Targeted base editing in the plastid genome of Arabidopsis thaliana

Nakazato, Issei; Okuno, Miki; Yamamoto, Hiroshi; Tamura, Yoshiko; Itoh, Takehiko; Shikanai, Toshiharu; Takanashi, Hideki; Tsutsumi, Nobuhiro; Arimura, Shin‐ichi

doi:10.1038/s41477-021-00954-6

Cited by 78 publications

(75 citation statements)

References 41 publications

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“…Although the technology to replace both Rubisco subunits was recently reported for tobacco ( 19 ), transformed plants must be able to produce sufficient amount of Rubisco to take advantage of improved kinetics. Emerging technologies such as targeted base editing of chloroplast genes ( 49 ) should expand the engineering of Rubisco to other plants where generation of stable chloroplast transformation is not available. The procedure in this study can be a blueprint to identify superior Rubiscos in other families to eventually enhance carbon fixation in agricultural crops such as rice and wheat.…”

Section: Discussionmentioning

confidence: 99%

Improving the efficiency of Rubisco by resurrecting its ancestors in the family Solanaceae

et al. 2022

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Plants and photosynthetic organisms have a remarkably inefficient enzyme named Rubisco that fixes atmospheric CO 2 into organic compounds. Understanding how Rubisco has evolved in response to past climate change is important for attempts to adjust plants to future conditions. In this study, we developed a computational workflow to assemble de novo both large and small subunits of Rubisco enzymes from transcriptomics data. Next, we predicted sequences for ancestral Rubiscos of the (nightshade) family Solanaceae and characterized their kinetics after coexpressing them in Escherichia coli . Predicted ancestors of C 3 Rubiscos were identified that have superior kinetics and excellent potential to help plants adapt to anthropogenic climate change. Our findings also advance understanding of the evolution of Rubisco’s catalytic traits.

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Section: Discussionmentioning

confidence: 99%

Improving the efficiency of Rubisco by resurrecting its ancestors in the family Solanaceae

et al. 2022

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“…DdCBEs have also been applied in chloroplasts. In A. thaliana , ptpTALECDs were obtained by modifying DdCBEs to make them suitable for A. thaliana , confirming that the base editing system could efficiently edit 16S , rpoC1 , and psbA ( Nakazato et al, 2021 ). As with mitochondria, chloroplast BEs based on CRISPR-Cas9 have not yet been developed, but based on what is available, the transformation of BEs in chloroplasts should allow base editing.…”

Section: Modified Gene-editing Systemsmentioning

confidence: 83%

Modified Gene Editing Systems: Diverse Bioengineering Tools and Crop Improvement

Zhu

2022

Front. Plant Sci.

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Gene-editing systems have emerged as bioengineering tools in recent years. Classical gene-editing systems include zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats (CRISPR) with CRISPR-associated protein 9 (Cas9) (CRISPR/Cas9), and these tools allow specific sequences to be targeted and edited. Various modified gene-editing systems have been established based on classical gene-editing systems. Base editors (BEs) can accurately carry out base substitution on target sequences, while prime editors (PEs) can replace or insert sequences. CRISPR systems targeting mitochondrial genomes and RNA have also been explored and established. Multiple gene-editing techniques based on CRISPR/Cas9 have been established and applied to genome engineering. Modified gene-editing systems also make transgene-free plants more readily available. In this review, we discuss the modifications made to gene-editing systems in recent years and summarize the capabilities, deficiencies, and applications of these modified gene-editing systems. Finally, we discuss the future developmental direction and challenges of modified gene-editing systems.

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“…Recent developments in plastid gene editing, also in cereals, may assist in generating and analyzing both types of mutations in barley and learn how they might modulate physiology and development of the plant under normal and high temperatures. Recent experiments suggest that most recent developments of TALLEN-based allele editing tested in Arabidopsis (Nakazato et al, 2021) could also be applied in barley (Fridman and Arimura, Personal communication) to allow such multi-layer analysis of isogenic mutants.…”

Section: Discussionmentioning

confidence: 99%

Plasmotype condition nuclear pleiotropic effects on clock and fitness in barley

Bdolach

Prusty

Tiwari

et al. 2021

Preprint

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In plants, the role of chloroplasts and mitochondria (plasmotype) in controlling circadian clock plasticity and overall plant robustness has not been elucidated. In this study, we investigated the rhythmicity of chlorophyll fluorescence (Chl F) clock output, and fitness in the field at optimal and elevated temperatures, in three different barley populations. First, we examined a reciprocal DH population between two wild barley (Hordeum vulgare ssp. spontaneum), in which we identified two pleiotropic QTLs (frp2.1 and amp7.1) that modulate clock and fitness including conditioning of these effects by plasmotype diversity. In the second population, a complete diallel consisting of 11 genotypes (reciprocal hybrids differing in plasmotype), we observed a gradual reduction in plasmotype, ranging from 26% and 15% for Chl F and clock measurements to 5.3% and 3.7% for growth and reproductive traits, respectively. The third population studied was a collection of cytolines in which nine different wild plasmotypes replaced the cultivated Noga (H. vulgare) plasmotype. Here, the order and magnitude of the effects of the plasmotypes differed from what we observed in the diallel population, with the greatest effect of plasmotype diversity observed for clock period and amplitude. Comparison of the chloroplast sequences suggests several candidate genes in the plastid-encoded RNA polymerase (PEP) complex that may be responsible for the observed plasmotype effects. Overall, our results unravel previously unknown cytonuclear epistatic interactions that controls clock performance while also having pleiotropic effects on a plant field characteristics.

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Targeted base editing in the plastid genome of Arabidopsis thaliana

Cited by 78 publications

References 41 publications

Improving the efficiency of Rubisco by resurrecting its ancestors in the family Solanaceae

Improving the efficiency of Rubisco by resurrecting its ancestors in the family Solanaceae

Modified Gene Editing Systems: Diverse Bioengineering Tools and Crop Improvement

Plasmotype condition nuclear pleiotropic effects on clock and fitness in barley

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