Reverse-engineering of gene regulation circuits: the temproal program of E. coli flagella assembly.

Uri Alon

Weizmann Institute, Rehovot

The recent advance in large scale monitoring of gene expression raises the challenge of 'reverse-engineering' systems based on kinetic expression data. To solve such an inverse problem, mapping genetic circuits from input-output measurements, requires new analysis and experimental methods.
Here, we examine this using one of the best-characterized gene regulation networks, the flagella system of Escherichia coli. Classical genetics ordered the 14 flagella operons into a three-class hierarchy.

We measured promoter activity at high temporal resolution using reporter plasmids. A temporal clustering algorithm captures not only the genetically defined hierarchy, but a much more detailed temporal program of transcription than was previously thought. The order of activation follows multiple steps of flagella basal body assembly, followed by flagella filament genes, and culminates with the chemotaxis 'computer'. A mechanism for temporal programming is proposed based on graded regulatory site affinities.
Thus, detailed analysis of expression kinetics might be a feasible high-throughput complement to genetics in ordering gene regulation and assembly cascades.