  Genomic and proteomic methods yield networks of biological regulatory
interactions but do not provide direct insight into how those interactions are
organized into functional modules, or how information flows from one module to
another. In this work we introduce an approach that provides this complementary
information and apply it to the bacterium Caulobacter crescentus, a paradigm
for cell-cycle control. Operationally, we use an inducible promoter to express
the essential transcriptional regulatory gene ctrA in a periodic, pulsed
fashion. This chemical perturbation causes the population of cells to divide
synchronously, and we use the resulting advance or delay of the division times
of single cells to construct a phase resetting curve. We find that delay is
strongly favored over advance. This finding is surprising since it does not
follow from the temporal expression profile of CtrA and, in turn, simulations
of existing network models. We propose a phenomenological model that suggests
that the cell-cycle network comprises two distinct functional modules that
oscillate autonomously and couple in a highly asymmetric fashion. These
features collectively provide a new mechanism for tight temporal control of the
cell cycle in C. crescentus. We discuss how the procedure can serve as the
basis for a general approach for probing network dynamics, which we term
chemical perturbation spectroscopy (CPS).
