Engineered CRISPRa enables programmable eukaryote-like gene activation in bacteria

Nat Commun. 2019 Aug 26;10(1):3693. doi: 10.1038/s41467-019-11479-0.

Abstract

Transcriptional regulation by nuclease-deficient CRISPR/Cas is a popular and valuable tool for routine control of gene expression. CRISPR interference in bacteria can be reliably achieved with high efficiencies. Yet, options for CRISPR activation (CRISPRa) remained limited in flexibility and activity because they relied on σ70 promoters. Here we report a eukaryote-like bacterial CRISPRa system based on σ54-dependent promoters, which supports long distance, and hence multi-input regulation with high dynamic ranges. Our CRISPRa device can activate σ54-dependent promoters with biotechnology relevance in non-model bacteria. It also supports orthogonal gene regulation on multiple levels. Combining our CRISPRa with dxCas9 further expands flexibility in DNA targeting, and boosts dynamic ranges into regimes that enable construction of cascaded CRISPRa circuits. Application-wise, we construct a reusable scanning platform for readily optimizing metabolic pathways without library reconstructions. This eukaryote-like CRISPRa system is therefore a powerful and versatile synthetic biology tool for diverse research and industrial applications.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • CRISPR-Cas Systems / genetics*
  • Clustered Regularly Interspaced Short Palindromic Repeats / genetics*
  • Escherichia coli / genetics*
  • Escherichia coli / metabolism
  • Escherichia coli Proteins / genetics*
  • Gene Expression / genetics
  • Gene Expression Regulation / genetics
  • Metabolic Networks and Pathways / genetics
  • Plasmids / genetics
  • Promoter Regions, Genetic / genetics
  • Protein Engineering / methods*
  • RNA Polymerase Sigma 54 / genetics*
  • RNA, Guide, CRISPR-Cas Systems / genetics
  • Transcriptional Activation / genetics

Substances

  • Escherichia coli Proteins
  • RNA, Guide, CRISPR-Cas Systems
  • rpoN protein, E coli
  • RNA Polymerase Sigma 54