Single-molecule fluorescence microscopy is allowing us to study low-abundance proteins inside live bacterial cells for the first time. We are using single-molecule imaging to study DNA polymerases in E. coli, in particular those that carry out translesion DNA synthesis (TLS) on damage DNA. When induced, TLS polymerases increase mutation rates of cells dramatically and play a demonstrated role in the development of de novo antibiotic resistance mutations.
We have discovered two novel mechanisms that limit the access of TLS polymerases to replisomes. DNA polymerase IV colocalises with replisomes during the early stages of the DNA damage response, but is suddenly ‘ejected’ from replisomes during the later stages. DNA polymerase V, on the other hand, is completely inactive in the early stages and becomes active once DNA polymerase IV is ejected from replisomes. Interestingly, DNA polymerase V activity is regulated spatially. When first expressed, the UmuC subunit is sequestered on the inner cell membrane, repressing mutagenesis. If damage persists beyond the initial repair stage, UmuC is released gradually into the cytosol and activated to its mutagenic form, pol V Mut (UmuD’2C-RecA-ATP). Cleavage of the UmuD protein acts not only as a biochemical switch that allows formation of active pol V Mut, but also a spatial switch that releases UmuC from the membrane. This spatial control mechanism, in which the membrane is used like a compartment, is unprecedented in bacteria.