The central idea of the review is metabolic reprogramming. Because plants are sessile organisms, they cannot flee environmental challenges; instead they must reorganise their internal chemistry in place. When stress strikes, cellular homeostasis collapses, photosynthesis falters and energy flows are diverted from growth toward defence. Melatonin, chemically N-acetyl-5-methoxytryptamine, intervenes at multiple points in this process. It shifts carbon fluxes through carbohydrate metabolism, alters amino acid biosynthesis, adjusts energy metabolism and stimulates the production of secondary metabolites such as phenolics, flavonoids and anthocyanins. The net effect is an accumulation of osmoprotectants, antioxidants and defence-related compounds that buffer the cell against damage and keep essential functions running under conditions that would otherwise be lethal.

One of the most striking aspects of the review is its emphasis on how modern analytical chemistry has transformed the field. High-throughput platforms such as liquid chromatography coupled to mass spectrometry, gas chromatography coupled to mass spectrometry and nuclear magnetic resonance spectroscopy now allow researchers to profile hundreds of stress-responsive metabolites simultaneously. These metabolomics approaches reveal, at a systems level, exactly which metabolic networks melatonin touches. When combined with transcriptomics, which measures changes in gene expression, and proteomics, which tracks shifts in protein abundance, metabolomics provides a multi-layered picture of how a single molecule can orchestrate such far-reaching changes. The authors highlight that this multi-omics integration is the key to understanding melatonin-mediated stress tolerance rather than viewing it as a collection of isolated physiological effects.

The mechanistic details are considerable. Melatonin biosynthesis in plants proceeds from tryptophan through a series of enzymatic steps, with serotonin N-acetyltransferases and related enzymes acting as key control points. Recent work cited in the review shows that manipulating these enzymes, for example by enhancing the expression of SNAT1 in kiwifruit, boosts melatonin biosynthesis, promotes growth and improves salt stress tolerance. Copy number variation in ASMT and COMT genes appears to drive differences in melatonin dosage between species, suggesting that breeders could select for naturally high-melatonin lines. This genetic dimension turns what might seem like an abstract biochemical story into a practical breeding target for climate-resilient agriculture.

Equally important is melatonin’s role as a signalling hub. The review describes extensive crosstalk with abscisic acid, auxin, cytokinin, gibberellin, ethylene, jasmonic acid, salicylic acid and strigolactones. In tomato, jasmonate and melatonin act synergistically to potentiate cold tolerance, while abscisic acid participates in melatonin-induced chilling tolerance in cucumber by regulating photosynthesis and the antioxidant system. In Arabidopsis, melatonin antagonises cytokinin responses to stimulate root growth, and cytokinin in turn modulates phytomelatonin responses under high light. Melatonin also represses auxin synthesis and polar auxin transport to regulate root meristem activity, and it can suppress ethylene biosynthesis during apple fruit ripening by inhibiting the transcription factor MdREM10. These interactions show that melatonin sits at a genuine crossroads of plant hormone networks, capable of both amplifying and damping specific hormonal signals depending on the stress context.

Reactive oxygen species and nitric oxide form another critical layer of this signalling web. Stress conditions cause bursts of reactive oxygen that damage membranes, proteins and DNA, but these molecules also serve as signals. Melatonin and its metabolites are exceptionally efficient radical scavengers, and the review documents how melatonin improves ROS metabolism and antioxidant defence responses in systems ranging from tomato seedlings exposed to copper to maize facing chromium toxicity. At the same time, melatonin engages nitric oxide in a stress-state-dependent signalling module, as recent work in Trends in Plant Science describes, allowing the plant to fine-tune its redox balance rather than simply eliminating all reactive species. This dual role, detoxifier and signal modulator, distinguishes melatonin from conventional antioxidants.

The review also covers melatonin’s contribution to defence against living attackers. In Arabidopsis, comparative metabolomic analysis has implicated sugars and glycerol in melatonin-mediated innate immunity against bacterial pathogens. Melatonin activates plant defence against root-knot nematodes through the jasmonate pathway, enhances resistance to Botrytis cinerea in tomato through a hierarchical cascade involving jasmonic acid and nitric oxide, and promotes jasmonic acid and phlorizin biosynthesis in pear against Botryosphaeria dothidea. Postharvest applications are particularly promising: melatonin treatment strengthens blueberry fruit defences by modulating jasmonic acid signalling and phenylpropanoid metabolites, and it improves chilling tolerance of peach fruit during cold storage by affecting jasmonate content and cell wall stability. There is even emerging evidence that melatonin may act as a natural antiviral compound in plant biocontrol.

Heavy metal and contaminant stress receives detailed treatment as well. Melatonin mitigates nickel toxicity in tomato seedlings by improving nutrient uptake, root architecture and antioxidant potential; it reduces heavy metal accumulation in pepper; it alleviates mercury toxicity in moss by modulating redox homeostasis and the urea cycle; and it helps rice cope with arsenic by reinforcing antioxidant defences and secondary metabolism. In alfalfa, melatonin alleviates aluminium toxicity, and in tomato, anthocyanin synthesis proves critical for melatonin-induced chromium tolerance. Combined applications are a recurring theme: melatonin with strigolactone mitigates salinity in maize through antioxidant defence, osmotic adjustment and ion homeostasis; melatonin with hydrogen sulfide modulates secondary metabolites and metal sequestration in arsenic-stressed tomato; and melatonin with salicylic acid improves drought performance in Brassica napus.

For agriculture, the practical implications are substantial. Exogenous melatonin application, whether as foliar spray, seed treatment or postharvest dip, has repeatedly improved crop performance under stress. In cotton, combined abscisic acid and melatonin application protects carbohydrate metabolism and yield under drought. In sugar beet, melatonin with jasmonic acid protects against heat stress by modulating enzymatic antioxidants and organic osmolytes. In sorghum, exogenous melatonin improves drought responses through defined physiological mechanisms. The review frames these findings within the broader push toward climate-smart agriculture, noting that melatonin-enabled omics approaches are helping researchers understand plant responses to single and combined stresses, which is precisely the kind of multifactorial challenge that field crops increasingly face as weather patterns become more erratic.

The authors conclude that integrating metabolomics with transcriptomics and proteomics offers the clearest path forward for decoding melatonin’s mechanisms and translating them into strategies for enhancing crop resilience and productivity. What was once considered merely an animal sleep hormone has turned out to be a versatile green signal, one that plants deploy to rewire their metabolism in the face of adversity. As sequencing costs fall and mass spectrometry becomes ever more sensitive, the coming years should reveal the precise regulatory circuits through which melatonin operates, opening the door to crops engineered or bred to harness this molecule’s remarkable protective chemistry. For a world where heatwaves, droughts and saline soils threaten harvests with growing frequency, melatonin’s journey from night hormone to agricultural ally may prove to be one of the more consequential stories in plant biology.

Subject of Research: Melatonin-mediated metabolic reprogramming and stress adaptation in plants

Article Title: Melatonin-mediated metabolic reprogramming and stress adaptation in plants

Article References: Hussain, B., Colgecen, H., Karahan, H., & Fariduddin, Q. (2026). Melatonin-mediated metabolic reprogramming and stress adaptation in plants. Plant Cell Reports, 45(11), Article 335. https://doi.org/10.1007/s00299-026-04016-z

Image Credits: AI Generated

DOI: 10.1007/s00299-026-04016-z

Keywords: melatonin, phytomelatonin, metabolic reprogramming, metabolomics, multi-omics, plant stress tolerance, reactive oxygen species, nitric oxide, phytohormone crosstalk, secondary metabolites, crop resilience, Plant Cell Reports

The gene at the heart of the story is SlGLK2, a transcription factor that controls the development of plastids, the tiny compartments inside plant cells where chlorophyll is built and where many of the compounds that make fruit nutritious are synthesized. In wild tomatoes, SlGLK2 is fully functional, and the fruit develops a pronounced green shoulder at the stem end, a patch of chlorophyll-rich tissue that signals healthy plastid development. But during the twentieth century, breeders selected a mutation called uniform ripening, or u, a single-base insertion in the SlGLK2 coding sequence that throws the gene’s reading frame out of alignment. The insertion creates a premature stop codon, truncating the protein before it can reach its DNA-binding and dimerization domains. The result is fruit that ripens into an even red without any green patches, a trait consumers found appealing, but one that comes with fewer plastids and lower levels of sugars and tocopherols in the ripe fruit.

That trade-off is a textbook example of what plant scientists call domestication-associated genetic trade-offs, where selecting for one desirable trait inadvertently fixes alleles that compromise others. The u allele has been widely adopted across cultivated tomato varieties, and its effects on fruit quality have been documented since Powell and colleagues first cloned the gene in 2012. But the JIRCAS team, Kentaro Ezura and Cheolwoo Park, wondered whether the damage could be repaired not by restoring the original wild-type sequence, which would require a precise repair template, but by introducing a second, compensatory mutation nearby that would shift the reading frame back into alignment. If the protein could tolerate a few extra or missing amino acids in a disordered linker region, the gene might be reactivated without ever needing to recreate the exact ancestral sequence.

To test the idea, the researchers turned to a temperature-tolerant version of LbCas12a, a CRISPR nuclease derived from a Lachnospiraceae bacterium, which carries a single D156R mutation that enhances its activity at low temperatures. Cas12a is particularly well suited to targeting A/T-rich sequences, and the insertion site in the u allele sits within just such a region, which had proven difficult to target with standard Cas9. The team built a genome editing vector carrying a crRNA directed against the SlGLK2 target site and introduced it into the Micro-Tom tomato cultivar, a miniature model system that carries the non-functional u allele. Agrobacterium-mediated transformation produced three independent T0 lines carrying mutations near the target site.

One of those lines, CR-Slglk2 #2, immediately caught the researchers’ attention because its mature green fruit developed green shoulders at the stem end, a phenotype resembling that of the functional U allele. Direct sequencing revealed that the plant carried biallelic mutations: a 4-bp deletion on one chromosome and a 13-bp deletion on the other. The 13-bp deletion, designated CR-Slglk2-4, caused a frameshift that restored the normal reading frame, while the 4-bp deletion, CR-Slglk2-3, produced another premature stop codon. The researchers then generated homozygous T1 lines for each allele and compared them side by side with unedited Micro-Tom. Fruits of the CR-Slglk2-3 line, which did not restore the reading frame, looked essentially identical to unedited fruit. But fruits of the CR-Slglk2-4 line, carrying the frame-restoring deletion, produced the green shoulder phenotype consistently, and accumulated significantly more chlorophyll at the immature green stage than either the unedited control or the CR-Slglk2-3 line.

Biochemical analysis of fully ripe fruit confirmed that the frame restoration had real consequences for fruit quality. Total soluble solids, measured as degrees Brix, rose from 6.3 in unedited Micro-Tom to 7.4 in the edited line, a significant increase that reflects higher sugar content. Total tocopherol content, comprising the α, β, γ, and δ forms of vitamin E, increased from 37.25 to 62.05 micrograms per gram of fresh weight, driven mainly by higher α- and γ-tocopherol levels. In contrast, lycopene and β-carotene contents, fruit weight, and fruit dimensions remained unchanged, suggesting that the restoration selectively enhanced several quality-related traits without substantially altering fruit morphology. Off-target analysis using Cas-OFFinder-bulge, which searched the tomato SL4.0 reference genome under both mismatch-only and bulge-permissive conditions, detected only the intended target site under standard conditions, and direct sequencing confirmed that the single additional candidate site identified under the bulge-permissive condition remained unedited.

To validate that the frame-restored allele had genuinely recovered SlGLK2 protein function, the researchers turned to a battery of molecular assays. Quantitative RT-PCR showed that SlGLK2 transcript levels were consistently higher in CR-Slglk2-4 fruit than in unedited fruit at all examined positions along the stem-to-tip axis, and that the characteristic spatial gradient of SlGLK2 expression, higher at the stem end than at the stylar end, was preserved in the edited line. This suggests that the uniform ripening phenotype of the u allele results primarily from loss of SlGLK2 protein activity rather than from an altered expression pattern, and that the frame-restored allele recovered protein function while maintaining the gene’s native spatial regulation. Full-length cDNA sequencing confirmed that the mutation did not affect splicing patterns, and predictions using LOCALIZER and NLStradamus showed that the additional deletion did not alter the nuclear localization signal upstream of the MYB-like DNA-binding domain.

Subcellular localization assays using sfGFP-tagged proteins expressed in Nicotiana benthamiana leaves showed that both the functional SlGLK2-U protein and the frame-restored SlGLK2-CR4 protein localized to the nucleus, whereas no fluorescent signal was detected for the truncated SlGLK2-u protein. Transcriptomic analysis of immature green fruit pericarps, performed with RNA-seq on an Illumina NovaSeq X Plus platform, identified 161 genes upregulated and 26 genes downregulated in the stem end of CR-Slglk2-4 fruit compared with the u allele. Of the 161 upregulated genes, 62 overlapped with genes upregulated in a previously published SlGLK2-overexpression line, and 34 of those 62 genes carried significant SlGLK2 binding signals in prior chromatin immunoprecipitation sequencing data, making them candidates for direct regulation. Gene ontology enrichment analysis of the commonly upregulated gene set revealed overrepresentation of chloroplast- and photosynthesis-associated terms, including chlorophyll biosynthetic process, photosystem I light harvesting, and chloroplast thylakoid lumen, confirming that the frame-restored allele had reactivated the downstream transcriptional program associated with plastid biogenesis.

Quantitative RT-PCR validation of seven genes present in both the transcriptomic and ChIP-seq datasets confirmed their elevated expression in CR-Slglk2-4 fruit. These included protochlorophyllide reductase B (SlPORB), Mg-protoporphyrin IX monomethyl ester cyclase (SlMPEC), geranylgeranyl diphosphate reductase (SlGGDR), chlorophyll a-b binding protein 1C (SlCAB1C), light-harvesting complex B2 (SlLHCB2), lycopene epsilon-cyclase (SlLCYE), and a CONSTANS-like zinc finger transcription factor. To directly test whether the frame-restored SlGLK2-CR4 protein retained transcriptional activation activity, the researchers performed a transient dual-luciferase reporter assay in Nicotiana benthamiana leaves using the promoter of SlLHCB2, a previously identified direct target of SlGLK2. Co-expression of SlGLK2-CR4 significantly increased the firefly-to-Renilla luciferase ratio compared with the sfGFP negative control, providing functional evidence that the reframed protein can activate a representative photosynthesis-related target gene.

The broader significance of the work lies in what it says about the latent potential hiding in crop genomes. Many domestication and improvement events have silently disabled genes through frameshift mutations and premature stop codons, converting them into non-processed pseudogenes whose transcripts may still be detectable even though the protein is truncated. The JIRCAS team notes that cultivated tomatoes carry several such disabled alleles, including an in-frame six-base insertion in the SlHAK20 transporter associated with salt tolerance loss, a C-to-T substitution in SlBBX18 that increases drought sensitivity, and a deleterious mutation in the SUPPRESSOR OF SP2 gene that was recently repaired by base editing to enable early fruit yield. The reframing strategy demonstrated here, which requires neither a repair template nor precise restoration of the wild-type sequence, offers a technically accessible route to recover useful gene functions directly within cultivated genetic backgrounds, avoiding the linkage drag that complicates conventional introgression from wild relatives. Its broader applicability will depend on the location and type of the original mutation, the availability of suitable target sites, and the structural tolerance of the encoded protein, but the approach expands the conventional use of nuclease-based genome editing from gene disruption to functional gene reactivation, opening a new chapter in the effort to recover traits lost during plant domestication.

Subject of Research: Restoration of the tomato uniform ripening gene SlGLK2 by compensatory frameshift genome editing

Article Title: Reactivation of a loss-of-function SlGLK2 allele by frame-restoring genome editing in tomato

Article References: Ezura, K., & Park, C. (2026). Reactivation of a loss-of-function SlGLK2 allele by frame-restoring genome editing in tomato. Plant Cell Reports, 45(11), Article 333. https://doi.org/10.1007/s00299-026-04024-z

Image Credits: AI Generated

DOI: 10.1007/s00299-026-04024-z

Keywords: SlGLK2, tomato, uniform ripening, CRISPR-Cas12a, genome editing, plastid development, chlorophyll, tocopherol, domestication trade-offs, Plant Cell Reports, Reactivation, loss-of-function

The story begins with a familiar horticultural tool: 6-benzylaminopurine, a synthetic cytokinin that growers and researchers use to stimulate bud activity. Cytokinins are plant hormones well known for promoting cell division and for encouraging axillary buds, the dormant embryonic shoots nestled in the angle between leaf and stem, to break out and grow into branches. When the team applied this synthetic cytokinin to apple plants, they noticed that MdAGL29 was consistently downregulated. In other words, the hormone that pushes buds toward growth simultaneously silences a gene that appears to suppress that very growth. That inverse relationship caught the researchers’ attention and became the central thread of their investigation.

To test whether MdAGL29 really influences branching, the team turned to a heterologous expression strategy, meaning they transferred the apple gene into a different organism to see what it would do. Their chosen host was poplar, a fast-growing tree that has long served as a model woody plant for forestry and molecular genetics because it is easy to transform and its architecture is readily quantified. When MdAGL29 was overexpressed in poplar, the effect was striking: the engineered trees produced fewer branches than control plants. The gene, it seemed, was not a passive bystander in the branching process but an active suppressor of it.

The poplar experiments also revealed a hormonal signature. After decapitation treatment, a standard experimental maneuver in which the shoot tip is removed to relieve apical dominance and provoke branching, the MdAGL29-overexpressing poplars contained lower levels of endogenous cytokinins than their non-engineered counterparts. This detail matters because cytokinins are among the primary promoters of bud outgrowth. A plant that makes less cytokinin in response to decapitation has less of the growth signal that normally coaxes axillary buds into shoots. The finding suggests that MdAGL29 may restrain branching partly by dampening the cytokinin pool, adding a hormonal dimension to its transcriptional role.

But where does MdAGL29 act in the genetic hierarchy of branching? To answer that question, the researchers performed yeast one-hybrid assays, a technique used to test whether a protein can physically bind to the regulatory DNA upstream of a target gene. Their results pointed to MdBRC1 and MdBRC2, the apple versions of BRANCHED1, a gene family famous in plant biology as a master inhibitor of bud outgrowth. BRANCHED1 was first characterized in Arabidopsis, where it acts as an integrator of branching signals within axillary buds, receiving inputs from auxin, strigolactone and other pathways and translating them into a decision: stay dormant or grow. In grasses, the equivalent gene TEOSINTE BRANCHED1 shaped crop domestication, and in trees, BRC1 mediates seasonal growth responses. The apple homologs fit this pattern as branch-negative regulators.

The yeast one-hybrid data were corroborated by dual-luciferase reporter assays, a complementary method performed in plant cells in which the promoter of the candidate target gene is wired to a luciferase enzyme. If the transcription factor activates the promoter, the cells glow more brightly. When MdAGL29 was supplied alongside the MdBRC1/2 promoters, luciferase activity rose, confirming that MdAGL29 positively regulates the expression of these branch inhibitors. The logic of the pathway therefore runs cleanly in one direction: MdAGL29 turns up the brakes, and branches stay suppressed. Remove or reduce MdAGL29, as happens when cytokinin is applied, and the brakes ease off, allowing buds to escape dormancy and develop into shoots.

This arrangement is elegant because it connects a hormone cue to a transcriptional switch through a single characterized step. Cytokinin application downregulates MdAGL29; MdAGL29 normally sustains the expression of MdBRC1/2; BRC1 proteins hold axillary buds in check. The new work thus adds a MADS-box link to the well-studied hormonal network of apical dominance, in which auxin flowing down from the shoot tip suppresses cytokinin biosynthesis in the nodes, and strigolactones moving up from the roots reinforce bud dormancy. Previous apple studies from the same research community had implicated cytokinin-responsive regulators such as MdRR9 and the MdWUS2-MdTCP12 module in bud activation, so MdAGL29 extends an emerging picture in which multiple transcription factors interpret hormonal signals at the bud.

Why should a MADS-box gene, a family best known for controlling floral organ identity, be pulling levers in shoot architecture? The answer is that MADS-box factors are versatile. In rice, the MADS-box protein OsMADS57 interacts with the tillering regulator OsTB1 to modulate branching via the strigolactone receptor DWARF14. In tomato, SlMBP11 and the type I factor SlMADS50 both influence plant architecture through hormonal pathways. The apple study fits squarely into this growing recognition that MADS-box transcription factors are recurring components of architectural networks across species, not merely specialists of the flower. That cross-species pattern also hints that similar modules may be waiting to be found in other woody crops, from pear to cherry.

The practical implications are considerable. Apple orchards increasingly rely on high-density planting systems in which tree size, branch number and branch angle determine how quickly a young orchard reaches commercial productivity. Recent horticultural research has quantified how lateral branch number and angle affect early growth and yield in high-density apple plantings, and growers currently manage these traits through labor-intensive pruning and training. A gene that reliably suppresses branching offers two possible routes. Overexpressing MdAGL29, or editing its regulatory regions, could produce naturally compact, low-branching trees that need less pruning. Conversely, suppressing the gene could encourage feathering, the production of well-placed lateral branches in nursery stock, reducing the need for chemical branching agents such as synthetic cytokinins in the nursery.

There are, of course, caveats. The overexpression experiments were carried out in poplar rather than apple, and while heterologous expression is a powerful and widely used dissection tool, the definitive test will be manipulating MdAGL29 in apple itself, whether through stable transformation, CRISPR editing or the identification of natural allelic variation among cultivars. It also remains to be seen how MdAGL29 interacts with the other branching regulators already known in apple, and whether its effect on cytokinin levels is a direct consequence of its transcriptional activity or an indirect downstream effect. Still, the study delivers something the field has lacked: a named, mechanistically supported negative regulator of branching in one of the world’s most valuable fruit crops, verified by binding and reporter assays and consistent across hormonal, molecular and whole-plant levels of analysis. For breeders chasing the ideal tree architecture, MdAGL29 is a target worth watching.

Subject of Research: Molecular regulation of shoot branching in apple by the MADS-box transcription factor MdAGL29

Article Title: MdAGL29 positively regulates MdBRC1/2 and negatively controls shoot branching in apple

Article References: Ji, M., Li, J.-W., Yang, F., Liu, J.-S., Zhang, D., & Ma, J.-J. (2026). MdAGL29 positively regulates MdBRC1/2 and negatively controls shoot branching in apple. Plant Cell Reports, 45(11), Article 332. https://doi.org/10.1007/s00299-026-04012-3

Image Credits: AI Generated

DOI: 10.1007/s00299-026-04012-3

Keywords: apple, MdAGL29, MADS-box transcription factor, shoot branching, MdBRC1/2, cytokinin, axillary buds, plant architecture, gene regulation, poplar, apical dominance, Plant Cell Reports

The organ in question is the sepal, the outermost floral whorl of the model plant Arabidopsis thaliana. Sepals are often dismissed as the plain, green wrappers of the flower, but they perform an essential protective role, shielding the delicate reproductive structures inside the bud until the moment of blooming. To do this well, a sepal must be neither too small, which would leave the bud exposed, nor excessively large, which would waste resources. Sepals have also become a favorite model system for studying organ size because their surface cells grow with striking variability, yet the organ as a whole achieves a reproducible final shape and dimensions through spatiotemporal averaging of that noisy growth. Understanding what halts sepal elongation at the right time therefore speaks to a fundamental problem in developmental biology.

The Zhejiang University team focused their investigation on a protein called histone deacetylase complex 1, or HDC1. Histone deacetylases are chromatin-associated enzymes that remove acetyl groups from histone proteins, the spools around which DNA is wound. When histones are highly acetylated, the chromatin tends to be open and genes are permissive to transcription; deacetylation generally compacts chromatin and silences genes. HDC1 was already known to be a versatile player in plant biology. Previous work had shown that its expression level titrates overall plant growth and abscisic acid sensitivity, that it facilitates hypocotyl elongation through a PIF4-dependent process, and that it helps remodel root architecture under low-phosphate conditions. What had remained unclear was whether HDC1 has any role in determining the final size of aerial reproductive organs.

Using a combination of genetic, transcriptomic, and physiological analyses in Arabidopsis, the researchers found that HDC1 acts as a critical regulator of sepal size specifically during the maturation phase of the organ. When HDC1 function is compromised, sepals fail to terminate their elongation properly, indicating that this protein is required to bring cell expansion to a controlled stop. The finding is significant because most studies of organ size have concentrated on the early, proliferative phase of growth, when cells divide rapidly and the organ primordium is established. The maturation phase, during which cells decide whether to keep expanding or to cease growth, has been far less well characterized, particularly for sepals.

The mechanistic story that emerges from the study is elegant and, in places, unexpected. During sepal maturation, HDC1 represses the expression of genes encoding protein phosphatase 2A, or PP2A, a family of serine/threonine phosphatases with well-documented roles in diverse signaling pathways, from abscisic acid responses in guard cells to microtubule organization. HDC1 achieves this repression through histone H3 deacetylation at the PP2A loci, a direct epigenetic mechanism. With PP2A expression dampened, the balance of phosphorylation within the cell shifts, and this shift has consequences for one of the most important hormonal systems in plants: ethylene biosynthesis.

Ethylene, the simple two-carbon gas that ripens fruit and promotes senescence, is synthesized from the amino acid methionine via a pathway whose rate-limiting enzymes are the ACC synthases. The activity and stability of these enzymes are famously controlled by phosphorylation. Prior work had established that mitogen-activated protein kinases can phosphorylate ACC synthases such as ACS6, stabilizing the protein and boosting ethylene production, while PP2A differentially regulates the turnover of ACC synthase isoforms. By repressing PP2A genes, HDC1 tips this regulatory balance: the ethylene biosynthetic enzymes become dephosphorylated and activated, and ethylene levels rise in the maturing sepal. In other words, an epigenetic change at the chromatin level is translated, through a phosphatase, into a change in hormone output.

The elevated ethylene then triggers the next link in the chain: accumulation of reactive oxygen species, or ROS. ROS are often portrayed as damaging byproducts of metabolism, but in the past two decades they have been recognized as bona fide signaling molecules that regulate cell expansion, vascular proliferation, root hair development, and stress adaptation throughout the plant. The interplay between ethylene and ROS is a recurring theme in plant signaling, with ethylene influencing ROS production through respiratory burst oxidase homolog enzymes such as RbohD. In the maturing sepal, the study found that increased ethylene facilitates ROS accumulation, and this oxidative burst serves a developmental purpose: it promotes sepal maturation and terminates sepal cell elongation, thereby fixing the final length of the organ.

Supporting this model, the team’s genetic evidence drew on an impressive collection of ethylene biosynthesis mutants, including the ACSDDD line and an acs octuple mutant lacking multiple ACC synthase genes, materials provided by collaborators at the Southern University of Science and Technology and elsewhere. Transcriptomic profiling of the relevant genotypes, with raw RNA sequencing data deposited in the National Genomics Data Center, allowed the researchers to connect HDC1’s chromatin activity to downstream changes in gene expression. The convergence of genetic, genomic, and physiological lines of evidence strengthens the conclusion that the HDC1–PP2A–ethylene–ROS pathway is a genuine regulatory module rather than a correlation of unrelated events.

The broader implications of the work extend beyond the sepal. Organ size control is a major determinant of crop yield, and genes that influence cell number and cell expansion, such as the maize cell number regulator CNR1, have long been viewed as targets for yield improvement. If the HDC1-mediated pathway identified here operates in other organs and crop species, it could offer breeders a handle on tuning final organ dimensions by manipulating either the epigenetic regulator itself or the hormonal module it controls. The study also adds to a growing appreciation that epigenetic machinery does not merely switch genes on and off in a static sense, but participates in dynamic developmental decisions, including the timing of growth cessation, flowering, and stress responses.

There remain open questions. How HDC1 is itself targeted to the PP2A genes specifically during sepal maturation, whether additional chromatin factors cooperate in this repression, and how the ROS signal is transduced into a cessation of cell expansion at the cellular level are all avenues for future work. It will also be interesting to see whether the same ethylene–ROS module governs size termination in other floral organs or in leaves, and whether mechanical feedback, known to restrict sepal growth and shape, intersects with this chemical signaling pathway. What is already clear, however, is that the humble sepal has once again proven its worth as a model, and that the answer to the old question of how organs know when to stop growing lies, at least in part, in a deceptively simple cascade: a histone modification silences a phosphatase, the phosphatase releases the brakes on a gaseous hormone, and the hormone ignites a burst of reactive oxygen that tells the cells their growing days are over.

Subject of Research: Epigenetic regulation of sepal organ size in Arabidopsis through the HDC1–PP2A–ethylene–ROS signaling module

Article Title: Histone deacetylase complex 1 modulates sepal length through the ethylene–ROS module

Article References: Xiang, D., Qiu, D., Zhang, R., He, X., Xu, S., Zhou, M., & Hong, L. (2026). Histone deacetylase complex 1 modulates sepal length through the ethylene–ROS module. Plant Cell Reports, 45(11), Article 330. https://doi.org/10.1007/s00299-026-04018-x

Image Credits: AI Generated

DOI: 10.1007/s00299-026-04018-x

Keywords: HDC1, histone deacetylase, sepal length, organ size, ethylene, reactive oxygen species, PP2A, Arabidopsis thaliana, epigenetics, plant development, cell elongation, Plant Cell Reports

The research team, led by Lichao Hu and Yaqiong Wu of Nanjing Forestry University and the Nanjing Botanical Garden, together with colleagues including Zefu Wang and Weilin Li, assembled 81 newly sequenced Rubus plastomes, drawing on 22 wild species and 59 cultivars. Chloroplast genomes, often called plastomes, are the circular DNA chromosomes housed inside the chloroplasts, the green organelles that perform photosynthesis. Because chloroplasts are inherited predominantly through the maternal line in most flowering plants, plastomes act like a genetic surname, allowing researchers to trace maternal ancestry even when centuries of hybridization have scrambled the nuclear genome.

Technically, the assembly pipeline followed the now-standard playbook for organelle genomics. High-quality reads were mapped and assembled de novo using tools such as GetOrganelle, structural verification was performed with visualization software including Bandage and CPGView, and annotations were checked against curated references. Every one of the 81 genomes displayed the canonical quadripartite architecture seen across most angiosperms: a large single-copy region and a small single-copy region separated by a pair of inverted repeats. Sizes ranged narrowly from 155,385 to 157,012 base pairs, and each plastome carried 130 annotated genes, corresponding to 113 unique functional genes once duplicates within the inverted repeats are counted once. That tight range is itself a finding, demonstrating that despite the morphological diversity of Rubus, from arching blackberry canes to upright red raspberry primocanes, the chloroplast chromosome has remained remarkably conservative in structure and gene order.

From the full set, the researchers distilled 16 representative cultivars whose plastomes captured every unique plastid sequence in the collection, and subjected these to a systematic comparative analysis. They catalogued repeat sequences, including simple sequence repeats and longer dispersed repeats, using tools such as MISA-web and REPuter. They quantified codon usage bias, the non-random preference for synonymous codons that reflects mutational pressures and translational selection in the plastid. And they scanned whole-genome alignments produced with MAFFT to locate hypervariable regions, the mutational hotspots where nucleotide diversity concentrates. Such hotspots, often found in intergenic spacers and in genes like matK that have long served as plant DNA barcodes, are the raw material from which species-discriminating markers are mined.

The phylogenetic analysis, performed with maximum-likelihood methods under frameworks such as RAxML-NG and IQ-TREE, placed the modern cultivars into three principal subgenera: Rubus, Idaeobatus, and Melanobatus. Red raspberries, as expected, fell within Idaeobatus, the subgenus of erect-caned raspberries, while blackberries clustered in subgenus Rubus. The more surprising result concerned black raspberry, the glossy, dark-fruited crop prized for its intense anthocyanin content: phylogenetically, it sits within Melanobatus rather than alongside its red namesake. For growers and breeders, this is more than a taxonomic footnote. It means that red and black raspberries, despite their culinary similarity, carry chloroplast lineages from distinct evolutionary branches, a divergence that shapes how their traits can be combined in breeding programs.

That divergence also created the opportunity for the study’s most applied contribution: molecular markers for species delimitation. By scanning the aligned plastomes for insertion-deletion polymorphisms, or InDels, stretches of DNA that are present in one lineage and absent in another, the team identified candidate sites that cleanly separate the major cultivated groups. From these candidates they developed and validated four InDel markers capable of distinguishing black raspberry, red raspberry, and raspberry-blackberry hybrids. In practice, such markers work like a genetic litmus test: a polymerase chain reaction assay produces fragments of diagnostic size depending on which plastid lineage a sample carries, and the pattern on a gel or capillary sequencer assigns the plant to its maternal group. Because InDels are codominant, easy to score, and highly reproducible across laboratories, they are among the most user-friendly marker types available for routine identification.

The practical value of this toolkit is hard to overstate. The nursery trade has wrestled with cultivar mislabeling for decades; as early as 1992, isoenzyme analysis was being used to detect mislabeled raspberry plants, and DNA fingerprinting later became the standard for verifying blackberry breeding lines. Misidentified stock propagates through nurseries, contaminates research collections, and undermines breeding decisions, particularly for raspberry-blackberry hybrids, whose intermediate morphology can fool even experienced eyes. A cheap, chloroplast-based assay that confirms whether a plant’s maternal parent was a black raspberry, a red raspberry, or a blackberry gives propagators, breeders, and gene bank curators a fast quality-control check that requires nothing more than a few milligrams of leaf tissue.

The study also matters for the future of hybrid breeding. Raspberry-blackberry hybrids, such as the loganberry and boysenberry lineages and modern primocane-fruiting hybrids, combine traits from across the genus, and breeders increasingly want to move disease resistance, fruit quality, and machine-harvestable architecture between subgenera. Knowing the maternal ancestry of every elite line, and having markers that verify it, helps breeders plan crosses that exploit cytoplasmic effects, including maternally inherited variation in photosynthesis and stress tolerance that plastid genomes can confer. The expanded plastome resource, with raw reads deposited in the Genome Sequence Archive under accession CRA043307 and assembled genomes available in GenBank under accession numbers PV528353 through PV528434, gives the global Rubus research community a reference panel that future studies of hybrid identification, cytoplasmic diversity, and domestication history can build upon immediately.

There is a broader evolutionary story here as well. Chloroplast genomes evolve slowly and mostly without recombination, which makes them ideal for reconstructing deep relationships, but it also means that a single plastome tree tells only the maternal side of a reticulate history. Rubus is notorious for apomixis, polyploidy, and interspecific hybridization, especially in the blackberries, where pseudogamous reproduction allows hybrid lineages to breed true while accumulating enormous nuclear diversity. The Melanobatus placement of black raspberry, and the clear separation of the three cultivated plastid lineages, provide a maternal scaffold onto which nuclear data can be layered, helping to disentangle which wild species contributed which genomes to modern cultivars. Comparative plastomics of this scale, following similar efforts in cotton, pea, and other crop genera, is rapidly turning the chloroplast into a workhorse for crop genealogy.

For a genus that most people encounter only as a summer treat, Rubus has now yielded a dataset of unusual completeness: 81 new plastomes, a resolved maternal framework for the major cultivated groups, a catalogue of repeats, codon preferences, and hypervariable regions, and four validated markers ready for deployment in nurseries and breeding stations. The work confirms that the existing taxonomic classification of cultivated Rubus holds up under genomic scrutiny, while giving breeders the molecular tools to keep that classification honest at the level of individual plants. As demand for berry crops grows and hybrid breeding accelerates, the humble chloroplast, inherited quietly from mother plant to seedling across generations of cultivation, has proven to be the most reliable witness to where these fruits really came from.

Subject of Research: Comparative chloroplast genome analysis of Rubus cultivars and development of InDel molecular markers for species delimitation

Article Title: Comparative analysis of plastomes of Rubus cultivars and development of molecular markers for species delimitation

Article References: Hu, L., Wu, Y., Zhao, Z., Wu, W., Cao, F., Wang, Z., & Li, W. (2026). Comparative analysis of plastomes of Rubus cultivars and development of molecular markers for species delimitation. Plant Cell Reports, 45(11), Article 324. https://doi.org/10.1007/s00299-026-04013-2

Image Credits: AI Generated

DOI: 10.1007/s00299-026-04013-2

Keywords: Rubus, plastome, chloroplast genome, raspberry, blackberry, phylogenetic analysis, molecular markers, InDel, species delimitation, hybrid breeding, Rosaceae, Plant Cell Reports

The study, led by Sujuan Xu, Xiaoyu Hu and Ting Li under the supervision of Nianjun Teng and Ze Wu at Nanjing Agricultural University, began with a sweeping computational survey. The researchers searched the genomes of three lily species — Lilium davidii var. unicolor, Lilium sargentiae and Lilium regale — for members of the heat shock transcription factor family, the master switches that plants flip when temperatures rise. What they found was striking: 48 heat shock factor genes in L. davidii var. unicolor, 62 in L. sargentiae and a remarkable 114 in L. regale. Those numbers are large by plant standards and reflect the enormous, duplicated genomes that lilies carry, which have been shaped by transposon insertions and polyploidization events over evolutionary time.

Heat shock transcription factors, or HSFs, sit at the top of the plant heat-response hierarchy. When a plant senses dangerous temperatures, these proteins bind to specific DNA sequences in the promoters of protective genes, switching on the production of heat shock proteins and other molecular chaperones that shield cells from damage. In the model plant Arabidopsis, the family is compact, but in crops and ornamentals it can be far more elaborate. The lily analysis showed that while the core protein domains — the DNA-binding domain and the oligomerization domain that lets HSFs pair up and grab DNA — have been conserved across the family, the genes themselves have expanded and diversified considerably, particularly within two branches known as class B and class C.

To understand what all this expansion means functionally, the team examined the regulatory regions upstream of each gene and profiled gene activity across heat treatments. Promoter analysis revealed that many lily HSF genes carry binding sites for stress, hormonal and developmental signals, suggesting they do more than simply respond to temperature — they may integrate a wide range of cues, from drought and salinity to growth hormones and flowering time. Transcriptome profiling confirmed that a substantial number of the genes are indeed heat-responsive, ramping up or down when temperatures climb. Among them, one gene stood out: LdHSFC1, a member of the class C branch, which was strongly induced by heat treatment.

That induction might sound like a good sign — a gene waking up to fight the heat — but the team’s functional experiments told a very different story. When they determined where the LdHSFC1 protein operates inside the cell, they found it accumulates in the nucleus, the expected location for a transcription factor. But when they tested its effect on gene expression, LdHSFC1 behaved as a transcriptional repressor, dampening the activity of the genes it contacted rather than activating them. In transient transformation assays in lily, plants carrying the gene showed clearly reduced thermotolerance, wilting under heat conditions that control plants handled better.

The mechanism behind this effect became clear when the researchers traced LdHSFC1’s influence across the heat-response network. Overexpressing LdHSFC1 suppressed the expression of four key protective genes: LdHSFA1, LdHSFA2, LdHSFA3 and LdMBF1c. Silencing the gene, by contrast, enhanced the expression of all four. This matters because HSFA2 is widely regarded as one of the most important positive regulators of acquired thermotolerance in plants — in Arabidopsis, it is required for plants to extend their heat protection after a mild warming episode, and HSFA3 works alongside it in complexes that drive transcriptional memory of heat stress. MBF1c, meanwhile, is a transcriptional coactivator that helps relay heat signals to the defense machinery. By holding these genes down, LdHSFC1 effectively applies a brake to the plant’s entire heat-defense program.

To prove the connection was direct rather than indirect, the team turned to two complementary molecular assays. Yeast one-hybrid experiments showed that the LdHSFC1 protein physically binds to the promoter region of LdHSFA2. Dual-luciferase assays, a standard technique for measuring transcriptional activity, then confirmed that this binding represses LdHSFA2 transcription. Together, the results establish LdHSFC1 as a negative regulator of thermotolerance that acts by directly suppressing the plant’s central heat-response activator — a finding that the authors describe as the first genome-wide overview of the lily HSF family combined with the identification of a clear functional villain in the heat-stress story.

The result is notable because it complicates a simple picture of heat shock factors as uniformly protective. Class B and class C HSFs in other species have shown mixed roles: some, like Arabidopsis HsfB1 and HsfB2b, repress heat-inducible genes yet still contribute positively to acquired thermotolerance, while others, such as rice OsHsfB2b, clearly undermine stress tolerance. In lily itself, earlier work from the same group showed that LlHSFC2 coordinates with class A factors to balance the heat response and actually improve tolerance, and that LdHSFB2a plays its own role in the network. LdHSFC1 now emerges as a class C member with the opposite effect, underscoring how evolutionarily related genes within the same family can evolve sharply divergent functions — and how dangerous it would be to assume that any heat-induced transcription factor is automatically a friend.

Why would a plant evolve a gene that weakens its own heat tolerance? The most likely answer lies in the economics of stress responses. Mounting a full heat-defense program — churning out chaperones, remodelling membranes, adjusting metabolism — is expensive, and plants must balance immediate survival against growth, reproduction and development. Repressors like LdHSFC1 may serve as tuning knobs, preventing the heat response from running too hot and too long when conditions do not warrant it. Under natural conditions this trade-off may be adaptive; under the increasingly extreme temperatures of a changing climate, it can become a liability. Understanding which genes act as brakes, and when, is therefore just as important for breeders as knowing which genes act as accelerators.

The practical implications reach well beyond basic biology. Lilies are among the most valuable cut flowers worldwide, and heat stress during cultivation reduces bloom quality, shortens vase life and narrows the geographic range where commercial growing is viable. The new genome-wide catalogue gives breeders and biotechnologists a complete parts list of lily heat-response regulators, and LdHSFC1 offers an obvious intervention point: silencing or editing the gene, or selecting natural variants with weaker repressor activity, could plausibly produce lilies that hold their blooms through hotter summers. The findings also carry lessons for other ornamental and crop species, where class B and class C HSFs remain underexplored. As the authors note, the work broadens understanding of heat-responsive transcriptional regulation in ornamental plants and highlights potential targets for enhancing lily thermotolerance — a small gene with an outsized role in deciding whether one of the world’s favorite flowers can keep its cool.

Subject of Research: Genome-wide analysis of heat shock transcription factor genes and the role of LdHSFC1 in heat stress tolerance in lily

Article Title: Genome-wide analysis of the HSF gene family in lily and functional characterization of LdHSFC1 under heat stress

Article References: Xu, S., Hu, X., Li, T., Feng, H., Ding, L., Wu, Z., & Teng, N. (2026). Genome-wide analysis of the HSF gene family in lily and functional characterization of LdHSFC1 under heat stress. Plant Cell Reports, 45(11), Article 323. https://doi.org/10.1007/s00299-026-03995-3

Image Credits: AI Generated

DOI: 10.1007/s00299-026-03995-3

Keywords: lily, heat shock transcription factors, LdHSFC1, thermotolerance, LdHSFA2, heat stress, genome-wide analysis, transcriptional repressor, Plant Cell Reports, ornamental plants, gene regulation, Lilium

The chemistry behind persulfidation is elegant in its simplicity. Cysteine residues within proteins carry reactive thiol groups, and when hydrogen sulfide reacts with these thiols, it converts them into persulfide groups, formally adding an extra sulfur atom. This seemingly small change can dramatically alter a protein’s behavior. Persulfidation can change a protein’s conformation, modify its enzymatic activity, alter its subcellular localization, protect cysteine residues from irreversible oxidation, or change how the protein interacts with partners and membranes. Because the modification is reversible, it functions as a dynamic molecular switch, allowing plant cells to respond rapidly and flexibly to developmental cues and environmental challenges without needing to synthesize new proteins.

Detecting this modification, however, has been one of the field’s greatest technical challenges, and the review devotes considerable attention to the methodological toolbox that has made persulfidation biology possible. The workhorse of the field is the modified biotin switch assay, an adaptation of a technique originally developed to detect S-nitrosylated proteins. In this approach, free thiols are blocked, persulfides are then selectively tagged, and the tagged proteins are pulled down and identified. Building on this foundation, researchers have developed mass spectrometry-based high-throughput workflows that can map persulfidation sites across thousands of proteins at once, generating whole-proteome persulfidation profiles in model plants such as Arabidopsis. These proteomic studies revealed that hundreds of proteins involved in wildly diverse processes carry the modification, hinting early on at the breadth of hydrogen sulfide’s regulatory reach.

Beyond the biotin switch family, the methodological landscape now includes antibody-dependent western blotting for targeted validation, electrophilic trapping strategies that exploit the distinctive nucleophilicity of persulfides, genetically encodable and small-molecule fluorescent probes that allow persulfidation to be visualized in living tissues, and alkylating compound-based approaches. Each technique comes with trade-offs in sensitivity, specificity and throughput, and the review emphasizes that careful controls remain essential. Notably, recent work has shown that some commonly used alkylating agents can convert persulfides into thioethers that escape detection, meaning that method choice can materially change experimental conclusions. Accurate detection, identification and quantification of persulfidation, the authors argue, is the indispensable foundation for understanding the modification’s biological functions and molecular mechanisms.

Where persulfidation truly shines, according to the synthesis, is in its role as a master fine-tuner of phytohormone signaling. The review documents how hydrogen sulfide modulates the pathways of ethylene, abscisic acid, auxin and melatonin by persulfidating key enzymes, receptors and transcription factors within each cascade. In the case of ethylene, the gas responsible for fruit ripening, hydrogen sulfide has been shown to negatively regulate ethylene biosynthesis by persulfidating the enzyme ACO in tomato plants under osmotic stress, creating a feedback loop that prevents runaway hormone production. Persulfidation of the transcription factor SlERF.D2 further interferes with ethylene signaling, while modification of the E3 ligase BRG3 delays tomato ripening by reducing ubiquitination of the ripening repressor WRKY71. Persulfidation and phosphorylation of the transcription factor SlWRKY6 have also been shown to differentially regulate tomato fruit ripening, illustrating how multiple post-translational modifications converge on the same regulatory proteins.

Abscisic acid, the hormone that governs stomatal closure and drought responses, provides perhaps the most mechanistically detailed examples. Hydrogen sulfide positively regulates abscisic acid signaling through persulfidation of SnRK2.6, a core protein kinase in guard cell signaling. Persulfidation-based modification of the cysteine desulfhydrase enzyme and the NADPH oxidase RBOHD controls guard cell abscisic acid signaling, linking sulfide production directly to the reactive oxygen species machinery that drives stomatal movement. Abscisic acid also triggers persulfidation of the cysteine protease ATG4, thereby regulating autophagy, while persulfidation of the glycosyltransferase UGT71C5 facilitates the reversible inactivation of abscisic acid itself. Through these targets, hydrogen sulfide influences everything from the opening and closing of stomata to the maintenance of hormone homeostasis, governing processes as visible as drought tolerance and as subtle as the balance of hormone pools within a single cell.

Auxin and melatonin signaling are likewise woven into the persulfidation network. Hydrogen sulfide alleviates osmotic stress-induced inhibition of root growth by promoting auxin homeostasis, and it alleviates salt stress through auxin signaling in Arabidopsis. The modification also antagonizes cytokinin signaling by persulfidating the cytokinin-degrading enzyme CKX2, reshaping root system architecture, and it acts downstream of methane to induce adventitious root development in cucumber. In the melatonin sphere, hydrogen sulfide aids osmotic stress resistance through the persulfidation of melatonin production-related enzymes in Arabidopsis, and the two molecules cooperate in modulating secondary metabolites and metal sequestration in arsenic-stressed tomato plants. Together, these findings paint a picture of hydrogen sulfide as a hub that sits at the intersection of multiple hormonal circuits, allowing a single gasotransmitter to coordinate root development, flowering, ripening and stress responses across the plant life cycle.

Beyond hormones, the review highlights a strikingly concrete mechanism by which persulfidation protects plants from salt and drought stress: the maintenance of cellular ion homeostasis. Excess sodium is toxic to plant cells, and survival under salinity depends on keeping sodium out while retaining potassium. Persulfidation executes what the authors describe as a coordinated ‘activate efflux, inhibit leak’ strategy. On the activation side, the modification enhances the activity of the plasma membrane H+-ATPase and the SOS1 Na+/H+ antiporter, the molecular pump that drives sodium extrusion from the cell. Persulfidation of PMA1, a plasma membrane proton pump, has been shown directly to improve salt tolerance in Arabidopsis. On the retention side, hydrogen sulfide inhibits inward potassium channels through persulfidation, preventing the loss of cellular potassium that would otherwise accompany salt stress. This dual action has been observed in systems ranging from Arabidopsis and cucumber to poplar and the salt-secreting mangrove Avicennia marina, suggesting an evolutionarily conserved ionic strategy.

The breadth of persulfidation’s targets extends even further. The modification maintains the activity of cytosolic glucose-6-phosphate dehydrogenases under salt stress by stabilizing their tetrameric structure and competing with cysteine sulfur oxidation, thereby protecting central carbon metabolism. Persulfidation of the flowering repressor BraFLCs promotes flowering in heading Chinese cabbage, and hydrogen sulfide-induced persulfidation has been implicated in barley’s resilience to drought and salinity. The review also situates plant persulfidation within a broader evolutionary context, noting that selective persulfide detection methods have revealed conserved anti-aging effects of protein S-sulfhydration in animals, and that hydrogen sulfide signaling through persulfidation regulates processes from autophagy to endoplasmic reticulum stress responses across kingdoms. What began as plant biochemistry is now clearly part of a universal redox signaling language.

The practical implications of this synthesis are considerable. Because persulfidation governs fruit ripening, stomatal movement, root development and osmotic stress adaptation, it represents a promising target for improving crop adaptation to the increasingly erratic conditions of a changing climate. Engineering or agronomically manipulating hydrogen sulfide signaling could, in principle, enhance salt and drought tolerance in staple and horticultural crops without the yield penalties often associated with conventional stress-resistance traits. The authors’ framework, supported by funding from the National Natural Science Foundation of China, provides researchers with a roadmap: refine detection methods to quantify persulfidation at specific sites, map the modification across crop genomes, and identify the persulfidation states that confer resilience. As the molecular details continue to accumulate, the once-maligned gas of rotten eggs looks increasingly like one of the most versatile regulatory molecules in the plant world, a sulfur-based switchboard quietly coordinating how plants grow, ripen and survive.

Subject of Research: Protein persulfidation as a hydrogen sulfide-mediated post-translational modification regulating plant hormone signaling, ion homeostasis and stress adaptation

Article Title: Protein persulfidation in plants: a central regulator of multiple signaling pathways

Article References: Yang, D., Huang, D., Chen, X., Li, A., Chen, H., & Liao, W. (2026). Protein persulfidation in plants: a central regulator of multiple signaling pathways. Plant Cell Reports, 45(9), Article 269. https://doi.org/10.1007/s00299-026-03954-y

Image Credits: AI Generated

DOI: 10.1007/s00299-026-03954-y

Keywords: persulfidation, hydrogen sulfide, post-translational modification, phytohormone signaling, abscisic acid, ethylene, auxin, melatonin, ion homeostasis, salt tolerance, drought stress, Plant Cell Reports

The stakes could hardly be higher. Global agriculture must deliver substantial yield gains by 2050 to feed a growing population while sharply reducing its environmental footprint. Today, pests and pathogens destroy between 20 and 40 percent of annual crop production, losses that are overwhelmingly managed with chemical pesticides carrying well-documented ecological and human health costs, from pollinator decline to contaminated waterways and rising greenhouse gas emissions associated with pesticide manufacture and application. RNA interference offers a fundamentally different approach: a mechanism that can be tuned with near-surgical precision to attack a single pest species while leaving beneficial insects, plants, and mammals untouched.

The underlying biology is elegant. RNAi is a natural gene-silencing pathway found across eukaryotes, first characterized by Andrew Fire and Craig Mello in the nematode Caenorhabditis elegans, work that earned the 2006 Nobel Prize in Physiology or Medicine. When a cell encounters double-stranded RNA, or dsRNA, an enzyme called Dicer slices it into small interfering RNAs. These fragments are loaded into the Argonaute-containing RNA-induced silencing complex, which uses one strand as a guide to find and degrade complementary messenger RNAs. If the dsRNA is designed to match a gene that is essential to a pest’s survival, ingesting it can shut down that gene and kill or debilitate the organism. Because the guide sequence can be chosen to match a target found only in the pest, the specificity of the approach far exceeds that of broad-spectrum chemical insecticides.

Two delivery strategies dominate the field. Host-induced gene silencing, or HIGS, builds the silencing construct directly into the crop’s genome, so the plant itself continuously produces dsRNA aimed at its attackers. Spray-induced gene silencing, or SIGS, instead applies dsRNA externally as a foliar spray, much like a conventional pesticide but with a biological active ingredient. HIGS delivered the first commercial success: the trait MON 87411, targeting western corn rootworm, was introduced in 2022 as part of SmartStax PRO maize, followed by additional RNAi-enabled products such as Bayer’s VT4PRO. SIGS reached the market more recently, when Calantha, developed by GreenLight Biosciences, became in 2023 the first foliar-applied RNA-based biopesticide registered by the United States Environmental Protection Agency, targeting the Colorado potato beetle.

Under controlled laboratory conditions, RNAi can achieve efficacy above 90 percent against susceptible target pests, a figure that rivals or exceeds many conventional insecticides. Yet responsiveness varies dramatically across taxa. Coleopteran insects such as beetles tend to be highly sensitive, while lepidopterans, the moths and butterflies that include some of the world’s most destructive caterpillar pests, often show weak or inconsistent responses. Research has traced this variability to several factors: differences in dsRNA uptake mechanisms, the activity of dsRNA-degrading nucleases in the gut and hemolymph, the efficiency of the core silencing machinery itself, and even the pH and enzymatic environment of the digestive tract. Some insects have also evolved outright resistance, as demonstrated in laboratory-selected populations of western corn rootworm and Colorado potato beetle, a reminder that any pest control technology must be deployed within a resistance management framework.

The second major barrier is environmental persistence. Naked dsRNA is fragile. It degrades rapidly in soil, on leaf surfaces, and in water, attacked by ubiquitous ribonucleases, ultraviolet radiation, and microbial activity. Studies of environmental fate have shown that dsRNA applied to soils typically dissipates within days, which is reassuring from an ecological risk perspective but problematic for growers who need a product to remain active long enough to protect the crop. This instability drives up the dose and frequency of application, and with it the cost, since dsRNA remains considerably more expensive to manufacture than conventional agrochemicals.

Formulation science is racing to close that gap. Nanoparticle carriers, including layered double hydroxide clay nanosheets, chitosan particles, lipid nanoparticles, carbon quantum dots, and engineered nanovesicles, can shield dsRNA from degradation and, in some systems, release it gradually over days or weeks. The BioClay platform, for example, has demonstrated prolonged protection against plant viruses and fungal pathogens by anchoring dsRNA on clay nanosheets that slowly desorb the payload. pH-responsive nanoparticles that release dsRNA in the alkaline midgut of target insects, cell-penetrating peptides that ferry RNA across membranes, and chemically modified dsRNAs that resist nuclease attack are all under active development. Meanwhile, microbial delivery systems are emerging as a complementary route: engineered bacteria and fungi can produce dsRNA in situ, and symbiotic microbes have been used to deliver silencing constructs to mosquito larvae and other targets.

Cost, too, is falling. Traditional dsRNA production relied on in vitro transcription, which is expensive at agricultural scale. Bacterial fermentation using strains optimized for dsRNA accumulation, cell-free production systems, and engineered microbes such as Corynebacterium glutamicum equipped with phage expression machinery have all been shown to yield long dsRNAs suitable for pest control at a fraction of the cost. Computational tools for dsRNA design, including multi-target chimeric designers and off-target prediction software, are simultaneously improving the precision and safety of candidate molecules by screening against the genomes of non-target organisms such as pollinators and natural enemies.

The third barrier is regulatory, and it may be the most consequential. Because RNAi products straddle the boundary between biotechnology and crop protection, jurisdictions classify them inconsistently: as biochemical pesticides, as plant-incorporated protectants, or as novel active substances requiring full GMO-style assessment. The United States has moved fastest, registering both transgenic RNAi traits and sprayable dsRNA products, while the European Union and many other regions are still defining their frameworks. This patchwork creates uncertainty for developers, delays market entry, and risks leaving growers in some regions without access to tools approved elsewhere. Review authors and other commentators have called for global regulatory cohesion, arguing that harmonized, science-based risk assessment frameworks are essential if RNAi biopesticides are to contribute meaningfully to sustainable food production and to the United Nations Sustainable Development Goals.

None of these challenges diminishes the underlying promise. RNAi aligns with the central demands of twenty-first-century agriculture: high specificity, low residues, minimal impact on non-target organisms, and compatibility with integrated pest management. The technology extends beyond pest killing, with demonstrated applications in improving shelf life, enhancing abiotic stress tolerance, modifying oil composition, and managing fungal, viral, and nematode pathogens. What the new review makes clear is that the remaining obstacles are engineering and governance problems rather than fundamental biological ones. If nanoparticle formulations, cheap microbial production, and coherent regulation mature together, RNA interference could indeed become a cornerstone of next-generation agriculture, turning a Nobel-winning discovery into the everyday toolkit of the sustainable farm.

Subject of Research: RNA interference as a sustainable crop protection technology and the barriers to its field deployment

Article Title: RNAi: the next wave of green agriculture, challenges, and bridging the translational gap

Article References: Abdullah, Z. K., Kong, L. L., Ariffin, N., & Wong, M. Y. (2026). RNAi: the next wave of green agriculture, challenges, and bridging the translational gap. Plant Cell Reports, 45(9), Article 271. https://doi.org/10.1007/s00299-026-03939-x

Image Credits: AI Generated

DOI: 10.1007/s00299-026-03939-x

Keywords: RNA interference, RNAi biopesticides, double-stranded RNA, spray-induced gene silencing, host-induced gene silencing, crop protection, sustainable agriculture, nanoparticle delivery, dsRNA stability, pest control, regulation, Plant Cell Reports

The study, published in Plant Cell Reports, combined physiology, transcriptomics, metabolomics, and enzyme assays to trace exactly how exogenous trehalose bolsters salt tolerance in tomato seedlings. The findings reveal that hydrogen sulfide acts as a central mediator in trehalose-induced protection, and that the downstream response funnels through two metabolic routes: the phenylpropanoid pathway, a workhorse of plant defense chemistry, and the less celebrated cyanoamino acid metabolism pathway, which processes cyanogenic compounds. The work offers a clearer mechanistic picture of how two stress-protective agents interact, and it hints at practical strategies for shielding crops from salinity.

Trehalose is no stranger to stress biology. This disaccharide, composed of two glucose units, accumulates in an astonishing range of organisms, from resurrection plants that survive near-total desiccation to yeast cells braving heat and dehydration. In plants, trehalose and its phosphorylated precursor trehalose-6-phosphate serve dual roles as osmoprotectants that stabilize proteins and membranes, and as sugar signals that rewire metabolism during stress. Previous studies had shown that spraying tomato seedlings with trehalose improves their performance under salt stress by modulating reactive oxygen species, photosynthesis, and osmolyte synthesis. Hydrogen sulfide, meanwhile, has shed its reputation as merely a toxic, rotten-egg-smelling gas. Over the past two decades, plant biologists have established that H2S functions as a genuine signaling molecule, regulating seed germination, stomatal closure, and a broad spectrum of abiotic stress responses, often through persulfidation, a chemical modification that alters the activity of target proteins.

What remained unknown was how these two protective agents relate to each other when deployed together. The Guangxi team, led by corresponding author Changxia Li with co-first authors Jin Qi and Zhang Zhang, designed a series of experiments to answer that question. They grew tomato seedlings under salt stress and treated them with trehalose alone, with sodium hydrosulfide (NaHS), a donor of hydrogen sulfide, alone, or with both compounds simultaneously. The physiological results were striking: both treatments significantly alleviated salt-induced growth inhibition, but the combined treatment produced the most pronounced protective effect, suggesting the two agents act in complementary or synergistic ways.

To dissect the direction of the relationship, the researchers turned to pharmacology. They applied validamycin A, an inhibitor of trehalose biosynthesis, and hypotaurine, a chemical scavenger that mops up hydrogen sulfide. The logic was simple but powerful: if removing hydrogen sulfide abolishes trehalose’s benefits, then trehalose must depend on the gas to work. The experiments delivered a clear verdict. The protective effect of trehalose was largely dependent on hydrogen sulfide, because scavenging the gas with hypotaurine substantially undermined trehalose-induced salt tolerance. In contrast, the efficacy of the NaHS donor was independent of trehalose, indicating a one-directional dependency: trehalose needs hydrogen sulfide, but hydrogen sulfide does not need trehalose. The authors are careful to note the limits of this interpretation. Their data mainly support a requirement for H2S in trehalose action rather than demonstrating that hydrogen sulfide alone is sufficient to reproduce the full trehalose response, and they call for further functional analyses to clarify the precise hierarchy between the two signals.

With the physiological dependency established, the team moved to the molecular level using RNA sequencing. The transcriptomic analysis showed that trehalose modulates the salt stress response of tomato seedlings at the transcriptional level via hydrogen sulfide, and it pinpointed phenylalanine biosynthesis as a core metabolic target. Phenylalanine is the gateway amino acid for the phenylpropanoid pathway, one of the most important specialized metabolic networks in plants. From phenylalanine, plants build an enormous arsenal of compounds, including lignin, which reinforces cell walls and forms apoplastic barriers against ion intrusion; flavonoids and anthocyanins, which act as antioxidants; and a variety of phenolic compounds that buffer oxidative damage. The second pathway flagged by the analysis was cyanoamino acid metabolism, the route that produces and processes cyanogenic glycosides, nitrogen-containing defense metabolites derived from amino acids.

The metabolomic data reinforced the transcriptomic picture. Compared with seedlings receiving salt plus trehalose, those that also received the hydrogen sulfide scavenger hypotaurine showed significantly reversed accumulation of protective metabolites. In the phenylpropanoid pathway, the compounds p-coumaryl alcohol and coniferyl alcohol, both monolignols that feed into lignin biosynthesis, accumulated in response to trehalose but dropped back when hydrogen sulfide was removed. In the cyanoamino acid pathway, the cyanogenic glycosides amygdalin and prunasin, compounds more famous for their roles in almond and stone fruit bitterness, followed the same pattern. This is a notable finding because it implicates a pathway usually discussed in the context of herbivore defense in abiotic stress tolerance, adding to a growing body of evidence that cyanogenic metabolism contributes to how plants cope with environmental challenges.

The enzymatic and gene expression data tied the whole story together. The salt plus trehalose treatment significantly elevated the activities of key enzymes in the phenylpropanoid biosynthesis pathway, including 4-coumarate-CoA ligase (4CL), caffeoyl-CoA O-methyltransferase (CCoAOMT), and peroxidase (POD), as well as enzymes in the cyanoamino acid metabolism pathway, namely mandelonitrile lyase (MDL) and beta-glucosidase (bglX). Consistent with these biochemical changes, the transcript levels of the corresponding encoding genes, including 4CL1, CCoAOMT, POD9, POD43, MDL3, and bglX1, were significantly upregulated. When hypotaurine was added to scavenge hydrogen sulfide, the trehalose-induced enhancement of both enzyme activities and gene expression was significantly reversed. At the molecular level, this confirms that hydrogen sulfide sits upstream of these metabolic changes, serving as a central mediator through which trehalose exerts its protective influence during salt stress.

Why does this matter beyond the laboratory? Salinity stress imposes a double burden on plants: excess sodium ions are toxic, and the osmotic stress they create makes it harder for roots to take up water. Plants respond with a suite of defenses, including osmolyte accumulation, ion homeostasis, and antioxidant systems that neutralize the reactive oxygen species generated under stress. The phenylpropanoid pathway sits at the heart of several of these defenses, supplying lignin for physical barriers and phenolic compounds for antioxidant protection. If trehalose triggers these defenses only through hydrogen sulfide, then breeding or engineering approaches might target the signaling relay itself, for instance by enhancing H2S production capacity or persulfidation of key regulatory proteins, to amplify a crop’s intrinsic stress response. Alternatively, combined field treatments of trehalose and hydrogen sulfide donors could be optimized to exploit the synergy observed in seedlings, though translating greenhouse pharmacology to open-field agriculture always demands careful validation.

The study also enriches a rapidly expanding literature on hydrogen sulfide as a master regulator of plant stress resilience. Recent work has shown that H2S promotes lateral root formation in peach through persulfidation of the SnRK1α kinase, balances hydrogen sulfide and hydrogen cyanide homeostasis in Arabidopsis under osmotic stress, and modulates phenolic metabolism to alleviate salt stress in tomato. The Guangxi findings slot neatly into this picture while adding a new layer: they position trehalose, a sugar signal, upstream of the gas, and they extend the downstream reach of the gas into cyanoamino acid metabolism, a pathway rarely invoked in salt tolerance research. The authors acknowledge that much remains to be resolved, particularly whether hydrogen sulfide alone can reproduce the complete trehalose response and what the precise hierarchical relationship between the two signals looks like under field conditions. But the core message is already compelling: in salt-stressed tomato seedlings, a protective sugar whispers its instructions through a stinky gas, and the plant listens by building stronger walls and richer chemistry. For a crop that feeds billions and a planet whose farmland grows saltier by the season, that conversation is worth every effort to understand and, ultimately, to harness.

Subject of Research: Hydrogen sulfide-dependent trehalose signaling that enhances salt tolerance in tomato seedlings through phenylpropanoid and cyanoamino acid metabolism

Article Title: H2S-dependent trehalose-induced salt tolerance in tomato involves phenylpropanoid and cyanoamino acid pathways

Article References: Qi, J., Zhang, Z., Li, S., Su, J., Tian, Y., Yu, W., & Li, C. (2026). H2S-dependent trehalose-induced salt tolerance in tomato involves phenylpropanoid and cyanoamino acid pathways. Plant Cell Reports, 45(10), Article 283. https://doi.org/10.1007/s00299-026-03969-5

Image Credits: AI Generated

DOI: 10.1007/s00299-026-03969-5

Keywords: trehalose, hydrogen sulfide, salt stress, tomato, phenylpropanoid pathway, cyanoamino acid metabolism, transcriptomics, plant stress signaling, sodium hydrosulfide, hypotaurine, antioxidant defense, Plant Cell Reports

The team’s strategy rests on a technique called intergeneric protoplast fusion. Fungi already possess a remarkable toolkit for dealing with arsenic: some species can biosorb the metal onto their cell walls, some methylate it into organic forms, some volatilize it into the atmosphere as gaseous compounds, and others oxidize the highly mobile and toxic arsenite into the less mobile arsenate. In nature, however, these talents are scattered across different fungal lineages that may be genetically incompatible with one another, making it impossible to simply mix strains and expect the traits to combine. Protoplast fusion sidesteps that barrier. Researchers strip away the cell walls of two fungal strains, leaving bare protoplasts that can be coaxed to merge, blending their genomes into a single stable hybrid cell that regenerates into a new organism carrying traits from both parents.

In this study, the researchers fused two soil fungal strains with complementary arsenic-detoxifying abilities. Strain FNBR-FA-03 was chosen for its capacity to methylate arsenic, converting inorganic arsenic into organic species, while strain FNBR-FA-06 was selected for its ability to oxidize arsenite, the form of arsenic that plants absorb most readily through the same silicon transport pathways they use for nutrients. Because the two strains belong to different fungal genera, the fusion was intergeneric, a more ambitious undertaking than fusing closely related strains, but one with the potential to produce genuinely novel combinations of detoxification machinery that neither parent could achieve alone.

After fusion, the team screened the resulting hybrid strains for the traits that mattered most: how efficiently they volatilized arsenic out of the system, how well they oxidized arsenite, whether they promoted plant growth, and, critically, whether they could reduce the arsenic burden in spinach grown in contaminated soil. One fusant, designated FU 26(4), emerged as the clear standout. Compared with its parents, this hybrid showed a 9.7-fold increase in arsenic volatilization relative to the methylating parent FNBR-FA-03 and a 3.6-fold increase in arsenite oxidation relative to the oxidizing parent FNBR-FA-06. In other words, the fusion did not merely average the parental abilities; it amplified them, producing a strain that detoxified arsenic through multiple mechanisms simultaneously and at levels neither parent could reach.

The greenhouse test that followed was the study’s centerpiece. Spinach plants were grown in soil artificially contaminated with arsenic at 20 milligrams per kilogram, a level representative of seriously polluted agricultural land. When the best fusant was introduced, the results were striking: arsenic content in spinach leaves dropped by 73.4 percent and arsenic in roots fell by 62.7 percent compared with plants grown without the fungus. For a leafy vegetable whose leaves are the harvested product, a nearly three-quarters reduction in foliar arsenic represents a potentially transformative food-safety intervention, achieved not by altering the crop’s genome but by reshaping the microbial community around its roots.

Just as important as the quantity of arsenic was its chemical form. Arsenic speciation, the identity of the specific molecular species present, determines toxicity. Inorganic arsenite and arsenate are classified as carcinogenic and far more dangerous than their organic counterparts. Using speciation analysis, the researchers detected methylated arsenic species, specifically monomethylarsenate, MMA(V), and dimethylarsenate, DMA(V), in the petioles and leaves of spinach grown with the fusant strains. These organic species are considerably less toxic than inorganic arsenic, meaning the fungi were not just blocking arsenic uptake but actively converting what did enter the plant into a safer chemical form. This dual action, reducing total accumulation while shifting the remaining arsenic toward less hazardous species, attacks the problem from two directions at once.

The fusants also carried plant growth-promoting traits inherited or amplified from the parental strains. The study reports that the hybrid strains exhibited characteristics capable of improving overall plant growth and physiology, which matters because arsenic stress typically stunts plants, damages chlorophyll, and triggers oxidative stress. A remediation microbe that merely detoxifies soil but leaves the crop weakened offers limited agricultural value. A strain that simultaneously lowers arsenic burden and supports vigorous growth is far more attractive to farmers, since the goal is not just safer food but a viable harvest from land that contamination has compromised.

The choice of protoplast fusion over other genetic improvement strategies is scientifically deliberate. Conventional microbial consortia, in which multiple strains are simply mixed, suffer from instability: community composition drifts, strains compete, and the desired combination of traits is never guaranteed. Genome editing tools such as CRISPR offer precision but require detailed knowledge of the genes involved and can face regulatory hurdles when applied to microorganisms destined for open-field use. Protoplast fusion occupies a middle ground. It can combine complex, multigene traits from genetically diverse organisms without the need to identify every underlying gene, and it produces stable fusants rather than transient mixtures. The authors note, however, an important caveat: fusants should be tested for long-term stability, since merged genomes can be unstable over many generations, and any strain intended for field deployment must retain its traits reliably across seasons and storage.

The broader context makes the work timely. Arsenic contamination of soil and irrigation water affects vast agricultural areas, particularly in South and Southeast Asia where arsenic-laden groundwater is used for irrigation, and the metalloid’s presence in the food chain is recognized as a threat to both food security and human health. Previous research has explored many mitigation routes, from silicon amendments that compete with arsenic at plant uptake channels, to mycorrhizal fungi that alter arsenic distribution within plant tissues, to genetically engineered bacteria designed to volatilize the element. The fusant approach adds a distinctive option to this arsenal: a single, self-replicating biological agent that combines methylation, oxidation, and volatilization in one package, and that can be produced through a relatively low-tech laboratory technique accessible to laboratories without advanced genome-engineering infrastructure.

There remain real questions before such strains could leave the greenhouse. The study was conducted under controlled conditions with a single arsenic concentration, and real fields present variable contamination levels, competing microbes, fluctuating moisture, and different crop species. The long-term genetic stability of the fusants, their ecological behavior once released into soil communities, and any regulatory considerations surrounding deliberately hybridized microorganisms all require attention. Yet the core demonstration stands: protoplast fusion can merge detoxification traits from genetically distant fungi into a single strain that outperforms both parents, cutting spinach arsenic levels by more than seventy percent while converting residual arsenic into less toxic forms. For millions of people whose vegetables carry an invisible burden of arsenic, that combination of simplicity and effectiveness is exactly the kind of innovation that could move from the laboratory bench to the contaminated field.

Subject of Research: Using intergeneric fungal protoplast fusion to reduce arsenic accumulation and toxicity in spinach

Article Title: Alleviating arsenic toxicity in Spinacia oleracea by modulating accumulation and speciation using fungal intergeneric fusant strains

Article References: Naseem, M., Gupta, A., Gupta, E., Singh, P. C., Raghuwanshi, R., Verma, P. C., & Srivastava, P. K. (2026). Alleviating arsenic toxicity in Spinacia oleracea by modulating accumulation and speciation using fungal intergeneric fusant strains. Plant Cell Reports, 45(10), Article 295. https://doi.org/10.1007/s00299-026-03984-6

Image Credits: AI Generated

DOI: 10.1007/s00299-026-03984-6

Keywords: arsenic, bioremediation, protoplast fusion, fungi, Spinacia oleracea, arsenic speciation, plant growth promotion, soil contamination, food safety, mycoremediation, fusant strains, Plant Cell Reports