Uncovering a novel function of the CCR4-NOT complex in phytochrome A-mediated light signalling in plants

JUNGBRUNNEN1, a Central Regulator of Plant Growth and Stress Response

Plants are under constant pressure to cope with ever-changing environmental conditions, requiring them to regulate their growth and stress response precisely. Transcription factors are key players in integrating stress-derived signals into developmental programs. One such transcription factor, JUNGBRUNNEN1 (JUB1), a member of the NAC family, has been identified as a central regulator of plant growth and stress responses. In this review, we discuss the structure of JUB1 and its recently identified alternatively spliced form and explore their potential modes of operation. We examine (i) how developmental and environmental cues regulate the expression of JUB1, (ii) its role as a negative regulator of leaf senescence while modulating tolerance to multiple abiotic and biotic stresses, and (iii) its function in regulating the trade-off between plant growth and defense. Furthermore, we provide insights into the regulation of JUB1, its interacting partners, and the potential conservation of its regulatory role across land plants. Given the climate crisis, we highlight the importance of identifying multitudinous stress response regulators such as JUB1 and emphasize the potential of its homologues in several important crop plants. Optimizing its application could make it an invaluable resource for improving crop resilience under changing climatic conditions.

Cryptochrome 1 promotes photomorphogenesis in Arabidopsis by displacing substrates from the COP1 ubiquitin ligase

In blue light, cryptochrome photoreceptors inhibit the key repressor of light signaling, the COP1/SPA ubiquitin ligase, to promote photomorphogenic responses. This inhibition relies on the direct interaction between COP1 and cryptochromes. Here, we analyzed the molecular mechanism of CRY1-mediated inhibition of COP1. We show that the VP motif in the C-terminal domain of CRY1 is essential for the COP1-CRY1 interaction in Arabidopsis. Phenotypic analysis of transgenic Arabidopsis plants harboring a mutation in the VP motif reveals that the VP motif of CRY1 is required for blue light-induced responses, such as seedling de-etiolation and anthocyanin biosynthesis. Via its VP motif, CRY1 inhibits the interaction between COP1 and the COP1 substrate transcription factors PAP2 and HY5. Replacing the VP motif of CRY1 with that of the human COP1 interactor TRIB1 produces a functional photoreceptor in transgenic plants. Since HY5, PAP2 and CRY1 interact with COP1 through their respective VP motifs, our results demonstrate that CRY1 inhibits the activity of COP1 by competitively displacing substrates from COP1. Taken together with previous results showing VP-dependent substrate displacement by photoactivated CRY2 and UVR8 photoreceptors, our results highlight the conservation of this mechanism across multiple photoreceptors.

Improvement in genomic prediction of maize with prior gene ontology information depends on traits and environmental conditions

Classical genomic prediction approaches rely on statistical associations between traits and markers rather than their biological significance. Biologically informed selection of genomic regions can help prioritize polymorphisms by considering underlying biological processes, making prediction models robust and accurate. Gene ontology (GO) terms can be used for this purpose, and the information can be integrated into genomic prediction models through marker categorization. It allows likely causal markers to account for a certain portion of genetic variance independently from the remaining markers. We systematically tested a list of 5110 GO terms for their predictive performance for physiological (platform traits) and productivity traits (field grain yield) in a maize (Zea mays L.) panel using genomic features best linear unbiased prediction (GFBLUP) model. Predictive abilities were compared to the classical genomic best linear unbiased prediction (GBLUP). Predictive gains with categorizing markers based on a given GO term strongly depend on the trait and on the growth conditions, as a term can be useful for a given trait in a given condition or somewhat similar conditions but not useful for the same trait in a different condition. Overall, results of all GFBLUP models compared to GBLUP show that the former might be less efficient than the latter. Even though we could not identify a prior criterion to determine which GO terms can offer benefit to a given trait, we could a posteriori find biological interpretations of the results, meaning that GFBLUP could be helpful if more about the gene functions and their relationships with the growth conditions was known.

The potato RNA metabolism machinery is targeted by the cyst nematode effector RHA1B for successful parasitism

The potato (Solanum tuberosum) cyst nematode Globodera pallida induces a multinucleate feeding site (syncytium) in potato roots as its sole source of nutrition. Here, we demonstrate that the G. pallida effector RING-H2 finger A1b (RHA1B), which is a functional ubiquitin ligase, interferes with the carbon catabolite repression 4 (CCR4)-negative on TATA-less (NOT) deadenylase-based RNA metabolism machinery that regulates syncytium development in G. pallida-infected potato. Specifically, RHA1B targets the CCR4-associated factor 1 (CAF1) and StNOT10 subunits of the CCR4-NOT complex for proteasome-mediated degradation, leading to upregulation of the cyclin gene StCycA2 involved in syncytium formation. The StCAF1 subunit of CCR4-NOT recruits the RNA binding protein StPUM5 to deadenylate StCycA2 mRNA, resulting in shortened poly-A tails of StCycA2 mRNA and subsequently reduced transcript levels. Knockdown of either subunit (StCAF1 or StNOT10) of the CCR4-NOT complex or StPUM5 in transgenic potato plants resulted in enlarged syncytia and enhanced susceptibility to G. pallida infection, which resembles the phenotypes of StCycA2 overexpression transgenic potato plants. Genetic analyses indicate that transgenic potato plants overexpressing RHA1B exhibit similar phenotypes as transgenic potato plants with knockdown of StNOT10, StCAF1, or StPUM5. Thus, our data suggest that G. pallida utilizes the RHA1B effector to manipulate RNA metabolism in host plants, thereby promoting syncytium development for parasitic success.

Population genomics and epigenomics of Spirodela polyrhiza provide insights into the evolution of facultative asexuality

Many plants are facultatively asexual, balancing short-term benefits with long-term costs of asexuality. During range expansion, natural selection likely influences the genetic controls of asexuality in these organisms. However, evidence of natural selection driving asexuality is limited, and the evolutionary consequences of asexuality on the genomic and epigenomic diversity remain controversial. We analyzed population genomes and epigenomes of Spirodela polyrhiza, (L.) Schleid., a facultatively asexual plant that flowers rarely, revealing remarkably low genomic diversity and DNA methylation levels. Within species, demographic history and the frequency of asexual reproduction jointly determined intra-specific variations of genomic diversity and DNA methylation levels. Genome-wide scans revealed that genes associated with stress adaptations, flowering and embryogenesis were under positive selection. These data are consistent with the hypothesize that natural selection can shape the evolution of asexuality during habitat expansions, which alters genomic and epigenomic diversity levels.

EID1 promotes the response to canopy shade in Arabidopsis thaliana by repressing the action of phytochrome A

The phytochrome (phy) system enables plants to adapt to canopy shade. By sensing the reduction of the red:far-red light ratio in shade, phyA and phyB trigger downstream signalling cascades which eventually lead to enhanced elongation growth. In this study, we show that the F-box protein EID1 takes on an essential function within the shade avoidance response in Arabidopsis thaliana by repressing phyA action and thereby allowing seedlings to elongate in shade. Thus, altering EID1 activity provides a means to adapt the shade response without affecting phyB action and could have played a role in the evolution of shade tolerance.

CmNAC25 targets CmMYB6 to positively regulate anthocyanin biosynthesis during the post-flowering stage in chrysanthemum

BACKGROUND

Anthocyanin is a class of important secondary metabolites that determines colorful petals in chrysanthemum, a famous cut flower. 'Arctic Queen' is a white chrysanthemum cultivar that does not accumulate anthocyanin during the flowering stage. During the post-flowering stage, the petals of 'Arctic Queen' accumulate anthocyanin and turn red. However, the molecular mechanism underlying this flower color change remains unclear.

RESULTS

In this study, by using transcriptome analysis, we identified CmNAC25 as a candidate gene promoting anthocyanin accumulation in the post-flowering stage of 'Arctic Queen'. CmNAC25 is directly bound to the promoter of CmMYB6, a core member of the MBW protein complex that promotes anthocyanin biosynthesis in chrysanthemum, to activate its expression. CmNAC25 also directly activates the promoter of CmDFR, which encodes the key enzyme in anthocyanin biosynthesis. CmNAC25 was highly expressed during the post-flowering stage, while the expression level of CmMYB#7, a known R3 MYB transcription factor interfering with the formation of the CmMYB6-CmbHLH2 complex, significantly decreased. Genetic transformation of both chrysanthemum and Nicotiana tabacum verified that CmNAC25 was a positive regulator of anthocyanin biosynthesis. Another two cultivars that turned red during the post-flowering stages also demonstrated a similar mechanism.

CONCLUSIONS

Altogether, our data revealed that CmNAC25 positively regulates anthocyanin biosynthesis in chrysanthemum petals during the post-flowering stages by directly activating CmMYB6 and CmDFR. Our results thus revealed a crucial role of CmNAC25 in regulating flower color change during petal senescence and provided a target gene for molecular design breeding of flower color in chrysanthemum.

Plants use molecular mechanisms mediated by biomolecular condensates to integrate environmental cues with development

This review highlights recent literature on biomolecular condensates in plant development and discusses challenges for fully dissecting their functional roles. Plant developmental biology has been inundated with descriptive examples of biomolecular condensate formation, but it is only recently that mechanistic understanding has been forthcoming. Here, we discuss recent examples of potential roles biomolecular condensates play at different stages of the plant life cycle. We group these examples based on putative molecular functions, including sequestering interacting components, enhancing dwell time, and interacting with cytoplasmic biophysical properties in response to environmental change. We explore how these mechanisms could modulate plant development in response to environmental inputs and discuss challenges and opportunities for further research into deciphering molecular mechanisms to better understand the diverse roles that biomolecular condensates exert on life.

Poplar CCR4-associated factor PtCAF1I is necessary for poplar development and defense response

Poplar is one of the most widely used tree species in afforestation projects. CCR4 associated factor 1 (CAF1) is a major member of CCR4-NOT and plays an important role in eukaryotic mRNA deadenylation. However, its role in poplar remains unclear. In this study, the full-length cDNA of the PtCAF1I gene was cloned from the poplar by screening the highly expressed PtCAF1I gene in the identified PtCAF1 gene family by poplar sterilization. PtCAF1I was localized in the nucleus. Through sequence alignment, it was found that the PtCAF1I sequence contains three motifs and is highly similar to the CAF1 protein sequence of other species. In the quantitative expression analysis of tissues, the expression of PtCAF1I in different tissues of Populus trichocarpa, 'Nanlin895', and Shanxinyang was not much different. In addition, the analysis of the expression of the PtCAF1I gene under different stress treatments showed that PtCAF1I responded to abscisic acid (ABA), salicylic acid (SA), methyl jasmonate (MeJA), NaCl, PEG₆₀₀₀, hydrogen peroxide (H₂O₂) and cold stress to different degrees. To study the potential biological functions of PtCAF1I, 6 transgenic lines were obtained through transformation using an Agrobacterium tumefaciens infection system. The transcriptome sequencing results showed that DEGs were mainly concentrated in pathways of phenylpropanoid biosynthesis, biosynthesis of secondary metabolites, carbon metabolism, and carotenoid biosynthesis. Compared with WT poplar, the contents of cellulose, hemicellulose, lignin, total sugar, and flavonoids, and the cell wall thickness of PtCAF1I overexpression poplars were significantly higher. Under Septotinia populiperda treatment, transgenic poplars clearly exhibited certain disease resistance. Meanwhile, upregulation of the expression of JA and SA pathway-related genes also contributed to improving the disease tolerance of transgenic poplar. In conclusion, our results suggest that PtCAF1I plays an important role in the growth and development of poplars and their resistance to pathogens.

Two environmental signal-driven RNA metabolic processes: Alternative splicing and translation

Plants live in fixed locations and have evolved adaptation mechanisms that integrate multiple responses to various environmental signals. Among the different components of these response pathways, receptors/sensors represent nodes that recognise environmental signals. Additionally, RNA metabolism plays an essential role in the regulation of gene expression and protein synthesis. With the development of RNA biotechnology, recent advances have been made in determining the roles of RNA metabolism in response to different environmental signals-especially the roles of alternative splicing and translation. In this review, we discuss recent progress in research on how the environmental adaptation mechanisms in plants are affected at the posttranscriptional level. These findings improve our understanding of the mechanism through which plants adapt to environmental changes by regulating the posttranscriptional level and are conducive for breeding stress-tolerant plants to cope with dynamic and rapidly changing environments.

Investigating Plant Protein-Protein Interactions Using FRET-FLIM with a Focus on the Actin Cytoskeleton

The study of protein-protein interactions is fundamental to understanding how actin-dependent processes are controlled through the regulation of actin-binding proteins by their interactors. FRET-FLIM (Förster resonance energy transfer-fluorescence lifetime imaging microscopy) is a sensitive bioimaging method to detect protein-protein interactions in living cells through measurement of FRET, facilitated by the interactions of fluorophore-tagged fusion protein. As a sensitive and noninvasive method for the spatiotemporal visualization of dynamic protein-protein interactions, FRET-FLIM holds several advantages over other methods of protein interaction assays. FRET-FLIM has been widely employed to characterize many plant protein interactions, including interactions between actin-regulatory proteins and their binding partners. As we increasingly understand the plant actin cytoskeleton to coordinate a diverse number of complex functions, the study of actin-regulatory proteins and their interactors becomes increasingly technically challenging. Sophisticated and sensitive in vivo methods such as FRET-FLIM are likely to be crucial to the study of protein-protein interactions as more complex and challenging hypotheses are addressed.

Role of plant microRNAs and their corresponding pathways in fluctuating light conditions

In recent years, it has been established that microRNAs (miRNAs) are critical for various plant physiological regulations in numerous species. Next-generation sequencing technologies have aided to our understandings related to the critical role of miRNAs during environmental stress conditions and plant development. Light influences not just miRNA accumulation but also their biological activities via regulating miRNA gene transcription, biosynthesis, and RNA-induced silencing complex (RISC) activity. Light-regulated routes, processes, and activities can all be affected by miRNAs. Here, we will explore how light affects miRNA gene expression and how conserved and novel miRNAs exhibit altered expression across different plant species in response to variable light quality. Here, we will mainly discuss recent advances in understanding how miRNAs are involved in photomorphogenesis, and photoperiod-dependent plant biological processes such as cell proliferation, metabolism, chlorophyll pigment synthesis and axillary bud growth. The review concludes by presenting future prospects via hoping that light-responsive miRNAs can be exploited in a better way to engineer economically important crops to ensure future food security.

SWAP1-SFPS-RRC1 splicing factor complex modulates pre-mRNA splicing to promote photomorphogenesis in Arabidopsis

Light signals perceived by a group of photoreceptors have profound effects on the physiology, growth, and development of plants. The red/far-red light-absorbing phytochromes (phys) modulate these aspects by intricately regulating gene expression at multiple levels. Here, we report the identification and functional characterization of an RNA-binding splicing factor, SWAP1 (SUPPRESSOR-OF-WHITE-APRICOT/SURP RNA-BINDING DOMAIN-CONTAINING PROTEIN1). Loss-of-function swap1-1 mutant is hyposensitive to red light and exhibits a day length-independent early flowering phenotype. SWAP1 physically interacts with two other splicing factors, (SFPS) SPLICING FACTOR FOR PHYTOCHROME SIGNALING and (RRC1) REDUCED RED LIGHT RESPONSES IN CRY1CRY2 BACKGROUND 1 in a light-independent manner and forms a ternary complex. In addition, SWAP1 physically interacts with photoactivated phyB and colocalizes with nuclear phyB photobodies. Phenotypic analyses show that the swap1sfps, swap1rrc1, and sfpsrrc1 double mutants display hypocotyl lengths similar to that of the respective single mutants under red light, suggesting that they function in the same genetic pathway. The swap1sfps double and swap1sfpsrrc1 triple mutants display pleiotropic phenotypes, including sterility at the adult stage. Deep RNA sequencing (RNA-seq) analyses show that SWAP1 regulates the gene expression and pre-messenger RNA (mRNA) alternative splicing of a large number of genes, including those involved in plant responses to light signaling. A comparative analysis of alternative splicing among single, double, and triple mutants showed that all three splicing factors coordinately regulate the alternative splicing of a subset of genes. Our study uncovered the function of a splicing factor that modulates light-regulated alternative splicing by interacting with photoactivated phyB and other splicing factors.

The phytochrome interacting proteins ERF55 and ERF58 repress light-induced seed germination in Arabidopsis thaliana

Seed germination is a critical step in the life cycle of plants controlled by the phytohormones abscisic acid (ABA) and gibberellin (GA), and by phytochromes, an important class of photoreceptors in plants. Here we show that light-dependent germination is enhanced in mutants deficient in the AP2/ERF transcription factors ERF55 and ERF58. Light-activated phytochromes repress ERF55/ERF58 expression and directly bind ERF55/ERF58 to displace them from the promoter of PIF1 and SOM, genes encoding transcriptional regulators that prevent the completion of germination. The same mechanism controls the expression of genes that encode ABA or GA metabolic enzymes to decrease levels of ABA and possibly increase levels of GA. Interestingly, ERF55 and ERF58 are themselves under transcriptional control of ABA and GA, suggesting that they are part of a self-reinforcing signalling loop which controls the completion of germination. Overall, we identified a role of ERF55/ERF58 in phytochrome-mediated regulation of germination completion.

Phytochrome A Mediates the Disassembly of Processing Bodies in Far-Red Light

Phytochromes are red- and far-red light receptors that control the growth and development of plants, enabling them to respond adequately to changing light conditions. It has been shown that halted mRNAs stored in RNA granules called processing bodies are released upon light perception and contribute to the adaptation to the light environment. However, the photophysiological background of this process is largely unknown. We found that light of different wavelengths can trigger the disassembly of processing bodies in a dose- and time-dependent manner. We show that phytochromes control this process in red- and far-red light and that cytoplasmic phytochrome A is sufficient and necessary for the far-red light-induced disassembly of processing bodies. This adds a novel, unexpected cytoplasmic function to the processes controlled by phytochrome A. Overall, our findings suggest a role of phytochromes in the control of translationally halted mRNAs that are stored in processing bodies. We expect our findings to facilitate understanding of how light and environmental cues control the assembly and disassembly of processing bodies, which could have broader implications for the regulation of non-membranous organelles in general.

Improvement of tomato salt tolerance by the regulation of photosynthetic performance and antioxidant enzyme capacity under a low red to far-red light ratio

The red light (R) to far-red light (FR) ratio (R:FR) regulates plant responses to salt stress, but the regulation mechanism is still unclear. In this study, tomato seedlings were grown under half-strength Hoagland solution with or without 150 mM NaCl at two different R:FR ratios (7.4 and 0.8). The photosynthetic capacity, antioxidant enzyme activities, and the phenotypes at chloroplast ultrastructure and whole plant levels were investigated. The results showed that low R:FR significantly alleviated the damage of tomato seedlings from salt stress. On day 4, 8, and 12 at low R:FR, the maximum photochemical quantum yields (F_v/F_m) of photosystem II (PSII) were increased by 4.53%, 3.89%, and 16.49%, respectively; the net photosynthetic rates (Pn) of leaves were increased by 16.21%, 90.81%, and 118.00%, respectively. Low R:FR enhanced the integrity and stability of the chloroplast structure of salinity-treated plants through maintaining the high activities of antioxidant enzymes and mitigated the degradation rate of photosynthetic pigments caused by reactive oxygen species (ROS) under salt stress. The photosynthesis, antioxidant enzyme-related gene expression, and transcriptome sequencing analysis of tomato seedlings under different treatments were also investigated. Low R:FR promoted the de novo synthesis of D1 protein via triggering psbA expression, and upregulated the transcripts of superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), and ascorbate peroxidase (APX) related genes. Meanwhile, the transcriptome analysis confirmed the positive function of low R:FR on enhancing tomato salinity stress tolerance from the regulation of photosynthesis and ROS scavenging systems.