VvprePIP, the Precursor of a PAMP-Induced Secreted Peptide, Stimulates Defence Responses and Improves Resistance to Plasmopora viticola in Grapevine

PRRs (Pattern-Recognition Receptors) distributed on plant cell membranes recognize not only PAMPs (Pathogen-Associated Molecular Patterns) released from the pathogens but also ligand peptides secreted from the plants, followed by eliciting defence responses. Here, we demonstrate that transcription of VvprePIP from grape (Vitis vinifera) encoding the precursor of a PIP (PAMP-Induced secreted Peptide) peptide is activated by Plasmopara viticola infection. Overexpression of VvprePIP increases the expression of defence-related genes and ROS (Reactive Oxygen Species) production, enhancing resistance to P. viticola in V. vinifera. A WRKY transcription factor VvWRKY8 interacts with VvprePIP promoter, upregulating its transcription directly. The immune reactions resulting from ectopic expression of VvprePIP are impaired in NbBAK1-silencing tobacco, implying BAK1 is necessary for the recognition between mature peptide VvPIP and its receptor. The conserved region at the C terminus of VvprePIP carries three typical SGPS-GH motifs, all of which contribute to provoke immune responses in plant. As synthetic VvPIP with a hydroxylated modification at the forth proline can mimic the functions of overexpression of the precursor, while synthetic unmodified VvPIP cannot, we reported that hydroxyproline is required for VvPIPs to serve as an active signal molecular. In conclusion, our studies reveal that VvprePIP plays a role in enhancing plant resistance to pathogens.

Branching under pressure: Influences of cell wall architecture and biomechanics on lateral root morphogenesis

Plants carry out a unique type of organogenesis in which cells do not move relative to each other but instead maintain their relative positions and grow in concert. The coordinated regulation of cell shape and size is thus essential for organ morphogenesis, but in a few developmental processes, most notably in invasive growth and the establishment of branched tissue architectures, cell and tissue growth in plants involves the displacement of surrounding or overlying tissues. Plant cells accomplish patterned developmental morphogenesis in part due to the mechanically complex architectures of their cell walls, which can anisotropically constrain the expansion that is facilitated in many cases by the cellular uptake of water that results in cell pressurization. Here, we focus on one example of patterned tissue growth and cell displacement, the formation and emergence of lateral roots, as a paradigm for understanding how cell wall architecture and cellular biomechanics influence the differentiation and growth of new organs in plants. We highlight recent advances in our knowledge of how hormone signaling, transcriptional regulation, cytoskeletal dynamics, and cell wall synthesis and remodeling influence lateral root initiation and emergence, and propose hypotheses and potential research directions for future studies of these complex but essential developmental processes.

Conserved role of the SERK-BIR module in development and immunity across land plants

SOMATIC EMBRYOGENESIS RECEPTOR-LIKE KINASES (SERKs), which are subfamily II of leucine-rich repeat receptor-like kinases (LRR-RLKs), play diverse roles in development and immunity in the angiosperm Arabidopsis thaliana. AtSERKs act as co-receptors for many LRR-RLKs, including BRASSINOSTEROID INSENSITIVE 1 (BRI1) and FLAGELLIN SENSITIVE 2 (FLS2).1,2,3,4 The conserved tyrosine (Y) residue in AtSERK3 is crucial for signaling specificity in differentiating BRI1- and FLS2-mediated pathways.5 BRI1-ASSOCIATED RECEPTOR KINASE 1 (BAK1)-INTERACTING RECEPTOR-LIKE KINASES (BIRs) interact with SERKs under resting conditions, negatively regulating SERK-mediated pathways.6,7 SERK and BIR are highly conserved in land plants, whereas BRI1 and FLS2 homologs are absent or poorly conserved in bryophyte lineages.8,9 The biological functions of SERK homologs in non-flowering plants are largely unknown. The genome of the liverwort Marchantia polymorpha encodes single homologs for SERK and BIR, namely MpSERK and MpBIR.9 We here show that Mpserk disruptants display growth and developmental defects with no observable sexual or vegetative reproduction. Complementation analysis revealed a contribution of the conserved Y residue of MpSERK to growth. Proximity-labeling-based interactomics identified MpBIR as a MpSERK interactor. Mpbir disruptants displayed defects in reproductive organ development. Patterns of development- and immunity-related gene expression in Mpserk and Mpbir were antagonistic, suggesting that MpBIR functions as an MpSERK repressor. The pathogenic bacterium Pseudomonas syringae pv. tomato DC3000 grew poorly on Mpbir, indicating a significant role of the MpSERK-MpBIR module in immunity. Taken together, we propose that the SERK-BIR functional module was already regulating both development and immunity in the last common ancestor of land plants.

RAPID LEAF FALLING 1 facilitates chemical defoliation and mechanical harvesting in cotton

Chemical defoliation stands as the ultimate tool in enabling the mechanical harvest of cotton, offering economic and environmental advantages. However, the underlying molecular mechanism that triggers leaf abscission through defoliant remains unsolved. In this study, we meticulously constructed a transcriptomic atlas through single-nucleus mRNA sequencing (snRNA-seq) of the abscission zone (AZ) from cotton petiole. We identified two newly-formed cell types, abscission cells and protection layer cells in cotton petiole AZ after defoliant treatment. GhRLF1 (RAPID LEAF FALLING 1), as one of the members of the cytokinin oxidase/dehydrogenase (CKX) gene family, was further characterized as a key marker gene unique to the abscission cells following defoliant treatment. Overexpression of GhRLF1 resulted in reduced cytokinin accumulation and accelerated leaf abscission. Conversely, CRISPR/Cas9-mediated loss of GhRLF1 function appeared to delay this process. Its interacting regulators, GhWRKY70, acting as "Pioneer" activator, and GhMYB108, acting as "Successor" activator, orchestrate a sequential modulation of GhWRKY70/GhMYB108-GhRLF1-CTK (cytokinin) within the AZ to regulate cotton leaf abscission. GhRLF1 not only regulates leaf abscission but also reduces cotton yield. Consequently, transgenic lines that exhibit rapid leaf falling and require less defoliant but show unaffected cotton yield were developed for mechanical harvesting. This was achieved using a defoliant-induced petiole-specific promoter, proPER21, to drive GhRLF1 (proPER21::RLF1). This pioneering biotechnology offers a new strategy for the chemical defoliation of machine-harvested cotton, ensuring stable production and reducing leaf debris in harvested cotton, thereby enhancing environmental sustainability.

Specific redox and iron homeostasis responses in the root tip of Arabidopsis upon zinc excess

Zinc (Zn) excess negatively impacts primary root growth in Arabidopsis thaliana. Yet, the effects of Zn excess on specific growth processes in the root tip (RT) remain largely unexplored. Transcriptomics, ionomics, and metabolomics were used to examine the specific impact of Zn excess on the RT compared with the remaining root (RR). Zn excess exposure resulted in a shortened root apical meristem and elongation zone, with differentiation initiating closer to the tip of the root. Zn accumulated at a lower concentration in the RT than in the RR. This pattern was associated with lower expression of Zn homeostasis and iron (Fe) deficiency response genes. A distinct distribution of Zn and Fe in RT and RR was highlighted by laser ablation inductively coupled plasma-mass spectrometry analysis. Specialized tryptophan (Trp)-derived metabolism genes, typically associated with redox and biotic stress responses, were specifically upregulated in the RT upon Zn excess, among those Phytoalexin Deficient 3 (PAD3) encoding the last enzyme of camalexin synthesis. In the roots of wild-type seedlings, camalexin concentration increased by sixfold upon Zn excess, and a pad3 mutant displayed increased Zn sensitivity and an altered ionome. Our results indicate that distinct redox and iron homeostasis mechanisms are key elements of the response to Zn excess in the RT.

The developmental basis of floral nectary diversity and evolution

Nectar is a central bridge between angiosperms and animal mutualists. It is produced by specialized structures termed nectaries, which can be found on different plant organs. Consumption of floral nectar by pollinators and the subsequent transfer of pollen contribute to the reproductive success of both angiosperms and their pollinators. Floral nectaries have evolved many times independently, feature diverse structural organizations, and produce nectars with various compositions, which cater to a wide range of pollinators. While the nectary and its nectar have been documented for two millennia, many aspects of nectary biology are still unknown. Recent advances in genetics, genomics, and comparative analyses across diverse species have accelerated our understanding of floral nectary structures and the genetic circuits behind their formation and evolution. In this review, we summarize the recent breakthroughs in nectary research and provide a macroevolutionary framework of floral nectary evolution, focusing on the genetic mechanisms that drive nectary development and shape nectary diversity.

miR858a-encoded peptide, miPEP858a, interacts with the miR858a promoter and requires the C-terminus for associated functions

MicroRNAs (miRNAs) are key regulators of gene expression and typically processed from primary transcripts (pri-miRNAs). Recent discoveries highlight that certain pri-miRNAs also encode miRNA-encoded peptides (miPEPs), which influence miRNA function. However, the molecular mechanisms underlying miPEP activity, including the specific domains or essential amino acid residues required for their function, remain largely unexplored. In this study, we elucidated that the pri-miR858a-derived peptide, miPEP858a, directly interacts with the promoter of the MIR858 gene in Arabidopsis (Arabidopsis thaliana). Notably, the C-terminal region of miPEP858a, composed of 14 amino acid residues, is critical for its functionality. Through DNA-protein interaction assays, including yeast 1-hybrid, chromatin immunoprecipitation (ChIP-qPCR), electrophoretic mobility shift assay, and promoter-reporter analyses, we demonstrated that miPEP858a binds to a specific region within the MIR858 promoter. Exogenous application of a synthetic peptide corresponding to the C-terminal region of miPEP858a resulted in enhanced MIR858 expression, leading to phenotypic changes similar to those observed with the full-length miPEP858a. Moreover, the truncated C-terminal peptide was able to complement mutant plants lacking endogenous miPEP858a, emphasizing its role in regulating miR858a expression and downstream target genes involved in flavonoid biosynthesis and plant development. These findings suggest that the full-length miPEP858a may not be necessary for its biological function, with the C-terminal region being sufficient to modulate miRNA expression. This discovery reveals opportunities for identifying functional domains in other miPEPs, potentially reducing peptide synthesis costs, and offering a more efficient strategy for enhancing agronomic traits in crop plants without the need for complex biotechnological interventions.

MhIDA small peptides modulate the growth and development of roots in Malus hupehensis

KEY MESSAGE

MhIDA small peptides promote apple root growth by enhancing auxin synthesis and cell wall remodeling gene expression, revealing a peptide-based strategy to improve root architecture. Although small peptides have been well documented as crucial regulators of plant growth and development, the molecular mechanisms underlying lateral root morphogenesis in Malus hupehensis remain poorly understood. In this research, exogenous application of 1 µM MhIDA-Like family peptides increased primary root (PR) length by 14.31-19.96% and lateral root (LR) number by 124.54-149.08%. MhIDA, predominant expression in the root tip and lateral root primordium, demonstrated the most substantial promoting effects on PR elongation, LR number and density when the treatment concentration reached 1 µM. Furthermore, similar effects were found in MhIDA-overexpression transgenic apple seedlings, with the number and density of transgenic LRs increase by 80.52 and 126.86%, respectively, compared with wild-type seedlings. More importantly, 1 µM MhIDA treatment induced significant hormonal alterations, with the content of auxin, salicylic acid and gibberellic acid increasing by 1.5-fold, 1.4-fold, and 2.1-fold, respectively, compared to control. The qRT-PCR results showed that MhIDA could induce the expression of auxin synthesis genes (MhTAA1 and MhYUCC1) that were up-regulated by about twofold, and the cell wall remodeling-related genes (MhEXP17, MhXTR6, MhPGAZAT and MhPGLR) were upregulated by about 2- to 4-fold after 1 µM MhIDA treatment, thereby regulating LR emergence and formation of Malus hupehensis. Overall, these findings suggested the MhIDA peptide can promote the growth and development of roots, laying the foundation for cultivating apple rootstocks with strong roots and higher resistance to abiotic stress.

Function in disorder: A review on the roles of the disordered dehydrin proteins in conferring stress tolerance

Water scarcity as a result of drought is considered to be among the most common forms of abiotic stress which directly hampers plant health. Such conditions often lead to various interlinked physiological conditions, including oxidative stress resulting from increased ROS levels that in turn, induce membranes dysfunction, leading to disruption in cellular ionic balance, and oxidation of macromolecules. Plants employ several mechanisms to counter these hostile conditions, which help them adapt to such unforgiving environments. Accumulation of specific types of proteins called dehydrins (DHNs) represents one such mechanism of adaptation. DHNs are ubiquitous in distribution and have been reported in different life forms; accumulating under a wide spectrum of stress. An important role of DHNs is to protect and maintain cell's macromolecular structure and function, thereby preserving membrane integrity, stabilizing proteins and nucleic acid, and conferring protection against oxidative stress. The present article explores different aspects of DHNs, including their structural compositions, architectures and conformational flexibility, and their role in combating a plethora of stress environments, with specific focus towards drought. Possible involvements of DHNs in intracellular biocondensates formation through phase separation and their role in stress sensing are also provided.

CRISPR mutant rapid identification in B. napus: RNA-Seq functional profiling and breeding technology application

Introduction

Traditional rapeseed breeding is inefficient and imprecise. CRISPR genome editing offers a precise alternative for trait improvement. Here, we edited the Bnaida gene in elite rapeseed cultivar ZS11 to study its role in floral organ abcission and enable rapid trait transfer to elite lines.

Methods

The BnaIDA gene was CRISPR-edited in ZS11. Phenotypes (petal adhesion time, cracking force of siliques) were statistically analyzed. And analyze the mutants using RNA -Seq. Edited alleles were introgressed into elite line SW1-6 via backcrossing. Locus-specific primers enabled efficient genotyping to distinguish hetero- and homozygous plants during selection.

Results and discussion

In this study, The Bnaida mutant by gene editing in the cv ZS11, which is widely used in rapeseed breeding. The phenotypic analysis showed that the petal was attached to the pod and pods were harder to crack in edited plants, and then we quickly introduced two Bnaida loci into the elite line of SW1-6 by backcrossing with edited ZS11 as the donor plant. Locus-specific primer combinations were designed to differentiate heterozygous and homozygous genotypes in backcrossing generations, enabling efficient and rapid selection. This study highlights the integration of gene editing and genotyping selection, offering insights into the future of gene editing-assisted breeding.

Cation recognition by benzene sandwich compounds - a DFT perspective

Cation-π interactions between alkali, alkaline earth and ammonium cations and sandwich compounds of benzene and the cyclopentadienyl (Cp) anion were studied using quantum chemical CCSD(T)/CBS and DFT (B3LYP/def2-TZVP) calculations. The results show significantly stronger interactions of sandwich compounds with respect to (uncoordinated) benzene. Moreover, very strong cation-π interactions of Cp sandwich compounds are furthermore surpassed by cation-π interactions of benzene sandwich compounds, which are capable of reaching a remarkable interaction energy value of -196.8 kcal mol-1 (Mg2+/W(benzene)2). While there are only small variations of interaction energy values for sandwich compounds of different transition metals (3d metals < 4d < 5d), cation-π interactions progressively become stronger in the following order: (uncoordinated) benzene < Cp sandwich < benzene sandwich. Aside from interaction energies, the cation-π interactions can be assessed by means of their influence on the geometries of sandwich compounds, which are found to strongly correlate with the strength of cation-π interactions. These results emphasize sandwich compounds, particularly those containing C6 aromatic rings, as promising candidates for new receptors for common metal cations.

Receptor kinase LecRK-I.9 regulates cell wall remodelling during lateral root formation in Arabidopsis

Assembling and remodelling the cell wall is essential for plant development. Cell wall dynamics are controlled by cell wall proteins, polysaccharide biosynthesis, and a variety of sensor and receptor systems. LecRK-I.9, an Arabidopsis thaliana plasma membrane-localized lectin receptor kinase, was previously shown to be involved in cell wall-plasma membrane contacts and to play roles in plant-pathogen interactions, but until now its role in development was not known. LecRK-I.9 is transcribed at a high level in root tissues including the pericycle. Comparative transcript profiling of a loss-of-function mutant versus the wild type identified LecRK-I.9 as a regulator of cell wall metabolism. Consistently, lecrk-I.9 mutants displayed an increased pectin methylesterification level correlated with decreased pectin methylesterase and increased polygalacturonase activities. Also, LecRK-I.9 negatively impacted lateral root development through the direct or indirect regulation of genes encoding (i) cell wall remodelling proteins during early events of lateral root initiation, and (ii) cell wall signalling peptides (CLE2 and CLE4) repressing lateral root emergence and growth. Furthermore, low nitrate reduced LecRK-I.9 expression in roots, particularly in the lateral root emergence zone: even in these conditions, the control of CLE2 and CLE4 expression is maintained. Altogether, the results show that LecRK-I.9 is a key player in negatively regulating both pre-branch site formation and lateral root emergence.

Cell wall remodeling during plant regeneration

Plant regeneration is the process during which differentiated tissues or cells can reverse or alter their developmental trajectory to repair damaged tissues or form new organs. In the plant regeneration process, the cell wall not only functions as a foundational barrier and scaffold supporting plant cells but also influences cell fates and identities. Cell wall remodeling involves the selective degradation of certain cell wall components or the integration of new components. Recently, accumulating evidence has underscored the importance of cell wall remodeling in plant regeneration. Wounding signals, transmitted by transcription factors, trigger the expressions of genes responsible for cell wall loosening, which is essential for tissue repair. In de novo organ regeneration and somatic embryogenesis, phytohormones orchestrate a transcriptional regulatory network to induce cell wall remodeling, which promotes cell fate reprogramming and organ formation. This review summarizes the effects of cell wall remodeling on various regenerative processes and provides novel insights into the future research of uncharacterized roles of cell wall in plant regeneration.

H3K36 methylation stamps transcription resistive to preserve development in plants

Eukaryotic euchromatin is the less-compact chromatin and is modified by many histone modifications such as H3 lysine 36 methylation (H3K36me). Here we report a new chromatin state, 'transcription resistive', which is differentiated from activation and silencing. Transcription resistive is stamped by H3K36me with almost undetectable transcription activity but open-chromatin state, and occupies most documented plant essential genes. Mutating SDG8, previously known as the major H3K36 methyltransferase in Arabidopsis, surprisingly elevates 78.7% of H3K36me3-marked resistive loci, which accounts for 39.4% of the coding genome. Genetically, SDG8 prevents H3K36me activity of SDG4 at short and intronless genes to secure plant fertility, while it collaborates with other H3K36me methyltransferases on long and intron-rich genes. Together, our results reveal that SDG8 is the primary sensor that suppresses excessive H3K36me, and uncovered that 'transcription resistive' is a conserved H3K36me-stamped novel transcription state in plants, highlighting the regulatory diversities and biological significance of H3K36 methylation in eukaryotes.

Comprehensive review of plant small signaling peptides: From stress adaptation mechanisms to practical solutions for crop resilience

Small signaling peptides (SSPs), short proteins of fewer than 100 amino acids, serve as pivotal signaling molecules with diverse structural features, post-translational modifications, and functional roles. They regulate various aspects of plant growth and development by modulating specific cellular signaling pathways. Research has shown that many SSPs are essential for mediating responses to environmental stresses. This review presents the structure, characteristics, and classification of plant SSPs and elucidates their roles in resistance signaling pathways through interactions with their specific receptors. We then summarize recent findings on the biological functions and regulatory mechanisms of SSPs in response to both biotic and abiotic stresses. Finally, we discuss the potential applications and future prospects of these peptides in plant protection. This review offers valuable insights for enhancing plant resilience to environmental stress and advancing sustainable agricultural practices, while also providing key references and perspectives to accelerate research on SSPs in plants.

MYB74 transcription factor guides de novo specification of epidermal cells in the abscission zone of Arabidopsis

The waxy cuticle layer is crucial for plant defence, growth and survival, and is produced by epidermal cells, which were thought to be specified only during embryogenesis. New surface cells are exposed during abscission, by which leaves, fruits, flowers and seeds are shed. Recent work has shown that nonepidermal residuum cells (RECs) can accumulate a protective cuticle layer after abscission, implying the potential de novo specification of epidermal cells by transdifferentiation. However, it remains unknown how this process occurs and what advantage this mechanism may offer over the other surface protection alternative, the wound healing pathways. Here we followed this transdifferentiation process with single-cell RNA sequencing analysis of RECs, showing that nonepidermal RECs transdifferentiate into epidermal cells through three distinct stages. During this vulnerable process, which involves a transient period when the protective layer is not yet formed, stress genes that protect the plant from environmental exposure are expressed before epidermis formation, ultimately facilitating cuticle development. We identify a central role for the transcription factor MYB74 in directing the transdifferentiation. In contrast to alternative protective mechanisms, our results suggest that de novo epidermal specification supports the subsequent growth of fruit at the abscission site. Altogether, we reveal a developmental programme by which plants use a transdifferentiation pathway to protect the plant while promoting growth.

The Gene SiPrx from Saussurea involucrata Enhances the Stress Resistance of Silphium perfoliatum L

Peroxiredoxin (Prx) plays a role in maintaining the balance of intracellular reactive oxygen species. The peroxidase SiPrx gene from the Tianshan Snow Lotus (Saussurea involucrata) has been proved to significantly enhance the stress resistance of plants. In this study, the SiPrx gene was expressed heterogeneously in high-quality herbage Silphium perfoliatum L. (SP). After treatment with NaCl, the transgenic SP only exhibited partial leaf wilting, whereas the wild-type (WT) plants were on the brink of death. Simultaneously, physiological and biochemical assays indicated that under high-salt conditions, the content of malondialdehyde in the transgenic plants was significantly lower than that in the WT plants, while the activity of antioxidant enzymes was significantly higher than that in the WT plants. The expression of the SiPrx gene has been shown to significantly enhance the salt stress resistance of transgenic SP. Furthermore, after treatment at -10 °C for 48 h, the leaves of transgenic plants were able to maintain a certain morphological structure, whereas the WT plants were completely wilted. Physiological and biochemical index measurements indicated that all indicators in the transgenic plants were significantly better than those in the WT plants. Based on these findings, this study plans to overexpress the SiPrx gene extracted from Saussurea involucrata in Comfrey using the Agrobacterium-mediated method and then study its effects on the stress resistance of transgenic SP. The research results indicate that the SiPrx gene shows significant application potential in enhancing the cold resistance and salt tolerance of SP. This study provides a certain research basis and scientific evidence for the mining of stress resistance genes in Saussurea involucrata and the cultivation of new varieties of SP.

H3K36me3 regulates subsets of photosynthesis genes in Sorghum bicolor potentially by counteracting H3K27me3 or H2A.Z

H3K36me3, catalyzed by ASHH proteins, serves as a positive histone mark associated with gene expression and plays a crucial role in plant development. In our study, we identified that sorghum SbASHH2 exhibits H3K36 methyltransferase activity. Immunoprecipitation analysis revealed that H3K36me3 rarely co-occurs with H3K27me3, and genome-wide profiling of these two marks indicates a non-overlapping distribution across the sorghum genome, underscoring the antagonistic relationship between H3K36me3 and H3K27me3. Furthermore, we observed that H2A.Z is deposited near the transcription start site (TSS) of genes enriched with H3K36me3, while genes with H2A.Z deposition in the gene body lack H3K36me3, suggesting an interplay between H3K36me3 and H2A.Z deposition. Our findings show that the high expression of photosynthesis genes in leaves is closely linked to H3K36me3 deposition, with only a small subset involving the removal of H3K27me3 or eviction of H2A.Z. This implies that H3K36me3 activates specific subsets of photosynthesis genes by antagonizing H3K27me3 or H2A.Z. Additionally, we found that the deposition of H3K36me3 on most photosynthesis genes is neither specific to mesophyll (M) nor bundle sheath (BS) cells and is independent of light induction. Our results emphasize the significance of H3K36me3 in the regulation of photosynthesis genes and lay the groundwork for further investigation into the mechanisms by which H3K36me3 contributes to gene regulation.

Research on the regulation mechanism of drought tolerance in wheat

Wheat (Triticum aestivum L.) is one of the most important crops in arid and semi-arid areas of the world, and its sustainable and efficient production is essential for ensuring food security in China and globally. However, with the global climate change, wheat production is increasingly endangered by abiotic stress, and drought stress has become the main abiotic stress factor restricting wheat production efficiently. Therefore, investigating drought resistance genes and elucidating the mechanisms underlying drought resistance regulation is crucial for the genetic enhancement of drought resistance and the development of new drought-resistant wheat varieties. This paper reviews the majority of research conducted on wheat drought resistance over the past five years, focusing on aspects, such as transcriptional regulation, protein post-translational modifications, and other regulatory mechanisms related to drought resistance in wheat. Additionally, this paper discusses future directions for the genetic improvement of drought resistance and the breeding of new drought-resistant wheat varieties.

A CW-type zinc finger protein is involved in RES-oxylipin signaling and the response to abiotic stress in Arabidopsis thaliana

Introduction

Oxylipins regulate the response of plants to biotic and abiotic stress factors and the tolerance of unfavorable conditions. While the signaling pathway of jasmonic acid has been intensively studied, little is known about the signal transduction that mediates the responses of reactive electrophile oxylipins such as 12-oxo phytodienoic acid and prostaglandins.

Methods and results

Here, a CW-type zinc finger protein (ZIFI1, At3g62900) was identified as a new signaling factor in a mutant screen. Transcriptome analysis of Arabidopsis mutants with a defect in this gene showed that the zinc finger protein is involved in regulating gene expression. Only about half (327 genes) of the about 646 genes induced by the reactive electrophilic oxylipin prostaglandin in the wild type was also up-regulated in the zifi1 mutant. The differentially expressed genes are enriched in genes related to detoxification and responses to stress factors such as oxidative stress. Therefore, it was tested whether a defect in the zinc finger gene resulted in altered sensitivity to stress factors. The sensitivity to the reactive oxygen species butyl hydroperoxide and to the xenobiotic triiodobenzoic acid was increased in the mutant. In addition, production of reactive oxygen species induced by the bacterial elicitor flg22 was accelerated.

Discussion

The results provide new insights into the factors involved in the signaling of reactive electrophiles and the connection of different stress signaling pathways.

Competitive binding of small antagonistic peptides to the OsER1 receptor optimizes rice panicle architecture

Rice panicle architecture is a pivotal trait that strongly contributes to grain yield. Small peptide ligands from the OsEPF/EPFL family synergistically control panicle architecture by recognition of the OsER1 receptor and subsequent activation of the OsMKKK10-OsMKK4-OsMPK6 cascade, indicating that specific ligand-receptor pairs orchestrate rice panicle development. However, how small homologous peptides fine-tune organ morphogenesis by targeting a common receptor remains to be clarified. Here, we report that the small peptide OsEPFL5 acts as a ligand of the OsER1 receptor that inactivates the OsMKKK10-OsMKK4-OsMPK6 cascade, suggesting that OsEPFL5 plays a role opposite to that of the OsEPFL6/7/8/9 subfamily in regulating spikelet number per panicle and grain size. Notably, OsEPFL5 competitively replaces binding of OsEPFL6, OsEPFL7, OsEPFL8, or OsEPFL9 to the OsER1 receptor, revealing antagonistic competition between these small homologous peptides. Specifically enhancing the expression of OsEPFL5 can significantly improve grain yield by suppressing functions of the ligand-receptor pairs OsEPFL6-OsER1, OsEPFL7-OsER1, OsEPFL8-OsER1, and OsEPFL9-OsER1, suggesting that competitive binding to the OsER1 receptor by small antagonistic peptides can optimize rice panicle architecture. Our findings clarify how a receptor agonist and antagonist define inductive and inhibitory cues to shape rice panicle architecture, thus providing a new method for rationally breaking yield-trait coupling by manipulating small antagonistic peptides.

Decoding small peptides: Regulators of plant growth and stress resilience

Small peptides (SPs) are pivotal signaling molecules that play essential roles in the precise regulation of plant growth, development, and stress responses. Recent advancements in sequencing technologies, bioinformatics approaches, and biochemical and molecular techniques have significantly enhanced the accuracy of SP identification, unveiling their diverse biological functions in plants. This review provides a comprehensive overview of the characteristics and methodologies for identifying SPs in plants. It highlights recent discoveries regarding the biological roles and signaling pathways of SPs in regulating plant growth, development, and plant-microbial interactions, as well as their contributions to plant resilience under various environmental stresses, including abiotic stress, nutrient deficiencies, and biotic challenges. Additionally, we discuss current insights into the potential applications of SPs and outline future research directions aimed at leveraging these molecules to enhance plant adaptation to environmental challenges. By integrating recent findings, this review lays a foundation for advancing the understanding and utilization of SPs to improve plant resilience and productivity.

Phytocytokine genes newly discovered in Malus domestica and their regulation in response to Erwinia amylovora and acibenzolar-S-methyl

Phytocytokines belong to a category of small secreted peptides with signaling functions that play pivotal roles in diverse plant physiological processes. However, due to low levels of sequence conservation across plant species and poorly understood biological functions, the accurate detection and annotation of corresponding genes is challenging. The availability of a high-quality apple (Malus domestica) genome has enabled the exploration of five phytocytokine gene families, selected on the basis of their altered expression profiles in response to biotic stresses. These include phytosulfokine, inflorescence deficient in abscission/-like, pathogen-associated molecular pattern induced secreted peptide, plant peptide containing sulfated tyrosine, and C-terminally encoded peptide. The genes encoding the precursors of these five families of signaling peptides were identified using a customized bioinformatics protocol combining genome mining, homology searches, and peptide motif detection. Transcriptomic analyses showed that these peptides were deregulated in response to Erwinia amylovora, the causal agent of fire blight in pome fruit trees, and in response to a chemical elicitor (acibenzolar-S-methyl). Finally, gene family evolution and the orthology relationships with Arabidopsis thaliana homologs were investigated.

Phytoremediation of microplastics by water hyacinth

Microplastics have emerged as pervasive environmental pollutants, posing significant risks to both terrestrial and aquatic ecosystems worldwide. Current remediation strategies-including physical, chemical, and microbial methods-are inadequate for large-scale, in situ removal of microplastics, highlighting the urgent need for alternative solutions. Phytoremediation, an eco-friendly and cost-effective technology, holds promise in addressing these challenges, though its application to microplastic pollution remains underexplored. Here we show the capacity of Eichhornia crassipes (water hyacinth), a fast-growing, floating aquatic plant, to remove microplastics from contaminated water. Our results show that within 48 h, water hyacinth achieved removal efficiencies of 55.3 %, 69.1 %, and 68.8 % for 0.5, 1, and 2 μm polystyrene particles, respectively, with root adsorption identified as the primary mechanism. Fluorescence microscopy revealed that the extremely large and abundant root caps, featuring a total surface area exceeding 150,000 mm2 per plant, serve as the principal sites for the entrapment of microplastics. Furthermore, a unique "vascular ring" structure within the stem prevents the translocation of microplastics to aerial tissues, safeguarding leaves for potential downstream applications. This study offers the first microstructural insight into the mechanisms underpinning water hyacinth's exceptional microplastic adsorption capacity and resilience, providing a promising framework for developing phytoremediation strategies to mitigate microplastic pollution in aquatic ecosystems.

MADS31 supports female germline development by repressing the post-fertilization programme in cereal ovules

The female germline of flowering plants develops within a niche of sporophytic (somatic) ovule cells, also referred to as the nucellus. How niche cells maintain their own somatic developmental programme, yet support the development of adjoining germline cells, remains largely unknown. Here we report that MADS31, a conserved MADS-box transcription factor from the B-sister subclass, is a potent regulator of niche cell identity. In barley, MADS31 is preferentially expressed in nucellar cells directly adjoining the germline, and loss-of-function mads31 mutants exhibit deformed and disorganized nucellar cells, leading to impaired germline development and partial female sterility. Remarkably similar phenotypes are observed in mads31 mutants in wheat, suggesting functional conservation within the Triticeae tribe. Molecular assays indicate that MADS31 encodes a potent transcriptional repressor, targeting genes in the ovule that are normally active in the seed. One prominent target of MADS31 is NRPD4b, a seed-expressed component of RNA polymerase IV/V that is involved in epigenetic regulation. NRPD4b is directly repressed by MADS31 in vivo and is derepressed in mads31 ovules, while overexpression of NRPD4b recapitulates the mads31 ovule phenotype. Thus, repression of NRPD4b by MADS31 is required to maintain ovule niche functionality. Our findings reveal a new mechanism by which somatic ovule tissues maintain their identity and support germline development before transitioning to the post-fertilization programme.

A close-up of regulatory networks and signaling pathways of MKK5 in biotic and abiotic stresses

Mitogen-activated protein Kinase Kinase 5 (MKK5) is a central hub in the complex phosphorylation chain reaction of the Mitogen-activated protein kinases (MAPK) cascade, regulating plant responses to biotic and abiotic stresses. This review manuscript aims to provide a comprehensive analysis of the regulatory mechanism of the MKK5 involved in stress adaptation. This review will delve into the intricate post-transcriptional and post-translational modifications of the MKK5, discussing how they affect its expression, activity, and subcellular localization in response to stress signals. We also discuss the integration of the MKK5 into complex signaling pathways, orchestrating plant immunity against pathogens and its modulating role in regulating abiotic stresses, such as: drought, cold, heat, and salinity, through the phytohormonal signaling pathways. Furthermore, we highlight potential applications of the MKK5 for engineering stress-resilient crops and provide future perspectives that may pave the way for future studies. This review manuscript aims to provide valuable insights into the mechanisms underlying MKK5 regulation, bridge the gap from numerous previous findings, and offer a firm base in the knowledge of MKK5, its regulating roles, and its involvement in environmental stress regulation.

Combination of PAMP-induced peptide signaling and its regulator SpWRKY65 boosts tomato resistance to Phytophthora infestans

Late blight, caused by Phytophthora infestans (P. infestans), seriously compromises tomato growth and yield. PAMP-induced peptides (PIPs) are secreted peptides that act as endogenous elicitors, triggering plant immune responses. Our previous research indicated that the exogenous application of PIP1 from Solanum pimpinelifolium L3708, named SpPIP1, enhances tomato resistance to P. infestans. However, little is known about the roles of additional family members in tomato resistance to P. infestans. In addition, there remains a significant gap in understanding the receptors of SpPIPs and the transcription factors (TFs) that regulate SpPIPs signaling in tomato defense, and the combination of SpPIPs signaling and TFs in defending against pathogens is rarely studied. This study demonstrates that the exogenous application of SpPIP-LIKE1 (SpPIPL1) also strengthens tomato resistance by affecting the phenylpropanoid biosynthesis pathway. Both SpPIP1 and SpPIPL1 trigger plant defense responses in a manner dependent on RLK7L. Tomato plants overexpressing the precursors of SpPIP1 and SpPIPL1 (SpprePIP1 and SpprePIPL1) exhibited enhanced expression of pathogenesis-related genes, elevated H2O2 and ABA levels, and increased lignin accumulation. Notably, SpWRKY65 was identified as a transcriptional activator of SpprePIP1 and SpprePIPL1. Disease resistance assays and gene expression analyses revealed that overexpression of SpWRKY65 (OEWRKY65) confers tomato resistance to P. infestans, while wrky65 knockout led to the opposite effect. Intriguingly, transgenic tomato studies showed that either spraying OEWRKY65 with SpPIPs or co-overexpressing SpprePIP1 and SpWRKY65 further augmented tomato resistance, underscoring the potential of gene stacking in enhancing disease resistance. In summary, this study offers new perspectives on controlling late blight and developing tomato varieties with improved resistance. The results emphasize the potential of exogenous SpPIPs application as an eco-friendly strategy for crop protection, laying a theoretical foundation for advancing crop breeding.

Comparative analysis of small secreted peptide signaling during defense response: insights from vascular and non-vascular plants

Small secreted peptides (SSPs) play an important role in modulating immune responses in all land plants. However, the evolution of stress peptide signaling in different plant phyla remains poorly understood. Here, we compared the expression of SSP genes in the pathogen-induced transcriptomes of vascular and non-vascular plants. We found 13, 19, 15, and 28 SSP families that were differentially expressed during infection in Physcomitrium patens, Zea mays, Brassica napus, and Solanum tuberosum, respectively. A comparative study of peptide motifs and predicted three-dimensional structures confirmed the similarity of SSPs across the examined plant species. In both vascular and non-vascular plants. However, only the RALF peptide family was differentially regulated under infection. We also found that EPFL peptides, which are involved in growth and development processes in angiosperms, were differentially regulated in P. patens in response to pathogen infection. The search for novel immune-specific peptides revealed a family of PSY-like peptides that are differentially regulated during infection in P. patens. The treatment with synthetic tyrosine-modified and non-modified PSY, and PSY-like peptides, as well as recombinant EPFL and MEG, validated their roles in the immune response and growth regulation. Thus, our study showed the complex nature of SSP signaling and shed light on the regulation of SSPs in different plant lineages during infection.

Cell wall dynamic changes and signaling during plant lateral root development

Lateral roots (LRs), are an important component of plant roots, playing a crucial role in anchoring the plant in the soil and facilitating the uptake of water and nutrients. As post-embryonic organs, LRs originate from the pericycle cells of the primary root, and their formation is characterized by precise regulation of cell division and complex intercellular interactions, both of which are closely tied to cell wall regulation. Considering the rapid advances in molecular techniques over the past three decades, we reframe the understanding of the dynamic change in cell wall during LR development by summarizing the factors that precipitate these changes and their effects, as well as the regulated signals involved. Additionally, we discuss current challenges in this field and propose potential solutions.

The TaCLE24b peptide signaling cascade modulates lateral root development and drought tolerance in wheat

Plant peptide hormones play an important role in regulating root development and stress responses. Here, we identify a root-derived CLAVATA3/Endosperm surrounding region-related (CLE) peptide TaCLE24b and its leucine-rich repeat receptor-like kinase CLAVATA1 (CLV1) TaCLV1, which together regulate the formation of lateral root primordium and the outgrowth of lateral root in wheat. Additionally, a loss-of-function mutation of TaSG-D1, encoding a Ser/Thr protein kinase glycogen synthase kinase 3 (STKc_GSK3), also enhances the formation of lateral root primordium and the outgrowth of lateral roots in wheat. Furthermore, TaCLV1 interacts with TaSG-D1, leading to phosphorylation and degradation of TaSG-D1. Whereas the presence of TaCLE24b enhances the binding affinity and phosphorylation ability of TaCLV1 to TaSG-D1, thereby positively fine-tuning lateral root development and contributing to drought tolerance in wheat. Overall, our findings provide new insights into the significance of the peptide signaling pathway in regulating lateral root development and responding to drought stress in wheat.

Antagonistic systemin receptors integrate the activation and attenuation of systemic wound signaling in tomato

Pattern recognition receptor (PRR)-mediated perception of damage-associated molecular patterns (DAMPs) triggers the first line of inducible defenses in both plants and animals. Compared with animals, plants are sessile and regularly encounter physical damage by biotic and abiotic factors. A longstanding problem concerns how plants achieve a balance between wound defense response and normal growth, avoiding overcommitment to catastrophic defense. Here, we report that two antagonistic systemin receptors, SYR1 and SYR2, of the wound peptide hormone systemin in tomato act in a ligand-concentration-dependent manner to regulate immune homeostasis. Whereas SYR1 acts as a high-affinity receptor to initiate systemin signaling, SYR2 functions as a low-affinity receptor to attenuate systemin signaling. The expression of systemin and SYR2, but not SYR1, is upregulated upon SYR1 activation. Our findings provide a mechanistic explanation for how plants appropriately respond to tissue damage based on PRR-mediated perception of DAMP concentrations and have implications for uncoupling defense-growth trade-offs.

Brems1 mutation induced tapetum deficiency leading to male sterility in Chinese cabbage (Brassica rapa L. ssp. pekinensis)

KEY MESSAGE

The mutation in Brems1 resulting in male sterility in Chinese cabbage were validated through two allelic mutations. Male sterile lines are ideal for hybrid seed production in Chinese cabbage. Herein, the complete male sterile mutants M5026 and M5073 were obtained through ethyl methanesulfonate (EMS) mutagenesis in the Chinese cabbage double haploid line 'FT'. Cytological observations revealed that M5026 exhibited an absence of the tapetum, an overabundance of microsporocytes, and abnormal exine formation in pollen. The male sterility phenotype of M5026 was controlled by a single recessive nuclear gene. Using mutmap sequencing and kompetitive allele-specific PCR (KASP) identification and gene cloning, two distinct SNPs in BraA10g029920.3.5C, encoding EMS1 (excess microsporocytes 1), were identified to be associated with the male sterility of M5026 and M5073. The gene was named as Brems1. M5026 and M5073 were determined to be allelic variants. Both BrEMS1 and Brems1 were subcellularly localized at the cell membrane. Brems1 exhibited the highest expression level in buds, while no expression was detected in roots. Transcriptomic analysis revealed that Brems1 mutations reduced the expression levels of genes associated with the tapetum, pollen tube, and LRR-RLK family. These results suggested that Brems1 played a critical role in pollen development and contributes to elucidating the molecular mechanisms underlying tapetum development and male sterility in Chinese cabbage.

Time-resolved oxidative signal convergence across the algae-embryophyte divide

The earliest land plants faced a significant challenge in adapting to environmental stressors. Stress on land is unique in its dynamics, entailing swift and drastic changes in light and temperature. While we know that land plants share with their closest streptophyte algal relatives key components of the genetic makeup for dynamic stress responses, their concerted action is little understood. Here, we combine time-course stress profiling using photophysiology, transcriptomics on 2.7 Tbp of data, and metabolite profiling analyses on 270 distinct samples, to study stress kinetics across three 600-million-year-divergent streptophytes. Through co-expression analysis and Granger causal inference we predict a gene regulatory network that retraces a web of ancient signal convergences at ethylene signaling components, osmosensors, and chains of major kinases. These kinase hubs already integrated diverse environmental inputs since before the dawn of plants on land.

Lights, location, action: shade avoidance signalling over spatial scales

Plants growing in dense vegetation need to flexibly position their photosynthetic organs to ensure optimal light capture in a competitive environment. They do so through a suite of developmental responses referred to as the shade avoidance syndrome. Below ground, root development is also adjusted in response to above-ground neighbour proximity. Canopies are dynamic and complex environments with heterogeneous light cues in the far-red, red, blue, and UV spectrum, which can be perceived by photoreceptors in spatially separated plant tissues. Molecular regulation of plant architecture adjustment via PHYTOCHROME-INTERACTING FACTOR transcription factors and growth-related hormones such as auxin, gibberellic acid, brassinosteroids, and abscisic acid were historically studied without much attention to spatial or tissue-specific context. Recent developments and technologies have, however, sparked strong interest in spatially explicit understanding of shade avoidance regulation. Other environmental factors such as temperature and nutrient availability interact with the molecular shade avoidance regulation network, often depending on the spatial location of the signals, and the responding organs. Here, we review recent advances in how plants respond to heterogeneous light cues and integrate these with other environmental signals.

SDG8 and HUB2 depositing euchromatin histone marks play important roles in meiosis and crossing-over regulation

Histone modifications play critical roles in plant growth and development. Crossing-over (CO) during meiosis, which constitutes a fundamental process ensuring sexual transmission of genetic material to the next generation and, meanwhile, generating diversity within species by creating new chromosome/allele combinations, occurs predominantly in euchromatin, which is enriched in active histone marks such as H3K4me3, H3K36me3, and H2Bub1. In plants, it is known that CO hotspots are correlated with H3K4me3 but the role of H3K36me3 and H2Bub1 during meiosis remains elusive so far. Here, we studied the Arabidopsis (Arabidopsis thaliana) sdg8-1 and hub2-2 mutants impeded in depositing H3K36me3 and H2Bub1, respectively. Chromosome spreading using 4',6-diamidino-2-phenylindole (DAPI) staining indicated that male meiotic stages are defective in the sdg8-1 mutant, and the defect increases synergistically in the sdg8-1hub2-2 double mutant. Defects in meiosis, seed formation, and silique length were also observed by RNAi-knockdown of SDG8 using the meiosis-specific gene DMC1 promoter. This corroborates to support a bona fide role of active histone marks during meiosis and plant reproduction. Using the tetrad-based visual reporter lines and immunostaining with antibodies against HEI10 and ZYP1, it was found that synapsis and pairing of homologous chromosomes are abnormal and CO rate increases in sdg8 mutants, pointing to a repressive role of SDG8 in Arabidopsis male meiotic homologous recombination.

Preventing inappropriate signals pre- and post-ligand perception by a toggle switch mechanism of ERECTA

Dynamic control of signaling events requires swift regulation of receptors at an active state. By focusing on the Arabidopsis ERECTA (ER) receptor kinase, which perceives peptide ligands to control multiple developmental processes, we report a mechanism preventing inappropriate receptor activity. The ER C-terminal tail (ER_CT) functions as an autoinhibitory domain: Its removal confers higher kinase activity and hyperactivity during inflorescence and stomatal development. ER_CT is required for the binding of a receptor kinase inhibitor, BKI1, and two U-box E3 ligases, PUB30 and PUB31, that trigger activated ER to degradation through ubiquitination. We further identify ER_CT as a phosphodomain transphosphorylated by the coreceptor BAK1. The phosphorylation impacts the tail structure, likely releasing ER from autoinhibition. The phosphonull version enhances BKI1 association, whereas the phosphomimetic version promotes PUB30/31 association. Thus, ER_CT acts as an off-on-off toggle switch, facilitating the release of BKI1 inhibition, enabling signal activation, and swiftly turning over the receptors afterward. Our results elucidate a mechanism that fine-tunes receptor signaling via a phosphoswitch module, maintaining the receptor at a low basal state while ensuring robust yet transient activation upon ligand perception.

Abscission zone metabolism impacts pre- and post-harvest fruit quality: a very attaching story

The function of abscission zones (AZs) determines the timing of fleshy fruit abscission, with important consequences not only for the optimal fruit harvest, but also on the overall final fruit quality. In this context, chemical treatments are commonly used at different stages of fruit development to control fruit abscission, which can also have positive or negative effects on fruit quality. In the current review, we examine commonly used chemicals that affect the metabolic activity in the AZs of fleshy fruit, in addition to their effects on fruit quality characteristics. The main hormone metabolism and signaling in the AZ include that of ethylene, auxin, abscisic acid and jasmonates, and the molecular components that are involved are covered and discussed, in addition to how these hormones work together to regulate AZ activity and hence, affect fruit quality. We focus on studies that have provided new insight into possible protein complexes that function in the AZ, including multiple MADS-box transcription factors, with potential overlapping regulatory roles which exist between AZ development, ethylene production, AZ activation, fruit ripening and overall fruit quality. The view of the AZ as a cross roads where multiple pathways and signals are integrated is discussed.

Peptide hormones in plants

Peptide hormones are defined as small secreted polypeptide-based intercellular communication signal molecules. Such peptide hormones are encoded by nuclear genes, and often go through proteolytic processing of preproproteins and post-translational modifications. Most peptide hormones are secreted out of the cell to interact with membrane-associated receptors in neighboring cells, and subsequently activate signal transductions, leading to changes in gene expression and cellular responses. Since the discovery of the first plant peptide hormone, systemin, in tomato in 1991, putative peptide hormones have continuously been identified in different plant species, showing their importance in both short- and long-range signal transductions. The roles of peptide hormones are implicated in, but not limited to, processes such as self-incompatibility, pollination, fertilization, embryogenesis, endosperm development, stem cell regulation, plant architecture, tissue differentiation, organogenesis, dehiscence, senescence, plant-pathogen and plant-insect interactions, and stress responses. This article, collectively written by researchers in this field, aims to provide a general overview for the discoveries, functions, chemical natures, transcriptional regulations, and post-translational modifications of peptide hormones in plants. We also updated recent discoveries in receptor kinases underlying the peptide hormone sensing and down-stream signal pathways. Future prospective and challenges will also be discussed at the end of the article.

Epigenetics in the modern era of crop improvements

Epigenetic mechanisms are integral to plant growth, development, and adaptation to environmental stimuli. Over the past two decades, our comprehension of these complex regulatory processes has expanded remarkably, producing a substantial body of knowledge on both locus-specific mechanisms and genome-wide regulatory patterns. Studies initially grounded in the model plant Arabidopsis have been broadened to encompass a diverse array of crop species, revealing the multifaceted roles of epigenetics in physiological and agronomic traits. With recent technological advancements, epigenetic regulations at the single-cell level and at the large-scale population level are emerging as new focuses. This review offers an in-depth synthesis of the diverse epigenetic regulations, detailing the catalytic machinery and regulatory functions. It delves into the intricate interplay among various epigenetic elements and their collective influence on the modulation of crop traits. Furthermore, it examines recent breakthroughs in technologies for epigenetic modifications and their integration into strategies for crop improvement. The review underscores the transformative potential of epigenetic strategies in bolstering crop performance, advocating for the development of efficient tools to fully exploit the agricultural benefits of epigenetic insights.

GmERF13 mediates salt inhibition of nodulation through interacting with GmLBD16a in soybean

While the genetic regulation of nodule formation has been well explored, the molecular mechanisms by which abiotic stresses, such as salt stress, impede nodule formation remain largely elusive. Here, we identify four APETALA2/Ethylene Responsive Factor (AP2/ERF) transcription factors, GmERF13s, that are induced by salt stress and play key roles in salt-repressed nodulation. Loss of GmERF13 function increases nodule density, while its overexpression suppresses nodulation. Moreover, salt stress-inhibited nodule formation is greatly attenuated in GmERF13 loss-of-function mutants, whereas it becomes more pronounced when GmERF13 is overexpressed. Furthermore, GmERF13s can interact with Lateral Organ Boundaries Domain 16 (GmLBD16a), which attenuates GmLBD16a's binding capacity on Expansin17c (GmEXP17c) promoter. Additionally, salt-induced GmERF13s expression relies on abscisic acid signaling, with direct promotion facilitated by GmABI5, illustrating their direct involvement in enhancing GmERF13s expression. Collectively, our study reveals a molecular mechanism by which salt stress impedes nodulation through the GmERF13-GmLBD16a-GmEXP17 module in soybean.

ABA-activated low-nanomolar Ca2+-CPK signalling controls root cap cycle plasticity and stress adaptation

Abscisic acid (ABA) regulates plant stress adaptation, growth and reproduction. Despite extensive ABA-Ca2+ signalling links, imaging ABA-induced increases in Ca2+ concentration has been challenging, except in guard cells. Here we visualize ABA-triggered [Ca2+] dynamics in diverse organs and cell types of Arabidopsis thaliana using a genetically encoded Ca2+ ratiometric sensor with a low-nanomolar Ca2+-binding affinity and a large dynamic range. The subcellular-targeted Ca2+ ratiometric sensor reveals time-resolved and unique spatiotemporal Ca2+ signatures from the initial plasma-membrane nanodomain, to cytosol, to nuclear oscillation. Via receptors and sucrose-non-fermenting1-related protein kinases (SnRK2.2/2.3/2.6), ABA activates low-nanomolar Ca2+ transient and Ca2+-sensor protein kinase (CPK10/30/32) signalling in the root cap cycle from stem cells to cell detachment. Surprisingly, unlike the prevailing NaCl-stimulated micromolar Ca2+ spike, salt stress induces a low-nanomolar Ca2+ transient through ABA signalling, repressing key transcription factors that dictate cell fate and enzymes that are crucial to root cap maturation and slough. Our findings uncover ABA-Ca2+-CPK signalling that modulates root cap cycle plasticity in adaptation to adverse environments.

Impact of water stress to plant epigenetic mechanisms in stress and adaptation

Water is the basic molecule in living beings, and it has a major impact on vital processes. Plants are sessile organisms with a sophisticated regulatory network that regulates how resources are distributed between developmental and adaptation processes. Drought-stressed plants can change their survival strategies to adapt to this unfavorable situation. Indeed, plants modify, change, and modulate gene expression when grown in a low-water environment. This adaptation occurs through several mechanisms that affect the expression of genes, allowing these plants to resist in dry regions. Epigenetic modulation has emerged as a major factor in the transcription regulation of drought stress-related genes. Moreover, specific molecular and epigenetic modifications in the expression of certain genetic networks lead to adapted responses that aid a plant's acclimatization and survival during repeated stress. Indeed, understanding plant responses to severe environmental stresses, including drought, is critical for biotechnological applications. Here, we first focused on drought stress in plants and their general adaptation mechanisms to this stress. We also discussed plant epigenetic regulation when exposed to water stress and how this adaptation can be passed down through generations.

The rise of CLAVATA: evidence for CLAVATA3 and WOX signaling in the fern gametophyte

CLAVATA3/EMBRYO SURROUNDING REGION (CLE) peptides are 12-13 amino acid-long peptides that serve as positional signals in plants. The core CLE signaling module consists of a CLE peptide and a leucine-rich repeat receptor-like kinase, but in flowering plants, WUSCHEL-RELATED HOMEOBOX (WOX) transcription factors are also incorporated to form negative feedback loops that regulate stem cell maintenance in the shoot and root. It is not known when WOX genes were co-opted into CLE signaling pathways, only that mosses and liverworts do not require WOX for CLE-regulated stem cell activities. We identified 11 CLE-encoding genes in the Ceratopteris genome, including one (CrCLV3) most similar to shoot meristem CLE peptide CLAVATA3. We performed the first functional characterization of a fern CLE using techniques including RNAi knockdown and synthetic peptide dosage. We found that CrCLV3 promotes cell proliferation and stem cell identity in the gametophyte meristem. Importantly, we provide evidence for CrCLV3 regulation of the WOX gene CrWOXA during the developmental stage when female gametangium formation begins. These discoveries open a new avenue for CLE peptide research in the fern and clarify the evolutionary timeline of CLE-WOX signaling in land plants.

The chromatin remodeling factor OsINO80 promotes H3K27me3 and H3K9me2 deposition and maintains TE silencing in rice

The INO80 chromatin remodeling complex plays a critical role in shaping the dynamic chromatin environment. The diverse functions of the evolutionarily conserved INO80 complex have been widely reported. However, the role of INO80 in modulating the histone variant H2A.Z is controversial. Moreover, whether INO80 helps regulate heterochromatin remains unknown. Here, we characterize the regulatory effects of OsINO80 on protein-coding genes and transposable elements (TEs) in rice. Upon OsINO80 overexpression in rice, we found three types of OsINO80-occupied regions with different chromatin signatures: type I (enriched with H2A.Z), type II (enriched with H3K9me2), and type III (deficient in H2A.Z/H3K9me2). Loss of OsINO80 results in a decrease in H3K27me3, but not H2A.Z, at type I regions as well as a decrease in H3K9me2 at type II regions, which correlates with TE activation and transposition. Our findings reveal that OsINO80 facilitates H3K27me3 establishment, promotes H3K9me2 deposition, and maintains TE silencing.

A regulatory network involving calmodulin controls phytosulfokine peptide processing during drought-induced flower abscission

Drought stress substantially decreases crop yields by causing flowers and fruits to detach prematurely. However, the molecular mechanisms modulating organ abscission under drought stress remain unclear. Here, we show that expression of CALMODULIN2 (CaM2) is specifically and sharply increased in the pedicel abscission zone in response to drought and plays a positive role in drought-induced flower drop in tomato (Solanum lycopersicum). Due to partial functional redundancy with SlCaM6, we generated the Slcam2 Slcam6 double mutant, which showed minimal flower drop under drought. SlCaM2 and SlCaM6 interacted with the transcription factor signal responsive 3L (SlSR3L), with the 3 proteins operating in the same pathway, based on genetic data. We identified Protease inhibitor26 (SlPI26) as a target gene of SlSR3L by DNA affinity purification sequencing and transcriptome analysis. SlPI26 specifically inhibited the activity of the phytaspase SlPhyt2, hence preventing the generation of active phytosulfokine peptide and negatively regulating drought-induced flower drop. SlCaM2 and SlCaM6 enhanced the repression of SlPI26 expression by SlSR3L, promoting drought-induced flower drop. In addition, the nonphototropic hypocotyl3 (SlNPH3)-Cullin3 (SlCUL3) complex, which relies on auxin, interacted with SlSR3L to induce its degradation. However, under drought conditions, SlNPH3-SlCUL3 function is compromised due to lower auxin concentration. These results uncover a regulatory network that precisely controls floral drop in response to drought stress.

CLAVATA3 INSENSITIVE RECEPTOR KINASEs regulate lateral root initiation and spacing in Arabidopsis

The root system architecture is very critical for plants to adapt to ever-changing environmental stimulations and is largely affected by lateral roots (LRs). Therefore, how plants regulate LR initiation and spacing is a key point for root system development. Previous studies have shown that RECEPTOR-LIKE KINASE 7 (RLK7) and its ligand TARGET OF LBD SIXTEEN 2 (TOLS2) control the initiation and spacing of LRs. However, the molecular mechanism underlying the perception and transduction of the TOLS2 signal by RLK7 remains to be elucidated. In this study, we explored whether CLAVATA3 INSENSITIVE RECEPTOR KINASEs (CIKs) are critical signaling components during Arabidopsis (Arabidopsis thaliana) LR development by investigating phenotypes of cik mutants and examining interactions between CIKs and members of the RLK7-mediated signaling pathway. Our results showed that high-order cik mutants generated more LRs because of more LR initiation and defective LR spacing. The cik mutants showed reduced sensitivity to applied TOLS2 peptides. TOLS2 application enhanced the interactions between CIKs and RLK7 and the RLK7-dependent phosphorylation of CIKs. In addition, overexpression of transcription factor PUCHI and constitutive activation of MITOGEN-ACTIVATED PROTEIN KINASE KINASE 4 (MKK4) and MKK5 partially rescued the spacing defects of LRs in cik and rlk7-3 mutants. Moreover, we discovered that auxin maximum in pericycle cells altered subcellular localization of CIKs to determine lateral root founder cells. These findings revealed that CIKs and RLK7 function together to perceive the TOLS2 signal and regulate LR initiation and spacing through the MKK4/5-MPK3/6-PUCHI cascade.

Characterization of DNA methylation reader proteins in Arabidopsis thaliana

In plants, cytosine DNA methylation (mC) is largely associated with transcriptional repression of transposable elements, but it can also be found in the body of expressed genes, referred to as gene body methylation (gbM). gbM is correlated with ubiquitously expressed genes; however, its function, or absence thereof, is highly debated. The different outputs that mC can have raise questions as to how it is interpreted-or read-differently in these sequence and genomic contexts. To screen for potential mC-binding proteins, we performed an unbiased DNA affinity pull-down assay combined with quantitative mass spectrometry using methylated DNA probes for each DNA sequence context. All mC readers known to date preferentially bind to the methylated probes, along with a range of new mC-binding protein candidates. Functional characterization of these mC readers, focused on the MBD and SUVH families, was undertaken by ChIP-seq mapping of genome-wide binding sites, their protein interactors, and the impact of high-order mutations on transcriptomic and epigenomic profiles. Together, these results highlight specific context preferences for these proteins, and in particular the ability of MBD2 to bind predominantly to gbM. This comprehensive analysis of Arabidopsis mC readers emphasizes the complexity and interconnectivity between DNA methylation and chromatin remodeling processes in plants.

Comparison of the Effects of UV-C Light in the Form of Flash or Continuous Exposure: A Transcriptomic Analysis on Arabidopsis thaliana L

Ultraviolet C (UV-C) flash treatment represents a promising method for priming plants. This study compared the effects of 1 s (flash) and 60 s (60 s) UV-C exposures on the transcriptome of Arabidopsis thaliana L. plants. A dose of 200 J m-2 delivered in one second was observed to effectively stimulate plant defenses without causing any adverse effects on plant health. A total of 3054 and 1865 differentially expressed genes (DEGs) were identified in the flash and 60 s treatments, respectively, in comparison to the control plants. Of these, 1131 were common to both treatments. The flash treatment affected a greater number of transcription factors (415 genes) than the 60 s treatment (254 genes), indicating more pronounced alterations in gene expression. The flash treatment resulted in a significant overexpression of heat shock proteins (HSPs), heat shock factors (HSFs), and their associated genes, which impacted oxidative stress, proteostasis, genome stability, cell survival, and thermotolerance. The majority of mitochondrial genes were found to be upregulated, while photosynthetic genes exhibited a downregulation. These expression patterns coordinate electron transport and crosstalk between the nucleus, chloroplasts, and mitochondria, eliciting an adaptive protective response to UV-C flash. Additionally, the flash treatment resulted in alterations to several genes involved in cell cycle regulation, division, and DNA replication. These included ATP BMMs, BRCA2 s, IQDs, kinesin complex, MCM complex, CYCs, and CDKs, which ultimately led to cell cycle arrest as a temporary preparation for subsequent conditions. The present study demonstrates that a 1 s exposure to UV-C induces distinctive plant responses through coordinated gene expression. The findings suggest that the flash treatment is an innovative method that triggers a unique cellular response, prioritizing repair mechanisms and potentially enhancing plant immunity, resilience, and priming. It can be used as a plant resistance inducer and stimulator.

Genome-Wide Identification of the SlSET Gene Family and the Function of SlSET6 Under Salt Stress

A comprehensive genome-wide identification of SET-domain-containing genes in Solanum lycopersicum (tomato) has revealed 46 members. Phylogenetic analysis showed that these SET genes, along with those from Arabidopsis thaliana and Oryza sativa, are divided into five subfamilies, with Subfamilies II and V being the largest. Motif and domain analyses identified 15 conserved motifs and revealed the presence of pre-SET and post-SET domains in several genes, suggesting functional diversification. Gene structure analysis further demonstrated variation in exon-intron organization, likely contributing to differential gene regulation. Promoter analysis identified cis-acting elements related to light responsiveness, plant growth, hormones, and stress, implicating SET genes in various biological processes. RNA-seq and qRT-PCR data revealed distinct expression patterns of SlSET genes under salt stress, with several genes showing significant upregulation, indicating their potential role in stress tolerance. In particular, SlSET6 silencing using VIGS reduced tomato's tolerance to salt stress, leading to higher lipid peroxidation, reduced antioxidant enzyme activity, and decreased proline content, further confirming its critical role in salt stress response. These findings provide valuable insights into the functional diversity, evolutionary history, and stress-related roles of SET domain genes in tomato, with potential applications for crop improvement strategies.

CEP signaling coordinates plant immunity with nitrogen status

Plant endogenous signaling peptides shape growth, development and adaptations to biotic and abiotic stress. Here, we identify C-TERMINALLY ENCODED PEPTIDEs (CEPs) as immune-modulatory phytocytokines in Arabidopsis thaliana. Our data reveals that CEPs induce immune outputs and are required to mount resistance against the leaf-infecting bacterial pathogen Pseudomonas syringae pv. tomato. We show that effective immunity requires CEP perception by tissue-specific CEP RECEPTOR 1 (CEPR1) and CEPR2. Moreover, we identify the related RECEPTOR-LIKE KINASE 7 (RLK7) as a CEP4-specific CEP receptor contributing to CEP-mediated immunity, suggesting a complex interplay of multiple CEP ligands and receptors in different tissues during biotic stress. CEPs have a known role in the regulation of root growth and systemic nitrogen (N)-demand signaling. We provide evidence that CEPs and their receptors promote immunity in an N status-dependent manner, suggesting a previously unknown molecular crosstalk between plant nutrition and cell surface immunity. We propose that CEPs and their receptors are central regulators for the adaptation of biotic stress responses to plant-available resources.