About

Xinnian Dong is an Arts and Sciences Distinguished Professor of Biology at Duke University, holding appointments since 2004 and 2007 respectively. His laboratory uses Arabidopsis thaliana as a model system to study the mechanisms of plant defense against microbial pathogens, with a focus on systemic acquired resistance (SAR). SAR is a response induced by local infection that provides long-lasting, systemic resistance against a broad spectrum of pathogens, with salicylic acid (SA) identified as the endogenous signal of SAR. His research involves genetic and molecular analyses to identify genes involved in SAR regulation, aiming to understand the gene functions and elucidate the SAR signaling pathway. These SAR-regulating genes are also targeted for molecular engineering of disease-resistant crops. Dr. Dong's work has contributed to understanding plant immune systems, immune hormone regulation, and plant stress responses, with recent publications exploring plant immune mechanisms and the regulation of immune responses through circadian clocks and translational control.

Research topics

• Biochemistry
• Cell biology
• Biology
• Immunology
• Chemistry
• Genetics
• Microbiology
• Medicine

Selected publications

• The redox rhythm gates immune-induced cell death distinctly from the genetic clock

  Proceedings of the National Academy of Sciences · 2025-09-10 · 5 citations

  articleOpen accessSenior authorCorresponding

  Organisms use circadian clocks to synchronize physiological processes to anticipate the Earth’s day-night cycles and regulate responses to environmental signals to gain competitive advantage. While divergent genetic clocks have been studied extensively in bacteria, fungi, plants, and animals, an ancient conserved circadian redox rhythm has been recently reported. However, its biological function and physiological outputs remain elusive. Here, we uncovered the coexistence of redox and genetic rhythms with distinct period lengths and transcriptional targets through concurrent metabolic and transcriptional time-course measurements in an Arabidopsis long-period clock mutant. Analysis of the target genes indicated regulation of the immune-induced programmed cell death (PCD) by the redox rhythm. Moreover, this time-of-day-sensitive PCD was eliminated by redox perturbations and by blocking the signaling pathway of the plant defense hormones jasmonic acid/ethylene, while remaining intact in genetic clock-defective backgrounds. This study shows that compared to robust genetic clocks, the more sensitive circadian redox rhythm serves as a signaling hub in regulating incidental energy-intensive processes, such as immune-induced PCD involving reprogramming of chloroplast and mitochondria activities, to provide organisms a flexible strategy to mitigate metabolic overload during stress responses.

  PublisherOA PDFDOI

• Core biological principles and tools stemming from basic Arabidopsis research

  The Plant Cell · 2025-06-06

  review

  The model plant Arabidopsis thaliana has been a cornerstone of research in plant biology, contributing transformative insights into fundamental biological processes across eukaryotes. In this vignette, we explore the role of Arabidopsis in elucidating immune mechanisms, where plant studies have informed mammalian immunity and translational regulation. We discuss how Arabidopsis-driven advancements in pangenomics and repeat expansions have reshaped our understanding of genomic variability and its implications for diseases like Friedreich's ataxia. Breakthroughs in synthetic biology and bioproduction underscore the role of Arabidopsis as a testbed for engineering specialized metabolites and advancing biotechnological applications. Finally, we examine how the development of tools like auxin-inducible degradation has extended beyond plant research, providing critical methodologies to study protein function and develop novel therapeutics.

  PublisherDOI

• H₂O₂ regulates rice defense via bHLH25 oxidation

  Cell Research · 2025-01-20 · 1 citations

  articleOpen accessSenior author
  PublisherOA PDFDOI

• Biomolecular condensates in plant immunity

  Cell Host & Microbe · 2025-08-01 · 9 citations

  articleOpen accessSenior author

  Plant defense against microbial pathogens relies on coordinated regulation of diverse molecular processes. Although much has been learned about these processes through traditional and modern approaches, recent findings indicate that they are orchestrated through membraneless biomolecular condensates formed via liquid-liquid phase separation and related phase transitions. The principle of subcellular compartmentalization is especially important for plants, as they lack specialized immune cells, requiring them to coordinate defense responses with other physiological functions. As a result, the dynamic spatiotemporal organization of immune-related molecules becomes a critical layer of regulation that has only recently become a research frontier. Here, we discuss the emerging roles of biomolecular condensates in plant immunity, identify critical questions for future research, and propose a framework for moving forward. By incorporating condensate biology into the study of plant defense, we suggest novel strategies for enhancing crop resilience and advancing sustainable agriculture.

  PublisherDOI

• Translational Regulation of Plant Stress Responses: Mechanisms, Pathways, and Applications in Bioengineering

  Annual Review of Phytopathology · 2025-06-02 · 11 citations

  reviewOpen accessSenior author

  Understanding how organisms regulate protein translation in response to stress is vital for both fundamental biology and biotechnological innovation. However, our knowledge of this area remains limited due to the inherent complexity of the translational regulatory process. Recent advances in multiomics and single-molecule technologies now allow for an integrated analysis of the multilayered regulation of translation in plants in response to biotic and abiotic stresses. In this review, we provide essential background information for newcomers to the field and synthesize recent discoveries in stress-induced translation into the following key areas: mRNA features (cap, Kozak sequence, uAUGs and uORFs, secondary structures, modifications, alternative splicing, small RNAs), ribosomal biogenesis and heterogeneity, tRNA and codon usage, master translation regulatory factors, spatial dynamics of translation, tools for studying translation regulation, and translational engineering for crop resilience. In assembling this review, we also uncovered significant knowledge gaps that represent exciting opportunities for future research.

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• Salicylic Acid Engages Central Metabolic Regulators SnRK1 and TOR to Govern Immunity by Differential Phosphorylation of NPR1

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-06-18 · 6 citations

  preprintOpen accessSenior authorCorresponding

  Immunity is a delicate balance between combating infection and preserving the metabolic functions vital for host survival. However, the mechanisms by which immune responses are coordinated with cellular metabolism remain largely unknown. Here, we show that NONEXPRESSER OF PR GENES 1 (NPR1), the central plant immune regulator of salicylic acid (SA)-mediated defense responses, is controlled by a cascade of posttranslational modifications (PTMs) involving two master nutrient-sensing kinases. Under normal growth conditions, TARGET OF RAPAMYCIN (TOR) inhibits NPR1 through phosphorylation at Ser-55/59. During defense responses, elevated SA enhances SNF1-RELATED KINASE 1 (SnRK1) activity, which in turn inhibits TOR signaling and phosphorylates NPR1 at Ser-557. This phosphorylation event activates NPR1 and facilitates its subsequent PTMs. Together, our results reveal an integral role of SA (the active metabolite of aspirin) in controlling central metabolic regulators SnRK1 and TOR to coordinate immune responses and growth through antagonistic modifications of NPR1.

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• Primary metabolism determines the outcome of salicylic acid-mediated immune induction

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-10-14

  preprintOpen accessSenior authorCorresponding

  ABSTRACT Controlling the deleterious effects of immune responses is as vital as fighting infection. In plants, this is achieved, in part, by circadian clock-mediated regulation, such as the synthesis of and response to the immune hormone salicylic acid (SA) 1,2 . Application of SA at the same concentration under light/dark cycles induces immunity with minimal impact on growth, however, prolonged darkness leads to plant death 2 . To uncover what determines this life-or-death outcome, we identified twenty survival of SA-induced death ( ssd ) mutants through genetic screening. These mutants are defective in starch, glucose, and nitrate metabolism, and circadian regulation, and accumulate excessive starch and/or glucose. Likewise, glucose application rescues SA-treated plants in prolonged darkness. Surprisingly, SA treatment does not deplete glucose, but instead, induces amino acid and fatty acid catabolism. Through transcriptomic analyses of glucose-rescued WT plants and ssd mutants for shared pathways, we found that SA triggers plant death in darkness by inducing oxidative stress, and water loss, while glucose antagonizes these processes, boosts ER protein processing and re-establishes the anabolism-catabolism balance. Interestingly, the programmed cell death induced by effector-triggered immunity shares common transcriptomic patterns with those observed during SA-induced cell death in darkness and could also be attenuated by glucose treatment. Therefore, coordination with the cellular metabolic context plays a central role in determining immune outcomes and optimizing plant health.

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• Leaf it to science: Uncovering plant immune systems through technological advances

  PLANT PHYSIOLOGY · 2025-11-22 · 1 citations

  articleOpen access1st authorCorresponding

  For the past 2 yr, I have been contemplating how best to write this review that not only reflects on a few significant and nostalgic moments in my more than 3 decades of professional career in the molecular plant-microbe interaction field, but also offers my personal outlook on the future aimed at inspiring young scientists to join this exciting discipline. Rather than a comprehensive overview, I would like to place greater emphasis on the "whys" and the "hows" than the "whats." I finally decided to use technological advancements critical for the development of our field as a thread to connect the past with the future.

  PublisherOA PDFDOI

• Next-generation mapping of the salicylic acid signaling hub and transcriptional cascade

  Molecular Plant · 2024-08-23 · 34 citations

  articleOpen accessSenior author

  For over 60 years, salicylic acid (SA) has been known as a plant immune signal required for basal and systemic acquired resistance. SA activates these immune responses by reprogramming ∼20% of the transcriptome through NPR1. However, components in the NPR1 signaling hub, which appears as nuclear condensates, and the NPR1 signaling cascade have remained elusive due to difficulties in studying this transcriptional cofactor, whose chromatin association is indirect and likely transient. To overcome this challenge, we applied TurboID to divulge the NPR1 proxiome, which detected almost all known NPR1 interactors as well as new components of transcription-related complexes. Testing of new components showed that chromatin remodeling and histone demethylation contribute to SA-induced resistance. Globally, the NPR1 proxiome has a striking similarity to the proxiome of GBPL3 that is involved in SA synthesis, except for associated transcription factors (TFs), suggesting that common regulatory modules are recruited to reprogram specific transcriptomes by transcriptional cofactors, like NPR1, through binding to unique TFs. Stepwise green fluorescent protein-tagged factor cleavage under target and release using nuclease (greenCUT&RUN) analyses showed that, upon SA induction, NPR1 initiates the transcriptional cascade primarily through association with TGACG-binding TFs to induce expression of secondary TFs, predominantly WRKYs. Further, WRKY54 and WRKY70 were identified to play a major role in inducing immune-output genes without interacting with NPR1 at the chromatin. Moreover, loss of condensate formation function of NPR1 decreases its chromatin association and transcriptional activity, indicating the importance of condensates in organizing the NPR1 signaling hub and initiating the transcriptional cascade. Collectively, this study demonstrates how combinatorial applications of TurboID and stepwise greenCUT&RUN transcend traditional genetic methods to globally map signaling hubs and transcriptional cascades for in-depth explorations.

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• m ⁶ A modification plays an integral role in mRNA stability and translation during pattern-triggered immunity

  Proceedings of the National Academy of Sciences · 2024-08-08 · 24 citations

  articleOpen accessSenior authorCorresponding

  Plants employ distinct mechanisms to respond to environmental changes. Modification of mRNA by N 6 -methyladenosine (m 6 A), known to affect the fate of mRNA, may be one such mechanism to reprogram mRNA processing and translatability upon stress. However, it is difficult to distinguish a direct role from a pleiotropic effect for this modification due to its prevalence in RNA. Through characterization of the transient knockdown-mutants of m 6 A writer components and mutants of specific m 6 A readers, we demonstrate the essential role that m 6 A plays in basal resistance and pattern-triggered immunity (PTI). A global m 6 A profiling of mock and PTI-induced Arabidopsis plants as well as formaldehyde fixation and cross-linking immunoprecipitation-sequencing of the m 6 A reader, EVOLUTIONARILY CONSERVED C-TERMINAL REGION2 (ECT2) showed that while dynamic changes in m 6 A modification and binding by ECT2 were detected upon PTI induction, most of the m 6 A sites and their association with ECT2 remained static. Interestingly, RNA degradation assay identified a dual role of m 6 A in stabilizing the overall transcriptome while facilitating rapid turnover of immune-induced mRNAs during PTI. Moreover, polysome profiling showed that m 6 A enhances immune-associated translation by binding to the ECT2/3/4 readers. We propose that m 6 A plays a positive role in plant immunity by destabilizing defense mRNAs while enhancing their translation efficiency to create a transient surge in the production of defense proteins.

  PublisherDOI

Recent grants

• Dynamic regulation of salicylic acid biosynthesis & perception in plant immunity

  NIH · $3.8M · 2004–2018

• Arabidopsis 2010: Expression Profiling of Plant Disease Resistance Pathways

  NSF · $3.6M · 2005–2011

• Elucidation of translational regulatory mechanisms of plant immune responses

  NSF · $925k · 2017–2022

• Salicylic Acid in Immunity and Health: A Small Phytohormone with Big Physiological Impacts

  NIH · $398k · 2016–2026

• Chromsome Modification and Transcription Repression in Regulation of Systemic Acquired Resistance

  NSF · $480k · 2005–2009

Frequent coauthors

• Lijing Liu

  43 shared

• Yangnan Gu

  University of California, Berkeley

  40 shared

• Musoki Mwimba

  Bridge University

  39 shared

• Joseph D. Clarke

  University of Birmingham

  35 shared

• Sophia G. Zebell

  Cold Spring Harbor Laboratory

  35 shared

• Wei Wang

  Peking University

  34 shared

• Raul Zavaliev

  Duke University

  32 shared

• Guoyong Xu

  Shanghai Zhangjiang Laboratory

  31 shared