Dynamic Gene Expression and Design Principles of Viral Infection Pathway

Abstract

The study of gene expression is often couched in the language of steady-states. On the other hand, non-steady-state conditions are clearly of critical importance. One example that opens a unique window to studying non-steady-state gene expression patterns is viral infection. The lytic pathway of most bacteriophages leads to production of the machinery of the virus and eventually the infected cells burst. Here we use phage lambda and E. coli as a model system to study the intracellular dynamics of viral products from the nucleic acid to protein level. We use single-molecule fluorescence in situ hybridization and fluorescence fusion proteins to quantify the copy number of viral nucleic acid and protein products in single cells during the lytic pathway as a function of time. We ask how the growth curves of the viral products can be explained by using simple master equations describing the replication/transcription/translation of the well-characterized phage lambda genetic regulatory circuit. We also examine the molecular balance in the viral production process, as balance in sub-components is a recurring principle in the biosynthesis of ribosome, protein complexes and metabolic pathways. In particular, how wasteful is the production compared to the burst size (the average number of viral particles released per cell as measured in titer experiments), and whether the viral components (for example the capsid protein to genome ratio) are produced to the correct stoichiometry that is well-defined from structural studies for mature viral particles.