Sulfur Homeostasis in Rice as a Dynamic Regulatory Network: Functional Genomics, Metabolic Crosstalk, and miR395-Mediated Control.

Functional Genomics of Sulfur Metabolism in Rice: Insights From Transgenic and MicroRNA‐Based Strategies

Sulfur (S) is an essential macronutrient that plays critical roles in plant growth, redox homeostasis, stress adaptation, and immunity. In rice (Oryza sativa), sulfur deficiency is becoming increasingly common due to modern agricultural practices, yet the molecular regulation of sulfur metabolism remains incompletely understood. Recent advances in functional genomics have provided new insights into the mechanisms governing sulfur uptake, transport, assimilation, and downstream metabolic regulation. This review synthesizes current knowledge of sulfur metabolism in rice, with particular emphasis on transgenic and microRNA‐based approaches. We discuss the functions of sulfate transporters, sulfur assimilation enzymes, and sulfur‐containing metabolites such as glutathione in regulating sulfur homeostasis, redox balance, and stress responses. Particular attention is given to the conserved miR395 regulatory module, which coordinates sulfur assimilation and allocation through posttranscriptional regulation of ATP sulfurylase genes. Evidence from functional genomics studies demonstrates that sulfur metabolism is closely integrated with redox signaling, stress tolerance, and plant immunity. Collectively, these findings support a view of sulfur metabolism as a dynamic regulatory network rather than a linear nutrient‐assimilation pathway. We further highlight key knowledge gaps, emerging research opportunities, and future directions for applying functional genomics to improve sulfur use efficiency and resilience in rice. This review provides a framework for advancing both the fundamental understanding and translational application of sulfur metabolism in sustainable rice production.

Sulfate starvation response modules connect sulfur metabolism to photorespiration and photosynthesis

SUMMARY Mineral nutrients are essential for plant growth and development. Sulfur (S), as a macronutrient, is incorporated into numerous critical S‐containing metabolites that play key roles in mitigating both abiotic and biotic stresses. Understanding how plants regulate S homeostasis and integrate it with other physiological processes is crucial for developing crops that can better withstand environmental challenges. Here, we demonstrate that the conserved sulfate starvation transcriptional response across Arabidopsis, tomato, rice, and Setaria is limited to only seven genes. We further characterize the roles of two of these genes, PYD4 (PYRIMIDINE 4) and MGL (METHIONINE GAMMA‐LYASE), in S metabolite regulation and the sulfate starvation response. Our genetic and biochemical analyses show that PYD4 is embedded within the S starvation network, positively regulating transcript levels of key S‐marker genes, including four of the seven conserved genes across these species, and serving as an integrator of S metabolism and photorespiration. MGL also positively regulates S‐marker genes, while additionally modulating diverse processes under sulfate starvation, such as photosynthesis and oxidoreductase homeostasis. Notably, MGL‐deficient lines fail to respond adequately to sulfate starvation and exhibit impaired mechanisms for maintaining photosynthetic efficiency. Overall, our findings indicate that the S starvation response is deeply embedded within primary plant metabolism. Disruption of its regulators alters metabolism at multiple levels, affecting traits central to crop improvement, such as photorespiration and photosynthesis.

A factorial multi-layer analysis reveals non-additive sulfur-iron interactions shaping metabolic and transcriptional responses in durum wheat.

Reciprocal iron-sulfur regulation in durum wheat converges on a few metabolic hubs that integrate nutrient status with plant growth and performance. Iron and sulfur availabilities were factorially modulated in hydroponically grown wheat to establish how each nutrient and their interaction shape growth, ionome, amino acid and organic acid metabolism, and the expression of key S- and Fe-homeostasis genes. Sulfur availability strongly shaped plant responses to iron availability, determining biomass allocation, ionomic patterns, and the expression of sulfate transporters, sulfur-assimilatory enzymes, and iron homeostasis genes. Metabolomics highlighted citrate, O-acetylserine, and methionine as root metabolites most consistently associated with combined Fe × S treatments. Correlation analysis linked these variables with markers of sulfate transport and assimilation, defining a reproducible interaction signature across biological layers. Sulfur deficiency, especially when combined with low iron, also increased free asparagine accumulation in vegetative tissues, indicating a strong reallocation in nitrogen metabolism under dual stress. Sulfur availability is a major modulator of iron-responsive phenotypic, transcriptional, and metabolic traits in durum wheat and provides a systems-level framework for future functional studies of Fe/S crosstalk.

Transcriptome Reversal in Sulfate Transporter Involves Abiotic Stress in Sesuvium portulacastrum L.

Sulfur is an essential nutrient involved in plant growth, redox regulation, and responses to environmental stresses. Sulfate transporters (SULTRs) control sulfate uptake and distribution, thereby affecting sulfur availability for metabolic processes and stress adaptation. However, the characteristics and stress-responsive functions of SULTRs in the halophyte Sesuvium portulacastrum remain unclear. In this study, we identified and characterized the SULTR family in S. portulacastrum through phylogenetic analysis, gene structure comparison, conserved motif analysis, promoter characterization, synteny analysis, and expression profiling. A total of 22 SpSULTRs were identified and classified into three subfamilies. Most SpSULTRs contained conserved Sulfate_transp and STAS domains and were predicted to localize to the plasma membrane. Transcriptome analysis combined with qRT-PCR validation revealed that SpSULTRs displayed diverse tissue-specific expression patterns under salt, cadmium, and copper stresses. Of these, SpSULTR3;1 and SpSULTR3;2 showed strong responses to salt stress and were mainly expressed in leaves. Protein interaction predictions suggested that these two transporters may be associated with sulfur assimilation, antioxidant metabolism, and stress-related pathways. These results reveal the structural diversification and stress-responsive characteristics of the SULTR family in S. portulacastrum and provide a basis for further investigation of sulfur transport mechanisms underlying halophyte adaptation.

Genome-wide identification, evolutionary dynamics, and abiotic stress response networks of the magnesium transporter gene family in foxtail millet (Setaria italica L.)

Magnesium (Mg²+) is an essential mineral nutrient for plant growth, playing a pivotal role in chlorophyll biosynthesis, enzyme activation, photosynthesis, and ion homeostasis. The magnesium transporters (MGTs) from the CorA/MRS2-ALR superfamily are crucial for Mg²+ uptake, translocation, and subcellular compartmentalization. Foxtail millet (Setaria italica L.), recognized as a drought-tolerant C4 cereal with a streamlined genome and robust environmental adaptability, presents an optimal model for investigating stress resilience and C4 photosynthesis. To date, the MGT gene family in foxtail millet has not been characterized. In this study, we identified nine SiMGT genes (SiMGT1–SiMGT9) through comprehensive genome-wide screening. These genes are distributed unevenly across chromosomes 4, 5, 7, and 9. Each SiMGT possesses conserved CorA domains and displays unique physicochemical attributes and subcellular localization patterns. Phylogenetic assessments categorized the SiMGTs into five distinct groups, indicating a close evolutionary relationship with graminaceous crops such as rice, maize, and sorghum, and suggesting functional conservation. Expression profiling highlighted that SiMGT1, SiMGT3, SiMGT6, SiMGT7, and SiMGT8 are consistently highly expressed. Notably, SiMGT7 is predominantly expressed in leaves, suggesting a potential association with leaf-related or photosynthesis-associated processes, while SiMGT6 shows preferential expression in panicles, indicating a possible role in reproductive development. When subjected to drought, low temperature, salinity, and ABA treatments, the SiMGTs exhibited varied temporal response patterns: SiMGT7 and SiMGT9 showed relatively strong responses to drought and cold stress; SiMGT2 responded prominently to salt treatment; and SiMGT1, SiMGT2, and SiMGT3 were rapidly induced at the early stage of ABA treatment. Haplotype analysis pinpointed superior haplotypes (Hap1) of both SiMGT6 and SiMGT7, which showed significant associations with panicle yield traits and stress-related traits, respectively. These findings provide insights into the evolutionary characteristics and expression divergence of the SiMGT family and offer candidate genes and molecular markers for future functional studies and the genetic improvement of foxtail millet.

GmHMGR6 enhances salt stress tolerance in soybean through modulation of nitrogen metabolism