Potential Use of CRISPR/Cas13 Machinery in Understanding Virus-Host Interaction.

Mahmoud Bayoumi,Muhammad Munir

doi:10.3389/fmicb.2021.743580

Abstract

Prokaryotes have evolutionarily acquired an immune system to fend off invading mobile genetic elements, including viral phages and plasmids. Through recognizing specific sequences of the invading nucleic acid, prokaryotes mediate a subsequent degradation process collectively referred to as the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)–CRISPR-associated (Cas) (CRISPR–Cas) system. The CRISPR–Cas systems are divided into two main classes depending on the structure of the effector Cas proteins. Class I systems have effector modules consisting of multiple proteins, while class II systems have a single multidomain effector. Additionally, the CRISPR–Cas systems can also be categorized into types depending on the spacer acquisition components and their evolutionary features, namely, types I–VI. Among CRISPR/Cas systems, Cas9 is one of the most common multidomain nucleases that identify, degrade, and modulate DNA. Importantly, variants of Cas proteins have recently been found to target RNA, especially the single-effector Cas13 nucleases. The Cas13 has revolutionized our ability to study and perturb RNAs in endogenous microenvironments. The Cas13 effectors offer an excellent candidate for developing novel research tools in virological and biotechnological fields. Herein, in this review, we aim to provide a comprehensive summary of the recent advances of Cas13s for targeting viral RNA for either RNA-mediated degradation or CRISPR–Cas13-based diagnostics. Additionally, we aim to provide an overview of the proposed applications that could revolutionize our understanding of viral–host interactions using Cas13-mediated approaches.

Highlights

Tugs-of-war usually occur between prokaryotes, including bacteria and archaea against viral phages
The generation of an all-in-one system that can express both Cas13b and two crRNAs for multiplexing was confirmed to attain superior RNA interference (Cui et al, 2020). They confirmed this finding after stable expression of the all-in-one system in MARC145 cell, achieving an almost complete degradation of the porcine reproductive and respiratory syndrome virus (PRRSV) genome (Cui et al, 2020). All these conclusions support the successful use of Cas13 proteins in controlling viral infection in the future, in either prophylactic or treatment conditions, and importantly, in engineering mammalian cells that stably express Cas13 effectors and poly-crRNAs targeting multiple viruses and could provide stable immunity in vitro
The platforms mentioned above and their improved versions highlight the successfulness of the guided RNases in viral diagnostic-based assays and biotechnological applications and suggest further improvements to develop an ideal approach for diagnosis (Abudayyeh and Gootenberg, 2021; Shinoda et al, 2021)

Summary

Introduction

Tugs-of-war usually occur between prokaryotes, including bacteria and archaea against viral phages. The Cas13 nucleases are novel effectors that could target viral RNA(s) using rationally designed crRNA(s).

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Results

Conclusion