Biology subjects

He, S. Y.

Publications and source records attributed to He, S. Y..

16 recordsLinked to original sources

bioRxiv2026

Iron as a principal mediator of dysbiosis prevention in the phyllosphere

Multicellular organisms require a correct microbiota composition for optimal health and fitness. Dysbiosis could lead to serious health consequences in humans and plants, and is pervasive during pathogen infections across systems. A recent study shows that carbon source availability plays a role in bacterial community assembly in Arabidopsis leaves [1]. However, whether carbon sources or other molecules are critical for leaf microbiota homeostasis remains unknown. Here, an unbiased in planta metatranscriptomic analysis of endophytic microbiota in leaves of wild-type and dysbiotic min7 fls2 efr cerk1 (mfec) mutant, which is defective in pattern-recognition receptor (PRR) signaling and MIN7-dependent vesicle trafficking, revealed that bacteria inside Arabidopsis leaves exhibit taxa-specific transcriptional responses. Most notably, iron starvation response was detected in Stenotrophomonas strains, a group of endophytic bacteria that cause dysbiotic symptoms. Elevated expression of canonical iron starvation genes confirmed low iron availability in mfec plants. This low iron environment was associated with a reduced level of the plasma membrane H-ATPase AHA2, resulting in a higher apoplastic pH that favors less-bioavailable ferric iron over soluble ferrous iron. Supplementing iron in mfec plants was sufficient to restore microbiota homeostasis and alleviate dysbiosis phenotypes. The role of iron in dysbiosis extends to Pseudomonas syringae foliar infection, which drives leaf dysbiosis through two iron-dependent mechanisms. Iron thus emerges as a surprising, key switch between healthy and dysbiotic microbiota in the endophytic spaces of plants.

plant biology↗

bioRxiv2026

Natural variation in temperature-resilient immunity in Arabidopsis

Elevated temperature has been shown to compromise salicylic acid (SA)-mediated immunity in plants. The Arabidopsis thaliana accession C24 retains constitutively elevated SA and resistance to the hemibiotrophic pathogen Pseudomonas syringae pv. tomato DC3000 (Pst DC3000) at elevated temperature. C24 exhibits reduced biomass compared to that of a commonly studied accession, Col-0, in which SA-mediated immunity is compromised at elevated temperature. Neither the genetic basis of temperature-resilient immunity (TRI) nor the apparent growth-defense tradeoff in C24 is known. Here, we show that a Col-0 x C24 recombinant inbred line (RIL) population resolves TRI to a chromosome 5 locus accounting for most of the mapped genetic variance. This locus (named TRI hereinafter) coincides with a hotspot of structural rearrangement between the two accessions and includes a calcium-sensor gene (CBL9) and several NLR-type paralogs found only in C24. Consistent with a calcium-dependent signaling component, C24 mounts an elevated cytosolic Ca{superscript 2} response to Pst DC3000. Surprisingly, across the RIL population, disease resistance and biomass are only weakly correlated, with some lines exhibiting both large biomass and high pathogen resistance. These results show that temperature-resilient disease resistance is not only genetically tractable in C24 but also can be uncoupled from biomass cost. The TRI locus in C24 therefore encodes a natural mechanism(s) of temperature-resilient immunity with the growth-defense tradeoff resolved.

plant biology↗

bioRxiv2026

The FERONIA receptor kinase is required for high humidity responses in Arabidopsis

High humidity greatly influences plant growth and development and triggers adaptive physiological responses such as leaf hyponasty (elongation of leaf petiole and upward leaf movement). A recent study identified Cyclic Nucleotide-Gated Ion Channels 2 and 4 (CNGC2/4)-mediated Ca2+ influx and Calmodulin Binding Transcription Activators 2 and 3 (CAMTA2/3)-mediated transcription as essential for high humidity response in Arabidopsis, but the upstream regulators that control these pathways remain unknown. Here, we show that the receptor-like kinase FERONIA and its co-receptor LORELEI-LIKE GPI-ANCHORED PROTEIN1 (LLG1) are required for a large portion of high humidity-associated Arabidopsis transcriptomic changes, including CNGC2, CAMTA-regulated genes, and cell wall remodeling genes, and for high humidity-induced leaf hyponasty. High humidity triggers a previously uncharacterized petiole-localized Ca2+ waves that precede hyponastic leaf movement. The petiole-localized Ca2+ signals were significantly altered in the fer-4 mutant. Thus, FERONIA is a key regulator of plant responses to extracellular high humidity. Highlights FERONIA plays a prominent role in transcriptomic responses to high humidity FERONIA is required for high humidity-induced leaf hyponasty High humidity induces petiole calcium waves FERONIA is required for normal petiole calcium waves in response to high humidity

plant biology↗

bioRxiv2026

Aimea gen. nov. defines a novel plant-associated yeast genus in Microbotryomycetes with three novel species

Plant tissues and surfaces are among the largest microbial habitats on Earth, and commensal yeasts are common members of these communities, where they can contribute to plant-microbe interactions including the biological control of plant diseases. Here, we describe a novel genus, Aimea, of unpigmented, plant-associated basidiomycete yeasts, in the class Microbotryomycetes, and name three new species (A. erigeronia, A. cardamina, and A. sorghi) represented by four isolates from leaves and roots of multiple hosts. We characterize these taxa through analyses of metabolic requirements, tolerance to differences in osmolarity, pH, and temperature, and enzymatic activities. In parallel, we generate near-chromosome-scale hybrid genomes annotated with transcriptome data. We employ whole-genome and multilocus phylogenetic approaches to infer the placement of these species within a monophyletic clade. We use comparative genomics to examine how the gene content of these yeasts differs from that of other members of the Microbotryomycetes, including an apparent proliferation of retrotransposons. We further demonstrate the genetic transformability of these taxa using Agrobacterium tumefaciens-mediated transformation. The description of these new species, together with high-quality genome resources and a genetic transformation protocol, establishes a foundation for experimental studies of these novel plant-associated yeasts and their interactions with hosts and other microbes.

genomics↗

bioRxiv2023

Warm temperature suppresses plant systemic acquired resistance by intercepting the N-hydroxypipecolic acid immune pathway

Climate warming influences disease development by targeting critical components of the plant immune system, including pattern-triggered immunity (PTI), effector-triggered immunity (ETI) and production of the central defence hormone salicylic acid (SA) at the primary pathogen infection site. However, it is not clear if and/or how temperature impacts systemic immunity. Here we show that pathogen-triggered systemic acquired resistance (SAR) in Arabidopsis thaliana is suppressed at elevated temperature. This was accompanied by global downregulation of SAR-induced genes at elevated temperature. Abolished SAR under warmer conditions was associated with reduced biosynthesis of the SAR metabolite N-hydroxypipecolic acid (NHP) in Arabidopsis and other plant species (such as tomato and rapeseed), as demonstrated by downregulation of NHP biosynthetic genes (ALD1 and FMO1) and reduced NHP and pipecolic acid (Pip) levels. Although multiple SAR signals have been shown previously, exogenous NHP or Pip was sufficient to restore disease protection at elevated temperature, indicating that heat-mediated SAR suppression is due to downregulation of the NHP pathway. Along with ALD1 and FMO1, local and systemic expression of the SA biosynthetic gene ICS1 were also suppressed at warm temperature. Finally, we define a transcriptional network controlling thermosensitive NHP pathway via the master transcription factors CBP60g and SARD1. Our findings demonstrate that warm temperatures impact not only local but also systemic immunity by impinging on NHP biosynthesis, providing a roadmap towards engineering climate-resilient plant immune systems.

plant biology↗

bioRxiv2023

Multiple host targets of Pseudomonas effector protein HopM1 form a protein complex regulating apoplastic immunity and water homeostasis

Bacterial type III effector proteins injected into the host cell play a critical role in mediating bacterial interactions with plant and animal hosts. Notably, some bacterial effectors are reported to target sequence-unrelated host proteins with unknown functional relationships. The Pseudomonas syringae effector HopM1 is such an example; it interacts with and/or degrades several HopM1-interacting (MIN) Arabidopsis proteins, including HopM1-interacting protein 2 (MIN2/RAD23), HopM1-interacting protein 7 (MIN7/BIG5), HopM1-interacting protein 10 (MIN10/14-3-3), and HopM1-interacting protein 13 (MIN13/BIG2). In this study, we purified the MIN7 complex formed in planta and found that it contains MIN7, MIN10, MIN13, as well as a tetratricopeptide repeat protein named HLB1. Mutational analysis showed that, like MIN7, HLB1 is required for pathogen-associated molecular pattern (PAMP)-, effector-, and benzothiadiazole (BTH)-triggered immunity. HLB1 is recruited to the trans-Golgi network (TGN)/early endosome (EE) in a MIN7-dependent manner. Both min7 and hlb1 mutant leaves contained elevated water content in the leaf apoplast and artificial water infiltration into the leaf apoplast was sufficient to phenocopy immune-suppressing phenotype of HopM1. These results suggest that multiple HopM1-targeted MIN proteins form a protein complex with a dual role in modulating water level and immunity in the apoplast, which provides an explanation for the dual phenotypes of HopM1 during bacterial pathogenesis.

plant biology↗

bioRxiv2023

Bacterial pathogens deliver water/solute-permeable channels as a virulence strategy

Many animal and plant pathogenic bacteria utilize a type III secretion system to deliver effector proteins into the host cell1,2. Elucidation of how these effector proteins function in the host cell is critical for understanding infectious diseases in animals and plants3-5. The widely conserved AvrE/DspE-family effectors play a central role in the pathogenesis of diverse phytopathogenic bacteria6. These conserved effectors are involved in the induction of "water-soaking" and host cell death that are conducive to bacterial multiplication in infected tissues. However, the exact biochemical functions of AvrE/DspE-family effectors have been recalcitrant to mechanistic understanding for three decades. Here we show that AvrE/DspE-family effectors fold into a {beta}-barrel structure that resembles bacterial porins. Expression of AvrE and DspE in Xenopus oocytes results in (i) inward and outward currents, (ii) permeability to water and (iii) osmolarity-dependent oocyte swelling and bursting. Liposome reconstitution confirmed that the DspE channel alone is sufficient to allow the passage of small molecules such as fluorescein dye. Targeted screening of chemical blockers based on the predicted pore size (15-20 [A]) of the DspE channel identified polyamidoamine (PAMAM) dendrimers as inhibitors of the DspE/AvrE channels. Remarkably, PAMAMs broadly inhibit AvrE/DspE virulence activities in Xenopus oocytes and during Erwinia amylovora and Pseudomonas syringae infections. Thus, we have unraveled the enigmatic function of a centrally important family of bacterial effectors with significant conceptual and practical implications in the study of bacterial pathogenesis.

plant biology↗

bioRxiv2023

Rapid intracellular acidification is a novel plant defense response countered by the brown planthopper

The brown planthopper (BPH) is the most destructive insect pest in rice. Through a stylet, BPH secrets a plethora of salivary proteins into rice phloem cells as a crucial step of infestation. However, how various salivary proteins function in rice cells to promote insect infestation is poorly understood. Among them, one of the salivary proteins is predicted to be a carbonic anhydrase (NlCA). The survival rate of the NlCA-RNA interference (RNAi) BPH insects was extremely low on rice, indicating a vital role of this salivary protein in BPH infestation. We generated NICA transgenic rice plants and found that NlCA expressed in rice plants could restore the ability of NlCA-RNAi BPH to survive on rice. Next, we produced rice plants expressing the ratiometric pH sensor pHusion and found that NlCA-RNAi BPH induced rapid intracellular acidification of rice cells during feeding. Further analysis revealed that both NlCA-RNAi BPH feeding and artificial of lowering intracellular pH activated plant defense responses, and that NICA-mediated intracellular pH stabilization is linked to diminished defense responses, including reduced callose deposition at the phloem sieve plates and suppressed defense gene expression. Given the importance of pH homeostasis across the kingdoms of life, discovery of NICA-mediated intracellular pH modulation uncovered a new dimension in the interaction between plants and piecing/sucking insect pests. The crucial role of NICA for BPH infestation of rice suggests that NICA is a promising target for chemical or trans-kingdom RNAi-based inactivation for BPH control strategies in plants. HighlightsO_LIRapid intracellular acidification is a novel plant defense response. C_LIO_LIBrown planthopper delivers into rice tissues a major virulence protein, carbonic anhydrase (NlCA), critical for survival. C_LIO_LINlCA counters intracellular acidification to suppress plant defense. C_LIO_LIResults implicate existence of pH-responsive regulators of defense responses in the rice-brown planthopper interaction. C_LI In briefThe brown planthopper (BPH) is the most devasting insect pest in rice. Jiang et al. discovered that BPH secretes a salivary carbonic anhydrase (NICA) to regulate the intracellular pH of the rice cell to facilitate its feeding and survival on rice plants and that NICA-counters host intracellular pH acidification to diminished defense responses. These findings uncovered that intracellular pH homeostasis is a previously uncharacterized battleground in plant-insect interactions, but also open a door to future discovery of pH-responsive intracellular regulators of defense responses, which could add a new research dimension in the study of plant-biotic interactions.

plant biology↗

bioRxiv2023

Roles of microbiota in autoimmunity in Arabidopsis

Over the past three decades, researchers have isolated plant mutants that display constitutively activated defense responses in the absence of pathogen infection. These mutants are called autoimmune mutants and are typically dwarf and/or bearing chlorotic/necrotic lesions. From a genetic screen for Arabidopsis genes involved in maintaining a normal leaf microbiota, we identified TIP GROWTH DEFECTIVE 1 (TIP1), which encodes a S-acyltransferase, as a key player in guarding leaves against abnormal microbiota level and composition under high humidity conditions. The tip1 mutant has several characteristic phenotypes of classical autoimmune mutants, including a dwarf stature, displaying lesions, and having a high basal level of defense gene expression. Gnotobiotic experiments revealed that the autoimmune phenotypes of the tip1 mutant are largely dependent on the presence of microbiota as axenic tip1 plants have markedly reduced autoimmune phenotypes. We found that the microbiota dependency of autoimmune phenotypes is shared by several "lesion mimic"-type autoimmune mutants in Arabidopsis. Interestingly, autoimmune phenotypes caused by mutations in NLR genes do not require the presence of microbiota and can even be partially alleviated by microbiota. Our results therefore suggest the existence of two classes of autoimmunity (microbiota-dependent vs. microbiota-independent) in plants. The observed interplay between autoimmunity and microbiota in the lesion mimic class of autoimmunity is reminiscent of the interactions between autoimmunity and dysbiosis in the animal kingdom.

plant biology↗

bioRxiv2023

A critical role of a eubiotic microbiota in gating proper immunocompetence in Arabidopsis

Although many studies have shown that microbes can ectopically stimulate or suppress plant immune responses, the fundamental question of whether the entire preexisting microbiota is indeed required for proper development of plant immune response remains unanswered. Using a recently developed peat-based gnotobiotic plant growth system we found that Arabidopsis grown in the absence of a natural microbiota lacked age-dependent maturation of plant immune response and were defective in several aspects of pattern-triggered immunity. Axenic plants exhibited hypersusceptibility to infection by the bacterial pathogen Pseudomonas syringae pv. tomato DC3000 and the fungal pathogen Botrytis cinerea. Microbiota-mediated immunocompetence was suppressed by rich nutrient conditions, indicating a tripartite interaction between the host, microbiota, and abiotic environment. A synthetic microbiota composed of 48 culturable bacterial strains from the leaf endosphere of healthy Arabidopsis plants was able to substantially restore immunocompetence similar to plants inoculated with a soil-derived community. In contrast, a 52-member dysbiotic synthetic leaf microbiota overstimulated the immune transcriptome. Together, these results provide evidence for a causal role of a eubiotic microbiota in gating proper immunocompetence and age-dependent immunity in plants.

plant biology↗

bioRxiv2021

Pseudomonas syringae effector AvrE associates with plant membrane nanodomains and binds phosphatidylinositides in vitro

Bacterial phytopathogens deliver effector proteins into host cells as key virulence weapons to cause disease. Extensive studies revealed diverse functions and biochemical properties of different effector proteins from pathogens. In this study, we show that the Pseudomonas syringae effector AvrE, the founding member of a broadly conserved and pathologically important bacterial effector family, binds to phosphatidylinositides (PIPs) in vitro and shares some properties with eukaryotic PROPPINs ({beta}-propellers that bind polyphosphoinositides). In planta pull down experiments with transgenic Arabidopsis plants expressing AvrE revealed that AvrE is associated with several plant proteins including plasma membrane lipid-raft proteins. These results shed new light on the properties of a bacterial effector that is crucial for bacterial virulence in plants.

pathology↗

bioRxiv2021

Phyllosphere-inhabiting endophytic bacteria feature a stationary phase-like lifestyle

Plants are in constant association with a variety of microbes, and although much is known about how symbiotic and pathogenic microbes interact with plants, less is known about the population dynamics, adaptive traits, and transcriptional features of endophytic commensal microbes that live inside leaves. In this study, we evaluated the long-term population and transcriptional dynamics of two bacterial microbiota endophytes and compared them to those of a commensal-simulating non-pathogenic mutant of the bacterial pathogen Pseudomonas syringae. We found that population densities of all three endophytic phyllosphere bacteria remained static over a long period of time, which was caused by a continual equilibrium between bacterial multiplication and death, as evidenced by treatment of plants with antibiotics that only targeted dividing bacteria or by in planta visualization of bacteria carrying a fluorescent division reporter. Population stasis could not be explained by a lack of resources, as Arabidopsis leaves could support population densities up to 100 times higher than the normal microbiota populations, nor was population stasis reversed by significantly quenching PAMP-triggered immunity. Long-term temporal in planta transcriptomic analysis of these three bacterial endophytes revealed up-regulation of protein translation, the generation of energy, and the response to stress, and interestingly, for the microbiota strains, the longer the bacteria remained inside plants, the greater the up-regulation of some of these processes. Further transcriptomic analysis of in planta populations of commensal-simulating Pseudomonas syringae revealed a remarkable resemblance to those of in vitro bacteria in stationary phase, a metabolically active physiological state in which the production of secondary metabolites and stress responses are induced. This study provides novel insight into how endophytic bacteria survive and thrive inside plant leaves, and reshapes our current understanding of what it means to be part of the endophytic microbiota in the phyllosphere.

microbiology↗

bioRxiv2020

Loss of a plant receptor kinase recruits beneficial rhizosphere-associated Pseudomonas

Maintaining microbiome structure is critical for the health of both plants1 and animals2. In plants, enrichment of beneficial bacteria is associated with advantageous outcomes including protection from biotic and abiotic stress3,4. However, the genetic and molecular mechanisms by which plants enrich for specific beneficial microbes without general dysbiosis have remained elusive. Here we show that through regulation of NADPH oxidase, FERONIA kinase negatively regulates beneficial Pseudomonas fluorescens in the Arabidopsis rhizosphere microbiome. By rescreening a collection of Arabidopsis mutants that affect root immunity under gnotobiotic conditions, followed by microbiome sequencing in natural soil, we identified a FERONIA mutant (fer-8) with a rhizosphere microbiome enriched in P. fluorescens without phylum-level dysbiosis. Using microbiome transplant experiments, we found that the fer-8 microbiome was beneficial and promoted plant growth. The effect of FER on rhizosphere Pseudomonads was independent of its immune coreceptor function, role in development, and jasmonic acid autoimmunity. We found that the fer-8 mutant has reduced basal levels of reactive oxygen species (ROS) in roots and that mutants deficient in NADPH oxidase showed elevated rhizosphere Pseudomonad levels. Overexpression of the ROP2 gene (encoding a client of FER and positive regulator of NADPH oxidase5) in fer-8 plants suppressed Pseudomonad overgrowth. This work shows that FER-mediated ROS production regulates levels of beneficial Pseudomonads in the rhizosphere microbiome.

plant biology↗

bioRxiv2020

Pattern-recognition receptors are required for NLR-mediated plant immunity

The plant immune system is fundamental to plant survival in natural ecosystems and productivity in crop fields. Substantial evidence supports the prevailing notion that plants possess a two-tiered innate immune system, called pattern-triggered immunity (PTI) and effector-triggered immunity (ETI). PTI is triggered by microbial patterns via cell surface-localized pattern-recognition receptors (PRRs), whereas ETI is activated by pathogen effector proteins via mostly intracellularly-localized receptors called nucleotide-binding, leucine-rich repeat proteins (NLRs)1-4. PTI and ETI are initiated by dist 30 inct activation mechanisms and are considered to act independently and have evolved sequentially5,6. Here we show that, contrary to the perception of PTI and ETI being separate immune signaling pathways, Arabidopsis PRR/co-receptor mutants, fls2/efr/cerk1 and bak1/bkk1/cerk1 triple mutants, are greatly impaired in ETI responses when challenged with incompatible Pseudomonas syrinage bacteria. We further show that the NADPH oxidase (RBOHD)-mediated production of reactive oxygen species (ROS) is a critical early signaling event connecting PRR and NLR cascades and that PRR-mediated phosphorylation of RBOHD is necessary for full activation of RBOHD during ETI. Furthermore, NLR signaling rapidly augments the transcript and protein levels of key PTI components at an early stage and in a salicylic acid-independent manner. Our study supports an alternative model in which PTI is in fact an indispensable component of ETI during bacterial infection, implying that ETI halts pathogen infection, in part, by directly co-opting the anti-pathogen mechanisms proposed for PTI. This alternative model conceptually unites two major immune signaling pathways in the plant kingdom and mechanistically explains the long-observed similarities in downstream defense outputs between PTI and ETI.

plant biology↗

bioRxiv2019

An oomycete RXLR effector triggers antagonistic plant hormone crosstalk to suppress host immunity

Understanding the mechanisms through which pathogens alter plant cell networks is essential for understanding plant-pathogen interactions and will inform efforts to reduce crop diseases. Oomycetes secrete diverse effector proteins into plant cells. The mechanisms through which these effectors promote virulence are largely unknown. We show that the HaRxL10 effector protein from the Arabidopsis thaliana pathogen Hyaloperonospora arabidopsidis (Hpa) targets a transcriptional repressor (JAZ3) involved in jasmonic acid (JA) signalling. This manipulation activates a regulatory cascade that inhibits salicylic acid (SA) signalling, which normally restricts Hpa infection. This virulence mechanism is functionally equivalent to but mechanistically distinct from activation of the antagonistic JA-SA hormone crosstalk by the bacterial JA-mimicking toxin coronatine and by bacterial Type III effectors. These results reveal a key role for JAZ3 in plant immunity and emphasize that JA-SA crosstalk is an Achilles heel in the plant immune system, vulnerable to manipulation by diverse microbes.

plant biology↗

bioRxiv2018

FlowPot axenic plant growth system for microbiota research

The presence of resident microbiota on and inside plants is hypothesized to influence many phenotypic attributes of the host. Likewise, host factors and microbe-microbe interactions are believed to influence microbial community assembly. Rigorous testing of these hypotheses necessitates the ability to grow plants in the absence or presence of resident or defined microbiota. To enable such experiments, we developed the scalable and inexpensive FlowPot growth platform. FlowPots have a sterile peat substrate amenable to colonization by microbiota, and the platform supports growth of the model plant Arabidopsis thaliana in the absence or presence of soil-derived microbial communities. Mechanically, the FlowPot system is unique in that it allows for total-saturation of the sterile substrate by \"flushing\" with water and/or nutrient solution via an irrigation port. The irrigation port also facilitates passive drainage of the substrate, preventing root anoxia. Materials to construct an individual FlowPot total [~]$2. A simple experiment with 12 FlowPots requires [~]4.5 h of labor following peat and seed sterilization. Plants are grown on FlowPots within a standard tissue culture microbox after inoculation, thus the Flowpot system is modular and does not require a sterile growth chamber. Here, we provide a detailed assembly and microbiota inoculation protocol for the FlowPot system. Collectively, this standardized suite of tools and colonization protocols empowers the plant microbiome research community to conduct harmonized experiments to elucidate the rules microbial community assembly, the impact of microbiota on host phenotypes, and mechanisms by which host factors influence the structure and function of plant microbiota.

plant biology↗