Journal of Experimental Botany最新文献

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.

Cyanobacteria rely on bicarbonate (HCO3-) as the primary inorganic carbon (Ci) source for photosynthesis in aquatic environments. To use this Ci source, cyanobacteria employ CO2 concentrating mechanisms that elevate cytoplasmic HCO3- via plasma membrane transporters, enhancing carboxylation by carboxysomal Rubisco. The sodium-dependent SbtA1 transporter family is well-characterized in freshwater cyanobacteria, but the related SbtA2 family, prevalent in marine α-cyanobacteria, remains uncharacterised. Here, we report functional characterisation of SbtA2 homologues from marine Synechococcus spp., which exhibit high Ci uptake flux with apparent chloride dependence and intermediate HCO3- affinity (K0.5 ≈ 150 µM), when assessed in E. coli. SbtA2 achieved internal Ci accumulation up to 24 mM within 30 seconds. Co-expression with the putative regulator SbtB2 reduced uptake activity, suggesting a regulatory role for this protein. These findings indicate that SbtA2 transporters contribute significantly to carbon acquisition in marine cyanobacteria. Given potential to enhance CO2 supply to Rubisco in C3 plants, we targeted SbtA2 to the tobacco chloroplast inner envelope membrane; however, this did not improve photosynthesis or growth. Our results highlight the functional diversity of cyanobacterial Ci transporters and suggest that additional components may be required for effective transfer of such systems into plant chloroplasts.

Flowering is a critical trait for reproduction and survival in plants, influenced by both temperature and photoperiod. Here, we explored the molecular basis of temperature- and photoperiod- insensitive flowering in the Arabidopsis natural accession IP-Svi-0. We identified genetic variations underlying the early flowering of IP-Svi-0 using whole-genome and RNA sequencing and verified them by generating transgenic plants that complemented or silenced the responsible genes. The complete insensitivity of IP-Svi-0 to temperature and photoperiod is due to its unique combination of polymorphisms at loci encoding floral repressor genes FLOWERING LOCUS C (FLC) and MADS AFFECTING FLOWERINGs (MAFs). Our data revealed that IP-Svi-0 carries large deletions in FLC, MAF2, and MAF3, resulting in gene knockouts. It also harbors promoter polymorphisms in FLM and MAF5, leading to reduced gene expression. This misregulation of the FLC-MAFs module causes de-repression of the floral activators FT and SOC1, resulting in unregulated early flowering. Flowering-time analysis showed that the fck (silenced MAF2-5 with flc flm mutations) phenocopies IP-Svi-0, and restoring FLC, MAF2, or MAF3 effectively delays its early flowering. Our findings indicate that temperature and photoperiod signals are integrated into the FLC-MAFs regulatory module to control flowering time in natural accessions. These results suggest a promising strategy to overcome seasonal barriers to flowering.

Inorganic nitrogen (N) is known to influence the composition and functioning of ectomycorrhizal (ECM) fungal communities. Research consistently highlights fungal traits related to carbon (C) use as key determinants of fungal sensitivity to elevated inorganic N, with more C-demanding ECM fungi declining along inorganic N gradients. This decline is often attributed to reduced C allocation from host trees to their fungal symbionts, yet the precise mechanisms underlying this reduction remain unclear, despite significant research efforts. Here, I examine recent advances in this field which highlight the role of fungal nutritional requirements and source-sink dynamics in regulating C flow to ECM fungi. Additionally, I explore how N-induced shifts in ECM fungal communities impact biogeochemical cycles, potentially leading to globally significant changes in decomposition and C-sequestration rates in forest soils. Given the scale of these potential effects, further research is essential to fully understand the complexity of N-driven changes in ECM fungal functioning.

The role of stems as a source of nitrogen (N) for the growing seeds has received little attention in soybean. This study evaluated N storage and mobilization from stems to seeds across 42 high-yielding environments under contrasting N supply: a "zero-N" treatment, in which crops relied on soil and biological N fixation, and a "full-N" treatment that received ample N fertilizer. We measured the accumulated N per organ before seed filling and subsequent N mobilization from vegetative organs to the seed. Vegetative storage protein (VSP) abundance in stems was quantified via proteomics. Average yield ranged from 4.2 to 7.3 Mg ha-1, with +11% yield in full-N (6.1 Mg ha-1) compared to zero-N (5.5 Mg ha-1). The full-N treatment resulted in a larger mobilized N from stems (+42%) and leaves (+22%) to seeds than the zero-N treatment, which was attributed to the larger N stored in stems and leaves before seed filling (+37% and +21%, respectively). Among the 5,335 identified proteins at the peak of N accumulation, VSPα (+1.4%) and VSPβ (+0.8%) showed the highest increase in full-N. We conclude that N stored in stems as VSPs before seed filling plays a key role in meeting the seed N demand in high-yielding soybean crops.