Jeremy Dale Murray

In animals and plants, the zygotene to pachytene transition of male meiocytes is marked by programmed mRNA degradation. In animals this is essential for meiotic progression, but in plants its role and underlying mechanism remain unknown. Here, we identify the tandem CCCH-type zinc finger proteins C3H14 and C3H15 as central regulators of RNA degradation in the microspore mother cells (MMCs) of Arabidopsis (Arabidopsis thaliana). We show that C3H14/15 are expressed at high levels in MMCs during the zygotene to pachytene transition, where they bind highly expressed mRNAs, including many that encode ribosomal, mitochondrial, and plastid proteins. Loss of C3H14/15 results in the formation of excess DNA:RNA hybrids, genomic instability, failure to progress beyond the pachytene stage of meiosis, and finally DNA degradation and cell death. Moreover, we show that C3H15 accumulates in P-bodies through its interaction with the decapping enzyme DCP1 for RNA degradation. Our findings establish mRNA decay mediated by C3H14/15 as a critical regulatory mechanism safeguarding meiosis in plants, highlighting the convergence of RNA metabolism and genome stability pathways during a key developmental transition.

The specific partnership between legumes and rhizobia relies on a chemical dialogue. Plant flavonoids activate the bacterial transcription factor NodD, which triggers production of Nod factors that are recognized by the plant. Structural studies of the Pisum sativum (pea) symbiont Rhizobium leguminosarum NodD revealed two pockets that are essential for its activation by flavonoids. Comparative studies with NodD1 of Sinorhizobium medicae , the symbiont of Medicago truncatula , revealed that this specificity is determined by the shape of the pocket and by specific amino acids. A chimeric NodD containing the flavonoid recognition residues from S. medicae NodD1 in the R. leguminosarum NodD backbone was sufficient to complement nitrogen fixation in M. truncatula by an S. medicae nodD1 mutant, confirming the critical role of flavonoid recognition in host range.

Nitrate is the primary source of nitrogen for plants in most environments. Nitrate uptake from the rhizosphere into root cells is mediated by Nitrate Transporter 2 (NRT2) and NRT1.1 proteins via proton symport, with the apoplast serving as an intermediate compartment. Using a simple root immersion system, we investigated the effects of NRT transporters on external media pH (pH _med ) and apoplastic pH (pH _apo ) in M. truncatula nitrate transporter mutants. Monitoring of pH _med showed that loss of NRT2.1 largely prevented nitrate induced alkalization of the media, while loss of NRT1.1A/B reduced media alkalization only during the initial stages of nitrate uptake, suggesting they have fundamentally different physiological roles. Use of the pH sensitive dye HPTS showed that the pH _apo of root cells initially decreased during nitrate uptake, and this required NRT1.1A/B. Unexpectedly, the observed changes in pH _med during nitrate uptake in WT and the mutants were not reflected in pH _apo . To explain these discrepancies, we propose a model in which the depletion of protons in the media occurring during nitrate symport is offset by the buffering of protons in the cell wall and the activity of the H ⁺ -ATPase, allowing a lower pH _apo to be maintained. Such a mechanism would enable efficient nitrate uptake across a range of external pH values.

The NIN-like protein 2 (NLP2) transcription factor is highly expressed in the infected cells of the N2 fixation zone of mature nodules in Medicago truncatula. In these cells, NLP2 directly activates the expression of leghemoglobin genes and is required for the full expression of nitrite reductase (NiR). Histological examination of nodules formed under different nitrate regimes revealed that the infected cells of nlp2 display abnormal vacuole morphology under high nitrate (5 mm KNO3). This phenotype is associated with starch accumulation, higher expression of starch biosynthesis genes, and increased levels of nitrite and nitric oxide. A transcriptomic comparison of nlp2 and wild-type nodules across nitrate concentrations revealed that under high nitrate, nlp2 shows lower expression of genes important for hypoxia adaptation, such as alcohol dehydrogenase and pyruvate decarboxylase (PDC), and increased expression of S-nitrosoglutathione reductase (GSNOR), which encodes a key enzyme for nitric oxide homeostasis. These changes in gene expression were associated with lower nodule ATP levels and a higher NAD+/NADH ratio, suggesting that energy metabolism is specifically compromised in nlp2 nodules under high nitrate. Transgenic expression of NiR in the nodules of nlp2-1 mutants grown under high nitrate rescued the vacuole phenotype and restored the expression of GSNOR and PDC to normal levels. Overall, our data indicate a role for NLP2 in the regulation of NiR in N2-fixing cells, suggesting a role for nitrate reduction in nodule energy homeostasis.

Panax quinquefolius is a globally valued medicinal plant rich in bioactive flavonoids, yet the molecular mechanisms underlying their biosynthesis remain poorly understood. In this study, we integrated transcriptomic and metabolomic analyses to investigate tissue-specific flavonoid accumulation and regulatory networks in roots, leaves, and flowers. Metabolomic profiling identified 141 flavonoid metabolites, with flavones, flavonols, and C-glycosylflavones predominantly enriched in aerial tissues (leaves and flowers), while specific glycosides like tricin 7-O-acetylglucoside showed root-specific accumulation. Transcriptome sequencing revealed 15,551–18,946 DEGs across tissues, and the reliability of the transcriptomic data was validated by qRT-PCR. KEGG and GO annotation analyses suggested that these DEGs may play a crucial role in the biosynthesis and metabolism of secondary metabolites. From the DEGs, UGTs and MYB TFs were identified and subjected to correlation analysis. Functional validation through in vitro enzymatic assays confirmed that PqUGT71A1 catalyzes apigenin and naringenin glycosylation at the 7-OH position. Additionally, subcellular localization and yeast one-hybrid assays demonstrated that PqMYB7 and PqMYB13 interact with the PqUGT71A1 promoter and activate its expression.. This study unveils the spatial dynamics of flavonoid metabolism in P. quinquefolius and establishes a MYB-UGT regulatory axis, providing critical insights for metabolic engineering and bioactive compound optimization in medicinal plants.

Understanding how numerous quantitative trait loci (QTL) shape phenotypic variation is an important question in genetics. To address this, we established a permanent population of 18,421 (18K) rice lines with reduced population structure. We generated reference-level genome assemblies of the founders and genotyped all 18K-rice lines through whole-genome sequencing. Through high-resolution mapping, 96 high-quality candidate genes contributing to variation in 16 traits were identified, including OsMADS22 and OsFTL1 verified as causal genes for panicle number and heading date, respectively. We identified epistatic QTL pairs and constructed a genetic interaction network with 19 genes serving as hubs. Overall, 170 masking epistasis pairs were characterized, serving as an important factor contributing to genetic background effects across diverse varieties. The work provides a basis to guide grain yield and quality improvements in rice.