Search Results (967)

Proteomic profiling using ultrafast chromatography–mass spectrometry provides valuable insights into plant responses to abiotic factors by linking molecular changes with physiological outcomes. Nanopriming, a novel approach involving the treatment of seeds with nanoparticles, has demonstrated potential for enhancing plant metabolism and productivity. However, the molecular mechanisms underlying nanoparticle-induced effects remain poorly understood. In this study, we investigated the impact of gold nanoparticle (Au-NP) seed priming on the proteome of wheat (Triticum aestivum L.) seedlings. Differentially regulated proteins (DRPs) were identified, revealing a pronounced reorganization of the photosynthetic apparatus (PSA). Both the light-dependent reactions and the Calvin cycle were affected, with significant upregulation of chloroplast-associated protein complexes, including PsbC (CP43), chlorophyll a/b-binding proteins, Photosystem I subunits (PsaA and PsaB), and the γ-subunit of ATP synthase. The large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCo) exhibited over a threefold increase in expression in Au-NP-treated seedlings. The proteomic changes in the large subunit RuBisCo L were corroborated by transcriptomic data. Importantly, the proteomic changes were supported by physiological and biochemical analyses, ultrastructural modifications in chloroplasts, and increased photosynthetic activity. Our findings suggest that Au-NP nanopriming triggers coordinated molecular responses, enhancing the functional activity of the PSA. Identified DRPs may serve as potential biomarkers for further elucidation of nanopriming mechanisms and for the development of precision strategies to improve crop productivity. Full article

Medicago falcata is one of the most important perennial forage legumes in the Medicago genus. In this study, we reported the complete chloroplast genome of two M. falcata ecotypes grown in different regions, and compared them with those of Medicago truncatula and Medicago sativa. We found that the M. falcata chloroplast genome lacks a typical quadripartite structure, containing 78 protein-coding genes, 30 tRNA genes, and four ribosomal RNA genes. They shared high conservation in size, genome structure, gene order, gene number and GC content with those of M. truncatula and M. sativa. High nucleotide diversity occurred in the coding gene regions of rps16, rps3, and ycf4 genes. Meanwhile, mononucleotide repeats are the most abundant repeat type, followed by the di-, tri-, tetra-, and pentanucleotides, and forward repeats were more abundant than reverse and palindrome repeats for all these three Medicago species. Phylogenetic analyses using both coding sequences and complete chloroplast genomes revealed that M. falcata shares the closest phylogenetic relationship with M. hybrida and M. sativa. This study provided valuable information for further studies on the genetic relationship of the Medicago genus. Full article

Objectives: Light intensity is a critical environmental factor regulating plant growth, development, and stress adaptation. However, the physiological and molecular mechanisms underlying light responses in Aconitum kusnezoffii, a valuable alpine medicinal plant, remain poorly understood. This study aimed to elucidate the adaptive strategies of A. kusnezoffii under different light intensities through integrated physiological and transcriptomic analyses. Methods: Two-year-old A. kusnezoffii plants were exposed to three controlled light regimes (790, 620, and 450 lx). Leaf anatomical traits were assessed via histological sectioning and microscopic imaging. Antioxidant enzyme activities (CAT, POD, and SOD), membrane lipid peroxidation (MDA content), osmoregulatory substances, and carbon metabolites were quantified using standard biochemical assays. Transcriptomic profiling was conducted using Illumina RNA-seq, with differentially expressed genes (DEGs) identified through DESeq2 and functionally annotated via GO and KEGG enrichment analyses. Results: Moderate light (620 lx) promoted optimal leaf structure by enhancing palisade tissue development and epidermal thickening, while reducing membrane lipid peroxidation. Antioxidant defense capacity was elevated through higher CAT, POD, and SOD activities, alongside increased accumulation of soluble proteins, sugars, and starch. Transcriptomic analysis revealed DEGs enriched in photosynthesis, monoterpenoid biosynthesis, hormone signaling, and glutathione metabolism pathways. Key positive regulators (PHY and HY5) were upregulated, whereas negative regulators (COP1 and PIFs) were suppressed, collectively facilitating chloroplast development and photomorphogenesis. Trend analysis indicated a “down–up” gene expression pattern, with early suppression of stress-responsive genes followed by activation of photosynthetic and metabolic processes. Conclusions: A. kusnezoffii employs a coordinated, multi-level adaptation strategy under moderate light (620 lx), integrating leaf structural optimization, enhanced antioxidant defense, and dynamic transcriptomic reprogramming to maintain energy balance, redox homeostasis, and photomorphogenic flexibility. These findings provide a theoretical foundation for optimizing artificial cultivation and light management of alpine medicinal plants. Full article

Nitric oxide is a gaseous signalling molecule produced by plants. Slight changes in endogenous NO levels have significant biochemical and physiological consequences. We investigated the structural and functional properties of NO-responsive antiporter genes in Arabidopsis thaliana. Phylogenetic analysis of 50 antiporter genes classified them into four subgroups based on the presence of NHX and CPA domains and the evolutionary similarity of the protein sequences. Antiporters were found scattered across the five chromosomes with unique physico-chemical properties and subcellular localisation in the plasma membrane, nucleus, chloroplasts, and vacuole. Furthermore, we performed QPCR analysis of eight different antiporter genes after infiltrating the plants with 1 mM CySNO (S-nitroso-L-cysteine), a nitric oxide donor, in WT and the loss-of-function atgsnor1-3 (disruptive S-nitrosoglutathione reductase 1 activity) plants. The AT1G79400 (CHX2), AT2G38170 (RCI4), and AT5G17400 (ER-ANT1) showed a significant increase in their expression in response to CySNO infiltration. However, their expression in atgsnor1-3 plants was found to be lower than in the WT plants, indicating a significant redundancy in the response of these genes to 1 mM levels of CySNO and physiological levels of SNOs in atgsnor1-3. On the other hand, a significant reduction in the expression of AT1G16380 (CHX1), AT2G47600 (MHX1), AT3G13320 (CAX2), and AT5G11800 (KEA6) was observed in WT plants after CySNO infiltration as well as in the leaves of atgsnor1-3 plants. Our study identified three NO-responsive antiporter genes in Arabidopsis, indicating their roles in stress responsiveness and ion homeostasis that could be used for further validation of their roles in NO signalling in plants. Full article

Chloroplasts, as the organelles primarily responsible for photosynthesis, require a substantial supply of iron ions. Conversely, due to Fe toxicity, the homeostasis of these ions is subject to tight regulation. Permease in chloroplast 1 (PIC1) has been identified as the primary iron importer into chloroplasts. However, previous studies suggested the existence of a distinct pathway for Fe transfer to chloroplasts, likely involving mitoferrin-like 1 (MFL1) protein. In this work, Arabidopsis MFL1 (AtMFL1) and its cucumber homolog (CsMFL1) were characterized using, among others, Arabidopsis protoplasts as well as both yeast and Arabidopsis mutants. Localization of both proteins in chloroplasts has been shown to be mediated via an N-terminal transit peptide. At the gene level, MFL1 expression profiles differed between the model plant and the crop plant under varying Fe availability. The expression of other genes involved in chloroplast Fe homeostasis, including iron acquisition, trafficking, and storage, was affected to some extent in both AtMFL1 knockout and overexpressing plants. Moreover, root growth and photosynthetic parameters changed unfavorably in the mutant lines. The obtained results imply that AtMFL1 and CsMFL1, as putative chloroplast iron transporters, play a role in both iron management and the proper functioning of the plant. Full article

Sheath blight (ShB), caused by the necrotrophic fungus Rhizoctonia solani (R. solani), poses severe threats to global rice production. Developing a resistant variety with an ShB-resistance gene is one of most efficient and economical approaches to control the disease. Here, we identified a highly conserved chloroplast-localized stem-loop-binding protein encoding gene (OsCSP41b), which shows great potential in developing an ShB-resistant variety. OsCSP41b-knockout mutants exhibit chlorotic leaves and increased ShB susceptibility, whereas OsCSP41b-overexpressing lines (CSP41b-OE) display significantly enhanced resistance to R. solani, as well as to drought, and salinity stresses. Notably, CSP41b-OE lines present a completely comparable grain yield to the wild type (WT). Transcriptomic analyses reveal that chloroplast transcripts and photosynthesis-associated genes maintain observably elevated stability in CSP41b-OE plants versus WT plants following R. solani infection, which probably accounts for the enhanced ShB resistance of CSP41b-OE. Our findings nominate the OsCSP41b gene as a promising molecular target for developing a rice variety with stronger resistance to both R. solani and multi-abiotic stresses. Full article

The main objective of this study was to reveal the molecular mechanism of the albinism in Schima superba and to identify the related functional genes to provide theoretical support for the optimization of S. superba seedling nursery technology. Combining third-generation SMRT sequencing with second-generation high-throughput sequencing technology, the transcriptomes of normal seedlings and albinism seedlings of S. superba were analyzed and the sequencing data were functionally annotated and deeply resolved. The results showed that 270 differentially expressed transcripts were screened by analyzing second-generation sequencing data. KEGG enrichment analysis of the annotation information revealed that, among the photosynthesis-antenna protein-related pathways, the expression of LHCA3 and LHCB6 was found to be down-regulated in S. superba albinism seedlings, suggesting that the down-regulation of photosynthesis-related proteins may affect the development of chloroplasts in leaves. Down-regulated expression of VDE in the carotenoid biosynthesis leads to impaired chlorophyll cycling. In addition, transcription factors (TFs), such as bHLH, MYB, GLK and NAC, were closely associated with chloroplast development in S. superba seedlings. In summary, the present study systematically explored the transcriptomic features of S. superba albinism seedlings, screened out key genes with significant differential expression and provide a reference for further localization and cloning of the key genes for S. superba albinism, in addition to laying an essential theoretical foundation for an in-depth understanding of the molecular mechanism of the S. superba albinism. The genes identified in this study that are associated with S. superba albinism will be important targets for genetic modification or molecular marker development, which is essential for improving the cultivation efficiency of S. superba. Full article

The genus Lysionotus belongs to the family Gesneriaceae and includes plants with both ornamental and medicinal value. However, genomic-level data on the genus remains scarce. Previous investigations of Lysionotus have predominantly centered on morphological classification, with only limited exploration of molecular phylogenetics. Comparative analysis of chloroplast genomes within the genus would provide valuable insights into the genetic variations and evolutionary patterns of Lysionotus plants. In this study, we present the analysis of 24 newly sequenced chloroplast genomes from Lysionotus-related members, including widely distributed and locally distributed species. The results showed that the 11 plastome sizes of widely distributed species ranged from 152,928 to 153,987 bp, with GC content of 37.43–37.49%; the 13 plastome sizes of locally distributed species ranged from 153,436 to 153,916 bp, with GC content of 37.43–37.48%. A total of 24 chloroplast genomes owned typical quadripartite structures, and the number of tRNA (36 tRNAs) and rRNA (4 rRNAs) were observed for all 24 genomes. However, the number of their protein-coding sequences (CDs) varied at individual levels. No contraction and expansion of IR borders, gene rearrangements, or inversions were detected. mVISTA and Pi showed inverted repeats (IR) region was more conserved than the single copy region, coding region was more conserved than the non-coding region. Additionally, the repeat sequences and codon usage bias of Lysionotus plastomes were also conserved. Our results offer a comprehensive understanding of the genetic differences among these species and shed light on their phylogenetic systematics. Full article

This study evaluated the influence of different male date palm cultivars, distinguished by their chloroplast haplotypes, on pollen quality, pollination efficiency, metaxenia effects, and gene expression during fruit development. Chloroplast DNA analysis of 37 male trees revealed multiple haplotypes, from which cultivars B25, P8, C22, and B46 were selected for further investigation. Pollen viability varied significantly among cultivars, with P8 and B25 exhibiting the highest germination rates and pollen tube elongation, while C22 showed the lowest. These differences correlated with pollination success: P8 and B25 achieved fertilization rates near 99%, whereas C22 remained below 43%. Pollination outcomes also varied in fruit traits. Despite its low pollen performance, C22 induced the production of larger fruits at the Bleh (Kimri) stage, potentially due to compensatory physiological mechanisms. Phytochemical profiling revealed significant cultivar effects: fruits from B25-pollinated trees had with lower moisture and polyphenol content but the higher sugar levels and soluble solids, suggesting accelerated maturation. Ripening patterns confirmed this finding, with B25 promoting the earliest ripening and B46 causing the most delayed. Gene expression analysis supported these phenotypic differences. Fruits pollinated by P8, B25, and B46 exhibited elevated levels of cell-division-related transcripts, particularly the PdCD_1 gene (PDK_XM_008786146.4, a gene encoding a cell division control protein), which was most abundant in P8. In contrast, fruits from C22-pollinated trees had the lowest expression of growth-related genes, suggesting a shift toward cell expansion rather than division. Overall, the results show the critical role of male genotype in influencing fertilization outcomes and fruit development, offering valuable insights for targeted breeding strategies at enhancing date palm productivity and fruit quality. Full article

Thylakoid rhodanese-like protein (TROL) serves as a thylakoid membrane hinge linking photosynthetic electron transport chain (PETC) complexes to nicotinamide adenine dinucleotide phosphate (NADPH) synthesis. TROL is the docking site for the flavoenzyme ferredoxin-NADP⁺ oxidoreductase (FNR). Our prior work indicates that the TROL-FNR complex maintains redox equilibrium in chloroplasts and systemically in plant cells. Improvement in the knowledge of redox regulation mechanisms is critical for engineering stress-tolerant plants in times of elevated global drought intensity. To further test this hypothesis and confirm our previous results, we monitored light-independent ROS propagation in the leaves of Arabidopsis wild type (WT), TROL knock-out (KO), and TROL ΔRHO (RHO-domain deletion mutant) mutant plants in situ by using confocal laser scanning microscopy with specific fluorescent probes for the three different ROS: O₂^·−, H₂O₂, and ¹O₂. Plants were grown under the conditions of normal substrate moisture and under drought stress conditions. Under the drought stress conditions, the TROL KO line showed ≈32% less O₂^·− while the TROL ΔRHO line showed ≈49% less H₂O₂ in comparison with the WT. This research confirms the role of dynamical TROL-FNR complex formation in redox equilibrium maintenance by redirecting electrons in alternative sinks under stress and also points it out as promising target for stress-tolerant plant engineering. Full article

Adansonia L. (1753) belongs to the family Malvaceae and is commonly known as the baobab tree. This species holds significant cultural and ecological value and is often referred to as the ‘tree of life.’ Although its nuclear genome has been reported, the mitogenome has not yet been studied. Mitogenome research is crucial for understanding the evolution of the entire genome. In this study, we assembled and analyzed the mitogenomes of four Adansonia species by integrating short-read and long-read data. The results showed that the mitogenomes of all four Adansonia species were resolved as single circular sequences. Their total genome lengths ranged from 507,138 to 607,344 bp and contained a large number of repetitive sequences. Despite extensive and complex rearrangements between the mitogenomes of Adansonia and other Malvaceae species, a phylogenetic tree constructed based on protein-coding genes clearly indicated that Adansonia is more closely related to the Bombax. Selection pressure analysis suggests that the rps4 gene in Adansonia may have undergone positive selection compared to other Malvaceae species, indicating that this gene may play a significant role in the evolution of Adansonia. Additionally, by analyzing intracellular gene transfer between the chloroplast, mitochondria, and nuclear genomes, we found that genes from the chloroplast and mitochondria can successfully transfer to each chromosome of the nuclear genome, and the psbJ gene from the chloroplast remains intact in both the mitochondrial and nuclear genomes. This study enriches the genetic information of Adansonia and provides important evidence for evolutionary research in the family Malvaceae. Full article

Investigations of endogenous plant circular RNAs (circRNAs) in several plant species have revealed changes in their circular RNA profiles in response to biotic and abiotic stresses. Recently, circRNAs have emerged as critical regulators of gene expression. The destructive impacts on agriculture due to plant viral infections necessitate better discernment of the involvement of plant circRNAs during viral infection. However, few such studies have been conducted hitherto. Sobemoviruses cause great economic impacts on important crops such as rice, turnip, alfalfa, and wheat. Our current study investigates the dynamics of plant circRNA profiles in the host Arabidopsis thaliana (A. thaliana) during infections with the sobemoviruses Turnip rosette virus (TRoV) and Rice yellow mottle virus (RYMV), as well as the small circular satellite RNA of the Lucerne transient streak virus (scLTSV), focusing on circRNA dysregulation in the host plants and its potential implications in triggering plant cellular defense responses. Towards this, two rounds of deep sequencing were conducted on the RNA samples obtained from infected and uninfected plants followed by the analysis of circular RNA profiles using RNA-seq and extensive bioinformatic analyses. We identified 760 circRNAs, predominantly encoded in exonic regions and enriched in the chloroplast chromosome, suggesting them as key sites for circRNA generation during viral stress. Gene ontology (GO) analysis indicated that these circRNAs are mostly associated with plant development and protein binding, potentially influencing the expression of their host genes. Furthermore, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed photosynthesis as the most affected pathway. Interestingly, the non-coding exogenous scLTSV specifically induced several circRNAs, some of which contain open reading frames (ORFs) capable of encoding proteins. Our biochemical assays demonstrated that transgenic expression of scLTSV in A. thaliana enhanced resistance to TRoV, suggesting a novel strategy for improving plant viral resistance. Our results highlight the complexity of circRNA dynamics in plant–virus interactions and offer novel insights into potential circRNA-based strategies for enhancing plant disease resistance by modulating the differential expression of circRNAs. Full article

As an auxin-responsive gene, Gretchen Hagen 3 (GH3) maintains hormonal homeostasis by conjugating excess auxin with amino acids in plant stress-related signaling pathways. GH3 genes have been characterized in many plant species, but the characteristics of pepper (Capsicum annuum L.) GH3 (CaGH3) gene family members in response to multiple stimulants are largely unknown. In this study, we systematically identified the CaGH3 gene family at the genome level and identified eight members on four chromosomes in pepper. CaGH3s were divided into two groups (I and III) and shared conserved motifs, domains, and gene structures. Moreover, CaGH3s had close evolutionary relationships with tomato (Solanum lycopersicum L.), and the promoters of most CaGH3 genes contained hormone and abiotic stress response elements. A protein interaction prediction analysis demonstrated that the CaGH3-3/3-6/3-7/3-8 proteins were possibly core members of the CaGH3 family interaction. In addition, qRT-PCR results showed that CaGH3 genes were differentially expressed in pepper tissues and could be induced by phytohormones (IAA, ABA, and MeJA) and abiotic stresses (salt, low temperature, and drought) with different patterns. In addition, CaGH3-5 and CaGH3-7 were cloned, and the sequences showed a high degree of conservation. Moreover, the results of subcellular localization indicated that they were located in the membrane and chloroplast. Notably, after overexpressing CaGH3-7 in tomato, RNA-seq was performed on wild-type and transgenic lines, and the differentially expressed genes were mainly enriched in response to external stimuli. This study not only lays the foundation for a comprehensive understanding of the function of the CaGH3 gene family during plant growth and stress responses but also provides potential genetic resources for pepper resistance breeding. Full article

Plant mitochondrial genomes exhibit extensive size variability and structural complexity. Here, we report the complete mitochondrial genome of Trichopus zeylanicus, an endemic medicinal plant from the Western Ghats. The mitochondrial genome was assembled using a combination of Illumina short-read and PacBio long-read sequencing technologies, followed by extensive annotation and comparative analysis. The circular mitogenome spans 709,127 bp with a GC content of 46%, encoding 32 protein-coding genes, 17 tRNAs, and three rRNAs. Comparative analysis with other monocot mitochondrial genomes revealed conserved gene clusters but also significant lineage-specific rearrangements. Despite genome size similarities, T. zeylanicus displayed marked divergence in gene order, suggesting that genome size does not necessarily correlate with structural conservation. The genome contains 6.7% chloroplast-derived sequences and 324 predicted RNA-editing sites, predominantly in the first and second codon positions. Phylogenetic analysis based on mitochondrial genes placed T. zeylanicus as a distinct lineage within Dioscoreales, supporting its evolutionary uniqueness. This work provides the first mitogenomic resource for Dioscoreales and advances our understanding of mitochondrial diversity and evolution in monocots. Full article

Phytoene synthase (PSY) is a multimeric enzyme that serves as the first enzyme in carotenoid synthesis within plant tissues and plays a crucial role in the production of carotenoids in plants. To understand the function of the PSY gene in Panax japonicus C. A. Meyer. fruit, the gene’s transcript was obtained by analyzing the transcriptome sequencing data of Panax japonicus fruit. The CDS sequence of the gene was cloned from Panax japonicus fruit using the RT-PCR cloning technique and named PjPSY1, which was then subjected to biosynthetic analysis and functional verification. The results showed that the open reading frame of the gene was 1269 bp, encoding 423 amino acids, with a protein molecular mass of 47,654.67 KDa and an isoelectric point (pI) of 8.63; the protein encoded by these amino acids was hydrophilic and localized in chloroplasts, and its three-dimensional structure was predicted by combining the pymol software to annotate the N site of action and active centre of the protein. Phylogenetic analysis demonstrated that PjPSY1 had the closest affinity to DcPSY from Daucus carota. Overexpression of PjPSY1 led to a significant increase in the content of carotenoid-related monomers in Arabidopsis thaliana, with Violaxanthin being synthesized in transgenic Arabidopsis thaliana but not in wild-type Arabidopsis thaliana. The PjPSY1 clone obtained in this study was able to promote carotenoid synthesis in the fruits of Panax japonicus, revealing that the mode of action of PjPSY1 in the carotenoid biosynthesis pathway of Panax japonicus fruits has a positive regulatory effect. Full article