The PPR-Domain Protein SOAR1 Regulates Salt Tolerance in Rice

K, Padaria JC, Singh PK, Alam B, Kumar S, Arunachalam A. Validation of stay-green and stem reserve mobilization QTLs: physiological and gene expression approach

Introduction

Abiotic stress significantly reduces the wheat yield by hindering several physiological processes in plant. Stay-green (SG) and stem reserve mobilization (SRM) are the two key physiological traits, which can contribute significantly to grain filling during stress period. Validation of genomic regions linked to SG and SRM is needed for its subsequent use in marker-assisted selection in breeding program.

Methods

Using a physiological and gene expression approach, quantitative trait loci (QTLs) for stay-green (SG) and stem reserve mobilization (SRM) were validated in a pot experiment study using contrasting recombinant inbred lines including its parental lines (HD3086/HI1500) in wheat. The experiment was laid down in a completely randomized design under normal (control, drought) and late sown (heat and combined stress) conditions during the 2022-2023 rabi season. Drought stress was imposed by withholding irrigation at the anthesis stage, whereas heat stress was imposed by 1-month late sowing compared to the normal sowing condition. Combined stress was imposed by 1-month late sowing along with restricted irrigation at the flowering stage. Superior lines (HDHI113 and HDHI87) had both SG and SRM traits, whereas inferior lines (HDHI185 and HDHI80) had contrasting traits, i.e., lower SG and SRM traits. HD3086 and HI1500 had SG and SRM traits respectively. Potential candidate genes were identified based on the flanking markers of the mapped QTLs using the BioMart tool in the Ensembl Plants database to validate the identified QTLs. Real-time gene expression was conducted with SG-linked genes in the flag leaf and SRM-linked genes in the peduncle.

Results and Discussion

In this study, HDHI113 and HDHI87 showed higher expression of SG-related genes in the flag leaf under stress conditions. Furthermore, HDHI113 and HDHI87 maintained higher chlorophyll a content of 7.08 and 6.62 mg/gDW, respectively, and higher net photosynthetic rates (PN) of 17.18 and 16.48 µmol CO2/m2/s, respectively, under the combined stress condition. However, these lines showed higher expression of SRM-linked genes in the peduncle under drought stress, indicating that drought stress aggravates SRM in wheat. HDHI113 and HDHI87 recorded higher 1,000-grain weights and spike weight differences under combined stress, further validating the identified QTLs being linked to SG and SRM traits. Henceforth, the identified QTLs can be transferred to developed wheat varieties through efficient breeding strategies for yield improvement in harsh climate conditions.

From genes to traits: Trends in RNA-binding proteins and their role in plant trait development: A review

RNA-binding proteins (RBPs) are essential for cellular functions by attaching to RNAs, creating dynamic ribonucleoprotein complexes (RNPs) essential for managing RNA throughout its life cycle. These proteins are critical to all post-transcriptional processes, impacting vital cellular functions during development and adaptation to environmental changes. Notably, in plants, RBPs are critical for adjusting to inconsistent environmental conditions, with recent studies revealing that plants possess, more prominent, and both novel and conserved RBP families compared to other eukaryotes. This comprehensive review delves into the varied RBPs covering their structural attributes, domain base function, and their interactions with RNA in metabolism, spotlighting their role in regulating post-transcription and splicing and their reaction to internal and external stimuli. It highlights the complex regulatory roles of RBPs, focusing on plant trait regulation and the unique functions they facilitate, establishing a foundation for appreciating RBPs' significance in plant growth and environmental response strategies.

RNA editing-induced structural and functional adaptations of NAD9 in Triticum aestivum under drought stress

Introduction

Mitochondria are essential organelles in eukaryotic cells, producing ATP through the electron transport chain to supply energy for cellular activities. Beyond energy production, mitochondria play crucial roles in cellular signaling, stress responses, and the regulation of reactive oxygen species. In plants, mitochondria are one of the keys to responding to environmental stresses which can significantly affect crop productivity, particularly in crops like wheat. RNA editing, a post-transcriptional RNA modification process in mitochondria, is linked to regulating these stress responses.

Methods

This study explores RNA editing patterns in the nad9 gene of wheat drought-tolerant (Giza168) and drought-sensitive (Gemmiza10) wheat cultivars under drought stress to understand plant adaptation mechanisms. RNA-seq data for these cultivars were analyzed using CLC Genomic Workbench to identify RNA editing sites in the nad9 gene, examining subsequent amino acid changes and predicting secondary structure modifications. These RNA editing sites were validated using qRT-PCR on drought-treated seedlings at 0, 2, and 12 hours post-treatment. Protein models were generated using AlphaFold, with functional predictions and structure verification conducted using various bioinformatics tools to investigate the effect of RNA editing on protein level.

Results

The results showed significant RNA editing events, especially C-to-T conversions, in the nad9 gene across different drought exposure times. Giza168 had 22 editing sites, while Gemmiza10 had 19, with several showing significant differences between control and stress conditions. RNA editing influenced the NAD9 protein's secondary structure, particularly beta sheets, and 3D modeling highlighted the structural impacts of these edits. The N-terminal region of NAD9 contained important regulatory motifs, suggesting a complex regulatory environment.

Discussion

This study reveals key editing sites that differ between drought-tolerant and sensitive wheat cultivars, impacting NAD9 protein structures and highlighting the role of RNA editing in enhancing drought resilience. Additionally, the study suggests potential regulatory mechanisms, including phosphorylation and ubiquitination that influence mitochondrial stability and function.

PPR proteins in plants: roles, mechanisms, and prospects for rice research

Pentatricopeptide repeat (PPR) proteins constitute one of the largest protein families in land plants, with over 300 members in various species. Nearly all PPR proteins are nuclear-encoded and targeted to the chloroplast and mitochondria, modulating organellar gene expression by participating in RNA metabolism, including mRNA stability, RNA editing, RNA splicing, and translation initiation. Organelle RNA metabolism significantly influences chloroplast and mitochondria functions, impacting plant photosynthesis, respiration, and environmental responses. Over the past decades, PPR proteins have emerged as a research focus in molecular biology due to their diverse roles throughout plant life. This review summarizes recent progress in understanding the roles and molecular mechanisms of PPR proteins, emphasizing their functions in fertility, abiotic and biotic stress, grain quality, and chloroplast development in rice. Furthermore, we discuss prospects for PPR family research in rice, aiming to provide a theoretical foundation for future investigations and applications.

Azospirillum brasilense improves rice growth under salt stress by regulating the expression of key genes involved in salt stress response, abscisic acid signaling, and nutrient transport, among others

Major food crops, such as rice and maize, display severe yield losses (30-50%) under salt stress. Furthermore, problems associated with soil salinity are anticipated to worsen due to climate change. Therefore, it is necessary to implement sustainable agricultural strategies, such as exploiting beneficial plant-microbe associations, for increased crop yields. Plants can develop associations with beneficial microbes, including arbuscular mycorrhiza and plant growth-promoting bacteria (PGPB). PGPB improve plant growth via multiple mechanisms, including protection against biotic and abiotic stresses. Azospirillum brasilense, one of the most studied PGPB, can mitigate salt stress in different crops. However, little is known about the molecular mechanisms by which A. brasilense mitigates salt stress. This study shows that total and root plant mass is improved in A. brasilense-inoculated rice plants compared to the uninoculated plants grown under high salt concentrations (100 mM and 200 mM NaCl). We observed this growth improvement at seven- and fourteen days post-treatment (dpt). Next, we used transcriptomic approaches and identified differentially expressed genes (DEGs) in rice roots when exposed to three treatments: 1) A. brasilense, 2) salt (200 mM NaCl), and 3) A. brasilense and salt (200 mM NaCl), at seven dpt. We identified 786 DEGs in the A. brasilense-treated plants, 4061 DEGs in the salt-stressed plants, and 1387 DEGs in the salt-stressed A. brasilense-treated plants. In the A. brasilense-treated plants, we identified DEGs involved in defense, hormone, and nutrient transport, among others. In the salt-stressed plants, we identified DEGs involved in abscisic acid and jasmonic acid signaling, antioxidant enzymes, sodium and potassium transport, and calcium signaling, among others. In the salt-stressed A. brasilense-treated plants, we identified some genes involved in salt stress response and tolerance (e.g., abscisic acid and jasmonic acid signaling, antioxidant enzymes, calcium signaling), and sodium and potassium transport differentially expressed, among others. We also identified some A. brasilense-specific plant DEGs, such as nitrate transporters and defense genes. Furthermore, our results suggest genes involved in auxin and ethylene signaling are likely to play an important role during these interactions. Overall, our transcriptomic data indicate that A. brasilense improves rice growth under salt stress by regulating the expression of key genes involved in defense and stress response, abscisic acid and jasmonic acid signaling, and ion and nutrient transport, among others. Our findings will provide essential insights into salt stress mitigation in rice by A. brasilense.

A Genome-Wide Analysis of the Pentatricopeptide Repeat Protein Gene Family in Two Kiwifruit Species with an Emphasis on the Role of RNA Editing in Pathogen Stress

Kiwifruit is a perennial fruit tree with high nutritional and economic value; however, various pathogen stresses have resulted in reductions in its yield and quality. Pentatricopeptide repeat proteins (PPRs), characterized by tandem repetitions of 35 amino acid motifs, play roles in RNA editing, mRNA stability, and splicing. They may also regulate plant development and growth. Nevertheless, the roles of PPRs in plant development and disease resistance remain unclear. In this study, we focused on the roles of PPRs in the fruit development and pathogen stress of kiwifruit and conducted a series of analyses of the PPR gene family in two representative kiwifruit species (Actinidia chinensis (Ach) and Actinidia eriantha (Ace)) with markedly different degrees of disease resistance. A total of 497 and 499 PPRs were identified in Ach and Ace, respectively. All the kiwifruit PPRs could be phylogenetically divided into four subfamilies. There were about 40.68% PPRs predicted to be localized to mitochondria or chloroplasts. A synteny analysis showed that the expansion of the kiwifruit PPRs mainly originated from segmental duplication. Based on RNA-seq data from the fruit over 12 periods of development and maturity, a weighted correlation network analysis suggested that two PPRs, Actinidia20495.t1 and Actinidia15159.t1, may be involved in fruit development and maturation. In addition, we observed different responses with respect to the expression of PPRs and RNA editing between resistant and susceptible kiwifruits following infection with pathogenic bacteria, indicating the regulatory role of PPRs in the stress response via the modulation of RNA editing. The differentially expressed upstream transcription factors of the PPRs were further identified; they may regulate resistance adaption by modulating the expression of the PPRs. Collectively, these results suggest that PPRs play roles in the development and disease resistance of kiwifruit and provide candidate genes for further clarifying the resistance mechanisms in kiwifruits.