Transcription kinetics in bacteria: What does it mean for a gene to be ‘on’?

Ido Golding, Department of Physics, University of Illinois at Urbana-Champaign

For a scientist with quantitative aspirations, traditional methods for measuring gene activity are highly unsatisfactory: a large number of cells is averaged; the measurements are made “off line” on extracts rather than in living cells; and results are only “semi-quantitative” with far from single-molecule resolution. Thus we cannot say what it actually means that a gene is “on” even for the simplest bacterial promoters. Does mRNA production occur as a simple Poisson process, with a constant probability per unit time of producing a new transcript, or is the temporal pattern more complex?
I will describe our strategy for measuring mRNA levels in individual growing cells, in real time, with single molecule resolution. We have found that transcription kinetics in E. coli can be explained by a simple “2-state” mechanism: An induced gene can switch into an active state with constant probability as a function of time. Whilst in this state, it can at each moment produce an mRNA molecule with a constant probability, but it can also switch back to the inactive “ground” state. The resulting time series is “bursty”, characterized by periods of transcriptional inactivity, interspersed with limited time windows of transcriptional activity.
Time permitting, I will discuss our plans to use the same experimental approach to deconstruct the regulatory network controlling the lysis/lysogeny switch in phage lambda.