Stephen Beungtae Ryu

In plants, effector-triggered immunity (ETI) is initiated when NLR receptors recognize pathogen effectors, yet the molecular signals linking this recognition to downstream defense activation remain poorly defined, in contrast to the well-characterized immunogenic signals of pattern-triggered immunity. Here, we show that a lysophospholipid is a previously unidentified ETI-mediating immune signal generated through host enzymatic conversion of pathogen membrane lipids. Upon recognition of avirulent Pseudomonas syringae, secretory phospholipase A2α (PLA2α) is rapidly induced and secreted into the apoplast, where it hydrolyzes bacterial phosphatidylethanolamine to produce lysophosphatidylethanolamines (LPEs), predominantly LPE18:1. Genetic ablation of PLA2α compromises local immunity, hypersensitive response confinement, and defense gene activation, all of which are fully rescued by exogenous LPE18:1. Mechanistically, LPE18:1 promotes ICS1-dependent salicylic acid biosynthesis and NPR1-mediated transcriptional reprogramming. Together, these findings support pathogen-derived LPE18:1 as a previously unrecognized lipid-based immune signal that links NLR activation to spatially confined defense responses. The evolutionary conservation of secretory PLA2 enzymes and lysophospholipid signaling from plants to mammals suggests that host-directed enzymatic remodeling of pathogen membranes into immune-activating lipid signals may constitute a fundamental and ancient strategy of innate immunity.

Natural rubber is usually synthesized in the rubber particles present in the latex of rubber-producing plants such as the Pará rubber tree (Hevea brasiliensis) and rubber dandelion (Taraxacum kok-saghyz). Since the detailed lipid compositions of fresh latex and rubber particles of the plants are poorly known, the present study reports detailed compound lipid composition, focusing on phospholipids and galactolipids in the latex and rubber particles of the plants. In the fresh latex and rubber particles of both plants, phospholipids were much more dominant (85–99%) compared to galactolipids. Among the nine classes of phospholipids, phosphatidylcholines (PCs) were most abundant, at ~80%, in both plants. Among PCs, PC (36:4) and PC (34:2) were most abundant in the rubber tree and rubber dandelion, respectively. Two classes of galactolipids, monogalactosyl diacylglycerol and digalactosyl diacylglycerol, were detected as 12% and 1%, respectively, of total compound lipids in rubber tree, whereas their percentages in the rubber dandelion were negligible (< 1%). Overall, the compound lipid composition differed only slightly between the fresh latex and the rubber particles of both rubber plants. These results provide fundamental data on the lipid composition of rubber particles in two rubber-producing plants, which can serve as a basis for artificial rubber particle production in the future.

Hevea brasiliensis, the most abundant rubber crop, is used widely for the commercial production of natural rubber. To reduce the risk of a shortage in the supply of natural rubber that may arise from a single major rubber crop, rubber dandelion (Taraxacum kok-saghyz) has been developed as an alternative rubber-producing crop by using a transgenic approach. However, it is necessary to identify a suitable promoter for the transfer of rubber biosynthesis-related genes to the species. In this study, the promoter region of H. brasiliensis PEP16, which was isolated as a potentially important component in rubber biosynthesis, was sequenced and a pPEP16::GUS fusion construct was introduced into T. kok-saghyz. Histological and fluorometric studies using transgenic T. kok-saghyz plants indicated that the HbPEP16 promoter was highly activated in a laticiferous tissue-specific manner under normal growth conditions and that promoter activation was tightly regulated by various hormones and external signals. These findings suggested that the HbPEP16 promoter may be a useful molecular tool for the manipulation of gene expression in the laticiferous tissues of T. kok-saghyz.

Summary: Natural rubber (NR) is a nonfungible and valuable biopolymer, used to manufacture ~50 000 rubber products, including tires and medical gloves. Current production of NR is derived entirely from the para rubber tree (Hevea brasiliensis). The increasing demand for NR, coupled with limitations and vulnerability of H. brasiliensis production systems, has induced increasing interest among scientists and companies in potential alternative NR crops. Genetic/metabolic pathway engineering approaches, to generate NR‐enriched genotypes of alternative NR plants, are of great importance. However, although our knowledge of rubber biochemistry has significantly advanced, our current understanding of NR biosynthesis, the biosynthetic machinery and the molecular mechanisms involved remains incomplete. Two spatially separated metabolic pathways provide precursors for NR biosynthesis in plants and their genes and enzymes/complexes are quite well understood. In contrast, understanding of the proteins and genes involved in the final step(s)—the synthesis of the high molecular weight rubber polymer itself—is only now beginning to emerge. In this review, we provide a critical evaluation of recent research developments in NR biosynthesis, in vitro reconstitution, and the genetic and metabolic pathway engineering advances intended to improve NR content in plants, including H. brasiliensis, two other prospective alternative rubber crops, namely the rubber dandelion and guayule, and model species, such as lettuce. We describe a new model of the rubber transferase complex, which integrates these developments. In addition, we highlight the current challenges in NR biosynthesis research and future perspectives on metabolic pathway engineering of NR to speed alternative rubber crop commercial development.

A central goal of systems neuroscience is to relate an organism’s neural activity to behavior. Neural population analysis often begins by reducing the dimensionality of the data to focus on the patterns most relevant to a given task. A major practical hurdle to data analysis is spike sorting, and this problem is growing rapidly as the number of neurons measured increases. Here, we investigate whether spike sorting is necessary to estimate neural dynamics. The theory of random projections suggests that we can accurately estimate the geometry of low-dimensional manifolds from a small number of linear projections of the data. We re-analyzed data from three previous studies and found that neural dynamics and scientific conclusions are quite similar using multi-unit threshold crossings in place of sorted neurons. This finding unlocks existing data for new analyses and informs the design and use of new electrode arrays for laboratory and clinical use.

Persimmon (Diospyros kaki Thunb.), which is a climacteric fruit, softens in 3–5 weeks after harvest. However, little is known regarding the transcriptional changes that underlie persimmon ripening. In this study, high-throughput de novo RNA sequencing was performed to examine differential expression between freshly harvested (FH) and softened (ST) persimmon fruit peels. Using the Illumina HiSeq platform, we obtained 259,483,704 high quality reads and 94,856 transcripts. After the removal of redundant sequences, a total of 31,258 unigenes were predicted, 1,790 of which were differentially expressed between FH and ST persimmon (1,284 up-regulated and 506 down-regulated in ST compared with FH). The differentially expressed genes (DEGs) were further subjected to KEGG pathway analysis. Several pathways were found to be up-regulated in ST persimmon, including “amino sugar and nucleotide sugar metabolism.” Pathways down-regulated in ST persimmon included “photosynthesis” and “carbon fixation in photosynthetic organisms.” Expression patterns of genes in these pathways were further confirmed using quantitative real-time RT-PCR. Ethylene gas production during persimmon softening was monitored with gas chromatography and found to be correlated with the fruit softening. Transcription involved in ethylene biosynthesis, perception and signaling was up-regulated. On the whole, this study investigated the key genes involved in metabolic pathways of persimmon fruit softening, especially implicated in increased sugar metabolism, decreased photosynthetic capability, and increased ethylene production and other ethylene-related functions. This transcriptome analysis provides baseline information on the identity and modulation of genes involved in softening of persimmon fruits and can underpin the future development of technologies to delay softening in persimmon.

Vesicle membrane-associated SCYL2 proteins are vital for plant development.

Summary: Geranylgeranyl pyrophosphate synthase (GGPS) is a key enzyme for a structurally diverse class of isoprenoid biosynthetic metabolites including gibberellins, carotenoids, chlorophylls and rubber. We expressed a chloroplast‐targeted GGPS isolated from sunflower (Helianthus annuus) under control of the cauliflower mosaic virus 35S promoter in tobacco (Nicotiana tabacum). The resulting transgenic tobacco plants expressing heterologous GGPS showed remarkably enhanced growth (an increase in shoot and root biomass and height), early flowering, increased number of seed pods and greater seed yield compared with that of GUS‐transgenic lines (control) or wild‐type plants. The gibberellin levels in HaGGPS‐transgenic plants were higher than those in control plants, indicating that the observed phenotype may result from increased gibberellin content. However, in HaGGPS‐transformant tobacco plants, we did not observe the phenotypic defects such as reduced chlorophyll content and greater petiole and stalk length, which were previously reported for transgenic plants expressing gibberellin biosynthetic genes. Fast plant growth was also observed in HaGGPS‐expressing Arabidopsis and dandelion plants. The results of this study suggest that GGPS expression in crop plants may yield desirable agronomic traits, including enhanced growth of shoots and roots, early flowering, greater numbers of seed pods and/or higher seed yield. This research has potential applications for fast production of plant biomass that provides commercially valuable biomaterials or bioenergy.