Expression of FRIGIDA in root inhibits flowering in Arabidopsis thaliana

"To remember or forget: Insights into the mechanisms of epigenetic reprogramming and priming in early plant embryos"

Chromatin is dynamically modified throughout the plant life cycle to regulate gene expression in response to environmental and developmental cues. Although such epigenetic information can be inherited across generations in plants, chromatin features that regulate gene expression are typically reprogrammed during plant gametogenesis and directly after fertilization. Nevertheless, environmentally induced epigenetic marks on genes can be transmitted across generations. Moreover, epigenetic information installed on early embryonic chromatin can be stably inherited during subsequent growth and influence how plants respond to environmental conditions much later in development. Here, we review recent breakthroughs towards deciphering mechanisms underlying epigenetic reprogramming and transcriptional priming during early plant embryogenesis.

NnSnRK1-NnATG1-mediated autophagic cell death governs flower bud abortion in shaded lotus

Many plants can terminate their flowering process in response to unfavourable environments, but the mechanisms underlying this response are poorly understood. In this study, we observed that the lotus flower buds were susceptible to abortion under shaded conditions. The primary cause of abortion was excessive autophagic cell death (ACD) in flower buds. Blockade of autophagic flux in lotus flower buds consistently resulted in low levels of ACD and improved flowering ability under shaded conditions. Further evidence highlights the importance of the NnSnRK1-NnATG1 signalling axis in inducing ACD in lotus flower buds and culminating in their timely abortion. Under shaded conditions, elevated levels of NnSnRK1 activated NnATG1, which subsequently led to the formation of numerous autophagosome structures in lotus flower bud cells. Excessive autophagy levels led to the bulk degradation of cellular material, which triggered ACD and the abortion of flower buds. NnSnRK1 does not act directly on NnATG1. Other components, including TOR (target of rapamycin), PI3K (phosphatidylinositol 3-kinase) and three previously unidentified genes, appeared to be pivotal for the interaction between NnSnRK1 and NnATG1. This study reveals the role of autophagy in regulating the abortion of lotus flower buds, which could improve reproductive success and act as an energy-efficient measure in plants.

Role of methylation in vernalization and photoperiod pathway: a potential flowering regulator?

Recognized as a pivotal developmental transition, flowering marks the continuation of a plant's life cycle. Vernalization and photoperiod are two major flowering pathways orchestrating numerous florigenic signals. Methylation, including histone, DNA and RNA methylation, is one of the recent foci in plant development. Considerable studies reveal that methylation seems to show an increasing potential regulatory role in plant flowering via altering relevant gene expression without altering the genetic basis. However, little has been reviewed about whether and how methylation acts on vernalization- and photoperiod-induced flowering before and after FLOWERING LOCUS C (FLC) reactivation, what role RNA methylation plays in vernalization- and photoperiod-induced flowering, how methylation participates simultaneously in both vernalization- and photoperiod-induced flowering, the heritability of methylation memory under the vernalization/photoperiod pathway, and whether and how methylation replaces vernalization/photoinduction to regulate flowering. Our review provides insight about the crosstalk among the genetic control of the flowering gene network, methylation (methyltransferases/demethylases) and external signals (cold, light, sRNA and phytohormones) in vernalization and photoperiod pathways. The existing evidence that RNA methylation may play a potential regulatory role in vernalization- and photoperiod-induced flowering has been gathered and represented for the first time. This review speculates about and discusses the possibility of substituting methylation for vernalization and photoinduction to promote flowering. Current evidence is utilized to discuss the possibility of future methylation reagents becoming flowering regulators at the molecular level.

Transcriptional repressor AGL79 positively regulates flowering time in Arabidopsis

The MADS-box gene family is widely distributed in higher plants and the members of the angiosperm-specific APETALA1/FRUITFULL (AP1/FUL) subfamily plays important roles in the regulation of plant reproductive development. Recent studies revealed that the AP1/FUL subfamily member Dt2, VEGETATIVE1/PsFRUITFULc (VEG1/PsFULc) and MtFRUITFULc (MtFULc) are essential for the stem growth, branching and inflorescence development in legume species soybean (Glycine max), pea (Pisum sativum) and Medicago truncatula. However, the biological function of their homologue in Arabidopsis thaliana, AGAMOUS-LIKE 79 (AGL79), has not been well elucidated. In this study, we investigated the developmental roles of Arabidopsis AGL79 by CRISPR/Cas9-mutagenesis and molecular and physiological analyses. We found that AGL79 mainly acts as a transcriptional repressor and positively regulates Arabidopsis flowering time. We further revealed that AGL79 interacts with SUPPRESSOR OF OVEREXPRESSION OF CO1 (SOC1) and represses the expression of TERMINAL FLOWER 1 (TFL1). Our results demonstrated the AGL79-mediated flowering regulation in Arabidopsis and added an additional layer of complexity to the understanding of flowering time regulation in dicot plants.

Microbiome-mediated signal transduction within the plant holobiont

Microorganisms colonizing the plant rhizosphere and phyllosphere play crucial roles in plant growth and health. Recent studies provide new insights into long-distance communication from plant roots to shoots in association with their commensal microbiome. In brief, these recent advances suggest that specific plant-associated microbial taxa can contribute to systemic plant responses associated with the enhancement of plant health and performance in face of a variety of biotic and abiotic stresses. However, most of the mechanisms associated with microbiome-mediated signal transduction in plants remain poorly understood. In this review, we provide an overview of long-distance signaling mechanisms within plants mediated by the commensal plant-associated microbiomes. We advocate the view of plants and microbes as a holobiont and explore key molecules and mechanisms associated with plant-microbe interactions and changes in plant physiology activated by signal transduction.

Brassinosteroid Signaling Downstream Suppressor BIN2 Interacts with SLFRIGIDA-LIKE to Induce Early Flowering in Tomato

Brassinosteroid (BR) signaling is very important in plant developmental processes. Its various components interact to form a signaling cascade. These components are widely studied in Arabidopsis; however, very little information is available on tomatoes. Brassinosteroid Insensitive 2 (BIN2), the downstream suppressor of BR signaling, plays a critical role in BR signal pathway, while FRIGIDA as a key suppressor of Flowering Locus C with overexpression could cause early flowering; however, how the BR signaling regulates FRIGIDA homologous protein to adjust flowering time is still unknown. This study identified 12 FRIGIDA-LIKE proteins with a conserved FRIGIDA domain in tomatoes. Yeast two-hybrid and BiFC confirmed that SlBIN2 interacts with 4 SlFRLs, which are sub-cellularly localized in the nucleus. Tissue-specific expression of SlFRLs was observed highly in young roots and flowers. Biological results revealed that SlFRLs interact with SlBIN2 to regulate early flowering. Further, the mRNA level of SlBIN2 also increased in SlFRL-overexpressed lines. The relative expression of SlCPD increased upon SlFRL silencing, while SlDWF and SlBIN2 were decreased, both of which are important for BR signaling. Our research firstly provides molecular evidence that BRs regulate tomato flowering through the interaction between SlFRLs and SlBIN2. This study will promote the understanding of the specific pathway essential for floral regulation.

Embryonic reactivation of FLOWERING LOCUS C by ABSCISIC ACID-INSENSITIVE 3 establishes the vernalization requirement in each Arabidopsis generation

Many over-wintering plants grown in temperate climate acquire competence to flower upon prolonged cold exposure in winter, through vernalization. In Arabidopsis thaliana, prolonged cold exposure induces the silencing of the potent floral repressor FLOWERING LOCUS C (FLC) through repressive chromatin modifications by Polycomb proteins. This repression is maintained to enable flowering after return to warmth, but is reset during seed development. Here, we show that embryonic FLC reactivation occurs in two phases: resetting of cold-induced FLC silencing during embryogenesis and further FLC activation during embryo maturation. We found that the B3 transcription factor (TF) ABSCISIC ACID-INSENSITIVE 3 (ABI3) mediates both FLC resetting in embryogenesis and further activation of FLC expression in embryo maturation. ABI3 binds to the cis-acting cold memory element at FLC and recruits a scaffold protein with active chromatin modifiers to reset FLC chromatin into an active state in late embryogenesis. Moreover, in response to abscisic acid (ABA) accumulation during embryo maturation, ABI3, together with the basic leucine zipper TF ABI5, binds to an ABA-responsive cis-element to further activate FLC expression to high level. Therefore, we have uncovered the molecular circuitries underlying embryonic FLC reactivation following parental vernalization, which ensures that each generation must experience winter cold prior to flowering.

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

Three of the nitrilases (NITs), NIT1, NIT2, and NIT3, are ubiquitously existing in plant kingdom, which catalyze indole-3-acetonitrile into the most important auxin indole-3-acetic acid. Auxin is an indispensable hormone, which plays the important roles in almost all processes of plant growth and development. However, there are few reports on the regulation of flowering-time mediated by auxin. Here, we found that in Arabidopsis, nit1/2/3 showed a late flowering phenotype in short days. To explore the molecular mechanism by which NIT1/2/3 regulate flowering time, we performed transcriptome sequencing of nit1/2/3. The results showed that the expression of a MADS-box transcription factor gene MADS AFFECTING FLOWERING4 (MAF4) was dramatically increased in nit1/2/3 comparing to wild type (WT). MAF4 is one of the paralogs of the potent flowering inhibitor FLOWERING LOCUS C (FLC). There are four other paralogs in FLC clade in Arabidopsis, including FLOWERING LOCUS M (FLM/MAF1), MAF2, MAF3, and MAF5. The late flowering phenotype of nit1/2/3 could not be observed in the maf4 background, indicating that the phenotype was specifically dependent on MAF4 rather than other FLC clade members. Interestingly, the expression of a lncRNA gene MAS, which is transcribed in the opposite direction of MAF4, was found significantly increased in nit1/2/3. Also, MAS has been reported to activate MAF4 transcription by promoting histone 3 lysine 4 trimethylation (H3K4me3). As expected, H3K4me3 deposition at MAF4 locus in nit1/2/3 was highly enriched and significantly higher than that of WT. In summary, we show that NITs, NIT1/2/3, positively regulate flowering by repressing MAF4 through manipulating H3K4me3 modification. Further study needs to be performed to explore the largely unknown mechanisms behind it.

Antagonistic activities of cotranscriptional regulators within an early developmental window set FLC expression level

Quantitative variation in expression of the Arabidopsis floral repressor FLC influences whether plants overwinter before flowering, or have a rapid cycling habit enabling multiple generations a year. Genetic analysis has identified activators and repressors of FLC expression but how they interact to set expression level is poorly understood. Here, we show that antagonistic functions of the FLC activator FRIGIDA (FRI) and the repressor FCA, at a specific stage of embryo development, determine FLC expression and flowering. FRI antagonizes an FCA-induced proximal polyadenylation to increase FLC expression and delay flowering. Sector analysis shows that FRI activity during the early heart stage of embryo development maximally delays flowering. Opposing functions of cotranscriptional regulators during an early embryonic developmental window thus set FLC expression levels and determine flowering time.

Root exudate signals in plant-plant interactions

Plant-to-plant signalling is a key mediator of interactions among plant species. Plants can perceive and respond to chemical cues emitted from their neighbours, altering survival and performance, impacting plant coexistence and community assembly. An increasing number of studies indicate root exudates as key players in plant-to-plant signalling. Root exudates mediate root detection and behaviour, kin recognition, flowering and production, driving inter- and intra-specific facilitation in cropping systems and mixed-species plantations. Altered interactions may be attributed to the signalling components within root exudates. Root ethylene, strigolactones, jasmonic acid, (-)-loliolide and allantoin are signalling chemicals that convey information on local conditions in plant-plant interactions. These root-secreted signalling chemicals appear ubiquitous in plants and trigger a series of belowground responses inter- and intra-specifically, involving molecular events in biosynthesis, secretion and action. The secretion of root signals, mainly mediated by ATP-binding cassette transporters, is critical. Root-secreted signalling chemicals and their molecular mechanisms are rapidly revealing a multitude of fascinating plant-plant interactions. However, many root signals, particularly species-specific signals and their underlying mechanisms, remain to be uncovered due to methodological limitations and root-soil interactions. A thorough understanding of root-secreted chemical signals and their mechanisms will offer many ecological implications and potential applications for sustainable agriculture.

Functional Characterization of the EMBRYONIC FLOWER 2 Gene Involved in Flowering in Ginkgo biloba

Ginkgo biloba has edible, medicinal, and ornamental value. However, the long juvenile phase prevents the development of the G. biloba industry, and there are few reports on the identification and functional analysis of genes regulating the flowering time of G. biloba. EMBRYONIC FLOWER 2 (EMF), an important protein in flower development, functions to promote vegetative growth and repress flowering. In this study, a novel EMF gene (GbEMF2) was cloned and characterized from G. biloba. GbEMF2 contains a 2,193 bp open reading frame (ORF) encoding 730 amino acids. GbEMF2 harbors conserved VEFS-Box domain by the plant EMF protein. The phylogenic analysis showed that GbEMF2 originated from a polycomb-group (Pc-G) protein ancestor and was a member of the EMF2 protein. The quantitative real-time PCR (qRT-PCR) analysis revealed that GbEMF2 was expressed in all detected organs, and it showed a significantly higher level in ovulating strobilus and microstrobilus than in other organs. Compared with emf2 mutant plants, overexpression of GbEMF2 driven by the CaMV 35S promoter in emf2 mutant Arabidopsis plants delayed flowering but earlier than wild-type (WT) plants. This result indicated that GbEMF2 repressed flowering in G. biloba. Moreover, the RNA-seq analysis of GbEMF2 transgenic Arabidopsis plants (GbEMF2-OE/emf2), WT plants, and emf2 mutants screened out 227 differentially expressed genes (DEGs). Among these DEGs, FLC, MAF5, and MAF5-1 genes were related to flower organ development and regulated by GbEMF2. In addition, some genes participating in sugar metabolism, such as Alpha-amylase 1 (AMY1), BAM1, and Sucrose synthase 3 (SUS3) genes, were also controlled by GbEMF2. Overall, our results suggested that GbEMF2 negatively regulates flowering development in G. biloba. This finding provided a foundation and target gene for shortening the Ginkgo juvenile period by genetic engineering technology.

EjFRI, FRIGIDA (FRI) Ortholog from Eriobotrya japonica, Delays Flowering in Arabidopsis

In the model species Arabidopsis thaliana, FRIGIDA (FRI) is a key regulator of flowering time and can inhibit flowering without vernalization. However, little information is available on the function in the Rosaceae family. Loquat (Eriobotrya japonica) belongs to the family Rosaceae and is a distinctive species, in which flowering can be induced without vernalization, followed by blooming in late-autumn or winter. To investigate the functional roles of FRI orthologs in this non-vernalization species, we isolated an FRI ortholog, dubbed as EjFRI, from loquat. Analyses of the phylogenetic tree and protein sequence alignment showed that EjFRI is assigned to eurosids I FRI lineage. Expression analysis revealed that the highest expression level of EjFRI was after flower initiation. Meanwhile, EjFRI was widely expressed in different tissues. Subcellular localization of EjFRI was only detected to be in the nucleus. Ectopic expression of EjFRI in wild-type Arabidopsis delayed flowering time. The expression levels of EjFRI in transgenic wild-type Arabidopsis were significantly higher than those of nontransgenic wild-type lines. However, the expression levels of AtFRI showed no significant difference between transgenic and nontransgenic wild-type lines. Furthermore, the upregulated AtFLC expression in the transgenic lines indicated that EjFRI functioned similarly to the AtFRI of the model plant Arabidopsis. Our study provides a foundation to further explore the characterization of EjFRI, and also contributes to illuminating the molecular mechanism about flowering in loquat.