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Summary: In flowering plants, the interaction of pollen tubes with female tissues is important for the accomplishment of double fertilization. Little information is known about the mechanisms that underlie signalling between pollen tubes and female tissues. In this study, two Arabidopsis pollen tube‐expressed CrRLK1L protein kinases, Buddha's Paper Seal 1 (BUPS1) and BUPS2, were identified as being required for normal tip growth of pollen tubes in the pistil. They are expressed prolifically in pollen and pollen tubes and are localized on the plasma membrane of the pollen tube tip region. Mutations in BUPS1 drastically reduced seed set. Most of the bups1 mutant pollen tubes growing in the pistil exhibited a swollen pollen tube tip, leading to failure of fertilization. The bups2 pollen tubes had a slightly abnormal morphology but could still accomplish double fertilization. The bups1 bups2 double mutant exhibited a slightly enhanced phenotype compared to the single bups1 mutants. The BUPS1 proteins could form homomers and heteromers with BUPS2, whereas BUPS2 could only form heteromers with BUPS1. The BUPS proteins could interact with the Arabidopsis pollen‐expressed RopGEFs in the yeast two‐hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays. The results indicated that the BUPSs may mediate normal polar growth of pollen tubes in the pistil. [ABSTRACT FROM AUTHOR]

This document is a profile of Martina Legris, a postdoctoral researcher at the Center for Integrative Genomics at the University of Lausanne in Switzerland. Martina's interest in plant science was inspired by her upbringing in a family of veterinarians and farmers, as well as her experiences playing with plants and animals in nature. She decided to pursue a career in research after participating in scientific meetings and outreach activities, where she met inspiring scientists and learned about their research. Martina is motivated by her love for her work and the sense of duty to contribute to society. She considers her mentors and female colleagues with children to be role models, and she appreciates the opportunity to choose her research topics and the variety of tasks in her everyday life. Martina's research focuses on plant development in response to light and temperature signals from the environment. She has published papers on the convergence of light and temperature signaling pathways in plants and the regulation of meristem activity. Martina's favorite plant is Ceiba speciosa, a large tree native to South America, and she also has a fondness for Arabidopsis thaliana, a tiny plant that has allowed her to uncover exciting aspects of plant biology. [Extracted from the article]

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Glucosylceramides (GlcCer), glucose-conjugated sphingolipids, are major components of the endomembrane system and plasma membrane in most eukaryotic cells. Yet the quantitative significance and cellular functions of GlcCer are not well characterized in plants and other multi-organ eukaryotes. To address this, we examined Arabidopsis lines that were lacking or deficient in GlcCer by insertional disruption or by RNA interference ( RNAi) suppression of the single gene for GlcCer synthase ( GCS, At2g19880), the enzyme that catalyzes GlcCer synthesis. Null mutants for GCS (designated ' gcs-1') were viable as seedlings, albeit strongly reduced in size, and failed to develop beyond the seedling stage. Heterozygous plants harboring the insertion allele exhibited reduced transmission through the male gametophyte. Undifferentiated calli generated from gcs-1 seedlings and lacking GlcCer proliferated in a manner similar to calli from wild-type plants. However, gcs-1 calli, in contrast to wild-type calli, were unable to develop organs on differentiation media. Consistent with a role for GlcCer in organ-specific cell differentiation, calli from gcs-1 mutants formed roots and leaves on media supplemented with the glucosylated sphingosine glucopsychosine, which was readily converted to GlcCer independent of GCS. Underlying these phenotypes, gcs-1 cells had altered Golgi morphology and fewer cisternae per Golgi apparatus relative to wild-type cells, indicative of protein trafficking defects. Despite seedling lethality in the null mutant, GCS RNAi suppression lines with ≤2% of wild-type GlcCer levels were viable and fertile. Collectively, these results indicate that GlcCer are essential for cell-type differentiation and organogenesis, and plant cells produce amounts of GlcCer in excess of that required for normal development. [ABSTRACT FROM AUTHOR]

SUMMARY: Root hairs are crucial in the uptake of essential nutrients and water in plants. This study showed that a zinc finger protein, GIS3 is involved in root hair growth in Arabidopsis. The loss‐of‐function gis3 and GIS3 RNAi transgenic line exhibited a significant reduction in root hairs compared to the wild type. The application of 1‐aminocyclopropane‐1‐carboxylic acid (ACC), an exogenous ethylene precursor, and 6‐benzyl amino purine (BA), a synthetic cytokinin, significantly restored the percentage of hair cells in the epidermis in gis3 and induced GIS3 expression in the wild type. More importantly, molecular and genetic studies revealed that GIS3 acts upstream of ROOT HAIR DEFECTIVE 2 (RHD2) and RHD4 by binding to their promoters. Furthermore, exogenous ACC and BA application significantly induced the expression of RHD2 and RHD4, while root hair phenotype of rhd2‐1, rhd4‐1, and rhd4‐3 was insensitive to ACC and BA treatment. We can therefore conclude that GIS3 modulates root hair development by directly regulating RHD2 and RHD4 expression through ethylene and cytokinin signals in Arabidopsis. Significance Statement: In this paper, we demonstrated that zinc finger protein GIS3 is the key regulator to control root hair development in Arabidopsis. Further experiments demonstrated that GIS3, RHD2, and RHD4 are required for root hair development in response to ethylene and cytokinin signaling. More importantly, the molecular and genetic experiments reveal that GIS3 directly binds to the promoter of RHD2 and RHD4 to regulate root hair elongation in Arabidopsis. These results will provide a novel function of zinc finger protein interacting with hormone signal to control root hair development and a better understanding of the network of zinc finger protein interact with root hair‐related genes to control root hair development in Arabidopsis. [ABSTRACT FROM AUTHOR]

This document is an interview with Debora Gasperini, a researcher in plant science. Gasperini explains that her interest in research began at a young age, inspired by her love for the natural world and engaging science classes. She chose to study molecular biology and became fascinated with plants due to their unique communication and resilience. Gasperini is motivated by the thrill of discovery and problem-solving, and she considers scientists like Rita Levi-Montalcini and Katherine Esau as role models for their passion and perseverance. She also discusses her favorite papers from the journal New Phytologist, which covers a wide range of plant science topics. Gasperini appreciates the adaptability and enduring nature of plants, which continue to inspire her research. [Extracted from the article]

This document is an interview with Ari Sadanandom, a Professor of Plant Molecular Sciences at the University of Durham. Sadanandom discusses his interest in plant science, his decision to pursue a career in research, and his motivations as a scientist. He also mentions his role models and inspirations throughout his career. Additionally, Sadanandom highlights some of his favorite papers from the journal New Phytologist, focusing on topics such as plant immunity, root development, and protein modifications. Finally, he shares his favorite plant, the Mimosa plant, and provides information about his research on protein modifications and its implications for agriculture. [Extracted from the article]

Cellular condensates can comprise membrane‐less ribonucleoprotein assemblies with liquid‐like properties. These cellular condensates influence various biological outcomes, but their liquidity hampers their isolation and characterization. Here, we investigated the composition of the condensates known as processing bodies (PBs) in the model plant Arabidopsis thaliana through a proximity‐biotinylation proteomics approach. Using in situ protein–protein interaction approaches, genetics and high‐resolution dynamic imaging, we show that processing bodies comprise networks that interface with membranes. Surprisingly, the conserved component of PBs, DECAPPING PROTEIN 1 (DCP1), can localize to unique plasma membrane subdomains including cell edges and vertices. We characterized these plasma membrane interfaces and discovered a developmental module that can control cell shape. This module is regulated by DCP1, independently from its role in decapping, and the actin‐nucleating SCAR–WAVE complex, whereby the DCP1–SCAR–WAVE interaction confines and enhances actin nucleation. This study reveals an unexpected function for a conserved condensate at unique membrane interfaces. Synopsis: Processing body (PB) composition remains incompletely characterized. Here, proximity interactome profiling of Arabidopsis PBs describes their dynamic nature and identifies the role of PB components in actin‐dependent regulation of tissue growth. The protein composition and proximity‐dependent interactome ("proxitome") of plant processing bodies are determined by proximity biotinylation approaches.Plant processing bodies are dynamic and include proteins linked to membrane remodeling and actin dynamics.Processing body component DCP1 associates with the plasma membrane and the actin‐nucleating complex SCAR/WAVE at cell vertices.DCP1 phosphorylation status regulates its localization and root growth. [ABSTRACT FROM AUTHOR]

Premise: We developed a novel, cost‐effective protocol that facilitates testing anoxia tolerance in plants without access to specialized equipment. Methods and Results: Arabidopsis thaliana and barley (Hordeum vulgare) seedlings were treated in airtight 2‐L Kilner jars. An anoxic atmosphere was generated using Oxoid AnaeroGen 2.5‐L sachets placed on in‐house, custom‐built wire stands. The performed experiments confirmed a higher sensitivity to low oxygen stress previously observed in anac017 A. thaliana mutants and the positive effect of exogenous sucrose on anoxia tolerance reported by previous studies in A. thaliana. Barley seedlings displayed typical responses to anoxia treatment, including shoot growth cessation and the induction of marker genes for anaerobic metabolism and ethylene biosynthesis in root tissue. Conclusions: The results validate the novel method as an inexpensive, simple alternative for testing anoxia tolerance in plants, where access to an anaerobic workstation is not possible. The novel protocol requires minimum investment and is easily adaptable. [ABSTRACT FROM AUTHOR]

DNA methylation and histone modifications are important epigenetic markers involved in transcriptional gene regulation in animals and plants. In Arabidopsis, IDM1 is a histone acetyltransferase that plays critical roles in preventing hypermethylation of DNA and transcriptional gene silencing, but the mechanism(s) by which IDM1 is targeted to specific genomic loci is still unclear. Here, we find two new components of the IDM1 complex, IDAP1 and IDAP2, which bear high similarities to the transposase and myb-like DNA-binding protein of PIF/Harbinger transposons, respectively. Dysfunction of IDAP1 or IDAP2 causes DNA hypermethylation and repression of reporter genes as well as endogenous genes. IDAP1 interacts with IDAP2, and they form a protein complex with IDM1. Furthermore, IDAP2 has DNA-binding activity, which facilitates the recruitment of IDM1 to its target loci. We propose that IDAP1 and IDAP2, co-opted from ancient PIF/Harbinger-like transposon proteins, act together with IDM1 to regulate active DNA demethylation in higher plants. [ABSTRACT FROM AUTHOR]

922I.922II.922III.925IV.925V.926VI.927VII.928VIII.929IX.930X.931XI.932XII.933XIII.Natural variation and genome‐wide association studies934XIV.934XV.935XVI.936XVII.937937References937 Summary: The year 2014 marked the 25th International Conference on Arabidopsis Research. In the 50 yr since the first International Conference on Arabidopsis Research, held in 1965 in Göttingen, Germany, > 54 000 papers that mention Arabidopsis thaliana in the title, abstract or keywords have been published. We present herein a citational network analysis of these papers, and touch on some of the important discoveries in plant biology that have been made in this powerful model system, and highlight how these discoveries have then had an impact in crop species. We also look to the future, highlighting some outstanding questions that can be readily addressed in Arabidopsis. Topics that are discussed include Arabidopsis reverse genetic resources, stock centers, databases and online tools, cell biology, development, hormones, plant immunity, signaling in response to abiotic stress, transporters, biosynthesis of cells walls and macromolecules such as starch and lipids, epigenetics and epigenomics, genome‐wide association studies and natural variation, gene regulatory networks, modeling and systems biology, and synthetic biology. [ABSTRACT FROM AUTHOR]

Thylakoid membranes in chloroplasts and cyanobacteria harbor the multisubunit protein complexes that catalyze the light reactions of photosynthesis. In plant chloroplasts, the thylakoid membrane system comprises a highly organized network with several subcompartments that differ in composition and morphology: grana stacks, unstacked stromal lamellae, and grana margins at the interface between stacked and unstacked regions. The localization of components of the photosynthetic apparatus among these subcompartments has been well characterized. However, less is known about the localization of proteins involved in the biogenesis and repair of the photosynthetic apparatus, the partitioning of proteins between two recently resolved components of the traditional margin fraction (refined margins and curvature), and the effects of light on these features. In this study, we analyzed the partitioning of numerous thylakoid biogenesis and repair factors among grana, curvature, refined margin, and stromal lamellae fractions of Arabidopsis thylakoid membranes, comparing the results from illuminated and dark‐adapted plants. Several proteins previously shown to localize to a margin fraction partitioned in varying ways among the resolved curvature and refined margin fractions. For example, the ALB3 insertase and FtsH protease involved in photosystem II (PSII) repair were concentrated in the refined margin fraction, whereas TAT translocon subunits and proteins involved in early steps in photosystem assembly were concentrated in the curvature fraction. By contrast, two photosystem assembly factors that facilitate late assembly steps were depleted from the curvature fraction. The enrichment of the PSII subunit OE23/PsbP in the curvature fraction set it apart from other PSII subunits, supporting the previous conjecture that OE23/PsbP assists in PSII biogenesis and/or repair. The PSII assembly factor PAM68 partitioned differently among thylakoid fractions from dark‐adapted plants and illuminated plants and was the only analyzed protein to convincingly do so. These results demonstrate an unanticipated spatial heterogeneity of photosystem biogenesis and repair functions in thylakoid membranes and reveal the curvature fraction to be a focal point of early photosystem biogenesis. [ABSTRACT FROM AUTHOR]

Summary: Thlaspi arvense (pennycress) has the potential for domestication as a new oilseed crop. Information from an extensive body of research on the related plant species Arabidopsis can be used to greatly speed this process. Genome‐scale comparisons in this paper documented that pennycress and Arabidopsis share similar gene duplication. This finding led to the hypothesis that it should be possible to isolate Arabidopsis‐like mutants in pennycress. This proved to be true, as forward genetic screens identified floral and vegetative pennycress mutants that were similar to mutants found in Arabidopsis. Extending this approach, it was shown that most of the pennycress genes responsible for the formation of oxidized tannins could be rapidly identified. The causative mutations in the pennycress mutants could be identified either by PCR amplification of candidate genes or through whole‐genome sequencing (WGS) analysis. In all, WGS was used to characterize 95 ethyl methane sulfonate mutants, which revealed a mutation rate of 4.09 mutations per megabase. A sufficient number of non‐synonymous mutations were identified to create a mutant gene index that could be used for reverse genetic approaches to identify pennycress mutants of interest. As proof of concept, a Ta‐max3‐like dwarf mutant and Ta‐kcs5/cer60‐like wax mutants deficient in the biosynthesis of long chain fatty acids were identified. Overall, these studies demonstrate that translational genomics can be used to promote the domestication of pennycress. Furthermore, the ease with which important findings could be made in pennycress makes this species a new potential model plant. Significance statement: The domestication of pennycress has the potential to create a new oilseed cash/cover crop that can be grown during the fallow period between traditional summer crops, such as between the >80 million acres undergoing corn/soybean rotation in the Upper Midwest of the USA. This report demonstrates that translational genomics using Arabidopsis can serve as a tool to help greatly speed up the domestication process. [ABSTRACT FROM AUTHOR]

Summary: The LATE ELONGATED HYPOCOTYL (LHY) transcription factor functions as part of the oscillatory mechanism of the Arabidopsis circadian clock. This paper reports the genome‐wide analysis of its binding targets and reveals a role in the control of abscisic acid (ABA) biosynthesis and downstream responses.LHY directly repressed expression of 9‐cis‐epoxycarotenoid dioxygenase enzymes, which catalyse the rate‐limiting step of ABA biosynthesis. This suggested a mechanism for the circadian control of ABA accumulation in wild‐type plants. Consistent with this hypothesis, ABA accumulated rhythmically in wild‐type plants, peaking in the evening. LHY‐overexpressing plants had reduced levels of ABA under drought stress, whereas loss‐of‐function mutants exhibited an altered rhythm of ABA accumulation.LHY also bound the promoter of multiple components of ABA signalling pathways, suggesting that it may also act to regulate responses downstream of the hormone. LHY promoted expression of ABA‐responsive genes responsible for increased tolerance to drought and osmotic stress but alleviated the inhibitory effect of ABA on seed germination and plant growth.This study reveals a complex interaction between the circadian clock and ABA pathways, which is likely to make an important contribution to plant performance under drought and osmotic stress conditions. See also the Commentary on this article by Belbin & Dodd, 220: 661–663. [ABSTRACT FROM AUTHOR]

Persistent homology, a topological data analysis (TDA) method, is applied to microarray data sets. Although there are a few papers referring to TDA methods in microarray analysis, the usage of persistent homology in the comparison of several weighted gene coexpression networks (WGCN) was not employed before to the very best of our knowledge. We calculate the persistent homology of weighted networks constructed from 38 Arabidopsis microarray data sets to test the relevance and the success of this approach in distinguishing the stress factors. We quantify multiscale topological features of each network using persistent homology and apply a hierarchical clustering algorithm to the distance matrix whose entries are pairwise bottleneck distance between the networks. The immunoresponses to different stress factors are distinguishable by our method. The networks of similar immunoresponses are found to be close with respect to bottleneck distance indicating the similar topological features of WGCNs. This computationally efficient technique analyzing networks provides a quick test for advanced studies. [ABSTRACT FROM AUTHOR]

Summary: In the plant apoplast, ascorbate is oxidised, via dehydroascorbic acid, to O‐oxalyl esters [oxalyl‐ l‐threonate (OxT) and cyclic oxalyl‐ l‐threonate (cOxT)]. We tested whether OxT and cOxT can donate the oxalyl group in transacylation reactions to form oxalyl‐polysaccharides, potentially modifying the cell wall. [oxalyl‐14C]OxT was incubated with living spinach (Spinacia oleracea) and Arabidopsis cell‐suspension cultures in the presence or absence of proposed acceptor substrates (carbohydrates). In addition, [14C]OxT and [14C]cOxT were incubated in vitro with cell‐wall enzyme preparations plus proposed acceptor substrates. Radioactive products were monitored electrophoretically. Oxalyltransferase activity was detected. Living cells incorporated oxalate groups from OxT into cell‐wall polymers via ester bonds. When sugars were added, [14C]oxalyl‐sugars were formed, in competition with OxT hydrolysis. Preferred acceptor substrates were carbohydrates possessing primary alcohols e.g. glucose. A model transacylation product, [14C]oxalyl‐glucose, was relatively stable in vivo (half‐life >24 h), whereas [14C]OxT underwent rapid turnover (half‐life ~6 h). Ionically wall‐bound enzymes catalysed similar transacylation reactions in vitro with OxT or cOxT as oxalyl donor substrates and any of a range of sugars or hemicelluloses as acceptor substrates. Glucosamine was O‐oxalylated, not N‐oxalylated. We conclude that plants possess apoplastic acyltransferase (oxalyltransferase) activity that transfers oxalyl groups from ascorbate catabolites to carbohydrates, forming relatively long‐lived O‐oxalyl‐carbohydrates. The findings increase the range of known metabolites whose accumulation in vivo indicates vitamin C catabolism. Possible signalling roles of the resulting oxalyl‐sugars can now be investigated, as can the potential ability of polysaccharide oxalylation to modify the wall's physical properties. [ABSTRACT FROM AUTHOR]

Abstract: The spatial deployment of lateral roots determines the ability of a plant to interact with the surrounding environment for nutrition and anchorage. This paper shows that besides the pericycle, the vascular cambium becomes active in Arabidopsis thaliana taproot at a later stage of development and is also able to form new lateral roots. To demonstrate the above, we implemented a two‐step approach in which the first step leads to development of a secondary structure in A. thaliana taproot, and the second applies a mechanical stress on the vascular cambium to initiate formation of a new lateral root primordium. GUS staining showed PRE3, DR5 and WOX11 signals in the cambial zone of the root during new lateral root formation. An advanced level of wood formation, characterized by the presence of medullar rays, was achieved. Preliminary investigations suggest the involvement of auxin and two transcription factors (PRE3/ATBS1/bHLH135/TMO7 and WOX11) in the transition of some vascular cambium initials from a role as producers of xylem/phloem mother cells to founder cells of a new lateral root primordium. [ABSTRACT FROM AUTHOR]

Extracellular vesicles (EVs) are membrane‐bound exosomes secreted into the apoplast. Two distinct populations of EVs have been described in Arabidopsis: PEN1‐associated and TET8‐associated. We previously noted early leaf senescence in the pen1 single and pen1pen3 double mutant. Both PEN1 and PEN3 are abundant in EV proteomes suggesting that EVs might regulate leaf senescence in soil‐grown plants. We observed that TET8 is more abundant in the apoplast of early senescing pen1 and pen1pen3 mutant rosettes and in older wild‐type (WT) rosettes. The increase in apoplast TET8 in the pen1 mutant did not correspond to increased TET8 mRNA levels. In addition, apoplast TET8 was more abundant in the early leaf senescence myb59 mutant, meaning the increase in apoplast TET8 protein during leaf senescence is not dependent on pen1 or pen3. Genetic analysis showed a significant delay in leaf senescence in tet3tet8 double mutants after 6 weeks of growth suggesting that these two tetraspanin paralogs operate additively and are positive regulators of leaf senescence. This is opposite of the effect of pen1 and pen1pen3 mutants that show early senescence and suggest PEN1 to be a negative regulator of leaf senescence. Our work provides initial support that apoplast‐localized TET8 in combination with TET3 positively regulates age‐related leaf senescence in soil‐grown Arabidopsis plants. [ABSTRACT FROM AUTHOR]

In Brassicaceae self‐incompatibility (SI), self‐pollen rejection is initiated by the S‐haplotype specific interactions between the pollen S cysteine‐rich/S‐locus protein 11 (SCR/SP11) ligands and the stigma S receptor kinases (SRK). In Brassica SI, a member of the Plant U‐Box (PUB) E3 ubiquitin ligases, ARM‐repeat containing 1 (ARC1), is then activated by SRK in this stigma and cellular events downstream of this cause SI pollen rejection by inhibiting pollen hydration and pollen tube growth. During the transition to selfing, Arabidopsis thaliana lost the SI components, SCR, SRK, and ARC1. However, this trait can be reintroduced into A. thaliana by adding back functional copies of these genes from closely related SI species. Both SCR and SRK are required for this, though the degree of SI pollen rejection varies between A. thaliana accessions, and ARC1 is not always needed to produce a strong SI response. For the A. thaliana C24 accession, only transforming with Arabidopsis lyrataSCR and SRK confers a strong SI trait (SI‐C24), and so here, we investigated if ARC1‐related PUBs were involved in the SI pathway in the transgenic A. thaliana SI‐C24 line. Two close ARC1 homologs, PUB17 and PUB16, were selected, and (Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR‐associated protein 9 (Cas9) technology was used to generate pub17 and pub16 mutations in the C24 accession. These mutants were then crossed into the transgenic A. thaliana SI‐C24 line and their potential impact on SI pollen rejection was investigated. Overall, we did not observe any significant differences in SI responses to implicate PUB17 and PUB16 functioning in the transgenic A. thaliana SI‐C24 stigma to reject SI pollen. [ABSTRACT FROM AUTHOR]

Information about transcription start sites ( TSSs) provides baseline data for the analysis of promoter architecture. In this paper we used paired- and single-end deep sequencing to analyze Arabidopsis TSS tags from several libraries prepared from roots, shoots, flowers and etiolated seedlings. The clustering of approximately 33 million mapped TSS tags led to the identification of 324 461 promoters that covered 79.7% (21 672/27 206) of protein-coding genes in the Arabidopsis genome. In addition we identified intragenic, antisense and orphan promoters that were not associated with any gene models. Of these, intragenic promoters exhibited unique characteristics regarding dinucleotide sequences at TSSs and core promoter element composition, suggesting that these promoters use different mechanisms of transcriptional initiation. An analysis of base composition with regard to promoter position revealed a low GC content throughout the promoter region and several local strand biases that were evident for TATA-type promoters, but not for Coreless-type promoters. Most observed strand biases coincided with strand biases of single nucleotide polymorphism rate. Our analysis also revealed that transcription of a gene is supported by an average of 2.7 genic promoters, among which one specific promoter, designated as a top promoter, substantially determines the expression level of the gene. [ABSTRACT FROM AUTHOR]

Phenotyping is important to understand plant biology, but current solutions are costly, not versatile or are difficult to deploy. To solve this problem, we present Phenotiki, an affordable system for plant phenotyping that, relying on off-the-shelf parts, provides an easy to install and maintain platform, offering an out-of-box experience for a well-established phenotyping need: imaging rosette-shaped plants. The accompanying software (with available source code) processes data originating from our device seamlessly and automatically. Our software relies on machine learning to devise robust algorithms, and includes an automated leaf count obtained from 2D images without the need of depth (3D). Our affordable device (~€200) can be deployed in growth chambers or greenhouse to acquire optical 2D images of approximately up to 60 adult Arabidopsis rosettes concurrently. Data from the device are processed remotely on a workstation or via a cloud application (based on CyVerse). In this paper, we present a proof-of-concept validation experiment on top-view images of 24 Arabidopsis plants in a combination of genotypes that has not been compared previously. Phenotypic analysis with respect to morphology, growth, color and leaf count has not been performed comprehensively before now. We confirm the findings of others on some of the extracted traits, showing that we can phenotype at reduced cost. We also perform extensive validations with external measurements and with higher fidelity equipment, and find no loss in statistical accuracy when we use the affordable setting that we propose. Device set-up instructions and analysis software are publicly available ( ). [ABSTRACT FROM AUTHOR]

Plant metabolism is more complex relative to individual microbes. In single‐celled microbes, transcriptional regulation by single transcription factors (TFs) is sufficient to shift primary metabolism. Corresponding genome‐level transcriptional regulatory maps of metabolism reveal the underlying design principles responsible for these shifts as a model in which master regulators largely coordinate specific metabolic pathways. Plant primary and specialized metabolism occur within innumerable cell types, and their reactions shift depending on internal and external cues. Given the importance of plants and their metabolites in providing humanity with food, fiber, and medicine, we set out to develop a genome‐scale transcriptional regulatory map of Arabidopsis metabolic genes. A comprehensive set of protein–DNA interactions between Arabidopsis thaliana TFs and gene promoters in primary and specialized metabolic pathways were mapped. To demonstrate the utility of this resource, we identified and functionally validated regulators of the tricarboxylic acid (TCA) cycle. The resulting network suggests that plant metabolic design principles are distinct from those of microbes. Instead, metabolism appears to be transcriptionally coordinated via developmental‐ and stress‐conditional processes that can coordinate across primary and specialized metabolism. These data represent the most comprehensive resource of interactions between TFs and metabolic genes in plants. SYNOPSIS: A transcription factor‐promoter interaction network of primary and specialized metabolism in Arabidopsis thaliana reveals transcriptional coordination across multiple metabolic pathways that is developmental and stress condition‐dependent. High‐throughput enhanced yeast one‐hybrid is used to map 27,485 interactions between 1930 TFs and 220 promoters of enzymes in primary and specialized metabolic pathways in Arabidopsis thaliana.Functional analyses reveal that TFs within the network influence expression of target genes across multiple metabolic pathways.Biologically validated TFs show that TFs incorporate developmental and environmental cues to regulate TCA cycle gene expression in a context‐dependent manner. [ABSTRACT FROM AUTHOR]

Cell‐specific transcriptional regulatory networks (TRNs) play vital roles in plant development and response to environmental stresses. However, traditional single‐cell mono‐omics techniques are unable to directly capture the relationships and dynamics between different layers of molecular information within the same cells. While advanced algorithm facilitates merging scRNA‐seq and scATAC‐seq datasets, accurate data integration remains a challenge, particularly when investigating cell‐type‐specific TRNs. By examining gene expression and chromatin accessibility simultaneously in 16,670 Arabidopsis root tip nuclei, the TRNs are reconstructed that govern root tip development under osmotic stress. In contrast to commonly used computational integration at cell‐type level, 12,968 peak‐to‐gene linkage is captured at the bona fide single‐cell level and construct TRNs at an unprecedented resolution. Furthermore, the unprecedented datasets allow to more accurately reconstruct the coordinated changes of gene expression and chromatin states during cellular state transition. During root tip development, chromatin accessibility of initial cells precedes gene expression, suggesting that changes in chromatin accessibility may prime cells for subsequent differentiation steps. Pseudo‐time trajectory analysis reveal that osmotic stress can shift the functional differentiation of trichoblast. Candidate stress‐related gene‐linked cis‐regulatory elements (gl‐cCREs) as well as potential target genes are also identified, and uncovered large cellular heterogeneity under osmotic stress. [ABSTRACT FROM AUTHOR]

Summary: The Elongator complex was originally identified as an interactor of hyperphosphorylated RNA polymerase II (RNAPII) in yeast and has histone acetyltransferase (HAT) activity. However, the genome‐wide regulatory roles of Elongator on transcriptional elongation and histone acetylation remain unclear. We characterized a maize miniature seed mutant, mn7 and map‐based cloning revealed that Mn7 encodes one of the subunits of the Elongator complex, ZmELP1. ZmELP1 deficiency causes marked reductions in the kernel size and weight. Molecular analyses showed that ZmELP1 interacts with ZmELP3, which is required for H3K14 acetylation (H3K14ac), and Elongator complex subunits interact with RNA polymerase II (RNAPII) C‐terminal domain (CTD). Genome‐wide analyses indicated that loss of ZmELP1 leads to a significant decrease in the deposition of H3K14ac and the CTD of phosphorylated RNAPII on Ser2 (Ser2P). These chromatin changes positively correlate with global transcriptomic changes. ZmELP1 mutation alters the expression of genes involved in transcriptional regulation and kernel development. We also showed that the decrease of Ser2P depends on the deposition of Elongator complex‐mediated H3K14ac. Taken together, our results reveal an important role of ZmELP1 in the H3K14ac‐dependent transcriptional elongation, which is critical for kernel development. [ABSTRACT FROM AUTHOR]

Cell walls surround all plant cells, and their composition and structure are tightly regulated to maintain cellular and organismal homeostasis. In response to wall damage, the cell wall integrity (CWI) system is engaged to ameliorate effects on plant growth. Despite the central role CWI plays in plant development, our current understanding of how this system functions at the molecular level is limited. Here, we investigated the transcriptomes of etiolated seedlings of mutants of Arabidopsis thaliana with defects in three major wall polysaccharides, pectin (quasimodo2), cellulose (cellulose synthase3je5), and xyloglucan (xyloglucan xylosyltransferase1 and 2), to probe whether changes in the expression of cell wall‐related genes occur and are similar or different when specific wall components are reduced or missing. Many changes occurred in the transcriptomes of pectin‐ and cellulose‐deficient plants, but fewer changes occurred in the transcriptomes of xyloglucan‐deficient plants. We hypothesize that this might be because pectins interact with other wall components and/or integrity sensors, whereas cellulose forms a major load‐bearing component of the wall; defects in either appear to trigger the expression of structural proteins to maintain wall cohesion in the absence of a major polysaccharide. This core set of genes functioning in CWI in plants represents an attractive target for future genetic engineering of robust and resilient cell walls. [ABSTRACT FROM AUTHOR]

Herbivorous insects and their host plants comprise most known species on Earth. Illuminating how herbivory repeatedly evolved in insects from nonherbivorous lineages is critical to understanding how this biodiversity is created and maintained. We characterized the trophic niche of Scaptomyza flava, a representative of a lineage nested within the Drosophila that transitioned to herbivory ~10–15 million years ago. We used natural history studies to determine whether S. flava is a true herbivore or a cryptic microbe‐feeder, given that the ancestral character state for the family Drosophilidae is likely microbe‐feeding. Specifically, we quantified oviposition substrate choice and larval viability across food types, trophic‐related morphological traits, and nitrogen isotope and sterol profiles across putatively herbivorous and nonherbivorous drosophilids. The results of these studies show that S. flava is an obligate herbivore of living plants. Paired with its genetic model host, Arabidopsis thaliana, S. flava is a novel and powerful system for exploring mechanisms underlying the evolution of herbivory, a complex trait that enabled the exceptional diversification of insects. [ABSTRACT FROM AUTHOR]

Plant stem cell niches ( SCNs) can be maintained in time through asymmetric cell divisions ( ACDs) that allow the production of new cell types while constantly renewing the pools of stem cells ( SCs). ACDs in plants require the asymmetric distribution of molecular components inside the cells as well as external asymmetric positional information. These two types of asymmetric information are controlled by inter- and intracellular signalling events. Phosphorylation of proteins is a major intermediate step in these signalling events, serving either as an activator or repressor of signalling, via fast auto- and trans-phosphorylation mechanisms. Whereas protein kinases, which phosphorylate proteins on serine, threonine or tyrosine residues, have been thoroughly studied, less attention has been given to protein phosphatases, which de-phosphorylate their protein targets on these same residues. Phosphatases modulate the activity of signalling pathways by balancing the action of kinases, and are therefore critical in the regulation of ACDs in plants. In this review, we first present the different types of ACDs that operate during Arabidopsis embryonic and post-embryonic development and participate in the construction and maintenance of its root and shoot SCNs; we then give a brief description of the main protein phosphatases so far described in the Arabidopsis genome; and finally discuss their functions toward the regulation of the ACDs introduced in the first part of the paper. [ABSTRACT FROM AUTHOR]

• In this paper we describe PATTERN-TRIGGERED IMMUNITY (PTI) COMPROMISED RECEPTOR-LIKE CYTOPLASMIC KINASE 1 (PCRK1) of Arabidopsis thaliana, an RLCK that is important for defense against the pathogen Pseudomonas syringae pv. maculicola ES4326 (Pma ES4326). • We examined defense responses such as bacterial growth, production of reactive oxygen species (ROS) and callose deposition in pcrk1 mutant plants to determine the role of PCRK1 during pathogen infection. • Expression of PCRK1 was induced following pathogen infection. Pathogen growth was significantly higher in pcrk1 mutant lines than in wild-type Col-0. Mutant pcrk1 plants showed reduced pattern-triggered immunity (PTI) against Pma ES4326 after pretreatment with peptides derived from flagellin (flg22), elongation factor-Tu (elf18), or an endogenous protein (pep1). Deposition of callose was reduced in pcrk1 plants, indicating a role of PCRK1 in activation of early immune responses. A PCRK1 transgene containing a mutation in a conserved lysine residue important for phosphorylation activity of kinases (K118E) failed to complement a pcrk1 mutant for the Pma ES4326 growth phenotype. • Our study shows that PCRK1 plays an important role during PTI and that a conserved lysine residue in the putative kinase domain is important for PCRK1 function. [ABSTRACT FROM AUTHOR]

The multinational Arabidopsis research community is highly collaborative and over the past thirty years these activities have been documented by the Multinational Arabidopsis Steering Committee (MASC). Here, we (a) highlight recent research advances made with the reference plant Arabidopsis thaliana; (b) provide summaries from recent reports submitted by MASC subcommittees, projects and resources associated with MASC and from MASC country representatives; and (c) initiate a call for ideas and foci for the "fourth decadal roadmap," which will advise and coordinate the global activities of the Arabidopsis research community. [ABSTRACT FROM AUTHOR]

Summary: Vascular wilt diseases caused by Fusarium oxysporum are a major threat to many agriculturally important crops. Genetic resistance is rare and inevitably overcome by the emergence of new races. To identify potentially durable and non‐race‐specific genetic resistance against Fusarium wilt diseases, we set out to identify effector targets in tomato that mediate susceptibility to the fungus. For this purpose, we used the SIX8 effector protein, an important and conserved virulence factor present in many pathogenic F. oxysporum isolates. Using protein pull‐downs and yeast two‐hybrid assays, SIX8 was found to interact specifically with two members of the tomato TOPLESS family: TPL1 and TPL2. Loss‐of‐function mutations in TPL1 strongly reduced disease susceptibility to Fusarium wilt and a tpl1;tpl2 double mutant exerted an even higher level of resistance. Similarly, Arabidopsis tpl;tpr1 mutants became significantly less diseased upon F. oxysporum inoculation as compared to wildtype plants. We conclude that TPLs encode susceptibility genes whose mutation can confer resistance to F. oxysporum. [ABSTRACT FROM AUTHOR]

Summary: During meiosis, recombination ensures allelic exchanges through crossovers (COs) between the homologous chromosomes. Advances in our understanding of the rules of COs have come from studies of mutations including structural chromosomal rearrangements that, when heterozygous, are known to impair COs in various organisms. In this work, we investigate the effect of a large heterozygous pericentric inversion on male and female recombination in Arabidopsis. The inversion was discovered in the Atmcc1 mutant background and was characterized through genetic and next‐generation sequencing analysis. Reciprocal backcross populations, each consisting of over 400 individuals, obtained from the mutant and the wild type, both crossed with Landsberg erecta, were analyzed genome‐wide by 143 single‐nucleotide polymorphisms. The negative impact of inversion became evident in terms of CO loss in the rearranged chromosome in both male and female meiosis. No single‐CO event was detected within the inversion, consistent with a post‐meiotic selection operating against unbalanced gametes. Cytological analysis of chiasmata in F1 plants confirmed that COs were reduced in male meiosis in the chromosome with inversion. Crossover suppression on the rearranged chromosome is associated with a significant increase of COs in the other chromosomes, thereby maintaining unchanged the number of COs per cell. The CO pattern observed in our study is consistent with the interchromosomal (IC) effect as first described in Drosophila. In contrast to male meiosis, in female meiosis no IC effect is visible. This may be related to the greater strength of interference that constrains the CO number in excess of the minimum value imposed by CO assurance in Arabidopsis female meiosis. Significance Statement: This work provides further information into the poorly described phenomenon of the interchromosomal (IC) effect in plants. Indeed, the few studies on this phenomenon in maize date back to the 1960s and 1970s and have low resolution, being limited to a few specific regions and genetic markers. In this paper we underscore the significance for plant scientists of the IC effect during meiosis and provide more detailed data and analyses. [ABSTRACT FROM AUTHOR]

Summary: Induction of high photosynthetic capacity is a key acclimation response to high light (HL) for many herbaceous dicot plants; however, the signaling pathways that control this response remain largely unknown. Here, a systems biology approach was utilized to characterize the induction of high photosynthetic capacity in strongly and weakly acclimating Arabidopsis thaliana accessions.Plants were grown for 5 wk in a low light (LL) regime, and time‐resolved photosynthetic physiological, metabolomic, and transcriptomic responses were measured during subsequent exposure to HL.The induction of high nitrogen (N) assimilation rates early in the HL shift was strongly predictive of the induction of photosynthetic capacity later in the HL shift. Accelerated N assimilation rates depended on the mobilization of existing organic acid (OA) reserves and increased de novo OA synthesis during the induction of high photosynthetic capacity. Enhanced sucrose biosynthesis capacity increased in tandem with the induction of high photosynthetic capacity, and increased starch biosynthetic capacity was balanced by increased starch catabolism.This systems analysis supports a model in which the efficient induction of N assimilation early in the HL shift begins the cascade of events necessary for the induction of high photosynthetic capacity acclimation in HL. [ABSTRACT FROM AUTHOR]

Summary: Meloidogyne enterolobii is an emerging root‐knot nematode species that overcomes most of the nematode resistance genes in crops. Nematode effector proteins secreted in planta are key elements in the molecular dialogue of parasitism. Here, we show the MeMSP1 effector is secreted into giant cells and promotes M. enterolobii parasitism.Using co‐immunoprecipitation and bimolecular fluorescent complementation assays, we identified glutathione‐S‐transferase phi GSTFs as host targets of the MeMSP1 effector. This protein family plays important roles in plant responses to abiotic and biotic stresses. We demonstrate that MeMSP1 interacts with all Arabidopsis GSTF. Moreover, we confirmed that the N‐terminal region of AtGSTF9 is critical for its interaction, and atgstf9 mutant lines are more susceptible to root‐knot nematode infection.Combined transcriptome and metabolome analyses showed that MeMSP1 affects the metabolic pathways of Arabidopsis thaliana, resulting in the accumulation of amino acids, nucleic acids, and their metabolites, and organic acids and the downregulation of flavonoids.Our study has shed light on a novel effector mechanism that targets plant metabolism, reducing the production of plant defence‐related compounds while favouring the accumulation of metabolites beneficial to the nematode, and thereby promoting parasitism. [ABSTRACT FROM AUTHOR]

SUMMARY: The first draft of the Arabidopsis genome was released more than 20 years ago and despite intensive molecular research, more than 30% of Arabidopsis genes remained uncharacterized or without an assigned function. This is in part due to gene redundancy within gene families or the essential nature of genes, where their deletion results in lethality (i.e., the dark genome). High‐throughput plant phenotyping (HTPP) offers an automated and unbiased approach to characterize subtle or transient phenotypes resulting from gene redundancy or inducible gene silencing; however, access to commercial HTPP platforms remains limited. Here we describe the design and implementation of OPEN leaf, an open‐source phenotyping system with cloud connectivity and remote bilateral communication to facilitate data collection, sharing and processing. OPEN leaf, coupled with our SMART imaging processing pipeline was able to consistently document and quantify dynamic changes at the whole rosette level and leaf‐specific resolution when plants experienced changes in nutrient availability. Our data also demonstrate that VIS sensors remain underutilized and can be used in high‐throughput screens to identify and characterize previously unidentified phenotypes in a leaf‐specific time‐dependent manner. Moreover, the modular and open‐source design of OPEN leaf allows seamless integration of additional sensors based on users and experimental needs. Significance Statement: Many bottlenecks still exist in the high‐throughput plant phenotyping (HTPP) field, including open access to algorithms, computing power for image processing, and a limited access to affordable HTPP platforms. Closing the genome‐to‐phenome gap requires more accessible open‐source and accessible HTPP options; hence, we developed an affordable open‐source top‐view automated phenotyping system that allows the quantification of traits at a whole rosette and leaf‐specific resolution. [ABSTRACT FROM AUTHOR]

SUMMARY: Success in plant reproduction is highly dependent on the correct timing of the floral transition, which is tightly regulated by the flowering pathways. In the model plant Arabidopsis thaliana, the central flowering repressor FLOWERING LOCUS C (FLC) is precisely regulated by multiple flowering time regulators in the vernalization pathway and autonomous pathway, including FPA. Here we report that Arabidopsis MEDIATOR SUBUNIT 8 (MED8) promotes floral transition in Arabidopsis by recruiting FPA to the FLC locus to repress FLC expression. Loss of MED8 function leads to a significant late‐flowering phenotype due to increased FLC expression. We further show that MED8 directly interacts with FPA in the nucleus and recruits FPA to the FLC locus. Moreover, MED8 is indispensable for FPA's function in controlling flowering time and regulating FLC expression. Our study thus reveals a flowering mechanism by which the Mediator subunit MED8 represses FLC expression by facilitating the binding of FPA to the FLC locus to ensure appropriate timing of flowering for reproductive success. Significance Statement: Initiation of flowering at the appropriate time is a fundamental trait in the life cycle of plants that have evolved to maximize plant reproductive success in various environmental conditions. We revealed that MED8 directly interacts with FPA in the nucleus and recruits FPA to the FLC locus to mediate FLC expression, thereby regulating flowering time. [ABSTRACT FROM AUTHOR]

SUMMARY: Despite the identification of clubroot resistance genes in various Brassica crops our understanding of the genetic basis of immunity to Plasmodiophora brassicae infection in the model plant Arabidopsis thaliana remains limited. To address this issue, we performed a screen of 142 natural accessions and identified 11 clubroot‐resistant Arabidopsis lines. Genome‐wide association analysis identified several genetic loci significantly linked with resistance. Three genes from two of these loci were targeted for deletion by CRISPR/Cas9 mutation in resistant accessions Est‐1 and Uod‐1. Deletion of Resistance to Plasmodiophora brassicae 1 (RPB1) rendered both lines susceptible to the P. brassicae pathotype P1+. Further analysis of rpb1 knock‐out Est‐1 and Uod‐1 lines showed that the RPB1 protein is required for activation of downstream defence responses, such as the expression of phytoalexin biosynthesis gene CYP71A13. RPB1 has recently been shown to encode a cation channel localised in the endoplasmic reticulum. The clubroot susceptible Arabidopsis accession Col‐0 lacks a functional RPB1 gene; when Col‐0 is transformed with RPB1 expression driven by its native promoter it is capable of activating RPB1 transcription in response to infection, but this is not sufficient to confer resistance. Transient expression of RPB1 in Nicotiana tabacum induced programmed cell death in leaves. We conclude that RPB1 is a critical component of the defence response to P. brassicae infection in Arabidopsis, acting downstream of pathogen recognition but required for the elaboration of effective resistance. [ABSTRACT FROM AUTHOR]

Aluminium (Al) toxicity is one of the major constraint for crop production in acidic soil, and the inappropriate utilization of nitrogen fertilizer can accelerate soil acidification. Despite previous studies investigating the regulation of nitrogen forms in Al toxicity of plants, the underlying mechanism, particularly at the molecular level, remains unclear. This study aims to uncover the potentially regulatory mechanism of nitrate (NO3−) in the Al resistance of maize and Arabidopsis. NO3− conservatively improves Al resistance in maize and Arabidopsis, with nitrate‐elevated citrate synthesis and exudation potentially playing critical roles in excluding Al from the root symplast. ZmSLAH2 in maize and AtSLAH1 in Arabidopsis are essential for the regulation of citrate exudation and NO3−‐promoted Al resistance, with ZmMYB81 directly targeting the ZmSLAH2 promoter to activate its activity. Additionally, NO3− transport is necessary for NO3−‐promoted Al resistance, with ZmNRT1.1A and AtNRT1.1 potentially playing vital roles. The suppression of NO3− transport in roots by ammonium (NH4+) may inhibit NO3−‐promoted Al resistance. This study provides novel insights into the understanding of the crucial role of NO3−‐mediated signalling in the Al resistance of plants and offers guidance for nitrogen fertilization on acid soils. Summary statement: This study demonstrates that nitrate improves Al resistance conservatively in maize and Arabidopsis by regulating the production and exudation of citrate, thereby promoting Al exclusion from roots. Maize ZmSLAH2 and Arabidopsis AtSLAH1 may play critical roles in this process. These findings provide new insights into understanding of the essential function of nitrate‐mediated signalling in plant Al resistance and offer guidance for soil fertilization in acidic environments. [ABSTRACT FROM AUTHOR]

The Salicaceae family is of growing interest in the study of dioecy in plants because the sex determination region (SDR) has been shown to be highly dynamic, with differing locations and heterogametic systems between species. Without the ability to transform and regenerate Salix in tissue culture, previous studies investigating the mechanisms regulating sex in the genus Salix have been limited to genome resequencing and differential gene expression, which are mostly descriptive in nature, and functional validation of candidate sex determination genes has not yet been conducted. Here, we used Arabidopsis to functionally characterize a suite of previously identified candidate genes involved in sex determination and sex dimorphism in the bioenergy shrub willow Salix purpurea. Six candidate master regulator genes for sex determination were heterologously expressed in Arabidopsis, followed by floral proteome analysis. In addition, 11 transcription factors with predicted roles in mediating sex dimorphism downstream of the SDR were tested using DAP‐Seq in both male and female S. purpurea DNA. The results of this study provide further evidence to support models for the roles of ARR17 and GATA15 as master regulator genes of sex determination in S. purpurea, contributing to a regulatory system that is notably different from that of its sister genus Populus. Evidence was also obtained for the roles of two transcription factors, an AP2/ERF family gene and a homeodomain‐like transcription factor, in downstream regulation of sex dimorphism. [ABSTRACT FROM AUTHOR]

Plasticity is an important component of the response of organism to environmental changes, but whether plasticity facilitates adaptation is still largely debated. Using transcriptomic and phenotypic data, we explored the evolution of ancestral plasticity during alpine colonization in Arabidopsis arenosa. We leveraged naturally replicated adaptation in four distinct mountain regions in Central Europe. We sampled seeds from ancestral foothill and independently formed alpine populations in each region and raised them in growth chambers under conditions approximating their natural environments. We gathered RNA‐seq and genetic data of 48 and 63 plants and scored vegetative and flowering traits in 203 and 272 plants respectively. Then, we compared gene expression and trait values over two treatments differing in temperature and irradiance and elevations of origin and quantified the extent of ancestral and derived plasticity. At the transcriptomic level, initial plastic changes tended to be more reinforced than reversed in adapted alpine populations. Genes showing reinforcement were involved in the stress response, developmental processes and morphogenesis and those undergoing reversion were related to the stress response (light and biotic stress). At the phenotypic level, initial plastic changes in all but one trait were also reinforced supporting a facilitating role of phenotypic plasticity during colonization of an alpine environment. Our results contrasted with previous studies that showed generally higher reversion than reinforcement and supported the idea that ancestral plasticity tends to be reinforced in the context of alpine adaptation. However, plasticity may also be the source of potential maladaptation, especially at the transcriptomic level. [ABSTRACT FROM AUTHOR]

SUMMARY: Arabidopsis thaliana diverged from A. arenosa and A. lyrata at least 6 million years ago. The three species differ by genome‐wide polymorphisms and morphological traits. The species are to a high degree reproductively isolated, but hybridization barriers are incomplete. A special type of hybridization barrier is based on the triploid endosperm of the seed, where embryo lethality is caused by endosperm failure to support the developing embryo. The MADS‐box type I family of transcription factors is specifically expressed in the endosperm and has been proposed to play a role in endosperm‐based hybridization barriers. The gene family is well known for its high evolutionary duplication rate, as well as being regulated by genomic imprinting. Here we address MADS‐box type I gene family evolution and the role of type I genes in the context of hybridization. Using two de‐novo assembled and annotated chromosome‐level genomes of A. arenosa and A. lyrata ssp. petraea we analyzed the MADS‐box type I gene family in Arabidopsis to predict orthologs, copy number, and structural genomic variation related to the type I loci. Our findings were compared to gene expression profiles sampled before and after the transition to endosperm cellularization in order to investigate the involvement of MADS‐box type I loci in endosperm‐based hybridization barriers. We observed substantial differences in type‐I expression in the endosperm of A. arenosa and A. lyrata ssp. petraea, suggesting a genetic cause for the endosperm‐based hybridization barrier between A. arenosa and A. lyrata ssp. petraea. Significance Statement: We address MADS‐box type I gene family evolution using de‐novo assembled genomes of A. arenosa and A. lyrata ssp. petraea and predict orthologs, copy number and structural genomic variation related to the type I loci. We observe substantial differences in MADS‐box type‐I expression in the endosperm suggesting a genetic cause for an endosperm‐based hybridization barrier. [ABSTRACT FROM AUTHOR]

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Summary: Drought is a major abiotic stress that impairs plant growth and development. Despite this, a comprehensive understanding of drought effects on the photosynthetic apparatus is lacking. In this work, we studied the consequences of 14‐d drought treatment on Arabidopsis thaliana.We used biochemical and spectroscopic methods to examine photosynthetic membrane composition and functionality.Drought led to the disassembly of PSII supercomplexes and the degradation of PSII core. The light‐harvesting complexes (LHCII) instead remain in the membrane but cannot act as an antenna for active PSII, thus representing a potential source of photodamage. This effect can also be observed during nonphotochemical quenching (NPQ) induction when even short pulses of saturating light can lead to photoinhibition. At a later stage, under severe drought stress, the PSI antenna size is also reduced and the PSI‐LHCI supercomplexes disassemble. Surprisingly, although we did not observe changes in the PSI core protein content, the functionality of PSI is severely affected, suggesting the accumulation of nonfunctional PSI complexes.We conclude that drought affects both photosystems, although at a different stage, and that the operative quantum efficiency of PSII (ΦPSII) is very sensitive to drought and can thus be used as a parameter for early detection of drought stress. [ABSTRACT FROM AUTHOR]

Summary: Reactive carbonyl species (RCS) derived from lipid peroxides can act as critical damage or signaling mediators downstream of reactive oxygen species by modifying target proteins. However, their biological effects and underlying mechanisms remain largely unknown in plants.Here, we have uncovered the mechanism by which the RCS 4‐hydroxy‐(E)‐2‐nonenal (HNE) participates in photosystem II (PSII) repair cycle of chloroplasts, a crucial process for maintaining PSII activity under high and changing light conditions.High Light Sensitive 1 (HLT1) is a potential NADPH‐dependent reductase in chloroplasts. Deficiency of HLT1 had no impact on the growth of Arabidopsis plants under normal light conditions but increased sensitivity to high light, which resulted from a defective PSII repair cycle. In hlt1 plants, the accumulation of HNE‐modified D1 subunit of PSII was observed, which did not affect D1 degradation but hampered the dimerization of repaired PSII monomers and reassembly of PSII supercomplexes on grana stacks. HLT1 is conserved in all photosynthetic organisms and has functions in overall growth and plant fitness in both Arabidopsis and rice under naturally challenging field conditions.Our work provides the mechanistic basis underlying RCS scavenging in light acclimation and suggests a potential strategy to improve plant productivity by manipulating RCS signaling in chloroplasts. [ABSTRACT FROM AUTHOR]

SUMMARY: Switch defective/sucrose non‐fermentable (SWI/SNF) chromatin remodeling complexes are evolutionarily conserved, multi‐subunit machinery that play vital roles in the regulation of gene expression by controlling nucleosome positioning and occupancy. However, little is known about the subunit composition of SPLAYED (SYD)‐containing SWI/SNF complexes in plants. Here, we show that the Arabidopsis thaliana Leaf and Flower Related (LFR) is a subunit of SYD‐containing SWI/SNF complexes. LFR interacts directly with multiple SWI/SNF subunits, including the catalytic ATPase subunit SYD, in vitro and in vivo. Phenotypic analyses of lfr‐2 mutant flowers revealed that LFR is important for proper filament and pistil development, resembling the function of SYD. Transcriptome profiling revealed that LFR and SYD shared a subset of co‐regulated genes. We further demonstrate that the LFR and SYD interdependently activate the transcription of AGAMOUS (AG), a C‐class floral organ identity gene, by regulating the occupation of nucleosome, chromatin loop, histone modification, and Pol II enrichment on the AG locus. Furthermore, the chromosome conformation capture (3C) assay revealed that the gene loop at AG locus is negatively correlated with the AG expression level, and LFR‐SYD was functional to demolish the AG chromatin loop to promote its transcription. Collectively, these results provide insight into the molecular mechanism of the Arabidopsis SYD‐SWI/SNF complex in the control of higher chromatin conformation of the floral identity gene essential to plant reproductive organ development. Significance Statement: This study provides insight into the molecular mechanism of the Arabidopsis SYD‐SWI/SNF complex in the control of higher chromatin conformation of the floral identity gene essential to plant reproductive organ development. [ABSTRACT FROM AUTHOR]

SUMMARY: Stomatal defences are important for plants to prevent pathogen entry and further colonisation of leaves. Apoplastic reactive oxygen species (ROS) generated by NADPH oxidases and apoplastic peroxidases play an important role in activating stomatal closure upon perception of bacteria. However, downstream events, particularly the factors influencing cytosolic hydrogen peroxide (H2O2) signatures in guard cells are poorly understood. We used the H2O2 sensor roGFP2‐Orp1 and a ROS‐specific fluorescein probe to study intracellular oxidative events during stomatal immune response using Arabidopsis mutants involved in the apoplastic ROS burst. Surprisingly, the NADPH oxidase mutant rbohF showed over‐oxidation of roGFP2‐Orp1 by a pathogen‐associated molecular pattern (PAMP) in guard cells. However, stomatal closure was not tightly correlated with high roGFP2‐Orp1 oxidation. In contrast, RBOHF was necessary for PAMP‐mediated ROS production measured by a fluorescein‐based probe in guard cells. Unlike previous reports, the rbohF mutant, but not rbohD, was impaired in PAMP‐triggered stomatal closure resulting in defects in stomatal defences against bacteria. Interestingly, RBOHF also participated in PAMP‐induced apoplastic alkalinisation. The rbohF mutants were also partly impaired in H2O2‐mediated stomatal closure at 100 μm while higher H2O2 concentration up to 1 mm did not promote stomatal closure in wild‐type plants. Our results provide novel insights on the interplay between apoplastic and cytosolic ROS dynamics and highlight the importance of RBOHF in plant immunity. Significance Statement: Whilst most studies have focused on the NADPH oxidase RBOHD, the role of RBOHF in plant defence responses to pathogens in Arabidopsis has been largely underestimated for decades. We show that RBOHF promotes stomatal immunity and Arabidopsis resistance to Pseudomonas syringae bacteria by affecting not only ROS signalling but also by modulating apoplastic pH, two processes probably interconnected via RBOHF during the response to pathogen‐associated molecular patterns. [ABSTRACT FROM AUTHOR]

Fluctuating light intensity challenges fluent photosynthetic electron transport in plants, inducing photoprotection while diminishing carbon assimilation and growth, and also influencing photosynthetic signaling for regulation of gene expression. Here, we employed in vivo chlorophyll‐a fluorescence and P700 difference absorption measurements to demonstrate the enhancement of photoprotective energy dissipation of both photosystems in wild‐type Arabidopsis thaliana after 6 h exposure to fluctuating light as compared with constant light conditions. This acclimation response to fluctuating light was hampered in a triple mutant lacking the thylakoid ion transport proteins KEA3, VCCN1, and CLCe, leading to photoinhibition of photosystem I. Transcriptome analysis revealed upregulation of genes involved in biotic stress and defense responses in both genotypes after exposure to fluctuating as compared with constant light, yet these responses were demonstrated to be largely upregulated in triple mutant already under constant light conditions compared with wild type. The current study illustrates the rapid acclimation of plants to fluctuating light, including photosynthetic, transcriptomic, and metabolic adjustments, and highlights the connection among thylakoid ion transport, photosynthetic energy balance, and cell signaling. [ABSTRACT FROM AUTHOR]

Mitogen‐activated protein kinase (MAPK) cascades play pivotal roles in plant defense against phytopathogens downstream of immune receptor complexes. The amplitude and duration of MAPK activation must be strictly controlled, but the underlying mechanism remains unclear. Here, we identified Arabidopsis CPL1 (C‐terminal domain phosphatase‐like 1) as a negative regulator of microbe‐associated molecular pattern (MAMP)‐triggered immunity via a forward‐genetic screen. Disruption of CPL1 significantly enhanced plant resistance to Pseudomonas pathogens induced by the bacterial peptide flg22. Furthermore, flg22‐induced MPK3/MPK4/MPK6 phosphorylation was dramatically elevated in cpl1 mutants but severely impaired in CPL1 overexpression lines, suggesting that CPL1 might interfere with flg22‐induced MAPK activation. Indeed, CPL1 directly interacted with MPK3 and MPK6, as well as the upstream MKK4 and MKK5. A firefly luciferase‐based complementation assay indicated that the interaction between MKK4/MKK5 and MPK3/MPK6 was significantly reduced in the presence of CPL1. These results suggest that CPL1 plays a novel regulatory role in suppressing MAMP‐induced MAPK cascade activation and MAMP‐triggered immunity to bacterial pathogens. [ABSTRACT FROM AUTHOR]