Journal of Experimental Botany最新文献

Alternative splicing (AS) of precursor mRNAs (pre-mRNAs) constitutes a major means to increase transcriptome complexity in higher eukaryotes and critically contributes to the re-programming of gene expression in response to internal and environmental signals. Technological advances have enabled us to determine transcriptome-wide AS patterns at unprecedented accuracy, depth, and throughput. Furthermore, powerful tools for examining the regulatory mechanisms underlying AS decisions have been successfully established for plants, including methods for profiling the in vivo interaction landscape of splicing regulatory proteins with their target pre-mRNAs. Combining these novel approaches with functional studies of individual AS events identified many critical components of the plant splicing code, consisting of cis-regulatory elements on the pre-mRNA and trans-acting factors, such as splicing regulatory proteins. Their concerted action affects splice site selection by the spliceosome, thereby generating highly dynamic and complex AS outputs. Here, we will review our current knowledge of AS regulation by RNA sequence and structural motifs in cis and networks of trans-acting splicing regulators. We will also discuss how, despite overall low complexity of the target motifs for binding of splicing regulators and their often-redundant functions, high levels of precision and specificity in AS can be achieved.

Effectors are small molecules secreted by microbial pathogens that disrupt host basal functioning and responses during infection by targeting various plant susceptibility factors. This study reports a candidate selection approach for identifying novel, potential plant nuclear localized effectors from Fusarium graminearum secretory proteins. From a dataset of core secretory proteins conserved across several Fusarium strains, candidates were selected based on predicted nuclear localization, structural characteristics, and expression profiles during infection. Transient expression in Nicotiana benthamiana confirmed accumulation in the plant nucleus, that were further confirmed in wheat protoplasts. One of these proteins was selected for yeast two-hybrid (Y2H) screening to identify wheat protein targets, using a Fusarium-infected wheat spike cDNA library specifically generated for this study. The screening identified a high confident interaction with a nuclear-localized wheat beta-amylase 2. The structural modeling of the protein complex between beta-amylase 2 and the putative effector was used to predict interacting amino acid residues and informed a deletion analysis to disrupt the interaction. This research identifies a Fusarium graminearum secretory core protein that interacts with a conserved wheat beta-amylase 2, showcasing a method to select pathogenicity factors conserved across multiple pathogens and host plants, with implications for developing broad-spectrum resistance strategies.

Genomic Selection (GS) has revolutionised breeding programs by enabling the prediction of phenotypes based on genetic data. However, GS often only explains a portion of the phenotypic variation. This review paper explores the potential of integrating various data types beyond genomics to enhance the prediction ability of phenotypes. The paper categorises data integration strategies into five categories: eliminate, facilitate, aggregate, incorporate, and modulate. Eliminating refers to removing the effect of non-genomic data on the phenotype, such as environmental data. Facilitating methods leverage non-genomic data to improve the accuracy of GS models. Aggregating approaches combine different data types for analysis, potentially revealing variation components not captured by individual data sources. Incorporation focuses on explicitly modelling interactions between data types. Modulating methods transform data into formats suitable for advanced models like deep learning convolutional neural networks (CNNs). The review discusses the advantages and limitations of each strategy, providing a comprehensive overview of the current state of the field. The paper concludes by emphasising the prospects of multi-data phenotypic prediction toward the development of a holistic prediction approach that facilitates a more comprehensive understanding of complex biological systems and significantly enhances prediction accuracy.

For many people, the culture of plant science, and science more broadly, can feel alienating and intimidating, which often leads to them leaving the discipline for other opportunities. However, studies show that there is a correlation between creative problem solving and increased diversity, and plant science cannot afford to lose talented individuals. Here we report on strategies to promote diversity, inclusion, and a sense of belonging for all within plant science. We address ways that institutions, organizations, communities, educators, and individuals can contribute to this needed cultural change. We urge all plant scientists to participate in these efforts; for each other, for the discipline, and for the future.

Alternative splicing (AS) represents a pivotal post-transcriptional regulatory mechanism, profoundly expanding proteomic diversity and functional complexity by enabling single genes to generate multiple mRNA isoforms. In plants, AS serves as a survival toolkit, dynamically modulating stress-responsive signaling pathways, transcriptional networks, and protein functional specialization to optimize environmental fitness. Recent advances in high-throughput sequencing technologies and computational tools have significantly deepened our understanding of AS regulation in plants. Notably, breakthroughs such as long-read transcriptome sequencing and single-cell RNA analysis have revolutionized the resolution at which we can characterize AS landscapes. These developments have collectively illuminated the critical role of AS in mediating plant responses to diverse abiotic stresses, including drought, salinity, and extreme temperatures. The resulting discoveries have opened transformative avenues for crop improvement through precision manipulation of splicing patterns. Innovative strategies such as CRISPR-Cas9-based splice editing and engineered SFs now provide powerful platforms for developing climate-resilient, high-yielding crop varieties with enhanced stress tolerance and nutritional quality. This review systematically examines the molecular mechanisms underlying AS-mediated plant stress responses, and cutting-edge applications of AS engineering in precision agriculture. By synthesizing fundamental insights with biotechnological innovations, we highlight the transformative potential of AS manipulation in addressing the pressing global agricultural challenges.

Phytochrome (phy) A and phyB are red and far-red photoreceptors that play essential roles in modulating seed germination. Despite extensive research on the roles of hormones and light signaling, the metabolic characteristics of phytochromes during the red-light-mediating seed germination remain largely unknown. Using high-throughput non-targeted metabolomics, this study profiled Arabidopsis seeds including the wild-type (Col-0), single mutants (phyA-211, phyB-9), double mutant phyAB, and the pifq mutant during red-light-induced germination, and identified a total of 164 metabolites linked to primary and secondary metabolism. Comparative analysis of the metabolome revealed that the levels of flavonols including quercetin, kaempferol and relevant glycosides were increased in phyA-211, decreased in Col-0 and phyB-9, and exhibited less change in phyAB, demonstrating that phyA and phyB antagonistically regulate flavonoid biosynthesis. Flavonoid biosynthesis was upregulated in pifq under red light. Exogenous quercetin and kaempferol treatment modestly inhibited Col-0 and pifq seed germination. Taken together, these results unveil the comprehensive metabolic networks, highlight the flavonoid metabolism under red light, and elucidate the synergistic and antagonistic roles of phyA and phyB in regulating seed metabolism. This study provides novel insight into the functional mechanisms of flavonoid metabolism and light signaling in plant development.

Growing evidence indicates that extracellular self-DNA (sDNA) acts as a damage-associated molecular pattern (DAMP) that elicits protective responses in conspecific plants. However, the mechanism by which plant senses or recognizes sDNA to initiate pattern-triggered immunity (PTI) remains unclear. In citrus fruit, sDNA treatment induced PTI responses, accompanied by jasmonic acid (JA)-dependent defense and reduced susceptibility to the fungus Penicillium digitatum. DNA methylation profiling showed that P. digitatum infection increased methylation genome-wide, whereas sDNA treatment reduced it extensively. Corresponding differentially methylated regions (DMRs) were significantly enriched in genes involved in the plant-pathogen interaction pathway. Notably, sDNA reduced the DNA methylation level of a critical LRR-RLK gene, CsSOBIR1, maintaining its high expression during P. digitatum infection. The subsequent interaction between CsSOBIR1 and CsRLP7 facilitated sDNA recognition, triggering PTI responses and activating the downstream CsMAPKKK1-CsMAPKK2-CsMAPK4 cascade along with JA signaling. The sDNA-induced DNA demethylation was associated with the upregulation of several demethylase-encoding genes, including CsDML1.1, CsDML1.2, and CsDME. Consistently, treatment with the DNA methylation inhibitor 5-azacytidine (5'-Aza) enhanced citrus resistance to fungal infection, supporting the positive correlation between sDNA-mediated demethylation and immune response. These findings suggest that DNA demethylation is an important epigenetic component of sDNA-mediated signaling that potentiates PTI-associated defenses in citrus fruit.

Post-translational modifications (PTMs) of key transcription factors constitute important switches that shape protein function and, consequently, signal transduction and cellular responses. Seed germination and seedling establishment are complex traits regulated by PTMs, which converge on key molecular devices such as the bZIP transcription factor ABI5. The latter represents a molecular hub in the abscisic acid (ABA) signaling pathway, which represses seed germination and seedling establishment. ABI5 is post-translationally modified by nitric oxide (NO) through Cys153-specific S-nitrosylation (SNO), leading to its degradation. Despite the physiological effects of redox-sensitive proteins, the specificity and molecular mechanisms underlying this type of regulation during seed germination and post-germination developmental checkpoints remain unknown. Here we show the effect of the redox environment on the formation of ABI5 complexes, emphasizing the relevance of Cys153. In addition, the mutation of this key residue and the phosphorylation status influence the subcellular localization of ABI5. Recent research points to the reversibility of redox-mediated modifications through the action of redoxins. We establish an enzymatic system underlying the reversibility of SNO mediated by thioredoxin h5 (TRXh5). Furthermore, seeds overexpressing the redoxins ROXY10 and ROXY21 show a dysregulation in germination and in the accumulation of the ABI5 protein. These results provide a physiological link between redox regulation and the ABA signaling pathway through the control of ABI5, which is crucial for a successful seedling establishment.

Glutathione S-transferases (GSTs) participate in diverse stress responses, but their function in heat responses remains poorly understood. Two rice varieties differing in heat tolerance, Yongyou15 (YY15) and Y-Liangyou1 (YLY1), were subjected to heat stress during anthesis. YY15 exhibited higher spikelet fertility than YLY1 under heat stress, primarily due to superior pollen germination on the stigma, enhanced pollen tube growth within the pistil, and lower reactive oxygen species (ROS) levels in the pistil. Transcriptome analysis and physiological assessments revealed that GSTs, glutathione (GSH), proanthocyanidins (PAs), and fructose (Fru) play pivotal roles in mediating the heat tolerance differences between the varieties. Specifically, these factors confer heat tolerance by maintaining ROS homeostasis. Exogenous GSTs enhancers, myristic acid (MA) and fulvic acid (FA), significantly improved spikelet fertility, GSTs activity, pollen germination, and pollen tube growth. They also substantially increased GSH content, PAs levels, Fru content, and antioxidant capacity, while concurrently reducing ROS levels. Conversely, application of the GSTs inhibitor ethacrynic acid reversed these beneficial effects. Importantly, exogenous application of FA, PAs, or Fru-either individually or in combination-significantly enhanced spikelet fertility under heat stress. This indicates that GSTs, mediating GSH, play a crucial role in preventing heat-induced pistil dysfunction through the PAs and Fru pathways.

Dehydration-Responsive Element-Binding (DREB) transcription factors play an important role in plant responses to drought. DREB subfamily A4, contains a sub-group named TINY. Previous studies in Arabidopsis suggest that TINYs suppress plant growth and mediate abscisic acid (ABA)-induced stomatal closure. In this study, we investigated the function of the tomato drought-induced TINY1. Under drought conditions, tiny1 mutant lost turgor and wilted more rapidly than control M82 plants. However, this sensitivity was attributed to its larger leaf area, rather than intrinsic differences in drought response. Measurements of stomatal conductance, leaf temperature, and osmotic adjustment revealed no significant differences between tiny1 and M82. Furthermore, whole plant daily transpiration of M82 and tiny1 with similar leaf area, showed no differences. Interestingly, the growth-promoting effect of tiny1 was confined to early developmental stages; enhanced embryo growth and hypocotyl elongation, and accelerated emergence of the first true leaves-trait that later contributed to increased leaf area. At later stages, the mutation had no observable impact on growth rate. Our results show increased gibberellin (GA) activity in the mature tiny1 embryo and suggest that TINY1 suppresses embryonic growth by repressing GA biosynthesis through downregulation of GA 20-oxidase 4 (GA20ox4) gene expression.