Journal
ACS SYNTHETIC BIOLOGY
Volume 8, Issue 2, Pages 391-402Publisher
AMER CHEMICAL SOC
DOI: 10.1021/acssynbio.8b00429
Keywords
CRISPR interference; isopentenol; metabolic flux redirection; simultaneous genome knockdown; Escherichia coli; mevalonate pathway
Categories
Funding
- US Department of Energy, Office of Science, Office of Biological and Environmental Research [DE-AC02-05CH11231]
- Regents of the University of California/Lawrence Berkeley National Laboratory and Technology Holding LLC [FP00003594]
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CRISPR interference (CRISPRi) via target guide RNA (gRNA) arrays and a deactivated Cas9 (dCas9) protein has been shown to simultaneously repress expression of multiple genomic DNA loci. By knocking down endogenous genes in competing pathways, CRISPRi technology can be utilized to redirect metabolic flux toward target metabolite. In this study, we constructed a CRISPRi-mediated multiplex repression system to silence transcription of several endogenous genes to increase precursor availability in a heterologous isopentenol biosynthesis pathway. To identify genomic knockdown targets in competing pathways, we first designed a single-gRNA library with 15 individual targets, where 3 gRNA cassettes targeting gene asnA, prpE, and gldA increased isopentenol titer by 18-24%. We then combined the 3 singleg-RNA cassettes into a two- or three-gRNA array and observed up to 98% enhancement in production by fine-tuning the repression level through titrating dCas9 expression. Our strategy shows that multiplex combinatorial knockdown of competing genes using CRISPRi can increase production of the target metabolite, while the repression level needs to be adjusted to balance the metabolic network and achieve the maximum titer improvement.
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