Conserved mechanical hallmark guides four-way junction avoidance during plant cytokinesis

When building an organ, adjacent cells coordinate to form topologically stable junctions by integrating mechanosensitive signaling pathways. Positioning the newly formed tricellular junction in walled multicellular organisms is critical, as cells cannot migrate. The cell division site must avoid existing cellular junctions to prevent unstable four-way junctions. The microtubule preprophase band (PPB) is a guideline for the plant cell's future cell division site. Yet, mutants impaired in PPB formation hardly display defects, suggesting the presence of an alternative mechanism. Here, we report the existence of a process that guides the cell division site close to an adjacent tricellular junction. This PPB-independent mechanism depends on the phosphoinositide phosphatase SUPPRESSION OF ACTIN 9 (SAC9): in the Arabidopsis mutant sac9-3, the cell plate abnormally attaches at two equidistant positions from an adjacent tricellular junction. Numerical simulations suggest that elastic energy accumulation at the subcellular level within walls, due to their rheological response to mechanical stresses, could act as positional cues revealing the positions of tricellular junctions. Moreover, perturbation of the root mechanical homeostasis results in four-way junction formation. This provides a scenario in which cells avoid four-way junction formation during cytokinesis through discrete subcellular mechanical hallmarks.

Exploitation of rhizosphere microbiome biodiversity in plant breeding

Climate change-induced stresses are perceived by plants at the root-soil interface, where they are alleviated through interactions between the host plant and the rhizosphere microbiome. The recruitment of specific microbiomes helps mitigate stress, increases resistance to pathogens, and promotes plant growth, development, and reproduction. The structure of the rhizosphere microbiome is shaped by crop domestication and variations in ploidy levels. Here we list key genes that regulate rhizosphere microbiomes and host genetic traits. We also discuss the prospects for rigorous analysis of symbiotic interactions, research needs, and strategies for systematically utilizing microbe-crop interactions to improve crop performance. Finally, we highlight challenges of maintaining live rhizosphere microbiome collections and mining heritable variability to enhance interactions between host plants and their rhizosphere microbiomes.

Transcriptome and metabolome analysis of senescent rice (Oryza sativa L.) seeds: insights into the mechanism of germination vigor and seedling morphogenesis

Seeds germination and seedlings growth are crucial factors in ensuring effective rice grain productivity. However, the mechanisms for maintaining seed vigor remains largely unknown. The seed aging phenomenon that occurs during storage poses a significant challenge to crop production, as it can lead to reduced germination rates and impaired seed vitality. The current study explored the underlying mechanisms that enable rice seeds to maintain high germination rates and seedling vigor after long - term storage. We employed transcriptomic and metabolomic techniques to identify metabolic changes and key genes associated with the aging of rice seeds during long - term storage. We utilized indicators such as imbibition rate (IR), germination rate (GR), mean germination time (MGT), germination coefficient (GC), germination index (GI), and germination potential (GP) to comprehensively assess germination activity. Traits including seedling emergence rate, seedling strength index, photosynthetic parameters, carbohydrate accumulation, and enzyme activity related to carbon metabolism were used to determine the impact of seed storage duration on seedling growth. Our research findings revealed significant differences in gene expression patterns and metabolic characteristics among seeds stored for different duration. Notably, IAA levels, the IAA/ABA ratio, and linoleic acid metabolism were identified as key factors affecting germination and seedling development. Results indicated that with the extension of storage duration, the germination potential and seedling development significantly declined. Current study provided a comprehensive understanding of the physiological and molecular mechanisms behind the germination and morphogenesis of rice seeds under different storage years. The insights gained from this study could be utilized to improve the storage and quality control of rice seeds, thereby ultimately enhancing agricultural productivity.

Trehalose-6-Phosphate Phosphatase SlTPP1 Adjusts Diurnal Carbohydrate Partitioning in Tomato

Trehalose 6-phosphate phosphatases (TPPs) play essential roles in carbohydrate distribution between source and sink organs in plants. Here, we show that TPPs also participate in regulating diurnal carbohydrate partitioning. In tomato, SlTPP1 exhibited high expression in leaves, particularly in phloem, with distinct diurnal variation. Overexpression of SlTPP1 promoted plant growth and biomass accumulation, whereas its knockout reduced both. Analysis of photosynthesis parameters revealed that overexpression of SlTPP1 accelerated the initiation of photosynthesis at dawn, promoting assimilate production. Additionally, SlTPP1 enhanced the stem's buffering capacity in diurnal carbohydrate partitioning, promoting daytime carbohydrate accumulation and facilitating nocturnal carbohydrate export to the roots, resulting in increased root carbohydrate levels. These results indicate that SlTPP1 regulates diurnal carbohydrate partitioning, establishing a positive feedback loop that promotes plant growth. Notably, overexpression of SlTPP1 reduced T6P concentration, whereas overexpression of SnRK1 (sucrose non-fermenting 1-related protein kinase) α subunit (SNF1) decreased biomass and did not enhance the stem's buffering capacity in carbohydrate partitioning. These findings suggest that SlTPP1's regulation of diurnal carbohydrate partitioning is at least partially independent of the classical T6P-SnRK1 pathway.

Flowering time regulation through the lens of evolution

Flowering, the onset of reproductive development, marks a critical transition in the angiosperm life cycle. In the model plant Arabidopsis thaliana, the process is tightly regulated by a complex network of approximately 300 genes organized into distinct pathways. This mini-review examines the genetic and molecular mechanisms regulating flowering time from an evolutionary perspective. Our analysis reveals that genes involved in the age and photoperiod pathways are evolutionarily ancient and highly conserved across bryophytes and vascular plants. In contrast, other regulatory modules appear to have evolved more recently, likely through the repurposing of existing genes or adaptations to environmental changes. We propose that future research should shift away from studying flowering regulation mechanisms in individual model plants to exploring the evolution of flowering time pathways and their underlying drivers. Adopting an evolutionary perspective may ultimately illuminate the fundamental principles governing the timing of reproductive development in plants.

Mutation of a gene with PWWP domain confers salt tolerance in rice

Salinity is a major problem due to the continuous increase in the salinization of agricultural lands, particularly, paddy fields. Using a forward genetics approach, salt-insensitive TILLING line 3, sitl3, was selected from a core population induced by gamma-ray irradiation. Under salt stress, sitl3 had greater fresh weight and chlorophyll content, and lower H2O2 and Na+ contents than the wild-type. In the gene (LOC_Os07g46180) with two PWWP domains (named Oyza sativa PWWP4, OsPWWP4) of sitl3, a premature stop was caused by an SNP, and was named OsPWWP4p.Gly462* (a stop gain occurred from the 462th amino acid residue). The OsPWWP4 and substrate proteins (OsEULS2, OsEULS3, and OsEULD2) were identified using yeast two-hybrid, bimolecular fluorescence complementation, in vitro pull-down, and in vitro methyltransferase assays. Subcellular localization of OsPWWP4 and OsPWWP4p.Gly462*GFP-tagged proteins revealed they were both localized in the nucleus, while OsEULS2, OsEULS3, and OsEULD2 GFP-tagged proteins were found in the nucleus and cytosol of rice protoplasts. The expression levels of OsEULS2, OsEULS3, OsEULD2 under salt stress were higher in sitl3 than in wild-type plants. In contrast, OsPWWP4 expression was higher in the latter. Genes involved in the salt overly sensitive (SOS) pathway showed higher expression in the aerial tissues of silt3 than in the wild-type. CRISPR/Cas9-mediated OsPWWP4 knock-out transgenic plants showed salt tolerance phenotypes with low Na+ contents and low Na+/K+ ratios. The data suggest that sitl3 is a valuable genetic resource for understanding protein post-translational regulation-related salinity tolerance mechanisms such as methyltransferase activities, and for improving salt tolerance in rice through breeding.

Disentangling serial chloroplast captures in willows

PREMISE

Chloroplast capture is a process through which the chloroplast of a focal species is replaced by the chloroplast from another species during repeated backcrossing of an initial hybrid. Here we investigated serial chloroplast capture from Salix nigra in willows during sequential hybridization events that led to the capture of the same chloroplast lineage across multiple Salix species.

METHODS

Previously generated sequences of nuclear and chloroplast regions from several Salix species were used to identify cases of cytonuclear phylogenetic discordance, a pattern indicating chloroplast capture. Serial chloroplast captures were identified by comparing phylogenetic topologies of the chloroplast trees to discriminate among (1) a single chloroplast capture and subsequent speciation of the lineage with the captured chloroplast, (2) multiple chloroplast captures from the same parent species, and (3) serial chloroplast captures. We also looked for hybridization in genes involved in cytonuclear interactions and in photosynthesis.

RESULTS

We identified cases of serial chloroplast capture and speciation after chloroplast capture in Salix. Although these chloroplast capture events were accompanied by signals of hybridization in the nuclear genomes, nuclear genes that functionally interact with chloroplast genes and nuclear genes involved in photosynthesis were no more likely to introgress in species with chloroplast captures than in species without chloroplast captures.

CONCLUSIONS

This study illuminates the complex evolution of the chloroplast genomes in Salix and the potential for hybridization and introgression to influence genomic evolution.

LEC2 induces somatic cell reprogramming through epigenetic activation of plant cell totipotency regulators

Many plant species can develop embryos from somatic cells without fertilization. During this process, known as somatic embryogenesis, changes in the DNA methylation patterns are characteristic of reprogramming somatic cells into an embryogenic state. However, the underlying mechanisms connecting DNA methylation and activating totipotency-regulating genes have remained largely unknown. Here, we show that during somatic embryogenesis induced by overexpressing the totipotency-regulating transcription factor LEAFY COTYLEDON2 (LEC2) in Arabidopsis, CHH hypermethylation is deposited by the LEC2-activated RNA-directed DNA methylation (RdDM) pathway. A reader complex composed of SU(VAR)3-9 HOMOLOGS (SUVH) and its chaperone SUVH-INTERACTING DNAJ DOMAIN-CONTAINING PROTEIN (SDJ) binds to the CHH hypermethylated regions and recruits AT-HOOK MOTIF CONTAINING NUCLEAR LOCALIZED (AHL) chromatin modification proteins to increase chromatin accessibility, resulting in the transcriptional activation of totipotency-regulating genes. Our work reveals a molecular framework of how epigenetic modifications mediate somatic cell reprogramming, offering a pathway toward enhancing somatic embryogenesis in agricultural regeneration biology.

The evolution of suppressed recombination between sex chromosomes and the lengths of evolutionary strata

The idea that sex-differences in selection drive the evolution of suppressed recombination between sex chromosomes is well-developed in population genetics. Yet, despite a now classic body of theory, empirical evidence that sexually antagonistic (SA) selection drives the evolution of recombination arrest remains equivocal and alternative hypotheses underdeveloped. Here, we investigate whether the length of "evolutionary strata" formed by chromosomal inversions (or other large-effect recombination modifiers) expanding the nonrecombining sex-linked region (SLR) on sex chromosomes can be informative of how selection influenced their fixation. We develop population genetic models to show how the length of an SLR-expanding inversion and the presence of partially recessive deleterious mutational variation affect the fixation probability of three different classes of inversions: (i) intrinsically neutral, (ii) directly beneficial (i.e., due to breakpoint or positional effects), and (iii) those capturing SA loci. Our models indicate that inversions capturing an SA locus initially in linkage disequilibrium with the ancestral SLR exhibit a strong fixation bias toward small inversions, while neutral, beneficial, and inversions capturing a genetically unlinked SA locus tend to favor larger inversions and exhibit similar distributions of fixed inversion lengths. The footprint of evolutionary stratum size left behind by different selection regimes is strongly influenced by parameters affecting the deleterious mutation load, the physical position of the ancestral SLR, and the distribution of new inversion lengths.

Cellular nitro-oxidative burden and survival through regulated cell death in the plants

Throughout the life of a plant, generations of different forms of reactive oxygen (ROS) and nitrogen species (RNS) are derived as a by-product of metabolic events. The quantum of ROS and RNS becomes higher once a plant encounters a perturbed situation either through biotic or abiotic factor. As each of reactive species is harmful to the cells beyond certain optimal level, it requires a mechanism to detoxify RONS induced cellular toxicity. For the purpose cell has instituted highly organized multi-layered defense mechanisms. In the first layer of defense, cell produces different antioxidant enzymes and non-enzyme molecules. Once generated, ROS and RNS become beyond the detoxification capacity of cellular antioxidant pool, another strategy comes into the operation wherein a few targeted cells undergo self-autolysis progression known as programmed cell death (PCD). The process of PCD has been partially dissected in plants emphasizing either under amplified ROS or RNS condition. However, there are evidences for reaction between species of ROS and RNS. It is unequivocally evident that superoxide has tendency to react with nitric oxide giving rise to a very potential oxidant called peroxynitrite that has ability to nitrosylate several biomolecules thus, altering cellular fate. This suggests that cellular damage caused by reactive species of nitrogen and oxygen is not only an outcome of accumulation of individual species of ROS and RNS, but a combinatorial product of ROS and RNS may have a key role to play. In this review, we intend to advocate role of cellular nitro-oxidative condition in PCD in plants.

Topping-induced transcriptome changes reveal PaSPL-mediated regulation of plant architecture in Platanus acerifolia

Plant architecture is one of the most important qualities of Platanus acerifolia Willd., enabling it to be known as "the king of street trees". However, there are few reports available on its molecular regulatory mechanisms. Shoot branching is a key process in regulating plant architecture. In this study, topping experiments and transcriptome sequencing analyses were performed to elucidate the molecular mechanisms underlying axillary bud growth and development in P. acerifolia. After 3 d of topping, the axillary buds in P. acerifolia exhibited significant growth, with the trend increasing over subsequent days. The KEGG enrichment analysis revealed considerable changes in the expression levels of genes involved in the auxin signal transduction pathway. Additionally, the expression of most PaSPL genes was downregulated after topping. While Pla-miR156f regulated Arabidopsis plant architecture, flowering transition and flower development, this regulation was not directly influenced by the topping pathway. These results contribute to a better understanding of P. acerifolia plant architecture regulation and provide valuable insights into the regulation of other plants, particularly woody plants.

Heterologous expression of the barley-specific HvbZIP87 transcription factor in wheat enhances broad-spectrum disease resistance with balanced yield

INTRODUCTION

NPR1, a protein that interacts with bZIP transcription factors known as TGAs, plays a pivotal role in coordinating systemic acquired resistance (SAR) in plants. Nevertheless, the molecular intricacies governing SAR in the Triticeae family, which includes crops like wheat and barley, are still largely enigmatic.

OBJECTIVES

We identified HvbZIP87, a barley-specific transcription factor, induced in SAR, more strongly in transgenic barley with HvNPR1 knocked down. The objective of this research is to explore the role of HvbZIP87 in SAR and the defense mechanisms of plants, focusing on transgenic wheat lines that have been engineered to overexpress HvbZIP87 (HvbZIP87-OE).

METHODS

Initially, the broad-spectrum disease resistance and SAR levels of HvbZIP87-OE lines were evaluated. Multiple techniques were employed to validate the direct protein interaction between HvbZIP87 and NPR1. RNA-seq and DAP-seq were performed to analyze the gene regulatory effects of HvbZIP87 in transgenic wheat lines.

RESULTS

Transgenic wheat lines expressing HvbZIP87 exhibited significantly enhanced SAR levels and improved plant defense to stripe rust, leaf rust, spot blotch, and Fusarium crown rot. Despite some adverse effects on agronomic traits, the heterologous expression of HvbZIP87 in wheat resulted in a balanced yield due to larger harvested seeds. Intriguingly, HvbZIP87 physically interacted with TaNPR1 in the plant cell nucleus. Transcriptome sequencing and DAP-seq have revealed the regulatory networks and cis-elements governed by HvbZIP87 in the wheat genome. The genes TaPR1, TaPR2, TaPR4, and TaPR5, among several PR genes, were forecasted to undergo direct regulation by HvbZIP87. Additionally, we identified TaMYC2 transcription factor as another protein interactor of HvbZIP87. Silencing TaMYC2 further enhanced wheat's resistance to stripe rust, suggesting its negative regulatory role in plant defense.

CONCLUSION

We have identified a unique protein that interacts with TaNPR1 in the SAR pathway of Triticeae species and have clarified its role in conferring resistance.

Large-scale transcriptome mining enables macrocyclic diversification and improved bioactivity of the stephanotic acid scaffold

Nearly 10,000 plant species are represented by RNA-seq datasets in the NCBI sequence read archive, which are difficult to search in unassembled format due to database size. Here, we optimize RNA-seq assembly to transform most of this public RNA-seq data to a searchable database for biosynthetic gene discovery. We test our transcriptome mining pipeline towards the diversification of moroidins, which are plant ribosomally-synthesized and posttranslationally-modified peptides (RiPPs) biosynthesized from copper-dependent peptide cyclases. Moroidins are bicyclic compounds with a conserved stephanotic acid scaffold, which becomes cytotoxic to non-small cell lung adenocarcinoma cells with an additional C-terminal macrocycle. We discover moroidin analogs with second ring structures diversified at the crosslink and the non-crosslinked residues including a moroidin analog from water chickweed, which exhibits higher cytotoxicity against lung adenocarcinoma cells than moroidin. Our study expands stephanotic acid-type peptides to grasses, Lowiaceae, mints, pinks, and spurges while demonstrating that large-scale transcriptome mining can broaden the medicinal chemistry toolbox for chemical and biological exploration of eukaryotic RiPP lead structures.

Nucleic acid nanobiosystems for cancer theranostics: an overview of emerging trends and challenges

Different cancers remain major global health challenges due to their diverse biological behaviors and significant treatment hurdles. The aging of populations and lifestyle factors increase cancer occurrence and place increasing pressure on healthcare systems. Despite continuous advancements, many cancers remain fatal due to late-stage diagnosis, tumor heterogeneity, and drug resistance, thus necessitating urgent development of innovative treatment solutions. Therapeutic nucleic acids, a new class of biological drugs, offer a promising approach to overcoming these challenges. The recent Nucleic Acids and Nanobiosystems in Cancer Theranostics (NANCT) conference brought together internationally recognized experts from 15 countries to discuss cutting-edge research, spanning from oncolytic viruses to anticancer RNA nanoparticles and other emerging nanotechnologies. This review captures key insights and developments, emphasizing the need for interdisciplinary translation of scientific advancements into clinical practice and shaping the future of personalized cancer treatments for improved therapeutic outcomes.

Fertilization-dependent phloem end gate regulates seed size

Seed formation is essential for plant propagation and food production. We present a novel mechanism for the regulation of seed size by a newly identified "gate" at the chalazal end of the ovule regulating nutrient transport into the developing seed. This gate is blocked by callose deposition in unfertilized mature ovules (closed state), but the callose is removed after central cell fertilization, allowing nutrient transport into the seed (open state). However, if fertilization fails, callose deposition persists, preventing transportation of nutrients from the funiculus. A mutant in an ovule-expressed β-1,3-glucanase gene (AtBG_ppap) showed incomplete callose degradation after fertilization and produced smaller seeds, apparently due to its partially closed state. By contrast, an AtBG_ppap overexpression line produced larger seeds due to continuous callose degradation, fully opening the gate for nutrient transport into the seed. The mechanism was also identified in rice, indicating that it potentially could be applied widely to angiosperms to increase seed size.

Intragenomic mutational heterogeneity: structural and functional insights from gene evolution

Variation of mutation rates between species has been documented over decades, but the variation between different regions of a genome has been less often discussed. Recent studies using high-quality sequence data have revealed previously unknown levels of intragenomic heterogeneity of mutation rates and their association with other structural and functional features of DNA sequences. This article reviews accumulating evidence of this intragenomic heterogeneity and speculates its cause and influence on organismal phenotypes.

Endophytic mycobiont provides growth benefits via a phenylpropanoid-auxin axis in host plants

Beneficial association with symbiotic fungi helps improve growth and fitness in most land plants and shows great potential as biofertilizers in precision agriculture. Here, we demonstrated that a root fungal endophyte, Tinctoporellus species isolate AR8, enabled yield improvement in Brassicaceae leafy green choy sum (Brassica rapa var. parachinensis). Mechanistically, AR8 colonized the root cortex/endosphere and channeled the metabolic flux to phenylpropanoids and requisite secondary metabolites to promote plant growth. AR8-assisted biosynthesis of auxin improved root growth and provided an intrinsic source for long-distance signaling that enhanced shoot biomass. Chemical complementation with exogenous p-coumaric acid restored auxin signaling and enhanced growth in AR8-inoculated pal1 mutant plants, thus implicating such a phenylpropanoid-auxin nexus as a pivotal regulator of symbiotic plant growth. Comparative metabolomics established hydroxycinnamic acid and p-coumaric acid as major plant-growth-promoting hubs that bridge the phenylpropanoid pathway and auxin signaling in the cross-kingdom AR8 symbiotic interaction model.

A single-nuclei transcriptome census of the Arabidopsis maturing root identifies that MYB67 controls phellem cell maturation

The periderm provides a protective barrier in many seed plant species. The development of the suberized phellem, which forms the outermost layer of this important tissue, has become a trait of interest for enhancing both plant resilience to stresses and plant-mediated CO2 sequestration in soils. Despite its importance, very few genes driving phellem development are known. Employing single-nuclei sequencing, we have generated an expression census capturing the complete developmental progression of Arabidopsis root phellem cells, from their progenitor cell type, the pericycle, through to their maturation. With this, we identify a whole suite of genes underlying this process, including MYB67, which we show has a role in phellem cell maturation. Our expression census and functional discoveries represent a resource, expanding our comprehension of secondary growth in plants. These data can be used to fuel discoveries and engineering efforts relevant to plant resilience and climate change.

The non-specific phospholipase C of common bean PvNPC4 modulates roots and nodule development

Plant phospholipase C (PLC) proteins are phospholipid-degrading enzymes classified into two subfamilies: phosphoinositide-specific PLCs (PI-PLCs) and non-specific PLCs (NPCs). PI-PLCs have been widely studied in various biological contexts, including responses to abiotic and biotic stresses and plant development; NPCs have been less thoroughly studied. No PLC subfamily has been characterized in relation to the symbiotic interaction between Fabaceae (legume) species and the nitrogen-fixing bacteria called rhizobia. However, lipids are reported to be crucial to this interaction, and PLCs may therefore contribute to regulating legume-rhizobia symbiosis. In this work, we functionally characterized NPC4 from common bean (Phaseolus vulgaris L.) during rhizobial symbiosis, findings evidence that NPC4 plays an important role in bean root development. The knockdown of PvNPC4 by RNA interference (RNAi) resulted in fewer and shorter primary roots and fewer lateral roots than were seen in control plants. Importantly, this phenotype seems to be related to altered auxin signaling. In the bean-rhizobia symbiosis, PvNPC4 transcript abundance increased 3 days after inoculation with Rhizobium tropici. Moreover, the number of infection threads and nodules, as well as the transcript abundance of PvEnod40, a regulatory gene of early stages of symbiosis, decreased in PvNPC4-RNAi roots. Additionally, transcript abundance of genes involved in autoregulation of nodulation (AON) was altered by PvNPC4 silencing. These results indicate that PvNPC4 is a key regulator of root and nodule development, underscoring the participation of PLC in rhizobial symbiosis.

Unveiling molecular mechanisms of iron and zinc dynamics in rice

Iron (Fe) and zinc (Zn) are essential micronutrients critical for human health, yet their deficiencies are widespread, particularly in rice-dependent populations. Rice, a staple food for over half the global population, lacks sufficient bioavailable Fe and Zn in its grains, contributing to global malnutrition. This review delves into the molecular mechanisms governing Fe and Zn transport in rice, focusing on gene families such as IRT, YSL, ZIP, and HMA, which regulate uptake, translocation, and storage. These transporters exhibit intricate interactions and crosstalk, influenced by environmental factors and shared pathways, underscoring the complexity of Fe-Zn homeostasis. Biofortification, through genetic engineering and conventional breeding, emerges as a promising solution to address Fe and Zn deficiencies. Genetic strategies include overexpression of ferritin and nicotianamine synthase genes, alongside manipulation of metal transporter genes, to enhance micronutrient accumulation in rice grains. The advanced breeding approaches including marker-assisted selection and quantitative trait loci (QTL) mapping, complement genetic engineering, offering non-transgenic alternatives for micronutrient enhancement. The common challenges such as regulatory barriers, public perception, and trait stability under diverse conditions necessitate interdisciplinary collaboration and technological advancements.

A fungal transcription factor converts a beneficial root endophyte into an anthracnose leaf pathogen

Plant-associated fungi exhibit diverse lifestyles. Fungal endophytes are resident inside plant tissue without showing any disease symptoms for at least a part of their life cycle, and some of them benefit plant growth and health. However, some can cause diseases in specific host environments or genotypes, implying a virulence mechanism, which may be induced by as-yet-unidentified regulatory factors in fungal endophytes. Here, we show that CtBOT6, a transcription factor encoded within a secondary metabolite gene cluster known as the abscisic acid (ABA)-botrydial gene (ABA-BOT) cluster in the root-associated fungus Colletotrichum tofieldiae, triggers virulence-related gene expression and drives the production of diverse metabolites encoded both within and outside the cluster. CtBOT6 overexpression is sufficient to shift a root-beneficial C. tofieldiae to a leaf pathogen, driving its transition along the mutualist-pathogen continuum. Our genetic analysis revealed that the ABA-BOT cluster is indispensable for fungal virulence caused by CtBOT6 activation, implying that compounds derived from the cluster affect these processes. Furthermore, transcriptome analysis of root colonization by C.tofieldiae strains overexpressing CtBOT6 revealed that the pathogenic state induced plant defense and senescence responses characteristic of necrotrophic interactions. Importantly, this state enabled the fungus to proliferate and reproduce in leaves, in addition to heavily colonizing roots, with these processes being partly dependent on the host ABA and ethylene pathways. Our findings indicate that the expression status of CtBOT6 serves as a critical determinant for the endophytic fungus to adapt to the different plant tissues and to manifest diverse infection strategies.

Divergent evolution of a thermospermine-dependent regulatory pathway in land plants

Plants adapted to life on land by developing diverse anatomical features across lineages. The molecular basis of these innovations often involves the emergence of new genes or establishing new connections between conserved elements, though evidence for evolutionary genetic circuit rewiring remains scarce. Here, we show that the thermospermine-dependent pathway regulating vascular cell proliferation in Arabidopsis thaliana operates as two distinct modules with different functions in the bryophyte Marchantia polymorpha. One module controls dichotomous branching at meristems, while the other one modulates gemmae and rhizoid production in the thallus. Heterologous assays and comparative expression analyses reveal that the molecular links between these modules, forming a unified circuit in vascular plants, emerged early in tracheophyte evolution. Our results illustrate how the thermospermine-dependent circuit elements followed two divergent evolutionary trajectories in bryophytes and tracheophytes, eventually influencing distinct developmental processes.

Mycorrhizal fungi drive Cd and P allocation strategies for the co-planting system of hyperaccumulator S. nigrum and upland rice

Arbuscular mycorrhizal fungi (AMF) enhance the remediation potential of hyperaccumulator-crop co-planting systems, yet the mechanisms governing cadmium (Cd) and phosphorus (P) allocation remain unclear. To investigate these strategies, pot experiments were conducted using Cd-contaminated soil (1.0 mg·kg-1 Cd) where the Cd hyperaccumulator Solanum nigrum (S. nigrum) was intercropped with upland rice under Funneliformis mosseae inoculation. Rhizospheric GRSP content, Cd/P allocation patterns, and microbial community structure were analyzed using in situ analysis using laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS), sequential chemical extraction, and 16S rRNA sequencing. Results showed that AMF increased total Cd accumulation in S. nigrum shoots by 25.37% while reducing Cd uptake in rice shoots and roots by 45.18% and 55.54%, respectively. AMF also enhanced the P uptake rate of S. nigrum by 1.76 times compared to non-inoculated conditions, thereby increasing the total P accumulation in S. nigrum by 25.62% under Cd stress. Conversely, AMF negatively impacted the P content and total P accumulation in neighboring rice. Rhizospheric GRSP content increased significantly, indicating AMF's role in reducing Cd availability for rice. In situ analysis of LA-ICP-MS confirmed lower Cd content in rice rhizosphere and root surfaces, with minimal effects on S. nigrum. Lower DTPA-Cd concentrations in the rhizosphere of intercropped rice further substantiated the mycorrhizal Cd-blocking effects of AMF. Furthermore, AMF inoculation was the principal factor influencing alterations in the bacterial community structure within the intercropping system, by increasing the abundance of phosphate-solubilizing bacteria (mainly Ramlibacter, Roseisolibacter, and Bacillus) in the rhizosphere. AMF reduced the relative abundance of metal-tolerant bacteria (primarily Flavisolibacter) in the S. nigrum rhizosphere while enhancing their presence in the rice rhizosphere. This work revealed the resource acquisition effect (especially P uptake) of AMF on S. nigrum, thereby promoting Cd uptake and its preferential strengthening of the Cd-defending effect of the intercropped rice.

48-Hour and 24-Hour Time-lapse Single-nucleus Transcriptomics Reveal Cell-type specific Circadian Rhythms in Arabidopsis

Functional circadian clock is critical to the adaptation and survival of organisms. In land plants, the comprehensive profiling of circadian gene expression at the single-cell level is largely unknown partly due to the challenges in obtaining precisely-timed single cells embedded within cell walls. To bridge this gap, we employ time-lapse single-nucleus RNA sequencing (snRNA-seq) on Arabidopsis seedlings collected over a 48-hour window at 4-hour intervals, as well as over a 24-hour day at 2-hour intervals, yielding a total of over 77,142 and 130,000 nuclei. Here, we find that four cell clusters in the shoot share a coherent rhythm, while around 3000 genes display cell-type specific rhythmic expression. Our analysis indicates that genes encoding circadian regulators oscillate in multiple cell types, and the majority of them are well-documented core clock genes, suggesting the snRNA-seq circadian data could be used to identify more clock components oscillating in a cell-autonomous way. We identify ABF1 as a circadian regulator, whose overexpression and shortens the circadian period. Our data provides a comprehensive resource for plant circadian rhythmicity at the single-cell level (hosted at https://zhailab.bio.sustech.edu.cn/sc_circadian ).

Structure of a photosystem II-FCPII supercomplex from a haptophyte reveals a distinct antenna organization

Haptophytes are unicellular algae that produce 30 to 50% of biomass in oceans. Among haptophytes, a subset named coccolithophores is characterized by calcified scales. Despite the importance of coccolithophores in global carbon fixation and CaCO3 production, their energy conversion system is still poorly known. Here we report a cryo-electron microscopic structure of photosystem II (PSII)-fucoxanthin chlorophyll c-binding protein (FCPII) supercomplex from Chyrostila roscoffensis, a representative of coccolithophores. This complex has two sets of six dimeric and monomeric FCPIIs, with distinct orientations. Interfaces of both FCPII/FCPII and FCPII/core differ from previously reported. We also determine the sequence of Psb36, a subunit previously found in diatoms and red algae. The principal excitation energy transfer (EET) pathways involve mainly 5 FCPIIs, where one FCPII monomer mediates EET to CP47. Our findings provide a solid structural basis for EET and energy dissipation pathways occurring in coccolithophores.

CsRAP2-7 negatively regulates cuticular wax biosynthesis and drought resistance in citrus by directly activating CsACO1

Cuticular wax plays an important role in enhancing plant stress tolerance. While positive regulators of cuticular wax biosynthesis are well-studied, negative regulators remain largely unexplored in citrus. In the present paper, we screened and cloned an AP2/ERF family gene, CsRAP2-7, from navel orange. This gene is localized to the nucleus and induced by drought and ABA treatments. Overexpression of CsRAP2-7 in lemon upregulates ethylene biosynthesis while concurrently inhibiting cuticular wax accumulation and reducing cuticular permeability, collectively leading to a marked decline in drought tolerance. CsRAP2-7 mediates its regulatory role by directly binding to the promoter of CsACO1, an ethylene biosynthetic gene, thereby activating its transcription. These results suggest that CsRAP2-7 play a negative role in regulating cuticular wax biosynthesis and drought resistance by directly mediating CsACO1 expression.

Protection of naringenin chalcone by a pathogenesis-related 10 protein promotes flavonoid biosynthesis in Marchantia polymorpha

Pathogenesis-related (PR) proteins are diverse stress- or pathogen-induced proteins. Some are associated with specialised metabolism, including proposed functions for anthocyanin biosynthesis. However, data are limited to a few angiosperm species, and the mode(s) of action are uncertain. Using the liverwort Marchantia polymorpha (Marchantia), we examined whether pathogenesis-related 10 (PR10) contributes to flavonoid biosynthesis in other land plant lineages and investigated its mode of action. Marchantia produces two major flavonoid types: flavones and the pigment auronidin. MpPR10.5 is a target of the auronidin regulator MpMYB14; therefore, Mppr10.5 mutants were generated using CRISPR/Cas9 and analysed for transcript abundance (via RNA sequencing) and for metabolite content. Recombinant MpPR10.5 protein was used for metabolite binding and stabilisation assays. Mppr10.5 mutants had reduced auronidin and flavone content, demonstrating that MpPR10.5 promotes flavonoid biosynthesis. Flavone and auronidin biosynthesis share a single flavonoid intermediate, naringenin chalcone (NC), suggesting MpPR10.5 acts on this compound. MpPR10.5 protein binds NC strongly (micromolar affinity), preventing spontaneous self-cyclisation in vitro. Several phenylpropanoid and flavonoid genes were downregulated in Mppr10.5 and Mpchalcone isomerase-like plants. This suggests PR10 proteins promote flavonoid biosynthesis by selectively binding unstable intermediates (NC), protecting them from degradation or undesirable nonenzymatic conversions and facilitating their transport to subsequent pathway steps.

Multiple transitions to high l-DOPA 4,5-dioxygenase activity reveal molecular pathways to convergent betalain pigmentation in Caryophyllales

Many specialized metabolic pathways have evolved convergently in plants, but distinguishing multiple origins from alternative evolutionary scenarios can be difficult. Here, we explore the evolution of l-3,4-dihydroxyphenylalanine (l-DOPA) 4,5-dioxygenase (DODA) enzymes to better resolve the convergent evolution of the betalain biosynthetic pathway within the flowering plant order Caryophyllales. We use yeast-based heterologous assays to quantify enzymatic activity of extant proteins and then employ ancestral sequence reconstruction to resurrect and assay ancestral DODA enzymes. We use a combination of ancestral sequence reconstruction, model-based methods, and structural modelling to describe patterns of molecular convergence. We confirm that high l-DOPA 4,5-dioxygenase activity is polyphyletic and show that high activity DODAs evolved at least three times from ancestral proteins with low activity. We show that molecular convergence is concentrated proximally to the binding pockets but also appears distally to active sites. Moreover, our analysis also suggests that many unique and divergent substitutions contribute to the evolution of DODA. Given the key role of DODA in betalain biosynthesis, our analysis further supports the convergent origins of betalains and illustrates how the iterative evolution of betalain biosynthesis has drawn on a complex mixture of convergent, divergent, and unique variation.

Wild Cicer species exhibit superior leaf photosynthetic phosphorus- and water-use efficiencies compared with cultivated chickpea under low-phosphorus conditions

Domesticated chickpea cultivars exhibit limited genetic diversity. This study evaluated the effects of chickpea domestication on phosphorus (P)-use efficiency (PUE) under low-P conditions, using a diverse Cicer collection, including wild species. Two wild Cicer species - 54 C. reticulatum accessions and 15 C. echinospermum accessions, and seven domesticated C. arietinum accessions were grown in low-P soil. All three species exhibited significant variation in physiological PUE, leaf gas exchange characteristics, photosynthetic PUE (PPUE), and photosynthetic N-use efficiency (PNUE), with greater variation in wild Cicer species than in domesticated C. arietinum. Domestication increased shoot growth and total leaf area but reduced root mass ratio. Compared with domesticated C. arietinum, wild Cicer species had lower stomatal conductance and higher leaf mass per area, associated with lower intercellular CO2 concentrations and higher water-use efficiency (WUE). Elevated leaf nitrogen concentrations in wild Cicer were likely associated with enhanced photosynthetic capacity, partially compensating for reduced stomatal conductance. Wild Cicer species demonstrated higher PPUE but lower PNUE than domesticated chickpea, with increased WUE exhibiting a trade-off with PNUE. These findings highlight the potential of wild Cicer species as valuable genetic resources for enhancing PPUE in chickpea improvement programmes.

PCP-B peptides and CrRLK1L receptor kinases control pollination via pH gating of aquaporins in Arabidopsis

During pollen-stigma interaction, pollen coat protein B-class peptides (PCP-Bs) compete with stigmatic rapid alkalinization factor (RALF) for interaction with FERONIA/ANJEA receptor kinases (FER/ANJ), stimulating pollen hydration and germination. However, the molecular mechanism underlying PCP-Bs-induced, FER/ANJ-regulated compatible responses remains largely unknown. Through PCP-Bγ-induced phosphoproteomic analysis, we characterized a series of pollination-related signaling pathways regulated by FER/ANJ. Interestingly, on stigmatic papillary cells, pollen PCP-Bγ induced an elevation in cytosolic pH near the plasma membrane (PM), sustained by stigmatic RALF23/33 through regulation of the autoinhibited H+-ATPase 1/2 (AHA1/2) activity. We further found that RALFs/PCP-Bs and FER/ANJ regulated the pH alterations via phosphorylation of AHA1/2 C terminus. Furthermore, RALF23/33-FER/ANJ maintained the protonation of H197 in plasma membrane intrinsic proteins (PIPs), whereas PCP-B relieved the protonation through AHA activity. Altogether, this study reveals that pollen PCP-Bs trigger FER/ANJ-controlled compatible responses, particularly the opening of aquaporins via AHA-mediated pH changes, thereby facilitating pollen hydration in Arabidopsis.

Distinct regulation of mRNA decay pathways by ABA enhances Nitrate Reductase 1/2-derived siRNAs production and stress adaptation

RNA degradation systems (e.g., RNA decay and RNA interference) and the phytohormone abscisic acid (ABA) are both essential for plant growth, development, and adaptation to stress. Although the interplay between these pathways has been recognized, the molecular mechanisms governing their coordination remain poorly understood. In this study, we revealed that mutations in the 5'-3' RNA-degrading enzyme Ethylene Insensitive 5 (EIN5) result in hypersensitivity to ABA in Arabidopsis, whereas defects in the 3'-5' RNA turnover machinery (ski mutants) do not. The ABA hypersensitivity of ein5 mutants was mitigated by mutating components of the post-transcriptional gene silencing (PTGS) pathway, including DICER-LIKE 2 (DCL2)/DCL4, RNA-Dependent RNA Polymerase 1 (RDR1)/RDR6, and ARGONAUTE 1 (AGO1). ABA treatment substantially increased the abundance of coding-transcript-derived small interfering RNAs (ct-siRNAs) in ein5, predominantly from two genes, Nitrate Reductase 1 (NIA1) and NIA2. Further analysis suggested that NIA1 and NIA2 negatively regulate both the ABA biosynthesis and signaling pathways. The key transcription factor Abscisic Acid Insensitive 3 (ABI3) represses SKI3 expression by directly binding to its promoter, thereby promoting the production of NIA1/NIA2-derived ct-siRNAs, leading to the ABA hypersensitivity of ein5. Conversely, ABA enhances the accumulation of EIN5 as well as DCL4 and AGO1, pointing to distinct regulation of the mRNA decay and PTGS pathways. Collectively, these findings demonstrate the pivotal roles of NIA1 and NIA2 in plant responses to abiotic stress and provide new insights into the interplay between the ABA response and RNA degradation pathways.

The stress-induced gene AtDUF569 positively regulates salt stress responses in Arabidopsis thaliana

BACKGROUND

Frequent drought and high soil salinity are significant stressors that hinder crop yields worldwide. Understanding gene regulation and underlying stress responses in plants is key to combating abiotic stress. Recent reports have implicated the domain-of-unknown-function (DUF) proteins in plant stress responses. In Arabidopsis, AtDUF569 regulates plant growth and development under oxidative as well as nitro-oxidative stress and modulates plant basal defense.

RESULTS

Here, we describe how AtDUF569 bolsters plant responses to salt stress. The atduf569 mutant plants demonstrated a salt-resistant phenotype. The expression of salt overly sensitive (SOS) pathway genes, nitrate reductase, abscisic acid (ABA)-dependent stress-induced genes, and other stress-related genes were altered in atduf569 plants in comparison to wild type. We also measured antioxidant activity, chlorophyll, polyphenol, flavonoid, total carotenoid, protein, malondialdehyde (MDA), ABA, and amino acid content; atduf569 plants had significantly lower levels of superoxide dismutase and polyphenol oxidase, total chlorophyll, polyphenol, flavonoid, carotenoid, protein, and ABA, though a significant increase in MDA content was observed.

CONCLUSION

These results indicate that AtDUF569 positively regulates plant responses to salt stress by modulating the expression of SOS pathway genes, potentially through transcriptional or indirect regulatory mechanisms, antioxidant defense and streamlining, photosynthesis, ABA, and secondary metabolites production.

Chelation and nanoparticle delivery of monomeric dopamine to increase plant salt stress resistance

Soil salinization hinders sustainable development of global agriculture. Dopamine (DA) delivery is promising for mitigating the detrimental effects of salt on plants. However, self-polymerization limits delivery and effectiveness. Here we chelated DA with ethylenediamine tetraacetic acid and zinc to reduce self-polymerization. To reduce soil adsorption, a sodium lignosulfonate and octadecyl dimethyl benzyl ammonium chloride nanocarrier is made for delivery to the plant. Compared with DA monomer, the soil adsorption rate of the DA in the nanocarrier is 46.02% lower. Salt stress experiments reveal, compared with NaCl and DA groups, the nanocarrier group exhibits significant increases in growth indicators for tomato plants. The beneficial effect is attributed to the increases in proline content, antioxidant capacity, and K+/Na+ ratios in the plants. Similar results are also observed with woody pear seedlings. These findings provide insights into alleviating crop salt stress.

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.

Response of different cotton genotypes to salt stress and re-watering

BACKGROUND

Cotton is a vital economic crop and reserve material and a pioneer crop planted on saline-alkaline soil. Improving the tolerance of cotton to saline alkaline environments is particularly important.

RESULTS

Salt-tolerant and salt-sensitive cotton plants at the three-leaf stage were subjected to 200 mM NaCl stress treatment, thereafter, microstructural observations beside physiological and biochemical analyses were performed on cotton leaves at 0 h (CK), 48 h (NaCl) and re-watering (RW) for 48 h. Salt stress altered microstructural observations and physiological and biochemical in ST and SS (p < 0.05). After re-watering, ST recovered fully, while SS sustained permanent oxidative and structural damage, indicating distinct salt tolerance. Transcriptome analysis was performed on cotton leaves under salt stress and re-watering conditions. KEGG analysis revealed that the response of cotton to salt stress and its adaptation to re-watering may be related to major protein families such as photosynthesis (ko 00195), photosynthesis-antenna protein (ko 00196), plant hormone signal transduction (ko 04075), starch and sucrose metabolism (ko 00500), and porphyrin and chlorophyll metabolism (ko 00860). A gray coexpression module associated with cotton restoration under salt stress was enriched according to WGCNA.

CONCLUSIONS

Salt stress did not only affect the physiological and biochemical levels of cotton but also induced structural changes in cells and tissues. Re-watering was relatively effective in stabilizing the physiological and biochemical parameters, as well as the leaf microstructure, of cotton plants under salt stress. WGCNA revealed enriched gray coexpression modules related to the recovery of cotton plants under salt stress, and screening of the pivotal genes in the gray module revealed five critical hubs, namely, GH_A01G1528, GH_A08G2688, GH_D08G2683, GH_D01G1620 and GH_A10G0617. Overall, our findings can provide new insights into enhancing cotton salt tolerance and exploring salt tolerance genes in cotton,including screening cotton genetic resources using those potential responsive genes. This study provides a theoretical basis for further exploration of the molecular mechanism of cotton salt tolerance and genetic resources for breeding salt-tolerant cotton.

LNK1/2 and COR27/28 Regulate Arabidopsis Photoperiodic Flowering in FKF1-Dependent and -Independent Pathways

The circadian clock allows plants to anticipate daily and seasonal environmental changes, thereby optimizing photoperiod-dependent flowering. While core clock components such as LNK1 and LNK2, as well as COR27 and COR28, have been implicated in photoperiodic flowering in Arabidopsis, their specific roles and interactions remain poorly understood. Here, genetic analysis revealed that LNK1/2 act upstream of COR27/28 under long-day (LD) conditions and contribute slight additively under short-day (SD) conditions. LNK1/2 directly bind the FKF1 promoter to promote its transcriptiontg, leading to upregulation of FT and floral induction. By contrast, COR27/28 enhance FT expression through an FKF1-independent mechanism. Transcriptional and protein-level assays, including qRT-PCR and split-luciferase complementation, revealed that both LNK1/2 and COR27/28 are regulated by photoperiod and form a protein complex enriched near ZT12. These findings suggest coordinated regulation of flowering via both shared and distinct pathways. Together, our results demonstrate that LNK1/2 and COR27/28 integrate photoperiodic signals to regulate FT expression through FKF1-dependent and -independent mechanisms, revealing a new layer of circadian control over seasonal flowering.

Auxin and tryptophan trigger common responses in the streptophyte alga Penium margaritaceum

Auxin is a signaling molecule that regulates multiple processes in the growth and development of land plants. Research gathered from model species, particularly Arabidopsis thaliana, has revealed that the nuclear auxin pathway controls many of these processes through transcriptional regulation. Recently, a non-transcriptional pathway based on rapid phosphorylation mediated by kinases has been described, complementing the understanding of the complexity of auxin-regulated processes. Phylogenetic inferences of both pathways indicate that only some of these components are conserved beyond land plants. This raises fundamental questions about the evolutionary origin of auxin responses and whether algal sisters share mechanistic features with land plants. Here, we explore auxin responses in the unicellular streptophyte alga Penium margaritaceum. By assessing physiological, transcriptomic, and cellular responses, we found that auxin triggers cell proliferation, gene regulation, and acceleration of cytoplasmic streaming. Notably, all these responses are also triggered by the structurally related tryptophan. These results identify shared auxin response features among land plants and algae and suggest that less chemically specific responses preceded the emergence of auxin-specific regulatory networks in land plants.

Overexpression of E. coli formaldehyde metabolic genes pleiotropically promotes Arabidopsis thaliana growth by regulating redox homeostasis

Formaldehyde (FA) is a hazardous pollutant causing acute and chronic poisoning in humans. While plants provide a natural method of removing FA pollution, their ability to absorb and degrade FA is limited. To improve the ability of plants to degrade FA, we introduced the E. coli FrmA gene into Arabidopsis thaliana alone (FrmAOE lines) or with FrmB (FrmA/BOE lines). The transgenic seedlings had approximately 30 % longer primary roots and a 20 % higher fresh weight than the control plants. The transgenic plants started flowering four days earlier and had about 30 % more kilo-seed weight than the wild type. FrmA/BOE and FrmAOE accumulated 40 % more reactive oxidative species (ROS) in mesophyll protoplasts and leaf tissue than wild-type plants under normal conditions. In the presence of FA, they produced 92 % and 26 % more glutathione (GSH) and 6 % and 4 % more ascorbate (AsA), respectively, compared to wild-type plants and thus scavenged FA-induced ROS more effectively. The degradation efficiency of the transgenic leaf extract for FA was 73 % and 44 % higher than that of the wild type, respectively, which was also emphasized by a 2 %-26 % increase in the activity of antioxidant enzymes such as SOD and APx. By revealing the functional divergence between microbial and plant FA metabolic pathways, our work has not only highlighted the promising pluripotency of microbial genes in promoting normal plant growth and detoxifying organic pollutants simultaneously, but also revealed another layer of complexity of plant defense mechanisms against organic toxins related to ROS scavenging.

Comparative spatial transcriptomics reveals root dryland adaptation mechanism in rice and HMGB1 as a key regulator

Drought severely threatens food security, and its detrimental effects will be exacerbated by climate change in many parts of the world. Rice production is water-consuming and particularly vulnerable to drought stress. Upland rice is a special rice ecotype that specifically adapts to dryland mainly due to its robust root system. However, the molecular and developmental mechanism underlying this adaption has remained elusive. In this study, by comparing the root development between upland and irrigated rice phenotypically and cytologically, we identified key developmental phenotypes that distinguish upland rice from irrigated rice. We further generated spatial transcriptomic atlases for coleoptilar nodes and root tips to explore their molecular differences in crown root formation and development, uncovering promising genes for enhancing rice drought resistance. Among the identified genes, HMGB1, a transcriptional regulator, functions as a key factor that facilitates root elongation and thickening in upland rice and thereby enhances drought resistance. In summary, our study uncovers spatially resolved transcriptomic features in roots of upland rice that contribute to its adaptation to dryland conditions, providing valuable genetic resources for breeding drought-resilient rice.

Structural comparison of three MoaE proteins in Mycobacterium tuberculosis: Insights into molybdopterin synthase assembly and specificity

Molybdoenzymes are essential for the survival and pathogenicity of Mycobacterium tuberculosis and require the molybdenum cofactor (MoCo). The biosynthesis of MoCo involves the molybdopterin (MPT) synthase complex, which is composed of the MoaD and MoaE subunits. The genome of M. tuberculosis encodes three homologs of MoaE: MoaE1, MoaE2, and MoaXE (the latter being a MoaE component of a MoaD-MoaE fusion protein known as MoaX), as well as three MoaD proteins. However, the structural basis for their functional specificity and interaction with MoaD partners remains unclear. We determined the crystal structures of all three MoaE proteins, revealing a conserved α/β hammerhead fold with distinct binding interface features resulting from minor sequence variations. Pull-down assays demonstrate that MoaE2 and MoaXE selectively interact with their cognate MoaD partners, while MoaE1 exhibits promiscuous binding to all MoaD forms. Although the structural plasticity of MoaE1 enables binding to three MoaD forms, it suggests that not all MoaE-MoaD combinations yield functional MPT synthase complexes, as structural rearrangements can lead to enzymatic inactivation. Our findings provide detailed insights into the molecular determinants that govern the assembly and specificity of MPT synthase in M. tuberculosis.

Two E-clade protein phosphatase 2Cs enhance ABA signaling by dephosphorylating ABI1 in Arabidopsis

ABA INSENSITIVE 1 (ABI1) and ABI2 are co-receptors of the phytohormone abscisic acid (ABA). Studies have demonstrated that phosphorylation of multiple amino acids on ABI1/2 augments their ability to inhibit ABA signaling in planta. However, whether and how the dephosphorylation of ABI1/2 is regulated to enhance plant sensitivity to ABA remain unknown. In this study, we identified two protein phosphatases, designated ABI1-Dephosphorylating E-clade PP2C 1 (ADEP1) and ADEP2, that interact with ABI1/2. Mutants lacking ADEP1, ADEP2, or both (adep1/2) exhibited reduced ABA inhibition of seed germination and root growth, as well as lower levels of ABA-induced stomatal closure. In addition, ABA-induced accumulation of ABI5 protein and expression of downstream target genes are reduced in the adep1/2 mutant compared with the wild type. These findings suggest that ADEP1/2 function as positive regulators of the ABA signaling pathway. Mass spectrometry analysis and two-dimensional electrophoresis identified Ser117 as a major ABA-induced phosphorylation site on the ABI1 protein. ADEP1/2 can dephosphorylate Ser117, leading to destabilization of the ABI1 protein and increased sensitivity of plants to ABA. Moreover, ABA treatment decreases the abundance of ADEP1/2 proteins. In summary, our study reveals two novel regulatory proteins that modulate ABA signaling and provides new insights into the regulatory network that fine-tunes plant ABA responses.

Redox-sensitive δ65Cu isotopic fractionation in the tissue of the scleractinian coral Stylophora pistillata: a biomarker of holobiont photophysiology following volcanic ash exposure

Volcanic ash is a significant source of micronutrients including iron (Fe), copper (Cu), and zinc (Zn) in oligotrophic tropical waters. These bioactive metals enhance primary productivity, influencing local and global biogeochemical cycles. This study explores how volcanic ash exposure affects trace metal uptake and photophysiological response, and how redox-sensitive metal stable isotope measurements in the tissues of the scleractinian coral Stylophora pistillata can provide crucial information on coral health. Controlled coral culture experiments were conducted in which coral nubbins were exposed to varying intensity and duration of volcanic ash. Throughout the experiment, coral symbionts showed enhanced photosynthetic performance irrespective of intensity or duration of ash exposure. Stable isotopes, such as δ65Cu and δ56Fe, in the coral tissue are marked by systematic variations, not associated with intensity or duration of ash exposure. Instead, we suggest biologically modulated redox-sensitive fractionation associated with ash exposure, linked to the coral host's oxidative stress state. This is evidenced by significant correlations between δ65Cu in coral hosts and photophysiology, with lighter Cu isotope ratios associated with higher photosynthetic performances. Hence, we propose that δ65Cu, and more generally redox-sensitive isotopic ratios (i.e. δ56Fe), in coral hosts serves as an indicator of the physiological state of symbiotic corals.

Microbe-mediated stress resistance in plants: the roles played by core and stress-specific microbiota

BACKGROUND

Plants in natural surroundings frequently encounter diverse forms of stress, and microbes are known to play a crucial role in assisting plants to withstand these challenges. However, the mining and utilization of plant-associated stress-resistant microbial sub-communities from the complex microbiome remains largely elusive.

RESULTS

This study was based on the microbial communities over 13 weeks under four treatments (control, drought, salt, and disease) to define the shared core microbiota and stress-specific microbiota. Through co-occurrence network analysis, the dynamic change networks of microbial communities under the four treatments were constructed, revealing distinct change trajectories corresponding to different treatments. Moreover, by simulating species extinction, the impact of the selective removal of microbes on network robustness was quantitatively assessed. It was found that under varying environmental conditions, core microbiota made significant potential contributions to the maintenance of network stability. Our assessment utilizing null and neutral models indicated that the assembly of stress-specific microbiota was predominantly driven by deterministic processes, whereas the assembly of core microbiota was governed by stochastic processes. We also identified the microbiome features from functional perspectives: the shared microbiota tended to enhance the ability of organisms to withstand multiple types of environmental stresses and stress-specific microbial communities were associated with the diverse mechanisms of mitigating specific stresses. Using a culturomic approach, 781 bacterial strains were isolated, and nine strains were selected to construct different SynComs. These experiments confirmed that communities containing stress-specific microbes effectively assist plants in coping with environmental stresses.

CONCLUSIONS

Collectively, we not only systematically revealed the dynamics variation patterns of rhizosphere microbiome under various stresses, but also sought constancy from the changes, identified the potential contributions of core microbiota and stress-specific microbiota to plant stress tolerance, and ultimately aimed at the beneficial microbial inoculation strategies for plants. Our research provides novel insights into understanding the microbe-mediated stress resistance process in plants. Video Abstract.

Adaptive dynamics of extrachromosomal circular DNA in rice under nutrient stress

Extrachromosomal circular DNAs (eccDNAs) have been identified in various eukaryotic organisms and are known to play crucial roles in genomic plasticity. However, in crop plants, the role of eccDNAs in responses to environmental cues, particularly nutritional stresses, remains unexplored. Rice (Oryza sativa ssp. japonica), a vital crop for over half the world's population and an excellent model plant for genomic studies, faces numerous environmental challenges during growth. Therefore, we conduct comprehensive studies investigating the distribution, sequence, and potential responses of rice eccDNAs to nutritional stresses. We describe the changes in the eccDNA landscape at various developmental stages of rice in optimal growth. We also identify eccDNAs overlapping with genes (ecGenes), transposable elements (ecTEs), and full-length repeat units (full-length ecRepeatUnits), whose prevalence responds to nitrogen (N) and phosphorus (P) deficiency. We analyze multiple-fragment eccDNAs and propose a potential TE-mediated homologous recombination mechanism as the origin of rice's multiple-fragment eccDNAs. We provide evidence for the role of eccDNAs in the rice genome plasticity under nutritional stresses and underscore the significance of their abundance and specificity.

PtrCWINV3 encoding a cell wall invertase regulates carbon flow to wood in Populus trichocarpa

Cell wall invertase (CWINV) catalyzes the hydrolysis of sucrose into glucose and fructose in the apoplastic unloading pathway, with carbon sources provided for sink tissues. However, its role in wood formation remains undetermined. Therefore, transgenic lines overexpressing PtrCWINV3 or with knocked-out PtrCWINV3 expression were generated in Populus trichocarpa. Compared with wild type, the PtrCWINV3-knockout lines showed decreased CWINV activity (by 7.4 %-10.8 %), which resulted in a 1.5 %-1.8 % decrease in cellulose content, a 0.82 %-0.98 % decrease in hemicellulose content, and an increase in lignin content (by 2.9 %-4.7 %). These changes in structural carbohydrate contents were accompanied with anomalies in the late stages of secondary xylem development, characterized by reduced width of the secondary xylem, fewer cell layers in secondary xylem, and thinner fiber cell walls. The lines overexpressing PtrCWINV3 under the control of the DX15 promoter in the developing xylem showed the opposite phenotype. Transcriptome data from the developing xylem indicated that PtrCWINV3 regulated the expression of genes involved in the biosynthesis of cellulose (CesA, EG, and CB), hemicellulose/pectin (UGD, AXS, GATL, UAM, PAE, and GAUT), and starch (GBSS), which suggested its involvement in multiple polysaccharide metabolic pathways. Ultimately, this facilitated the synthesis of structural carbohydrate components such as cellulose and hemicellulose, which promoted the later stages of secondary xylem development. These findings not only demonstrate the significant role of CWINV activity in wood formation, but also highlight an excellent candidate gene for breeding new poplar varieties with high cellulose and low lignin contents.

Shaping the future: Unravelling regulators modulating plant architecture for next-generation crops

Plant architecture traits in crops are modulated through intricate interactions of various genetic pathways, which helps them to adapt to diverse environmental conditions. Key developmental pathways involved in forming plant architecture include the LAZY-TAC (Tiller Angle Control) module regulating branch and tiller angle, the CLAVATA-WUSCHEL pathway controlling shoot apical meristem fate and the GID1-DELLA pathway governing plant height and tillering in major food crops. These pathways function in concert to shape the overall architecture of plants, which is essential for optimizing light capture, resource allocation, reproductive success and eventual crop yield enhancement. Presently, plant architecture of modern crops has been shaped especially by artificial selection of natural alleles that target yield traits. Recent advances in CRISPR-Cas-based genome editing and genomics-assisted breeding strategies have enabled precise genetic manipulation of natural alleles in the functionally relevant genes regulating plant architecture traits in crops. This will assist researchers to select and introgress superior natural alleles in popular cultivars strategically for restructuring their desirable plant-types suitable for mechanical harvesting as well as enhancing the crop yield potential.

Dynamics of cytosolic and organellar gene transcripts in wild and cultivated genotypes of pigeon pea due to simulated herbivory

Pigeon pea (Cajanus cajan), widely grown in India, suffers significant yield losses due to pod borers (Helicoverpa armigera and Maruca vitrata). Therefore, studying the host resistance mechanism is pivotal for crop improvement. In this study, we conducted transcriptome analysis on two wild-type (WT) Cajanus scarabaeoides accessions (ICP-15761 and ICP-15738) having high levels of resistance to pod borers and two cultivated C. cajan genotypes, ICPL-332 (moderately resistant) and ICPL-87 (susceptible), following simulated herbivory with H. armigera oral secretions (OS). Differential gene expression analysis identified 3573 and 4677 differentially expressed genes (DEGs) in ICP-15761 and ICP-15738, whereas 4149 and 3639 DEGs were documented in ICPL-332 and ICPL-87, respectively. Genes related to chloroplast biogenesis, photosynthesis, and chlorophyll metabolism exhibited significant differential expression, indicating chloroplast reprogramming under simulated herbivory. Significant upregulation of key defense genes, including chitinases and cysteine proteases, in C. scarabaeoides accessions highlighted robust defense pathway activation. A genotype-specific shift in transcription factors, phytohormones, and calcium signaling-related gene expression was noted. Higher levels of expression of aspartic proteinases and pathogenesis-related proteins in cultivated genotypes suggesting adaptive evolutionary traits. This is a novel insight on molecular mechanism of defense in a wild type, C. scarabaeoides and cultivated genotypes of pigeon pea under simulated herbivory. The information on cytosolic and organellar gene changes in pigeon pea due to H. armigera OS mediated-simulated herbivory may help develop pigeon pea varieties that are resistant to pod borer infestations.

RABC1-ABI1 module coordinates lipid droplet mobilization and post-germination growth arrest in Arabidopsis

Abscisic acid (ABA) promotes post-germination growth arrest (PGGA), thereby enhancing plant survival under adverse conditions such as high salinity. Lipid droplets (LDs) are universally conserved dynamic organelles that can store and mobilize neutral lipids for their multiple cellular roles. The molecular mechanism whereby a plant coordinates LD mobilization and PGGA in response to environmental stresses remains poorly understood. Here, we report that RABC1 deficiency enhances PGGA, which could be efficiently mitigated by either inhibiting ABA biosynthesis or promoting LD breakdown. ABI1 interacts with and dephosphorylates RABC1 and promotes the interactions between RABC1 and its effectors SEIPIN2 and SEIPIN3, consequently enhancing LD mobilization. Taken together, these results report a regulatory mechanism of LD mobilization for plant stress tolerance and highlight a concerted interplay between lipid metabolism and hormonal signaling.

Kinase domain diversification drives specificity in BRI1 and non-BRI1 RLKs in brassinosteroid signaling

Receptor-like kinases (RLKs) are one of the largest families of Eukaryotic protein kinases (EPKs) that evolved through repeated duplication and diversification events in plants. RLKs regulate diverse roles of plant growth and development. Brassinosteroid Insensitive 1 (BRI1) and its family members BRI1-Like 1 (BRL1/3), BRL2, Excess Microsporocytes 1 (EMS1), and Nematode-Induced LRR-RLK 1 (NILR1) that belong to the LRR-RLK family of RLKs, control distinct biological functions through a conserved brassinosteroid (BR) signaling pathway. We previously demonstrated that the kinase specificity between BRI1 and GASSHO1 (GSO1) is allosterically regulated by merely two subdomains, raising a question of how different RLKs control distinct biological functions through their conserved kinase domain (KD). Here, we engineered chimeric receptors by fusing the extracellular domain (ECD) of BRI1 with KD of the BRI1 family and with non-BRI1 family RLKs, including BAK1-Interacting Receptor-like Kinase 1 (BIR1), BIR2, TOAD2 (RPK2), Barely Any Meristem (BAM1), CLAVATA 1 (CLV1), SOBIR1, Elongation Factor (EF-Tu) Receptor (EFR), Glycan Perception 4 (IGP4), and Strubbelig-Receptor Family 8 (SRF8), and confirmed that only the BRI1 family achieved BR signal output but not the others. We then replaced the S1 and S2 subdomains of the chimeric receptors with the corresponding S1 and S2 subdomains of the BRI1 kinase and found that except GSO1BRI1-S1S2, no other chimeric receptor could induce BR signaling in bri1-301 mutants. However, chimeric receptors RPK2BRI1-S1(E)S2, EFRBRI1-S1(E)S2, IGP4BRI1-S1(E)S2, BAM1BRI1-S1(E)S2, and SRF8BRI1-S1(E)S2 with an extended S1 subdomain S1(E) of BRI1 not only rescued bri1-301, but also achieved molecular phenotypes. In conclusion, this study provides evidence that signaling specificity of the RLKs has evolved through evolution of the S1 and S2 subdomains.

All roads lead to dome: Multicellular dynamics during de novo meristem establishment in shoot regeneration

Shoot apical meristems (SAMs) harbor persistent stem cells and give rise to above-ground organs throughout life. In tissue culture-based shoot regeneration, a subpopulation of pluripotent callus cells is specified into SAMs. How callus cells decide whether or not to become SAMs stands as an important question in developmental biology. Furthermore, the developmental basis underlying the de novo construction of dome-shaped SAMs remained largely unknown. Recent high-resolution analyses have revealed the spatiotemporal dynamics of cell fate determination and meristem establishment during shoot regeneration. Cell fates to become meristem are actively determined through interactions between neighboring cells, rather than by cell-autonomous fate transition. Inter-cell layer communication via mobile signal or mechanical cue may enable meristem construction. By integrating recent insights from the two-step tissue culture system in Arabidopsis together with other shoot regeneration systems, we depict the process of de novo meristem establishment as a dynamic multicellular system.