Global Characterization of Transcription Factor Localization and Partitioning in Escherichia Coli

Abstract

Despite the lack of cytoskeletal molecular motors and membrane-bound organelles, the bacterial cell exhibits surprising complexity in subcellular structure and organization. To isolate the localization behavior of bacterial proteins at the genome-scale, we combine high-throughput time-lapse fluorescence microscopy and automated image analysis to capture the cell-cycle localization dynamics of nearly every protein in E. coli that exhibits a non-diffuse localization pattern. We capture hundreds of complete cell cycles for each protein, which facilitates quantitative analysis of cell-cycle dynamics and cell-to-cell variation. We exploit this unique data set to characterize the localization behavior of a subset of proteins that exhibit large variability in localization patterns: DNA-binding transcription factors. We find that many transcription factors form well localized punctate foci with significant complexity in positioning, both spatially and temporally. Principal components analysis reveals that these proteins occupy diverse yet overlapping localization groups, many of which are cell-cycle dependent. Finally, we find numerous examples of non-trivial partitioning of transcription factors at cell division, including proteins that appear to be preferentially partitioned as a function of cell age. This complex localization behavior may be evidence of a new global model for the function of transcription factors in bacterial cells.