Applications of CRISPR/Cas13-Based RNA Editing in Plants

Abstract

The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated (Cas) system is widely used as a genome-editing tool in various organisms, including plants, to elucidate the fundamental understanding of gene function, disease diagnostics, and crop improvement. Among the CRISPR/Cas systems, Cas9 is one of the widely used nucleases for DNA modifications, but manipulation of RNA at the post-transcriptional level is limited. The recently identified type VI CRISPR/Cas systems provide a platform for precise RNA manipulation without permanent changes to the genome. Several studies reported efficient application of Cas13 in RNA studies, such as viral interference, RNA knockdown, and RNA detection in various organisms. Cas13 was also used to produce virus resistance in plants, as most plant viruses are RNA viruses. However, the application of CRISPR/Cas13 to studies of plant RNA biology is still in its infancy. This review discusses the current and prospective applications of CRISPR/Cas13-based RNA editing technologies in plants.

TemStaPro: protein thermostability prediction using sequence representations from protein language models

“…Sequence dataset of Class II effector proteins Initial datasets of Cas12 and Cas9 were taken from (a recently accepted paper, to be cited upon publication) and (17), respectively. Cas13 sequence dataset was constructed by building HMMER (25) sequence profiles for Cas13 groups (26) and using them to search NR (27), UniRef100 (28), MGnify (29), and IMG/VR v4 (30) databases with hmmsearch (25). Only sequences with E-value ≤ 1e-20 were extracted.…”

“…Initial datasets of Cas12 and Cas9 were taken from (Sasnauskas et al, 2023) and (Gasiunas et al, 2020), respectively. Cas13 sequence dataset was constructed by building HMMER (Eddy, 2011) sequence profiles for Cas13 groups (Kavuri et al, 2022) and using them to search NR (Sayers et al, 2022), UniRef100 (Suzek et al, 2007), MGnify (Richardson et al, 2023), and IMG/VR v4 (Camargo et al, 2023) databases with hmmsearch (Eddy, 2011). Only sequences with E-value ≤1e-20 were extracted.…”

Genomic surveillance urgently needed to control wheat blast pandemic spreading across continents

“…The Cas9 system for DNA modification has recently been used to enhance disease resistance in rice against rice blast disease caused by M. oryzae [6], suggesting similar potential for wheat, too. More recently, the RNA editing Cas13 system also provides an avenue to explore to generate Wheat Blast-resistant wheat varieties [7]. However, these genome editing systems also enable manipulation of the M. oryzae genome, creating mutants with reduced growth, differential pathogenicity, or altered germination qualities.…”

“…oryzae [ 6 ], suggesting similar potential for wheat, too. More recently, the RNA editing Cas13 system also provides an avenue to explore to generate Wheat Blast–resistant wheat varieties [ 7 ]. However, these genome editing systems also enable manipulation of the M .…”

Applications of Synthetic Pentatricopeptide Repeat Proteins

“…2016 ). Much of the work in engineering RBPs has focused on the use of the bacterial RBP Cas13 fused to functional domains such as adenosine deaminase acting on RNA to edit RNAs or degrade viral RNA via RNA interference ( Kavuri et al. 2022 ).…”