Nitrilases NIT1/2/3 Positively Regulate Flowering by Inhibiting MAF4 Expression in Arabidopsis

Genetic Analyses, BSA-Seq, and Transcriptome Analyses Reveal Candidate Genes Controlling Leaf Plastochron in Rapeseed (Brassica napus L.)

The leaf plastochron serves as an indicator of the rate of leaf appearance, biomass accumulation, and branch number, while also impacting plant architecture and seed yield. However, research on the leaf plastochron of crops remains limited. In this study, 2116C exhibited a rapid leaf plastochron compared to ZH18 during both rosette and bud periods. There were significant positive correlations among the leaf plastochron and primary branch number of the F2 populations (r ranging from 0.395 to 0.635, p < 0.01). Genetic analyses over two years demonstrated that two equally dominant genes might govern the leaf plastochron. Through bulk segregant analysis sequencing (BSA-seq), three novel genomic intervals were identified on chromosomes A02 (9.04-9.48 Mb and 13.52-13.66 Mb) and A04 (19.84-20.14 Mb) of ZS11 and Darmor-bzh reference genomes. By gene functional annotations, single-nucleotide variation (SNV) analyses, transcriptome data from parents, genetic progeny, and natural accessions, we identified ten candidate genes within the intervals, including FLOWERING LOCUS T, RGL1, MYB-like, CYP96A8, BLH3, NIT2, ASK6, and three CLAVATA3/ESR (CLE)-related genes. These findings lay the molecular foundation for further exploration into the leaf plastochron and the implications in plastochron-related breeding in rapeseed.

The role of DNA content in shaping chromatin architecture and gene expression

Whole-genome duplication is an evolutionary force that drives speciation in all living kingdoms and is notably prevalent in plants. The evolutionary history of plants involved at least two genomic duplications that significantly expanded the plant morphology and physiology spectrum. Many important crops are polyploids, showing valuable features relative to morphological and stress response traits. After genome duplication, diploidization processes facilitate genomic adjustments to restore disomic inheritance. However, little is known about the chromatin changes triggered by nuclear DNA content alterations. Here, we report that synthetically induced genome duplication leads to chromatinization and significant changes in gene expression, resulting in a transcriptional landscape resembling a natural tetraploid. Interestingly, synthetic diploidization elicits only minor alterations in transcriptional activity and chromatin accessibility compared to the more pronounced effects of tetraploidization. We identified epigenetic factors, including specific histone variants, that showed increased expression following genome duplication and decreased expression after genome reduction. These changes may play a key role in the epigenetic mechanisms underlying the phenotypic complexity after tetraploidization in plants. Our findings shed light on the mechanisms that modulate chromatin accessibility remodeling and gene transcription regulation underlying plant genome adaptation in response to changes in genome size.

Nitrilases NIT1/2/3 Positively Regulate Resistance to Pseudomonas syringae pv. tomato DC3000 Through Glucosinolate Metabolism in Arabidopsis

Nitrilases, found to have a common presence in the plant kingdom, are capable of converting nitriles into their corresponding carboxylic acids through hydrolysis. In Arabidopsis, the nitrilases NIT1, NIT2, and NIT3 catalyze the formation of indole-3-acetonitrile (IAN) into indole-3-acetic acid (IAA). Notably, IAN can originate from the breakdown products of indole glucosinolates. Glucosinolates, which are plant secondary metabolites commonly found in cruciferous plants, and their breakdown products, are crucial for plant defense against pathogens. In our study, we found that nitrilases positively regulate resistance to Pseudomonas syringae pv. tomato DC3000 (PstDC3000) in mature Arabidopsis. Transcriptome data showed that after PstDC3000 treatment, genes related to the auxin pathway in nit1nit2nit3 changed more dramatically than in the wild type. Moreover, the enhancement of disease resistance through exogenous aliphatic glucosinolate application relies on NIT1/2/3. Hence, it is hypothesized that NIT1/2/3 may serve a dual role in disease resistance and defense mechanisms. After infection with PstDC3000, NIT1/2/3 catalyzes the biosynthesis of auxin, thereby triggering certain disease-related responses. On the other hand, NIT1/2/3 can also break down nitriles generated from aliphatic glucosinolate degradation to enhance disease resistance. Our study elucidates the regulatory mechanism of nitrilases in Arabidopsis disease resistance, offering a theoretical foundation for enhancing disease resistance in cruciferous plants.

Functional characterization of Arabidopsis hydroxynitrile lyase in response to abiotic stress and the regulation of flowering time

BACKGROUND

Hydroxynitrile lyases (HNLs) are a class of hydrolytic enzymes from a wide range of sources, which play crucial roles in the catalysis of the reversible conversion of carbonyl compounds derived from cyanide and free cyanide in cyanogenic plant species. HNLs were also discovered in non-cyanogenic plants, such as Arabidopsis thaliana, and their roles remain unclear even during plant growth and reproduction.

METHODS AND RESULTS

The pattern of expression of the HNL in A. thaliana (AtHNL) in different tissues, as well as under abiotic stresses and hormone treatments, was examined by real-time quantitative reverse transcription PCR (qRT-PCR) and an AtHNL promoter-driven histochemical β-glucuronidase (GUS) assay. AtHNL is highly expressed in flowers and siliques, and the expression of AtHNL was dramatically affected by abiotic stresses and hormone treatments. The overexpression of AtHNL resulted in transgenic A. thaliana seedlings that were more tolerance to mannitol and salinity. Moreover, transgenic lines of A. thaliana that overexpressed this gene were less sensitive to abscisic acid (ABA). Altered expression of ABA/stress responsive genes was also observed in hnl mutant and AtHNL-overexpressing plants, suggesting AtHNL may play functional roles on regulating Arabidopsis resistance to ABA and abiotic stresses by affecting ABA/stress responsive gene expression. In addition, the overexpression of AtHNL resulted in earlier flowering, whereas the AtHNL mutant flowered later than the wild type (WT) plants. The expression of the floral stimulators CONSTANS (CO), SUPPRESSOR OF OVER EXPRESSION OF CO 1 (SOC1) and FLOWERING LOCUS T (FT) was upregulated in plants that overexpressed AtHNL when compared with the WT plants. In contrast, expression of the floral repressor FLOWERING LOCUS C (FLC) was upregulated in AtHNL mutants and downregulated in plants that overexpressed AtHNL compared to the WT plants.

CONCLUSION

This study revealed that AtHNL can be induced under abiotic stresses and ABA treatment, and genetic analysis showed that AtHNL could also act as a positive regulator of abiotic stress and ABA tolerance, as well as flowering time.

Decoding the functionality of plant transcription factors

Transcription factors (TFs) intricately govern cellular processes and responses to external stimuli by modulating gene expression. TFs help plants to balance the trade-off between stress tolerance and growth, thus ensuring their long-term survival in challenging environments. Understanding the factors and mechanisms that define the functionality of plant TFs is of paramount importance for unravelling the intricate regulatory networks governing development, growth, and responses to environmental stimuli in plants. This review provides a comprehensive understanding of these factors and mechanisms defining the activity of TFs. Understanding the dynamic nature of TFs has practical implications for modern molecular breeding programmes, as it provides insights into how to manipulate gene expression to optimize desired traits in crops. Moreover, recent studies also report the functional duality of TFs, highlighting their ability to switch between activation and repression modes; this represents an important mechanism for attuning gene expression. Here we discuss what the possible reasons for the dual nature of TFs are and how this duality instructs the cell fate decision during development, and fine-tunes stress responses in plants, enabling them to adapt to various environmental challenges.

Prediction of plant complex traits via integration of multi-omics data

The formation of complex traits is the consequence of genotype and activities at multiple molecular levels. However, connecting genotypes and these activities to complex traits remains challenging. Here, we investigate whether integrating genomic, transcriptomic, and methylomic data can improve prediction for six Arabidopsis traits. We find that transcriptome- and methylome-based models have performances comparable to those of genome-based models. However, models built for flowering time using different omics data identify different benchmark genes. Nine additional genes identified as important for flowering time from our models are experimentally validated as regulating flowering. Gene contributions to flowering time prediction are accession-dependent and distinct genes contribute to trait prediction in different genotypes. Models integrating multi-omics data perform best and reveal known and additional gene interactions, extending knowledge about existing regulatory networks underlying flowering time determination. These results demonstrate the feasibility of revealing molecular mechanisms underlying complex traits through multi-omics data integration.

Flavin-containing monooxygenases FMOGS-OXs integrate flowering transition and salt tolerance in Arabidopsis thaliana

Salt stress substantially leads to flowering delay. The regulation of salt-induced late flowering has been studied at the transcriptional and protein levels; however, the involvement of secondary metabolites has rarely been investigated. Here, we report that FMOGS-OXs (EC 1.14.13.237), the enzymes that catalyze the biosynthesis of glucosinolates (GSLs), promote flowering transition in Arabidopsis thaliana. It has been reported that WRKY75 is a positive regulator, and MAF4 is a negative regulator of flowering transition. The products of FMOGS-OXs, methylsulfinylalkyl GSLs (MS GSLs), facilitate flowering by inducing WRKY75 and repressing the MAS-MAF4 module. We further show that the degradation of MS GSLs is involved in salt-induced late flowering and salt tolerance. Salt stress induces the expression of myrosinase genes, resulting in the degradation of MS GSLs, thereby relieving the promotion of WRKY75 and inhibition of MAF4, leading to delayed flowering. In addition, the degradation products derived from MS GSLs enhance salt tolerance. Previous studies have revealed that FMOGS-OXs exhibit alternative catalytic activity to form trimethylamine N-oxide (TMAO) under salt stress, which activates multiple stress-related genes to promote salt tolerance. Therefore, FMOGS-OXs integrate flowering transition and salt tolerance in various ways. Our study shed light on the functional diversity of GSLs and established a connection between flowering transition, salt resistance, and GSL metabolism.

Transcription Factors and Their Regulatory Roles in the Male Gametophyte Development of Flowering Plants

Male gametophyte development in plants relies on the functions of numerous genes, whose expression is regulated by transcription factors (TFs), non-coding RNAs, hormones, and diverse environmental stresses. Several excellent reviews are available that address the genes and enzymes associated with male gametophyte development, especially pollen wall formation. Growing evidence from genetic studies, transcriptome analysis, and gene-by-gene studies suggests that TFs coordinate with epigenetic machinery to regulate the expression of these genes and enzymes for the sequential male gametophyte development. However, very little summarization has been performed to comprehensively review their intricate regulatory roles and discuss their downstream targets and upstream regulators in this unique process. In the present review, we highlight the research progress on the regulatory roles of TF families in the male gametophyte development of flowering plants. The transcriptional regulation, epigenetic control, and other regulators of TFs involved in male gametophyte development are also addressed.

Research progress on the roles of lncRNAs in plant development and stress responses

Long non-coding RNAs (lncRNAs) are RNAs of more than 200 nucleotides in length that are not (or very rarely) translated into proteins. In eukaryotes, lncRNAs regulate gene expression at the transcriptional, post-transcriptional, and epigenetic levels. lncRNAs are categorized according to their genomic position and molecular mechanism. This review summarized the characteristics and mechanisms of plant lncRNAs involved in vegetative growth, reproduction, and stress responses. Our discussion and model provide a theoretical basis for further studies of lncRNAs in plant breeding.