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C4 photosynthesis increases the efficiency of carbon fixation by spatially separating high concentrations of molecular oxygen from Rubisco. The specialized leaf anatomy required for this separation evolved independently many times. The morphology of C4 root systems is also distinctive and adapted to support high rates of photosynthesis; however, little is known about the molecular mechanisms that have driven the evolution of C4 root system architecture. Using a mutant screen in the C4 model plant Setaria italica, we identify Siaux1-1 and Siaux1-2 as root system architecture mutants. Unlike in S. viridis, AUX1 promotes lateral root development in S. italica. A cell by cell analysis of the Siaux1-1 root apical meristem revealed changes in the distribution of cell volumes in all cell layers and a dependence of the frequency of protophloem and protoxylem strands on SiAUX1. We explore the molecular basis of the role of SiAUX1 in seedling development using an RNAseq analysis of wild-type and Siaux1-1 plants and present novel targets for SiAUX1-dependent gene regulation. Using a selection sweep and haplotype analysis of SiAUX1, we show that Hap-2412TT in the promoter region of SiAUX1 is an allele which is associated with lateral root number and has been strongly selected for during Setaria domestication.

C4 photosynthesis increases the efficiency of carbon fixation by spatially separating high concentrations of molecular oxygen from rubisco. The specialized leaf anatomy required for this separation evolved independently many times. C4 root systems are highly branched, an adaptation thought to support high rates of photosynthesis; however, little is known about the molecular mechanisms that have driven the evolution of C4 root system architecture (RSA). Using a mutant screen in the C4 model plant Setaria italica, we identify siaux1-1 and siaux1-2 as RSA mutants, and use CRISPR/cas9-mediated genome editing and overexpression to confirm the importance of the locus. As AUX1 is not necessary for lateral root emergence in S. viridis, the species from which S. italica was domesticated, we conducted an analysis of auxin responsive elements in the promoters of auxin-responsive gene families in S. italica, and explore the molecular basis of SiAUX1’s role in seedling development using an RNAseq analysis of wild type and siaux1-1 plants. Finally, we use a root coordinate system to compare cell-by-cell meristem structures in siaux1-1 and wild type Setaria plants, observing changes in the distribution of cell volumes in all cell layers and a dependence in the frequency of protophloem and protoxylem strands on siAUX1.

The transport of auxin controls the rate, direction and localization of plant growth and development. The course of auxin transport is defined by the polar subcellular localization of the PIN proteins, a family of auxin efflux transporters. However, little is known about the composition and regulation of the PIN protein complex. Here, using blue‐native PAGE and quantitative mass spectrometry, we identify native PIN core transport units as homo‐ and heteromers assembled from PIN1, PIN2, PIN3, PIN4 and PIN7 subunits only. Furthermore, we show that endogenous flavonols stabilize PIN dimers to regulate auxin efflux in the same way as does the auxin transport inhibitor 1‐naphthylphthalamic acid (NPA). This inhibitory mechanism is counteracted both by the natural auxin indole‐3‐acetic acid and by phosphomimetic amino acids introduced into the PIN1 cytoplasmic domain. Our results lend mechanistic insights into an endogenous control mechanism which regulates PIN function and opens the way for a deeper understanding of the protein environment and regulation of the polar auxin transport complex., Identification of native PIN‐FORMED (PIN) auxin transporter complexes in Arabidopsis thaliana shows formation of dimers that are stabilized by the auxin transport inhibitor NPA and natural flavonols.

Root system development is crucial for optimal growth and yield in plants, especially in sub-optimal soil conditions. The architecture of a root system is environmentally responsive, enabling the plant to exploit regions of high nutrient density whilst simultaneously minimizing abiotic stress. Despite the vital contribution of root systems to the growth of both model and crop species, we know little of the mechanisms which regulate their architecture. One factor which is relatively well understood is the transport of auxin, a plant growth regulator which defines the frequency of lateral root (LR) initiation and the rate of LR outgrowth. Here we describe a search for proteins which regulate RSA by interacting directly with a key auxin transporter, PIN1. The native separation of PIN1 identified several co-purifying proteins. Among them, AZG1 was subsequently confirmed as a PIN1 interactor. AZG1-GFP fusions co-localized with PIN1 in procambium cells of the root meristem. Roots of azg1 plants contained less PIN1 and blocking proteolysis restored PIN1 levels, observations which are consistent with PIN1 being stabilized by AZG1 in the plasma membrane. Furthermore, we show that AZG1 is a cytokinin import protein; accordingly, azg1 plants are insensitive to exogenously applied cytokinin. In wild-type plants, the frequency of LRs falls with increasing salt concentration, a response which is not observed in azg1 x azg2 plants, although their drought response is unimpaired. This report therefore identifies a potential point for auxin:cytokinin crosstalk in the environmentally-responsive determination of root system architecture.

Cell death, autophagy and endosomal sorting contribute to many physiological, developmental and immunological processes in plants. They are mechanistically interconnected and interdependent, but the molecular basis of their mutual regulation has only begun to emerge in plants. Here, we describe the identification and molecular characterization of CELL DEATH RELATED ENDOSOMAL FYVE/SYLF PROTEIN 1 (CFS1). The CFS1 protein interacts with the ENDOSOMAL SORTING COMPLEX REQUIRED FOR TRANSPORT I (ESCRT-I) component ELCH (ELC) and is localized at ESCRT-I-positive late endosomes likely through its PI3P and actin binding SH3YL1 Ysc84/Lsb4p Lsb3p plant FYVE (SYLF) domain. Mutant alleles of cfs1 exhibit auto-immune phenotypes including spontaneous lesions that show characteristics of hypersensitive response (HR). Autoimmunity in cfs1 is dependent on ENHANCED DISEASE SUSCEPTIBILITY 1 (EDS1)-mediated effector-triggered immunity (ETI) but independent from salicylic acid. Additionally, cfs1 mutants accumulate the autophagy markers ATG8 and NBR1 independently from EDS1. We hypothesize that CFS1 acts at the intersection of autophagosomes and endosomes and contributes to cellular homeostasis by mediating autophagosome turnover.

Systems biology orientates signaling pathways in their biological context. This aim invariably requires models that ignore extraneous factors and focus on the most crucial pathways of any given process. The developing embryo encapsulates many important processes in plant development; understanding their interaction will be key to designing crops able to maximize yield in an ever-more challenging world. Here, we briefly summarize the role of auxin during embryo development. We highlight recent advances in our understanding of auxin signaling and discuss implications for a systems understanding of development.

The Endosomal Sorting Complex Required for Transport (ESCRT) regulates important functions in the secretory system of yeast and animals. The main responsibilities that have been described so far are sorting of biosynthetic cargo and receptor-downregulation. The scope of my PhD thesis was the analysis of the Arabidopsis ELCH protein that is similar to Vps23p and TSG101. These proteins represent the core components of ESCRT I complex in yeast and animals. I could show that ubiquitin binding and complex formation is conserved between Arabidopsis, yeast and animals, supporting the idea that ESCRT mediated protein sorting is a general strategy in eukaryotic organisms. New ELCH/ESCRT-I interacting proteins were isolated by immunoprecipitation and subsequent mass spectrometry. By this approach a plant specific protein containing a UBiquitin Associated (UBA) domain and several subunits of the vacuolar (H+)-ATPase were identified. The VHA-a3 subunit of the vacuolar (H+)-ATPase was analysed in more detail for ubiquitin modifications because mono-ubiquitination constitutes the sorting signal for the ESCRT pathway. Two colour western analysis showed that VHA-a3 is mono-ubiquitinated indicating that VHA-a3 might be a target of ELCH/ESCRT-I. Similar to the ESCRT pathway the V-ATPase is involved in the sorting of biosynthetic cargo and receptor-downregulation in yeast. No interaction between the ESCRT pathway and the V-ATPase has been reported so far. A T-DNA mutation in the ELCH gene of Arabidopsis results in multiple nuclei in a minority of epidermal cells. As multinucleated cells can be an indication for a cell division defect, trichomes, pavement cells and stomata were examined in respect to incomplete cell walls. Cell wall stubs were observed in pavement cells and stomata but not in trichomes. Similar defects have not been observed in yeast vps23 but the multinucleated phenotype of elch resembles the phenotype observed in TSG101 mutant cell lines. Furthermore cytokinesis defects are reported in Arabidopsis mutants lacking the VHA-E subunit of the V-ATPase. Plants mutant for VHA-E are embryonic lethal and display incomplete cell walls, multiple nuclei and aberrant vacuoles (Strompen et al., 2005). Although mutations in ELCH, TSG101 and VHA-E cause a similar phenotype only vague ideas exist why compromising the ESCRT pathway or the V-ATPase lead to cell division defects. A cue was provided by genetic analysis, which suggests that ELCH influences cell division by regulating microtubules. This is apparent because a double mutant with tubulin-folding cofactor a (tfc-a) shows a strong synergistic phenotype. Cell wall development during plant cell division depends heavily on a plant specific structure, the phragmoplast. The secretory system and microtubules are the main components of the phragmoplast. Therefore it seems reasonable to assume that subtle protein sorting defects, mislocalization of membranes or misregulation of microtubules can lead to the observed cell division defect.

Sorting of transmembrane proteins into the inner vesicles of multivesicular bodies for subsequent delivery to the vacuole/lysosome can be induced by attachment of a single ubiquitin or K63-linked ubiquitin chains to the cytosolic portion of the cargo in yeast and mammals. In plants, large efforts have been undertaken to elucidate the mechanisms of vacuolar trafficking of soluble proteins. Sorting of transmembrane proteins, by contrast, is still largely unexplored. As a proof of principle, that ubiquitin is involved in vacuolar sorting in plants we show that a translational fusion of a single ubiquitin to the Arabidopsis plasma membrane ATPase PMA-EGFP is sufficient to induce its endocytosis and sorting into the vacuolar lumen. Sorting of the artificial reporter is not dependent on ubiquitin chain formation, but involves ubiquitin’s hydrophobic patch and can be inhibited by coexpression of a dominant-negative version of the ESCRT (endosomal sorting complex required for transport) related protein AtSKD1 (SUPPRESSOR OF K+ TRANSPORT GROWTH DEFECT1). Our results suggest that ubiquitin can in principle act as vacuolar sorting signal in plants.

The vacuole is the most prominent organelle of plant cells. Despite its importance for many physiological and developmental aspects of plant life, little is known about its biogenesis and maintenance. Here we show that Arabidopsis plants expressing a dominant-negative version of the AAA (ATPase associated with various cellular activities) ATPase AtSKD1 (SUPPRESSOR OF K+ TRANSPORT GROWTH DEFECT1) under the control of the trichome-specific GLABRA2 (GL2) promoter exhibit normal vacuolar development in early stages of trichome development. Shortly after its formation, however, the large central vacuole is fragmented and finally disappears completely. Secretion assays with amylase fused to the vacuolar sorting signal of Sporamin show that dominant-negative AtSKD1 inhibits vacuolar trafficking of the reporter that is instead secreted. In addition, trichomes expressing dominant-negative AtSKD1 frequently contain multiple nuclei. Our results suggest that AtSKD1 contributes to vacuolar protein trafficking and thereby to the maintenance of the large central vacuole of plant cells, and might play a role in cell-cycle regulation.

In yeast, endosomal sorting of monoubiquitylated transmembrane proteins is performed by a subset of the 19 “class E vacuolar protein sorting” proteins. The core machinery consists of 11 proteins that are organised in three complexes termed ESCRT I-III (endosomal sorting complex required for transport I-III) and is conserved in eukaryotic cells. While the pathway is well understood in yeast and animals, the plant ESCRT system is largely unexplored. At least one sequence homolog for each ESCRT component can be found in the Arabidopsis genome. Generally, sequence conservation between yeast/animals and the Arabidopsis proteins is low. To understand details about participating proteins and complex organization we have performed a systematic pairwise yeast two hybrid analysis of all Arabidopsis proteins showing homology to the ESCRT core machinery. Positive interactions were validated using bimolecular fluorescence complementation. In our experiments, most putative ESCRT components exhibited interactions with other ESCRT components that could be shown to occur on endosomes suggesting that despite their low homology to their yeast and animal counterparts they represent functional components of the plant ESCRT pathway.

The vacuole is the most prominent organelle of plant cells. Despite its importance for many physiological and developmental aspects of plant life, little is known about its biogenesis and maintenance. Here we show that Arabidopsis plants expressing a dominant-negative version of the AAA (ATPase associated with various cellular activities) ATPase AtSKD1 (SUPPRESSOR OF K+ TRANSPORT GROWTH DEFECT1) under the control of the trichome-specific GLABRA2 (GL2) promoter exhibit normal vacuolar development in early stages of trichome development. Shortly after its formation, however, the large central vacuole is fragmented and finally disappears completely. Secretion assays with amylase fused to the vacuolar sorting signal of Sporamin show that dominant-negative AtSKD1 inhibits vacuolar trafficking of the reporter that is instead secreted. In addition, trichomes expressing dominant-negative AtSKD1 frequently contain multiple nuclei. Our results suggest that AtSKD1 contributes to vacuolar protein trafficking and thereby to the maintenance of the large central vacuole of plant cells, and might play a role in cell-cycle regulation.