Systematic analysis of the Serine/Arginine-Rich Protein Splicing Factors (SRs) and focus on salt tolerance of PtSC27 in Populus trichocarpa

Identification of pine SF3B1 protein and cross-species comparison highlight its conservation and biological significance in pre-mRNA splicing regulation

As a key component of the largest subunit of the splicing machinery, SF3B1 plays essential roles in eukaryotic growth and development. However, only a few studies have focused on the evolutionary features and functions of this protein in plants. In this study, with the assistance of a bioinformatic analysis, we determined the complete coding sequence of the gene encoding the pine SF3B1 protein using RT-PCR and DNA sequencing. The evolutionary features of SF3B1 proteins were further examined based on a phylogenetic tree of SF3B1 homologous proteins from different eukaryotes, along with comprehensive comparisons of their functional domains, conserved motifs, and cis-regulatory elements and the structures of the corresponding genes. Furthermore, the effects of the splicing modulator GEX1a on several plant species were analysed, confirming that the re-identified SF3B1, with a full-length HEAT repeat domain, is expressed and functions in pre-mRNA splicing regulation in pines. In summary, we conducted a systematic cross-species comparison of SF3B1 homologous proteins, with an emphasis on complete sequence determination and the functional confirmation of pine SF3B1, illustrating the conservation of homologous proteins in plants. This study provides a valuable reference for understanding functional and regulatory mechanisms, as well as the potential applications of SF3B1.

Alternative Splicing Dynamics in Plant Adaptive Responses to Stress

Plants thrive in dynamic environments by activating sophisticated molecular networks that fine-tune their responses to stress. A key component of these networks is gene regulation at multiple levels, including precursor messenger RNA (pre-mRNA) splicing, which shapes the transcriptome and proteome landscapes. Through the precise action of the spliceosome complex, noncoding introns are removed and coding exons are joined to produce spliced RNA transcripts. While constitutive splicing always generates the same messenger RNA (mRNA), alternative splicing (AS) produces multiple mRNA isoforms from a single pre-mRNA, enriching proteome diversity. Remarkably, 80% of multiexon genes in plants generate multiple isoforms, underscoring the importance of AS in shaping plant development and responses to abiotic and biotic stresses. Recent advances in CRISPR-Cas genome and transcriptome editing technologies offer revolutionary tools to dissect AS regulation at molecular levels, unveiling the functional significance of specific isoforms. In this review, we explore the intricate mechanisms of pre-mRNA splicing and AS in plants, with a focus on stress responses. Additionally, we examine how leveraging AS insights can unlock new opportunities to engineer stress-resilient crops, paving the way for sustainable agriculture in the face of global environmental challenges.

Polyethylene terephthalate nanoplastics affect potassium accumulation in foxtail millet (Setaria italica) seedlings

BACKGROUND

As modern industrial activities have advanced, the prevalence of microplastics and nanoplastics in the environment has increased, thereby impacting plant growth. Potassium is one of the most crucial nutrient cations for plant biology. Understanding how polyethylene terephthalate (PET) treatment affects potassium uptake will deepen our understanding of plant response mechanisms to plastic pollution.

RESULTS

In this study, we examined the impact of PET micro- and nanoplastics on foxtail millet seedling growth and potassium accumulation. Additionally, we measured reactive oxygen species (ROS) production, antioxidant enzyme activities, and the expression levels of the corresponding enzyme-encoding genes. Our findings indicated that the germination and seedling growth of foxtail millet were not significantly affected by exposure to PET plastics. However, the ROS levels in foxtail millet increased under these conditions. This increase in ROS led to the upregulation of several genes involved in K+ uptake and transport (SiHAK1, SiHAK2, SiAKT2/3, SiHKT2;2, SiHKT1;1, SiGORK, and SiSKOR), thereby increasing K+ accumulation in foxtail millet leaves. Further research revealed that higher K+ concentrations in plant leaves were correlated with increased expression of the antioxidant-related genes SiCAT1, SiPOD1, and SiSOD3, as well as increased activities of the corresponding antioxidant enzymes. This response helps mitigate the excessive accumulation and damage caused by ROS in plant cells after PET nanoplastic treatment, suggesting a potential stress response mechanism in foxtail millet against nanoplastic pollution.

CONCLUSIONS

Our research indicates that PET nanoplastic treatment induces the expression of genes related to K+ uptake in foxtail millet through ROS signaling, leading to increased K+ accumulation in the leaves. This process mitigates the ROS damage caused by PET nanoplastic treatment by increasing the expression and activity of genes encoding antioxidant enzymes. The present research has unveiled the K+ accumulation-related response mechanism of foxtail millet to PET nanoplastic treatment, contributing significantly to our understanding of both the potassium absorption regulation mechanism in plants and the broader impact of plastic pollution on agricultural crops. This discovery not only highlights the complexity of plant responses to environmental stressors but also underscores the importance of considering such responses when evaluating the ecological and agricultural implications of plastic pollution.

Genome-wide identification of the MED25 BINDING RING-H2 PROTEIN gene family in foxtail millet (Setaria italica L.) and the role of SiMBR2 in resistance to abiotic stress in Arabidopsis

MAIN CONCLUSION

The SiMBR genes in foxtail millet were identified and studied. Heterologous expression of SiMBR2 in Arabidopsis can improve plant tolerance to drought stress by decreasing the level of reactive oxygen species. Foxtail millet (Setaria italica L.), a C4 crop recognized for its exceptional resistance to drought stress, presents an opportunity to improve the genetic resilience of other crops by examining its unique stress response genes and understanding the underlying molecular mechanisms of drought tolerance. In our previous study, we identified several genes linked to drought stress by transcriptome analysis, including SiMBR2 (Seita.7G226600), a member of the MED25 BINDING RING-H2 PROTEIN (MBR) gene family, which is related to protein ubiquitination. Here, we have identified ten SiMBR genes in foxtail millet and conducted analyses of their structural characteristics, chromosomal locations, cis-acting regulatory elements within their promoters, and predicted transcription patterns specific to various tissues or developmental stages using bioinformatic approaches. Further investigation of the stress response of SiMBR2 revealed that its transcription is induced by treatments with salicylic acid and gibberellic acid, as well as by salt and osmotic stresses, while exposure to high or low temperatures led to a decrease in its transcription levels. Heterologous expression of SiMBR2 in Arabidopsis thaliana enhanced the plant's tolerance to water deficit by reducing the accumulation of reactive oxygen species under drought stress. In summary, this study provides support for exploring the molecular mechanisms associated with drought resistance of SiMBR genes in foxtail millet and contributing to genetic improvement and molecular breeding in other crops.

Pan-transcriptomic analysis reveals alternative splicing control of cold tolerance in rice

Plants have evolved complex mechanisms to adapt to harsh environmental conditions. Rice (Oryza sativa) is a staple food crop that is sensitive to low temperatures. However, its cold stress responses remain poorly understood, thus limiting possibilities for crop engineering to achieve greater cold tolerance. In this study, we constructed a rice pan-transcriptome and characterized its transcriptional regulatory landscape in response to cold stress. We performed Iso-Seq and RNA-Seq of 11 rice cultivars subjected to a time-course cold treatment. Our analyses revealed that alternative splicing-regulated gene expression plays a significant role in the cold stress response. Moreover, we identified CATALASE C (OsCATC) and Os03g0701200 as candidate genes for engineering enhanced cold tolerance. Importantly, we uncovered central roles for the 2 serine-arginine-rich proteins OsRS33 and OsRS2Z38 in cold tolerance. Our analysis of cold tolerance and resequencing data from a diverse collection of 165 rice cultivars suggested that OsRS2Z38 may be a key selection gene in japonica domestication for cold adaptation, associated with the adaptive evolution of rice. This study systematically investigated the distribution, dynamic changes, and regulatory mechanisms of alternative splicing in rice under cold stress. Overall, our work generates a rich resource with broad implications for understanding the genetic basis of cold response mechanisms in plants.

Comprehensive investigation of BZR gene family in four dicots and the function of PtBZR9 and PtBZR12 under drought stress

Brassinazole-resistant (BZR) transcription factor plays an important role in plant growth and stress resistance through brassinosteroid (BR) signal transduction. However, systematic analysis of the BZR family in dicots remains limited. In this study, we conducted a genome-wide study of four typical dicots: Arabidopsis thaliana, Carica papaya, Vitis vinifera and Populus trichocarpa. Thirty-four BZR gene family members were identified and classified them into three subfamilies. Analysis of promoter and expression patterns revealed crucial role of a pair of homologous BZR genes, PtBZR9 and PtBZR12, in poplar may play a critical role under abiotic stress. PtBZR9 and PtBZR12 were localised in the nucleus and exhibited mutual interactions. Moreover, transient overexpression (OE) of PtBZR9 and PtBZR12 in poplar enhanced tolerance to drought stress. The phenotypic and physiological characteristics of PtBZR9 and PtBZR12 OE in Arabidopsis mirrored those of transient OE in the poplar. Additionally, PtBZR9 and PtBZR12 can bind to the E-box element. Under exogenous BR treatment, transgenic lines displayed a greater decrease in root length than the wild type. Thus, these findings provide a solid foundation for future research on the complex regulatory mechanisms of BZR genes.

OsSCL30 overexpression reduces the tolerance of rice seedlings to low temperature, drought and salt

Rice is one of the main food crops for the world population. Various abiotic stresses, such as low temperature, drought, and high salinity, affect rice during the entire growth period, determining its yield and quality, and even leading to plant death. In this study, by constructing overexpression vectors D-163 + 1300:OsSCL30 and D-163 + 1300-AcGFP:OsSCL30-GFP, the mechanism of action of OsSCL30 in various abiotic stresses was explored. Bioinformatics analysis showed that OsSCL30 was located on the chromosome 12 of rice Nipponbare, belonging to the plant-specific SCL subfamily of the SR protein family. The 1500 bp section upstream of the open reading frame start site contains stress-related cis-acting elements such as ABRE, MYC, and MYB. Under normal conditions, the expression of OsSCL30 was higher in leaves and leaf sheaths. The results of reverse transcription polymerase chain reaction showed that the expression of OsSCL30 decreased after low temperature, drought and salt treatment. In root cells OsSCL30 was localized in the nuclei. The results of the rice seedling tolerance and recovery tests showed that overexpression of OsSCL30 diminished the resistance to low temperature, drought and salt stresses in transgenic rice and resulted in larger accumulation of reactive oxygen species. This study is of great significance for exploring the response mechanisms of SR proteins under abiotic stresses.