Takuya Kaji

Plant oxylipins include the jasmonates, lipid-derived hormones that control growth–defense trade-offs. In tracheophytes, (3R,7S)-jasmonoyl-L-isoleucine (JA-Ile) is the principal bioactive ligand that assembles the COI1–JAZ co-receptor together with inositol polyphosphates, leading to JAZ degradation and transcriptional reprogramming. By contrast, bryophytes employ dn-cis/iso-12-oxo-phytodienoic acid (OPDA) and related species, revealing evolutionary diversity in ligand identity and receptor matching. This review synthesizes chemical perspectives on jasmonate signaling. First, we outline the ‘molecular glue’ logic of COI1–JAZ assembly and the current structural gap beyond Arabidopsis that limits lineage-level, structure-guided discussion. Second, we summarize multilayered metabolic circuits that sculpt signal intensity, duration, and spatial distribution: oxidation of JA-Ile to 12-OH- and 12-COOH-JA-Ile; hydrolysis; and hydroxylation of the JA backbone. Notably, 12-OH-JA-Ile can function as a weak and ‘biased’ agonist, whereas 12-COOH-JA-Ile is receptor silent; in Marchantia, dn-iso-OPDA is chiefly inactivated by conjugation with amino acids, paralleling auxin logic. Third, we review evidence for co-evolution of ligands with COI1/JAZ components across land plants. Finally, we highlight the design of COI1–JAZ subtype-selective agonists and antagonists—often based on coronatine scaffolds—that preferentially recruit specific JAZ proteins to promote ERF/ORA outputs while sparing MYC branch responses. These chemical levers suggest practical routes to amplify defense with reduced growth costs, offering opportunities for stress-resilient crop improvement.

Jasmonoyl-L-isoleucine (JA-Ile) is a pivotal oxylipin plant hormone that regulates numerous physiological processes and stress responses. Because JA-Ile is synthesized from jasmonic acid (JA), the cellular level of JA is tightly controlled. Although the oxidative catabolism of JA to 12-hydroxy-JA (12-OH-JA) is well-characterized, the biosynthesis, accumulation dynamics, and biological functions of 11-hydroxy-JA (11-OH-JA) remain poorly understood. Here, we conducted a comprehensive investigation of 11-OH-JA in Arabidopsis thaliana , encompassing its chemical synthesis, accumulation patterns, biological activity, and biosynthetic pathways. Using chemically synthesized 11-OH-JA of naturally occurring (3 R ,7 S )-stereochemistry, we identified 11-OH-JA as the predominant hydroxylated JA derivative that accumulates following wounding. Enzymatic assays and in silico docking studies revealed that JOX1/2/3/4 exclusively catalyze the conversion of JA to 11-OH-JA, whereas 12-OH-JA is produced by distinct pathways. Notably, the quadruple mutant joxQ completely abolished 11-OH-JA accumulation without affecting 12-OH-JA levels. Furthermore, 11-OH-JA exhibited no binding affinity for the COI1-JAZ co-receptor, indicating that it acts as a biologically inactive shunt product of JA catabolism. Our findings establish JOX-mediated 11-hydroxylation of JA as a primary inactivation pathway, separate from 12-hydroxylation. Parallel, non-redundant inactivation routes deliver layered signal termination of costly defense signals. This study provides new insights into JA catabolism, highlighting 11-OH-JA as a crucial factor in the attenuation of jasmonate signaling, and thereby redefining the framework of JA turnover in A. thaliana .

Jasmonates (JAs) are a family of oxylipin phytohormones regulating plant development and growth and mediating ‘defense versus growth’ responses. The upstream JA biosynthetic precursor cis-(+)-12-oxo-phytodienoic acid (cis-OPDA) acts independently of CORONATIVE INSENSITIVE 1 (COI1)-mediated JA signaling in several stress-induced and developmental processes. However, its perception and metabolism are only partially understood. A few years ago, a low abundant isoleucine analog of the biologically active JA-Ile, OPDA-Ile, was detected years ago in wounded leaves of flowering plants, opening up the possibility that conjugation of cis-OPDA to amino acids might be a relevant mechanism for cis-OPDA regulation. Here, we extended the analysis of amino acid conjugates of cis-OPDA and identified naturally occurring OPDA-Val, OPDA-Phe, OPDA-Ala, OPDA-Glu, and OPDA-Asp accumulating in response to biotic and abiotic stress in Arabidopsis (Arabidopsis thaliana). The OPDA-amino acid conjugates displayed cis-OPDA-related plant responses in a JA-Ile-dependent manner. We also showed that the synthesis and hydrolysis of cis-OPDA amino acid conjugates are mediated by members of the amidosynthetase GRETCHEN HAGEN 3 (GH3) and the amidohydrolase INDOLE-3-ACETYL-LEUCINE RESISTANT 1 (ILR1)/ILR1-like (ILL) families. Thus, OPDA amino acid conjugates function in the catabolism or temporary storage of cis-OPDA in stress responses instead of acting as chemical signals per se.

Jasmonates are important phytohormones that regulate plant tolerance to biotic and abiotic stresses, and developmental processes. Distinct jasmonates in different plant lineages activate a conserved signalling pathway that mediates these responses: dinor-12-oxo-phytodienoic acid (dn-OPDA) isomers in bryophytes and lycophytes, and JA-Ile in most vascular plants. In many cases, the final responses triggered by these phytohormones depend on the accumulation of specialized metabolites. To identify compounds regulated by the dn-OPDA pathway in the liverwort Marchantia polymorpha, untargeted metabolomic analyses were carried out in response to wounding, a stress that activates the dn-OPDA pathway. A previously unreported group of molecules was identified from these analyses: dn-OPDA-amino acid conjugates (dn-OPDA-aas). Their accumulation after wounding and herbivory was confirmed by targeted metabolic profiling in Marchantia and in all species in which we previously detected dn-iso-OPDA. Mutants in GRETCHEN-HAGEN 3A (MpGH3A) failed to accumulate dn-OPDA-aa conjugates and showed a constitutive activation of the OPDA pathway and increased resistance to herbivory. Our results show that dn-iso-OPDA bioactivity is reduced by amino acid conjugation. Therefore, jasmonate conjugation in land plants plays dichotomous roles: jasmonic acid (JA) conjugation with isoleucine (Ile) produces the bioactive JA-Ile in tracheophytes, whereas conjugation of dn-iso-OPDA with different amino acids deactivates the phytohormone in bryophytes and lycophytes.

Jasmonates are important phytohormones activating plant tolerance to biotic and abiotic stress, as well as different development processes. A conserved signalling pathway activated by distinct hormones in different plant species mediates these responses: dinor-12-oxo-phytodienoic acid (dn-OPDA) isomers in bryophytes and lycophytes, and JA-Ile in most vascular plants. The final responses depend, in many cases, on the accumulation of specialized metabolites. To identify novel compounds regulated by the dn-OPDA pathway in Marchantia, untargeted metabolomic analyses were carried out in response to dn-OPDA-regulated stress. A novel group of molecules were identified as dn-OPDA-amino acid conjugates (dn-OPDA-aas), and their accumulation after wounding and herbivory confirmed by targeted metabolic profiling in Marchantia and all species in which we previously found dn- iso -OPDA. Mutants in GRETCHEN-HAGEN 3A (Mp GH3A ) failed to accumulate dn-OPDA-aa conjugates, and showed a constitutive activation of the OPDA pathway and increased resistance to herbivory. Our results show that dn- iso -OPDA bioactivity is reduced by conjugation with amino acids. Therefore, a dichotomous role of jasmonate conjugation in land plants is highlighted: jasmonic acid (JA) conjugation with isoleucine (Ile) produce the bioactive JA-Ile in tracheophytes, whereas conjugation of dn- iso -OPDA with different amino acids disactivate the hormone in bryophytes and lycophytes.

Lysocin E, a 37-membered natural depsipeptide, induces rapid bacteriolysis in methicillin-resistant Staphylococcus aureus via a unique menaquinone-dependent mechanism, presenting a promising therapeutic lead. Despite the great medical importance, exploring the potential utility of its derivatives as new platform structures for antibiotic development has remained a significant challenge. Here, we report a high-throughput strategy that enabled the preparation of thousands of analogues of lysocin E and large-scale structure-activity relationship analyses. We integrate 26-step total synthesis of 2401 cyclic peptides, tandem mass spectrometry-sequencing, and two microscale activity assays to identify 23 candidate compounds. Re-synthesis of these candidates shows that 11 of them (A1–A11) exhibit antimicrobial activity superior or comparable to that of lysocin E, and that lysocin E and A1–A11 share l-Leu-6 and l-Ile-11. Therefore, the present strategy allows us to efficiently decipher biologically crucial residues and identify potentially useful agents for the treatment of infectious diseases.

Synthetic methods that provide control over macrocycle conformation represent valuable tools for the discovery of bioactive molecules. Incorporation of heterocycles into cyclic peptides may offer a way to stabilize their solution conformations. Herein, we used N-(isocyanimino)triphenylphosphorane (Pinc) to install an oxadiazole ring and an endocyclic amine into peptide macrocycles. To elucidate the conformational effect of this constellation of functionalities, we performed synthesis, variable temperature NMR analysis, and NOE-based molecular dynamics simulation of a range of macrocycles in DMSO. As part of this study, we conducted experiments to compare macrocycle conformation in aqueous and DMSO solutions. The obtained solution structures suggest that the reduced amide bond/heterocycle (RAH) motif can stabilize macrocycle conformations in both water and DMSO, which addresses an enduring challenge in molecular design. The conformational effect of the RAH was used in an effort to mimic the biologically relevant secondary structure of MAdCAM-1. This resulted in the discovery of a novel α₄β₇ integrin antagonist.

WAP-8294A2 (lotilibcin, 1) is a potent antibiotic with superior in vivo efficacy to vancomycin against methicillin-resistant Staphylococcus aureus (MRSA). Despite the great medical importance, its molecular mode of action remains unknown. Here we report the total synthesis of complex macrocyclic peptide 1 comprised of 12 amino acids with a β-hydroxy fatty-acid chain, and its deoxy analogue 2. A full solid-phase synthesis of 1 and 2 enabled their rapid assembly and the first detailed investigation of their functions. Compounds 1 and 2 were equipotent against various strains of Gram-positive bacteria including MRSA. We present evidence that the antimicrobial activities of 1 and 2 are due to lysis of the bacterial membrane, and their membrane-disrupting effects depend on the presence of menaquinone, an essential factor for the bacterial respiratory chain. The established synthetic routes and the menaquinone-targeting mechanisms provide valuable information for designing and developing new antibiotics based on their structures.