Metabolic excretion associated with nutrient–growth dysregulation promotes the rapid evolution of an overt metabolic defect

Abstract

In eukaryotes, conserved mechanisms ensure that cell growth is coordinated with nutrient availability. Overactive growth during nutrient limitation ("nutrient-growth dysregulation") can lead to rapid cell death. Here, we demonstrate that cells can adapt to nutrient-growth dysregulation by evolving major metabolic defects. Specifically, when yeast lysine-auxotrophic mutant lys − encountered lysine limitation, an evolutionarily novel stress, cells suffered nutrient-growth dysregulation. A subpopulation repeatedly evolved to lose the ability to synthesize organosulfurs (lys − orgS −). Organosulfurs, mainly reduced glutathione (GSH) and GSH conjugates, were released by lys − cells during lysine limitation when growth was dysregulated, but not during glucose limitation when growth was regulated. Limiting organosulfurs conferred a frequency-dependent fitness advantage to lys − orgS − by eliciting a proper slow growth program, including autophagy. Thus, nutrient-growth dysregulation is associated with rapid organosulfur release, which enables the selection of organosulfur auxotrophy to better tune cell growth to the metabolic environment. We speculate that evolutionarily novel stresses can trigger atypical release of certain metabolites, setting the stage for the evolution of new ecological interactions.

Pleiotropic mutations can rapidly evolve to directly benefit self and cooperative partner despite unfavorable conditions

“…We randomly isolated evolved L - H + colonies from CoSMO and subjected them to whole-genome sequencing. Nearly every sequenced clone harbored one or more of the following mutations: ecm21 , rsp5 , and duplication of chromosome 14 ( DISOMY14 ) ( Table 1 , top), consistent with our earlier studies ( Waite and Shou, 2012 ; Hart et al, 2019a ; Hart et al, 2019b ; Green et al, 2020 ). Mutations in RSP5 , an essential gene, mostly involved point mutations (e.g., rsp5 ( P772L )), while mutations in ECM21 mostly involved premature stop codons and frameshift mutations ( Table 1 , top; Figure 2—figure supplement 1 ).…”

“…For chemostat evolution of L - H + , device fabrication and setup are described in detail in Green et al, 2020 . Briefly, the device allowed the evolution of six independent cultures, each at an independent doubling time.…”

Adaptive evolution of nontransitive fitness in yeast

“…Frequency-dependent selection can be either negative, where rare genotypes are favored, or positive, where rare genotypes are disfavored. Of the two, negative frequency-dependent selection is more commonly observed in experimental evolution, arising, for example, from nutrient cross-feeding ( Helling et al, 1987 ; Turner et al, 1996 ; Spencer et al, 2008 ; Kinnersley et al, 2014 ; Plucain et al, 2014 ; Green et al, 2020 ) and spatial structuring ( Rainey and Travisano, 1998 ; Frenkel et al, 2015 ). Positive frequency-dependent selection, in contrast, is not typically observed in experimental evolution.…”

Acetate and glycerol are not uniquely suited for the evolution of cross-feeding in E. coli

“…Third, we cannot rule out that the consumption of acetate or glycerol might give an advantage to the consumer strain that derives from more than just their role as carbon sources. A precedent for this possibility exists [ 39 ]. When a population of yeast cells auxotrophic for lysine encountered lysine limitation, coexistence of the ancestral lysine auxotroph strain and a mutant organosulfur auxotroph repeatedly evolved.…”

“…The organosulfur auxotroph strain persisted in the population, because it consumed organosulfurs excreted by the ancestral strain. Organosulfur auxotrophy conferred an advantage to the mutant strain, because it recovered the proper nutrient-driven growth regulation that had been impaired in the ancestral strain [ 39 ]. Fourth, cross-feeding interactions may be transient.…”