Phenotypic heterogeneity follows a growth-viability tradeoff in response to amino acid identity

• Published in: Nature communications Vol. 15; no. 1; pp. 6515 - 16
• Main Authors: Shabestary, Kiyan, Klemm, Cinzia, Carling, Benedict, Marshall, James, Savigny, Juline, Storch, Marko, Ledesma-Amaro, Rodrigo
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 02.08.2024; Nature Publishing Group; Nature Portfolio
• Subjects: 14; 14/34; 14/35; 14/56; 45/91; 49/31; 631/1647/2017; 631/326/2565/855; 631/61/252/318; Adaptation; Amino acids; Amino Acids - metabolism; Biosensors; Cell differentiation; Fungi; Gene sequencing; Growth conditions; Heterogeneity; Humanities and Social Sciences; Life span; MAP kinase; Metabolic response; Metabolism; Microorganisms; multidisciplinary; Natural environment; Nitrogen; Nitrogen - metabolism; Nitrogen sources; Phenotype; Saccharomyces; Saccharomyces cerevisiae - genetics; Saccharomyces cerevisiae - growth & development; Saccharomyces cerevisiae - metabolism; Saccharomyces cerevisiae Proteins - genetics; Saccharomyces cerevisiae Proteins - metabolism; Science; Science (multidisciplinary); Single-Cell Analysis; Subpopulations; Viability
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-024-50602-8

In their natural environments, microorganisms mainly operate at suboptimal growth conditions with fluctuations in nutrient abundance. The resulting cellular adaptation is subject to conflicting tasks: growth or survival maximisation. Here, we study this adaptation by systematically measuring the impact of a nitrogen downshift to 24 nitrogen sources on cellular metabolism at the single-cell level. Saccharomyces lineages grown in rich media and exposed to a nitrogen downshift gradually differentiate to form two subpopulations of different cell sizes where one favours growth while the other favours viability with an extended chronological lifespan. This differentiation is asymmetrical with daughter cells representing the new differentiated state with increased viability. We characterise the metabolic response of the subpopulations using RNA sequencing, metabolic biosensors and a transcription factor-tagged GFP library coupled to high-throughput microscopy, imaging more than 800,000 cells. We find that the subpopulation with increased viability is associated with a dormant quiescent state displaying differences in MAPK signalling. Depending on the identity of the nitrogen source present, differentiation into the quiescent state can be actively maintained, attenuated, or aborted. These results establish amino acids as important signalling molecules for the formation of genetically identical subpopulations, involved in chronological lifespan and growth rate determination. Microbes frequently encounter suboptimal conditions. Here, Shabestary et al. show that phenotypic heterogeneity is an important feature of Saccharomyces species adaptation where amino acid identity serves as an environmental cue driving this adaptive process.