Suppose organism Y has a system composed of a kinase, phosphatase, and transcription factor(s) that is controlled via phosphorylation. This entire system can be transplanted into organism X (e.g. E. coli), with each component under the control of different promoters.
This will give some control at the protein level, because the equilibrium concentrations of the phosphorylated and unphosphorylated proteins can be controlled by regulating the levels of the kinase and phosphotase. Of course, the control is still at the transcription level, but the phosphorylation will serve as a fast-acting system -- i.e. producing a few kinases will activate many transcription factors.