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- Garoff, Linnéa, et al.
(författare)
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Population Bottlenecks Strongly Influence the Evolutionary Trajectory to Fluoroquinolone Resistance in Escherichia coli
- 2020
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Ingår i: Molecular biology and evolution. - : Oxford University Press (OUP). - 0737-4038 .- 1537-1719. ; 37:6, s. 1637-1646
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Tidskriftsartikel (refereegranskat)abstract
- Experimental evolution is a powerful tool to study genetic trajectories to antibiotic resistance under selection. A confounding factor is that outcomes may be heavily influenced by the choice of experimental parameters. For practical purposes (minimizing culture volumes), most experimental evolution studies with bacteria use transmission bottleneck sizes of 5 x 10(6) cfu. We currently have a poor understanding of how the choice of transmission bottleneck size affects the accumulation of deleterious versus high-fitness mutations when resistance requires multiple mutations, and how this relates outcome to clinical resistance. We addressed this using experimental evolution of resistance to ciprofloxacin in Escherichia coli. Populations were passaged with three different transmission bottlenecks, including single cell (to maximize genetic drift) and bottlenecks spanning the reciprocal of the frequency of drug target mutations (10(8) and 10(10)). The 10(10) bottlenecks selected overwhelmingly mutations in drug target genes, and the resulting genotypes corresponded closely to those found in resistant clinical isolates. In contrast, both the 10(8) and single-cell bottlenecks selected mutations in three different gene classes: 1) drug targets, 2) efflux pump repressors, and 3) transcription-translation genes, including many mutations with low fitness. Accordingly, bottlenecks smaller than the average nucleotide substitution rate significantly altered the experimental outcome away from genotypes observed in resistant clinical isolates. These data could be applied in designing experimental evolution studies to increase their predictive power and to explore the interplay between different environmental conditions, where transmission bottlenecks might vary, and resulting evolutionary trajectories.
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| 2. |
- Pietsch, Franziska, et al.
(författare)
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Evolutionary Trajectories Dependent on Bottleneck Size and a New Class of Genes Selected During the Development of Ciprofloxacin Resistance in Escherichia coli
- 2018
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- The evolution of resistance to ciprofloxacin (CIP) in Escherichia coli is strongly associated with the accumulation of multiple chromosomal mutations. Mutations are selected in genes encoding subunits of the target enzymes, and genes encoding direct or indirect regulators of drug efflux. We asked whether and how transmission bottleneck size would affect the evolutionary trajectory of chromosomal mutation accumulation. Independent lineages of E. coli were selected for growth at increasing concentrations of ciprofloxacin up to and above the clinical resistance breakpoint. Evolution experiments were made with three different transmission bottlenecks: single cell, ≈ 3x108, and ≈ 3x1010 cfu. Whole genome sequencing was used to analyse selected clones and populations at different stages during evolution. Under all conditions mutations in gyrA were the first to be selected and to approach or reach fixation. Evolution with the largest population bottleneck selected combinations of mutations similar to those found in resistant clinical isolates (gyrA S83, D87, with parC S80). As predicted by population genetics theory, evolution with a single cell bottleneck resulted in a greater diversity of mutations. Mutations were selected in genes directly regulating drug efflux, and in novel genes involved in transcription and translation, at least some of which are known to indirectly affect drug efflux. Evolution with the intermediate bottleneck, ≈ 3x108, also selected for mutations in a wide variety of genes, similar to the profile associated with the single cell bottleneck. The data suggest that the order of chromosomal mutations accumulated under selection for resistance to ciprofloxacin is highly predictable but the precise evolutionary trajectories differ significantly as a function of transmission bottleneck size.
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| 3. |
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| 4. |
- Schwelm, Arne, et al.
(författare)
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The Plasmodiophora brassicae genome reveals insights in its life cycle and ancestry of chitin synthases
- 2015
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 5
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Tidskriftsartikel (refereegranskat)abstract
- Plasmodiophora brassicae causes clubroot, a major disease of Brassica oil and vegetable crops worldwide. P. brassicae is a Plasmodiophorid, obligate biotrophic protist in the eukaryotic kingdom of Rhizaria. Here we present the 25.5 Mb genome draft of P. brassicae, developmental stage-specific transcriptomes and a transcriptome of Spongospora subterranea, the Plasmodiophorid causing powdery scab on potato. Like other biotrophic pathogens both Plasmodiophorids are reduced in metabolic pathways. Phytohormones contribute to the gall phenotypes of infected roots. We report a protein (PbGH3) that can modify auxin and jasmonic acid. Plasmodiophorids contain chitin in cell walls of the resilient resting spores. If recognized, chitin can trigger defense responses in plants. Interestingly, chitin-related enzymes of Plasmodiophorids built specific families and the carbohydrate/chitin binding (CBM18) domain is enriched in the Plasmodiophorid secretome. Plasmodiophorids chitin synthases belong to two families, which were present before the split of the eukaryotic Stramenopiles/Alveolates/Rhizaria/Plantae and Metazoa/Fungi/Amoebozoa megagroups, suggesting chitin synthesis to be an ancient feature of eukaryotes. This exemplifies the importance of genomic data from unexplored eukaryotic groups, such as the Plasmodiophorids, to decipher evolutionary relationships and gene diversification of early eukaryotes.
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