Plants and animals respond to pathogens through pattern recognition receptor and Nod-like receptor proteins1. Pathogens commonly use protein effectors to suppress host immunity for successful infection2. However, the existence of non-protein effector classes remains comparatively understudied. Here we report an RNA-RNA recognition mechanism governing pathogen-host interaction, mediated by a regulatory RNA-encoding DNA sequence that separately generates two complementary regulatory RNAs. Specifically, a long non-coding RNA transcribed from this DNA region in the fungal pathogen Magnaporthe oryzae translocates into host rice cells and sequesters a complementary microRNA (miRNA), derived from a distinct host DNA region, thereby subverting host immunity. In turn, this rice-derived miRNA promotes disease resistance by repressing the expression of PKR1, a gene that encodes a negative regulator of host immunity. Sequestration of the host miRNA by the fungal long non-coding RNA releases PKR1 expression to facilitate fungal infection. We discovered that this regulatory RNA-encoding DNA sequence is probably widely present across diverse life species, mediating interactions between pathogens and their plant hosts. Collectively, our findings provide an approach for effective disease control using miRNAs derived from this important DNA region.

Genomic selection (GS) has provided a comprehensive framework for efficient breeding by linking phenotypes to genome-wide markers. However, research has predominantly focused on improving genotype-to-phenotype prediction models, often overlooking optimal cross design, which determines the potential of progeny selection and plays a critical role in crop breeding. In this study, an efficient GS framework, EMLGP (ensemble machine-learning for genomic prediction), was proposed for optimal cross design in crop breeding. EMLGP first employs machine-learning algorithms to train precise genotype-to-phenotype prediction models in a germplasm population and then integrates with genome simulations to predict optimal crosses in a breeding population. GS model training of 14 soybean traits demonstrated that EMLGP achieved superior performance, with the highest prediction accuracy (correlation coefficient) reaching 0.92. The prediction accuracy showed a maximum improvement of 35.85% over the classical GBLUP method. Further simulation studies confirmed that EMLGP exhibited robust performance under conditions of small-to-moderate sample sizes (300–5000), low-to-moderate trait heritabilities (0.4–0.6), and complex genetic architectures (100 causal loci). Validation using real data of rice, maize, cotton, sorghum, and switchgrass consistently affirmed EMLGP’s superiority, outperforming GBLUP and deep learning methods. Among the 14 soybean traits analyzed, 13 traits exhibited transgressive segregation potential in the progeny. Specifically, seed linolenic acid content in the northern China showed the highest recombination potential, exceeding the maximum parental value by 16.89%. In conclusion, EMLGP optimizes parental selection and phenotypic prediction, offering a robust framework for efficient, intelligence-driven crop breeding.

Papain-like cysteine proteases (PLCPs) are key enzymes involved in protein hydrolysis and play critical roles in plant growth, development, and responses to stresses. Although PLCPs have been systematically identified in various plant species, their functions in tomato remain largely unexplored, particularly their roles in salt stress adaptation. In this study, we identified 32 PLCP genes in the tomato genome and classified them into nine subfamilies. We found that the promoter regions of SlPLCP genes are enriched with stress-responsive elements. Combining transcriptome data and qRT-PCR analysis showed that SlRD19B was the most significantly upregulated gene under salt stress. Further functional studies demonstrated that silencing SlRD19B enhanced tomato sensitivity to salt stress, as evidenced by severe leaf wilting, increased membrane damage, reduced osmotic adjustment capacity, inhibited root growth, and an elevated Na⁺/K⁺ ratio. Additionally, SlRD19B-silenced plants exhibited excessive reactive oxygen species (ROS) accumulation and disrupted antioxidant enzyme activities under salt stress, characterized by increased superoxide dismutase (SOD) and catalase (CAT) activities but decreased peroxidase (POD) activity. This study systematically reveals the crucial role of the SlPLCP gene family in tomato salt stress response and provides new insights into the functional mechanisms of PLCP genes in plants.

Epigenetic engineering is rapidly emerging as a transformative frontier for unlocking the untapped yield potential of cottonseed oil. This review highlights the role of epigenetic mechanisms, including DNA methylation, histone modifications, and small RNAs, in regulating pathways for oil accumulation in cotton. We discuss epigenomic findings that reveal tissue and developmental stage-specific patterns affecting oil biosynthesis, including distinct regulatory signatures in the embryo versus mitochondrial/nuclear compartments. The application of advanced tools, including CRISPR-based systems and RNA-directed DNA methylation, for precise epigenetic engineering is examined, alongside challenges such as off-target effects and regulatory considerations. Future directions should extend beyond promoter editing to incorporate the regulation of distal enhancer elements. Critical steps include generating high-resolution chromatin interaction maps from developing embryos/endosperms to identify candidate enhancers for key oil genes, which can then be manipulated using CRISPR-dCas9-based activators. Integrating this enhancer biology with non-transgenic approaches, such as pollen priming, bacteriophages and nanoparticle delivery, will be essential for practical applications. We propose a framework that leverages these strategies to address oil-protein trade-offs and develop a holistic epigenetic breeding approach, underscoring the transformative potential of epigenetics for sustainable cottonseed oil yield improvement.

N6-methyladenosine (m6A) is the most prevalent methylation modification present in mRNAs, which has been confirmed to participate in many developmental and biological processes. However, the biological function and specific regulatory mechanism of m6A modification in relation to salt tolerance of potato remain obscure. Here, we generated a transcriptome-wide m6A map using salt-resistant and salt-sensitive potato varieties under salt stress conditions to uncover patterns of m6A methylation in the potato response to salt stress. MeRIP-seq revealed that m6A is significantly enriched in the CDS region in potato, by recognising the conserved motifs including RRACH and URRUAY. Numerous differential m6A-deposited transcripts have been identified, which were significantly enriched in ABA-signalling and flavonoids biosynthesis pathway in two potato varieties after salt stress. Notably, a positive correlation was observed between the m6A enrichment and mRNA abundance based on combined analysis of MeRIP-seq and mRNA-seq. StALKBH10B was identified as an m6A demethylase for decreasing m6A modification levels, inhibiting mRNA stability and translation efficiency of ABA signal-related genes (StABF3, StAAO3, and StZEP7) and flavonoids biosynthesis genes (StPAL3, StCHS, and StFLS), and overexpression of StALKBH10B suppressed salt resistance in potato. Collectively, we uncover a novel mechanism of post-transcriptional modification involved in affecting salt stress response in potato, via StALKBH10B-mediated m6A demethylation on targeted transcripts in the ABA signalling and flavonoids biosynthesis pathway, thereby providing candidate genes for the breeding of stress-tolerant potato cultivars.

Phosphoglycerate kinase (PGK) is a vital glycolytic enzyme that provides energy and carbon skeletons to support fatty acid synthesis. However, the PGK gene family has not been characterized in soybean (Glycine max), and its role in soybean oil accumulation remains unclear. Here, we identified six GmPGK genes in soybean, all of which encode proteins containing conserved PGK domains. Phylogenetic analysis clustered soybean PGK proteins into three groups. Analysis of GmPGK promoters revealed relatively abundant cis-elements related to plant growth, development, and phytohormone response. Expression profiling showed that GmPGK5 transcript abundance increases progressively with oil accumulation during seed development, and is significantly higher in the high-oil variety NN1138-2. Overexpression of GmPGK5 significantly increased total fatty acid content in soybean hairy roots. A single nucleotide polymorphism (SNP) located at Chr15:49447855 within the GmPGK5 promoter was significantly associated with both seed oil content and seed weight in natural soybean accessions. Based on this SNP, a derived cleaved amplified polymorphic sequence (dCAPS) marker was developed to facilitate soybean molecular breeding. Our findings suggest that GmPGK5 may positively regulate fatty acid accumulation in soybean. The identified natural variation and dCAPS marker provide potential valuable tools for marker-assisted selection to improve soybean oil content and seed weight.

Selenium-enriched vegetables have high nutritional value and good flavor, which are beneficial to human health. To improve the selenium uptake of watercress, a pot experiment was conducted to study the effects of selenium combined with 400-fold diluted extracts of Artemisia argyi and tartary buckwheat (Fagopyrum tataricum) straw on its growth and selenium accumulation. Both extracts promoted root and shoot biomass, increased leaf chlorophyll and carotenoid contents, and enhanced POD activity. Compared with single selenium treatment, A. argyi straw extract raised root and above-ground selenium accumulation by 46.38% and 16.69%, while tartary buckwheat extract increased it by 39.10% and 5.41%. Their combined treatment increased selenium accumulation by 47.28% and 19.64%. The correlation analysis showed that the selenium content in the roots and above-ground parts of watercress had a positive correlation with the biomass of watercress, chlorophyll content, carotenoid content, and POD activity. In conclusion, the two extracts can promote watercress growth and selenium enrichment, and their combined application achieves a better effect.

Improving disease resistance in plants often incurs growth and yield penalty. Therefore, identifying and utilizing genetic resources that enhance resistance without compromising yield is an urgent need in crop breeding. In this study, we identified miR439 as a key regulator of both fungal disease resistance and yield-related traits in rice. Blocking or knockout of miR439 enhances grain yield and resistance to blast and sheath blight, whereas its overexpression compromises both traits. miR439 targets and suppresses Wall-associated receptor kinase-like protein 14 (WAKL14) and Subtilisin-like protease 20 (Sub20). Overexpression of these 2 targets simultaneously enhance disease resistance and yield. WAKL14 and Sub20 function as major downstream mediators contributing to miR439-regulated immunity, basal defense responses, and panicle number. Time-course expression analysis revealed that the accumulation of miR439 and the transcript levels of WAKL14 and Sub20 in leaves and tiller buds are dynamically and inversely correlated throughout the growth period, orchestrating normal development and resistance in rice. Our findings establish a model in which miR439 coordinately regulates rice yield and immunity via 2 targets genes and demonstrate that MIR439a represents a promising genetic target for breeding rice varieties with improved disease resistance and yield.

Ascorbic acid (AsA), an essential nutrient for human health predominantly obtained from fresh vegetables and fruits, demonstrates considerable genetic complexity in its accumulation mechanisms. This study investigates the genetic regulation of AsA biosynthesis in non-heading Chinese cabbage (NHCC), a crucial leafy vegetable in China. Through comprehensive quantitative trait locus (QTL) analysis across multiple environments, we identified 19 AsA-associated QTLs distributed over 10 linkage groups, explaining 3.15% to 18.04% of phenotypic variance. An environmentally stable QTL (qAsA.A01.1) was prioritized for further investigation. Integrated QTL mapping and comparative transcriptome analysis revealed 297 candidate genes, among which the GATA transcription factor CYTOKININ-RESPONSIVE GATA FACTOR 1 (BcCGA1) emerged as a candidate regulator through allelic variation analysis, gene description analysis, and association analysis. Functional validation via gene silencing and overexpression confirmed the suppressive role of BcCGA1 in AsA biosynthesis. Mechanistic studies established that BcCGA1 plays a direct transcriptional repressor of AsA biosynthesis by binding to the promoters of GDP-L-GALACTOSE PHOSPHORYLASE c (BcGGP.c), GDP-MANNOSE PYROPHOSPHORYLASE b (BcGMP.b), and KONJAC c (BcKJC.c). Furthermore, we identified an interaction between BcCGA1 and the chloroplast-localized protein PS II OXYGEN-EVOLVING COMPLEX 1 (BcPSBO1), which exhibits dual regulatory effects. While BcPSBO1 attenuated BcCGA1's DNA-binding capacity in vitro, it paradoxically enhanced transcriptional repression of target genes in vivo. Our findings elucidate a sophisticated regulatory framework involving transcriptional and protein interaction mechanisms that substantially advances our understanding of AsA accumulation genetics and provides a theoretical basis for nutrient-enhanced NHCC cultivars.

Cotton (Gossypium hirsutum) is globally cultivated for its high-quality fiber; yet, its seed, rich in oil and protein, offers untapped potential for various applications, including food, feed, and industry. With cottonseed oil gaining renewed attention as a valuable co-product, efforts to enhance oil content must contend with long-standing breeding priorities focused on lint yield and fiber quality. A central challenge lies in the complex and often antagonistic genetic relationships between oil accumulation and key agronomic traits. Notably, negative correlations between seed oil content and fiber yield, as well as the pleiotropic nature of several regulatory genes and Quantitative Trait Loci (QTLs), present significant barriers to dual-trait improvement. This review synthesizes current knowledge on the genetic and molecular interplay between cottonseed oil content and other agronomic traits. We examine the architecture of oil-related QTLs and pleiotropic loci, co-expression patterns of shared transcriptional regulators, and metabolic trade-offs influencing carbon allocation between seed and fiber. Recent advances in genomics, transcriptomics, and systems biology are explored as tools to disentangle these trait interactions. We highlight strategies such as multi-trait genomic selection, CRISPR-based uncoupling of antagonistic loci, and the use of wild and exotic germplasm to overcome linkage drag. By providing an integrative overview of the constraints and opportunities at the intersection of oil and agronomic trait improvement, this review lays the groundwork for the development of dual-purpose cotton ideotypes. We propose a conceptual framework for breeding programs to simultaneously enhance fiber yield and oil productivity in a sustainable and climate-resilient manner.

Eukaryotic genomes are pervasively transcribed, producing a vast repertoire of RNA molecules. In plants, diverse RNA species play pivotal roles in regulating growth, development, and responses to environmental stimuli. The activities of RNAs are determined not only by their nucleotide sequences but are also shaped by multiple regulatory mechanisms, including processing, turnover, chemical modifications, and higher-order structure formation-each contributing critically to phenotypic outcomes. Over the past decade, technological advances, particularly in high-throughput sequencing and genome editing, have substantially deepened our understanding of RNA regulation; concurrently, research in this field has expanded from foundational studies in Arabidopsis to encompass a broad range of crop species. Building upon this expanded knowledge, this review provides a comprehensive overview of the regulation and functions of RNAs in plants. Specifically, we discuss the roles and molecular mechanisms of diverse RNA types, the roles of RNA structures and modifications in regulatory processes, and the translational application of RNA-based strategies for improving agronomic traits. Finally, we outline future research directions and offer perspectives on harnessing RNA regulation to advance crop improvement.

Root architecture is intricately linked to the acquisition of water and nutrients in maize seedlings. Despite its functional importance, few genes controlling root development have been targeted for drought resistance in breeding. Here, we performed a genome-wide association analysis to detect genetic variants linked to primary root length (PRL) across 307 inbred lines grown under hydroponic conditions. We identified 28 SNPs significantly associated with 25 candidate genes, accounting for 6.09%–11.07% of the phenotypic variation. Among them, ZmHSP20-5, encoding a cytoplasm-localized small heat shock protein (sHSP) with preferential expression particularly in lateral root primordia emerged as a promising candidate. Functional validation using knockout mutants revealed that disruption of ZmHSP20-5 impaired root architecture, causing reduced primary root elongation, shorter lateral roots, decreased lateral root density, and compromised drought tolerance. Further analysis revealed that InDel-1224 in the ZmHSP20-5 promoter likely contributed to differential gene expression and variation in root development among inbred lines. Evolutionary evidence suggested that the ZmHSP20-5 locus may have undergone selection during domestication, with the favorable ZmHSP20-5In-1224 allele increasing in frequency over time. Overall, these findings establish that natural variation in ZmHSP20-5, particularly the ZmHSP20-5In-1224 allele, contributes to root growth and drought resistance, providing a valuable genetic resource for the breeding of drought-resistant maize varieties with optimized root systems.

Leaf color directly affects the appearance quality and nutritional quality of leafy vegetables, thereby determining their economic value. Here, we identified a golden leaf mutant, Mut298, from an ethyl methanesulfonate (EMS)-induced mutant library of Chinese cabbage. Through the approach of forward genetics, it has been demonstrated that the phenotype of Mut298 is due to a single nucleotide substitution from C to T that changes glycine to arginine in the conserved domain of BrPRPL1, which encodes the large subunit ribosomal protein L1 of the chloroplast. Because the PRPL1 mutation causes embryonic lethality in Arabidopsis, the function of PRPL1 in leaf development remains elusive. In this study, the mutation of BrPRPL1 causes a substantial reduction in the expression of key chloroplast-encoded proteins (RbcL, PsaA, and PsaB) and disrupts chloroplast development. Moreover, the chlorophyll content and photosynthetic parameters are significantly lower in Mut298 plants than in wild-type plants, resulting in golden yellow leaves in Chinese cabbage. This study reveals the impact of PRPL1 mutation on ribosome translation within chloroplasts and provides a theoretical a foundation for future research into the regulatory roles of PRPL1 in plant growth and development.

The membrane-bound proteins belonging to DUF677 (domain of unknown function 677) are found mainly in green plants. The function of the DUF677 gene (AT14A) has been investigated in Arabidopsis and tomato in relation to drought stress tolerance. Overexpression of AT14A improves drought tolerance in tomato, promotes growth in Arabidopsis during drought stress, and confers tolerance against oxidative damage caused by drought stress in suspension-cultured A. thaliana. However, the role of the DUF677 gene family has not yet been reported in cotton. We identified 148 DUF677 genes from 15 selected plant species using domain-based and homology-supported bioinformatics approaches and classified them into two major groups (I and II) based on phylogenetic analysis. Group I is further divided into two sub-groups (IA and IB). Structural analysis revealed the presence of a few introns in the DUF677 genes. The evolution and expansion of the DUF677 protein family were primarily driven by segmental duplication. Seventy-one miRNAs were predicted to target 29 GhDUF677 genes, including Ghi-MIR397, Ghi-MIR8722, and Ghi-MIRN1429. Several cis-elements, such as MBS, ABRE, TCA elements, and W-Box, which were known to play a role in abiotic stress response, were observed in the promoter region of GhDUF677 genes. RNA-seq data were analyzed for tissue-specific expression, and qRT‒PCR was performed on six selected genes. The outcomes revealed high levels of GhDUF677 gene expression across different tissues under abiotic stress conditions. This study provides a genome-wide bioinformatics and expression-based characterization of the DUF677 gene family in cotton, identifying candidate genes potentially associated with drought and salt stress responses. While the findings are based on evolutionary, regulatory, and transcriptomic evidence, they do not constitute direct functional validation. Instead, this study establishes a theoretical and genomic foundation for future functional studies aimed at elucidating the precise roles of DUF677 genes in cotton stress tolerance.

Panax notoginseng (P. notoginseng) is a valuable traditional Chinese medical herb with multiple pharmacological effects, and Acremonium sp. D212 is a symbiotic fungus. The symbiotic relationship between fungi and plants is widely present in nature, but the molecular mechanism of the symbiotic relationship between P. notoginseng and its symbiotic microorganisms is unknown. This study found that Acremonium sp. D212 altered the gene expression of P. notoginseng under different lights, and this change was associated with the miRNAs transferred from Acremonium sp. D212 to P. notoginseng. Transferred miRNAs can not only regulate P. notoginseng target genes, but also trigger the production of phased siRNAs to regulate more target genes, thereby forming a cascaded regulatory network. P. notoginseng target genes are associated with trans-membrane transporting and plant hormone metabolism, suggesting that these small RNAs may have potential influence on the growth and development of P. notoginseng. This study discovers an underlying molecular mechanism of the interactions between P. notoginseng and its symbiotic fungus Acremonium sp. D212, and provide a new perspective for further research on the gene interaction between plants and symbiotic fungi.

Potato growth and development are inhibited by drought stress, which in extreme situations jeopardises tuber yield and quality. Despite progress in understanding drought stress responses, the full regulatory network remains unclear. In this study, we found that the cell wall-localised expansin gene StEXLB1 was significantly induced by polyethylene glycol 6000 (PEG6000) and abscisic acid (ABA). StEXLB1-Overexpression (OE) reduced stomatal density and aperture, accompanied by enhancing drought tolerance. Conversely RNA interference (RNAi) lines exhibited the opposite effects. Further investigation revealed that the transcription factor StMYB55 directly promotes StEXLB1 transcription. Notably, StMYB55-OE resulted in stomatal phenotypes similar to those in StEXLB1-OE lines. Conversely, StMYB55-RNAi increased stomatal density and aperture, as well as reduced drought tolerance. StMYB55 interacts with the ABA receptor StPYL8 and the molecular chaperone StDnaJ3, respectively. This complex then acts to differentially suppress the transcript levels of key stomatal development factors (StSPCH and StFAMA). Genetic evidence showed that StPYL8-RNAi resulted in increased stomatal density and aperture, which was associated with decreased drought tolerance in potato. Collectively, this study suggests that the StMYB55/StPYL8-StEXLB1 module may participate in drought stress response, potentially via stomatal regulation, and provides candidate genes for breeding drought-tolerant potato varieties.

BackgroundThe YUCCA (YUC) genes play a pivotal regulatory role in plant growth and development; however, those in cotton have not been systematically characterized.ResultsIn this study, 104 YUC members were identified across four cotton species using bioinformatics analysis. Phylogenetic analysis revealed that the YUC genes clustered into four distinct clades, and both gene structures and motif compositions were highly conserved within each subgroup. Additionally, cis-acting elements associated with growth and development, hormone response, and abiotic stress were found in the promoter regions of GhYUCs. GhYUC19 is a homologous gene of AtYUC1/4 in Arabidopsis thaliana. The quantitative reverse transcription polymerase chain reaction (qRT-PCR) analysis demonstrated that GhYUC19 was highly expressed in the main shoot apex, young leaves, and flower buds of cotton plants. Overexpression of GhYUC19 in Arabidopsis resulted in increased plant height, downward-curling leaves, reduced silique size, and lower fertility. Conversely, downregulation of GhYUC19 via virus-induced gene silencing (VIGS) in cotton resulted in abnormal floral organ development, including missing petals and fewer stamens.ConclusionsThis study conducted a systematic analysis of the YUC gene family members and validated the regulatory role of GhYUC19 in plant height, branching, and flower and fruit development. These findings provide a foundation for further investigation into the biological functions of GhYUCs in cotton.

Semigamy is a rare fertilization anomaly in plants that enables haploid induction (HI), a valuable strategy for accelerating crop breeding; however, its molecular basis remains largely unexplored. We investigated transcriptional and epigenetic mechanisms underlying semigamy mutant VSg in island cotton (Gossypium barbadense), which exhibits a high haploid induction rate during double fertilization. We combined cytological observations with time-resolved transcriptome profiling and whole-genome bisulfite sequencing across key fertilization stages. This integrative approach captured dynamic molecular changes associated with gamete nuclear fusion and early zygotic development. Compared with the wild-type, which displayed rapid polar nuclei fusion and normal free nuclear endosperm formation, the semigamy mutant showed delayed polar nuclei fusion and impaired sperm-egg nuclear fusion. Transcriptomic analyses identified differentially expressed genes enriched in membrane fusion processes, while epigenomic profiling revealed dynamic DNA methylation changes in genes encoding transmembrane proteins, cyclins, and kinesins, suggesting disrupted regulation of membrane dynamics and cell cycle progression. These results indicate that coordinated transcriptional and epigenetic regulation of nuclear fusion and cell cycle pathways underlie semigamy-induced developmental arrest and haploid induction. The study provides mechanistic insights into fertilization biology and highlights semigamy as a promising system for improving haploid breeding strategies in crops.

Tree peony (Paeonia suffruticosa), a high-value ornamental, is prone to dwarfism and bud abortion in container cultivation owing to limited sucrose supply. Previous studies have shown that the sucrose transporter PsSUT1 facilitates sucrose transport and thereby promotes vegetative growth and flowering. We functionally characterized the PsSUT1 promoter, identified upstream ABA-responsive transcription factors, and validated their functions. Using chromosome walking, we cloned the 1,606-bp PsSUT1 promoter containing ABRE motifs. In tree peony, PsSUT1 expression was highest in petioles and lowest in roots; ABA increased transcripts across tissues, with 5-fold induction in petioles. The pSUT1::GUS reporter confirmed promoter activity in transient Nicotiana benthamiana assays and in Arabidopsis thaliana promoter::GUS lines, with expression in seedlings, roots, leaves, and siliques and clear ABA-inducibility. To identify upstream regulators, we cloned four ABF transcription factors involved in ABA signaling (PsABF1/2/3/7), which were highly expressed in petioles and strongly positively correlated with PsSUT1 expression. Yeast one-hybrid assays verified binding to the PsSUT1 promoter, and transient tobacco dual-luciferase/LUC imaging demonstrated positive transcriptional regulation of PsSUT1. PsABF7-OE lines were more vigorous than WT, with significantly greater height and rosette diameter. They had lower sucrose levels in rosette leaves but higher levels in stems and siliques, and showed enhanced growth under high-sucrose conditions, suggesting more efficient exogenous sucrose utilization. Together, our data elucidate the promoter architecture and upstream regulation of PsSUT1 and provide a foundation for breeding and cultivation strategies to alleviate sucrose limitation in container-grown tree peony.

Lysosomes are central to lipid metabolism, yet how gut microbiota-derived metabolites regulate lysosomal function to influence host lipid homeostasis remains unknown. Here, we identify a mechanism in which bacterial tryptophan metabolism activates lysosomal activity to promote lipid breakdown in Caenorhabditis elegans, and show that the bacterial tryptophan metabolite indole recapitulates these effects in mammalian hepatocytes. By developing a lysosomal-responsive lipid reporter in C. elegans to screen for bacterial metabolic states that modulate host lipid storage, we discover that Escherichia coli tryptophan catabolism via tryptophanase TnaA induces lysosomal lipid chaperone LBP-8, driving lipid mobilization. Moreover, tryptophan metabolite indole enhanced lysosomal acidification and degradation capacity, while genetic disruption of lysosomal regulators reversed these effects. Strikingly, bacterial tryptophan metabolism further promoted mitochondrial β-oxidation through lysosomal lipase activity. This pathway was conserved in mammalian hepatocytes, where E. coli-derived tryptophan metabolite indole enhances lysosomal function and reduce lipid accumulation. Our work uncovers microbiota-regulated lysosomal activation as a critical axis in lipid homeostasis, highlighting its potential as a therapeutic target for metabolic disorders linked to lysosomal dysfunction.