Biology subjects

Itami, K.

Publications and source records attributed to Itami, K..

5 recordsLinked to original sources

bioRxiv2026

Synthetic activation of gibberellin signaling reveals spatial coordination of root growth

Gibberellins (GAs) influence cell division and elongation, profoundly shaping plant architecture and yield. GA perception occurs when bioactive GAs bind the receptor GID1, promoting DELLA degradation and activating transcriptional programs. While GA signaling in the root endodermis is essential for promoting root elongation, functions of other layers in spatial control of GA responses have not been explored. Here, we developed a synthetic GA (sGA) that does not bind endogenous GID1, together with a modified GID1 (mGID1) engineered to selectively recognize sGA, enabling cell-specific activation of GA signaling in vivo. Using this system in Arabidopsis, we demonstrate that coordinated action of GA signaling in the endodermis, epidermis, and other layers is required for full root elongation. Moreover, cell type-specific expression of GA biosynthetic enzymes indicates the existence of intercellular GA transport. The sGA-mGID1 system provides a versatile platform for spatially precise reprogramming of hormone signaling, enabling synthetic control of developmental processes such as root-shoot growth balance, thereby advancing applications in plant synthetic biology and sustainable crop improvement.

plant biology↗

bioRxiv2024

Chemical genetics reveals cross-activation of plant developmental signaling by the immune peptide-receptor pathway

Cells sense and integrate multiple signals to coordinate development and defence. A receptor-kinase signaling pathway for plant stomatal development shares components with the immunity pathway. The mechanism ensuring their signal specificities remains unclear. Using chemical genetics, here we report the identification of a small molecule, kC9, that triggers excessive stomatal differentiation by inhibiting the canonical ERECTA receptor-kinase pathway. kC9 binds to and inhibits the downstream MAP kinase MPK6, perturbing its substrate interaction. Strikingly, activation of immune signaling by a bacterial flagellin peptide nullified kC9s effects on stomatal development. This cross-activation of stomatal development by immune signaling depends on the immune receptor FLS2 and occurs even in the absence of kC9 if the ERECTA-family receptor population becomes suboptimal. Furthermore, proliferating stomatal-lineage cells are vulnerable to the immune signal penetration. Our findings suggest that the signal specificity between development and immunity can be ensured by MAP Kinase homeostasis reflecting the availability of upstream receptors, thereby providing a novel view on signal specificity.

plant biology↗

bioRxiv2023

Chemical inhibition of stomatal differentiation by perturbation of the master-regulatory bHLH heterodimer via an ACT-Like domain

Selective perturbation of protein interactions with chemical compounds enables dissection and control of developmental processes. Differentiation of stomata, cellular valves vital for plant growth and survival, is specified by the basic-helix-loop-helix (bHLH) heterodimers. Harnessing a new amination reaction, we here report a synthesis, derivatization, target identification, and mode of action of an atypical doubly-sulfonylated imidazolone, Stomidazolone, which triggers stomatal stem cell arrest. Our forward chemical genetics followed by biophysical analyses elucidated that Stomidazolone directly binds to the C-terminal ACT-Like (ACTL) domain of MUTE, a master regulator of stomatal differentiation, and perturbs its heterodimerization with a partner bHLH, SCREAM in vitro and in plant cells. On the other hand, Stomidazolone analogs that are biologically inactive did not bind to MUTE or disrupt the SCREAM-MUTE heterodimers. Guided by structural docking modeling, we rationally designed MUTE with reduced Stomidazolone binding. These engineered MUTE proteins are fully functional and confer Stomidazolone resistance in vivo. Our study identifies doubly-sulfonylated imidazolone as a direct inhibitor of the stomatal master regulator, further expanding the chemical space for perturbing bHLH-ACTL proteins to manipulate plant development.

plant biology↗

bioRxiv2020

A unique small molecule pair controls the plant circadian clock

Circadian clocks are the biological time keeping systems that coordinate genetic, metabolic, and physiological behaviors with the external day-night cycle. Previous studies have suggested possible molecular mechanisms for the circadian clock in Arabidopsis thaliana (Arabidopsis), but there might be additional mechanisms that have been hidden due to genetic redundancy. A clock reporter line of Arabidopsis was screened against the 10,000 chemicals in the Maybridge Hitfinder10K chemical library, and a structure-activity relationship study of hit compounds was conducted. Clock mutants were treated with two of the small molecules to gain insight into their mode of action. The screening identified 5-(3,4-dichlorophenyl)-1-phenyl-1,7-dihydro-4H-pyrazolo[3,4-d]pyrimidine-4,6(5H)-dione (TU-892) as a period lengthening molecule. From a structure-activity relationship study, we found that a molecule possessing 2,4-dichlorophenyl instead of a 3,4-dichlorophenyl group (TU-923) had period shortening activity. The period shortening activity of TU-923 was reversed to a lengthening activity in double mutants lacking PSEUDO-RESPONSE REGULATOR 9 (PRR9) and PRR7 (prr9-10 prr7-11). Our study provides a unique small molecule pair that regulates the pace of the clock in opposite ways, likely by targeting unknown factors. Small differences at the atomic level can reverse the period tuning activities. PRR9 and PRR7 are essential for the activity of TU-923 in period shortening.

plant biology↗

bioRxiv2020

Effect of nanocarbon molecules on the Arabidopsis thaliana transcriptome

Nanocarbons, such as fullerenes, carbon nanotubes, and graphene have attracted a great deal of attention as next-generation materials because of their unprecedented structures and unique physicochemical properties; however, almost all nanocarbons reported previously were used as mixtures. Thus, there are still many unsolved issues about their biological functions at the molecular level. Our synthetic campaign in the last decade has synthesized structurally uniform and atomically precise nanocarbons, leading to the preparation of a library consisting of eighty structurally diverse nanocarbon molecules. This resource motivated us to explore the as yet uncovered biological functions of these nanocarbon molecules in organisms. Recently, nanotubes were used to deliver genes to plants; however, the effects of the molecules on plants are not well known. To monitor the effects of nanocarbon molecules on plants, we analyzed the transcriptome of Arabidopsis thaliana seedlings treated with [9]cycloparaphenylene (CPP), decaborylated warped nanographene (WNG), and dimethoxyhexabenzotetracene (HBT). Clustering analysis indicated few effects of nanocarbon molecules on the transcriptome, perhaps suggesting a low toxicity of nanocarbon molecules on plants. We found that AT1G05880 (ARIADNE 12) gene, categorized into response to hypoxia genes, was up-regulated by nanocarbon molecules, suggesting that this gene is usable as maker for treatment of nanocarbon molecules.

plant biology↗