Getting better all the time — recent progress in the development of CRISPR/Cas-based tools for plant genome engineering

Capdeville, Niklas; Schindele, Patrick; Puchta, Holger

doi:10.1016/j.copbio.2022.102854

Cited by 19 publications

(13 citation statements)

References 62 publications

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“…Thus, deletions ranging from 10 to 40 bp are difficult to obtain using existing tools. Previously, it could be shown that overexpressing or fusing exonucleases to Cas endonucleases increases the size of the induced deletions ( Cerm ak et al, 2017;Clements et al, 2017;Weiss et al, 2020;Zhang et al, 2020). However, the efficiency of the fusion-based approach might have still been limited by the fact that only one copy of the exonuclease was present at the break site.…”

Section: Discussionmentioning

confidence: 99%

“…The CRISPR/Cas system has revolutionized molecular biology by enabling the targeted induction of mutations. Multiple tools have been developed in the last years, enabling the induction of a wide variety of changes in the plant genome (Capdeville et al., 2023). While the repair of Cas9‐induced DSB predominantly results in small insertions, Cas12a‐mediated mutagenesis often leads to the generation of small deletions of about 5–10 bp (Zhang et al., 2021).…”

Section: Discussionmentioning

confidence: 99%

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Increasing deletion sizes and the efficiency of CRISPR/Cas9‐mediated mutagenesis by SunTag‐mediated TREX1 recruitment

Capdeville,

Schindele,

Puchta

2023

The Plant Journal

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SUMMARYPreviously, it has been shown that mutagenesis frequencies can be improved by directly fusing the human exonuclease TREX2 to Cas9, resulting in a strong increase in the frequency of smaller deletions at the cut site. Here, we demonstrate that, by using the SunTag system for recruitment of TREX2, the mutagenesis efficiency can be doubled in comparison to the direct fusion in Arabidopsis thaliana. Therefore, we also tested the efficiency of the system for targeted deletion formation by recruiting two other 3′‐5′ exonucleases, namely the human TREX1 and E. coli ExoI. It turns out that SunTag‐mediated recruitment of TREX1 not only improved the general mutation induction efficiency slightly in comparison to TREX2, but that, more importantly, the mean size of the induced deletions was also enhanced, mainly via an increase of deletions of 25 bp or more. EcExoI also yielded a higher amount of larger deletions. However, only in the case of TREX1 and TREX2, the effect was predominately SunTag‐dependent, indicating efficient target‐specific recruitment. Using SunTag‐mediated TREX1 recruitment at other genomic sites, we were able to obtain similar deletion patterns. Thus, we were able to develop an attractive novel editing tool that is especially useful for obtaining deletions in the range from 20 to 40 bp around the cut site. Such sizes are often required for the manipulation of cis‐regulatory elements. This feature is closing an existing gap as previous approaches, based on single nucleases or paired nickases or nucleases, resulted in either shorter or longer deletions, respectively.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Increasing deletion sizes and the efficiency of CRISPR/Cas9‐mediated mutagenesis by SunTag‐mediated TREX1 recruitment

Capdeville,

Schindele,

Puchta

2023

The Plant Journal

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“…The toolkit of CRISPR-Cas applications has expanded to around twenty different techniques that allow diverse targeted modifications in the genome ( Villalobos-López et al., 2022 ; Capdeville et al., 2023 ). On the one hand, Cas enzymes from different bacteria have been characterized and adopted for use.…”

Section: Genome Editing: a Tool For Developing Stress Resistant Forag...mentioning

confidence: 99%

Improving abiotic stress tolerance of forage grasses – prospects of using genome editing

Sustek-Sánchez

Rognli²,

Rostoks³

et al. 2023

Front. Plant Sci.

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Due to an increase in the consumption of food, feed, and fuel and to meet global food security needs for the rapidly growing human population, there is a necessity to obtain high-yielding crops that can adapt to future climate changes. Currently, the main feed source used for ruminant livestock production is forage grasses. In temperate climate zones, perennial grasses grown for feed are widely distributed and tend to suffer under unfavorable environmental conditions. Genome editing has been shown to be an effective tool for the development of abiotic stress-resistant plants. The highly versatile CRISPR-Cas system enables increasingly complex modifications in genomes while maintaining precision and low off-target frequency mutations. In this review, we provide an overview of forage grass species that have been subjected to genome editing. We offer a perspective view on the generation of plants resilient to abiotic stresses. Due to the broad factors contributing to these stresses the review focuses on drought, salt, heat, and cold stresses. The application of new genomic techniques (e.g., CRISPR-Cas) allows addressing several challenges caused by climate change and abiotic stresses for developing forage grass cultivars with improved adaptation to the future climatic conditions. Genome editing will contribute towards developing safe and sustainable food systems.

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“…In the last 10 yr, biology in general and especially plant breeding has been transformed by applying the CRISPR/Cas system for different kinds of genome manipulations (Gao, 2021; Nasti & Voytas, 2021; Capdeville et al ., 2023; Wang & Doudna, 2023). Especially, the nucleases Cas9 and Cas12a have proven to be extremely efficient tools for cutting at almost any position in the plant genome.…”

Section: Inducing Chromosomal Inversions By Crispr/cas To Redirect Me...mentioning

confidence: 99%

Plant chromosome engineering – past, present and future

Puchta,

Houben

2023

New Phytologist

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SummarySpontaneous chromosomal rearrangements (CRs) play an essential role in speciation, genome evolution and crop domestication. To be able to use the potential of CRs for breeding, plant chromosome engineering was initiated by fragmenting chromosomes by X‐ray irradiation. With the rise of the CRISPR/Cas system, it became possible to induce double‐strand breaks (DSBs) in a highly efficient manner at will at any chromosomal position. This has enabled a completely new level of predesigned chromosome engineering. The genetic linkage between specific genes can be broken by inducing chromosomal translocations. Natural inversions, which suppress genetic exchange, can be reverted for breeding. In addition, various approaches for constructing minichromosomes by downsizing regular standard A or supernumerary B chromosomes, which could serve as future vectors in plant biotechnology, have been developed. Recently, a functional synthetic centromere could be constructed. Also, different ways of genome haploidization have been set up, some based on centromere manipulations. In the future, we expect to see even more complex rearrangements, which can be combined with previously developed engineering technologies such as recombinases. Chromosome engineering might help to redefine genetic linkage groups, change the number of chromosomes, stack beneficial genes on mini cargo chromosomes, or set up genetic isolation to avoid outcrossing.

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Getting better all the time — recent progress in the development of CRISPR/Cas-based tools for plant genome engineering

Cited by 19 publications

References 62 publications

Increasing deletion sizes and the efficiency of CRISPR/Cas9‐mediated mutagenesis by SunTag‐mediated TREX1 recruitment

Increasing deletion sizes and the efficiency of CRISPR/Cas9‐mediated mutagenesis by SunTag‐mediated TREX1 recruitment

Improving abiotic stress tolerance of forage grasses – prospects of using genome editing

Plant chromosome engineering – past, present and future

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