Search Results (2,537)

Chitinases have been demonstrated to enhance plant resistance to fungi in various pathosystems. Although there is evidence of the effectiveness of these proteins in coffee–fungus interactions, no genome-wide identification or characterization of coffee chitinases has been performed. In this study, we employed phylogenetic analysis, domain architecture, gene structure analysis, and subcellular localization to identify and characterize putative genes and proteins in the genomes of Coffea arabica and its progenitors, Coffea canephora and Coffea eugenioides. A total of 113, 47, and 69 putative chitinase proteins were identified in C. arabica, C. canephora, and C. eugenioides, respectively. These chitinases were classified according to their catalytic domains, GH18 and GH19, and into Classes I, II, III, IV, and V, as determined through phylogenetic analysis based on the Arabidopsis thaliana classification. Furthermore, based on orthologous analysis, we identified ten, six, and seven putative chitinases associated with fungal defense responses in C. arabica, C. canephora, and C. eugenioides, respectively. These findings are valuable for future studies focusing on coffee chitinases, particularly on genetic programs involved in plant pathogen resistance. Full article

Arabidopsis thaliana is a widely used model in plant biology, where histology (HT), histochemistry (HC), immunohistochemistry (IHC), and immunofluorescence (IF) are applied to study cellular structures, macromolecules, and antigens. Despite their extensive use, protocols lack standardization and exhibit substantial variability in critical aspects such as reagent handling, exposure times, and the proper use of controls. This methodological heterogeneity represents a major gap, limiting reproducibility and comparability between studies. Unlike previous methodological reviews, this work focuses exclusively on A. thaliana, systematically identifies reporting omissions, and proposes a roadmap for standardization. A narrative review of literature retrieved from Scopus and Web of Science was conducted with the aim of analyzing methodological approaches, identifying inconsistencies, and offering recommendations for improved laboratory practices. The analysis revealed frequent omissions in the reporting of critical steps such as dehydration, clearing, antigen retrieval, enzyme blocking, and the incorporation of positive and negative controls, which compromise the reliability of results and hinder inter-laboratory validation. Based on this evidence, three key recommendations are emphasized: (i) organ-specific selection and explicit justification of fixatives and stains; (ii) mandatory incorporation of positive and negative controls in IHC and IF; and (iii) adoption of a minimum reporting checklist to enhance reproducibility. Beyond cell morphology, the reviewed studies demonstrate applications in plant physiology, phytogenetics, and pathophysiology. By combining critical analysis with actionable guidelines, this review contributes a practical reference to strengthen methodological rigor in histological and immunological studies of plants. Full article

Leaf senescence is the final, programmed stage of leaf development, marked by nutrient remobilization and tightly regulated molecular events. Although alternative splicing has emerged as a major regulator of plant development, its role in isoform switching during leaf aging remains poorly understood. To address this, we conducted a genome-wide analysis of isoform switching in Arabidopsis, leveraging publicly available RNA-seq data from mature (16-day-old) and senescent (30-day-old) leaves, analyzed with the IsoformSwitchAnalyzeR package. Between these two developmental stages, we identified 269 genes exhibiting 377 significant isoform switches collectively predicted to alter protein localization, coding potential, and transcript stability. Experimental validation confirmed predicted switching at the PUS3 (Pseudouridine Synthase 3) locus, with sequence analysis revealing an age-dependent shift from mitochondrial-targeted to cytoplasmic isoforms. Gene Ontology enrichment analysis of switching genes revealed 82 significant terms, prominently associated with metabolism, gene expression, developmental regulation, and stress responses. Interestingly, we found nearly one-third of switching genes to overlap with known targets of the splicing factor SR45, with enrichment in pathways related to nucleotide and amino acid metabolism, energy production, and developmental processes. Correspondingly, dark-induced senescence assays revealed accelerated senescence in the sr45 mutant, confirming SR45′s role in regulating leaf aging. Specific complementation of SR45′s two isoforms revealed contrasting functions, with SR45.1 restoring normal senescence timing while SR45.2 failed to complement. Taken together, our findings demonstrate that differential isoform usage, orchestrated by specific splicing regulators, plays a critical role in leaf aging. This insight opens new avenues for manipulating senescence and engineering stay-green traits in crops. Full article

Poacic acid is a novel natural antifungal agent. It inhibits the growth of fungal cells, including budding yeast Saccharomyces cerevisiae, by inhibiting the synthesis of β-1,3-glucan, which is a major component of the fungal cell wall. Although poacic acid is expected to be a candidate pesticide owing to its antifungal activity, its effects on plant cells have not been investigated. In this study, we analyzed the effects of poacic acid on lily (Lilium longiflorum) pollen. Poacic acid inhibited lily pollen germination and tube growth at concentrations lower than those that inhibited budding yeast growth. While poacic acid did not inhibit callose (β-1,3-glucan) synthesis in pollen tubes, it inhibited membrane traffic, including endocytosis and secretion, and the organization of the actin cytoskeleton within pollen tubes. Since these processes have been shown to play essential roles in pollen tube growth, our study indicates that poacic acid affects lily pollen tube growth differently than it affects budding yeast. Poacic acid also inhibited the growth of Arabidopsis thaliana pollen tubes and root. Full article

Acetolactate synthase (ALS) is an important enzyme in plant branched-chain amino acid biosynthesis and the target of several major herbicide classes. Despite its agronomic importance, the role of ALS genes in stress adaptation in the invasive weed Amaranthus palmeri remains unstudied. In this study, four ApALS genes with high motif conservation were identified and analyzed in A. palmeri. Phylogenetic analysis classified ApALS and other plant ALS proteins into two distinct clades, and the ApALS proteins were predicted to localize to the chloroplast. Gene expression analysis demonstrated that ApALS genes are responsive to multiple stresses, including salt, heat, osmotic stress, glufosinate ammonium, and the ALS-inhibiting herbicide imazethapyr, suggesting roles in both early and late stress responses. Herbicide response analysis using an Arabidopsis thaliana ALS mutant (AT3G48560) revealed enhanced imazethapyr resistance, associated with higher chlorophyll retention. Furthermore, high sequence homology between AT3G48560 and ApALS1 suggests a conserved role in protecting photosynthetic function during herbicide stress. This study provides the first comprehensive analysis of the ALS gene family in A. palmeri and offers important insights into its contribution to stress resilience. These findings establish a vital foundation for developing novel strategies to control this pervasive agricultural weed and present potential genetic targets for engineering herbicide tolerance in crops. Full article

Cucumber green mottle mosaic virus (CGMMV, Tobamovirus viridimaculae) is a tobamovirus that induces leaf green mottling, mosaic patterns, bleaching, fruit sponginess, rotting, and malformation symptoms in various cucurbit crops. The underlying mechanisms by which CGMMV elicits these symptoms have yet to be elucidated. In the present study, we observed that the infection of CGMMV in bottle gourd, but not in N. benthamiana, led to the significant upregulation of a key gene involved in chlorophyll degradation, Chlorophyllase 1 (CLH1). This induction may be closely linked to chlorophyll degradation, particularly that of chlorophyll a (Clh a) in bottle gourd plants. Phylogenetic analysis showed that the amino acid sequence of BgCLH1 has a closer relationship with those of CLH1 from other cucurbit crops and has a relatively farther relationship with those of the well-studied CLH1 from Arabidopsis thaliana and Citrus sinensis. Further, confocal microscopy analysis indicated that BgCLH1 may be localized to the cytoplasm instead of the chloroplast. Moreover, silencing of the BgCLH1 gene not only reduced viral accumulation but also resulted in an increase in chlorophyll content. Similar results were also observed in watermelon, suggesting that this regulatory mechanism may be conserved across cucurbit crops. Our findings thus reveal a complex and intricate interplay between viral infection and the chlorophyll metabolic pathway. Full article

The glyoxalase pathway intermediate S-d-lactoylglutathione was recently implicated in protein post-translational modifications in animal systems. Here, we examined the spontaneous modification of the Arabidopsis thaliana cytosolic glyceraldehyde-3-phosphate dehydrogenase C1 (GAPC1) by this compound. Incubation of GAPC1 with S-d-lactoylglutathione resulted in the inhibition of enzyme activity. The inhibitory effect was concentration dependent and increased at alkaline pHs. Furthermore, the inhibition of GAPC1 by S-d-lactoylglutathione was favored by oxidative conditions and reversed by reduction with dithiothreitol. Analyses of the S-d-lactoylglutathione-treated protein by nanoLC-MS/MS revealed S-glutathionylation of its two Cys residues and N-lactoylation of six Lys residues. Protein structure predictions showed that the double S-glutathionylation is accommodated by the GAPC1 catalytic pocket, which likely explains enzyme inhibition. N-lactoylated sites overlap partially with previously reported N-acetylated sites at the surface of the GAPC1 tetramer. The efficiency of cytosolic glutaredoxin and thioredoxin isoforms was tested for reversing the S-d-lactoylglutathione-induced modification. In these assays, recovery of GAPC1 activity after inhibition by S-d-lactoylglutathione treatment was used as indicator of efficiency. The results show that both types of redoxins were able to reverse inhibition. We propose a model describing the mechanisms involved in the two types of post-translational modifications found on GAPC1 following exposure to S-d-lactoylglutathione. The possible involvement of these findings for the control over glycolytic metabolism is discussed. Full article

Arabinogalactan proteins (AGPs: hydroxyproline-rich glycoproteins) are ubiquitous in plants and play various functions in cases of development and reproduction. In Arabidopsis thaliana some AGPs can work as markers for gametophytic cell differentiation (among others embryological structures they mark generative cell wall and/or plasma membrane, and also sperm cells). However, apart from Arabidopsis, this labeling of generative cell and sperm cells in pollen grains has only been observed in a few flowering plant species belonging to dicotyledons. No such studies are available in monocotyledons. The main aim of our study was to see whether AGPs would be present at the generative cell–vegetative cell interface in different monocotyledons (representatives of Asparagaceae, Amarylidaceae and Liliaceae), and we also wanted to test whether they would be the same AGPs as in dicotyledons. For the study, we selected Gagea lutea (L.) Ker Gawl., Ornithogalum nutans L. and Galanthus nivalis L. species that differ in shape and size of generative cells. Antibodies against arabinogalactan proteins AGPs were used, including JIM8, JIM13, JIM14, MAC207, LM2, LM14, JIM15 and JIM4. The localization of the examined compounds was determined using immunohistochemistry techniques. The key finding was that AGPs (detected with JIM8 and JIM13 antibodies) consistently mark the boundary between the generative cell and the surrounding vegetative cytoplasm, suggesting their association with the generative cell–vegetative cell interface in all species studied. Identifying such molecular markers in male gametophyte may enhance the understanding of gametophytic cell fate, sperm cell identity and the molecular mechanisms underlying fertilization. Such labeling may also be useful in studies on pollen development, species comparisons, or responses to environmental stresses. Full article

14-3-3 proteins are highly conserved regulatory molecules in plants. In grapevine (Vitis vinifera L.), 14-3-3 proteins are studied under abiotic stress. However, the role of 14-3-3 proteins in the interaction between grapevine and downy mildew is yet to be studied. In this study, we identified a highly conserved 14-3-3 protein in grapevine and performed a phylogenetic analysis, revealing a close relationship between one of its homologs, 14-3-3ω proteins from Arabidopsis thaliana and Nicotiana benthamiana. We designated this homolog as Vv14-3-3ω. Subcellular localization studies showed that Vv14-3-3ω resides in the plasma membrane and cytoplasm. Expression analysis revealed a strong induction of Vv14-3-3ω at early time points following Plasmopara viticola infection, correlating with enhanced pathogen sporulation in grapevine. Furthermore, transient overexpression of Vv14-3-3ω in N. benthamiana increased susceptibility to the Phytophthora capsici pathogen and suppressed Flg22-induced pattern-triggered immunity (PTI) responses. Overexpression of Vv14-3-3ω in Nb14-3-3-silenced N. benthamiana plants resulted in increased susceptibility to P. capsici, suggesting functional conservation of this isoform. These findings indicate that Vv14-3-3ω functions as a susceptibility factor, facilitating pathogen infection and disease progression in grapevine, and highlight its potential role for improving resistance against downy mildew. Full article

Light-dependent protochlorophyllide oxidoreductase (LPOR, E.C.1.3.1.33) plays a crucial role in the biosynthesis of chlorophyll in plants. Therefore, inactivating LPOR can hinder the production of chlorophyll to achieve the effect of weed control. In this research, utilizing an active substructure splicing method, 20 new 1,2,4-oxadiazole compounds targeting LPOR were synthesized. Among them, compounds 5j, 5k and 5q exhibited superior inhibitory efficacy in greenhouse herbicidal trials. In vitro enzyme activity assays indicated that 5q significantly inhibited Arabidopsis thaliana LPOR (AtLPOR), with an IC₅₀ value of 17.63 μM. Furthermore, compound 5q exhibited superior crop safety and holds potential application prospects for weed management in cotton. Molecular docking and dynamic simulations were employed to elucidate the binding mode and molecular mechanism of 5q with AtLPOR. These experimental and theoretical results indicate that 5q is a promising candidate for the development of novel herbicides targeting LPOR. Full article

Brassinosteroids (BRs) are essential regulators of plant development and stress responses, but the distinct contributions of BR biosynthesis and signaling to hormonal crosstalk remain poorly defined. Here, we investigated the effects of the BR biosynthesis inhibitor brassinazole (BRZ) and the BR-insensitive mutant bri1-6 on endogenous phytohormone profiles in Arabidopsis thaliana. Using multivariate analysis and targeted hormone quantification, we show that BRZ treatment and BRI1 disruption alter hormone balance through partially overlapping but mechanistically distinct pathways. Principal component analysis (PCA) and hierarchical clustering revealed that BRZ and the bri1-6 mutation do not phenocopy each other and that BRZ still alters hormone profiles even in the bri1-6 mutant, suggesting potential BRI1-independent effects. Both BRZ treatment and the bri1-6 mutation tend to influence cytokinins and auxin conjugates divergently. On the contrary, their effects on stress-related hormones converge: BRZ decreases salicylic acid (SA), jasmonic acid (JA), and abscisic acid (ABA) in the WT leaves; similarly, bri1-6 mutants show reduced SA, JA, and ABA. These results indicate that BR biosynthesis and BRI1-mediated perception may contribute independently to hormonal reprogramming, with BRZ eliciting additional effects, possibly via metabolic feedback, compensatory signaling, or off-target action. Hormone correlation analyses revealed conserved co-regulation clusters that reflect underlying regulatory modules. Altogether, our findings provide evidence for a partial uncoupling of BR levels and BR signaling and illustrate how BR pathways intersect with broader hormone networks to coordinate growth and stress responses. Full article

Evidence indicates that light can trigger an increase in triacylglycerol (TAG) accumulation in eukaryotic microalgae without reducing cell division. In connection with this, we have recently reported that the expression of the chloroplast enzyme diacylglycerol acyltransferase 3 (DGAT3) is induced by light in concert with TAG accumulation in Chlamydomonas reinhardtii. In this work, we report the identification of two phytyl ester synthases (PES) in C. reinhardtii, named PESα and PESβ. These are homologous to chloroplast PES1 and PES2 of Arabidopsis thaliana, which play a role in the synthesis of fatty acid phytyl esters (FAPEs) and TAGs. We demonstrate that PESα and PESβ transcript levels are transiently induced upon transferring cell cultures from a growth condition of low light to high light, and this occurs in parallel to an increase in TAG levels. In a pesα knockdown mutant, DGAT3 transcripts and TAG levels are significantly higher than in the parental strain at the end of the low-light period, and remain elevated after shifting pesα cells to the high-light condition. On the contrary, in a pesβ knockdown mutant, TAG levels, as well as DGAT3 expression, are similar to those of the control strain. These results suggest that PESα and PESβ are non-redundant in TAG metabolism and that PESα is functionally related to DGAT3. Full article

TCP transcription factors represent a crucial family of plant regulators that contribute significantly to growth and developmental processes. Although the TCP gene family has been extensively studied in various plant species, research on Chimonanthus praecox (wintersweet) remains limited. Here, we performed genome-wide identification and analysis of the TCP gene family in C. praecox and identified 22 CpTCP genes. We further systematically examined the associated physicochemical properties, evolutionary relationships, gene structures, and regulatory features. Analysis revealed that all CpTCP proteins possess a conserved TCP domain, and subcellular localization prediction indicated their localization in the nucleus. Promoter analysis revealed that multiple cis-elements are associated with abiotic stress responses and plant growth regulation. Further analysis revealed high CpTCP2 expression in the leaves and stamen, with significantly increased levels during flower senescence. CpTCP2 expression was upregulated in response to methyl jasmonate (MeJA), salicylic acid, abscisic acid, and shade. CpTCP2 overexpression in Arabidopsis thaliana resulted in a reduced leaf area, delayed flowering, and increased rosette leaf numbers. Moreover, MeJA treatment accelerated leaf senescence in CpTCP2 transgenic Arabidopsis. These findings provide insights into the evolutionary characteristics of the TCP family in C. praecox, highlighting the functional role of CpTCP2 in regulating leaf development and flowering time in Arabidopsis, thereby offering valuable genetic resources for wintersweet molecular breeding. Full article

Terpene synthases (TPS) facilitate terpenoid production, influencing the flavor, color, and medicinal properties of Crocus sativus (saffron), a triploid geophyte of significant commercial importance. Despite its importance, the CsTPS gene family remains poorly characterized, limiting genetic enhancements in saffron’s agronomic features. This research performed a comprehensive genome-wide analysis of CsTPS genes using genomic, transcriptomic, and in silico approaches. BLASTP and PfamScan discovered thirty CsTPS genes, demonstrating conserved TPS domains, varied exon–intron architectures, and chromosomal clustering indicative of tandem duplications. Phylogenetic research categorized these genes into five subfamilies (TPS-a to TPS-e), with the prevalence of TPS-a suggesting a role in sesquiterpene biosynthesis. RNA-seq data (PRJNA976833, PRJNA400472) revealed tissue-specific expression, with CsTPS1 and CsTPS5 expressed in reproductive tissues and CsTPS2 in vegetative tissues. Stress-responsive genes (CsTPS1, CsTPS4) exhibited upregulation in response to cold and pathogen stress, with cis-regulatory elements (e.g., ARE, ABRE) indicating hormone control. The in-silico validation of CsTPS1, chosen for its elevated GMQE score (0.89), included primer design, ePCR, and vector optimization for expression in Arabidopsis thaliana. This study elucidates the contribution of the CsTPS family to saffron terpenoid diversity, providing a foundation for enhancing flavor, yield, and stress tolerance through genetic engineering. Full article

Seed dormancy and germination is regulated by internal hormones and exogenous environment cues. Ethylene is one of the hormones that break seed dormancy and induce seed germination. Our previous study showed that N-degron pathway gene, proteolysis6 (PRT6) was involved in dormancy release by ethylene, the defection of which exhibiting ethylene-insensitivity in Arabidopsis thaliana. In the present study, through screening an ethyl methyl sulfonate-mutagenized (EMS) population of prt6−1, we isolated a recessive mutant that acted as a suppressor of prt6 that rescued its insensitivity to ethylene as well as a phenotype of shorter silique length. Further bulk segregant analysis on F2 population identified a premature termination located in the third exon of LONGIFOLIA1 (LNG1), previously reported in the regulation of longitudinal cell elongation. Mutation of LNG1 in prt6−1 background by CRISPR-Cas9 confirmed that LNG1 was epistatic to PRT6 in seed responsiveness to ethylene. Our finding proposed the pleiotropic effect of LNG1 in seed dormancy breakage by ethylene via PRT6, providing novel functional component at the downstream of the coordinated PRT6 and ethylene signaling pathway. Full article