Bipartite anchoring of SCREAM enforces stomatal initiation by coupling MAP Kinases to SPEECHLESS, bioRxiv, 2019-03-24
AbstractCell-fate in eukaryotes is regulated by MAP Kinases (MAPKs) that translate external cues to cellular responses. In plants, two MAPKs, MPK36, regulate diverse processes of development, environmental response, and immunity. Yet, the mechanism bridging these shared signaling components with a specific target remains unresolved. Focusing on the development of stomata, epidermal valves for gas exchange and transpiration, we report here that the bHLH protein SCREAM functions as a scaffold by recruiting MPK36 to downregulate SPEECHLESS, a transcription factor initiating stomatal cell lineages. SCREAM directly binds with MPK36 through an evolutionarily-conserved yet unconventional bipartite motif. Mutations in this motif abrogate association, phosphorylation and degradation of SCREAM, unmask hidden non-redundancies between MPK3 and MPK6, and result in uncontrolled stomatal differentiation. Structural analyses of MPK6 at the 2.75Å resolution unraveled bipartite binding of SCREAM with MPK6, that is distinct from an upstream MAPKK. Our findings elucidate, at the atomic resolution, the mechanism directly linking extrinsic signals to transcriptional reprogramming during the establishment of stomatal cell-fate, and highlight a unique substrate-binding mode adopted by plant MAPKs.
biorxiv plant-biology 0-100-users 2019Convergent gene loss in aquatic plants predicts new components of plant immunity and drought response, bioRxiv, 2019-03-11
AbstractThe transition of plants from sea to land sparked an arms race with pathogens. The increased susceptibility of land plants is largely thought to be due to their dependence on micro-organisms for nutrients; the ensuing co-evolution has shaped the plant immune system. By profiling the immune receptors across flowering plants, we identified species with low numbers of NLR immune receptors. Interestingly, four of these species represent distinct lineages of monocots and dicots that returned to the aquatic lifestyle. Both aquatic monocot and dicot species lost the same well-known downstream immune signalling complex (EDS1-PAD4). This observation inspired us to look for other genes with a similar loss pattern and allowed us to predict putative new components of plant immunity. Gene expression analyses confirmed that a group of these genes was differentially expressed under pathogen infection. Excitingly, another subset of these genes was differentially expressed upon drought. Collectively, our study reveals the minimal plant immune system required for life under water, and highlights additional components required for the life of land plants.Author summaryPlant resistance to pathogens is commonly mediated by a complex gene family, known as NLRs. Upon pathogen infection, changes in the cellular environment trigger NLR activation and subsequent defence responses. Despite the dependence of agricultural practices on NLR genes to control pathogen load, relatively little is known about this gene family outside of model crop species. In this study, we identified a convergent reduction in the NLR gene family among two lineages of aquatic plants. Furthermore, we established that NLR reduction occurred in conjunction with the loss of a common immune signalling pathway. Subsequently, we identified other genes convergently lost in aquatic species and propose these as candidate components of the plant immune signalling pathway. In addition, we revealed components of the agronomically important drought response to be lost in aquatic plants. This study adds to our understanding of the complex interactions between environment and response to biotic stress, widely known as the disease triangle. The pathways identified in this study shed further light on the link between responses to drought and disease.
biorxiv plant-biology 100-200-users 2019Convergent loss of an EDS1PAD4 signalling pathway in several plant lineages predicts new components of plant immunity and drought response, bioRxiv, 2019-03-11
AbstractPlant innate immunity relies on NLR receptors that recognize pathogen derived molecules and activate downstream signalling pathways. We analyzed the variation in copy number of NLR genes across flowering plants, and identified a number of species with a low number of NLRs relative to sister species. Two distinct lineages, one monocot (Lentibulariaceae) and one dicot (Alismatales) encapsulate four species with particularly few NLR genes. In these lineages, loss of NLRs coincided with loss of the well-known downstream immune signalling complex (EDS1-PAD4). When we expanded our analysis across the whole proteomes, we were able to identify other characterized immune genes absent only in Lentibulariaceae and Alismatales. Additionally, we identified a small subset of genes with unknown function convergently lost in all four species. We predicted that some of these genes may have a role in plant immunity. Gene expression analyses confirmed that a group of these genes was differentially expressed under pathogen infection. Another subset of these genes was differentially expressed upon drought providing further evidence of a link between the drought and plant immunity.
biorxiv plant-biology 100-200-users 2019Cytokinin functions as an asymmetric and anti-gravitropic signal in lateral roots, bioRxiv, 2019-03-10
AbstractDirectional organ growth allows the plant root system to strategically cover its surroundings. Intercellular auxin transport is aligned with the gravity vector in the primary root tips, facilitating downward organ bending at the lower root flank. Here we show that cytokinin signaling functions as a lateral root specific anti-gravitropic component, promoting the radial distribution of the root system. We performed a genome-wide association study and revealed that signal peptide processing of Cytokinin Oxidase 2 (CKX2) affects its enzymatic activity and, thereby, determines the degradation of cytokinins in natural Arabidopsis thaliana accessions. Cytokinin signaling interferes with growth at the upper lateral root flank and thereby prevents downward bending. Our interdisciplinary approach revealed that two phytohormonal cues at opposite organ flanks counterbalance each other’s negative impact on growth, suppressing organ growth towards gravity and allow for radial expansion of the root system.
biorxiv plant-biology 100-200-users 2019Auxin export from proximal fruits drives arrest in competent inflorescence meristems, bioRxiv, 2019-02-06
A well-defined set of regulatory pathways control entry into the reproductive phase in flowering plants. Conversely, little is known about the mechanisms that control the end of the reproductive phase (floral arrest), despite this being a critical process for optimising fruit and seed production. Complete fruit removal or lack of fertile fruit-set in male sterile mutants, for example male sterile1 (ms1), prevents timely floral arrest in the model plant Arabidopsis. These observations formed the basis for Hensel and colleagues model in which end-of-flowering was proposed to result from a cumulative fruitseed-derived signal that caused simultaneous global proliferative arrest (GPA) in all inflorescences. Recent studies have suggested that end-of-flowering involves gene expression changes at the floral meristem which are at least in part controlled by the FRUITFULL-APETELA2 pathway, however there is limited understanding of how this process is controlled and the communication needed at the whole plant level. Here, we provide new information providing a framework for the fruit-to-meristem (F-M) communication implied by the GPA model. We show that floral arrest in Arabidopsis is not global and does not occur synchronously between branches, but rather that the arrest of each inflorescence is a local process, driven by auxin export from fruit proximal to the inflorescence meristem (IM). Furthermore, we show that inflorescence meristems are only competent for floral arrest once they reach a certain developmental age. Understanding the regulation of floral arrest is of major importance for the future manipulation of flowering to extend and maximise crop yields.
biorxiv plant-biology 0-100-users 2019The Arabidopsis thaliana pan-NLRome, bioRxiv, 2019-02-01
Disease is both among the most important selection pressures in nature and among the main causes of yield loss in agriculture. In plants, resistance to disease is often conferred by Nucleotide-binding Leucine-rich Repeat (NLR) proteins. These proteins function as intracellular immune receptors that recognize pathogen proteins and their effects on the plant. Consistent with evolutionarily dynamic interactions between plants and pathogens, NLRs are known to be encoded by one of the most variable gene families in plants, but the true extent of intraspecific NLR diversity has been unclear. Here, we define the majority of the Arabidopsis thaliana species-wide 'NLRome'. From NLR sequence enrichment and long-read sequencing of 65 diverse A. thaliana accessions, we infer that the pan-NLRome saturates with approximately 40 accessions. Despite the high diversity of NLRs, half of the pan-NLRome is present in most accessions. We chart the architectural diversity of NLR proteins, identify novel architectures, and quantify the selective forces that act on specific NLRs, domains, and positions. Our study provides a blueprint for defining the pan-NLRome of plant species.
biorxiv plant-biology 100-200-users 2019