  Multiplex and multi-directional control of metabolic pathways is crucial for
metabolic engineering to improve product yield of fuels, chemicals, and
pharmaceuticals. To achieve this goal, artificial transcriptional regulators
such as CRISPR-based transcription regulators have been developed to
specifically activate or repress genes of interest. Here, we found that by
deploying guide RNAs to target on DNA sites at different locations of genetic
cassettes, we could use just one synthetic CRISPR-based transcriptional
regulator to simultaneously activate and repress gene expressions. By using the
pairwise datasets of guide RNAs and gene expressions, we developed a
data-driven predictive model to rationally design this system for fine-tuning
expression of target genes. We demonstrated that this system could achieve
programmable control of metabolic fluxes when using yeast to produce versatile
chemicals. We anticipate that this master CRISPR-based transcription regulator
will be a valuable addition to the synthetic biology toolkit for metabolic
engineering, speeding up the design-build-test cycle in industrial
biomanufacturing as well as generating new biological insights on the fates of
eukaryotic cells.
