Chemical Tag on Histones Governs Rice Immunity Against Viruses and Insect Pests

Rice feeds more people on Earth than almost any other crop, yet every growing season its fields are besieged by pathogens and insects that can devastate yields. A new study published in Genome Biology has uncovered an unexpected layer of the plant’s defensive machinery: a small chemical modification attached to histone proteins, the spools around which DNA is wound, appears to act as a master switch controlling how rice responds to both viral infections and chewing herbivores. The finding opens a potential route toward breeding or engineering rice varieties with broad-spectrum resistance to several of the crop’s most damaging enemies at once.

The modification in question is lysine succinylation, a post-translational change in which a succinyl group is chemically attached to a lysine amino acid residue on a protein. Lysine succinylation is known to influence metabolism and transcription in a range of organisms, and previous work had charted its behavior during rice development. What remained largely unexplored was whether this modification plays a role in biotic stress — the umbrella term for damage inflicted on plants by living attackers such as viruses, bacteria, and insects. The new research, led by Lei Yang and Shuai Li together with colleagues at Yangzhou University, the Jiangsu Academy of Agricultural Sciences, and Anhui Normal University, demonstrates that it does, and in strikingly consequential ways.

To probe the question, the team performed quantitative succinylome profiling, a mass-spectrometry-based survey that measures lysine succinylation across thousands of proteins simultaneously. They applied the technique to rice plants subjected to viral infection and to herbivore infestation, and the results revealed extensive, stress-responsive succinylation on both histone and non-histone proteins. The modification preferentially decorated highly abundant proteins and was concentrated in pathways tied to photosynthesis and core metabolism. Notably, the data showed that herbivore attack increased lysine succinylation while suppressing the expression of photosynthetic pathway-related proteins, hinting that the modification tracks the metabolic reorganization plants undergo when under attack.

A central technical achievement of the study was the application of CUT&Tag analysis — a genome-mapping method that pinpoints where a particular histone modification sits along the chromosomes — to lysine succinylation in rice. The mapping showed strong enrichment of the mark at the promoters of defense-related genes, particularly genes involved in plant hormone signal transduction. Crucially, the researchers found a positive correlation between lysine succinylation occupancy at these regulatory regions and the expression levels of the corresponding genes. In other words, when the succinyl mark was present at a gene’s promoter, that gene was more likely to be actively transcribed. This positions lysine succinylation not as a passive byproduct of cellular chemistry but as an active participant in defense-related transcriptional control.

Because a modification’s abundance reflects a balance between the enzymes that add it and those that remove it, the team went hunting for desuccinylases — enzymes that strip succinyl groups from lysine residues. Working in rice, they identified three histone deacetylases as major desuccinylases: OsSRT702, OsHDA714, and OsHDA716. The researchers purified an OsHDA714-His fusion protein and validated its desuccinylation activity in vitro, confirming that the enzyme could directly remove the mark. They also generated CRISPR/Cas9-mediated knockout mutations in the corresponding genes and verified the edits by DNA sequencing, providing a clean genetic system in which to test the enzymes’ biological roles.

The functional results were dramatic. Disrupting OsHDA714 markedly enhanced rice resistance to rice stripe virus and rice black-streaked dwarf virus, two important viral pathogens of the crop, and also to the brown planthopper and the striped stem borer, two of the most destructive insect pests in rice-growing regions. A single gene knockout thus broadened resistance across two viral and two insect attackers, a breadth that conventional single-resistance breeding rarely achieves. This pattern suggests that OsHDA714 normally functions as a negative regulator of immunity — a brake on the plant’s defensive responses — and that releasing the brake, by removing the enzyme, activates a wider defense program.

To understand what that defense program consists of, the researchers integrated transcriptomic data with their CUT&Tag maps. Genes upregulated in the hda714 knockout mutant turned out to be predominantly enriched in the phenylpropanoid biosynthesis pathway, a metabolic route that produces an arsenal of antimicrobial and anti-herbivore compounds, and many of these genes carried lysine succinylation marks in their promoter regions. In parallel, jasmonate-associated defense pathways were activated in the mutant. Jasmonates are plant hormones best known for orchestrating responses to wounding and herbivory, and their involvement links the epigenetic machinery of succinylation directly to classical hormonal defense signaling. Phytohormone measurements in the mutant and in wild-type ZH11 plants supported this remodeling of hormone pathways.

Taken together, the results sketch a coherent mechanistic model. Under normal conditions, OsHDA714 — aided by OsSRT702 and OsHDA716 — keeps lysine succinylation levels in check, limiting succinyl marks at defense gene promoters and thereby restraining the expression of hormone-signaling and phenylpropanoid genes. When viruses or herbivores attack, this regulation is perturbed, succinylation accumulates on histones and key metabolic proteins, and defense transcription is reprogrammed. Removing OsHDA714 genetically locks the system into a primed state, in which the plant constitutively deploys the biochemical tools needed to fend off a diverse range of attackers. The authors propose that OsHDA714-mediated desuccinylation modulates hormone signaling and phenylpropanoid metabolism to control broad-spectrum resistance in rice.

The study carries practical implications for crop protection. Rather than stacking individual resistance genes against specific pathogens — a strategy that pathogens and pests frequently circumvent — agricultural scientists could target a regulatory hub like OsHDA714 to bolster multiple defenses simultaneously. Because the work was performed with genome editing tools such as CRISPR/Cas9, the pathway from discovery to improved germplasm is conceptually straightforward, although field performance, agronomic trade-offs, and potential effects on growth and yield would need careful evaluation, since defense activation often competes with productivity. More broadly, the research expands the known repertoire of histone modifications that regulate plant immunity, positioning lysine succinylation alongside better-characterized marks such as acetylation and methylation as a genuine epigenetic regulator of defense. It also raises questions for future work: how the cell senses viral or herbivore attack and translates it into altered succinylation, what non-histone succinylated proteins contribute to the response, and whether parallel systems operate in other crops. For now, the study provides the clearest evidence yet that a chemical tag on rice histones sits at the heart of the plant’s ability to defend itself against some of agriculture’s most persistent enemies.

Subject of Research: Role of lysine succinylation in rice defense responses against viral pathogens and herbivorous insects

Article Title: Lysine succinylation mediates defense responses against viruses and herbivores in rice

Article References: Yang, L., Li, S., Deng, X., Zhao, R., Meng, Y., Li, C., Qin, L., Liu, B., Sun, Y., Fang, J., Ji, R., & He, Z. (2026). Lysine succinylation mediates defense responses against viruses and herbivores in rice. Genome Biology. https://doi.org/10.1186/s13059-026-04271-z

Image Credits: AI Generated

DOI: 10.1186/s13059-026-04271-z

Keywords: rice, lysine succinylation, histone modification, OsHDA714, plant immunity, rice stripe virus, brown planthopper, jasmonate signaling, phenylpropanoid biosynthesis, CUT&Tag, CRISPR/Cas9, epigenomics