Stress biology最新文献

Understanding plant-pathogen interactions requires a systems-level perspective that single-omics approaches, such as genomics, transcriptomics, proteomics, or metabolomics alone, often fail to provide. While these methods are informative, they are limited in their ability to capture the complexity of the dynamic molecular interactions between host and pathogen. Multi-omics strategies offer a powerful solution by integrating complementary data types, enabling a more comprehensive view of the molecular networks and pathways involved in disease progression and defence. Although technological advances have made omics analyses more accessible and affordable, their integration remains underutilised in plant science. This review highlights the limitations of single-omics studies in dissecting plant-pathogen interactions and emphasises the value of multi-omics approaches. We discuss available computational tools for data integration and visualisation, outline current challenges, including data heterogeneity, normalisation issues, and computational demands, and explore future directions such as the exploitation of artificial intelligence-based approaches and single-cell omics. We conclude that the increasing accessibility and affordability of omics analysis means that multi-omics strategies are now indispensable tools to investigate complex biological processes such as plant-pathogen interactions.

Asian soybean rust, caused by Phakopsora pachyrhizi, is a devastating fungal disease threatening global soybean production, particularly in tropical regions where chemical control is increasingly unsustainable. This study employed cutting-edge 4D-DIA proteomics to investigate molecular defense mechanisms in resistant (SX6907) and susceptible (Tianlong 1) soybean cultivars during early infection (12 hpi and 3 dpi). We identified 12,852 proteins, with 1,510 differentially expressed proteins (DEPs) revealing genotype-specific responses. Resistant plants exhibited sustained upregulation of immune receptors (CRKs, LRR-RLKs), MAPK signaling components, and cell wall reinforcement proteins (peroxidases, XTHs), alongside dynamic modulation of calcium signaling and ROS homeostasis. These patterns suggest key pathways enriched in resistance may include phenylpropanoid biosynthesis, isoflavonoid production, and ER stress responses, while susceptible plants showed suppression of photosynthesis and defense pathways. Weighted Protein Co-expression Network Analysis(WPCNA) highlighted co-expression modules linked to resistance, potentially including NLR-mediated effector-triggered immunity. Crucially, DIR proteins and organelle-specific defense hubs (e.g., chloroplasts, nuclei) were implicated in rust resistance. Validation by qPCR confirmed concordance for 84% of tested DEPs. Our findings provide a protein-level blueprint of soybean rust resistance, identifying candidate targets for marker-assisted breeding and genetic engineering to develop durable resistant varieties, reducing reliance on fungicides.

Gayal (Bos frontalis) an endangered bovine species inhabitingChina, India, Bangladesh, Myanmar and Bhutan, has a mysterious evolutionary origin. Shaped by natural selection, its unique traits make it a valuable genetic resource; however, its populations are rapidly declining. In this study, comprehensive whole-genome resequencing of fifty-eight samples of Gayal from China, India, Myanmar and Bangladesh was performed. We identified over 44 million SNPs across four Gayal populations. Nucleotide diversity analysis revealed variations in genetic diversity, with the lowest occurring in India and the highest occurring in China. Phylogenetic tree analysis revealed three distinct clades representing China, India and Bangladesh-Myanmar, which were further confirmed by principal component and admixture analyses. The genetic exchanges between Gayal and other bovine species indicate limited influence from domestic cattle in both the Chinese and Bangladeshi Gayal populations. Mitochondrial DNA sequences and a phylogenetic tree highlighted the unique mitochondrial genome of Gayal. Genome-wide selection signals pinpointed candidate genes linked to mitochondrial function, immunity, musculoskeletal development, reproduction and growth performance. Distinct haplotype patterns emerged for the CCDC157, KIAA0753 and MTFP1 genes in the Chinese and Bangladesh-Myanmar Gayal populations, indicating artificial selection in the Chinese population. KEGG pathway and gene ontology enrichment analyses provided insights into processes related to neurodevelopment, cardiac function, tissue growth, immunity and metabolism. In summary, our study enhances our understanding of Gayal genetics, population structure and selection signals across four countries. This knowledge is crucial for conserving this endangered species amid its rapid decline.

Modification of proteins by ubiquitin is a dynamic and reversible process. It is unclear whether rice stripe virus (RSV) can modulate the plant deubiquitination pathway. In this study, we found that RSV infection can specifically upregulate the expression of the deubiquitinase NbUBP16. Further analysis revealed that NbUBP16 stabilizes serine hydroxymethyltrasferase (SHMT1) by binding to NbSHMT1 and removing its polyubiquitination modification mediated by E3 ligase MEL, which inhibits downstream SHMT1-mediated ROS accumulation and thereby facilitates RSV infection. Our findings provide new insights into the molecular arms race between pathogens and plants, demonstrating how a plant virus can undermine plant defenses by hijacking host deubiquitination pathways.

As a barrier between the cell and its environment, the plant cell wall provides structural support during development and stress response. Plants are able to sense their surroundings and adjust their activities accordingly. A crucial mechanism involved in these adaptive changes is the cell wall integrity (CWI) maintenance mechanism, which monitors and maintains the integrity of cell walls via changes in cell and cell wall metabolism without destroying cell wall organization. Different abiotic stresses and changes in plant developmental phases disrupt CWI. However, emerging evidence has demonstrated the initiation of CWI signaling mechanisms as key in promoting plant growth in complex situations. This review discusses recent advances in the Catharanthus roseus receptor-like kinase 1-like (CrRLK1L) protein function in plant cell wall signaling during adaptation to changing environments and development. We conclude by highlighting how current spatially resolved transcriptomics may be used to advance the role of CrRLK1L members in plant cell wall signaling during development and stress response.

Sheath blight (ShB), caused by the necrotrophic fungus Rhizoctonia solani, is a globally destructive rice disease responsible for significant yield losses. However, the absence of characterized genes conferring high potential resistance to sheath blight within natural rice germplasm constrains resistance breeding. A recent study published in Nature Genetics uncovered the ShB resistance receptor-like kinase 1 (SBRR1) as a key gene associated with disease resistance. SBRR1-R, an elite resistance allele mainly presented in indica rice and distinguished by a 256-bp promoter insertion, confers strong resistance without obvious yield penalty. SBRR1 is the first gene with major effects underlying natural variation in sheath blight resistance, offering significant potential for rice breeding. Furthermore, the discovery of the "bHLH57-SBRR1-R-SIP1-Chit3/4" defense module provides fundamental insights into rice immunity and a molecular module with substantial breeding potential.

Heavy metal pollution severely impacts plant health by inhibiting growth, photosynthesis, enzyme activities, and causing oxidative stress. Plants respond to such stress by activating complex defense mechanisms involving reactive oxygen species and different signaling pathways. These pathways are pivotal in triggering plant defense responses and are currently a major focus of research. Understanding the complex mechanisms of heavy metal uptake, transport, chelation, and signaling can guide strategies to improve plant resilience and stress tolerance. In this review, we aim to highlight the key heavy metals found in soil and the environment, along with their mechanisms of accumulation in plants. We also explore the defense responses of plants through various signaling pathways such as calcium (Ca²⁺), MAP kinase, and hormone signaling. Additionally, we emphasize the importance of understanding advanced omics technologies, including transcriptomics, metabolomics, and bioinformatic tools, in enhancing our knowledge of plant resilience and stress tolerance.

Plant cells exhibit an extraordinary regenerative potential, achieving cellular totipotency by dedifferentiating to form new tissues. While significant progress has been made in understanding cell fate mechanisms, the regulatory networks governing callus cell development remain insufficiently explored, particularly regarding cell classification, morphology, and regulatory processes. This study provides a detailed investigation into the developmental dynamics and transcriptomic profiles of callus cells in Arabidopsis at key stages: initiation, proliferation, and greening. Employing single-cell RNA sequencing and UMAP-based clustering, we annotated cell clusters based on highly enriched gene expressions. Developmental trajectories were further mapped through pseudotime analysis, revealing distinct transcription factor networks. Additionally, functional analysis of key regulatory genes was conducted using mutant and overexpression lines, affirming their roles in callus development. Gene Ontology analysis highlighted the involvement of environmental factors-low oxygen and salinity promoted callus formation, while light inhibited it, though essential for greening. These findings shed light on the complex regulatory landscape of plant tissue regeneration and guide future research avenues.

Understanding the genetic mechanism of cold adaptation in cashmere goats and dairy goats is very important to improve their production performance. The purpose of this study was to comprehensively analyze the genetic basis of goat adaptation to cold environments, clarify the impact of environmental factors on genome diversity, and lay the foundation for breeding goat breeds to adapt to climate change. A total of 240 dairy goats were subjected to genome resequencing, and the whole genome sequencing data of 57 individuals from 6 published breeds were incorporated. By integrating multiple approaches such as phylogenetic analysis, population structure analysis, gene flow and population history exploration, selection signal analysis, and genome-environment association analysis, an in-depth investigation was carried out. Phylogenetic analysis unraveled the genetic relationships and differentiation patterns among dairy goats and other goat breeds. Through signal analysis (θπ, FST, XP-CLR), we identified numerous candidate genes associated with cold adaptation in dairy goats (STRIP1, ALX3, HTR4, NTRK2, MRPL11, PELI3, DPP3, BBS1) and cashmere goats (MED12L, MARC2, MARC1, DSG3, C6H4orf22, CHD7, MYPN, KIAA0825, MITF). Genome-environment association (GEA) analysis confirmed the link between these genes and environmental factors. Moreover, a detailed analysis of the critical genes C6H4orf22 and STRIP1 demonstrated their significant roles in the geographical variations of cold adaptation and allele frequency differences among different breeds. This study contributes to understanding the genetic basis of cold adaptation, providing crucial theoretical support for precision breeding programs aimed at improving production performance in cold regions by leveraging adaptive alleles, thereby ensuring sustainable animal husbandry.

Nucleotide-binding leucine-rich repeat (NLR) proteins assemble into genetically linked pairs to mediate effector-triggered immunity (ETI) in plants. Here, we characterize the paired NLRs NRCX and NARY (NRCX adjacent resistance gene Y) in Nicotiana benthamiana. CRISPR/Cas9 knockout of NRCX caused severe dwarfism and constitutively activated immunity, marked by PR1 upregulation and enhanced resistance to Phytophthora capsici. Co-silencing or double knockout of the adjacent NLR NARY partially rescued the nrcx phenotype, revealing NARY as a compensatory regulator that modulates growth and immunity. Structural analysis revealed that NARY harbors non-canonical Walker B and MHD motifs, which lack autoactivation capacity despite their divergence from canonical NLR executors. Split-luciferase and co-immunoprecipitation assays showed that NRCX and NARY interact exclusively through their CC domains, forming a non-canonical regulatory complex. Notably, simultaneous silencing of NRC2/3 and NARY incompletely restored growth in nrcx mutants, implicating additional factors in immune modulation. Our findings establish NARY as a compensatory NLR partner of NRCX that fine-tunes immunity without triggering cell death, revealing a novel mechanism for balancing growth and defense in Solanaceae.