|dc.description.abstract||Decision-making influences the development of life over multiple levels. Understanding the core mechanisms of this complex process could yield new insights into the treatment of diseases and the evolution of lifeforms. To study the universal subject of decision-making, we investigate the simple bacteriophage lambda model to distill complicated decision-making into fundamental biological questions. Lambda is a virus that infects E. coli, choosing between alternative modes of propagation, lysis or lysogeny, as its decision. Despite a history of research spanning decades, the underlying mechanisms of lambda decision-making are unclear. Using fluorescence microscopy for quantitative, high-resolution study, we explore an established paradigm with a new perspective to discover the inner workings of cellular decision-making.
In our studies, we find that phages within single cells behave analogous to advanced organisms within their niches. For lambda, we find that their viral DNA molecules compete with each other inside the cell over replication resources. This allows phages to dominate each other, particularly during lysis, when DNA replication is important. Conversely, cooperation is prevalent during lysogeny, allowing viruses to benefit each other during a different path of development. These behaviors play a role in evolutionary fitness, where both strategic domination and cooperation may minimize the chances of extinction. We then study the spatial organization of phage development in the cell. We build tools to specifically characterize the coordinates of lambda DNA replication, resource sequestration, transcription, and virion assembly. We find that lambda manipulates its environment by hoarding resources and confining replicated viral genomes spatially. We observe that phage transcripts are localized nearby the phage genomes, and that virion assembly transpires in the same location, resembling a phage factory. Through our analysis, we find that multiple factories arise in cells and may be quantitatively distinct, suggesting this to be the origin of viral individuality. Indeed, we observe that different transcription programs, corresponding to different fates, occur in single cells, corroborating our hypothesis that individual phages can vote for decisions within cells. Finally, we incorporate our quantitative data and new models into computational simulations of this biological process to work towards a more complete quantitative understanding of decision-making.||en