Resource plasticity-driven carbon-nitrogen budgeting enables specialization and division of labor in a clonal community.

Previously, we found that in glucose-limited Saccharomyces cerevisiae colonies, metabolic constraints drive cells into groups exhibiting gluconeogenic or glycolytic states. In that study, threshold amounts of trehalose - a limiting, produced carbon-resource, controls the emergence and self-organization of cells exhibiting the glycolytic state, serving as a carbon source that fuels glycolysis (Varahan et al., 2019). We now discover that the plasticity of use of a non-limiting resource, aspartate, controls both resource production and the emergence of heterogeneous cell states, based on differential metabolic budgeting. In gluconeogenic cells, aspartate is a carbon source for trehalose production, while in glycolytic cells using trehalose for carbon, aspartate is predominantly a nitrogen source for nucleotide synthesis. This metabolic plasticity of aspartate enables carbon-nitrogen budgeting, thereby driving the biochemical self-organization of distinct cell states. Through this organization, cells in each state exhibit true division of labor, providing growth/survival advantages for the whole community.

Metabolic constraints drive self-organization of specialized cell groups.

How phenotypically distinct states in isogenic cell populations appear and stably co-exist remains unresolved. We find that within a mature, clonal yeast colony developing in low glucose, cells arrange into metabolically disparate cell groups. Using this system, we model and experimentally identify metabolic constraints sufficient to drive such self-assembly. Beginning in a uniformly gluconeogenic state, cells exhibiting a contrary, high pentose phosphate pathway activity state, spontaneously appear and proliferate, in a spatially constrained manner. Gluconeogenic cells in the colony produce and provide a resource, which we identify as trehalose. Above threshold concentrations of external trehalose, cells switch to the new metabolic state and proliferate. A self-organized system establishes, where cells in this new state are sustained by trehalose consumption, which thereby restrains other cells in the trehalose producing, gluconeogenic state. Our work suggests simple physico-chemical principles that determine how isogenic cells spontaneously self-organize into structured assemblies in complimentary, specialized states.

Under certain conditions, single-celled microbes such as yeast and bacteria form communities of many cells. In some cases, the cells in these communities specialize to perform specific roles. By specializing, these cells may help the whole community to survive in difficult environments. These co-dependent communities have some similarities to how cells specialize and work together in larger living things ­ like animals or plants ­ that in some cases can contain trillions of cells. Research has already identified the genes involved in creating communities from a population of identical cells. It is less clear how cells within these communities become specialized to different roles. The budding yeast Saccharomyces cerevisiae can help to reveal how genetic and environmental factors contribute to cell communities. By growing yeast in conditions with a low level of glucose, Varahan et al. were able to form cell communities. The communities contained some specialized cells with a high level of activity in a biochemical system called the pentose phosphate pathway (PPP). This is unusual in low-glucose conditions. Further examination showed that many cells in the community produce a sugar called trehalose and, in parts of the community where trehalose levels are high, cells switch to the high PPP state and gain energy from processing trehalose. These findings suggest that the availability of a specific nutrient (in this case, trehalose), which can be made by the cells themselves, is a sufficient signal to trigger specialization of cells. This shows how simple biochemistry can drive specialization and organization of cells. Certain infections are caused by cell communities called biofilms. These findings could also contribute to new approaches to preventing biofilms. This knowledge could in turn reveal how complex multi-cellular organisms evolved, and it may also be relevant to studies looking into the development of cancer.

In silico Evolution of Lysis-Lysogeny Strategies Reproduces Observed Lysogeny Propensities in Temperate Bacteriophages.

Bacteriophages are the most abundant organisms on the planet and both lytic and temperate phages play key roles as shapers of ecosystems and drivers of bacterial evolution. Temperate phages can choose between (i) lysis: exploiting their bacterial hosts by producing multiple phage particles and releasing them by lysing the host cell, and (ii) lysogeny: establishing a potentially mutually beneficial relationship with the host by integrating their chromosome into the host cell's genome. Temperate phages exhibit lysogeny propensities in the curiously narrow range of 5-15%. For some temperate phages, the propensity is further regulated by the multiplicity of infection, such that single infections go predominantly lytic while multiple infections go predominantly lysogenic. We ask whether these observations can be explained by selection pressures in environments where multiple phage variants compete for the same host. Our models of pairwise competition, between phage variants that differ only in their propensity to lysogenize, predict the optimal lysogeny propensity to fall within the experimentally observed range. This prediction is robust to large variation in parameters such as the phage infection rate, burst size, decision rate, as well as bacterial growth rate, and initial phage to bacteria ratio. When we compete phage variants whose lysogeny strategies are allowed to depend upon multiplicity of infection, we find that the optimal strategy is one which switches from full lysis for single infections to full lysogeny for multiple infections. Previous attempts to explain lysogeny propensity have argued for bet-hedging that optimizes the response to fluctuating environmental conditions. Our results suggest that there is an additional selection pressure for lysogeny propensity within phage populations infecting a bacterial host, independent of environmental conditions.