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Biology subjects

Osakabe, Y.

Publications and source records attributed to Osakabe, Y..

6 recordsLinked to original sources

Sequentially Self-Assembled Supramolecular Nanocomplexes Enable Systemic Cas9 RNP Delivery and In Vivo Tumor Genome Editing

In vivo genome editing with CRISPR-Cas9 ribonucleoproteins (RNPs) holds substantial therapeutic promise, yet rapid bloodstream clearance and the absence of delivery systems capable of systemic tumor targeting have hindered its clinical translation. Herein, a supramolecular ternary complex platform is reported in which Cas9/sgRNA RNPs are co-assembled with tannic acid (TA) and phenylboronic acid (PBA)-conjugated polymers through sequential self-assembly, producing [~]30 nm core-shell ternary complexes that protect RNPs from enzymatic degradation and dissociate selectively at endosomal pH. Upon intravenous administration in subcutaneous tumor-bearing mice, these ternary complexes exhibit prolonged blood circulation and preferential tumor accumulation, achieving 37.2% gene editing at tumor sites compared with only 1.5% for free RNPs. The platform successfully knocks out previously undruggable oncogenes including mutant KRAS and polo-like kinase 1 (PLK1), markedly suppressing tumor growth in vivo. By integrating sequential supramolecular self-assembly with stimuli-responsive cargo release, this strategy establishes a generalizable framework for systemically administered in vivo CRISPR therapeutics.

bioengineering↗

Stacked mutations disrupting syringyl and p-coumaroylated lignin biosynthesis in rice result in lignin dominated by guaiacyl units: insights into grass-specific lignin monomer biosynthesis and polymerization mechanisms

O_LIThe aromatic composition of lignin significantly impacts the usability of lignocellulosic biomass. In eudicots, transgenic and mutant lines with elevated guaiacyl (G) or syringyl (S) lignin units have been successfully generated by manipulating the expression level of CONIFERALDEHYDE 5-HYDROXYLASE (CAld5H). However, this bioengineering approach has proven less effective in grasses, implicating the potential existence of a grass-specific alternative pathway for S lignin biosynthesis. C_LIO_LIThrough characterization of genome-edited rice mutants, we demonstrated that S lignin in rice can be virtually eliminated by disrupting genes encoding CAld5H along with p- COUMAROYL-COENZYME A:MONOLIGNOL TRANSFERASE (PMT), a grass-specific enzyme essential for the biosynthesis of monolignol p-coumarate conjugates. In contrast, individual mutations in either CAld5H or PMT genes resulted in incomplete elimination of S lignin. These findings provide strong evidence that rice possesses a CAld5H-independent pathway leading to the grass-specific monolignol p-coumarate conjugates. C_LIO_LIIn-depth structural characterizations of G-dominated lignins from rice and Arabidopsis mutants, natural gymnosperm pine, and G-type synthetic lignin revealed pronounced effects of lineage-dependent cell wall environments on the linkage patterns and molecular weight distributions of the resulting lignin polymers. C_LIO_LIOverall, our findings highlight previously overlooked lineage-specific lignin monomer biosynthesis and polymerization patterns in grasses. C_LI

plant biology↗

Essential Yet Dispensable: The Role of CINNAMATE 4-HYDROXYLASE in Rice Cell Wall Lignification

A comprehensive understanding of the intricate lignin biosynthesis in grasses could contribute to enhancing our ability to utilize grass biomass. CINNAMATE 4-HYDROXYLASE (C4H), in conjunction with PHENYLALANINE AMMONIA-LYASE (PAL), initiates the entry of phenylalanine into the cinnamate/monolignol pathway, leading to the production of diverse phenylpropanoids, including lignin monomers. Despite extensive research on C4H in eudicots, genetic studies of C4H in grasses remain considerably limited. Notably, the role of C4H in the presence of PHENYLALANINE/TYROSINE AMMONIA-LYASE (PTAL), a grass-specific ammonia-lyase that can bypass the conserved PAL-C4H pathway by recruiting tyrosine into the cinnamate/monolignol pathway, remains unclear. To address this gap, a set of genome-edited rice mutants harboring knockout mutations in rice C4H genes were generated and subjected to the analysis of growth phenotype and cell wall chemotype, alongside isotopic feeding and chemical inhibitor assays to test the contributions of the PAL-C4H and PTAL pathways. The phenotype and chemotype characterizations of C4H-knockout rice mutants demonstrated that class I (OsC4H1/CYP73A38) and class II (OsC4H2a/CYP73A39 and OsC4H2b/CYP73A40) C4Hs cooperatively contribute to lignin biosynthesis in rice. Nevertheless, the impacts of C4H-deficiency on plant development and lignin formation in rice appeared to be less prominent compared to those reported in eudicots. The 13C-labeled phenylalanine and tyrosine feeding experiments demonstrated that even with the phenylalanine-derived PAL-C4H pathway completely blocked, the C4H-knockout rice can still produce significant levels of lignin and maintain sound cell walls by utilizing the tyrosine-derived PTAL pathway. Overall, this study demonstrates the essential but dispensable role of C4H in grass cell wall lignification.

plant biology↗

The trans-zeatin-type side-chain modification of cytokinins controls rice growth

Cytokinins (CKs), a class of phytohormones with vital roles in growth and development, occur naturally with various side-chain structures, including N6-({Delta}2-isopentenyl)adenine-, cis-zeatin- and trans-zeatin (tZ)-types. Recent studies in a model dicot plant Arabidopsis demonstrated that tZ-type CKs are biosynthesized via cytochrome P450 monooxygenase (P450) CYP735A, and have a specific function in shoot growth promotion. Although the function of some of these CKs has been demonstrated in a few dicotyledonous plant species, the significance of these variations and their biosynthetic mechanism and function in monocots and in plants with distinctive side-chain profiles than Arabidopsis, such as Oryza sativa (rice), remain elusive. In this study, we characterized CYP735A3 and CYP735A4 to investigate the role of tZ-type CKs in rice. Complementation test of the Arabidopsis CYP735A-deficient mutant and CK profiling of loss-of-function rice mutant, cyp735a3 cyp735a4, demonstrated that CYP735A3 and CYP735A4 encode P450s required for tZ-type side-chain modification in rice. CYP735As are expressed in both roots and shoots. The cyp735a3 cyp735a4 mutants exhibited growth retardation concomitant with reduction in CK activity in both roots and shoots, indicating that tZ-type CKs function in growth promotion of both organs. Expression analysis revealed that tZ-type CK biosynthesis is negatively regulated by auxin, abscisic acid, and cytokinin and positively by dual nitrogen nutrient signals, namely glutamine-related and nitrate-specific signals. These results suggest that the physiological role of tZ-type CKs in rice is different from that in Arabidopsis and they control growth of both roots and shoots in response to internal and environmental cues in rice.

plant biology↗

The histidine phosphotransfer AHP4 plays a negative role in Arabidopsis plant response to drought

Cytokinin plays an important role in plant stress responses via a multistep signaling pathway, involving the histidine phosphotransfer proteins (HPs). In Arabidopsis thaliana, the AHP2, AHP3 and AHP5 proteins are known to impact drought responses; however, the role of AHP4 in drought adaptation remains undetermined. In the present study, using a loss-of-function approach we showed that AHP4 possesses a negative regulatory role in Arabidopsiss response to drought. This is evidenced by both higher survival rates of ahp4 than wild-type (WT) plants under drought conditions, and the down-regulated AHP4 expression in WT during periods of dehydration. Comparative transcriptome analysis of ahp4 and WT plants revealed AHP4-mediated expression of several dehydration- and/or abscisic acid (ABA)-responsive genes involved in regulation of various physiological and biochemical processes important for plant drought acclimation. In comparison with WT, ahp4 plants showed increased wax crystal accumulation in stems, thicker cuticles in leaves, greater sensitivity to exogenous ABA at germination, narrow stomatal apertures, heightened leaf temperatures during dehydration, and longer root length under osmotic stress. Additionally, ahp4 plants showed greater photosynthetic efficiency, lower levels of reactive oxygen species (ROS), reduced electrolyte leakage and lipid peroxidation, and increased anthocyanin contents under drought, when compared with WT. These differences displayed in ahp4 plants are likely due to up-regulation of genes that encode enzymes involved in ROS-scavenging and non-enzymatic antioxidant metabolism. The role of AHP4 in negative regulation of multiple protective mechanisms associated with drought tolerance could make editing of AHP4 a promising approach for the production of drought-tolerant crop plants. Significance statementLoss-of-function analysis of the cytokinin signaling member AHP4 revealed its function in Arabidopsis adaptation to drought as a negative regulator, affecting various physiological and biochemical processes by modulating the expression of a large set of genes potentially in a crosstalk with ABA. AHP4 and its homologs are promising candidates for gene editing to develop drought-tolerant crop cultivars.

plant biology↗

Genome editing in mammals and plants using CRISPR type I-D nuclease

Adoption of the CRISPR-Cas system has revolutionized genome engineering in recent years; however, application of genome editing with CRISPR type I--the most abundant CRISPR system in bacteria--has been less developed. Type I systems in which Cas3 nuclease degrades the target DNA are known; in contrast, for the sub-type CRISPR type I-D (TiD), which lacks a typical Cas3 nuclease in its cascade, the mechanism of target DNA degradation remains unknown. Here, we found that Cas10d--a nuclease in TiD--is multi-functional in PAM recognition, stabilization and target DNA degradation. TiD can be used for targeted mutagenesis of genomic DNA in human cells, directing both bi-directional long-range deletions and short insertions/deletions. TiD off-target effects, which were dependent on the mismatch position in the protospacer of TiD, were also identified. Our findings suggest TiD as a unique effector pathway in CRISPR that can be repurposed for genome engineering in eukaryotic cells.

molecular biology↗