Flagellin from the rice avirulent N1141 strain of Acidovorax avenae, functions as a pathogen-associated molecular pattern （PAMP） and induces PAMP-triggered immunity （PTI） in rice.　To study the recognition mechanism of flagellin in rice, the region（s） definition of the flagellin protein required to activate the PTI response was attempted.　Among four fragments of N1141 flagellin, the C-terminal CD2-1 fragment induced PTI responses in cultured rice cells.　Synthetic flg22, which is sufficient to produce the flagellin response in Arabidopsis elicited no immune responses in rice.　In addition, CD2-1 triggered resistance to coinfection with pathogenic bacteria.　Taken together, these data suggest that rice mainly recognizes flagellin CD2-1, and that this epitope recognition leads to PTI responses.　To identify additional PAMPs from A. avenae N1141, cell extracts were isolated from flagellin-deficient N1141.　The cell extracts still induced PTI responses, suggesting that flagellin-deficient N1141 possesses an additional PAMP distinct from flagellin.　We showed that elongation factor Tu （EF-Tu）, one of the most abundant bacterial proteins, act as a PAMP in rice and causes several PTI responses.　Synthetic elf18, which is sufficient to produce the EF-Tu response in Arabidopsis, did not cause any immune responses in rice, whereas an EF-Tu middle region comprising Lys176 to Gly225, termed EFa50, is fully active as a PAMP in rice.　These data demonstrate that rice recognizes EFa50, which is distinct from elf18, and that this epitope induces PTI re­sponses.

Low temperature is a major factor that limits plant growth and productivity.　I have identified the OsMKK6-OsMPK3 chilling stress sig­naling pathway in rice.　The OsMKK6-OsMPK3 pathway is regulated by redox and activated by Reactive Oxygen Species （ROS） generated by mild chilling stress.　Constitutive activation of the OsMKK6-OsMPK3 pathway resulted in tolerance against sever chilling stress.　I also identified that trehalose biosynthesis is activated in response to mild chilling stress.　Decreasing trehalose 6-phosphate level by OsTPP1 may contribute to chilling tolerance through regulating photosynthesis under chilling.　In contrast, winter crops such as wheat are chilling tolerant and develop freezing tolerance through cold acclimation （CA）.　Among many genes induced through CA, I focused our research on the cold shock domain proteins （CSPs）.　Arabidopsis AtCSP3 functions as an RNA chaperone and positively regulates freezing tolerance independent of the CBF regulatory pathway.　CA also induces a set of pathogenesis related proteins which may contribute to the defense against snow mold fungus during overwintering.　

The moss Physcomitrella patens does not respond to active gibberellins （GAs）, and GAs have not been detected in the moss.　However, P. patens has a partial GA biosynthetic pathway that mediates the biosynthesis of the GA intermediate ent-kaurenoic acid （KA）.　Previous work demonstrated that P. patens KA-deficient mutants have defects in protonemal cell differentiation, which are restored by the application of KA but not by GAs.　Recently, I demonstrated that a KA-derived diterpenoid functions as a potent regulator of protonemal cell differentiation in the moss.　Bioassay-guided exploration with a KA-deficient mutant led to the detection of a bioactive metabolite from KA, and its structure was elucidated as ent-3β-hydroxy-kaurenoic acid.　Transcriptome analysis identified a gene encodes a putative 2-oxoglutarate-dependent dioxygenase involved in the oxidation of KA to ent-2α-hydroxy-kaurenoic acid, an inactive metabolite in protonemal cell differentiation.　My study showed that P. patens converts KA to an active form by 3-oxidation and to an inactive form by 2-oxidation, identifying a potential activation/inactivation system for GA biosynthesis in flowering plants.　Here I summarize the biosynthetic studies on GA-like plant growth regulators in a P. patens.

Amino acids, an essential component that constitutes proteins in vivo, are also known to play as a signaling molecule that regulates various physiological functions in the living organism.　Ionotropic glutamate receptors （iGluRs） are ligand-gated channels that specifically transmit amino acid signals in the central nervous system.　Surprisingly, homologs of iGluRs, known as glutamate receptor-like channels （GLRs）, were also found in higher plant genomes.　However, their physiological roles or molecular functions are still obscure.　Here, I review the latest research of plant GLRs and discuss their roles in plant signaling including environmental adaptation and cell-to-cell communications.

Various studies on flavonoid pigments related to the color development of blue flowers and their biosynthetic genes have been conducted for over 100 years.　Today, molecular breeding of blue flowers has become possible via the genetic manipulation of the pigment biosynthetic pathway present in some flowers.　Recently, blue transgenic chrysanthemums have been successfully generated by synthesizing artificial anthocyanins that interact with endogenous flavonoids.　In this review, I will describe and discuss the recent advances in blue-flower color breeding and the blue coloration mechanisms that help generate blue transgenic chrysanthemums.

Nitrate promotes seed germination in many plant species.　Its effect can be seen at low concentrations （< 1 mM） and even in the nitrate reductase deficient mutant, suggesting that nitrate itself, not assimilates, acts as a signal to promote seed germination.　Arabidopsis molecular genetics research have revealed that nitrate-induced expression of CYP707A2, encoding an abscisic acid （ABA） catabolism enzyme, play an important role in this process.　This regulation involves NIN-LIKE PROTEIN 8 （NLP8） transcription factor.　Nitrate activates NLP8, which allows directly binding the Nitrate Responsive Element （NRE） in the CYP707A2 promoter.　The induction of CYP707A2 leads to the decrease in seed ABA contents, which in turn promotes seed germination.　Understanding the function of nitrate in plants will be useful to create crops with low nitrogen use.

Chloroplasts change their intracellular position in response to environmental alterations.　What is being most studied is the relocation induced by light.　For example, chloroplasts move towards weak light, maximizing photosynthesis.　However, when ambient temperature decreases, chloroplasts escape from the weak light.　We call the cold-induced phenomenon “the chloroplast cold-avoidance response”.　In this review, I would like to summarize the findings on the chloroplast cold-avoidance response during the past over 100 years, and also propose a new hypothesis on biological thermosensing.

Strigolactones have diverse functions as plant hormones and as ecological signals to communicate with soil microbes.　Strigolactones are also exploited by parasitic plants, including noxious parasitic weeds called Striga hermonthica, as germination cues that enable efficient parasitism to their host plants.　Recent understanding for the mechanism of strigolactone perception by α/β-hydrolase receptors has provided opportunities to dissect the diverse functions with synthetic strigolactones.　Here, we introduce the design principle of the synthetic strigolactones, which relies on a hybrid of two functions encoded in the two substructures, ABC-ring and D-ring.　The principle discussed here has been applied to develop a Striga-selective suicide germination stimulant acting at femtomolar-range.

Tricholoma matsutake, a basidiomycete, forms ectomycorrhizas with Pinus densiflora as the host tree.　Its fruiting body, “matsutake” in Japanese, is an edible and highly prized mushroom, and it grows in a circle called a fairy ring.　Beneath the fairy ring of T. matsutake, a whitish mycelium-soil aggregated zone, called “shiro” in Japanese, develops.　The front of the shiro, an active mycorrhizal zone, functions to gather nutrients from the soil and roots to nourish the fairy ring.　Bacteria and sporulating fungi decrease from the shiro front, whereas they increase inside and outside the shiro front.　Ohara and Hamada demonstrated that the shiro front exhibited antimicrobial activity, but the antimicrobial substance has remained unidentified for 50 years.　We have identified the antimicrobial substance as the （oxalato）aluminate complex, known as a reaction product of oxalic acid and insoluble aluminum phosphate to release soluble phosphorus.　The complex protects the shiro from micro­organisms, and contributes to its development.

Functional roles of small coding genes tend to be ignored in 20 years because small coding genes have not been identified in even highly accurate genomes of model organisms.　In plants, it is recognized that small coding genes play essential roles within a single cell as well as intercellular signal transductions like hormone-like peptides.　However, many of small coding genes are not annotated in plant genomes even if novel hormone-like peptides encoded by small coding genes tend to be hidden in plant genomes.　Here, we introduce transcriptome database （HanaDB-AT） and transgenic library of overexpression with focusing on Arabidopsis novel and annotated small coding genes.　The database and transgenic library should be useful tools to discover novel hormone-like peptides as well as other functional peptides in small coding genes.

Pith parenchyma cells store water in many plants.　These cells are important for producing sugar and ethanol from the sugar juice of grass stems.　A gene, long referred to as D, in a promising energy grass, Sorghum bicolor, that is responsible for reducing stem water content, has recently been identified.　Sorghum varieties with functional D had stems enriched with dry, dead pith parenchyma cells, whereas those with non-functional D had stems enriched with juicy, living pith parenchyma cells.　An Arabidopsis D homolog, ANAC074, was also required for the death of stem pith parenchyma cells.　D encodes a NAC transcription factor, which activates the autolytic enzymes involved in programmed cell death of plants.　These results suggest that D is the master transcriptional switch for executing programmed death of pith parenchyma cells in sorghum stems.　Thus, identifying D will provide a new approach to breeding crops for sugar and ethanol production.

The plant phloem system transports both essential nutrients and long-distance signaling agents.　Recent transcriptomics studies and grafting experiments have demonstrated that several thousand mRNAs and various small noncoding RNAs are moved over long-distances via the phloem.　Therefore, by using grafting, it is possible to deliver artificial RNAs which are derived from a designed DNA construct in the transgenic plant into the graft partner plant, and to induce heritable TGS （transcriptional gene silencing） via RdDM （RNA directed DNA Methylation）.　We developed an epigenome editing system of an endogenous gene of potato （Solanum tuberosum）.　We address potential function of siRNA（small interfering RNA） in grafting system with respect to epigenetic breeding.

To produce recombinant proteins and identify the gene functions, such as subcellular localization, one of the strongest agro-infiltration-based transient protein expression system for plant cells, termed ‘Tsukuba system’ has been established.　By using this system, about 4 mg/g fresh weight of protein expression was detected in Nicotiana benthamiana.　Furthermore, the system is also applicable to various plant species, including eggplant, tomato cultivars and wild species, lettuce, hot pepper, soybean, common bean, and orchid.　The vector pBYR2HS contains a geminiviral replication system and a double terminator.　Thus, the system is an effective and valuable tool for rapid transient expression to obtain a bunch of proteins and to examine gene function.

We have developed the vaccine rice for cedar pollen allergy and have been trying to commercialize it since then.　At first, we aimed to commercialize it as food for specified health use, but the Ministry of Health, Labour and Welfare had a different opinion.　Then, we had made efforts to bring it out as the medicine by consulting with Pharmaceuticals and Medical Devices Agency （PMDA）.　However, any pharmaceutical companies embarked on this challenging project.　Now, we are trying to accumulate the evidence in clinical studies in collaboration with medical institutions.　Hopefully, a new functional food category between medicine and food will be established in near future and the vaccine rice will be approved as a functional food by receiving a big boost from patients suffer from pollinosis.