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Intensification of agricultural practices has severely reduced weed diversity in arable fields, which affects the delivery of ecosystem services. However, in parallel, some species have benefited from intensive farming and have vastly increased their abundance, as is the case for Lolium rigidum and Avena sterilis in cereal fields. These highly competitive species severely reduce yields but can also compete with other weed species, and, when less intensive practices are applied, they might limit the recovery of weed diversity and the success of arable species reintroductions. A gradient of infestation was established in a winter wheat field in Catalonia (north-eastern Spain) by sowing seeds of both species at three different densities to test their effects on the abundance, diversity and composition of the natural weed community. The emergence of seeds and the survival and biomass of transplanted seedlings of two rare species, Agrostemma githago and Vaccaria hispanica, were also evaluated. Avena sterilis and L. rigidum infestations reduced the diversity, abundance and biomass and changed the composition of the natural weed community, even at low infestation densities. Moreover, infestations of both species affected the overall performance of A. githago and V. hispanica. This study reveals that A. sterilis and L. rigidum are highly competitive and that their infestations might hamper the recovery of diverse weed communities. Their densities should be considered when selecting suitable sites for promoting diversity and reintroducing rare species. [ABSTRACT FROM AUTHOR]

Fertiliser application is considered crucial for determining the crop-weed competition relationship by stimulating plant growth and modulating the competition for below-ground (soil nutrients) and above-ground resources (e.g. light and space). Segetal species, those preferentially inhabiting cereal fields, have suffered a strong decline, owing to agricultural intensification. Under continued pressure, particularly the rarest species may disappear. In this study, we aimed to assess the competitive ability of common and rare segetal species when growing with wheat and how this competitive relationship is modulated by the type (organic and mineral) and dose (low or high) of fertilisation in a pot experiment. The segetal species grew better at higher doses of fertilisers when growing alone. However, when growing with wheat, they were outcompeted by the cereal plants. Overall, flowering was not affected by the competition with wheat under the different fertiliser regimes. Only the onset of flowering of some segetal weeds tended to be delayed by crop competition. Some rare species were more affected by the competition with wheat, indicating that they may be disadvantaged in a community context. However, not all rare segetal species tested responded in the same way, which highlights that competitiveness alone is a poor predictor of the rarity of segetal species. [ABSTRACT FROM AUTHOR]

Vacuoles are essential for cellular metabolism and growth and the maintenance of internal turgor pressure. They sequester lytic enzymes, ions and secondary metabolites that, if leaked into the cytosol, could lead to cell death. Despite their pivotal roles, quality control pathways that safeguard vacuolar integrity have remained elusive in plants. Here we describe a conserved vacuolar quality control pathway that is activated upon cell wall damage in a turgor-pressure-dependent manner. Cell wall perturbations induce a distinct modification-ATG8ylation-on the vacuolar membrane (tonoplast) that is regulated by the V-ATPase and ATG8 conjugation machinery. Genetic disruption of tonoplast ATG8ylation impairs vacuolar integrity, leading to cell death. Together, our findings reveal a homeostatic pathway that preserves vacuolar integrity upon cell wall damage., Competing Interests: Competing interests: The authors declare no competing interests., (© 2025. The Author(s).)

Programmed cell death (PCD) is fundamentally important for plant development, abiotic stress responses and immunity, but our understanding of its regulation remains fragmented. Building a stronger research community is required to accelerate progress in this area through knowledge exchange and constructive debate. In this Viewpoint, we aim to initiate a collective effort to integrate data across a diverse set of experimental models to facilitate characterisation of the fundamental mechanisms underlying plant PCD and ultimately aid the development of a new plant cell death classification system in the future. We also put forward our vision for the next decade of plant PCD research stemming from discussions held during the 31 st New Phytologist workshop, 'The Life and Death Decisions of Plant Cells' that took place at University College Dublin in Ireland (14-15 June 2023). We convey the key areas of significant progress and possible future research directions identified, including resolving the spatiotemporal control of cell death, isolation of its molecular and genetic regulators, and harnessing technical advances for studying PCD events in plants. Further, we review the breadth of potential impacts of plant PCD research and highlight the promising new applications of findings from this dynamically evolving field., (© 2024 The Authors. New Phytologist © 2024 New Phytologist Foundation.)

Iron is critical during host-microorganism interactions 1-4 . Restriction of available iron by the host during infection is an important defence strategy, described as nutritional immunity 5 . However, this poses a conundrum for externally facing, absorptive tissues such as the gut epithelium or the plant root epidermis that generate environments that favour iron bioavailability. For example, plant roots acquire iron mostly from the soil and, when iron deficient, increase iron availability through mechanisms that include rhizosphere acidification and secretion of iron chelators 6-9 . Yet, the elevated iron bioavailability would also be beneficial for the growth of bacteria that threaten plant health. Here we report that microorganism-associated molecular patterns such as flagellin lead to suppression of root iron acquisition through a localized degradation of the systemic iron-deficiency signalling peptide Iron Man 1 (IMA1) in Arabidopsis thaliana. This response is also elicited when bacteria enter root tissues, but not when they dwell on the outer root surface. IMA1 itself has a role in modulating immunity in root and shoot, affecting the levels of root colonization and the resistance to a bacterial foliar pathogen. Our findings reveal an adaptive molecular mechanism of nutritional immunity that affects iron bioavailability and uptake, as well as immune responses., (© 2024. The Author(s), under exclusive licence to Springer Nature Limited.)

Stress granules (SGs) are highly conserved cytoplasmic condensates that assemble in response to stress and contribute to maintaining protein homeostasis. These membraneless organelles are dynamic, disassembling once the stress is no longer present. Persistence of SGs due to mutations or chronic stress has been often related to age-dependent protein-misfolding diseases in animals. Here, we find that the metacaspase MC1 is dynamically recruited into SGs upon proteotoxic stress in Arabidopsis (Arabidopsis thaliana). Two predicted disordered regions, the prodomain and the 360 loop, mediate MC1 recruitment to and release from SGs. Importantly, we show that MC1 has the capacity to clear toxic protein aggregates in vivo and in vitro, acting as a disaggregase. Finally, we demonstrate that overexpressing MC1 delays senescence and this phenotype is dependent on the presence of the 360 loop and an intact catalytic domain. Together, our data indicate that MC1 regulates senescence through its recruitment into SGs and this function could potentially be linked to its remarkable protein aggregate-clearing activity., Competing Interests: Conflict of interest statement. None declared., (© The Author(s) 2023. Published by Oxford University Press on behalf of American Society of Plant Biologists.)

Controlled primary cell wall remodeling allows plant growth under stressful conditions, but how these changes are conveyed to adjust cellulose synthesis is not understood. Here, we identify the TETRATRICOPEPTIDE THIOREDOXIN-LIKE (TTL) proteins as new members of the cellulose synthase complex (CSC) and describe their unique and hitherto unknown dynamic association with the CSC under cellulose-deficient conditions. We find that TTLs are essential for maintaining cellulose synthesis under high-salinity conditions, establishing a stress-resilient cortical microtubule array, and stabilizing CSCs at the plasma membrane. To fulfill these functions, TTLs interact with CELLULOSE SYNTHASE 1 (CESA1) and engage with cortical microtubules to promote their polymerization. We propose that TTLs function as bridges connecting stress perception with dynamic regulation of cellulose biosynthesis at the plasma membrane.

In plants, regulated cell expansion determines organ size and shape. Several members of the family of redundantly acting Small Auxin Up RNA (SAUR) proteins can stimulate plasma membrane (PM) H+-ATPase proton pumping activity by inhibiting PM-associated PP2C.D phosphatases, thereby increasing the PM electrochemical potential, acidifying the apoplast, and stimulating cell expansion. Similarly, Arabidopsis thaliana SAUR63 was able to increase growth of various organs, antagonize PP2C.D5 phosphatase, and increase H+-ATPase activity. Using a gain-of-function approach to bypass genetic redundancy, we dissected structural requirements for SAUR63 growth-promoting activity. The divergent N-terminal domain of SAUR63 has a predicted basic amphipathic α-helix and was able to drive partial PM association. Deletion of the N-terminal domain decreased PM association of a SAUR63 fusion protein, as well as decreasing protein level and eliminating growth-promoting activity. Conversely, forced PM association restored ability to promote H+-ATPase activity and cell expansion, indicating that SAUR63 is active when PM-associated. Lipid binding assays and perturbations of PM lipid composition indicate that the N-terminal domain can interact with PM anionic lipids. Mutations in the conserved SAUR domain also reduced PM association in root cells. Thus, both the N-terminal domain and the SAUR domain may cooperatively mediate the SAUR63 PM association required to promote growth., Competing Interests: The authors have declared that no competing interests exist.

Membrane lipids, and especially phosphoinositides, are differentially enriched within the eukaryotic endomembrane system. This generates a landmark code by modulating the properties of each membrane. Phosphatidylinositol 4,5-bisphosphate [PI(4,5)P 2 ] specifically accumulates at the plasma membrane in yeast, animal, and plant cells, where it regulates a wide range of cellular processes including endocytic trafficking. However, the functional consequences of mispatterning PI(4,5)P 2 in plants are unknown. Here, we functionally characterized the putative phosphoinositide phosphatase SUPPRESSOR OF ACTIN9 (SAC9) in Arabidopsis thaliana ( Arabidopsis ). We found that SAC9 depletion led to the ectopic localization of PI(4,5)P 2 on cortical intracellular compartments, which depends on PI4P and PI(4,5)P 2 production at the plasma membrane. SAC9 localizes to a subpopulation of trans -Golgi Network/early endosomes that are enriched in a region close to the cell cortex and that are coated with clathrin. Furthermore, it interacts and colocalizes with Src Homology 3 Domain Protein 2 (SH3P2), a protein involved in endocytic trafficking. In the absence of SAC9, SH3P2 localization is altered and the clathrin-mediated endocytosis rate is reduced. Together, our results highlight the importance of restricting PI(4,5)P 2 at the plasma membrane and illustrate that one of the consequences of PI(4,5)P 2 misspatterning in plants is to impact the endocytic trafficking., Competing Interests: AL, MD, AF, VB, JL, FR, MM, LA, RB, MS, MF, BM, SÜ, YJ, MC No competing interests declared, (© 2022, Lebecq, Doumane et al.)

Maintaining soil quality for agricultural production is a critical challenge, especially in the tropics. Due to the focus on environmental performance and the provision of soil ecosystem services, organic farming and agroforestry systems are proposed as alternative options to conventional monoculture farming. Soil processes underlying ecosystem services are strongly mediated by microbes; thus, increased understanding of the soil microbiome is crucial for the development of sustainable agricultural practices. Therefore, we measured and related soil quality indicators to bacterial and fungal community structures in five cocoa production systems, managed either organically or conventionally for 12 years, with varying crop diversity, from monoculture to agroforestry. In addition, a successional agroforestry system was included, which uses exclusively on-site pruning residues as soil inputs. Organic management increased soil organic carbon, nitrogen and labile carbon contents compared to conventional. Soil basal respiration and nitrogen mineralisation rates were highest in the successional agroforestry system. Across the field sites, fungal richness exceeded bacterial richness and fungal community composition was distinct between organic and conventional management, as well as between agroforestry and monoculture. Bacterial community composition differed mainly between organic and conventional management. Indicator species associated with organic management were taxonomically more diverse compared to taxa associated with conventionally managed systems. In conclusion, our results highlight the importance of organic management for maintaining soil quality in agroforestry systems for cocoa production., Competing Interests: Declaration of competing interest The authors declare that they have no competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 The Authors. Published by Elsevier B.V. All rights reserved.)

Phosphoinositides are low-abundant lipids that participate in the acquisition of membrane identity through their spatiotemporal enrichment in specific compartments. Phosphatidylinositol 4-phosphate (PI4P) accumulates at the plant plasma membrane driving its high electrostatic potential, and thereby facilitating interactions with polybasic regions of proteins. PI4Kα1 has been suggested to produce PI4P at the plasma membrane, but how it is recruited to this compartment is unknown. Here, we pin-point the mechanism that tethers Arabidopsis thaliana phosphatidylinositol 4-kinase alpha1 (PI4Kα1) to the plasma membrane via a nanodomain-anchored scaffolding complex. We established that PI4Kα1 is part of a complex composed of proteins from the NO-POLLEN-GERMINATION, EFR3-OF-PLANTS, and HYCCIN-CONTAINING families. Comprehensive knockout and knockdown strategies revealed that subunits of the PI4Kα1 complex are essential for pollen, embryonic, and post-embryonic development. We further found that the PI4Kα1 complex is immobilized in plasma membrane nanodomains. Using synthetic mis-targeting strategies, we demonstrate that a combination of lipid anchoring and scaffolding localizes PI4Kα1 to the plasma membrane, which is essential for its function. Together, this work opens perspectives on the mechanisms and function of plasma membrane nanopatterning by lipid kinases., (© The Author(s) 2021. Published by Oxford University Press on behalf of American Society of Plant Biologists.)

Plants are able to orient their growth according to gravity, which ultimately controls both shoot and root architecture. 1 Gravitropism is a dynamic process whereby gravistimulation induces the asymmetric distribution of the plant hormone auxin, leading to asymmetric growth, organ bending, and subsequent reset of auxin distribution back to the original pre-gravistimulation situation. 1-3 Differential auxin accumulation during the gravitropic response depends on the activity of polarly localized PIN-FORMED (PIN) auxin-efflux carriers. 1-4 In particular, the timing of this dynamic response is regulated by PIN2, 5 , 6 but the underlying molecular mechanisms are poorly understood. Here, we show that MEMBRANE ASSOCIATED KINASE REGULATOR2 (MAKR2) controls the pace of the root gravitropic response. We found that MAKR2 is required for the PIN2 asymmetry during gravitropism by acting as a negative regulator of the cell-surface signaling mediated by the receptor-like kinase TRANSMEMBRANE KINASE1 (TMK1). 2 , 7-10 Furthermore, we show that the MAKR2 inhibitory effect on TMK1 signaling is antagonized by auxin itself, which triggers rapid MAKR2 membrane dissociation in a TMK1-dependent manner. Our findings suggest that the timing of the root gravitropic response is orchestrated by the reversible inhibition of the TMK1 signaling pathway at the cell surface., Competing Interests: Declaration of Interests The authors declare no competing interests., (Copyright © 2020 The Author(s). Published by Elsevier Inc. All rights reserved.)

Under the hypothesis that organically managed cacao agroforestry systems report a lower global warming potential (GWP) and reduce other environmental pressure indicators compared with conventionally managed systems and monocultures, this work discusses how global transportation can cut back the ecological advantage of the production phase. For this purpose, the life cycle assessment (LCA) of 1 kg of dark chocolate manufactured with Ecuadorian cacao has been performed (cradle-to-retailer approach), including the indirect impacts of transportation and estimating the equilibrium distances beyond which organic chocolate would have a higher impact than chocolate manufactured from cacao grown in monocultures and/or conventionally managed systems. To articulate the discussion, the carbon footprint (CF) of cacao/chocolate was analyzed together with 10 additional LCA-related impact categories. Three management systems-conventional monoculture (CM) and agroforestry (CA), and organic agroforestry (OA)-and three different supply chain scenarios with different weights in the transportation phase were studied. Expanding on the concept of "food miles", the equivalent kilometers of the impact of emissions (km-eq) (or cumulated energy demand, eutrophication, etc.) were defined as the variable distance that a certain means of transportation can travel in relation to a fixed level of GHG emissions (or MJ, kg PO 4 -eq, etc.). The CF of the life cycle of cacao/chocolate was estimated at between 2.04 and 4.66 kg CO 2 -eq kg -1 . The relative weight of transportation in relation to the total GHG emissions ranged between 8.9% and 51.1%, with cacao/chocolate traveling between 1380 and 9155 km-eq. The CF of chocolate made from cacao grown in OA systems was 22.7%-34.2% and 6.3%-10.7% lower than the CF of chocolate produced from cacao grown in CM and CA and manufactured and transported under the same conditions. The equilibrium distances between managements were estimated at 1213 and 5275 km-eq. Beyond those equivalent kilometers, organic chocolate would have a larger CF than chocolate manufactured from cacao grown, respectively, in CA and CM systems. Our results indicate that transportation would cancel out this and most other comparative ecological advantages of producing organic cacao analyzed in this work. Directly exporting chocolate from cacao-producing countries and relocating chocolate manufacture would help reduce GHG emissions and other environmental impacts of the supply chain., (Copyright © 2020 Elsevier Ltd. All rights reserved.)

: The definition of "arable weeds" remains contentious. Although much attention has been devoted to specialized, segetal weeds, many taxa found in arable fields also commonly occur in other habitats. The extent to which adjacent habitats are favorable to the weed flora and act as potential sources of colonizers in arable fields remains unclear. In addition, weeds form assemblages with large spatiotemporal variability, so that many taxa in weed flora are rarely observed in plot-based surveys. We thus addressed the following questions: How often do weeds occur in other habitats than arable fields? How does including field edges extend the taxonomic and ecological diversity of weeds? How does the weed flora vary across surveys at different spatial and temporal scales? We built a comprehensive dataset of weed taxa in France by compiling weed flora, lists of specialized segetal weeds, and plot-based surveys in agricultural fields, with different spatial and temporal coverages. We informed life forms, biogeographical origins and conservation status of these weeds. We also defined a broader dataset of plants occupying open habitats in France and assessed habitat specialization of weeds and of other plant species absent from arable fields. Our results show that many arable weeds are frequently recorded in both arable fields and non-cultivated open habitats and are, on average, more generalist than species absent from arable fields. Surveys encompassing field edges included species also occurring in mesic grasslands and nitrophilous fringes, suggesting spill-over from surrounding habitats. A total of 71.5% of the French weed flora was not captured in plot-based surveys at regional and national scales, and many rare and declining taxa were of Mediterranean origin. This result underlines the importance of implementing conservation measures for specialist plant species that are particularly reliant on arable fields as a habitat, while also pointing out biotic homogenization of agricultural landscapes as a factor in the declining plant diversity of farmed landscapes. Our dataset provides a reference species pool for France, with associated ecological and biogeographical information ., Competing Interests: The authors declare no conflict of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.

Rho guanosine triphosphatases (GTPases) are master regulators of cell signaling, but how they are regulated depending on the cellular context is unclear. We found that the phospholipid phosphatidylserine acts as a developmentally controlled lipid rheostat that tunes Rho GTPase signaling in Arabidopsis Live superresolution single-molecule imaging revealed that the protein Rho of Plants 6 (ROP6) is stabilized by phosphatidylserine into plasma membrane nanodomains, which are required for auxin signaling. Our experiments also revealed that the plasma membrane phosphatidylserine content varies during plant root development and that the level of phosphatidylserine modulates the quantity of ROP6 nanoclusters induced by auxin and hence downstream signaling, including regulation of endocytosis and gravitropism. Our work shows that variations in phosphatidylserine levels are a physiological process that may be leveraged to regulate small GTPase signaling during development., (Copyright © 2019 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.)

Farmers expect yield reduction of cash crops like cocoa when growing in agroforestry systems compared to monocultures, due to competition for resources, e.g. nutrients and water. However, complementarities between species in the use of resources may improve resource use efficiency and result in higher system performance. Cocoa trees have a shallow rooting system while the rooting characteristics of the associated trees are mainly unknown. This work investigates fine root distribution and production in five cocoa production systems: two monocultures and two agroforestry systems under conventional and organic farming, and a successional agroforestry system. In the organic systems a perennial leguminous cover crop was planted and compost was added, while herbicides and chemical fertilizers were applied in the conventional ones. We measured cocoa fine root parameters in the top 10cm of soil and annual total fine root production at 0-25 and 25-50cm depth. We related the root data with both the aboveground performance (tree and herbaceous biomass), and the cocoa and system yields. Cocoa fine roots were homogenously distributed over the plot area. Around 80% of the total fine roots were located in the upper 25cm of soil. The total fine root production was 4-times higher in the agroforestry systems and the organic monoculture than in the conventional monoculture. The roots of the associated tree species were located in the same soil space as the cocoa roots and, in principle, competed for the same soil resources. The cocoa yield was lower in the agroforestry systems, but the additional crops generated a higher system yield and aboveground biomass than the conventional cocoa monocultures, implying effective resource exploitation. The leguminous cover crop in the organic monoculture competed with the cocoa trees for nutrients, which may explain the lower cocoa yield in this system in contrast with the conventional monoculture., (Copyright © 2018 Elsevier B.V. All rights reserved.)

Premise of the Study: Despite long-term research efforts, a comprehensive perspective on the ecological and functional properties determining plant weediness is still lacking. We investigated here key functional attributes of arable weeds compared to non-weed plants, at large spatial scale., Methods: We used an intensive survey of plant communities in cultivated and non-cultivated habitats to define a pool of plants occurring in arable fields (weeds) and one of plants occurring only in open non-arable habitats (non-weeds) in France. We compared the two pools based on nine functional traits and three functional spaces (LHS, reproductive and resource requirement hypervolumes). Within the weed pool, we quantified the trait variation of weeds along a continuum of specialization to arable fields., Key Results: Weeds were mostly therophytes and had higher specific leaf area, earlier and longer flowering, and higher affinity for nutrient-rich, sunny and dry environments compared to non-weeds, although functional spaces of weeds and non-weeds largely overlapped. When fidelity to arable fields increased, the spectrum of weed ecological strategies decreased as did the overlap with non-weeds, especially for the resource requirement hypervolume., Conclusions: Arable weeds constitute a delimited pool defined by a trait syndrome providing tolerance to the ecological filters of arable fields (notably, regular soil disturbances and fertilization). The identification of such a syndrome is of great interest to predict the weedy potential of newly established alien plants. An important reservoir of plants may also become weeds after changes in agricultural practices, considering the large overlap between weeds and non-weeds., (© 2019 Botanical Society of America.)

Membrane surface charge is critical for the transient, yet specific recruitment of proteins with polybasic regions to certain organelles. In eukaryotes, the plasma membrane (PM) is the most electronegative compartment of the cell, which specifies its identity. As such, membrane electrostatics is a central parameter in signaling, intracellular trafficking, and polarity. Here, we explore which are the lipids that control membrane electrostatics using plants as a model. We show that phosphatidylinositol-4-phosphate (PI4P), phosphatidic acidic (PA), and phosphatidylserine (PS) are separately required to generate the electrostatic signature of the plant PM. In addition, we reveal the existence of an electrostatic territory that is organized as a gradient along the endocytic pathway and is controlled by PS/PI4P combination. Altogether, we propose that combinatorial lipid composition of the cytosolic leaflet of organelles not only defines the electrostatic territory but also distinguishes different functional compartments within this territory by specifying their varying surface charges., (Copyright © 2018 Elsevier Inc. All rights reserved.)

Cocoa beans are produced all across the humid tropics under different environmental conditions provided by the region but also by the season and the type of production system. Agroforestry systems compared to monocultures buffer climate extremes and therefore provide a less stressful environment for the understory cocoa, especially under seasonally varying conditions. We measured the element concentration as well as abiotic stress indicators (polyamines and total phenolic content) in beans derived from five different production systems comparing monocultures and agroforestry systems and from two harvesting seasons. Concentrations of N, Mg, S, Fe, Mn, Na, and Zn were higher in beans produced in agroforestry systems with high stem density and leaf area index. In the dry season, the N, Fe, and Cu concentration of the beans increased. The total phenolic content increased with proceeding of the dry season while other abiotic stress indicators like spermine decreased, implying an effect of the water availability on the chemical composition of the beans. Agroforestry systems did not buffer the variability of stress indicators over the seasons compared to monocultures. The effect of environmental growing conditions on bean chemical composition was not strong but can contribute to variations in cocoa bean quality.

The directional transport of auxin, known as polar auxin transport (PAT), allows asymmetric distribution of this hormone in different cells and tissues. This system creates local auxin maxima, minima, and gradients that are instrumental in both organ initiation and shape determination. As such, PAT is crucial for all aspects of plant development but also for environmental interaction, notably in shaping plant architecture to its environment. Cell to cell auxin transport is mediated by a network of auxin carriers that are regulated at the transcriptional and post-translational levels. Here we review our current knowledge on some aspects of the 'non-genomic' regulation of auxin transport, placing an emphasis on how phosphorylation by protein and lipid kinases controls the polarity, intracellular trafficking, stability, and activity of auxin carriers. We describe the role of several AGC kinases, including PINOID, D6PK, and the blue light photoreceptor phot1, in phosphorylating auxin carriers from the PIN and ABCB families. We also highlight the function of some receptor-like kinases (RLKs) and two-component histidine kinase receptors in PAT, noting that there are probably RLKs involved in co-ordinating auxin distribution yet to be discovered. In addition, we describe the emerging role of phospholipid phosphorylation in polarity establishment and intracellular trafficking of PIN proteins. We outline these various phosphorylation mechanisms in the context of primary and lateral root development, leaf cell shape acquisition, as well as root gravitropism and shoot phototropism., (© The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.)

Many signalling proteins permanently or transiently localize to specific organelles. It is well established that certain lipids act as biochemical landmarks to specify compartment identity. However, they also influence membrane biophysical properties, which emerge as important features in specifying cellular territories. Such parameters include the membrane inner surface potential, which varies according to the lipid composition of each organelle. Here, we found that the plant plasma membrane (PM) and the cell plate of dividing cells have a unique electrostatic signature controlled by phosphatidylinositol-4-phosphate (PtdIns(4)P). Our results further reveal that, contrarily to other eukaryotes, PtdIns(4)P massively accumulates at the PM, establishing it as a critical hallmark of this membrane in plants. Membrane surface charges control the PM localization and function of the polar auxin transport regulator PINOID as well as proteins from the BRI1 KINASE INHIBITOR1 (BKI1)/MEMBRANE ASSOCIATED KINASE REGULATOR (MAKR) family, which are involved in brassinosteroid and receptor-like kinase signalling. We anticipate that this PtdIns(4)P-driven physical membrane property will control the localization and function of many proteins involved in development, reproduction, immunity and nutrition.

The protein kinase CK2 is a ubiquitous and highly conserved enzyme, the activity of which is vital for eukaryotic cells. We recently demonstrated that CK2 modulates salicylic acid (SA) homeostasis in Arabidopsis thaliana, and that functional interplay between CK2 and SA sustains transcriptional expression of PIN-FORMED (PIN) genes. In this work, we show that CK2 also plays a key role in the transcriptional regulation of PINOID (PID), an AGC protein kinase that modulates the apical/basal localization of auxin-efflux transporters. We show that PID transcription is up-regulated by auxin and by SA and that CK2 is involved in both pathways. On the one hand, CK2 activity is required for proteosome-dependent degradation of AXR3, a member of the AUX/IAA family of auxin transcriptional repressors that must be degraded to activate auxin-responsive gene expression. On the other hand, the role of CK2 in SA homeostasis and, indirectly, in SA-driven PID transcription, was confirmed by using Arabidopsis NahG transgenic plants, which cannot accumulate SA. In conclusion, our results evidence a role for CK2 as a functional link in the negative cross-talk between auxin- and SA-signaling.

We have previously reported that CK2-defective Arabidopsis thaliana plants (CK2mut plants) were impaired severely in root development and auxin polar transport, and exhibited transcriptional misregulation of auxin-efflux transporters (Plant J., 67, 2011a, 169). In this work we show that CK2mut roots accumulate high levels of salicylic acid (SA) and that the gene that encodes isochorismate synthase (SID2) is overexpressed, strongly suggesting that CK2 activity is required for SA biosynthesis via the shikimate pathway. Moreover, SA activates transcription of CK2-encoding genes and, thus, SA and CK2 appear to be part of an autoregulatory feed-back loop to fine-tune each other's activities. We also show that exogenous SA and constitutive high SA levels in cpr mutants reproduce the CK2mut root phenotypes (decrease of root length and of number of lateral roots), whereas inhibition of CK2 activity in SA-defective and SA-signalling mutants lead to less severe phenotypes, suggesting that the CK2mut root phenotypes are SA-mediated effects. Moreover, exogenous SA mediates transcriptional repression of most of PIN-FORMED (PIN) genes, which is the opposite effect observed in CK2mut roots. These results prompted us to propose a model in which CK2 acts as a link between SA homeostasis and transcriptional regulation of auxin-efflux transporters. We also show that CK2 overexpression in Arabidopsis has neither impact on SA biosynthesis nor on auxin transport, but it improves the Arabidopsis root system. Thus, unlike the outcome in mammals, an excess of CK2 in plant cells does not produce neoplasia, but it might be advantageous for plant fitness., (© 2014 The Authors The Plant Journal © 2014 John Wiley & Sons Ltd.)

The multifunctional protein kinase CK2 is involved in several aspects of the DNA damage response (DDR) in mammals. To gain insight into the role of CK2 in plant genome maintenance, we studied the response to genotoxic agents of an Arabidopsis CK2 dominant-negative mutant (CK2mut plants). CK2mut plants were hypersensitive to a wide range of genotoxins that produce a variety of DNA lesions. However, they were able to activate the DDR after exposure to γ irradiation, as shown by accumulation of phosphorylated histone H2AX and up-regulation of sets of radio-modulated genes. Moreover, functional assays showed that mutant plants quickly repair the DNA damage produced by genotoxins, and that they exhibit preferential use of non-conservative mechanisms, which may explain plant lethality. The chromatin of CK2mut plants was more sensitive to digestion with micrococcal nuclease, suggesting compaction changes that agreed with the transcriptional changes detected for a number of genes involved in chromatin structure. Furthermore, CK2mut plants were prone to transcriptional gene silencing release upon genotoxic stress. Our results suggest that CK2 is required in the maintenance and control of genomic stability and chromatin structure in plants, and that this process affects several functions, including the DNA damage response and DNA repair., (© 2012 The Authors. The Plant Journal © 2012 Blackwell Publishing Ltd.)

The use of composted manures and of legumes in crop rotations may control the quality and quantity of soil organic matter and may affect nutrient retention and recycling. We studied soil organic C and N stocks and N mineralization in organically and conventionally managed dryland arable soils. We selected 13 extensive organic fields managed organically for 10 yr or more as well as adjacent fields managed conventionally. Organic farmers applied composted manures ranging from 0 to 1380 kg C ha yr and incorporated legumes in crop rotations. In contrast, conventional farmers applied fresh manures combined with slurries and/or mineral fertilizers ranging from 200 to 1900 kg C ha yr and practiced a cereal monoculture. Despite the fact that the application of organic C was similar in both farming systems, organically managed soils showed higher C and similar N content and lower bulk density than conventionally managed soils. Moreover, organic C stocks responded to the inputs of organic C in manures and to the presence of legumes only in organically managed soils. In contrast, stocks of organic N increased with the inputs of N or C in both farming systems. In organically managed soils, organic N stocks were less mineralizable than in conventional soils. However, N mineralization in organic soils was sensitive to the N fixation rates of legumes and to application rate and C/N ratio of the organic fertilizers., (Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.)

Despite increasing progress in the study of CK2 activity in plants, a clear understanding of its functional role remains elusive. The high pleiotropic nature of the enzyme, the fact that it is absolutely necessary to maintain life, and the existence of multiple isoforms have made it difficult to obtain loss-of-function mutants with which to study the impact of CK2 depletion in the organisms. To avoid all these difficulties, we have used a dominant-negative mutant approach, by constructing a CK2α kinase-inactive subunit (CKA3mut) that was cloned downstream of an inducible promoter. Stably transformed Arabidopsis plants showed that longtime inductions of the transgene were lethal, causing growth and development arrests and ultimately resulting in plant death. However, short-time inductions were not lethal and revealed broad phenotypical changes that uncovered novel functions of CK2 in plants. The high pleiotropy of CK2 was sustained by analysis of global transcript profiles that showed a huge number of genes affected, involved in a wide variety of cellular processes.