Biological Insights from a Computational Simulation of the M13 Bacteriophage Life Cycle

As the biotechnological applications of M13 phage particles continue to expand in scope and complexity, a quantitative, holistic understanding of the biological processes and interactions that govern the life cycle of the phage will foster the creation of new platforms with rationally designed control elements that are more amenable to engineering. The filamentous phage life cycle employs 11 phage-encoded proteins to direct a complex and coordinated program of action in the infected cell. Unique among bacteriophage, the filamentous phages act as true parasites of bacteria: infected cells continue to grow and divide as progeny phage particles are continuously produced. To be a successful parasite the phage must invade the cell and quickly establish itself in a limited manner that allows the cell to survive while at the same time avoiding the cell’s attempts to dislodge it. Bacteriophage M13, the most well studied F-pilus specific filamentous phage of E. coli, is able to co-opt the infected cell and control the extent and timing of progeny production across many cellular generations. We have constructed a genetically-structured, experimentally-based computational simulation of the life cycle of M13 to evaluate and expand the system level understanding of this biotechnologically-relevant phage. Our deterministic chemical kinetic simulation integrates 50 years of experimental observations and explicitly includes the molecular details of phage DNA replication, mRNA transcription, protein translation and phage particle assembly, as well as the competing protein-protein and protein-nucleic acid interactions that control the timing and extent of phage production. Many aspects of M13 biology are faithfully reproduced by the simulation, including the production levels and timing of the shift between replicative form and preassembly complex DNA, quantities of phage mRNA and proteins, and the time course of assembly and release of progeny phage. Extending the simulation across multiple cell generations recapitulated the dynamic steady state behavior observed in infected cell populations and elucidated underappreciated elements of the controlling architecture of the phage life process, in particular the role of translational attenuation in resource allocation by phage protein p5. The p5 translational attenuation control mechanism was originally hypothesized to be central to the coordinated control of the levels of phage DNA in in the cell and the switch from replicative form to single-stranded DNA synthesis. Subsequent experiments called this central role into question. Our simulation of the phage life cycle matches the behavior of experiments that indicated that translational attenuation of the DNA synthesis initiation protein p2 were unimportant, but finds a role for translational self-attenuation of p5 in controlling resource allocation. Our simulation not only provides a quantitative description of phage biology, but also highlights gaps in the present understanding of M13 biology. Understanding the subtleties of regulation will be important for maximally exploiting the phage as scaffolds for nanoscale devices from biosensors to batteries. Our simulation should find utility helping to prioritize future biochemical experiments and design new synthetic phage-like systems.