Plant genome editing by CRISPR–Cas systems

Since its first appearance, CRISPR–Cas9 has been developed extensively as a programmable genome-editing tool, opening a new era in plant genome engineering. However, CRISPR–Cas9 still has some drawbacks, such as limitations of the protospacer-adjacent motif (PAM) sequence, target specificity, and the large size of the cas9 gene. To combat invading bacterial phages and plasmid DNAs, bacteria and archaea have diverse and unexplored CRISPR–Cas systems, which have the potential to be developed as a useful genome editing tools. Recently, discovery and characterization of additional CRISPR–Cas systems have been reported. Among them, several CRISPR–Cas systems have been applied successfully to plant and human genome editing. For example, several groups have achieved genome editing using CRISPR–Cas type I-D and type I-E systems, which had never been applied for genome editing previously. In addition to higher specificity and recognition of different PAM sequences, recently developed CRISPR–Cas systems often provide unique characteristics that differ from well-known Cas proteins such as Cas9 and Cas12a. For example, type I CRISPR–Cas10 induces small indels and bi-directional long-range deletions ranging up to 7.2 kb in tomatoes (Solanum lycopersicum L.). Type IV CRISPR–Cas13 targets RNA, not double-strand DNA, enabling highly specific knockdown of target genes. In this article, we review the development of CRISPR–Cas systems, focusing especially on their application to plant genome engineering. Recent CRISPR–Cas tools are helping expand our plant genome engineering toolbox

Genome engineering of woody plants : past, present and future

Engineered endonucleases that digest the specific sequences can be used to modify target genomes precisely. This is called “genome editing” and is used widely to modify the genome of various organisms. The DNA-binding domains of zinc finger (ZF) proteins were the first to be used as a genome editing tool, in the form of designed ZF nucleases and, more recently, transcription activator-like effector as well as the clustered, regularly interspaced, short palindromic repeats and CRISPR-associated protein 9 (CRISPR/Cas9) system that targets RNA–DNA rather than protein–DNA interactions have been used successfully. These are powerful tools with which targeted gene modifications can be introduced in various organisms, including various plant species. A key step in genome editing is the generation of a double-stranded DNA break that is specific to the target gene. This is achieved using custom-designed endonucleases, which enable site-directed mutagenesis via a non-homologous end joining repair pathway and/or gene targeting via homologous recombination to occur efficiently at specific sites in the genome. This review provides an overview of the current status of genomics and genetic engineering of woody plants, and recent advances in genome editing technologies in plants as well as fungi. We also discuss how these strategies can provide insights into molecular breeding technology for woody plants

Precision genome editing in plants : state-of- the-art in CRISPR/Cas9-based genome engineering

Traditionally, generation of new plants with improved or desirable features has relied on laborious and time-consuming breeding techniques. Genome-editing technologies have led to a new era of genome engineering, enabling an effective, precise, and rapid engineering of the plant genomes. Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (CRISPR/Cas9) has emerged as a new genome-editing tool, extensively applied in various organisms, including plants. The use of CRISPR/Cas9 allows generating transgene-free genome-edited plants (“null segregants”) in a short period of time. In this review, we provide a critical overview of the recent advances in CRISPR/Cas9 derived technologies for inducing mutations at target sites in the genome and controlling the expression of target genes. We highlight the major breakthroughs in applying CRISPR/Cas9 to plant engineering, and challenges toward the production of null segregants. We also provide an update on the efforts of engineering Cas9 proteins, newly discovered Cas9 variants, and novel CRISPR/Cas systems for use in plants. The application of CRISPR/Cas9 and related technologies in plant engineering will not only facilitate molecular breeding of crop plants but also accelerate progress in basic research

Genome editing in mammalian cells using the CRISPR type I-D nuclease

Adoption of CRISPR–Cas systems, such as CRISPR–Cas9 and CRISPR–Cas12a, has revolutionized genome engineering in recent years; however, application of genome editing with CRISPR type I—the most abundant CRISPR system in bacteria—remains less developed. Type I systems, such as type I-E, and I-F, comprise the CRISPR-associated complex for antiviral defense (‘Cascade’: Cas5, Cas6, Cas7, Cas8 and the small subunit) and Cas3, which degrades the target DNA; in contrast, for the sub-type CRISPR–Cas type I-D, which lacks a typical Cas3 nuclease in its CRISPR locus, the mechanism of target DNA degradation remains unknown. Here, we found that Cas10d is a functional nuclease in the type I-D system, performing the role played by Cas3 in other CRISPR–Cas type I systems. The type I-D system can be used for targeted mutagenesis of genomic DNA in human cells, directing both bi-directional long-range deletions and short insertions/deletions. Our findings suggest the CRISPR–Cas type I-D system as a unique effector pathway in CRISPR that can be repurposed for genome engineering in eukaryotic cells

Multiplex Genome Editing in Tomato

Several expression systems for multiple guide RNA (gRNAs) have been developed in the CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/CRISPR associated protein 9) system to induce multiple-gene modifications in plants. Here, we evaluated mutation efficiencies in the tomato genome using multiplex CRISPR/Cas9 vectors consisting of various Cas9 expression promoters with multiple gRNA expression combinations. In transgenic tomato calli induced with these vectors, mutation patterns varied depending on the promoters used to express Cas9. By using the tomato ELONGATION FACTOR-1α (SlEF1α) promoter to drive Cas9, occurrence of various types of mutations with high efficiency was detected in the tomato genome. Furthermore, sequence analysis showed that the majority of mutations using the multiplex system with the SlEF1α promoter corresponded to specific mutation pattern of deletions produced by self-ligation at two target sites of CRISPR/Cas9 with low mosaic mutations. These results suggest that optimizing the Cas9 expression promoter used in CRISPR/Cas9-mediated mutation improves multiplex genome editing, and could be used effectively to disrupt functional domains precisely in the tomato genome

Geotaxis and leaf-surface preferences mitigate negative effects of a predatory mite on an herbivorous mite.

Reproductive success and population growth of an herbivorous mite are limited by activities of phytoseiid predators. However, occurrences on upper versus lower leaf surfaces are sometimes mismatched between these prey and predators. The mismatch potentially mitigates predation risk for the prey species. We assessed factors that affect mite distributions on leaf surfaces, testing whether the presence of the phytoseiid mite Phytoseius nipponicus alters the leaf-surface distribution and reproductive success of the herbivorous false spider mite Brevipalpus obovatus. The host plant was Viburnum erosum var. punctatum (Adoxaceae). Leaves were set in natural (TRUE) and reversed (upside down; INVERTED) orientations using experimental devices. Both surfaces were accessible to mites. We detected lower and abaxial leaf-surface preferences in P. nipponicus. In contrast, upper and adaxial surfaces were preferred by B. obovatus. Thus, prey and predatory mites accumulated on different sides of leaves. Presence of the predator also indirectly decreased egg production in B. obovatus. Brevipalpus obovatus females actively avoided leaf surfaces with elevated predator numbers; these females shifted their distributions and changed oviposition sites to leaf surfaces with fewer predators. In consequence, B. obovatus eggs on the upper sides of leaves were less frequently preyed upon than were those on lower sides. We suggest that upper leaf-surface exploitation in this particular herbivorous mite species mitigates predation risk from phytoseiid mites, which prefer lower leaf surfaces

Note on the Graphite-Free Corundum-K feldspar Gneiss in the Hida Metamorphic Belt, Central Japan

The association of corundum-K feldspar in a graphite-free rock is newly found in the western portion of the Hida Metamorphic Belt, central Japan. The equilibrium assemblage of the rock is corundum-K feldspar-plagioclase-biotite-apatite-zircon-ore with no graphite. Ore minerals are characterized by the abundance of rutile and by the absence of ilmenite and/or magnetite. Corundum and K feldspar had been in direct contact with each other before the formation of kelyphitic rims of muscovite aggregates around corundum crystals. The association of corundum-K feldspar in the graphite-free system must suggest the formation by the breakdown of muscovite under the condition when PH2O is not so low. Therefore, the breakdown must occur more or less near the maximum temperature expected. The metamorphic conditions have been estimated by the stable associations of zincian spinel-garnet-biotite-sillimanite-K feldspar-plagioclase and clinopyroxene-garnet in the metamorphites from the area to be around 700°C and 6 kb, which are not inconsistent with the condition deduced from the association now discussed

Procyanidins in Theobroma cacao Reduce Plasma Cholesterol Levels in High Cholesterol-Fed Rats

We evaluated the effect of cacao procyanidins (CP) on plasma lipid levels in high cholesterol-fed rats. Animals were divided into 4 groups, and each group was fed on either a normal diet, high cholesterol diet (HCD) containing 1% cholesterol (HCD without CP), HCD with 0.5% (HCD with 0.5% CP) or 1.0% CP (HCD with 1.0% CP) for 4 weeks. Plasma cholesterol level was significantly higher in the HCD without CP group than the normal diet group (p<0.01). Supplementation of CP significantly decreased plasma cholesterol (p<0.01) to levels similar to those of the normal diet group. The liver cholesterol and triglyceride levels in all HCD groups were significantly higher (p<0.01), but 1.0% CP feeding significantly reduced this increase. Fecal excretion of neutral sterol and triglyceride was significantly increased in all HCD groups (p<0.01), and the excreted amounts tended to be higher in the HCD with CP groups. The procyanidins dose-dependently reduced micellar solubility of cholesterol and this activity increased with increasing molecular weight. These results suggest that one of the mechanisms of CP to lower plasma cholesterol is inhibition of intestinal absorption of cholesterol

SlIAA9 Controls Tomato Elongation

Tomato INDOLE-3-ACETIC ACID9 (SlIAA9) is a transcriptional repressor in auxin signal transduction, and SlIAA9 knockout tomato plants develop parthenocarpic fruits without fertilization. We generated sliaa9 mutants with parthenocarpy in several commercial tomato cultivars (Moneymaker, Rio Grande, and Ailsa Craig) using CRISPR-Cas9, and null-segregant lines in the T1 generation were isolated by self-pollination, which was confirmed by PCR and Southern blot analysis. We then estimated shoot growth phenotypes of the mutant plants under different light (low and normal) conditions. The shoot length of sliaa9 plants in Moneymaker and Rio Grande was smaller than those of wild-type cultivars in low light conditions, whereas there was not clear difference between the mutant of Ailsa Craig and the wild-type under both light conditions. Furthermore, young seedlings in Rio Grande exhibited shade avoidance response in hypocotyl growth, in which the hypocotyl lengths were increased in low light conditions, and sliaa9 mutant seedlings of Ailsa Craig exhibited enhanced responses in this phenotype. Fruit production and growth rates were similar among the sliaa9 mutant tomato cultivars. These results suggest that control mechanisms involved in the interaction of AUX/IAA9 and lights condition in elongation growth differ among commercial tomato cultivars