Pleiotropic mutations can rapidly evolve to directly benefit self and cooperative partner despite unfavorable conditions
- Fred Hutchinson Cancer Research Center, Division of Basic Sciences, United States
- University College London, Department of Genetics, Evolution and Environment, Centre for Life's Origins and Evolution (CLOE), United Kingdom
Figures
Figure 1
Win-win mutation in a nascent cooperative community.
(A) CoSMO (Cooperation that is Synthetic and Mutually Obligatory) consists of two non-mating cross-feeding yeast strains, each engineered to overproduce a metabolite required by the partner strain. …
Figure 2 with 2 supplements
Self-serving mutations stabilize the high affinity lysine permease Lyp1 on cell membrane and improve cell growth rates at low lysine.
(A) Recurrent mutations are self-serving. We measured growth rates of mutant and ancestral strains in minimal SD medium with various lysine concentrations, using a calibrated fluorescence microscopy …
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Figure 2—source data 1
Growth parameters of ancestral and mutant strains.
- https://cdn.elifesciences.org/articles/57838/elife-57838-fig2-data1-v2.xlsx
Figure 2—figure supplement 1
Functional domains and positions of mutations in Ecm21 and Rsp5 proteins.
Mutations and their locations are marked with respect to the functional domains of the proteins. Numbers indicate amino acid positions, except in non-coding regions. Domain structures are obtained …
Figure 2—figure supplement 2
ecm21Δ rapidly outcompetes ancestor in lysine-limited chemostats.
We competed ancestor (expressing the mCherry fluorescent protein) and ecm21Δ (expressing the blue fluorescent protein) in four independent lysine-limited chemostats (represented by different …
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Figure 2—figure supplement 2—source data 1
Population dynamics of strain competition.
- https://cdn.elifesciences.org/articles/57838/elife-57838-fig2-figsupp2-data1-v2.xlsx
Figure 3 with 1 supplement
ecm21Δ improves hypoxanthine release rate per lysine consumption.
(A) Hypoxanthine accumulates to a higher level in ecm21Δ chemostats than in ancestor chemostats. We cultured individual strains in lysine-limited chemostats (20 µM input lysine) at 6 hr doubling …
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Figure 3—source data 1
Dynamics and exchange ratios measured in chemostats.
- https://cdn.elifesciences.org/articles/57838/elife-57838-fig3-data1-v2.xlsx
Figure 3—figure supplement 1
Population dynamics in chemostats.
We cultured ancestor and mutant strains in lysine-limited chemostats (20 µM input lysine) at 6 hr doubling time (similar to Cooperation that is Synthetic and Mutually Obligatory [CoSMO] doubling …
Figure 4
ecm21Δ increases the growth rate of community and of partner.
To prevent rapid evolution, we grew CoSMO containing ancestral H-L+ and ancestral or ecm21Δ L-H+ in a spatially structured environment on agarose pads, and periodically measured the absolute …
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Figure 4—source data 1
Community growth dynamics.
- https://cdn.elifesciences.org/articles/57838/elife-57838-fig4-data1-v2.xlsx
Tables
Table 1
Mutations that repeatedly arose in independent lines.
Single-nucleotide polymorphisms (SNPs) and chromosomal duplications from Illumina re-sequencing of L-H+ from Cooperation that is Synthetic and Mutually Obligatory (CoSMO) communities (top) and …
| L-H+ | Line | Generation | ecm21 | rsp5 | Chromosome duplicated | Strain |
|---|---|---|---|---|---|---|
| CoSMO comm. | A1 | 24 | Glu316 -> Stop | – | 11, 14 | WY1588 |
| – | Pro772 -> Leu | 11 | WY1589 | |||
| 151 | – | Pro772 -> Leu | – | WY1590 | ||
| – | Pro772 -> Leu | 11, 14, 16 | WY1591 | |||
| B1 | 25 | Leu812->Stop | – | 14 | WY1584 | |
| 49 | – | Gly689 -> Cys | 14 | WY1585 | ||
| 76 | – | Gly689 -> Cys | – | WY1586 | ||
| Gly689 -> Cys | 14 | WY2467 | ||||
| – | Gly689 -> Cys | 14 | WY1587 | |||
| B3 | 14 | – | – | – | WY1592 | |
| – | – | 14 | WY1593 | |||
| 34 | Arg742 -> Stop | – | 14, 16 | WY1594 | ||
| Arg742 -> Stop | – | 14, 16 | WY1595 | |||
| 63 | Arg742 -> Stop | Arg742 -> His | 12, 14 | WY1596 | ||
| Lysine-limited chemostat mono-culture | 7.Line1 | 30 | Asp652 frameshift | 14 | WY1601 | |
| Glu216 -> Stop | 14 | WY1602 | ||||
| 7.Line2 | 30 | Pro886 -> Ser | 11, 14, 16 | WY1603 | ||
| 7.Line3 | 30 | Thr586 frameshift | 14 | WY1604 | ||
| Thr586 frameshift | 14 | WY1605 | ||||
| 11.Line1 | 19 | Glu688 -> Stop | 14, 16 | WY1606 | ||
| G(−281) ->A | – | WY1608 | ||||
| 11.Line2 | 19 | A(−304) -> G | – | WY1607 | ||
| 50 | Glu793 frameshift | 14 | WY1609 |
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Table 1—source data 1
Summary of mutations.
- https://cdn.elifesciences.org/articles/57838/elife-57838-table1-data1-v2.xlsx
Additional files
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Supplementary file 1
List of strains.
- https://cdn.elifesciences.org/articles/57838/elife-57838-supp1-v2.xlsx
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Transparent reporting form
- https://cdn.elifesciences.org/articles/57838/elife-57838-transrepform-v2.docx
