Prieurianin/endosidin 1 is an actin-stabilizing small molecule identified from a chemical genetic screen for circadian clock effectors in Arabidopsis thaliana

Insights into the Mechanism of Action of the Degraded Limonoid Prieurianin

Limonoids are extremely diversified in plants, with many categories of products bearing an intact, rearranged or fragmented oxygenated scaffold. A specific subgroup of fragmented or degraded limonoids derives from the tetranortriterpenoid prieurianin, initially isolated from the tree Trichilia prieuriana but also found in other plants of the Meliaceae family, including the more abundant species Aphanamixis polystachya. Prieurianin-type limonoids include about seventy compounds, among which are dregeanin and rohitukin. Prieurianin and analogs exhibit insecticidal, antimicrobial, antiadipogenic and/or antiparasitic properties but their mechanism of action remains ill-defined at present. Previous studies have shown that prieurianin, initially known as endosidin 1, stabilizes the actin cytoskeleton in plant and mammalian cells via the modulation of the architecture and dynamic of the actin network, most likely via interference with actin-binding proteins. A new mechanistic hypothesis is advanced here based on the recent discovery of the targeting of the chaperone protein Hsp47 by the fragmented limonoid fraxinellone. Molecular modeling suggested that prieurianin and, to a lesser extent dregeanin, can form very stable complexes with Hsp47 at the protein-collagen interface. Hsp-binding may account for the insecticidal action of the product. The present review draws up a new mechanistic portrait of prieurianin and provides an overview of the pharmacological properties of this atypical limonoid and its chemical family.

A Small-Molecule Modulator Affecting the Clock-Associated PSEUDO-RESPONSE REGULATOR 7 Amount

Circadian clocks are biological timekeeping systems that coordinate genetic, metabolic and physiological behaviors with the external day-night cycle. The clock in plants relies on the transcriptional-translational feedback loops transcription-translation feedback loop (TTFL), consisting of transcription factors including PSUEDO-RESPONSE REGULATOR (PRR) proteins, plant lineage-specific transcriptional repressors. Here, we report that a novel synthetic small-molecule modulator, 5-(3,4-dichlorophenyl)-1-phenyl-1,7-dihydro-4H-pyrazolo[3,4-d] pyrimidine-4,6(5H)-dione (TU-892), affects the PRR7 protein amount. A clock reporter line of Arabidopsis was screened against the 10,000 small molecules in the Maybridge Hitfinder 10K chemical library. This screening identified TU-892 as a period-lengthening molecule. Gene expression analyses showed that TU-892 treatment upregulates CIRCADIAN CLOCK-ASSOCIATED 1 (CCA1) mRNA expression. TU-892 treatment reduced the amount of PRR7 protein, a transcriptional repressor of CCA1. Other PRR proteins including TIMING OF CAB EXPRESSION 1 were altered less by TU-892 treatment. TU-892-dependent CCA1 upregulation was attenuated in mutants impaired in PRR7. Collectively, TU-892 is a novel type of clock modulator that reduces the levels of PRR7 protein.

Chemical biology to dissect molecular mechanisms underlying plant circadian clocks

Circadian clocks regulate the diel rhythmic physiological activities of plants, enabling them to anticipate and adapt to day-night and seasonal changes. Genetic and biochemical approaches have suggested that transcription-translation feedback loops (TTFL) are crucial for Arabidopsis clock function. Recently, the study of chemical chronobiology has emerged as a discipline within the circadian clock field, with important and complementary discoveries from both plant and animal research. In this review, we introduce recent advances in chemical biology using small molecules to perturb plant circadian clock function through TTFL components. Studies using small molecule clock modulators have been instrumental for revealing the role of post-translational modification in the clock, or the metabolite-dependent clock input pathway, as well as for controlling clock-dependent flowering time.

Selective chemical probes can untangle the complexity of the plant cell endomembrane system

The endomembrane system is critical for plant growth and development and understanding its function and regulation is of great interest for plant biology research. Small-molecule targeting distinctive endomembrane components have proven powerful tools to dissect membrane trafficking in plant cells. However, unambiguous elucidation of the complex and dynamic trafficking processes requires chemical probes with enhanced precision. Determination of the mechanism of action of a compound, which is facilitated by various chemoproteomic approaches, opens new avenues for the improvement of its specificity. Moreover, rational molecule design and reverse chemical genetics with the aid of virtual screening and artificial intelligence will enable us to discover highly precise chemical probes more efficiently. The next decade will witness the emergence of more such accurate tools, which together with advanced live quantitative imaging techniques of subcellular phenotypes, will deepen our insights into the plant endomembrane system.

Investigation of Drug Efficacy by Screening Bioactive Chemical Effects on Plant Cell Subcellular Architecture

New biologically active compounds are regularly discovered through screening procedures using microorganisms. This very cheap procedure is followed by drug discovery that is usually seen as a highly focused approach, testing new compounds on animals or cell lines. In vivo assays of candidate drugs in mammals are expensive and sometimes not affordable at the preliminary stages of drug development. Early screening approaches in transgenic plants would allow chemotherapeutic drug candidates further selection before their characterization in expensive biological models. The proposed screening approach is based on cell subcellular architecture observations in transgenic plants within a short time of treatment, which is better than observing the effects of compounds on growth.

Chemical Perturbation of Chloroplast-Related Processes Affects Circadian Rhythms of Gene Expression in Arabidopsis: Salicylic Acid Application Can Entrain the Clock

The plant circadian system reciprocally interacts with metabolic processes. To investigate entrainment features in metabolic–circadian interactions, we used a chemical approach to perturb metabolism and monitored the pace of nuclear-driven circadian oscillations. We found that chemicals that alter chloroplast-related functions modified the circadian rhythms. Both vitamin C and paraquat altered the circadian period in a light-quality-dependent manner, whereas rifampicin lengthened the circadian period under darkness. Salicylic acid (SA) increased oscillatory robustness and shortened the period. The latter was attenuated by sucrose addition and was also gated, taking place during the first 3 h of the subjective day. Furthermore, the effect of SA on period length was dependent on light quality and genotype. Period lengthening or shortening by these chemicals was correlated to their inferred impact on photosynthetic electron transport activity and the redox state of plastoquinone (PQ). Based on these data and on previous publications on circadian effects that alter the redox state of PQ, we propose that the photosynthetic electron transport and the redox state of PQ participate in circadian periodicity. Moreover, coupling between chloroplast-derived signals and nuclear oscillations, as observed in our chemical and genetic assays, produces traits that are predicted by previous models. SA signaling or a related process forms a rhythmic input loop to drive robust nuclear oscillations in the context predicted by the zeitnehmer model, which was previously developed for Neurospora. We further discuss the possibility that electron transport chains (ETCs) are part of this mechanism.

Movement of small RNAs in and between plants and fungi

RNA interference is a biological process whereby small RNAs inhibit gene expression through neutralizing targeted mRNA molecules. This process is conserved in eukaryotes. Here, recent work regarding the mechanisms of how small RNAs move within and between organisms is examined. Small RNAs can move locally and systemically in plants through plasmodesmata and phloem, respectively. In fungi, transportation of small RNAs may also be achieved by septal pores and vesicles. Recent evidence also supports bidirectional cross-kingdom communication of small RNAs between host plants and adapted fungal pathogens to affect the outcome of infection. We discuss several mechanisms for small RNA trafficking and describe evidence for transport through naked form, combined with RNA-binding proteins or enclosed by vesicles.

Progress in using chemical biology as a tool to uncover novel regulators of plant endomembrane trafficking

The regulated dynamic transport of materials among organelles through endomembrane trafficking pathways is essential for plant growth, development, and environmental adaptation, and thus is a major topic of plant biology research. Large-scale chemical library screens have identified small molecules that could potentially inhibit different plant endomembrane trafficking steps. Further characterization of these molecules has provided valuable tools for understanding plant endomembrane trafficking and uncovered novel regulators of trafficking processes.

3,4-Dibromo-7-Azaindole Modulates Arabidopsis Circadian Clock by Inhibiting Casein Kinase 1 Activity

The circadian clock is a timekeeping system for regulation of numerous biological daily rhythms. One characteristic of the circadian clock is that period length remains relatively constant in spite of environmental fluctuations, such as temperature change. Here, using the curated collection of in-house small molecule chemical library (ITbM chemical library), we show that small molecule 3,4-dibromo-7-azaindole (B-AZ) lengthened the circadian period of Arabidopsis thaliana (Arabidopsis). B-AZ has not previously been reported to have any biological and biochemical activities. Target identification can elucidate the mode of action of small molecules, but we were unable to make a molecular probe of B-AZ for target identification. Instead, we performed other analysis, gene expression profiling that potentially reveals mode of action of molecules. Short-term treatment of B-AZ decreased the expression of four dawn- and morning-phased clock-associated genes, CIRCADIAN CLOCK-ASSOCIATED 1 (CCA1), LATE ELONGATED HYPOCOTYL (LHY), PSEUDO-RESPONSE REGULATOR 9 (PRR9) and PRR7. Consistently, amounts of PRR5 and TIMING OF CAB EXPRESSION 1 (TOC1) proteins, transcriptional repressors of CCA1, LHY, PRR9 and PRR7 were increased upon B-AZ treatment. B-AZ inhibited Casein Kinase 1 family (CK1) that phosphorylates PRR5 and TOC1 for targeted degradation. A docking study and molecular dynamics simulation suggested that B-AZ interacts with the ATP-binding pocket of human CK1 delta, whose amino acid sequences are highly similar to those of Arabidopsis CK1. B-AZ-induced period-lengthening effect was attenuated in prr5 toc1 mutants. Collectively, this study provides a novel and simple structure CK1 inhibitor that modulates circadian clock via accumulation of PRR5 and TOC1.

Casein kinase 1 family regulates PRR5 and TOC1 in the Arabidopsis circadian clock

The mechanisms of eukaryotic circadian clocks rely on transcriptional-translational feedback loops (TTFLs), but components of TTFLs from different phylogenetic lineages are thought to be evolutionarily diverse. Posttranslational modification is also required for clock function, but those within the plant clock are less studied, likely due to genetic redundancy. Here, we identified a small synthetic molecule that lengthened the Arabidopsis circadian period. Using an affinity probe, we found that the molecule inhibited multiple members of the casein kinase I (CK1) family, which is also essential in animal, fungal, and algal clocks. The CK1 family modulated plant-specific clock-associated transcriptional repressors. With other studies, our results established the prominent role of CK1 family to control circadian clocks among vastly divergent phylogenetic lineages.

The circadian clock provides organisms with the ability to adapt to daily and seasonal cycles. Eukaryotic clocks mostly rely on lineage-specific transcriptional-translational feedback loops (TTFLs). Posttranslational modifications are also crucial for clock functions in fungi and animals, but the posttranslational modifications that affect the plant clock are less understood. Here, using chemical biology strategies, we show that the Arabidopsis CASEIN KINASE 1 LIKE (CKL) family is involved in posttranslational modification in the plant clock. Chemical screening demonstrated that an animal CDC7/CDK9 inhibitor, PHA767491, lengthens the Arabidopsis circadian period. Affinity proteomics using a chemical probe revealed that PHA767491 binds to and inhibits multiple CKL proteins, rather than CDC7/CDK9 homologs. Simultaneous knockdown of Arabidopsis CKL-encoding genes lengthened the circadian period. CKL4 phosphorylated transcriptional repressors PSEUDO-RESPONSE REGULATOR 5 (PRR5) and TIMING OF CAB EXPRESSION 1 (TOC1) in the TTFL. PHA767491 treatment resulted in accumulation of PRR5 and TOC1, accompanied by decreasing expression of PRR5- and TOC1-target genes. A prr5 toc1 double mutant was hyposensitive to PHA767491-induced period lengthening. Together, our results reveal posttranslational modification of transcriptional repressors in plant clock TTFL by CK1 family proteins, which also modulate nonplant circadian clocks.

High-Throughput Screening of Chemical Compound Libraries for Modulators of Salicylic Acid Signaling by In Situ Monitoring of Glucuronidase-Based Reporter Gene Expression

Salicylic acid (SA) is a vital phytohormone that is intimately involved in coordination of the complex plant defense response to pathogen attack. Many aspects of SA signaling have been unraveled by classical genetic and biochemical methods using the model plant Arabidopsis thaliana, but many details remain unknown, owing to the inherent limitations of these methods. In recent years, chemical genetics has emerged as an alternative scientific strategy to complement classical genetics by virtue of identifying bioactive chemicals or probes that act selectively on their protein targets causing either activation or inhibition. Such selective tools have the potential to create conditional and reversible chemical mutant phenotypes that may be combined with genetic mutants. Here, we describe a facile chemical screening methodology for intact Arabidopsis seedlings harboring the β-glucuronidase (GUS) reporter by directly quantifying GUS activity in situ with 4-methylumbelliferyl-β-D-glucuronide (4-MUG) as substrate. The quantitative nature of this screening assay has an obvious advantage over the also convenient histochemical GUS staining method, as it allows application of statistical procedures and unbiased hit selection based on threshold values as well as distinction between compounds with strong or weak bioactivity. We show pilot screens for chemical activators or inhibitors of salicylic acid-mediated defense signaling using the Arabidopsis line expressing the SA-inducible PR1p::GUS reporter gene. Importantly, the screening methodology provided here can be adopted for any inducible GUS reporter line.

Identification of Chemical Inducers of the Phosphate-Starvation Signaling Pathway in A. thaliana Using Chemical Genetics

In spite of its importance for agriculture and 30 years of genetic studies, the phosphate-starvation signaling pathway, that allows plants to detect, respond, and adapt to changes in the phosphate concentration of the rhizosphere, remains poorly known. Chemical genetics has been increasingly and successfully used as a complementary approach to genetics for the dissection of signaling pathways in diverse organisms. Screens can be designed to identify chemicals interfering specifically with a pathway of interest. We designed a screen that led to the discovery of the first chemical capable to induce specifically the phosphate-starvation signaling pathway in Arabidopsis thaliana. This procedure, described here, can be adapted for the discovery of inducers or repressors of other pathways.

The Root Growth-Regulating Brevicompanine Natural Products Modulate the Plant Circadian Clock

Plant growth regulating properties of brevicompanines (Brvs), natural products of the fungus Penicillium brevicompactum, have been known for several years, but further investigations into the molecular mechanism of their bioactivity have not been performed. Following chemical synthesis of brevicompanine derivatives, we studied their activity in the model plant Arabidopsis by a combination of plant growth assays, transcriptional profiling, and numerous additional bioassays. These studies demonstrated that brevicompanines cause transcriptional misregulation of core components of the circadian clock, whereas other biological read-outs were not affected. Brevicompanines thus represent promising chemical tools for investigating the regulation of the plant circadian clock. In addition, our study also illustrates the potential of an unbiased -omics-based characterization of bioactive compounds for identifying the often cryptic modes of action of small molecules.

Chemical Genetic Dissection of Membrane Trafficking

The plant endomembrane system is an extensively connected functional unit for exchanging material between compartments. Secretory and endocytic pathways allow dynamic trafficking of proteins, lipids, and other molecules, regulating a myriad of biological processes. Chemical genetics-the use of compounds to perturb biological processes in a fast, tunable, and transient manner-provides elegant tools for investigating this system. Here, we review how chemical genetics has helped to elucidate different aspects of membrane trafficking. We discuss different strategies for uncovering the modes of action of such compounds and their use in unraveling membrane trafficking regulators. We also discuss how the bioactive chemicals that are currently used as probes to interrogate endomembrane trafficking were discovered and analyze the results regarding membrane trafficking and pathway crosstalk. The integration of different expertises and the rational implementation of chemical genetic strategies will improve the identification of molecular mechanisms that drive intracellular trafficking and our understanding of how trafficking interfaces with plant physiology and development.

Review: Post-translational cross-talk between brassinosteroid and sucrose signaling

A direct link has been elucidated between brassinosteroid function and perception, and sucrose partitioning and transport. Sucrose regulation and brassinosteroid signaling cross-talk at various levels, including the well-described regulation of transcriptional gene expression: BZR-like transcription factors link the signaling pathways. Since brassinosteroid responses depend on light quality and quantity, a light-dependent alternative pathway was postulated. Here, the focus is on post-translational events. Recent identification of sucrose transporter-interacting partners raises the question whether brassinosteroid and sugars jointly affect plant innate immunity and plant symbiotic interactions. Membrane permeability and sensitivity depends on the number of cell surface receptors and transporters. More than one endocytic route has been assigned to specific components, including brassinosteroid-receptors. The number of such proteins at the plasma membrane relies on endocytic recycling, internalization and/or degradation. Therefore, vesicular membrane trafficking is gaining considerable attention with regard to plant immunity. The organization of pattern recognition receptors (PRRs), other receptors or transporters in membrane microdomains participate in endocytosis and the formation of specific intracellular compartments, potentially impacting biotic interactions. This minireview focuses on post-translational events affecting the subcellular compartmentation of membrane proteins involved in signaling, transport, and defense, and on the cross-talk between brassinosteroid signals and sugar availability.

Facile high-throughput forward chemical genetic screening by in situ monitoring of glucuronidase-based reporter gene expression in Arabidopsis thaliana

The use of biologically active small molecules to perturb biological functions holds enormous potential for investigating complex signaling networks. However, in contrast to animal systems, the search for and application of chemical tools for basic discovery in the plant sciences, generally referred to as "chemical genetics," has only recently gained momentum. In addition to cultured cells, the well-characterized, small-sized model plant Arabidopsis thaliana is suitable for cultivation in microplates, which allows employing diverse cell- or phenotype-based chemical screens. In such screens, a chemical's bioactivity is typically assessed either through scoring its impact on morphological traits or quantifying molecular attributes such as enzyme or reporter activities. Here, we describe a facile forward chemical screening methodology for intact Arabidopsis seedlings harboring the β-glucuronidase (GUS) reporter by directly quantifying GUS activity in situ with 4-methylumbelliferyl-β-D-glucuronide (4-MUG) as substrate. The quantitative nature of this screening assay has an obvious advantage over the also convenient histochemical GUS staining method, as it allows application of statistical procedures and unbiased hit selection based on threshold values as well as distinction between compounds with strong or weak bioactivity. At the same time, the in situ bioassay is very convenient requiring less effort and time for sample handling in comparison to the conventional quantitative in vitro GUS assay using 4-MUG, as validated with several Arabidopsis lines harboring different GUS reporter constructs. To demonstrate that the developed assays is particularly suitable for large-scale screening projects, we performed a pilot screen for chemical activators or inhibitors of salicylic acid-mediated defense signaling using the Arabidopsis PR1p::GUS line. Importantly, the screening methodology provided here can be adopted for any inducible GUS reporter line.

GIGANTEA - an emerging story

GIGANTEA (GI) is a plant specific nuclear protein and functions in diverse physiological processes such as flowering time regulation, light signaling, hypocotyl elongation, control of circadian rhythm, sucrose signaling, starch accumulation, chlorophyll accumulation, transpiration, herbicide tolerance, cold tolerance, drought tolerance, and miRNA processing. It has been five decades since its discovery but the biochemical function of GI and its different domains are still unclear. Although it is known that both GI transcript and GI protein are clock controlled, the regulation of its abundance and functions at the molecular level are still some of the unexplored areas of intensive research. Since GI has many important pleotropic functions as described above scattered through literature, it is worthwhile and about time to encapsulate the available information in a concise review. Therefore, in this review, we are making an attempt to summarize (i) the various interconnected roles that GI possibly plays in the fine-tuning of plant development, and (ii) the known mutations of GI that have been instrumental in understanding its role in distinct physiological processes.

Signaling to actin stochastic dynamics

Advances in microscopy techniques applied to living cells have dramatically transformed our view of the actin cytoskeleton as a framework for cellular processes. Conventional fluorescence imaging and static analyses are useful for quantifying cellular architecture and the network of filaments that support vesicle trafficking, organelle movement, and response to biotic stress. However, new imaging techniques have revealed remarkably dynamic features of individual actin filaments and the mechanisms that underpin their construction and turnover. In this review, we briefly summarize knowledge about actin and actin-binding proteins in plant systems. We focus on the quantitative properties of the turnover of individual actin filaments, highlight actin-binding proteins that participate in actin dynamics, and summarize the current genetic evidence that has been used to dissect specific aspects of the stochastic dynamics model. Finally, we describe some signaling pathways in which recent data implicate changes in actin filament dynamics and the associated cytoplasmic responses.

Considerations for designing chemical screening strategies in plant biology

Traditionally, biologists regularly used classical genetic approaches to characterize and dissect plant processes. However, this strategy is often impaired by redundancy, lethality or pleiotropy of gene functions, which prevent the isolation of viable mutants. The chemical genetic approach has been recognized as an alternative experimental strategy, which has the potential to circumvent these problems. It relies on the capacity of small molecules to modify biological processes by specific binding to protein target(s), thereby conditionally modifying protein function(s), which phenotypically resemble mutation(s) of the encoding gene(s). A successful chemical screening campaign comprises three equally important elements: (1) a reliable, robust, and quantitative bioassay, which allows to distinguish between potent and less potent compounds, (2) a rigorous validation process for candidate compounds to establish their selectivity, and (3) an experimental strategy for elucidating a compound's mode of action and molecular target. In this review we will discuss details of this general strategy and additional aspects that deserve consideration in order to take full advantage of the power provided by the chemical approach to plant biology. In addition, we will highlight some success stories of recent chemical screenings in plant systems, which may serve as teaching examples for the implementation of future chemical biology projects.

A moving view: subcellular trafficking processes in pattern recognition receptor-triggered plant immunity

A significant challenge for plants is to induce localized defense responses at sites of pathogen attack. Therefore, host subcellular trafficking processes enable accumulation and exchange of defense compounds, which contributes to the plant on-site defenses in response to pathogen perception. This review summarizes our current understanding of the transport processes that facilitate immunity, the significance of which is highlighted by pathogens reprogramming membrane trafficking through host cell translocated effectors. Prominent immune-related cargos of plant trafficking pathways are the pattern recognition receptors (PRRs), which must be present at the plasma membrane to sense microbes in the apoplast. We focus on the dynamic localization of the FLS2 receptor and discuss the pathways that regulate receptor transport within the cell and their link to FLS2-mediated immunity. One emerging theme is that ligand-induced late endocytic trafficking is conserved across different PRR protein families as well as across different plant species.

Trafficking modulator TENin1 inhibits endocytosis, causes endomembrane protein accumulation at the pre-vacuolar compartment and impairs gravitropic response in Arabidopsis thaliana

Auxin gradients are established and maintained by polarized distribution of auxin transporters that undergo constitutive endocytic recycling from the PM (plasma membrane) and are essential for the gravitropic response in plants. The present study characterizes an inhibitor of endomembrane protein trafficking, TE1 (trafficking and endocytosis inhibitor 1/TENin1) that reduces gravitropic root bending in Arabidopsis thaliana seedlings. Short-term TE1 treatment causes accumulation of PM proteins, including the BR (brassinosteroid) receptor BRI1 (BR insensitive 1), PIP2a (PM intrinsic protein 2a) and the auxin transporter PIN2 (PIN-FORMED 2) in a PVC (pre-vacuolar related compartment), which is sensitive to BFA (Brefeldin A). This compound inhibits endocytosis from the PM and promotes trafficking to the vacuole, consistent with inhibition of retrieval of proteins to the TGN (trans-Golgi network) from the PVC and the PM. However, trafficking of newly synthesized proteins to the PM is unaffected. The short-term protein trafficking inhibition and long-term effect on plant growth and survival caused by TE1 were fully reversible upon drug washout. Structure-activity relationship studies revealed that only minor modifications were possible without loss of biological activity. Diversity in Arabidopsis ecotypes was also exploited to identify two Arabidopsis accessions that display reduced sensitivity to TE1. This compound and the resistant Arabidopsis accessions may be used as a resource in future studies to better understand endomembrane trafficking in plants.

Measure for measure: determining, inferring and guessing auxin gradients at the root tip

The plant hormone auxin is transported from sites of synthesis to sites of action. Auxin responses are mediated by fast (non-transcriptional) and slow (transcriptional; ubiquitinylation) responses, which affect physiological changes at cellular and organismal scales. As such, auxin transport vectors regulate programmed and plastic growth responses to optimize growth and development. Here we address some common problems in extrapolating 'universal' understanding of auxin transport streams from analyses of loss-of-function mutants and auxin transport inhibitors. We also discuss the analytical methods and tools used to directly quantify, measure and infer auxin gradients within the plant [DR5:GUS/GFP (beta-glucuronidase/green fluorescent protein), DII-VENUS; surface electrodes, direct quantification]. We discuss the assumptions and limitations of each of these analyses, present comparative summaries of auxin transport methods and assay conditions (diffusion, non-specific transport and relevant assay conditions), and consider what is actually being transported and measured [labeled-indole-3-acetic acid (IAA), IAA metabolites].

The availability of filament ends modulates actin stochastic dynamics in live plant cells

A network of individual filaments that undergoes incessant remodeling through a process known as stochastic dynamics comprises the cortical actin cytoskeleton in plant epidermal cells. From images at high spatial and temporal resolution, it has been inferred that the regulation of filament barbed ends plays a central role in choreographing actin organization and turnover. How this occurs at a molecular level, whether different populations of ends exist in the array, and how individual filament behavior correlates with the overall architecture of the array are unknown. Here we develop an experimental system to modulate the levels of heterodimeric capping protein (CP) and examine the consequences for actin dynamics, architecture, and cell expansion. Significantly, we find that all phenotypes are the opposite for CP-overexpression (OX) cells compared with a previously characterized cp-knockdown line. Specifically, CP OX lines have fewer filament-filament annealing events, as well as reduced filament lengths and lifetimes. Further, cp-knockdown and OX lines demonstrate the existence of a subpopulation of filament ends sensitive to CP concentration. Finally, CP levels correlate with the biological process of axial cell expansion; for example, epidermal cells from hypocotyls with reduced CP are longer than wild-type cells, whereas CP OX lines have shorter cells. On the basis of these and other genetic studies in this model system, we hypothesize that filament length and lifetime positively correlate with the extent of axial cell expansion in dark-grown hypocotyls.

Live cell imaging reveals actin-cytoskeleton-induced self-association of the actin-bundling protein WLIM1

Crosslinking of actin filaments into bundles is essential for the assembly and stabilization of specific cytoskeletal structures. However, relatively little is known about the molecular mechanisms underlying actin bundle formation. The two LIM-domain-containing proteins define a novel and evolutionarily conserved family of actin-bundling proteins whose actin-binding and -crosslinking activities primarily rely on their LIM domains. Using TIRF microscopy, we describe real-time formation of actin bundles induced by tobacco NtWLIM1 in vitro. We show that NtWLIM1 binds to single filaments and subsequently promotes their interaction and zippering into tight bundles of mixed polarity. NtWLIM1-induced bundles grew by both elongation of internal filaments and addition of preformed fragments at their extremities. Importantly, these data are highly consistent with the modes of bundle formation and growth observed in transgenic Arabidopsis plants expressing a GFP-fused Arabidopsis AtWLIM1 protein. Using two complementary live cell imaging approaches, a close relationship between NtWLIM1 subcellular localization and self-association was established. Indeed, both BiFC and FLIM-FRET data revealed that, although unstable NtWLIM1 complexes can sporadically form in the cytosol, stable complexes concentrate along the actin cytoskeleton. Remarkably, disruption of the actin cytoskeleton significantly impaired self-association of NtWLIM1. In addition, biochemical analyses support the idea that F-actin facilitates the switch of purified recombinant NtWLIM1 from a monomeric to a di- or oligomeric state. On the basis of our data, we propose a model in which actin binding promotes the formation and stabilization of NtWLIM1 complexes, which in turn might drive the crosslinking of actin filaments.

Synthesis of the B-seco limonoid core scaffold

Synthetic investigations towards the structurally complex and highly decorated framework of B-seco limonoid natural products by means of a [3,3]-sigmatropic rearrangement are described. Detailed model studies reveal, that an Ireland-Claisen rearrangement can be employed to construct the central C9-C10 bond thereby giving access to the B-seco limonoid scaffold. However, application of the developed strategy ended up failing in more complex and sterically demanding systems.

ACTIN DEPOLYMERIZING FACTOR4 regulates actin dynamics during innate immune signaling in Arabidopsis

Conserved microbe-associated molecular patterns (MAMPs) are sensed by pattern recognition receptors (PRRs) on cells of plants and animals. MAMP perception typically triggers rearrangements to actin cytoskeletal arrays during innate immune signaling. However, the signaling cascades linking PRR activation by MAMPs to cytoskeleton remodeling are not well characterized. Here, we developed a system to dissect, at high spatial and temporal resolution, the regulation of actin dynamics during innate immune signaling in plant cells. Within minutes of MAMP perception, we detected changes to single actin filament turnover in epidermal cells treated with bacterial and fungal MAMPs. These MAMP-induced alterations phenocopied an ACTIN DEPOLYMERIZING FACTOR4 (ADF4) knockout mutant. Moreover, actin arrays in the adf4 mutant were unresponsive to a bacterial MAMP, elf26, but responded normally to the fungal MAMP, chitin. Together, our data provide strong genetic and cytological evidence for the inhibition of ADF activity regulating actin remodeling during innate immune signaling. This work is the first to directly link an ADF/cofilin to the cytoskeletal rearrangements elicited directly after pathogen perception in plant or mammalian cells.

Actin dynamics in the cortical array of plant cells

The actin cytoskeleton changes in organization and dynamics as cellular functions are reprogrammed following responses to diverse stimuli, hormones, and developmental cues. How this is choreographed and what molecular players are involved in actin remodeling continues to be an area of intense scrutiny. Advances in imaging modalities and fluorescent fusion protein reporters have illuminated the strikingly dynamic behavior of single actin filaments at high spatial and temporal resolutions. This led to a model for the stochastic dynamic turnover of actin filaments and predicted the actions and responsibilities of several key actin-binding proteins. Recently, aspects of this model have been tested using powerful genetic strategies in both Arabidopsis and Physcomitrella. Collectively, the latest data emphasize the importance of filament severing activities and regulation of barbed-end availability as key facets of plant actin filament turnover.

Regulation of cytoskeletal dynamics by phospholipase D and phosphatidic acid

Plants respond to diverse biotic and abiotic stimuli as well as to endogenous developmental cues. Many of these stimuli result in altered activity of phospholipase D (PLD), an enzyme that hydrolyzes structural phospholipids producing phosphatidic acid (PA). PA is a key signaling intermediate in animals, but its targets in plants are relatively uncharacterized. Recent studies have demonstrated that the cytoskeleton is a major target of PLD-PA signaling and identified a positive feedback loop between actin turnover and PLD activity. Moreover, two cytoskeletal proteins, capping protein and MAP65-1, have been identified as PA-binding proteins regulating actin and microtubule organization and dynamics. In this review, we highlight the role of the PLD-PA module as an important hub for housekeeping and stress-induced regulation of membrane-associated cytoskeletal dynamics.

Cell polarity and patterning by PIN trafficking through early endosomal compartments in Arabidopsis thaliana

PIN-FORMED (PIN) proteins localize asymmetrically at the plasma membrane and mediate intercellular polar transport of the plant hormone auxin that is crucial for a multitude of developmental processes in plants. PIN localization is under extensive control by environmental or developmental cues, but mechanisms regulating PIN localization are not fully understood. Here we show that early endosomal components ARF GEF BEN1 and newly identified Sec1/Munc18 family protein BEN2 are involved in distinct steps of early endosomal trafficking. BEN1 and BEN2 are collectively required for polar PIN localization, for their dynamic repolarization, and consequently for auxin activity gradient formation and auxin-related developmental processes including embryonic patterning, organogenesis, and vasculature venation patterning. These results show that early endosomal trafficking is crucial for cell polarity and auxin-dependent regulation of plant architecture.

Auxin is a unique plant hormone, which is actively and directionally transported in plant tissues. Transported auxin locally accumulates in the plant body and triggers a multitude of responses, including organ formation and patterning. Therefore, regulation of the directional auxin transport is very important in multiple aspects of plant development. The PIN-FORMED (PIN) family of auxin transporters is known to localize at specific sides of cells and export auxin from the cells, enabling the directional transport of auxin in the tissues. PIN proteins are rapidly shuttling between the plasma membrane and intracellular compartments, potentially allowing dynamic changes of the asymmetric localization according to developmental and environmental cues. Here, we discovered that a mutation in the Sec1/Munc18 family protein VPS45 abolishes its own early endosomal localization and compromises intracellular trafficking of PIN proteins. By genetic and pharmacological inhibition of early endosomal trafficking, we also revealed that another early endosomal protein, ARF GEF BEN1, is involved in early endosomal trafficking at a distinct step. Furthermore, we showed that these components play crucial roles in polar localization and dynamic repolarization of PIN proteins, which underpin various developmental processes. These findings highlight the indispensable roles of early endosomal components in regulating PIN polarity and plant architecture.

Rab-A1c GTPase defines a population of the trans-Golgi network that is sensitive to endosidin1 during cytokinesis in Arabidopsis

In plant cells, Rab-A proteins have been implicated to play important roles in membrane trafficking from the trans-Golgi network (TGN) to the plasma membrane/cell wall and to the newly formed cell plate in cytokinesis. But how different Rab-A proteins may work in the TGN is not well studied. We show here that RAB-A1c defines a population of TGN that is partially overlapped with the VHA-a1 marked-TGN. Interestingly, the morphology of RAB-A1c defined-TGN is sensitive to endosidin 1 (ES1), but not to wortmannin. In mitotic cells, RAB-A1c is relocated to the cell plate. We revealed that this process could be interrupted by ES1, but not by wortmannin. In addition, root growth and cytokinesis in root mitotic cells of rab-a1a/b/c triple mutant seedlings are hypersensitive to lower concentrations of ES1. ES1 is known to selectively block the transport of several plasma membrane auxin transporters, including PIN2 and AUX1 at the TGN. Together with the known facts that members of Rab-A1 proteins are involved in auxin-mediated responses in root growth and that mutations in TRAPPII, a protein complex that acts upstream of RAB-A1c, also selectively impair the transport of PIN2 and AUX1 at the TGN, we propose that the Rab-A1-mediated trafficking pathways around the TGN, but not Rab-A1s directly, are the target of ES1.

Global approaches for telling time: omics and the Arabidopsis circadian clock

The circadian clock is an endogenous timer that anticipates and synchronizes biological processes to the environment. Traditional genetic approaches identified the underlying principles and genetic components, but new discoveries have been greatly impeded by the embedded redundancies that confer necessary robustness to the clock architecture. To overcome this, global (omic) techniques have provided a new depth of information about the Arabidopsis clock. Our understanding of the factors, regulation, and mechanistic connectivity between clock genes and with output processes has substantially broadened through genomic (cDNA libraries, yeast one-hybrid, protein binding microarrays, and ChIP-seq), transcriptomic (microarrays, RNA-seq), proteomic (mass spectrometry and chemical libraries), and metabolomic (mass spectrometry) approaches. This evolution in research will undoubtedly enhance our understanding of how the circadian clock optimizes growth and fitness.

Capping protein modulates the dynamic behavior of actin filaments in response to phosphatidic acid in Arabidopsis

Remodeling of actin filament arrays in response to biotic and abiotic stimuli is thought to require precise control over the generation and availability of filament ends. Heterodimeric capping protein (CP) is an abundant filament capper, and its activity is inhibited by membrane signaling phospholipids in vitro. How exactly CP modulates the properties of filament ends in cells and whether its activity is coordinated by phospholipids in vivo is not well understood. By observing directly the dynamic behavior of individual filament ends in the cortical array of living Arabidopsis thaliana epidermal cells, we dissected the contribution of CP to actin organization and dynamics in response to the signaling phospholipid, phosphatidic acid (PA). Here, we examined three cp knockdown mutants and found that reduced CP levels resulted in more dynamic activity at filament ends, and this significantly enhanced filament-filament annealing and filament elongation from free ends. The cp mutants also exhibited more dense actin filament arrays. Treatment of wild-type cells with exogenous PA phenocopied the actin-based defects in cp mutants, with an increase in the density of filament arrays and enhanced annealing frequency. These cytoskeletal responses to exogenous PA were completely abrogated in cp mutants. Our data provide compelling genetic evidence that the end-capping activity of CP is inhibited by membrane signaling lipids in eukaryotic cells. Specifically, CP acts as a PA biosensor and key transducer of fluxes in membrane signaling phospholipids into changes in actin cytoskeleton dynamics.

Bundling actin filaments from membranes: some novel players

Progress in live-cell imaging of the cytoskeleton has significantly extended our knowledge about the organization and dynamics of actin filaments near the plasma membrane of plant cells. Noticeably, two populations of filamentous structures can be distinguished. On the one hand, fine actin filaments which exhibit an extremely dynamic behavior basically characterized by fast polymerization and prolific severing events, a process referred to as actin stochastic dynamics. On the other hand, thick actin bundles which are composed of several filaments and which are comparatively more stable although they constantly remodel as well. There is evidence that the actin cytoskeleton plays critical roles in trafficking and signaling at both the cell cortex and organelle periphery but the exact contribution of actin bundles remains unclear. A common view is that actin bundles provide the long-distance tracks used by myosin motors to deliver their cargo to growing regions and accordingly play a particularly important role in cell polarization. However, several studies support that actin bundles are more than simple passive highways and display multiple and dynamic roles in the regulation of many processes, such as cell elongation, polar auxin transport, stomatal and chloroplast movement, and defense against pathogens. The list of identified plant actin-bundling proteins is ever expanding, supporting that plant cells shape structurally and functionally different actin bundles. Here I review the most recently characterized actin-bundling proteins, with a particular focus on those potentially relevant to membrane trafficking and/or signaling.