Classification of CRISPR/Cas system and its application in tomato breeding

Abstract

Remarkable diversity in the domain of genome loci architecture, structure of effector complex, array of protein composition, mechanisms of adaptation along with difference in pre-crRNA processing and interference have led to a vast scope of detailed classification in bacterial and archaeal CRISPR/Cas systems, their intrinsic weapon of adaptive immunity. Two classes: Class 1 and Class 2, several types and subtypes have been identified so far. While the evolution of the effector complexes of Class 2 is assigned solely to mobile genetic elements, the origin of Class 1 effector molecules is still in a haze. Majority of the types target DNA except type VI, which have been found to target RNA exclusively. Cas9, the single effector protein, has been the primary focus of CRISPR-mediated genome editing revolution and is an integral part of Class 2 (type II) system. The present review focuses on the different CRISPR types in depth and the application of CRISPR/Cas9 for epigenome modification, targeted base editing and improving traits such as abiotic and biotic stress tolerance, yield and nutritional aspects of tomato breeding.

Comprehending the evolution of gene editing platforms for crop trait improvement

“…The effector module of the CRISPR/Cas system is divided into three stages: the adaptation stage, the expression and processing stage, and the interference stage. In class 1 CRISPR/Cas systems (with types I, III, and IV), type I and type III systems employ a multi-protein complex called the Cascade complex along with Cas3 nuclease-helicase and the Cmr complex for type I, type III-A, and type IIIB CRISPR/Cas systems, respectively ( Koonin and Makarova, 2019 ; Chaudhuri et al, 2022 ). However, class 2 CRISPR/Cas systems (with types II, V, and VI) employ only one effector protein.…”

“…In type II and type V CRISPR/Cas systems, the expression and processing of the crRNA are regulated by a single protein such as Cas9 and Cpf1, respectively ( Makarova et al, 2015 ; Amitai and Sorek, 2016 ). Type VI systems have been recently discovered and are the only CRISPR/Cas systems to target RNA specifically ( Chaudhuri et al, 2022 ). In Class 1 CRISPR Cas systems, type 1 and type III are more prevalent than type IV in diverse bacterial and archaeal populations.…”

“…Class 1 CRISPR systems, types I and III, bear structural similarities suggesting evolution via a common ancestor ( Chaudhuri et al, 2022 ). In addition, they employ Cas9 endonuclease to process crRNA.…”

“…The type III systems are divided into four subtypes, type III-A, III-B, III-C, and III-D, based on variation in adaptation, recognition, and interference modules of the effector protein complex. Chaudhuri et al (2022) discussed the further classification of type I and type III into subtypes at length. Class 2 CRISPR/Cas system is divided into three types, types II, V, and VI.…”

Genome Editing for Sustainable Crop Improvement and Mitigation of Biotic and Abiotic Stresses

“…Further experimentation and analysis have further divided the classification into 2 classes, 6 types and 33 subtypes [48]. As the classification of CRISPR has been described in earlier reviews [49,50], we are not explaining it in detail in this paper.…”