Diversity of molecular mechanisms used by anti-CRISPR proteins: the tip of an iceberg?

Abstract

Bacteriophages (phages) and their preys are engaged in an evolutionary arms race driving the co-adaptation of their attack and defense mechanisms. In this context, phages have evolved diverse anti-CRISPR proteins to evade the bacterial CRISPR–Cas immune system, and propagate. Anti-CRISPR proteins do not share much resemblance with each other and with proteins of known function, which raises intriguing questions particularly relating to their modes of action. In recent years, there have been many structure–function studies shedding light on different CRISPR–Cas inhibition strategies. As the anti-CRISPR field of research is rapidly growing, it is opportune to review the current knowledge on these proteins, with particular emphasis on the molecular strategies deployed to inactivate distinct steps of CRISPR–Cas immunity. Anti-CRISPR proteins can be orthosteric or allosteric inhibitors of CRISPR–Cas machineries, as well as enzymes that irreversibly modify CRISPR–Cas components. This repertoire of CRISPR–Cas inhibition mechanisms will likely expand in the future, providing fundamental knowledge on phage–bacteria interactions and offering great perspectives for the development of biotechnological tools to fine-tune CRISPR–Cas-based gene edition.

A diverse repertoire of anti-defense systems is encoded in the leading region of plasmids

“…However, their location in this region strongly indicates that they likely encode for anti-defense-related functions. Focusing the search on the leading region of conjugative elements could facilitate the discovery of new anti-defense systems, such as anti-CRISPR proteins, which are challenging to detect due to their small size and high variability 77,78 .…”

A short overview of the CRISPR-Cas adaptation stage

“…Several mechanisms for anti-CRISPR proteins have also been discovered, revealing that different ACR proteins target different Cas proteins. For example, binding of the ACR to Cas proteins prevented binding or cleaving of nucleic acids (Bondy-Denomy et al 2015;Dong et al 2017;Harrington et al 2017;Shin et al 2017;Yang and Patel 2017;Hardouin and Goulet 2020;Marino et al 2020;Davidson et al 2020). A nomenclature for ACRs has been proposed and an online spreadsheet is available to avoid names being used twice in this fast-growing field (Bondy-Denomy et al 2018).…”

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

“…Other type II Acrs, such as AcrIIA6 and AcrIIC3, carry out their function as allosteric inhibitors, i.e., they induce conformation changes, which preclude CRISPR-Cas9 working, upon interaction with non-functional Cas9 sites. Finally, AcrAII5 was shown to behave as an enzyme and cleave the guide RNA at multiple places, outside the spacer sequence ( Hardouin and Goulet, 2020 ).…”