Disentangling strictly self-serving mutations from win-win mutations in a mutualistic microbial community
- Fred Hutchinson Cancer Research Center, United States
Figures
Figure 1 with 1 supplement
Mutation types predicted to be favored during the evolution of a mutualistic community.
(A) Direct fitness effects. To define direct effects, we use a framework similar to Chapter 10 of Peters et al. (2017). For simplicity, consider a commensal community where population A benefits …
Figure 1—figure supplement 1
Lysine overproduction incurs a fitness cost.
Exponentially-growing isogenic strain pairs were competed in triplicate cocultures (circle, square, and triangle) at 30°C in minimal SD medium with adenine supplemented in excess (108.6 μM) when …
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Figure 1—figure supplement 1—source data 1
Data plotted in Figure 1—figure supplement 1.
- https://doi.org/10.7554/eLife.44812.005
Figure 2 with 2 supplements
DISOMY14 improves L-H+ growth rate under lysine limitation via duplication of the high-affinity lysine permease LYP1.
Exponentially-growing cells were washed free of lysine, starved in minimal medium SD for 3~5 hrs to deplete vacuolar lysine storage, and incubated in microtiter wells containing SD supplemented with …
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Figure 2—source data 1
Data plotted in Figure 2.
- https://doi.org/10.7554/eLife.44812.009
Figure 2—figure supplement 1
Micro-colony assay distinguishes ancestral from evolved L-H+ clones.
An ancestral clone (left) and two evolved L-H+ clones (center and right) were plated on SD plates supplemented with 1.5 µM lysine. Ancestral cells (WY1335, left) failed to divide (arrows). Cells …
Figure 2—figure supplement 2
Whole genome sequencing Nextera V2.
Schematic for whole genome sequencing using Nextera V2. Sequences for primers can be found in Supplementary file 4. The cyan and orange regions right next to gDNA are added by the transposase during …
Figure 3 with 5 supplements
Chromosome truncation reveals the genomic region responsible for increased hypoxanthine release rate.
(A) Chromosome truncation scheme. Recombination occurs between a chromosome and a truncation cassette containing a homology region, a drug resistance marker, and a telomere (Materials and methods, …
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Figure 3—source data 1
Data plotted in Figure 3.
- https://doi.org/10.7554/eLife.44812.018
Figure 3—figure supplement 1
Starvation batch culture release assay.
This figure is adapted from Figure 5 of Hart et al. (2019a) (original figure published under a CC-BY 4.0 license, https://creativecommons.org/licenses/by/4.0/). (A) Hypoxanthine release during …
Figure 3—figure supplement 2
Evolved L-H+ clones with improved hypoxanthine release rates harbored Chromosome 14 duplication.
Our previous work has established that hypoxanthine is released by live L-H+ cells (Hart et al., 2019a), and that hypoxanthine release rate is relatively constant regardless of whether cells are …
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Figure 3—figure supplement 2—source data 1
Data plotted in Figure 3—figure supplement 2.
- https://doi.org/10.7554/eLife.44812.013
Figure 3—figure supplement 3
Increased hypoxanthine release rate segregates with DISOMY14.
We crossed evolved clones JR30 (WY1593; black) and 38RL1 (WY1584; black) containing DISOMY14 with an ancestral strain containing one copy of chromosome 14. When we dissected tetrads (four …
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Figure 3—figure supplement 3—source data 2
Data plotted in Figure 3—figure supplement 3.
- https://doi.org/10.7554/eLife.44812.015
Figure 3—figure supplement 4
RADseq.
Schematic for RADseq using TruSeq. For detailed information, see Materials and methods ‘RADseq’. Sequences for primers can be found in Supplementary file 5.
Figure 3—figure supplement 5
Bioassay.
This figure is adapted from S3 Fig of Hart et al. (2019a) (original figure published under a CC-BY 4.0 license, https://creativecommons.org/licenses/by/4.0/). The final turbidity of an ade8- …
Figure 4 with 3 supplements
Despite increased release rate per cell, DISOMY14 is not partner-serving.
(A) WHI3 duplication is responsible for increased hypoxanthine release rate per cell. Introducing an extra copy of WHI3 into the ancestral background (WY2357 ~2359) increased hypoxanthine release …
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Figure 4—source data 1
Data plotted in Figure 4.
- https://doi.org/10.7554/eLife.44812.023
Figure 4—figure supplement 1
WHI3 duplication increases cell size and lysine utilization per birth.
Introducing an extra copy of WHI3 into the ancestral background (WY2357 ~2359) increased cell size and lysine utilization per birth. Deleting the duplicated WHI3 from DISOMY14 (WY2350 ~2352) …
Figure 4—figure supplement 2
In chemostats, DISOMY14 and ancestor share identical exchange ratio.
(A) Chemostat population dynamics. Ancestor (WY1335, magenta) or DISOMY14 (WY2349, blue) L-H+ cells were grown in separate, lysine-limited chemostats (Materials and methods, ‘Chemostat’). Live and …
Figure 4—figure supplement 3
CoSMO growth dynamics.
(A) Exponential community growth lasting to 108 total cells. (B) Examples of CoSMO dynamics consisting of ancestral or DISOMY14 L-H+. The duration of the lag phase can vary with the area of the …
Figure 5
Schematic illustration of partner-serving mutations.
(A) Transient interaction. At the initial stage of an interaction, DISOMY14 with an increased release rate per cell (2x thick purple arrow) is more partner-serving than the ancestor (1x thick purple …
Additional files
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Supplementary file 1
Foresight, hindsight, insight, and the blur in-between.
- https://doi.org/10.7554/eLife.44812.025
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Supplementary file 2
Strain table.
- https://doi.org/10.7554/eLife.44812.026
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Supplementary file 3
Mutations in evolved L-H+.
- https://doi.org/10.7554/eLife.44812.027
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Supplementary file 4
Whole genome sequencing primer sequences.
- https://doi.org/10.7554/eLife.44812.028
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Supplementary file 5
RADseq primer sequences.
- https://doi.org/10.7554/eLife.44812.029
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Transparent reporting form
- https://doi.org/10.7554/eLife.44812.030
