ASK1/SKP1-type proteins. Due to gene duplication, the gene family has expanded rapidly, with 94 DUF295-related genes in Arabidopsis thaliana alone. Two DUF295 family subgroups have uniquely evolved and quickly expanded within Brassicaceae. One of these subgroups has completely lost the F-box, but instead obtained strongly predicted mitochondrial targeting peptides. We show that several representatives of this DUF295 Organellar group are effectively targeted to plant mitochondria and chloroplasts. Furthermore, many DUF295 Organellar genes are induced by mitochondrial dysfunction, whereas F-Box DUF295 genes are not. In agreement, several Brassicaceae-specific DUF295 Organellar genes were incorporated in the evolutionary much older ANAC017-dependent mitochondrial retrograde signaling pathway. Finally, a representative set of DUF295 T-DNA insertion mutants was created. No obvious aberrant phenotypes during normal growth and mitochondrial dysfunction were observed, most likely due to the large extent of gene duplication and redundancy. Overall, this study provides insight into how novel mitochondrial proteins can be created via “intercompartmental” gene duplication events. Moreover, our analysis shows that these newly evolved genes can then be specifically integrated into relevant, pre-existing coexpression networks

Poor Reproducibility of Allergic Rhinitis SNP Associations

10.1371/journal.pone.0053975PLoS ONE81

Recombination promotes canalization against deleterious mutations in sexual haploid organisms

Deleterious mutations are an unavoidable part of life. In sufficiently large populations, all such mutations are removed by natural selection, though always with a concomitant loss of population fitness equal to the mutation rate. A natural question to ask is then: What happens if at another locus a rare allele appears (selectively neutral in itself) that decreases, but does not abolish, the negative phenotypic effect of mutations at the first locus ? or, in other words, makes the organism more canalized against the mutational damage? In the long run this new allele will not affect the mean fitness of the population, since the mutation load will always equal the mutation rate, but will this modifying allele be favoured in some indirect way? The answer is yes, but it is interesting to note how recombination affects this process: With less linkage between the two loci, the easier it becomes for the modifying allele to spread. Thus, recombination promotes mutational canalization in sexual haploids, in a manner that is impossible in asexual haploids. This result is easy to derive but has been surprisingly overlooked, probably because the underlying question was originally discussed in diploids and then phrased in terms of "the evolution of dominance". The secondary selective forces involved are, however, easier to grasp in haploid organisms, where the process instead becomes a question of the "evolution of canalization". That the outlined secondary selective force may be of evolutionary importance is shown by studying a modifying allele that acts on the trait-output of many loci. The force of secondary selection favouring canalization does then depend on the sum of all the mutation rates involved, which gives the process a chance to become evolutionarily effective

Analysis on yeast short-term Crabtree effect and its origin.

The short-term Crabtree effect is defined as the immediate appearance of aerobic alcoholic fermentation upon a pulse of excess sugar to sugar-limited yeast cultures. In this paper we characterized ten different yeast species, having a clearly defined phylogenetic relationship. Yeast species were cultivated under glucose-limited conditions, and upon a glucose pulse we studied their general carbon metabolism. We generated an extensive collection of data on glucose and oxygen consumption, and ethanol and carbon dioxide generation. We conclude that Pichia, Debaryomyces, Eremothecium and Kluyveromyces marxianus yeasts did not exhibit any significant ethanol formation, while Kluyveromyces lactis behaved as an intermediate yeast, and Lachancea, Torulaspora, Vanderwaltozyma and Saccharomyces yeasts exhibited rapid ethanol accumulation. Based on our previous data set covering over forty yeast species for the presence of the long-term Crabtree effect and our present data, we can speculate that the origin of the short-term effect may coincide with the origin of the long-term Crabtree effect in the Saccharomycetales lineage, taking place approximately 150 million years ago. This article is protected by copyright. All rights reserved

Evolution of hordein gene organization in three Hordeum species.

The inheritance pattern of hordein, the seed storage protein in barley, has been studied in two wild Hordeum species, H. murinum and H. pusillum. Three different diploid populations of each species were crossed, and the F1 plants were self-pollinated. The seeds with an F2 genotype were studied by sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE). Several differences could be observed in the banding patterns of the parental populations. The analysis of recombinant banding patterns showed that in H. murinum there are at least four segregating loci, of which two code for B- and two for C-hordein. All the loci are linked on the same chromosome. In H. pusillum at least six segregating loci were found, of which three code for B and three for C-hordein. Five of the loci are linked, while the sixth showed independent segregation. The organization of the hordein genes differs not only between these two species but also between them and the different forms of H. vulgare, as well as with other species belonging to the tribe Triticeae. Extensive rearrangements must obviously have taken place among the members of the hordein gene family since the divergence of the species in the Hordeum genus. The possibility is discussed that the genes have been moved through transposition, a possible mechanism for the physical divergence of tandemly repeated sequences

Yeast "make-accumulate-consume" life strategy evolved as a multi-step process that predates the whole genome duplication.

When fruits ripen, microbial communities start a fierce competition for the freely available fruit sugars. Three yeast lineages, including baker's yeast Saccharomyces cerevisiae, have independently developed the metabolic activity to convert simple sugars into ethanol even under fully aerobic conditions. This fermentation capacity, named Crabtree effect, reduces the cell-biomass production but provides in nature a tool to out-compete other microorganisms. Here, we analyzed over forty Saccharomycetaceae yeasts, covering over 200 million years of the evolutionary history, for their carbon metabolism. The experiments were done under strictly controlled and uniform conditions, which has not been done before. We show that the origin of Crabtree effect in Saccharomycetaceae predates the whole genome duplication and became a settled metabolic trait after the split of the S. cerevisiae and Kluyveromyces lineages, and coincided with the origin of modern fruit bearing plants. Our results suggest that ethanol fermentation evolved progressively, involving several successive molecular events that have gradually remodeled the yeast carbon metabolism. While some of the final evolutionary events, like gene duplications of glucose transporters and glycolytic enzymes, have been deduced, the earliest molecular events initiating Crabtree effect are still to be determined