Slow-growing cells within isogenic populations have increased RNA polymerase error rates and DNA damage

Abstract

Isogenic cells show a large degree of variability in growth rate, even when cultured in the same environment. Such cell-to-cell variability in growth can alter sensitivity to antibiotics, chemotherapy and environmental stress. To characterize transcriptional differences associated with this variability, we have developed a method—FitFlow—that enables the sorting of subpopulations by growth rate. The slow-growing subpopulation shows a transcriptional stress response, but, more surprisingly, these cells have reduced RNA polymerase fidelity and exhibit a DNA damage response. As DNA damage is often caused by oxidative stress, we test the addition of an antioxidant, and find that it reduces the size of the slow-growing population. More generally, we find a significantly altered transcriptome in the slow-growing subpopulation that only partially resembles that of cells growing slowly due to environmental and culture conditions. Slow-growing cells upregulate transposons and express more chromosomal, viral and plasmid-borne transcripts, and thus explore a larger genotypic—and so phenotypic — space.

Mitochondrial heterogeneity, metabolic scaling and cell death

“…For simulation details, see Supporting Information Section S3. proliferation rate of yeast is heritable, and that slow-growing cells have higher oxidative stress whose proliferation rate may be rescued with an anti-oxidant, suggesting a link to mitochondrial functionality [56]. Further studies are required to determine whether this is true for a larger class of systems, including mammalian cells.…”

“…The biological mechanism for the heritability of mitochondrial functionality was unclear from that study, although one may speculate that the inherited concentration of mitochondrial fusion proteins may be a feasible explanation for this. Indeed, recent evidence suggests that the proliferation rate of yeast is heritable, and that slow-growing cells have higher oxidative stress whose proliferation rate may be rescued with an anti-oxidant, suggesting a link to mitochondrial functionality [56]. Further studies are required to determine whether this is true for a larger class of systems, including mammalian cells.…”

Single-cell RNA-seq reveals intrinsic and extrinsic regulatory heterogeneity in yeast responding to stress

“…For example, some isogenic cells within cultures of Saccharomyces cerevisiae can survive extreme heat stress whereas most cells in the culture cannot (10). Stress-tolerant individuals may be in an altered state, since they often display transiently reduced growth and markers of the stress response (1,(10)(11)(12). But whether this state mimics that of stress-treated cells that have fully mounted a stress response or instead emerges from partial, stochastic events is unclear.…”

Stochasticity of cellular growth: sources, propagation and consequences

“…Recent work showed that such fluctuations can impact the mean population growth 49 , implying that these mechanistic parameters may be subject to evolutionary pressure. Cellular physiology could seize this degree of freedom and use it to shape noise to its benefit, for instance, as an evolutionary bet-hedging strategy [50][51][52] . The model could be put to use in in numero evolutionary experiments to test the specific benefits of noise architectures in different environments and retrace possible evolutionary paths.…”