An Arabidopsis Retention and Splicing complex regulates root and embryo development through pre-mRNA splicing

Pre-mRNA Splicing Functions in Plant Sexual Reproduction Development

Precursor messenger RNA (pre-mRNA) splicing is a critical post-transcriptional regulatory mechanism in gene expression. The precise splicing of pre-mRNAs is essential for plant development and responding to genetic and environmental signals. In plant sexual reproduction, gene expression regulation relies on the accurate processing of pre-mRNAs, which is fundamental for coordinating developmental programs. The alternation of generations in plants involves two key phases: gametophyte development, which produces gametes, and fertilization, which leads to the formation of a diploid sporophyte. Gametophyte and embryo development represent essential processes in plant sexual reproduction. This review focuses on summarizing and analyzing the current evidence regarding the role of pre-mRNA splicing in plant sexual reproduction, with an emphasis on its involvement in gametophyte formation and embryo development. Future challenges in understanding RNA splicing regulation in plant sexual reproduction are also discussed, particularly in modulating splicing factor levels and activities and identifying target mRNAs and non-coding RNAs regulated by these factors. This review provides crucial insights into the molecular mechanisms of plant reproductive development and offers a theoretical basis for improving plant fertility and adaptability via RNA splicing regulation.

The splicing factor U2AF65B regulates cytosine methylation through interacting with DEFECTIVE IN MERISTEM SILENCING 3 in Arabidopsis

U2AF65B is one of the splicing factors that are involved in the recognition of the 3' splicing site and it plays an important role in plant development and stress response through its mRNA splicing function. However, it is not clear whether U2AF65B regulates gene expression in a splicing-independent manner. Through mutant screening and map-based cloning, protein-protein interaction, transcriptomic sequencing, whole-genome bisulfite sequencing and chromatin immunoprecipitation analysis, we investigated the function of U2AF65B in gene silencing in Arabidopsis thaliana. We found in the u2af65b mutant that the exogenous transgene 35S::HYG is activated in expression with decreased DNA methylation on the 35S core-promoter compared with that in the wild-type. Loss of U2AF65B function also globally decreased the methylation of CG, CHG and CHH with a profound effect on CHH methylation in transposons and intergenic sequences. Among the hypomethylated non-CG cytosines in u2af65b, nearly half of them are also hypomethylated in the dms3 mutant. Interestingly, U2AF65B interacts with the RNA-directed DNA methylation (RdDM) pathway component DMS3, and loss of U2AF65B function significantly decreased the enrichment of DMS3 on the targets, including the 35S::HYG transgene and endogenous RdDM loci. Our findings suggest that U2AF65B is a crucial player in RdDM-mediated DNA methylation, partially through promoting the RdDM pathway by interacting with and recruiting DMS3 to the target sequences.

Proteomic and metabolomic insights into oxidative stress response activation in mouse embryos generated by in vitro fertilization

STUDY QUESTION

How different is the global proteomic and metabolic profile of mouse blastocysts generated by IVF, cultured in optimal (5% O2) or stressful (20% O2) conditions, compared to in vivo generated blastocysts?

SUMMARY ANSWER

We found that in IVF-generated embryos: (i) the proteome was more sensitive to high oxygen levels than the global metabolomic profile; (ii) enzymes involved in splicing and the spliceosome are altered; (iii) numerous metabolic pathways, particularly amino acids metabolism, are altered (iv) there is activation of the integrated stress response (ISR) and downregulation of mTOR pathways.

WHAT IS KNOWN ALREADY

IVF culture conditions are known to affect the gene expression of embryos. However, comprehensive data on the global metabolic and proteomic changes that occur in IVF-generated embryos are unknown.

STUDY DESIGN SIZE DURATION

Mouse embryos were generated by natural mating (in vivo control or flushed blastocyst-FB-group) or by IVF using KSOM medium and two distinct oxygen concentrations: 5% O2 (optimal) and 20% O2 (stressful). Proteomic and metabolomic analyses were performed using state-of-the-art mass spectrometry techniques in triplicate (n = 100 blastocysts per replicate), allowing for detailed profiling of protein and metabolite alterations in each group.

PARTICIPANTS/MATERIALS SETTING METHODS

Mouse blastocysts were collected from CD-1 and B6D2F1 strains as specified above. High-resolution liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used for proteomics, while high-performance liquid chromatography coupled with mass spectrometry (HILIC-MS) was used for metabolomics. In addition, Immunofluorescence was used to assess the activation of stress response pathways, including the ISR.

MAIN RESULTS AND THE ROLE OF CHANCE

Proteomic analysis revealed significant changes in protein expression in embryos cultured under 20% O2 compared to 5% O2 and in vivo embryos. Compared to in vivo embryos, IVF embryos cultured under 20% O2 exhibited 599 differentially expressed proteins, with an increase in proteins involved in oxidative stress responses, aminoacyl-tRNA synthesis, and spliceosome pathways. In contrast, IVF embryos cultured under 5% O2 showed fewer changes, with 426 differentially expressed proteins, though still reflecting significant alterations compared to in vivo embryos. These results indicate that embryos in stressful conditions (20% O2) exhibit a stronger stress response and alterations in critical pathways for protein synthesis and DNA repair. Metabolomic analysis revealed that embryos cultured under 20% O2 showed changes in branch-chained amino acid levels, and decreased levels of key metabolites of the TCA cycle and pentose phosphate pathway. Embryos cultured under 5% O2 had increased pyruvate levels, suggesting altered glycolysis. Immunofluorescence confirmed that oxidative stress markers such as GCN2, EIF2α, and ATF4 were upregulated in IVF embryos, indicating ISR activation. Overall, IVF and embryo culture have a direct impact on embryo proteomes and metabolomes affecting amino acid metabolism and stress-related pathways.

LARGE SCALE DATA

N/A.

LIMITATIONS REASONS FOR CAUTION

Results in a murine model should be extrapolated with caution to human embryos.

WIDER IMPLICATIONS OF THE FINDINGS

These findings offer valuable insights into how different IVF culture conditions, specifically oxygen levels, impact the global metabolic and proteomic profiles of embryos. These findings provide critical insights into the profound impact of IVF culture conditions, particularly oxygen levels, on the global metabolic and proteomic landscapes of embryos. By identifying key metabolic pathways disrupted by oxidative stress, we highlight the potential clinical importance of proteomic and metabolomic analyses in understanding embryo quality, improving ART, and ultimately enhancing pregnancy outcomes. The integration of metabolomic and proteomic data offers a comprehensive understanding of how oxidative stress influences cellular function. These insights have direct clinical relevance, providing a foundation for optimizing ART protocols to mitigate oxidative stress.

STUDY FUNDING/COMPETING INTERESTS

This work was supported by grant R01 HD108166-01A1 from the National Institute of Child Health and Human Development (NICHD) to P.F.R. The authors declare that there is no conflict of interest that could be perceived as prejudicing the impartiality of the research reported.

The splicing auxiliary factor OsU2AF35a enhances thermotolerance via protein separation and promoting proper splicing of OsHSA32 pre-mRNA in rice

Heat stress significantly impacts global rice production, highlighting the critical need to understand the genetic basis of heat resistance in rice. U2AF (U2 snRNP auxiliary factor) is an essential splicing complex with critical roles in recognizing the 3'-splice site of precursor messenger RNAs (pre-mRNAs). The U2AF small subunit (U2AF35) can bind to the 3'-AG intron border and promote U2 snRNP binding to the branch-point sequences of introns through interaction with the U2AF large subunit (U2AF65). However, the functions of U2AF35 in plants are poorly understood. In this study, we discovered that the OsU2AF35a gene was vigorously induced by heat stress and could positively regulate rice thermotolerance during both the seedling and reproductive growth stages. OsU2AF35a interacts with OsU2AF65a within the nucleus, and both of them can form condensates through liquid-liquid phase separation (LLPS) following heat stress. The intrinsically disordered regions (IDR) are accountable for their LLPS. OsU2AF35a condensation is indispensable for thermotolerance. RNA-seq analysis disclosed that, subsequent to heat treatment, the expression levels of several genes associated with water deficiency and oxidative stress in osu2af35a-1 were markedly lower than those in ZH11. In accordance with this, OsU2AF35a is capable of positively regulating the oxidative stress resistance of rice. The pre-mRNAs of a considerable number of genes in the osu2af35a-1 mutant exhibited defective splicing, among which was the OsHSA32 gene. Knocking out OsHSA32 significantly reduced the thermotolerance of rice, while overexpressing OsHSA32 could partially rescue the heat sensitivity of osu2af35a-1. Together, our findings uncovered the essential role of OsU2AF35a in rice heat stress response through protein separation and regulating alternative pre-mRNA splicing.

A tripartite transcriptional module regulates protoderm specification during embryogenesis in Arabidopsis

Protoderm formation is a crucial step in early embryo patterning in plants, separating the precursors of the epidermis and the inner tissues. Although key regulators such as ARABIDOPSIS THALIANA MERISTEM LAYER1 (ATML1) and PROTODERMAL FACTOR2 (PDF2) have been identified in the model plant Arabidopsis thaliana, the genetic pathways controlling protoderm specification remain largely unexplored. Here, we combined genetic, cytological, and molecular approaches to investigate the regulatory mechanisms of protoderm specification in Arabidopsis thaliana. We report a novel role of the β-importin KETCH1 in protoderm specification. KETCH1 loss-of-function leads to aberrant protoderm cell morphology and absent ATML1 transcription in embryos. We further demonstrate that KETCH1 directly interacts with an RNA Polymerase II (Pol-II) cofactor JANUS, mediating its nuclear accumulation. Furthermore, JANUS directly interacts with the WUS HOMEOBOX2 (WOX2) protein, which is critical for WOX2-activated ATML1 expression. Consequently, JANUS, KETCH1, and WOX2 loss-of-function results in similar protoderm defects. Our results identify the tripartite KETCH1/JANUS/WOX2 transcriptional module as a novel regulatory axis in Arabidopsis protoderm specification.

AtSNU13 modulates pre-mRNA splicing of RBOHD and ALD1 to regulate plant immunity

Pre-mRNA splicing is a significant step for post-transcriptional modifications and functions in a wide range of physiological processes in plants. Human NHP2L binds to U4 snRNA during spliceosome assembly; it is involved in RNA splicing and mediates the development of human tumors. However, no ortholog has yet been identified in plants. Therefore, we report At4g12600 encoding the ortholog NHP2L protein, and AtSNU13 associates with the component of the spliceosome complex; the atsnu13 mutant showed compromised resistance in disease resistance, indicating that AtSNU13 is a positive regulator of plant immunity. Compared to wild-type plants, the atsnu13 mutation resulted in altered splicing patterns for defense-related genes and decreased expression of defense-related genes, such as RBOHD and ALD1. Further investigation shows that AtSNU13 promotes the interaction between U4/U6.U5 tri-snRNP-specific 27 K and the motif in target mRNAs to regulate the RNA splicing. Our study highlights the role of AtSNU13 in regulating plant immunity by affecting the pre-mRNA splicing of defense-related genes.

Importance of pre-mRNA splicing and its study tools in plants

Alternative splicing (AS) significantly enriches the diversity of transcriptomes and proteomes, playing a pivotal role in the physiology and development of eukaryotic organisms. With the continuous advancement of high-throughput sequencing technologies, an increasing number of novel transcript isoforms, along with factors related to splicing and their associated functions, are being unveiled. In this review, we succinctly summarize and compare the different splicing mechanisms across prokaryotes and eukaryotes. Furthermore, we provide an extensive overview of the recent progress in various studies on AS covering different developmental stages in diverse plant species and in response to various abiotic stresses. Additionally, we discuss modern techniques for studying the functions and quantification of AS transcripts, as well as their protein products. By integrating genetic studies, quantitative methods, and high-throughput omics techniques, we can discover novel transcript isoforms and functional splicing factors, thereby enhancing our understanding of the roles of various splicing modes in different plant species.

Heterologous Expression of Two Brassica campestris CCCH Zinc-Finger Proteins in Arabidopsis Induces Cytoplasmic Foci and Causes Pollen Abortion

The membrane-less organelles in cytoplasm that are presented as cytoplasmic foci were successively identified. Although multiple CCCH zinc-finger proteins have been found to be localized in cytoplasmic foci, the relationship between their specific localization and functions still needs further clarification. Here, we report that the heterologous expression of two Brassica campestris CCCH zinc-finger protein genes (BcMF30a and BcMF30c) in Arabidopsis thaliana can affect microgametogenesis by involving the formation of cytoplasmic foci. By monitoring the distribution of proteins and observing pollen phenotypes, we found that, when these two proteins were moderately expressed in pollen, they were mainly dispersed in the cytoplasm, and the pollen developed normally. However, high expression induced the assembly of cytoplasmic foci, leading to pollen abortion. These findings suggested that the continuous formation of BcMF30a/BcMF30c-associated cytoplasmic foci due to high expression was the inducement of male sterility. A co-localization analysis further showed that these two proteins can be recruited into two well-studied cytoplasmic foci, processing bodies (PBs), and stress granules (SGs), which were confirmed to function in mRNA metabolism. Together, our data suggested that BcMF30a and BcMF30c play component roles in the assembly of pollen cytoplasmic foci. Combined with our previous study on the homologous gene of BcMF30a/c in Arabidopsis, we concluded that the function of these homologous genes is conserved and that cytoplasmic foci containing BcMF30a/c may participate in the regulation of gene expression in pollen by regulating mRNA metabolism.

A molecular framework underlying low-nitrogen-induced early leaf senescence in Arabidopsis thaliana

Nitrogen (N) deficiency causes early leaf senescence, resulting in accelerated whole-plant maturation and severely reduced crop yield. However, the molecular mechanisms underlying N-deficiency-induced early leaf senescence remain unclear, even in the model species Arabidopsis thaliana. In this study, we identified Growth, Development and Splicing 1 (GDS1), a previously reported transcription factor, as a new regulator of nitrate (NO₃^-) signaling by a yeast-one-hybrid screen using a NO₃^- enhancer fragment from the promoter of NRT2.1. We showed that GDS1 promotes NO₃^- signaling, absorption and assimilation by affecting the expression of multiple NO₃^- regulatory genes, including Nitrate Regulatory Gene2 (NRG2). Interestingly, we observed that gds1 mutants show early leaf senescence as well as reduced NO₃^- content and N uptake under N-deficient conditions. Further analyses indicated that GDS1 binds to the promoters of several senescence-related genes, including Phytochrome-Interacting Transcription Factors 4 and 5 (PIF4 and PIF5) and represses their expression. Interestingly, we found that N deficiency decreases GDS1 protein accumulation, and GDS1 could interact with Anaphase Promoting Complex Subunit 10 (APC10). Genetic and biochemical experiments demonstrated that Anaphase Promoting Complex or Cyclosome (APC/C) promotes the ubiquitination and degradation of GDS1 under N deficiency, resulting in loss of PIF4 and PIF5 repression and consequent early leaf senescence. Furthermore, we discovered that overexpression of GDS1 could delay leaf senescence and improve seed yield and N-use efficiency (NUE) in Arabidopsis. In summary, our study uncovers a molecular framework illustrating a new mechanism underlying low-N-induced early leaf senescence and provides potential targets for genetic improvement of crop varieties with increased yield and NUE.

The role of forkhead-associated (FHA)-domain proteins in plant biology

The forkhead-associated (FHA) domain, a well-characterized small protein module that mediates protein-protein interactions by targeting motifs containing phosphothreonine, is present in many regulatory molecules like protein kinase, phosphatases, transcription factors, and other functional proteins. FHA-domain containing proteins in yeast and human are involved in a large variety of cellular processes such as DNA repair, cell cycle arrest, or pre-mRNA processing. Since the first FHA-domain protein, kinase-associated protein phosphatase (KAPP) was found in plants, the interest in plant FHA-containing proteins has increased dramatically, mainly due to the important role of FHA domain-containing proteins in plant growth and development. In this review, we provide a comprehensive overview of the fundamental properties of FHA domain-containing proteins in plants, and systematically summarized and analyzed the research progress of proteins containing the FHA domain in plants. We also emphasized that AT5G47790 and its homologs may play an important role as the regulatory subunit of protein phosphatase 1 (PP1) in plants.