The RALF story began in tobacco, where the peptide was first identified as a growth inhibitor. RALFs are small, cysteine-rich peptides of roughly five kilodaltons that earned their name from their ability to rapidly raise the pH of the space outside plant cells, the apoplast. Mature RALF peptides are cut from larger precursor proteins at a specific recognition site for a protease called SITE-1 PROTEASE, and they carry two signature features: a YISY motif essential for binding to receptors, and four conserved cysteines that form disulfide bonds holding the peptide in its active three-dimensional shape. Once released, RALF1 binds its receptor and triggers phosphorylation of a proton pump called AHA2, shutting down the flow of protons into the cell wall. The resulting alkalinization blocks cell expansion, which is how the peptide restrains root growth. The RALF family has expanded dramatically across the plant kingdom, with 37 members in Arabidopsis, 43 in rice, 18 in soybean, and 34 in maize, and comparative analysis of 795 RALFs from 51 species places them into four major clades that diversified rapidly after the split of eudicots and monocots roughly 145 million years ago.

FERONIA itself belongs to the CrRLK1L family of receptor-like kinases, a group of 17 proteins in Arabidopsis distinguished by two malectin-like domains in their extracellular region. These domains share homology with carbohydrate-binding modules, hinting at the family’s role in monitoring the cell wall. To understand where FER came from, the review’s authors searched 26 plant genomes for FER-like proteins and found 50 homologs, but none in green algae. Their phylogenetic analysis, built from 67 proteins across mosses, lycophytes, ferns, gymnosperms, and flowering plants, revealed a striking pattern: the FER-like proteins of early-diverging lineages cluster with non-FER CrRLK1L members rather than with true FER, suggesting that FER as we know it originated early in the differentiation of flowering plants. The domain architecture proved highly conserved, with nearly all homologs carrying the characteristic malectin-like domains, a transmembrane segment, and an intracellular kinase domain, though the kinases split between serine/threonine and tyrosine types with no obvious lineage pattern.

What makes FERONIA extraordinary is its pleiotropy. In reproduction, the receptor performs a dual role: it ensures sperm delivery and blocks polyspermy. When a pollen tube arrives at the female gametophyte, FER, together with the GPI-anchored protein LORELEI and the calcium channel NORTIA, senses pollen-derived RALF peptides and triggers a calcium-dependent surge of reactive oxygen species that ruptures the pollen tube and releases the sperm cells. After fertilization, FER, ANJEA, and HERCULES RECEPTOR KINASE 1 detect pollen tube-specific RALFs secreted into the septum, establishing a polytubey block that prevents additional pollen tubes from entering the same ovule. On the stigma, a lock-and-key system operates: stigmatic RALF1/22/23/33 peptides bound to FER complexes form a barrier against unwanted pollen tubes, while compatible pollen carries its own RALF peptides that outcompete the stigmatic ligands and unlock the gate. In roots, FER regulates root hair growth through the RAC/ROP signaling pathway and NADPH oxidase-dependent ROS production, and it controls vacuolar expansion through interactions with cell wall proteins of the LRX family.

The same module also underpins abiotic stress tolerance. Under high salinity, the protease S1P cleaves RALF22, and the mature peptide, together with RALF23, drives FER internalization, part of the LRX3/4/5-RALF22/23-FER module that modulates jasmonic acid, salicylic acid, abscisic acid, and ROS levels. FER additionally phosphorylates the photoreceptor phytochrome B, linking salt stress to growth suppression through nuclear phyB accumulation. Loss-of-function mutants are hypersensitive to both cold and heat, and in apple, the FER-like kinase MdMRLK2 enhances cold resistance by promoting the accumulation of water-insoluble pectin, lignin, cellulose, and hemicellulose, while also improving drought tolerance by modulating energy metabolism and free amino acid production. Cadmium stress represses FER expression in roots, and fer mutants accumulate roughly half the cadmium of wild-type seedlings, implicating the receptor in metal ion homeostasis as well.

The review’s central focus, however, is immunity, and here the picture becomes genuinely dramatic. FER acts as a scaffold receptor that facilitates the formation of immune complexes between the pattern recognition receptors EFR and FLS2 and their coreceptor BAK1, the assembly that initiates pattern-triggered immunity upon detection of bacterial flagellin or elongation factor peptides. But the same receptor can be turned against the plant. Fungi and nematodes encode their own RALF-like peptides, and at least some of these molecular mimics are functionally active. The fungus Fusarium oxysporum secretes a RALF that Arabidopsis FER perceives, raising the pH around the root and promoting fungal infection. Root-knot nematodes of the species Meloidogyne incognita express two RALF-like genes, MiRALF1 and MiRALF3, in their esophageal glands during the parasitic stages; both peptides bind directly to the extracellular domain of FER, and both the peptides and the receptor are required for successful nematode parasitism in Arabidopsis and rice. Whether fungal RALFs arose through horizontal gene transfer or convergent evolution remains unresolved.

The experimental evidence across crops reveals a receptor with context-dependent, sometimes contradictory effects. In Arabidopsis, fer mutations increase resistance to Fusarium oxysporum, the powdery mildew Golovinomyces orontii, and Botrytis cinerea, yet heighten susceptibility to the oomycete Hyaloperonospora arabidopsidis, the anthracnose fungus Colletotrichum higginsianum, and the necrotroph Sclerotinia sclerotiorum. Synthetic RALF22 peptide induces resistance to Sclerotinia in wild-type plants, an effect abolished in fer mutants. In rice, mutations in the FERONIA-like gene FLR2 confer broad-spectrum resistance to the blast fungus Magnaporthe oryzae, cutting fungal biomass to 10 to 20 percent of wild-type levels, and remarkably, this resistance comes with no growth penalty, a rare and valuable combination for breeders. In tomato, the FER homolog SlFERL positively regulates immunity to Botrytis, whereas in apple, MdMRLK2 negatively regulates resistance to Valsa canker. In soybean, the malectin-like receptor kinase GmLMM1 suppresses resistance to Phytophthora sojae and to bacterial pathogens. The direction of FER’s effect evidently depends on the pathogen’s lifestyle, the host species, and the tissue involved.

Mechanistically, the review catalogues at least nine ways FER shapes immune outcomes. Beyond scaffolding PRR complexes, FER organizes the nanoscale distribution of FLS2 and BAK1 within the plasma membrane, keeping these immune receptors properly positioned for signaling. It senses cell wall integrity through interactions with pectin and LRX proteins, and cooperates with CELLULOSE SYNTHASE-INTERACTIVE PROTEIN 1 to monitor wall status. It generates ROS through the RAC/ROP and RIPK-RBOHD pathways, activates MAP kinase cascades, and undergoes regulated endocytosis and recycling through clathrin-dependent trafficking. Perhaps most striking is a recent discovery: rhizobacteria trigger accumulation of the metalloproteinase At2-MMP, which cleaves FER within its intracellular juxtamembrane region, and the truncated receptor then translocates into the nucleus to activate antimicrobial responses in specific root zones. FER also phosphorylates and destabilizes MYC2, the master transcription factor of jasmonic acid signaling, thereby bolstering salicylic acid-mediated immunity against the bacterium Pseudomonas syringae, while RALF23 reverses this effect and favors infection.

The translational implications are considerable, even if no RALF-FER-based crop protection strategy has yet reached the field. The rice FLR2 result demonstrates that manipulating this pathway can deliver durable, broad-spectrum disease resistance without sacrificing yield, addressing the central trade-off that has long plagued resistance breeding. The authors identify several open questions that will determine how quickly the pair can be exploited: the binding specificity of individual RALFs for FER, the dose-dependent effects that distinguish protective peptides from immunosuppressive ones, the possibility of FER-independent RALF signaling suggested by recent structural work on RALF22 in the cell wall, and the interplay between FER-mediated cell wall integrity sensing and the newly discovered SCOOP18-MIK2 immune module. As pathogens continue to deploy peptide mimics against plant surveillance systems, understanding this master ligand-receptor pair may prove essential for building the next generation of disease-resistant crops.

Subject of Research: The RALF-FERONIA ligand-receptor signaling pair in plant immunity, development, and pathogen interactions

Article Title: RALF-FER, a master ligand‒receptor pair in plant health

Article References: Chen, X.-Y., Chen, J., Xu, F., & Cai, X.-Z. (2025). RALF-FER, a master ligand‒receptor pair in plant health. Crop Health, 3(1), Article 4. https://doi.org/10.1007/s44297-024-00040-1

Image Credits: AI Generated

DOI: 10.1007/s44297-024-00040-1

Keywords: FERONIA, RALF peptides, plant immunity, receptor-like kinases, pattern-triggered immunity, fungal pathogens, nematode parasitism, crop resistance, cell wall integrity, reactive oxygen species, peptide signaling, plant-pathogen interactions

The core of the story lies in RNA interference, or RNAi, a gene-regulation system shared across much of life. Small interfering RNAs and microRNAs can be loaded into Argonaute proteins to form silencing complexes that seek out and destroy matching messenger RNAs. What has stunned researchers is that these molecules do not respect species barriers. A fungal pathogen can ship its own small RNAs into a plant cell, where they hijack the host’s Argonaute machinery and switch off immunity genes. Conversely, a plant can package its small RNAs into extracellular vesicles and send them into an invading fungus, where they silence the very genes the pathogen needs to cause disease.

The evidence is strikingly specific. The gray mold fungus Botrytis cinerea secretes small RNAs such as Bc-siR3.1 and Bc-siR5 into plant cells, where they co-opt the host AGO1 complex to suppress immunity-related genes. The wheat rust pathogen Puccinia striiformis delivers a microRNA-like RNA called Pst-milR1 that silences PR2, a gene encoding beta-1,3-glucanase involved in degrading fungal cell walls. In the banana-wilting Fusarium oxysporum system, fungal milRNAs target banana transcription factors and receptor-like kinases, dismantling early defense signaling. Rhizoctonia solani deploys a battery of milRNAs against rice, suppressing vacuolar sorting receptors, NB-ARC immune receptors, and F-box proteins to blunt the hypersensitive response. Even Valsa mali, the apple canker pathogen, uses a single milRNA to silence two receptor-like kinases and reduce reactive oxygen accumulation and callose deposition in host tissue.

Crucially, the traffic runs both ways. Plants selectively load small RNAs into extracellular vesicles with the help of RNA-binding proteins including AGO1, the helicases RH11 and RH37, and the annexins ANN1 and ANN2, which sort, stabilize, and transport the cargo. Encapsulation shields the RNA from extracellular nucleases during the journey. In the Brachypodium distachyon and Fusarium graminearum system, researchers identified 258 plant-derived small RNAs that target fungal messenger RNAs and significantly reduce pathogenicity. Wheat roots even send microRNAs into the beneficial fungus Clonostachys rosea, where they fine-tune fungal secondary metabolism rather than triggering defense, showing that RNA exchange also shapes cooperative relationships, not just conflict.

Bacteria play this game too, though the evidence is younger. The rice pathogen Xanthomonas oryzae pv. oryzicola packages a small RNA called Xosr001 into outer membrane vesicles, which deliver it into rice cells to silence OsJMT1, a jasmonate metabolism gene, thereby suppressing stomatal immunity. In the opposite direction, Arabidopsis plants have been shown to silence virulence genes of Pseudomonas syringae, reducing bacterial colonization and impairing stomatal reopening, with the silencing RNAs exported through both vesicle-associated and non-vesicular routes. Plant-derived small RNAs can also suppress gene expression in Ralstonia pseudosolanacearum, the agent of bacterial wilt. Even mutualistic partnerships show RNA crosstalk: Bradyrhizobium japonicum produces tRNA-derived fragments that accumulate in soybean nodules and use the host AGO1 machinery to regulate plant transcripts involved in nodulation.

Viruses occupy a special place in this landscape. Because viral RNA replicates continuously inside host cells, the review’s authors treat plant-virus systems as a closely related but mechanistically distinct model rather than classical cross-kingdom transfer. Still, the dynamics are instructive. Plants process viral double-stranded RNA with Dicer-like enzymes into virus-derived small interfering RNAs that guide sequence-specific degradation of viral genomes. Viruses fight back with silencing suppressor proteins such as the NS3 protein of Rice stripe virus, which binds small RNAs and interferes with microRNA biogenesis. Virus-derived siRNAs from Rice black-streaked dwarf virus directly target host genes in rice and maize, while virally activated siRNAs extend RNA regulation to endogenous plant transcripts during infection, creating layered, bidirectional control networks.

These discoveries have crystallized into three agricultural technologies that share a common RNAi mechanism but differ in delivery. Spray-induced gene silencing, or SIGS, applies double-stranded RNAs directly onto plant surfaces, where they are taken up by tissues and silence invading pathogens. It is non-transgenic, rapid, and flexible, and has been shown to suppress gray mold, Fusarium head blight, stem rot, powdery mildew, and late blight across cereals, vegetables, fruits, and ornamentals. Artificial vesicles and nanocarriers such as layered double-hydroxide nanosheets dramatically extend the persistence of sprayed RNAs, with encapsulated double-stranded RNAs protecting tomato and grape tissues for up to ten days and grape leaves for up to twenty-one days.

Host-induced gene silencing, or HIGS, takes the opposite approach: the plant itself is genetically engineered to continuously produce silencing RNAs directed at pathogen genes. Stable HIGS lines have delivered durable resistance in sugarcane against Pokkah boeng and smut, in rice against Bakanae disease and blast, in potato against late blight, and in apple against ring rot. In one notable strategy, transgenic Arabidopsis expressing short tandem target mimics effectively blocked the immune-suppressing small RNAs of Botrytis cinerea, reducing gray mold infection. HIGS offers long-lasting, tissue-specific protection, but it inherits the regulatory hurdles, biosafety debates, and public concerns that surround genetically modified crops, and it demands years of development time.

The newest and perhaps most intriguing strategy is microbe-induced gene silencing, or MIGS, which recruits beneficial microorganisms as living RNA delivery vehicles. Engineered Trichoderma harzianum strains colonizing the rhizosphere produce small RNAs that silence virulence genes in Verticillium dahliae and Fusarium oxysporum. Even more remarkably, engineered Bacillus subtilis and Pseudomonas putida can package double-stranded RNAs into extracellular vesicles and deliver them across kingdoms to fungal pathogens, suppressing Botrytis and Verticillium infections in Arabidopsis and tomato. Because microbes protect their RNA cargo from environmental degradation and can be produced at relatively low cost, MIGS could overcome the two biggest weaknesses of sprayed RNA: instability and expense.

The field is moving from laboratory proof-of-concept toward commercial reality. RNA-based pesticides are a rapidly growing industry, and China has officially released the first batch of registered RNA pesticide products, targeting Tobacco Mosaic Virus. The review argues that the safest and most effective targets will come from cross-kingdom small RNAs themselves, molecules already filtered through millions of years of co-evolution, whose natural trafficking suggests low off-target risk and environmental compatibility. Pairing these evolutionarily optimized sequences with microbial bio-factories for production and delivery, the authors contend, could dissolve the techno-economic barriers that have slowed RNA biopesticides. Significant questions remain, including how RNAs are packaged and recognized by recipient cells, how stable they are under field conditions, and what ecological effects engineered microbes might have on soil biodiversity. But the direction is clear: the quiet molecular conversation between plants and microbes is becoming a blueprint for agriculture that protects crops with the precision of a key in a lock rather than the blunt force of a chemical spray.

Subject of Research: Cross-kingdom RNA communication between plants and microbes and its application in RNA interference-based crop protection

Article Title: Cross-kingdom RNA in plant–microbe interactions: from molecular interactions to next-generation crop protection

Article References: Cross-kingdom RNA in plant–microbe interactions: from molecular interactions to next-generation crop protection. (n.d.). https://doi.org/10.1007/s44154-026-00337-x

Image Credits: AI Generated

DOI: 10.1007/s44154-026-00337-x

Keywords: cross-kingdom RNA, RNA interference, plant-microbe interactions, spray-induced gene silencing, host-induced gene silencing, microbe-induced gene silencing, small RNAs, extracellular vesicles, RNA pesticides, fungal pathogens, plant immunity, sustainable agriculture