SERKs regulate embryonic cuticle integrity through the TWS1-GSO1/2 signaling pathway in Arabidopsis

Challenges of translating Arabidopsis insights into crops

The significance of research conducted on Arabidopsis thaliana cannot be overstated. This focus issue showcases how insights from Arabidopsis have opened new areas of biology and directly advanced our understanding of crops. Here, experts intimately involved in bridging between Arabidopsis and crops share their perspectives on the challenges and opportunities for translation. First, we examine the translatability of genetic modules from Arabidopsis into maize, emphasizing the need to publish well-executed translational experiments, regardless of outcome. Second, we highlight the landmark success of HB4, the first GM wheat cultivar on the market, whose abiotic tolerance is borne from direct translation and based on strategies first outlined in Arabidopsis. Third, we discuss the decades-long journey to engineer oilseed crops capable of producing omega-3 fish oils, with Arabidopsis serving as a critical intermediary. Fourth, we explore how direct translation of starch synthesizing proteins characterized in Arabidopsis helped uncover novel mechanisms and functions in crops, with potential valuable applications. Finally, we illustrate how shared molecular factors between Arabidopsis and barley exhibit distinct molecular wiring as exemplified in cuticular and stomatal development. Together, these vignettes underscore the pivotal role of Arabidopsis as a foundational model plant while highlighting the challenges of translating discoveries into field-ready, commercial cultivars with enhanced knowledge-based traits.

Genome-Wide Identification of the CIF Gene Family and Protein Interaction with GSO1s Under the p-HBA-Induced Continuous Cropping Obstacle in Pogostemon cablin

Casparian strip integrity factors (CIFs), which are tyrosine-sulfated small peptides, are crucial genes involved in the formation and regulation of the Casparian strip and play an important role in the regulation of plant stress response. In order to explore the evolution, characteristics, role, and function of CIFs in response to continuous cropping obstacles (CCOs), the bioinformatics and gene expression analysis of CIF genes in Pogostemon cablin was carried out by determining the phylogenetic relationship, chromosome location, gene structure, and RT-qPCR results. Results showed that a total of 12 PatCIF family genes were identified on 12 different chromosomes. Promoter prediction analysis revealed 16 different cis-regulatory elements. A systematic evolutionary study of 33 species indicates CIF family genes originated from Spermatophyta. Collinearity analysis revealed P. cablin shared 19 syntenic genes with Solanum lycopersicum and only 8 with Oryza sativa. Transcriptome analysis indicated that the expression of PatCIF1-4 and PatGSO1b/1c/1f genes decreased under p-hydroxybenzoic acid treatment, and further RT-qPCR validation of four PatCIF genes was consistent with the results. AlphaFold prediction showed a protein interaction region between PatCIF1-4 mature peptide and PatGSO1b/1c/1f via the LRR domain, which provides a key binding surface for mature PatCIFs. This study offers a theoretical basis to investigate the roles of PatCIFs and PatGSO1s in CCOs and their protein interactions in P. cablin.

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.

Sulfated peptides and their receptors: Key regulators of plant development and stress adaptation

Four distinct types of sulfated peptides have been identified in Arabidopsis thaliana. These peptides play crucial roles in regulating plant development and stress adaptation. Recent studies have revealed that Xanthomonas and Meloidogyne can secrete plant-like sulfated peptides, exploiting the plant sulfated peptide signaling pathway to suppress plant immunity. Over the past three decades, receptors for these four types of sulfated peptides have been identified, all of which belong to the leucine-rich repeat receptor-like protein kinase subfamily. A number of regulatory proteins have been demonstrated to play important roles in their corresponding signal transduction pathways. In this review, we comprehensively summarize the discoveries of sulfated peptides and their receptors, mainly in Arabidopsis thaliana. We also discuss their known biological functions in plant development and stress adaptation. Finally, we put forward a number of questions for reference in future studies.

Defects in the cell wall and its deposition caused by loss-of-function of three RLKs alter root hydrotropism in Arabidopsis thaliana

Root tips can sense moisture gradients and grow into environments with higher water potential. This process is called root hydrotropism. Here, we report three closely related receptor-like kinases (RLKs) that play critical roles in root hydrotropism: ALTERED ROOT HYDROTROPIC RESPONSE 1 (ARH1), FEI1, and FEI2. Overexpression of these RLKs strongly reduce root hydrotropism, but corresponding loss-of-function mutants exhibit an increased hydrotropic response in their roots. All these RLKs show polar localization at the plasma membrane regions in root tips. The biosynthesis of the cell wall, cutin, and wax (CCW) is significantly impaired in root tips of arh1-2 fei1-C fei2-C. A series of known CCW mutants also exhibit increased root hydrotropism and reduced osmotic tolerance, similar to the characteristics of the triple mutant. Our results demonstrat that the integrity of the cell wall, cutin, and root cap wax mediate a trade-off between root hydrotropism and osmotic tolerance.

SERKs and NIKs: Coreceptors or signaling hubs in a complex crosstalk between growth and defense?

SOMATIC EMBRYOGENESIS RECEPTOR-LIKE KINASES (SERKs) and NUCLEAR SHUTTLE PROTEIN-INTERACTING KINASES (NIKs) belong to superfamily II of leucine-rich repeat receptor-like kinases, which share cytosolic kinase conservation and a similar ectodomain configuration. SERKs have been extensively demonstrated to function as coreceptors of receptor-like kinases, which sense biotic or developmental signals to initiate specific responses. NIKs, on the other hand, have emerged as downstream components in signaling cascades, not functioning as coreceptors but rather serving as hubs that converge information from both biotic and abiotic signals, resulting in a unified response. Like SERKs, NIKs play a crucial role as information spreaders in plant cells, forming hubs of high centrality. However, unlike SERKs, which function as coreceptors and assemble paired receptor-specific responses, NIKs employ a shared signaling circuit to transduce diverse biotic and abiotic signals into the same physiological response. Therefore, this review highlights the concept of signaling hubs that differ from coreceptors in signaling pathways.

The EPFL-ERf-SERK signaling controls integument development in Arabidopsis

As the seed precursor, the ovule produces the female gametophyte (or embryo sac), and the subsequent double fertilization occurs in it. The integuments emerge sequentially from the integument primordia at the early stages of ovule development and finally enwrap the embryo sac gradually during gametogenesis, protecting and nursing the embryo sac. However, the mechanisms regulating integument development are still obscure. In this study, we show that SOMATIC EMBRYOGENESIS RECEPTOR-LIKE KINASES (SERKs) play essential roles during integument development in Arabidopsis thaliana. The serk1/2/3 triple mutant shows arrested integuments and abnormal embryo sacs, similar defects also found in the triple loss-of-function mutants of ERECTA family (ERf) genes. Ovules of serk1/2/3 er erl1/2 show defects similar to er erl1/2 and serk1/2/3. Results of yeast two-hybrid analyses, bimolecular fluorescence complementation (BiFC) analyses, and co-immunoprecipitation assays demonstrated that SERKs interact with ERf, which depends on EPIDERMAL PATTERNING FACTOR-LIKE (EPFL) family small peptides. The sextuple mutant epfl1/2/3/4/5/6 shows integument defects similar to both of er erl1/2 and serk1/2/3. Our results demonstrate that ERf-SERK-mediated EPFL signaling orchestrates the development of the female gametophyte and the surrounding sporophytic integuments.

Apple SUMO E3 ligase MdSIZ1 regulates cuticular wax biosynthesis by SUMOylating transcription factor MdMYB30

A key function of SUMOylation is the coordinated modification of numerous proteins to optimize plant growth and resistance to environmental stress. Plant cuticular wax is deposited on the surface of primary plant organs to form a barrier that provides protection against changes in terrestrial environments. Many recent studies have examined cuticular wax biosynthetic pathways and regulation. However, whether SUMOylation is involved in the regulation of cuticle wax deposition at the posttranslational level remains unclear. Here, we demonstrate that a small ubiquitin-like modifier (SUMO) E3 ligase, SAP AND MIZ1 DOMAIN CONTAINING LIGASE1 (MdSIZ1), regulates wax accumulation and cuticle permeability in apple (Malus domestica Borkh), SUMO E2 CONJUGATING ENZYME 1(MdSCE1) physically interacts with MdMYB30, a transcription factor involved in the regulation of cuticle wax accumulation. MdSIZ1 mediates the SUMOylation and accumulation of MdMYB30 by inhibiting its degradation through the 26S proteasome pathway. Furthermore, MdMYB30 directly binds to the β-KETOACYL-COA SYNTHASE 1 (MdKCS1) promoter to activate its expression and promote wax biosynthesis. These findings indicate that the MdSIZ1-MdMYB30-MdKCS1 module positively regulates cuticular wax biosynthesis in apples. Overall, the findings of our study provide insights into the regulation pathways involved in cuticular wax biosynthesis.

PlantPhoneDB: A manually curated pan-plant database of ligand-receptor pairs infers cell-cell communication

Ligand-receptor pairs play important roles in cell-cell communication for multicellular organisms in response to environmental cues. Recently, the emergence of single-cell RNA-sequencing (scRNA-seq) provides unprecedented opportunities to investigate cellular communication based on ligand-receptor expression. However, so far, no reliable ligand-receptor interaction database is available for plant species. In this study, we developed PlantPhoneDB (https://jasonxu.shinyapps.io/PlantPhoneDB/), a pan-plant database comprising a large number of high-confidence ligand-receptor pairs manually curated from seven resources. Also, we developed a PlantPhoneDB R package, which not only provided optional four scoring approaches that calculate interaction scores of ligand-receptor pairs between cell types but also provided visualization functions to present analysis results. At the PlantPhoneDB web interface, the processed datasets and results can be searched, browsed, and downloaded. To uncover novel cell-cell communication events in plants, we applied the PlantPhoneDB R package on GSE121619 dataset to infer significant cell-cell interactions of heat-shocked root cells in Arabidopsis thaliana. As a result, the PlantPhoneDB predicted the actively communicating AT1G28290-AT2G14890 ligand-receptor pair in atrichoblast-cortex cell pair in Arabidopsis thaliana. Importantly, the downstream target genes of this ligand-receptor pair were significantly enriched in the ribosome pathway, which facilitated plants adapting to environmental changes. In conclusion, PlantPhoneDB provided researchers with integrated resources to infer cell-cell communication from scRNA-seq datasets.

Cloning and expression analysis of SERK1 gene in Diospyros lotus

Somatic embryogenesis receptor-like kinases (SERKs), a subfamily of receptor-like kinases, play important roles in response to abiotic stresses in addition to apomictic reproductive development in numerous plant species. The purpose of the present work was to determine if an ortholog of the SERK gene is present in the Diospyros lotus genome, isolate it and analyze its expression during embryogeny and abiotic stress. An ortholog of the SERK gene was isolated from the D. lotus genome, and designated as DlSERK1. The physical and chemical properties, protein structure, and evolutionary relationship of the DlSERK1 protein were analyzed by bioinformatics methods, and the expression of DlSERK1 gene during embryonic development and under low-temperature, salt, and drought stresses was examined through real-time quantitative PCR analysis. DlSERK1 contained 1,881 bp open reading frame encoding 626 amino acids, with a molecular mass of 69.18 kDa and pI of 5.34. DlSERK1 had strong hydrophilic property, signal peptide cleavage sites, and two transmembrane regions, indicating that DlSERK1 is a secretory protein. The secondary structure of DlSERK1 was consistent with the tertiary structure, both of which were dominated by random curls and alpha-helices. DlSERK1 had the typical structure of SERK proteins, and harbored multiple phosphorylation and glycosylation sites. Quantitative analysis showed that DlSERK1 was expressed during the embryonic development period, and the highest expression level was at 10 days post-flowering. The DlSERK1 expression level was down-regulated under low-temperature stress and up-regulated under drought and salt stresses. Our study showed that DlSERK1 was expressed in embryo development and could respond to low-temperature, drought, and salt stresses, which lays a foundation for further research on the function of SERK1 in the apomixis growth and development of environmental adaptation in D. lotus.

Arabidopsis ROOT ELONGATION RECEPTOR KINASES negatively regulate root growth putatively via altering cell wall remodeling gene expression

Receptor-like kinases (RLKs) play key roles in regulating various physiological aspects in plant growth and development. In Arabidopsis thaliana, there are at least 223 leucine-rich repeat (LRR) RLKs. The functions of the majority of RLKs in the LRR XI subfamily were previously revealed. Only three RLKs were not characterized. Here we report that two independent triple mutants of these RLKs, named ROOT ELONGATION RECEPTOR KINASES (REKs), exhibit increased cell numbers in the root apical meristem and enhanced cell size in the elongation and maturation zones. The promoter activities of a number of Quiescent Center marker genes are significantly up-regulated in the triple mutant. However, the promoter activities of several marker genes known to control root stem cell niche activities are not altered. RNA-seq analysis revealed that a number of cell wall remodeling genes are significantly up-regulated in the triple mutant. Our results suggest that these REKs play key roles in regulating root development likely via negatively regulating the expression of a number of key cell wall remodeling genes.

Receptor-like protein kinases in plant reproduction: Current understanding and future perspectives

Reproduction is a crucial process in the life span of flowering plants, and directly affects human basic requirements in agriculture, such as grain yield and quality. Typical receptor-like protein kinases (RLKs) are a large family of membrane proteins sensing extracellular signals to regulate plant growth, development, and stress responses. In Arabidopsis thaliana and other plant species, RLK-mediated signaling pathways play essential roles in regulating the reproductive process by sensing different ligand signals. Molecular understanding of the reproductive process is vital from the perspective of controlling male and female fertility. Here, we summarize the roles of RLKs during plant reproduction at the genetic and molecular levels, including RLK-mediated floral organ development, ovule and anther development, and embryogenesis. In addition, the possible molecular regulatory patterns of those RLKs with unrevealed mechanisms during reproductive development are discussed. We also point out the thought-provoking questions raised by the research on these plant RLKs during reproduction for future investigation.