  The molecular network in an organism consists of transcription/translation
regulation, protein-protein interactions/modifications and a metabolic network,
together forming a system that allows the cell to respond sensibly to the
multiple signal molecules that exist in its environment. A key part of this
overall system of molecular regulation is therefore the interface between the
genetic and the metabolic network. A motif that occurs very often at this
interface is a negative feedback loop used to regulate the level of the signal
molecules. In this work we use mathematical models to investigate the steady
state and dynamical behaviour of different negative feedback loops. We show, in
particular, that feedback loops where the signal molecule does not cause the
dissociation of the transcription factor from the DNA respond faster than loops
where the molecule acts by sequestering transcription factors off the DNA. We
use three examples, the bet, mer and lac systems in E. coli, to illustrate the
behaviour of such feedback loops.
