Gene location and DNA density determine transcription factor distributions in Escherichia coli

Abstract

• The steady-state spatial distribution of the canonical lac repressor transcription factor, LacI, is not homogeneous in E. coli.

• The spatial distribution of LacI depends upon the location of the encoding gene and the compaction state of DNA, which changes in response to growth conditions.

• When DNA becomes highly condensed, proteins are excluded from the nucleoid volume.

• These observations suggest mechanisms driving the spatial organization of the E. coli genome and regulation of global transcription patterns.

Abstract

The diffusion coefficient of the transcription factor LacI within living Escherichia coli has been measured directly by in vivo tracking to be D=0.4  μm ²/s. At this rate, simple models of diffusion lead to the expectation that LacI and other proteins will rapidly homogenize throughout the cell. Here, we test this expectation of spatial homogeneity by single-molecule visualization of LacI molecules non-specifically bound to DNA in fixed cells. Contrary to expectation, we find that the distribution depends on the spatial location of its encoding gene. We demonstrate that the spatial distribution of LacI is also determined by the local state of DNA compaction, and that E. coli can dynamically redistribute proteins by modifying the state of its nucleoid. Finally, we show that LacI inhomogeneity increases the strength with which targets located proximally to the LacI gene are regulated. We propose a model for intranucleoid diffusion that can reconcile these results with previous measurements of LacI diffusion, and we discuss the implications of these findings for gene regulation in bacteria and eukaryotes.