Search Results (797)

Bacterial cell morphology might result from natural selection to gain a competitive advantage under environmentally stressful conditions such as nutrient limitation. In nutrient-limited conditions, a higher surface-to-volume ratio is crucial for cell survival because it allows for a more efficient exchange of nutrients and waste products. A bacterial strain YC6860^T isolated from the rhizosphere of rice (Oryza sativa L.) showed pleomorphic behavior with smooth cell morphology and wrinkled surface rods depending upon nutritional conditions. Based on scanning and transmission electron microscopy studies, we hypothesized that the surface-to-volume ratio of cells would increase with decreasing nutrient concentrations and tested this quantitatively. The transition from smooth to wrinkled cell surface morphology could be one of the adaptation strategies by which YC6860^T maximizes its ability to access available nutrients. To characterize the properties of the wrinkled strain, we performed taxonomic and phylogenetic analyses. 16S rRNA gene sequencing results showed that the strain represented a novel, deep-rooting lineage within the order Rhizobiales with the highest similarity of 94.2% to Pseudorhodoplanes sinuspersici RIPI 110^T. Whole-genome sequencing was also performed to characterize its genetic features. The low phylogenetic and genetic similarity is probably related to the wrinkled morphology of the strain. Therefore, we propose that the strain YC6860^T might belong to a new genus and species, named Rugositalea oryzae. In addition, taxonomic analysis showed that YC6860^T is Gram-negative, aerobic, and rod-shaped with regular surface wrinkles under nutrient-limiting conditions, resembling a delicate twist of fusilli, with groove depths of 48.8 ± 3.7 nm and spacing of 122.5 ± 16.9 nm. This unique cell structure with regular rugosity could be the first finding that has not been reported in the existing bacterial morphology. Full article

Potato (Solanum tuberosum L.) is a globally significant staple crop that faces constant threats from Phytophthora infestans, the causative agent of late blight (LB). The battle between Phytophthora infestans and its host is driven by the molecular interplay of RXLR-encoded avirulence (PiAvr) effectors and nucleotide-binding leucine-rich repeat (NLR) immune receptors in potato. This review provides a comprehensive analysis of the structural characteristics, functional diversity, and evolutionary dynamics of RXLR effectors and the mechanisms by which NLR receptors recognize and respond to them. The study elaborates on both direct and indirect modes of effector recognition by NLRs, highlighting the gene-for-gene interactions that underlie resistance. Additionally, we discuss the molecular strategies employed by P. infestans to evade host immunity, including effector polymorphism, truncation, and transcriptional regulation. Advances in structural biology, functional genomics, and computational modeling have provided valuable insights into effector–receptor interactions, paving the way for innovative resistance breeding strategies. We also discuss the latest approaches to engineering durable resistance, including gene stacking, synthetic NLRs, and CRISPR-based modifications. Understanding these molecular mechanisms is critical for developing resistant potato cultivars and mitigating the devastating effects of LB. This review aims to bridge current knowledge gaps and guide future research efforts in plant immunity and disease management. Full article

In molecular biology studies, suitable vectors are fundamental tools; however, most vectors can only express one target gene, which limits the ability to study multiple genes simultaneously within the same plant tissue. The traditional method for achieving multi-gene co-expression involves co-transferring multiple plasmids into plant tissues, but this approach is often inefficient due to the difficulty of successfully transforming multiple plasmids at once. To overcome this limitation, we have developed a series of vectors, called pMAGs (Multigene Assembly Genetic vectors), capable of simultaneously expressing or silencing two or three different genes in plants. These vectors not only provide an optimal solution for a wide range of biological experiments but also work effectively across numerous plant species. Full article

RNA polymerase II (Pol II) has been shown to participate in various biological processes in plants, but its function in response to abiotic stress in cotton remains unclear. This study aimed to elucidate the role of the third-largest subunit of Pol II (NRBP3) in the response of cotton to drought and salt stress through molecular biology and physiological methods. Real-time fluorescence quantitative PCR was used to analyze the expression pattern of NRPB3 in roots, stems, leaves, and cotyledons and to detect changes in its expression under drought, NaCl, and ABA treatments. Using virus-induced gene silencing (VIGS) technology, NRPB3-silenced plants were obtained, and their physiological indicators under drought and salt stress, as well as the expression levels of the drought stress-related genes GhRD22 and GhRD26, were measured. This study revealed that NRPB3 is widely expressed in roots, stems, leaves, and cotyledons and that its expression is significantly induced by drought, NaCl, and ABA treatments. Compared to wild-type plants, the drought resistance, survival rate, and peroxidase activity of the GhNRPB3-silenced plants significantly increased, whereas the malondialdehyde content significantly decreased. Moreover, the expression levels of the drought-responsive genes GhRD22 and GhRD26 significantly increased. The salt tolerance of the GhNRPB3-silenced plants also increased, as reflected by decreased leaf wilting and significant increases in root growth parameters (including root length, root area, and root volume). These results indicate that NRPB3 plays a crucial role in mediating the adaptation of cotton to drought and salt stress by regulating the expression of stress-related genes. Full article

Plants must contend with oxidative stress, a paradoxical phenomenon in which reactive oxygen species (ROS) can cause cellular damage while also serving as key signaling molecules. Environmental stressors, such as drought, salinity, and temperature extremes, promote ROS accumulation, affecting plant growth and productivity. To maintain redox homeostasis, plants rely on antioxidant systems comprising enzymatic defenses, such as superoxide dismutase, catalase, and ascorbate peroxidase, and non-enzymatic molecules, including ascorbate, glutathione, flavonoids, and emerging compounds such as proline and nano-silicon. This review provides an integrated overview of antioxidant responses and their modulation through recent biotechnological advances, emphasizing the role of emerging technologies in advancing our understanding of redox regulation and translating molecular insights into stress-resilient phenotypes. Omics approaches have enabled the identification of redox-related genes, while genome editing tools, particularly those based on clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) proteins, offer opportunities for precise functional manipulation. Artificial intelligence and systems biology are accelerating the discovery of regulatory modules and enabling predictive modeling of antioxidant networks. We also highlight the contribution of synthetic biology to the development of stress-responsive gene circuits and address current regulatory and ethical considerations. Overall, this review aims to provide a comprehensive perspective on molecular, biochemical, and technological strategies to enhance oxidative stress tolerance in plants, thereby contributing to sustainable agriculture and food security in a changing climate. Full article

Powdery mildew, predominantly caused by Podosphaera xanthii and Golovinomyces orontii, presents a major constraint to cucurbitaceous crop production worldwide. Despite intensive research, the complex interplay between pathogen virulence factors and host immune responses remains only partially understood. Recent advances in genomics, transcriptomics, and gene editing technologies have shed light on key molecular mechanisms underlying host susceptibility, quantitative resistance, and potential durable control strategies. In this review, we summarize the biology of powdery mildew fungi infecting cucurbits, the latest findings on pathogen effectors, plant defense signaling, and the genetic basis of resistance. We also discuss novel breeding and biotechnological approaches for durable powdery mildew resistance and outline future directions for integrative disease management strategies. Full article

The WRKY gene family is a widely distributed and highly conserved transcription factor (TF) family in plants, with its members playing key roles in plant growth and development, stress response, and metabolism. Although WRKY TFs have been extensively studied in many plant species, research on the WRKY gene family in Vaccinium bracteatum Thunb. remains limited. Therefore, integrating molecular biology and bioinformatics approaches to further explore the WRKY gene family in V. bracteatum is of considerable scientific importance. In this study, we employed various online tools to obtain genomic and expression data, which were subsequently analyzed to determine the composition, evolutionary relationships, and functions of WRKY family genes in V. bracteatum. A total of 66 WRKY genes (VaWRKY) were identified, named based on homology alignment. Phylogenetic analysis classified the 66 VaWRKYs into three major clades and seven subclades. Sequence and structural analyses of VaWRKY genes provided insights into their evolutionary and functional characteristics. Expression profile analysis revealed significant differences in the expression of 12 VaWRKY genes at various stages of fruit development. Protein interaction analysis further indicated that VaWRKY genes are functionally diverse, playing important roles in stress response, seed germination regulation, and plant growth and development. In summary, we have a deeper understanding of VaWRKY genes, and systematic analysis of structure, evolutionary characteristics, and expression patterns plays an important role in analyzing its biological functions, molecular breeding, and enhancing economic value. Full article

Long non-coding RNAs (lncRNAs) are emerging as crucial regulators of various biological processes in plants, including development, stress responses, and pathogen defense. Advances in multi-omics sequencing analysis and molecular biology methods have significantly expanded our understanding of the plant lncRNA landscape, revealing novel lncRNAs across diverse species. In this review, we provided an overview of the essential roles of lncRNAs in multilevel regulatory functions in plant growth, development, and stress responses. Moreover, we bridged the module network among these different conditions. One of the most important functions of lncRNA is gene expression regulation. Thus, we summarized the plant lncRNAs acting in cis/trans and as endogenous target mimics (eTMs) to influence the expression of target genes in transcription and post-transcription regulation. This review also sheds light on several application values in agricultural production and development of plant-specific databases and bioinformatic tools. These datasets facilitated the exploration of lncRNA function, enabling the identification of their expression patterns, phylogenetic relationships, and molecular interactions. As research progresses, multi-omics approaches will provide deeper insights into the regulatory mechanisms of lncRNAs, offering promising strategies for enhancing crop resilience and productivity in response to climate change. Full article

Climate change, population growth and the increasing demand for food and nutritional security necessitate the development of climate-resilient cereal crops. This requires first gaining mechanistic insights into the molecular mechanisms underpinning plant abiotic and biotic stress tolerance. Although this is challenging, recent conceptual and technological advances in functional genomics, coupled with computational biology, high-throughput plant phenotyping and artificial intelligence, are now aiding our uncovering of the molecular mechanisms underlying plant stress tolerance. Integrating other innovative approaches such as genome editing, modern plant breeding and synthetic biology facilitates the development of climate-smart cereal crops. Here, we discuss major recent advances in plant functional genomic approaches and techniques such as third-generation sequencing, transcriptomics, pangenomes, genome-wide association studies and epigenomics, which have advanced our understanding of the molecular basis of stress tolerance and development of stress-resilient cereals. Further, we highlight how these genomics approaches are successfully integrated into new plant breeding methods for effective development of stress-tolerant crops. Overall, harnessing these advances and improved knowledge of crop stress tolerance could accelerate development of climate-resilient cereals for global food and nutrition security. Full article

Green synthesis of copper oxide (CuO) nanoparticles offers a sustainable alternative to conventional chemical methods that often involve toxic reagents and harsh conditions. This study investigates the use of Tithonia diversifolia, an invasive species in Sri Lanka, as a bioreductant for the eco-friendly fabrication of CuO nanoparticles. Using copper sulfate (CuSO₄·5H₂O) as a precursor, eight treatments were conducted by varying precursor concentration, temperature, and reaction time to determine optimal conditions. A visible color change in the reaction mixture initially indicated nanoparticle formation. Among all the conditions, treatment T4 (5 mM CuSO₄, 80 °C, 2 h) yielded the most favorable results in terms of stability, morphology, and crystallinity. UV-Vis spectroscopic analysis confirmed the synthesis, with absorbance peaks between 265 and 285 nm. FTIR analysis revealed organic functional groups and characteristic metal–oxygen vibrations in the fingerprint region (500–650 cm⁻¹), confirming formation. SEM imaging showed that particles were mainly spherical to polygonal, averaging 125–150 nm. However, dynamic light scattering showed larger diameters (~240 nm) due to surface capping agents. Zeta potential values ranged from −16.0 to −28.0 mV, indicating stability. XRD data revealed partial crystallinity with CuO-specific peaks. These findings support the potential of T. diversifolia in green nanoparticle synthesis, suggesting a low-cost, eco-conscious strategy for future applications. Full article

Stomata, highly specialized structures that evolved on the aerial surfaces of plants, play a crucial role in regulating hydration, mitigating the effects of abiotic stress. Stomatal lineage development involves a series of coordinated events, such as initiation, stem cell proliferation, and cell fate determination, ultimately leading to the differentiation of guard cells. While core transcriptional regulators and signaling pathways controlling stomatal cell division and fate determination have been characterized over the past twenty years, the molecular mechanisms linking stomatal development to dynamic environmental cues remain poorly understood. Therefore, stomatal development is considered an active and compelling frontier in plant biology research. On the one hand, this review aims to provide an understanding of the molecular networks governing stomatal ontogenesis, which relies on the activation and function of the transcription factors SPEECHLESS (SPCH), MUTE, and FAMA; the EPF–TMM and ERECTA receptor systems; and downstream MAPK signaling. On the other hand, it synthesizes current discoveries of how hormonal signaling pathways regulate stomatal development in response to environmental changes. As the climate crisis intensifies, the understanding of the complex interplay between stress stimuli and key factors regulating stomatal development may reveal key mechanisms that enhance plant resilience under adverse environmental conditions. Full article

Plant diseases resulting from pathogens and pests constitute a persistent threat to global food security. Pathogenic infections of plants are influenced by environmental factors; a concept encapsulated in the “disease triangle” model. It is important to elucidate the complex molecular mechanisms underlying the interactions among plants, their pathogens and various environmental factors in the disease triangle. This review aims to highlight recent advancements in the application of systems biology to enhance understanding of the plant disease triangle within the context of microbiome rising to become the 4th dimension. Recent progress in microbiome research utilizing model plant species has begun to illuminate the roles of specific microorganisms and the mechanisms of plant–microbial interactions. We will examine (1) microbiome-mediated functions related to plant growth and protection, (2) advancements in systems biology, (3) current -omics methodologies and new approaches, and (4) challenges and future perspectives regarding the exploitation of plant defense mechanisms via microbiomes. It is posited that systems biology approaches such as single-cell RNA sequencing and mass spectrometry-based multi-omics can decode plant defense mechanisms. Progress in this significant area of plant biology has the potential to inform rational crop engineering and breeding strategies aimed at enhancing disease resistance without compromising other pathways that affect crop yield. Full article

Plants are constantly exposed to environmental stressors such as drought, salinity, and extreme temperatures, which threaten their growth and productivity. To counter these challenges, they employ complex molecular defense systems, including epigenetic modifications that regulate gene expression without altering the underlying DNA sequence. This review comprehensively examines the emerging roles of reactive oxygen species (ROS) and reactive nitrogen species (RNS) as central signaling molecules orchestrating epigenetic changes in response to abiotic stress. In addition, biotic factors such as pathogen infection and microbial interactions are considered for their ability to trigger ROS/RNS generation and epigenetic remodeling. It explores how ROS and RNS influence DNA methylation, histone modifications, and small RNA pathways, thereby modulating chromatin structure and stress-responsive gene expression. Mechanistic insights into redox-mediated regulation of DNA methyltransferases, histone acetyltransferases, and microRNA expression are discussed in the context of plant stress resilience. The review also highlights cutting-edge epigenomic technologies such as whole-genome bisulfite sequencing (WGBS), chromatin immunoprecipitation sequencing (ChIP-seq), and small RNA sequencing, which are enabling precise mapping of stress-induced epigenetic landscapes. By integrating redox biology with epigenetics, this work provides a novel framework for engineering climate-resilient crops through the targeted manipulation of stress-responsive epigenomic signatures. Full article

Trichomes—microscopic appendages on the plant epidermis—play vital roles as both protective barriers and specialized biosynthetic factories. Acting as the first line of defense against environmental stressors, they also produce a wide range of pharmaceutically valuable secondary metabolites. This mini-review highlights recent advances in understanding the development, structure, and function of trichomes, with a focus on glandular secretory trichomes (GSTs) in key species such as Artemisia annua and Solanum lycopersicum. We explore how insights from these systems are driving innovation in plant synthetic biology, including modular genetic engineering and metabolic channeling strategies. These breakthroughs are paving the way for scalable, plant-based platforms to produce high-value compounds. By integrating molecular mechanisms with emerging technologies, this review outlines a forward-looking framework for leveraging trichomes in sustainable agriculture, natural product discovery, and next-generation biomanufacturing. Full article

Redox signaling is central to plant adaptation, influencing metabolic regulation, stress responses, and developmental processes through thiol-based oxidative post-translational modifications (oxiPTMs) of redox-sensitive proteins. These modifications, particularly those involving cysteine (Cys) residues, act as molecular switches that alter protein function, structure, and interactions. Advances in mass spectrometry-based redox proteomics have greatly enhanced the identification and quantification of oxiPTMs, enabling a more refined understanding of redox dynamics in plant cells. In parallel, the emergence of computational modeling, artificial intelligence (AI), and machine learning (ML) has revolutionized the ability to predict redox-sensitive residues and characterize redox-dependent signaling networks. This review provides a comprehensive synthesis of methodological advancements in redox proteomics, including enrichment strategies, quantification techniques, and real-time redox sensing technologies. It also explores the integration of computational tools for predicting S-nitrosation, sulfenylation, S-glutathionylation, persulfidation, and disulfide bond formation, highlighting key models such as CysQuant, BiGRUD-SA, DLF-Sul, and Plant PTM Viewer. Furthermore, the functional significance of redox modifications is examined in plant development, seed germination, fruit ripening, and pathogen responses. By bridging experimental proteomics with AI-driven prediction platforms, this review underscores the future potential of integrated redox systems biology and emphasizes the importance of validating computational predictions, through experimental proteomics, for enhancing crop resilience, metabolic efficiency, and precision agriculture under climate variability. Full article