Biology subjects

Kuroiwa, K.

Publications and source records attributed to Kuroiwa, K..

4 recordsLinked to original sources

bioRxiv2026

Alternative splicing expands the functional portfolio of a plant virus to control the viral cycle

Viruses frequently have limited coding space, yet efficiently manipulate complex hosts by deploying intricate, often poorly understood strategies. Geminiviruses, devastating plant pathogens with small single-stranded (ss) DNA genomes, replicate in the nucleus aided by the viral replication-associated protein (Rep), the most conserved protein within this family and related ssDNA viruses. Rep initiates viral DNA replication and represses its own promoter to regulate the infection cycle. The molecular mechanisms enabling this dual functionality are so far unknown. Here, we show that the geminivirus tomato yellow leaf curl virus (TYLCV) exploits the host spliceosome to produce novel Rep splice variants. Splicing generates Rep isoforms lacking the central oligomerization domain that cannot initiate replication but strongly repress the Rep promoter. Conversely, Rep mutants deficient in splicing promote replication but fail to repress transcription. Reduced Rep splicing interferes with the viral gene expression hierarchy and decreases infectivity. Our findings therefore reveal a previously unrecognized viral strategy in which alternative splicing produces functionally specialized viral protein isoforms, providing a mechanistic explanation for the dual role of Rep in viral replication and gene regulation. Splicing events with potentially similar functional consequences in related viruses suggest that this strategy may have convergently evolved across diverse viral lineages infecting different domains of life.

plant biology↗

bioRxiv2025

Restricted edition of ALS is required during co-edition in order to maintain normal tomato development

Co-editing strategies have emerged as an approach to facilitate the selection of CRISPR/Cas-mediated mutants in a transgene-free manner: the gene of interest is edited together with a reporter gene, whose mutation can be selected visually or pharmacologically. In this work, we asses the impact of editing the well-used reporter Acetolactate synthase (ALS) on plant development and metabolome. We show that the desired mutation in ALS1 (P186S) conferring selectable herbicide resistance trait does not show significant impact on the plant morphology and physiology but that the additional mutations resulting from the same sgRNA can result in reduced vegetative vigor and altered metabolomic profiles in tomato.

plant biology↗

bioRxiv2024

Tunicate-specific protein Epi-1 is essential for conferring hydrophilicity to the larval tunic in the ascidian Ciona

Animals must avoid adhesion to objects in the environment to maintain their mobility and independence. The marine invertebrate chordate ascidians are characterized by an acellular matrix tunic enveloping their entire body for protection and swimming. The tunic of ascidian larvae consists of a surface cuticle layer and inner matrix layer. Hydrophilic substances coat the cuticle; this modification is thought to be for preventing adhesion. However, the molecule responsible for regulating this modification has not been clarified. We here found that the tunicate-specific protein Epi-1 is responsible for preventing adhesiveness of the tunic in the ascidian Ciona intestinalis Type A. Ciona mutants with homozygous knockouts of Epi-1 exhibited adhesion to plastic plates and to other individuals. The cuticle of the Epi-1 mutants was fragile, and it lost the glycosaminoglycans supplied by test cells, the accessory cells that normally attach to the tunic surface. Although it has an apparent signal peptide for membrane trafficking, we showed that the Epi-1 protein is localized to the cytosol of the epidermal cells. Our study demonstrated that the emergence of the tunicate-specific protein Epi-1 accelerated the immediate ancestor of tunicates to evolve a tunic by providing a way to avoid the adhesiveness of this structure. HighlightsO_LIThe ascidian Ciona tunic has a glycosaminoglycan (GAG)-coated hydrophilic cuticle. C_LIO_LIEpi-1 is a protein expressed in the epidermis of tunicates during embryogenesis. C_LIO_LIEpi-1 Ciona mutants have GAG-free, hydrophobic and therefore sticky cuticles. C_LIO_LIEpi-1 acquisition may have prevented adhesion of tunicates to environmental objects. C_LI

developmental biology↗

bioRxiv2022

An iterative gene editing strategy broadens eIF4E1 genetic diversity in Solanum lycopersicum and generates resistance to several potyvirus isolates

Resistance to potyviruses in plants have been largely provided by the selection of natural variant alleles of eukaryotic initiation factors (eIF) 4E in many crops. However, the sources of such variability for breeding can be limited for certain crop species, while new virus strains continue to emerge. Different methods of mutagenesis have been applied to inactivate the eIF4E genes to generate virus resistance, but with limited success due to the physiological importance of translation factors and their redundancy. Here, we employed genome editing approaches at the base level to induce non-synonymous mutations in the eIF4E1 gene and create genetic diversity in cherry tomato (Solanum lycopersicum var. cerasiforme). We sequentially edited the genomic sequences coding for two regions of eIF4E1 protein, located around the cap-binding pocket and known to be important for susceptibility to potyviruses. We show that the editing of only one of the two regions, by gene knock-in and base-editing, respectively, is not sufficient to provide resistance. However, combining amino acid mutations in both regions resulted in resistance to multiple potyviruses without affecting its functionality in translation initiation. Meanwhile, we report that extensive base editing in exonic region can alter RNA splicing pattern, resulting in gene knockout. Altogether our work demonstrates that precision editing allows to design plant factors based on the knowledge on evolutionarily selected alleles and enlarge the gene pool to potentially provide advantageous phenotypes such as pathogen resistance.

plant biology↗