Alternative splicing (AS) of pre-mRNAs promotes transcriptome and proteome diversity and plays important roles in a wide range of biological processes. However, the role of AS in maintaining mineral nutrient homeostasis in plants are largely unknown. To clarify this role, we obtained whole transcriptome RNA sequencing data from rice (Oryza sativa) roots grown in the presence or absence of several mineral nutrients (Fe, Zn, Cu, Mn, and P). Our systematic analysis revealed 13,291 alternatively spliced genes, representing ~53.3% of the multiexon genes in the rice genome. As the overlap between differentially expressed genes and differentially alternatively spliced genes is small, a molecular understanding of the plant9s response to mineral deficiency is limited by analyzing differentially expressed genes alone. We found that the targets of AS are highly nutrient-specific. To verify the role of AS in mineral nutrition, we characterized mutants in genes encoding Ser/Arg (SR) proteins that function in AS. We identified several SR proteins as critical regulators of Zn, Mn, and P nutrition and showed that three SR protein-encoding genes regulate P uptake and remobilization between leaves and shoots of rice, demonstrating that AS has a key role in regulating mineral nutrient homeostasis in rice.-

Salinity is one of the major factors limiting the growth, development, and yield of cotton. Although the mechanisms of cotton tolerance to salt stress have been studied, the regulatory roles and mechanisms of protein kinases and phosphatases in cotton salt response remain poorly understood. Here, we identify Type One Protein Phosphatase 4aD (GhTOPP4aD), belonging to the Type One Protein Phosphatase (TOPP) family, as a negative regulator in cotton salt stress response. To reveal the post-translational modification mechanism by which GhTOPP4aD regulates salt stress response in cotton, phosphoproteome analysis was performed. A total of 6055 phosphoproteins with 12,608 phosphosites were identified. In VIGS-Ctrl plants, there were 935 upregulated and 35 downregulated phosphoproteins, while there were 1026 upregulated and 89 downregulated phosphoproteins in VIGS-GhTOPP4aD plants after NaCl treatment. Moreover, a class of tyrosine kinases responsive to abscisic acid (ABA) was significantly enriched at upregulated, differentially phosphorylated sites that were induced by NaCl in GhTOPP4aD-silenced plants, suggesting that these proteins could be regulated by dephosphorylation mediated by GhTOPP4aD in response to salt stress. Among them, Raf-like Kinase 36 (GhRAF36), FERONIA (GhFER), and Lysin Motif-containing Receptor-like Kinase 3 (GhLYK3) interacted with GhTOPP4aD and their kinase activities were inhibited by GhTOPP4aD. VIGS-GhRAF36, VIGS-GhFER, and VIGS-GhLYK3 plants were sensitive to salt stress, suggesting that these kinases may play important roles in the regulation of cotton salt stress response mediated by GhTOPP4aD. These studies provide new insights into the mechanisms of cotton salt stress tolerance and the potential molecular targets for breeding salt-tolerant cotton varieties.

MicroRNAs (miRNAs) are non-coding, endogenous, small-molecule RNAs. They are involved in cell proliferation, differentiation, apoptosis, and metabolism. Additionally, they play an essential role in the development and progression of various malignancies. Recent research has revealed that miR-18a plays an important role in cancer development. However, its role in lymphoma is not yet fully understood. In this study, we investigated the clinicopathological characteristics and potential functional roles of miR-18a in lymphomas. First, we predicted the potential downstream genes of miR-18a using miRTarBase software and subjected these downstream genes to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses to determine the potential mechanisms of action of these genes. We found that these target genes were closely related to cellular senescence, the p53 signaling pathway, and other signaling pathways. From the predicted downstream target genes, ATM and p53 were selected as the target genes; their deletion in patients with lymphoma was detected using the fluorescence in situ hybridization technique. The results showed that some patients with lymphoma have a deletion of the ATM and p53 genes. In addition, the deletion rates of ATM and p53 were positively correlated with the expression of miR-18a. Next, the expression levels of miR-18a and the deletion rates of ATM and p53 were used for correlation and prognostic analyses with patient clinical information. The findings revealed a significant difference in disease-free survival (DFS) between patients with lymphoma with ATM deletion and those with a normal ATM gene expression (p < 0.001). Moreover, a significant difference in overall survival (OS) and DFS between patients with p53 deletion and those with normal p53 expression was observed (p < 0.001). The results indicate that the deletion of ATM and p53 downstream of miR-18a is closely associated with the development of lymphoma. Thus, these biomarkers may serve as key prognostic biomarkers for lymphomas.