Li J, Zeng T, Xu H
… +3 more, Kang X, Liang M, Wu R
J Integr Plant Biol
· 2026 May · PMID 41645413
·
Full text
Alkaloids, renowned for their pivotal physiological roles in plant defense and chemical medium, constitute a structurally diverse class of bioactive natural products with substantial therapeutic potential in modern drug...Alkaloids, renowned for their pivotal physiological roles in plant defense and chemical medium, constitute a structurally diverse class of bioactive natural products with substantial therapeutic potential in modern drug development. There is currently no dedicated alkaloid database, highlighting an urgent need for such a resource. Here, we present AlkaPlorer (https://alkaplorer.qmclab.com/), the first systematic alkaloid database, which has compiled over 130,000 alkaloids from 12,250 species, with reported activity against 6,583 biological targets. AlkaPlorer not only integrates comprehensive experimentally validated data and computationally predicted properties for each alkaloid, but also establishes standardized notation and associations among various data elements, forming a correlative-type dataset. Extensive chemoinformatic analyses on structural scaffolds, biosynthetic precursors, physicochemical properties, and phylogenetic distributions across plant taxa are performed based on AlkaPlorer, providing new insights into the chemical diversity, structural evolution, and biosynthetic regularity of plant alkaloids. AlkaPlorer enables easy access and efficient retrieval and provides a foundational resource for AI-driven applications in plant metabolism and alkaloid research.
The unfolded protein response (UPR) serves as a crucial regulatory mechanism that enables eukaryotic cells to mitigate endoplasmic reticulum (ER) stress and plays a significant role in plant antiviral immunity. In this s...The unfolded protein response (UPR) serves as a crucial regulatory mechanism that enables eukaryotic cells to mitigate endoplasmic reticulum (ER) stress and plays a significant role in plant antiviral immunity. In this study, we show that V2 protein encoded by the tomato yellow leaf curl virus (TYLCV) induces severe necrotic symptoms in Nicotiana benthamiana and tomato plants. V2 activates the host UPR, and this activation promotes TYLCV infection. Furthermore, we demonstrate that V2 directly interacts with NbFKBP13, a rate-limiting enzyme in protein folding, and inhibits its enzymatic activity. Genetic analysis revealed that NbFKBP13 significantly attenuates V2-induced UPR activation and cell death while enhancing N. benthamiana resistance against TYLCV infection. Similarly, V2 interacts with SlFKBP13, the tomato homolog of NbFKBP13, and SlFKBP13 improves tomato resistance to TYLCV infection. Moreover, both TYLCV infection and V2 expression induce autophagy, a process in which NbFKBP13 plays a crucial role. Notably, the activation of autophagy inhibits TYLCV infection. Our results unveil a molecular mechanism through which the geminivirus V2 protein manipulates the host UPR to facilitate viral infection. These findings significantly advance our understanding of the evolutionary arms race between plants and viruses.
This commentary on Wang et al. (2025) and Phan et al. (2025) highlights previously undiscovered Xanthomonas pathways for nutrition acquisition, explains how Xanthomonas bacteria hijack host molecular machinery through th...This commentary on Wang et al. (2025) and Phan et al. (2025) highlights previously undiscovered Xanthomonas pathways for nutrition acquisition, explains how Xanthomonas bacteria hijack host molecular machinery through their effector proteins, and discusses how these studies can be used to develop new disease resistance mechanisms.
Tension wood (TW), a type of reaction wood that develops in angiosperm trees in response to gravistimulation, serves as an ideal model for investigating the regulatory mechanisms underlying xylem cell differentiation and...Tension wood (TW), a type of reaction wood that develops in angiosperm trees in response to gravistimulation, serves as an ideal model for investigating the regulatory mechanisms underlying xylem cell differentiation and cell wall deposition. The initial biological signals that induce the formation of reaction wood in response to gravitational stimuli remain poorly understood. In this study, we utilized pharmacological and genetic approaches to modulate Ca levels in hybrid white poplar (Populus alba × P. glandulosa) and examine the role of calcium signaling during the early stages of gravitropic responses. Our findings revealed differential cytosolic Ca signal distribution in gravistimulated stems during the early phase of gravity induction, characterized by lower Ca levels on the upper side (where TW forms) and higher Ca levels on the lower side (where opposite wood forms). Consistent with this hypothesis, plants treated with LaCl and those with genetically disrupted calcium channels (PagGLR3.3 knockout using the CRISPR/Cas9 system) showed reduced Ca signals and developed characteristic TW features. These results suggest that decreased Ca levels induce the formation of TW. Furthermore, PagGLR3.3 knockout plants with TW-like stems displayed diminished sensitivity to gravistimulation. Transcriptomic analysis revealed that the knockout of PagGLR3.3 resulted in the upregulation of genes associated with TW formation and reactive oxygen species (ROS) production. Notably, superoxide anion (O ) levels were significantly elevated in the cambium zone of stems subjected to gravistimulation, LaCl treatment, or PagGLR3.3 knockout, indicating that reduced Ca levels promote TW formation through increased O accumulation. This study offers novel insights into the critical role of Ca in gravitropism and TW induction in poplar.
This commentary highlights emerging strategies for efficient plant regeneration through control of morphogenic regulators that govern cell identity. Synthetic expression systems, enabled by high-throughput discovery plat...This commentary highlights emerging strategies for efficient plant regeneration through control of morphogenic regulators that govern cell identity. Synthetic expression systems, enabled by high-throughput discovery platforms, can direct plant cells to form new tissues or organs, opening new possibilities for efficient genetic engineering of agronomically important crops.
Global warming imposes a major threat to plant survival by disrupting growth homeostasis, yet plants adapt to elevated temperatures through thermomorphogenesis. Although auxin signaling is known to orchestrate these adap...Global warming imposes a major threat to plant survival by disrupting growth homeostasis, yet plants adapt to elevated temperatures through thermomorphogenesis. Although auxin signaling is known to orchestrate these adaptive responses, how temperature perception is integrated with auxin remains poorly understood. Here, we identify the CrRLK1L-family receptor kinase FERONIA (FER) as a central regulator of thermomorphogenesis in Arabidopsis thaliana. Under warm-temperature conditions, FER undergoes proteolytic cleavage, releasing its cytosolic domain FER, which translocates into the nucleus via an importin-dependent pathway. Once in the nucleus, FER phosphorylates the non-canonical AUX/IAA protein IAA29, thereby relieving its inhibition of ARF19 and promoting hypocotyl elongation. Transcriptomic analyses further reveal that FER and ARF19 co-regulate thermo-inducible genes involved in auxin signaling and cell wall remodeling. Together, these findings uncover the mechanism by which FER integrates thermal cues through proteolytic activation and phosphorylation-dependent modulation of auxin signaling, establishing a new paradigm for receptor kinase-mediated environmental adaptation in plants.
While plant salicylic acid (SA) signaling via NPR1-PR1 is well-characterized in pathogen resistance, its role against piercing-sucking insects remains unclear in rice. Here, we demonstrate that leafhopper infestation in...While plant salicylic acid (SA) signaling via NPR1-PR1 is well-characterized in pathogen resistance, its role against piercing-sucking insects remains unclear in rice. Here, we demonstrate that leafhopper infestation in rice induces SA-mediated resistance, which defends against insect infestation via pathogenesis-related protein OsPR1a. However, prolonged infestation triggers autophagy-dependent degradation of OsPR1a through its interaction with OsATG8b, fine-tuning immunity to prevent excessive defense activation. Strikingly, this autophagy-mediated OsPR1a degradation represents a conserved regulatory mechanism in rice during brown planthopper infestation. A rice rhabdovirus in leafhopper vectors secretes glycoprotein on virion envelopes to rice phloem, where it binds OsATG6b and OsPR1a to enhance autophagic OsPR1a turnover, ultimately facilitating insect vector feeding and viral transmission by leafhopper vectors. Our work reveals an adaptive mechanism by which a vector-borne virus hijacks plant autophagy to evade SA immunity, highlighting OsPR1a as a critical convergence point in plant-insect-virus interactions.
Photorespiration is essential for maintaining plant photosynthesis and growth under aerobic conditions. While environmental factors like light-dark transitions and high light modulate this pathway, the underlying molecul...Photorespiration is essential for maintaining plant photosynthesis and growth under aerobic conditions. While environmental factors like light-dark transitions and high light modulate this pathway, the underlying molecular regulatory mechanisms remain unclear. Here, we report that the activity of phosphoglycolate phosphatase (PGLP), the first enzyme in the photorespiratory pathway, is redox-regulated in response to environmental light conditions. Specifically, Arabidopsis PGLP enzymatic activity enhanced under reducing conditions and light, but suppressed under oxidative conditions and darkness. Light-dark transitions dynamically alter the oligomeric state of PGLP1, as darkness promotes oligomer assembly, while light triggers disassembly, a process critically dependent on cysteine 320 (Cys320) of PGLP1. Thioredoxin (Trx) f directly interacts with PGLP1, modulating both; its light-dependent oligomeric state and enzymatic activity. Complementation of the Arabidopsis pglp1-2 mutant with wild-type PGLP1 or the Cys320 mutant (C320S) revealed that C320S-complemented lines show greater tolerance to high-light and fluctuating light conditions. Collectively, our study identifies a redox-dependent post-translational modification mechanism that fine-tunes PGLP activity, thereby optimizing photorespiratory metabolism to enhance plant photosynthetic efficiency and environmental adaptability.
Floral induction in plants represents a critical developmental transition from vegetative growth to the reproductive phase, which is vital for reproductive success. Identifying new genes that control flowering time and u...Floral induction in plants represents a critical developmental transition from vegetative growth to the reproductive phase, which is vital for reproductive success. Identifying new genes that control flowering time and understanding their regulatory mechanisms is crucial for improving our knowledge of plant adaptability to the environment. Here, we identify VQ motif-containing proteins VQ18 and VQ26 as novel promoters of flowering that function redundantly to regulate this process in Arabidopsis. The VQ18 and VQ26 proteins promote flowering in Arabidopsis through their interaction with the CONSTANS (CO) protein. This interaction enhances the stability of the CO protein and augments its transcriptional activation of the FLOWERING LOCUS T (FT) gene. Furthermore, VQ18 and VQ26 exhibit binding affinity for the TARGET OF EAT1 (TOE1) and TOE2 proteins, thereby diminishing the binding affinity and inhibitory effects of TOEs on FT, which alleviates the repression of flowering by TOEs. Additionally, VQ18 and VQ26 are implicated in the regulation of flowering timing by competing with TOEs for interaction with CO. Our findings broaden the functions of VQ proteins and reveal new regulatory interactions in the flowering network, providing insights into how plants balance positive and negative signals to regulate flowering time.
This commentary highlights how antagonistic actions between MORC proteins and the DNA demethylase ALKBH1 shape three-dimensional chromatin organization in rice. By balancing gene silencing and activation at stress-respon...This commentary highlights how antagonistic actions between MORC proteins and the DNA demethylase ALKBH1 shape three-dimensional chromatin organization in rice. By balancing gene silencing and activation at stress-responsive loci, this mechanism provides insights into chromatin regulation and offers potential applications for developing stress-resilient crop varieties through epigenomic breeding.
Soybean is a major crop that produces high-quality seed oil for global consumption. However, the regulatory mechanisms underlying seed oil content remain poorly understood. In this study, GmGT-2F, a trihelix transcriptio...Soybean is a major crop that produces high-quality seed oil for global consumption. However, the regulatory mechanisms underlying seed oil content remain poorly understood. In this study, GmGT-2F, a trihelix transcription factor, was identified as a positive regulator of seed oil content. It was observed that GmGT-2F expression gradually increased during seed development. Furthermore, GmGT-2F overexpression elevated seed oil content and increased the proportion of oleic and linoleic acids in fatty acid composition. However, knocking out GmGT-2F improved seed protein content and seed size. We demonstrated that GmGT-2F binds to the GmAGAL promoter and activates its transcription. Moreover, knockout of GmAGAL and GmGT-2F/GmAGAL reduced α-galactosidase activity and decreased seed oil content. The metabolomic and seed sucrose content analyses of the gmagal and wild-type (WT) plants showed that GmGT-2F affects the transcription of GmAGAL to regulate the activity of α-galactosidase and may control the oil content by influencing the generation and distribution of sucrose in the seed. In addition, GmCYP2 interacts with GmGT-2F, reducing its promoter-binding activity and inhibiting GmAGAL transcription. Haplotype diversity analyses of GmGT-2F, GmCYP2, and GmAGAL revealed combinations associated with increased oil or protein content. This study elucidates the regulatory mechanism by which GmGT-2F regulates seed oil content, expands understanding of trihelix transcription factor function in seed quality trait regulation, and provides new insights for high-quality soybean breeding.
This commentary on Tsai et al. (2025) highlights glutamine's important role in attracting beneficial bacteria to colonize plant roots, deciphers its links to casparian strip integrity, and explores its dual functions. Th...This commentary on Tsai et al. (2025) highlights glutamine's important role in attracting beneficial bacteria to colonize plant roots, deciphers its links to casparian strip integrity, and explores its dual functions. This finding reveals how plants use chemical signals to shape their root microbiome for better health.
TnpB, a compact RNA-guided nuclease ancestral to Cas12, is optimized for plant genome editing. A 99-nt enhanced RNA and T5 exonuclease fusion generate TnpBe5, boosting rice editing 2.5-fold. Coupling with a single-strand...TnpB, a compact RNA-guided nuclease ancestral to Cas12, is optimized for plant genome editing. A 99-nt enhanced RNA and T5 exonuclease fusion generate TnpBe5, boosting rice editing 2.5-fold. Coupling with a single-strands annealing (SSA)-responsive HYYG surrogate (TnpBmax) enriches edited cells, achieving up to 81.5% efficiency and high homozygosity across rice and tomato.
This commentary describes a study displaying the dynamic process of bacterial recruitment from plants through the leakage of glutamine from a defect in the endodermis layer. Leakage of glutamine from the root and bacteri...This commentary describes a study displaying the dynamic process of bacterial recruitment from plants through the leakage of glutamine from a defect in the endodermis layer. Leakage of glutamine from the root and bacterial chemotaxis both contribute to the colonization and proliferation of bacteria.
Identification of pesticide targets is of great significance for the development of new pesticides. The new compound GLY-15, containing a pyrimidine heterocycle and a moroxydine skeleton structure, has good anti-TMV acti...Identification of pesticide targets is of great significance for the development of new pesticides. The new compound GLY-15, containing a pyrimidine heterocycle and a moroxydine skeleton structure, has good anti-TMV activity, but the underlying molecular targets and mechanism of action remain elusive. Here, host malate dehydrogenase (MDH), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), and tobacco mosaic virus (TMV) coat protein (CP) were identified as potential targets of GLY-15 using activity-based protein profiling (ABPP) and drug affinity responsive target stability (DARTS), and their interactions with GLY-15 were validated by microscale thermophoresis (MST) and pull-down analysis. Functional analyses demonstrate that MDH silencing significantly reduces TMV accumulation, while transient overexpression of MDH results in elevated viral infection. Meanwhile, yeast two-hybrid (Y2H), co-immunoprecipitation (Co-IP), and bimolecular fluorescence complementation (BiFC) analysis uncover that MDH interacts with CP, and their interaction is effectively inhibited by GLY-15. Site-directed mutagenesis identifies E225 as a critical residue for both GLY-15/MDH binding and MDH/CP interaction. Further investigations reveal that GLY-15 functions as an MDH inhibitor and affects its interaction with CP. Meanwhile, we showed that GLY-15 targeting MDH indicates broad antiviral activity against pepper mild mottle virus (PMMoV) and potato virus Y (PVY). This investigation systematically reveals novel insights into the anti-TMV mechanisms of GLY-15, establishing a valuable theoretical basis for antiviral target discovery and plant disease resistance breeding.
CRISPR/Cas12i3 belongs to the type V-I Cas system, characterized by its smaller protein size and less restricted canonical "TTN" protospacer adjacent motif. Developments of Cas12i3-mediated base editing systems for eithe...CRISPR/Cas12i3 belongs to the type V-I Cas system, characterized by its smaller protein size and less restricted canonical "TTN" protospacer adjacent motif. Developments of Cas12i3-mediated base editing systems for either C-to-T or A-to-G transitions will expand the editing scope and enrich the plant base editing toolkits for crop improvement. However, while the Cas12i3-based cytosine base editor (CBE) only shows very low editing efficiency in plants, its adenine base editor (ABE) has not been documented as yet. Here, we engineered a series of Cas12i3 (5M)-based CBEs (V0-V5) and ABEs (V0-V5) by fusing a deactivated dCas12i3 (5M) with a transactivation module VP64, a single-stranded DNA-binding domain Rad51, or a double-stranded DNA-binding domain HMG-D, or in combinations, and systemically evaluated their performance in rice protoplasts. Our results demonstrated that synergistic combinations of both VP64 and HMG-D outperformed other architectures and significantly boosted the efficiencies of Cas12i3 (5M)-based CBE and ABE for C-to-T and A-to-G base editing and expanded the editing window. In stable lines, in comparison to the non-fusion control, the optimized Cas12i3 (5M)-based CBE-V5 and ABE-V5 enabled up to 4.78- and 3.35-fold higher editing efficiencies, with the maximum C-to-T and A-to-G efficiencies reaching 32.35% and 38.24%, respectively, and a higher proportion of homozygous mutants in the T generation. Furthermore, we generated herbicide-resistant rice germplasm by using CBE-V5 and ABE-V5, demonstrating their potential for precision breeding in crops. Together, here, we report novel Cas12i3 (5M)-based CBE and ABE that substantially enrich base editing toolkits for improvement of rice and potentially other crops.
CRISPR-Cas9 is a widely used platform for plant genome editing, but its outcomes are typically dominated by small insertions and deletions (indels). Such limited mutation profiles restrict its utility in functional studi...CRISPR-Cas9 is a widely used platform for plant genome editing, but its outcomes are typically dominated by small insertions and deletions (indels). Such limited mutation profiles restrict its utility in functional studies of non-coding RNAs and regulatory elements, such as microRNAs (miRNAs), untranslated regions (UTRs), and promoter sequences, where larger sequence disruptions are often required. Here, we developed enhanced exonuclease-Cas9 platforms, termed multiple nucleotide deletion Cas9 (MND-Cas9) systems, for efficient generation of large deletions in rice. By screening four exonucleases (RecJ, T5, TREX2, and SbcB), we established MND-Cas9v1 systems based on TREX2 or SbcB that produced substantially larger deletions without reducing editing efficiency. Further optimization with an inserted DNA-binding domain (DBD) between Cas9 and exonuclease yielded MND-Cas9v2, which simultaneously enhanced efficiency and deletion size. To expand PAM compatibility, we introduced PAM-relaxed Cas9-NG and SpG variants, generating MND-Cas9-NG/SpGv2 systems with broader targeting scope and superior performance compared to their parental nucleases. Finally, we demonstrated the utility of these systems in two applications: MND-Cas9v2 efficiently knocked out the miRNA gene OsMIR530, producing larger seeds, and generated extended deletions in the 3'UTR of OsGhd2, which upregulated its expression and increased grain size. These results demonstrate that MND-Cas9 systems enable high-efficiency generation of extended deletions and facilitate functional analyses of non-coding RNAs and regulatory sequences. Overall, this work establishes a versatile and expandable exonuclease-Cas9 platform that substantially broadens the mutational spectrum and application potential of CRISPR-Cas9 for plant genome engineering.
Jasmonic acid (JA), a key phytohormone in plant defense, plays essential roles in regulating plant stress responses and growth. However, how JA signaling and nitrate signaling regulate nitrate uptake in maize (Zea mays L...Jasmonic acid (JA), a key phytohormone in plant defense, plays essential roles in regulating plant stress responses and growth. However, how JA signaling and nitrate signaling regulate nitrate uptake in maize (Zea mays L.) remains elusive. Here, we report that low-nitrate stress promotes JA accumulation in maize roots, and JA treatment leads to a low-nitrate phenotype. JA triggers ZmbHLH99 expression, encoding a transcription factor that binds to ZmNLP3.2 promoter and inhibits ZmNLP3.2 expression, thereby regulating nitrate uptake. In addition, the JA ZIM-domain (JAZ) transcriptional repressor ZmZIM13 interacts with ZmbHLH99 to release its inhibitory effect on the ZmNLP3.2-ZmNRT cascade and promotes ZmNLP3.2 expression. Furthermore, loss of ZmbHLH99 or overexpression of ZmZIM13 promotes plant growth and nitrate uptake, leading to higher grain yield. These findings reveal the transcriptional regulatory landscape of how JA signaling regulates nitrate uptake via the ZmZIM13-ZmbHLH99-ZmNLP3.2 module and integrates with nitrate signaling to coordinate plant growth and stress responses.
Small G proteins, functioning as monomeric GTPases, are critical molecular switches that regulate diverse processes in plants. However, little is known about their protein homeostasis during immune responses. Here, we de...Small G proteins, functioning as monomeric GTPases, are critical molecular switches that regulate diverse processes in plants. However, little is known about their protein homeostasis during immune responses. Here, we demonstrate that OsRab11C1, encoding a Rab-type GTPase, is transcriptionally upregulated upon Magnaporthe oryzae infection. Strikingly, loss of OsRab11C1 enhances rice blast resistance, concomitant with increased defense gene expression, MAPK activation, and ROS burst. Mechanistically, we identify the E3 ubiquitin ligase EL5 as an interactor that ubiquitinates and targets OsRab11C1 for degradation via the 26S proteasome. Consistently, EL5 acts upstream of OsRab11C1 and positively regulates rice immunity. Further analysis reveals that OsRab11C1 interacts with and stabilizes mitogen-activated protein kinase kinase OsMKK6, thereby facilitating its autophosphorylation activity. In return, OsMKK6 acts as a negative regulator of rice programmed cell death and immunity. Collectively, our findings unveil a dynamic EL5-OsRab11C1-OsMKK6 signaling module that orchestrates rice immunity against pathogen invasion.
Supplementation of Driver and Kuniyuki Walnut Medium with phloroglucinol enhanced regeneration efficiency in tomato tissue culture. Heterologous expression of an Arabidopsis growth-regulating factor gene, GROWTH-REGULATI...Supplementation of Driver and Kuniyuki Walnut Medium with phloroglucinol enhanced regeneration efficiency in tomato tissue culture. Heterologous expression of an Arabidopsis growth-regulating factor gene, GROWTH-REGULATING FACTOR5 (GRF5), in tomato improved regeneration and transformation efficiency, suggesting a synergistic effect between phloroglucinol treatment and GRF-mediated pathways.