The Genomic Landscape of Compensatory Evolution

Adaptive evolution is generally assumed to progress through the accumulation of beneficial mutations. However, as deleterious mutations are common in natural populations, they generate a strong selection pressure to mitigate their detrimental effects through compensatory genetic changes. This process can potentially influence directions of adaptive evolution by enabling evolutionary routes that are otherwise inaccessible. Therefore, the extent to which compensatory mutations shape genomic evolution is of central importance. Here, we studied the capacity of the baker's yeast genome to compensate the complete loss of genes during evolution, and explored the long-term consequences of this process. We initiated laboratory evolutionary experiments with over 180 haploid baker's yeast genotypes, all of which initially displayed slow growth owing to the deletion of a single gene. Compensatory evolution following gene loss was rapid and pervasive: 68% of the genotypes reached near wild-type fitness through accumulation of adaptive mutations elsewhere in the genome. As compensatory mutations have associated fitness costs, genotypes with especially low fitnesses were more likely to be subjects of compensatory evolution. Genomic analysis revealed that as compensatory mutations were generally specific to the functional defect incurred, convergent evolution at the molecular level was extremely rare. Moreover, the majority of the gene expression changes due to gene deletion remained unrestored. Accordingly, compensatory evolution promoted genomic divergence of parallel evolving populations. However, these different evolutionary outcomes are not phenotypically equivalent, as they generated diverse growth phenotypes across environments. Taken together, these results indicate that gene loss initiates adaptive genomic changes that rapidly restores fitness, but this process has substantial pleiotropic effects on cellular physiology and evolvability upon environmental change. Our work also implies that gene content variation across species could be partly due to the action of compensatory evolution rather than the passive loss of genes

The genomic landscape of compensatory evolution.

Adaptive evolution is generally assumed to progress through the accumulation of beneficial mutations. However, as deleterious mutations are common in natural populations, they generate a strong selection pressure to mitigate their detrimental effects through compensatory genetic changes. This process can potentially influence directions of adaptive evolution by enabling evolutionary routes that are otherwise inaccessible. Therefore, the extent to which compensatory mutations shape genomic evolution is of central importance. Here, we studied the capacity of the baker's yeast genome to compensate the complete loss of genes during evolution, and explored the long-term consequences of this process. We initiated laboratory evolutionary experiments with over 180 haploid baker's yeast genotypes, all of which initially displayed slow growth owing to the deletion of a single gene. Compensatory evolution following gene loss was rapid and pervasive: 68% of the genotypes reached near wild-type fitness through accumulation of adaptive mutations elsewhere in the genome. As compensatory mutations have associated fitness costs, genotypes with especially low fitnesses were more likely to be subjects of compensatory evolution. Genomic analysis revealed that as compensatory mutations were generally specific to the functional defect incurred, convergent evolution at the molecular level was extremely rare. Moreover, the majority of the gene expression changes due to gene deletion remained unrestored. Accordingly, compensatory evolution promoted genomic divergence of parallel evolving populations. However, these different evolutionary outcomes are not phenotypically equivalent, as they generated diverse growth phenotypes across environments. Taken together, these results indicate that gene loss initiates adaptive genomic changes that rapidly restores fitness, but this process has substantial pleiotropic effects on cellular physiology and evolvability upon environmental change. Our work also implies that gene content variation across species could be partly due to the action of compensatory evolution rather than the passive loss of genes

Mutually opposing activity of PIN7 splicing isoforms is required for auxin-mediated tropic responses in Arabidopsis thaliana

Summary Advanced transcriptome sequencing has uncovered that the majority of eukaryotic genes undergo alternative splicing (AS). Nonetheless, little effort has been dedicated to investigating the functional relevance of particular splicing events, even those in the key developmental and hormonal regulators. Combining approaches of genetics, biochemistry and advanced confocal microscopy, we describe the impact of alternative splicing on the PIN7 gene in the plant model Arabidopsis thaliana. PIN7 encodes a polarly localized transporter for the phytohormone auxin and produces two evolutionary-conserved transcripts PIN7a and PIN7b. PIN7a and PIN7b, differing in a 4-amino acid motif, exhibit almost identical expression pattern and subcellular localization. We reveal that they closely associate and mutually influence their mobility within the plasma membrane. Phenotypic complementation tests indicate that the functional contribution of PIN7b per se is minor, but it markedly reduces the prominent PIN7a activity, which is required for correct seedling apical hook formation and auxin-mediated tropic responses. Our results establish alternative splicing of the PIN family as a conserved, functionally relevant mechanism, unveiling an additional regulatory level of auxin-mediated plant development.Advanced transcriptome sequencing has revealed that the majority of eukaryotic genes undergo alternative splicing (AS). Nonetheless, little effort has been dedicated to investigating the functional relevance of particular splicing events, even those in the key developmental and hormonal regulators. Combining approaches of genetics, biochemistry and advanced confocal microscopy, we describe the impact of alternative splicing on the PIN7 gene in the model plant Arabidopsis thaliana. PIN7 encodes a polarly localized transporter for the phytohormone auxin and produces two evolutionarily conserved transcripts, PIN7a and PIN7b. PIN7a and PIN7b, differing in a four amino acid stretch, exhibit almost identical expression patterns and subcellular localization. We reveal that they are closely associated and mutually influence each other's mobility within the plasma membrane. Phenotypic complementation tests indicate that the functional contribution of PIN7b per se is minor, but it markedly reduces the prominent PIN7a activity, which is required for correct seedling apical hook formation and auxin-mediated tropic responses. Our results establish alternative splicing of the PIN family as a conserved, functionally relevant mechanism, revealing an additional regulatory level of auxin-mediated plant development.Peer reviewe

Bacterial evolution of antibiotic hypersensitivity.

The evolution of resistance to a single antibiotic is frequently accompanied by increased resistance to multiple other antimicrobial agents. In sharp contrast, very little is known about the frequency and mechanisms underlying collateral sensitivity. In this case, genetic adaptation under antibiotic stress yields enhanced sensitivity to other antibiotics. Using large-scale laboratory evolutionary experiments with Escherichia coli, we demonstrate that collateral sensitivity occurs frequently during the evolution of antibiotic resistance. Specifically, populations adapted to aminoglycosides have an especially low fitness in the presence of several other antibiotics. Whole-genome sequencing of laboratory-evolved strains revealed multiple mechanisms underlying aminoglycoside resistance, including a reduction in the proton-motive force (PMF) across the inner membrane. We propose that as a side effect, these mutations diminish the activity of PMF-dependent major efflux pumps (including the AcrAB transporter), leading to hypersensitivity to several other antibiotics. More generally, our work offers an insight into the mechanisms that drive the evolution of negative trade-offs under antibiotic selection

The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis

Clathrin-mediated endocytosis in plants is an essential process but the underlying mechanisms are poorly understood, not least because of the extreme intracellular turgor pressure acting against the formation of endocytic vesicles. In contrast to other models, plant endocytosis is independent of actin, indicating a mechanistically distinct solution. Here, by using biochemical and advanced microscopy approaches, we show that the plant-specific TPLATE complex acts outside of endocytic vesicles as a mediator of membrane bending. Cells with disrupted TPLATE fail to generate spherical vesicles, and in vitro biophysical assays identified protein domains with membrane bending capability. These results redefine the role of the TPLATE complex as a key component of the evolutionarily distinct mechanism mediating membrane bending against high turgor pressure to drive endocytosis in plant cells. One Sentence Summary While plant CME is actin independent, we identify that the evolutionarily ancient octameric TPLATE complex mediates membrane bending against high turgor pressure in plant clathrin-mediated endocytosis

Genome-wide analysis captures the determinants of the antibiotic cross-resistance interaction network

Understanding how evolution of antimicrobial resistance increases resistance to other drugs is a challenge of profound importance. By combining experimental evolution and genome sequencing of 63 laboratory-evolved lines, we charted a map of cross-resistance interactions between antibiotics in Escherichia coli, and explored the driving evolutionary principles. Here, we show that (1) convergent molecular evolution is prevalent across antibiotic treatments, (2) resistance conferring mutations simultaneously enhance sensitivity to many other drugs and (3) 27% of the accumulated mutations generate proteins with compromised activities, suggesting that antibiotic adaptation can partly be achieved without gain of novel function. By using knowledge on antibiotic properties, we examined the determinants of cross-resistance and identified chemogenomic profile similarity between antibiotics as the strongest predictor. In contrast, cross-resistance between two antibiotics is independent of whether they show synergistic effects in combination. These results have important implications on the development of novel antimicrobial strategies

Parlagok és természetvédelmi célú gyepesítések értékelése Ásotthalom, Tiszaalpár és Kardoskút határában

Három alföldi területen (Alpár-Bokrosi ártéri öblözet, Ásotthalmi Láprétek TT és Kardoskúti puszta) vizsgáltuk a természetvédelmi kezelők által végrehajtott gyepesítési kísérleteket. Célunk az volt, hogy a spontán regenerációt, illetve a lucernával, valamint kommersz fűmaggal való bevetés hatásosságát természetvédelmi szempontból értékeljük. Öt lokalitásban, összesen 13 gyepesített- és 5 referencia-területen készítettünk cönológiai felvételeket. A felvételeket a természetességre utaló fajok száma és összborítása alapján értékeltük, figyelembe vettük a gyomok és a tájidegen fajok mennyiségét is. Megállapítottuk, hogy a spontán regeneráció már három év alatt a természeteshez közeli állapotot képes létrehozni, ha a talajvízszint a felszín közelében van. A kereskedelemben jelenleg kapható, intenzív gyepgazdálkodás céljából előállított gyepvetőmag keverékek nem segítették a regenerációt, és a lucerna vetése sem javasolható, mert évekig akadályozza a természetes gyepfajok betelepülését. Eredményeink szerint a spontán regenerációt kell előnyben részesíteni természetvédelmi célú gyepesítés esetén. Elméleti és gyakorlati szempontból egyaránt fontosnak tartjuk, hogy minél több természetvédelmi célú beavatkozás értékelését elvégezzük

Root adaptation to H2O2-induced oxidative stress by ARF-GEF BEN1- and cytoskeleton-mediated PIN2 trafficking

Abiotic stress poses constant challenges for plant survival and is a serious problem for global agricultural productivity. On a molecular level, stress conditions result in elevation of reactive oxygen species (ROS) production causing oxidative stress associated with oxidation of proteins and nucleic acids as well as impairment of membrane functions. Adaptation of root growth to ROS accumulation is facilitated through modification of auxin and cytokinin hormone homeostasis. Here, we report that in Arabidopsis root meristem, ROS-induced changes of auxin levels correspond to decreased abundance of PIN auxin efflux carriers at the plasma membrane (PM). Specifically, increase in H2O2 levels affects PIN2 endocytic recycling. We show that the PIN2 intracellular trafficking during adaptation to oxidative stress requires the function of the ADP-ribosylation factor (ARF)-guanine-nucleotide exchange factor (GEF) BEN1, an actin-associated regulator of the trafficking from the PM to early endosomes and, presumably, indirectly, trafficking to the vacuoles. We propose that H2O2 levels affect the actin dynamics thus modulating ARF-GEF-dependent trafficking of PIN2. This mechanism provides a way how root growth acclimates to stress and adapts to a changing environment

The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis

Clathrin-mediated endocytosis in plants is an essential process but the underlying mechanisms are poorly understood, not least because of the extreme intracellular turgor pressure acting against the formation of endocytic vesicles. In contrast to other models, plant endocytosis is independent of actin, indicating a mechanistically distinct solution. Here, by using biochemical and advanced microscopy approaches, we show that the plant-specific TPLATE complex acts outside of endocytic vesicles as a mediator of membrane bending. Cells with disrupted TPLATE fail to generate spherical vesicles, and in vitro biophysical assays identified protein domains with membrane bending capability. These results redefine the role of the TPLATE complex as a key component of the evolutionarily distinct mechanism mediating membrane bending against high turgor pressure to drive endocytosis in plant cells

Comparisons of the transcriptome profiles of wild-type, ancestor, and evolved lines.

<p>(A) Heatmaps of transcriptome profiles of deletion mutants <i>Δrpl43a</i>, <i>Δpop2</i>, <i>Δmdm34</i>, <i>Δrsc2</i>, <i>Δifm1</i>, <i>Δrpb9</i>, and <i>Δbud20</i> and their corresponding evolved lines. For each deletion mutant, the fold-changes (FC) are shown for the ancestor strain versus the wild type, the evolved strain versus the wild type and the evolved strain versus the ancestor strain (<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001935#pbio.1001935.s008" target="_blank">Table S3</a>). Color scales as indicated. Individual transcripts are depicted if they change significantly (FC>1.7, <i>p</i><0.05) at least once in one of these comparisons. (B) The Euclidean distances of microarray profiles of the evolved evolutionary line from its ancestor and from wild type (WT) were calculated and normalized to the ancestor–wild type distance for each genotype. The distances of the points in the figure are proportional to the calculated profile distances. For each genotype triplet, distances were calculated on the basis of those genes that are differentially expressed in at least one of the pairwise comparisons. For each deletion strain, the edges of the triangle represent Euclidean distances of log₂ mRNA expression fold-changes between the wild-type (WT), ancestor (anc), and evolved (evo) lines. To calculate these distances we used the average of four replicate expression measurements (two biological and two technical replicates). Circles around average values represent the Euclidean distance between the two biological replicates (calculated as the average based on the two technical replicates). For each genotype triplet, distances were calculated on the basis of those genes that are differentially expressed (FC>1.7, <i>p</i><0.05) in at least one of the pairwise comparisons (<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001935#pbio.1001935.s011" target="_blank">Table S6</a>). (C) Within the subset of genes that showed expression change upon gene deletion, the barplot shows the fraction of these genes that changed expression during evolution in the opposite direction (i.e., evolution towards restoration of wild-type expression level; see inset). With one major exception (lines disrupted in <i>mdm34</i>), only a small fraction of the expression changes were restored in the evolved lines (<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001935#pbio.1001935.s011" target="_blank">Table S6</a>). The threshold for expression change was 1.7-fold-change and <i>p</i><0.05, as in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001935#pbio.1001935-vanWageningen1" target="_blank">[62]</a>.</p