Anti-CRISPR protein applications: natural brakes for CRISPR-Cas technologies

Abstract

Co-evolutionary arms races are fertile ground for innovation. The strong selective pressures exerted by mobile genetic elements (MGEs) on their prokaryotic hosts exemplify this, yielding robust technologies such as restriction enzymes and CRISPR-Cas nucleases. Clustered, regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) genes, a diverse family of prokaryotic adaptive immune systems, have emerged as a biotechnological tool and therapeutic. The discovery of protein inhibitors of CRISPR-Cas systems, called "anti-CRISPRs" (Acrs), enables the development of more controllable and precise CRISPR-Cas tools. The applications of Acr proteins for post-translational control of CRISPR-Cas systems in prokaryotic and mammalian cells, organisms, and ecosystems will be discussed here.CRISPR-Cas systems provide prokaryotes with adaptive immunity from their pathogens. These multi-protein (Class 1) or single protein (Class 2) nuclease complexes use a guide or CRISPR RNA (gRNA or crRNA) to target invasive nucleic acids. The specificity and easily programmable nature of CRISPR-Cas nucleases have been repurposed for various molecular, biotechnological, and medical applications, including gene editing, gene

Exploring the synthetic biology potential of bacteriophages for engineering non-model bacteria

“…These modulators constitute a goldmine of revolutionary, strain-optimized tools to expand the SynBio toolbox, as we illustrate here using selected examples. First, when entering the cell, the phage protects itself from several host defence mechanisms by using anti-CRISPR proteins (Acr) or by integrating non-canonical nucleotides into their genome to avoid host restriction enzymes 111 , 112 . Since the discovery of Acr proteins in Pseudomonas phages, many other Acr proteins have been identified and used in a range of SynBio applications, including regulation of CRISPR-Cas-based tools at multiple stages, reduction of CRISPR-Cas toxicity and the development of Acr-based CRISPRi and selection markers (Fig.…”

“…Since the discovery of Acr proteins in Pseudomonas phages, many other Acr proteins have been identified and used in a range of SynBio applications, including regulation of CRISPR-Cas-based tools at multiple stages, reduction of CRISPR-Cas toxicity and the development of Acr-based CRISPRi and selection markers (Fig. 3 (12)) 112 . In contrast, the DNA manipulation enzymes still need to find their way to the in vivo SynBio field, but could for example be used to protect DNA sequences from nucleases in restriction-based DNA assembly methods.…”

Types I and V Anti-CRISPR Proteins: From Phage Defense to Eukaryotic Synthetic Gene Circuits

“…Upon expression of AcrIE1 or AcrIF3, Cascade-crRNA binds the substrate DNA stably without triggering any DNA degradation. Therefore, AcrIE1 and AcrIF3 are a means to regulate gene transcription (Luo et al, 2015;Marino et al, 2020). In 2015, Rath et al (2015) utilized the Csy complex as a repressor of GFP in E. coli and Salmonella typhimurium.…”

“…Besides, they used, as a positive control, a strain without a CRISPR-Cas system ( CRISPR-Cas) and, as a negative control, a strain containing an inactive Cas3 mutant (H89A/D90A). AcrIE1 led to a decrease in pyocyanin production-as in the negative control-compared to the positive control that showed normal pyocyanin production (Marino et al, 2020). Type V anti-CRISPR proteins have been adopted, mainly, in gene editing.…”

Discovery of multiple anti-CRISPRs uncovers anti-defense gene clustering in mobile genetic elements

“…antibiotic resistance) across microbiomes. Practically, Acr proteins also benefit phage-based therapeutics and plasmid-based delivery platforms and provide a means to control CRISPR-Cas-derived biotechnologies (Marino et al, 2020).…”