@Article{IPB-265, author = {Nietzschmann, L. and Smolka, U. and Perino, E. H. B. and Gorzolka, K. and Stamm, G. and Marillonnet, S. and Bürstenbinder, K. and Rosahl, S. and}, title = {{The secreted PAMP-induced peptide StPIP1\_1 activates immune responses in potato}}, year = {2023}, pages = {20534}, journal = {Sci. Rep.}, doi = {10.1038/s41598-023-47648-x}, url = {https://doi.org/10.1038/s41598-023-47648-x}, volume = {13}, abstract = {Treatment of potato plants with the pathogen-associated molecular pattern Pep-13 leads to the activation of more than 1200 genes. One of these, StPIP1\_1, encodes a protein of 76 amino acids with sequence homology to PAMP-induced secreted peptides (PIPs) from Arabidopsis thaliana. Expression of StPIP1\_1 is also induced in response to infection with Phytophthora infestans, the causal agent of late blight disease. Apoplastic localization of StPIP1\_1-mCherry fusion proteins is dependent on the presence of the predicted signal peptide. A synthetic peptide corresponding to the last 13 amino acids of StPIP1\_1 elicits the expression of the StPIP1\_1 gene itself, as well as that of pathogenesis related genes. The oxidative burst induced by exogenously applied StPIP1\_1 peptide in potato leaf disks is dependent on functional StSERK3A/B, suggesting that StPIP1\_1 perception occurs via a receptor complex involving the co-receptor StSERK3A/B. Moreover, StPIP1\_1 induces expression of FRK1 in Arabidopsis in an RLK7-dependent manner. Expression of an RLK from potato with high sequence homology to AtRLK7 is induced by StPIP1\_1, by Pep-13 and in response to infection with P. infestans. These observations are consistent with the hypothesis that, upon secretion, StPIP1\_1 acts as an endogenous peptide required for amplification of the defense response.} } @Article{IPB-231, author = {Dahiya, P. and Bürstenbinder, K. and}, title = {{The making of a ring: Assembly and regulation of microtubule-associated proteins during preprophase band formation and division plane set-up}}, year = {2023}, pages = {102366}, journal = {Curr. Opin. Plant Biol.}, doi = {10.1016/j.pbi.2023.102366}, url = {https://doi.org/10.1016/j.pbi.2023.102366}, volume = {73}, abstract = {The preprophase band (PPB) is a transient cytokinetic structure that marks the future division plane at the onset of mitosis. The PPB forms a dense cortical ring of mainly microtubules, actin filaments, endoplasmic reticulum, and associated proteins that encircles the nucleus of mitotic cells. After PPB disassembly, the positional information is preserved by the cortical division zone (CDZ). The formation of the PPB and its contribution to timely CDZ set-up involves activities of functionally distinct microtubule-associated proteins (MAPs) that interact physically and genetically to support robust division plane orientation in plants. Recent studies identified two types of plant-specific MAPs as key regulators of PPB formation, the TON1 RECRUITMENT MOTIF (TRM) and IQ67 DOMAIN (IQD) families. Both families share hallmarks of disordered scaffold proteins. Interactions of IQDs and TRMs with multiple binding partners, including the microtubule severing KATANIN1, may provide a molecular framework to coordinate PPB formation, maturation, and disassembly.} } @Article{IPB-226, author = {Bürstenbinder, K. and Schwarzerová, K. and}, title = {{European Plant Cytoskeletal Club meeting: A vital platform for advancing plant cytoskeleton research}}, year = {2023}, pages = {397-399}, journal = {Cytoskeleton}, doi = {10.1002/cm.21780}, url = {https://doi.org/10.1002/cm.21780}, volume = {80}, abstract = {This contribution reports on a meeting of plant cytoskeleton scientists-the European Plant Cytoskeletal Club 2023 conference.} } @Article{IPB-222, author = {Bao, Z. and Guo, Y. and Deng, Y. and Zang, J. and Zhang, J. and Deng, Y. and Ouyang, B. and Qu, X. and Bürstenbinder, K. and Wang, P. and}, title = {{Microtubule-associated protein SlMAP70 interacts with IQ67-domain protein SlIQD21a to regulate fruit shape in tomato}}, year = {2023}, pages = {4266-4283}, journal = {Plant Cell}, doi = {10.1093/plcell/koad231}, url = {https://doi.org/10.1093/plcell/koad231}, volume = {35}, abstract = {Tomato (Solanum lycopersicum) fruit shape is related to microtubule organization and the activity of microtubule-associated proteins (MAPs). However, insights into the mechanism of fruit shape formation from a cell biology perspective remain limited. Analysis of the tissue expression profiles of different microtubule regulators revealed that functionally distinct classes of MAPs, including members of the plant-specific MICROTUBULE-ASSOCIATED PROTEIN 70 (MAP70) and IQ67 DOMAIN (IQD, also named SUN in tomato) families, are differentially expressed during fruit development. SlMAP70-1–3 and SlIQD21a are highly expressed during fruit initiation, which relates to the dramatic microtubule pattern rearrangements throughout this developmental stage of tomato fruits. Transgenic tomato lines overexpressing SlMAP70-1 or SlIQD21a produced elongated fruits with reduced cell circularity and microtubule anisotropy, while their loss-of-function mutants showed the opposite phenotype, harboring flatter fruits. Fruits were further elongated in plants coexpressing both SlMAP70-1 and SlIQD21a. We demonstrated that SlMAP70s and SlIQD21a physically interact and that the elongated fruit phenotype is likely due to microtubule stabilization induced by the SlMAP70–SlIQD21a interaction. Together, our results identify SlMAP70 proteins and SlIQD21a as important regulators of fruit elongation and demonstrate that manipulating microtubule function during early fruit development provides an effective approach to alter fruit shape.} } @INBOOK{IPB-1, author = {Klemm, S. and Buhl, J. and Möller, B. and Bürstenbinder, K. and}, title = {{Methods in Molecular Biology}}, year = {2023}, pages = {43-61}, chapter = {{Quantitative analysis of microtubule organization in leaf epidermis pavement cells}}, journal = {The Plant Cytoskeleton}, editor = {Hussey, P.J., Wang, P.}, doi = {10.1007/978-1-0716-2867-6_4}, url = {https://doi.org/10.1007/978-1-0716-2867-6_4}, volume = {2604}, abstract = {Leaf epidermis pavement cells form highly complex shapes with interlocking lobes and necks at their anticlinal walls. The microtubule cytoskeleton plays essential roles in pavement cell morphogenesis, in particular at necks. Vice versa, shape generates stress patterns that regulate microtubule organization. Genetic or pharmacological perturbations that affect pavement cell shape often affect microtubule organization. Pavement cell shape and microtubule organization are therefore closely interconnected. Here, we present commonly used approaches for the quantitative analysis of pavement cell shape characteristics and of microtubule organization. In combination with ablation experiments, these methods can be applied to investigate how different genotypes (or treatments) affect the organization and stress responsiveness of the microtubule cytoskeleton.} } @Article{IPB-2510, author = {Bao, Z. and Guo, Y. and Deng, Y. and Zang, J. and Zhang, J. and Ouyang, B. and Qu, X. and Bürstenbinder, K. and Wang, P. and}, title = {{The microtubule-associated protein SlMAP70 interacts with SlIQD21 and regulates fruit shape formation in tomato}}, year = {2022}, doi = {10.1101/2022.08.08.503161}, url = {https://doi.org/10.1101/2022.08.08.5031}, abstract = {The shape of tomato fruits is closely correlated to microtubule organization and the activity of microtubule associated proteins (MAP), but insights into the mechanism from a cell biology perspective are still largely elusive. Analysis of tissue expression profiles of different microtubule regulators revealed that functionally distinct classes of MAPs are highly expressed during fruit development. Among these, several members of the plant-specific MAP70 family are preferably expressed at the initiation stage of fruit development. Transgenic tomato lines overexpressing SlMAP70 produced elongated fruits that show reduced cell circularity and microtubule anisotropy, while SlMAP70 loss-of-function mutant showed an opposite effect with flatter fruits. Microtubule anisotropy of fruit endodermis cells exhibited dramatic rearrangement during tomato fruit development, and SlMAP70-1 is likely implicated in cortical microtubule organization and fruit elongation throughout this stage by interacting with SUN10/SlIQD21a. The expression of SlMAP70 (or co-expression of SlMAP70 and SUN10/SlIQD21a) induces microtubule stabilization and prevents its dynamic rearrangement, both activities are essential for fruit shape establishment after anthesis. Together, our results identify SlMAP70 as a novel regulator of fruit elongation, and demonstrate that manipulating microtubule stability and organization at the early fruit developmental stage has a strong impact on fruit shape.} } @Article{IPB-408, author = {Yang, B. and Stamm, G. and Bürstenbinder, K. and Voiniciuc, C. and}, title = {{Microtubule‐associated IQD9 orchestrates cellulose patterning in seed mucilage}}, year = {2022}, pages = {1096-1110}, journal = {New Phytol.}, doi = {10.1111/nph.18188}, url = {https://doi.org/10.1111/nph.18188}, volume = {235}, abstract = {Arabidopsis seeds release large capsules of mucilaginous polysaccharides, which are shaped by an intricate network of cellulosic microfibrils. Cellulose synthase complexes are guided by the microtubule cytoskeleton, but it is unclear which proteins mediate this process in the seed coat epidermis. Using reverse genetics, we identified IQ67 DOMAIN 9 (IQD9) and KINESIN LIGHT CHAIN-RELATED 1 (KLCR1) as two highly expressed genes during seed development and comprehensively characterized their roles in cell wall polysaccharide biosynthesis. Mutations in IQD9 as well as in KLCR1 lead to compact mucilage capsules with aberrant cellulose distribution, which can be rescued by transgene complementation. IQD9 physically interacts with KLCR1 and localizes to cortical MTs to maintain their organization in SCE cells. IQD9 as well as a previously identified TONNEAU1 (TON1) RECRUITING MOTIF 4 (TRM4) protein act to maintain cellulose synthase velocity. Our results demonstrate that IQD9, KLCR1 and TRM4 are MT-associated proteins that are required for seed mucilage architecture. This study provides the first direct evidence that members of the IQD, KLCR and TRM families have overlapping roles in cell wall biosynthesis. Therefore, SCE cells provide an attractive system to further decipher the complex genetic regulation of polarized cellulose deposition.} } @Article{IPB-2515, author = {Yang, B. and Stamm, G. and Bürstenbinder, K. and Voiniciuc, C. and}, title = {{Microtubule-associated IQD9 guides cellulose synthase velocity to shape seed mucilage}}, year = {2021}, journal = {bioRxiv}, doi = {10.1101/2021.12.11.472226}, url = {https://doi.org/10.1101/2021.12.11.472226}, abstract = {SummaryArabidopsis seeds release large capsules of mucilaginous polysaccharides, which are shaped by an intricate network of cellulosic microfibrils. Cellulose synthase complexes is guided by the microtubule cytoskeleton, but it is unclear which proteins mediate this process in the seed coat epidermis (SCE).Using reverse genetics, we identified IQ67 DOMAIN 9 (IQD9) and KINESIN LIGHT CHAIN-RELATED 1 (KLCR1) as two highly expressed genes during seed development and comprehensively characterized their roles for cell wall polysaccharide biosynthesis and cortical microtubule (MT) organization.Mutations in IQD9 as well as in KLCR1 lead to compact mucilage capsules with aberrant cellulose distribution, which can be rescued by transgene complementation. Double mutant analyses revealed that their closest paralogs (IQD10 and KLCR2, respectively) are not required for mucilage biosynthesis. IQD9 physically interacts with KLCR1 and localizes to cortical MTs to maintain their organization in SCE cells. Similar to the previously identified TONNEAU1 (TON1) RECRUITING MOTIF 4 (TRM4) protein, IQD9 is required to maintain the velocity of cellulose synthases.Our results demonstrate that IQD9, KLCR1 and TRM4 are MT-associated proteins that are required for seed mucilage architecture. This study provides the first direct evidence that members of the IQD, KLCR and TRM families have overlapping roles in guiding the distribution of cell wall polysaccharides. Therefore, SCE cells provide an attractive system to further decipher the complex genetic regulation of polarized cellulose deposition.} } @Article{IPB-527, author = {Zang, J. and Klemm, S. and Pain, C. and Duckney, P. and Bao, Z. and Stamm, G. and Kriechbaumer, V. and Bürstenbinder, K. and Hussey, P. J. and Wang, P. and}, title = {{A novel plant actin-microtubule bridging complex regulates cytoskeletal and ER structure at ER-PM contact sites}}, year = {2021}, pages = {1251-1260}, journal = {Curr. Biol.}, doi = {10.1016/j.cub.2020.12.009}, url = {https://doi.org/10.1016/j.cub.2020.12.009}, volume = {31}, abstract = {In plants, the cortical endoplasmic reticulum (ER) network is connected to the plasma membrane (PM) through the ER-PM contact sites (EPCSs), whose structures are maintained by EPCS resident proteins and the cytoskeleton.1-7 Strong co-alignment between EPCSs and the cytoskeleton is observed in plants,1,8 but little is known of how the cytoskeleton is maintained and regulated at the EPCS. Here, we have used a yeast-two-hybrid screen and subsequent in vivo interaction studies in plants by fluorescence resonance energy transfer (FRET)-fluorescence lifetime imaging microscopy (FLIM) analysis to identify two microtubule binding proteins, KLCR1 (kinesin-light-chain-related protein 1) and IQD2 (IQ67-domain 2), that interact with the actin binding protein NET3C and form a component of plant EPCS that mediates the link between the actin and microtubule networks. The NET3C-KLCR1-IQD2 module, acting as an actin-microtubule bridging complex, has a direct influence on ER morphology and EPCS structure. Their loss-of-function mutants, net3a/NET3C RNAi, klcr1, or iqd2, exhibit defects in pavement cell morphology, which we suggest is linked to the disorganization of both actin filaments and microtubules. In conclusion, our results reveal a novel cytoskeletal-associated complex, which is essential for the maintenance and organization of cytoskeletal structure and ER morphology at the EPCS and for normal plant cell morphogenesis.} } @Article{IPB-521, author = {Vaddepalli, P. and de Zeeuw, T. and Strauss, S. and Bürstenbinder, K. and Liao, C.-Y. and Ramalho, J. J. and Smith, R. S. and Weijers, D. and}, title = {{Auxin-dependent control of cytoskeleton and cell shape regulates division orientation in the Arabidopsis embryo}}, year = {2021}, pages = {4946-4955}, journal = {Curr. Biol.}, doi = {10.1016/j.cub.2021.09.019}, url = {https://doi.org/10.1016/j.cub.2021.09.019}, volume = {31}, abstract = {Premitotic control of cell division orientation is critical for plant development, as cell walls prevent extensive cell remodeling or migration. While many divisions are proliferative and add cells to existing tissues, some divisions are formative and generate new tissue layers or growth axes. Such formative divisions are often asymmetric in nature, producing daughters with different fates. We have previously shown that, in the Arabidopsis thaliana embryo, developmental asymmetry is correlated with geometric asymmetry, creating daughter cells of unequal volume. Such divisions are generated by division planes that deviate from a default “minimal surface area” rule. Inhibition of auxin response leads to reversal to this default, yet the mechanisms underlying division plane choice in the embryo have been unclear. Here, we show that auxin-dependent division plane control involves alterations in cell geometry, but not in cell polarity axis or nuclear position. Through transcriptome profiling, we find that auxin regulates genes controlling cell wall and cytoskeleton properties. We confirm the involvement of microtubule (MT)-binding proteins in embryo division control. Organization of both MT and actin cytoskeleton depends on auxin response, and genetically controlled MT or actin depolymerization in embryos leads to disruption of asymmetric divisions, including reversion to the default. Our work shows how auxin-dependent control of MT and actin cytoskeleton properties interacts with cell geometry to generate asymmetric divisions during the earliest steps in plant development.Graphical abstract} } @Article{IPB-425, author = {Bao, Z. and Xu, Z. and Zang, J. and Bürstenbinder, K. and Wang, P. and}, title = {{The Morphological Diversity of Plant Organs: Manipulating the Organization of Microtubules May Do the Trick}}, year = {2021}, pages = {649626}, journal = {Front Cell Dev Biol}, doi = {10.3389/fcell.2021.649626}, url = {https://doi.org/10.3389/fcell.2021.649626}, volume = {9}, } @Article{IPB-469, author = {Kumari, P. and Dahiya, P. and Livanos, P. and Zergiebel, L. and Kölling, M. and Poeschl, Y. and Stamm, G. and Hermann, A. and Abel, S. and Müller, S. and Bürstenbinder, K. and}, title = {{IQ67 DOMAIN proteins facilitate preprophase band formation and division-plane orientation}}, year = {2021}, pages = {739-747}, journal = {Nat. Plants}, doi = {10.1038/s41477-021-00923-z}, url = {https://doi.org/10.1038/s41477-021-00923-z}, volume = {7}, abstract = {Spatiotemporal control of cell division is essential for the growth and development of multicellular organisms. In plant cells, proper cell plate insertion during cytokinesis relies on the premitotic establishment of the division plane at the cell cortex. Two plant-specific cytoskeleton arrays, the preprophase band (PPB) and the phragmoplast, play important roles in division-plane orientation and cell plate formation, respectively1. Microtubule organization and dynamics and their communication with membranes at the cortex and cell plate are coordinated by multiple, mostly distinct microtubule-associated proteins2. How division-plane selection and establishment are linked, however, is still unknown. Here, we report members of the Arabidopsis IQ67 DOMAIN (IQD) family3 as microtubule-targeted proteins that localize to the PPB and phragmoplast and additionally reside at the cell plate and a polarized cortical region including the cortical division zone (CDZ). IQDs physically interact with PHRAGMOPLAST ORIENTING KINESIN (POK) proteins4,5 and PLECKSTRIN HOMOLOGY GTPase ACTIVATING (PHGAP) proteins6, which are core components of the CDZ1. The loss of IQD function impairs PPB formation and affects CDZ recruitment of POKs and PHGAPs, resulting in division-plane positioning defects. We propose that IQDs act as cellular scaffolds that facilitate PPB formation and CDZ set-up during symmetric cell division.} } @Article{IPB-2524, author = {Zang, J. and Klemm, S. and Pain, C. and Duckney, P. and Bao, Z. and Stamm, G. and Kriechbaumer, V. and Bürstenbinder, K. and Hussey, P. J. and Wang, P. and}, title = {{A Novel Plant Actin-Microtubule Bridging Complex Regulates Cytoskeletal and ER Structure at Endoplasmic Reticulum-Plasma Membrane Contact Sites (EPCS)}}, year = {2020}, journal = {SSRN Electronic Journal}, doi = {10.2139/ssrn.3581370}, url = {http://dx.doi.org/10.2139/ssrn.3581370}, abstract = {In plants, the cortical ER network is connected to the plasma membrane through the ER-PM contact sites (EPCS), whose structures are maintained by EPCS resident proteins and the cytoskeleton. Strong co-alignment between EPCS and the cytoskeleton is observed in plants, but little is known of how the cytoskeleton is maintained and regulated at the EPCS. Here we have used a yeast-two-hybrid screen and subsequent in vivo interaction studies in plants by FRET-FLIM analysis, to identify two microtubule binding proteins, KLCR1 (Kinesin Light Chain Related protein 1) and IQD2 (IQ67-Domain 2) that interact with the actin binding protein NET3C and form a component of plant EPCS, that mediates the link between the actin and microtubule networks. The NET3C-KLCR1-IQD2 module, acting as an actin-microtubule bridging complex, has a direct influence on ER morphology. Their loss of function mutants, net3a/NET3C RNAi, 0klcr1 or iqd2, exhibit defects in pavement cell morphology which we suggest is linked to the disorganization of both actin filaments and microtubules. In conclusion, our results reveal a novel cytoskeletal associated complex, which is essential for the maintenance and organization of both cytoskeletal structure and ER morphology at the EPCS, and for normal plant cell morphogenesis.} } @INBOOK{IPB-21, author = {Poeschl, Y. and Möller, B. and Müller, L. and Bürstenbinder, K. and}, year = {2020}, pages = {349-363}, chapter = {{User-friendly assessment of pavement cell shape features with PaCeQuant: Novel functions and tools}}, journal = {Methods Cell Biol.}, editor = {Charles T. Anderson, Elizabeth S. Haswell, Ram Dixit}, doi = {10.1016/bs.mcb.2020.04.010}, url = {https://doi.org/10.1016/bs.mcb.2020.04.010}, volume = {160}, abstract = {Leaf epidermis pavement cells develop complex jigsaw puzzle-like shapes in many plant species, including the model plant Arabidopsis thaliana. Due to their complex morphology, pavement cells have become a popular model system to study shape formation and coordination of growth in the context of mechanically coupled cells at the tissue level. To facilitate robust assessment and analysis of pavement cell shape characteristics in a high-throughput fashion, we have developed PaCeQuant and a collection of supplemental tools. The ImageJ-based MiToBo plugin PaCeQuant supports fully automatic segmentation of cell contours from microscopy images and the extraction of 28 shape features for each detected cell. These features now also include the Largest Empty Circle criterion as a proxy for mechanical stress. In addition, PaCeQuant provides a set of eight features for individual lobes, including the categorization as type I and type II lobes at two- and three-cell junctions, respectively. The segmentation and feature extraction results of PaCeQuant depend on the quality of input images. To allow for corrections in case of local segmentation errors, the LabelImageEditor is provided for user-friendly manual postprocessing of segmentation results. For statistical analysis and visualization, PaCeQuant is supplemented with the R package PaCeQuantAna, which provides statistical analysis functions and supports the generation of publication-ready plots in ready-to-use R workflows. In addition, we recently released the FeatureColorMapper tool which overlays feature values over cell regions for user-friendly visual exploration of selected features in a set of analyzed cells.} } @Article{IPB-699, author = {Mitra, D. and Klemm, S. and Kumari, P. and Quegwer, J. and Möller, B. and Poeschl, Y. and Pflug, P. and Stamm, G. and Abel, S. and Bürstenbinder, K. and}, title = {{Microtubule-associated protein IQ67 DOMAIN5 regulates morphogenesis of leaf pavement cells in Arabidopsis thaliana}}, year = {2019}, pages = {529-543}, journal = {J. Exp. Bot.}, doi = {10.1093/jxb/ery395}, volume = {70}, abstract = {Plant microtubules form a highly dynamic intracellular network with important roles for regulating cell division, cell proliferation and cell morphology. Its organization and dynamics are coordinated by various microtubule-associated proteins (MAPs) that integrate environmental and developmental stimuli to fine-tune and adjust cytoskeletal arrays. IQ67 DOMAIN (IQD) proteins recently emerged as a class of plant-specific MAPs with largely unknown functions. Here, using a reverse genetics approach, we characterize Arabidopsis IQD5 in terms of its expression domains, subcellular localization and biological functions. We show that IQD5 is expressed mostly in vegetative tissues, where it localizes to cortical microtubule arrays. Our phenotypic analysis of iqd5 loss-of-function lines reveals functions of IQD5 in pavement cell (PC) shape morphogenesis. Histochemical analysis of cell wall composition further suggests reduced rates of cellulose deposition in anticlinal cell walls, which correlate with reduced anisotropic expansion. Lastly, we demonstrate IQD5-dependent recruitment of calmodulin calcium sensors to cortical microtubule arrays and provide first evidence for important roles of calcium in regulation of PC morphogenesis. Our work thus identifies IQD5 as a novel player in PC shape regulation, and, for the first time, links calcium signaling to developmental processes that regulate anisotropic growth in PCs.} } @Article{IPB-686, author = {Kölling, M. and Kumari, P. and Bürstenbinder, K. and}, title = {{Calcium- and calmodulin-regulated microtubule-associated proteins as signal-integration hubs at the plasma membrane–cytoskeleton nexus}}, year = {2019}, pages = {387-396}, journal = {J. Exp. Bot.}, doi = {10.1093/jxb/ery397}, volume = {70}, abstract = {Plant growth and development are a genetically predetermined series of events but can change dramatically in response to environmental stimuli, involving perpetual pattern formation and reprogramming of development. The rate of growth is determined by cell division and subsequent cell expansion, which are restricted and controlled by the cell wall–plasma membrane–cytoskeleton continuum, and are coordinated by intricate networks that facilitate intra- and intercellular communication. An essential role in cellular signaling is played by calcium ions, which act as universal second messengers that transduce, integrate, and multiply incoming signals during numerous plant growth processes, in part by regulation of the microtubule cytoskeleton. In this review, we highlight recent advances in the understanding of calcium-mediated regulation of microtubule-associated proteins, their function at the microtubule cytoskeleton, and their potential role as hubs in crosstalk with other signaling pathways.} } @Article{IPB-702, author = {Naumann, C. and Müller, J. and Sakhonwasee, S. and Wieghaus, A. and Hause, G. and Heisters, M. and Bürstenbinder, K. and Abel, S. and}, title = {{The Local Phosphate Deficiency Response Activates Endoplasmic Reticulum Stress-Dependent Autophagy}}, year = {2019}, pages = {460-476}, journal = {Plant Physiol.}, doi = {10.1104/pp.18.01379}, volume = {179}, abstract = {Inorganic phosphate (Pi) is often a limiting plant nutrient. In members of the Brassicaceae family, such as Arabidopsis (Arabidopsis thaliana), Pi deprivation reshapes root system architecture to favor topsoil foraging. It does so by inhibiting primary root extension and stimulating lateral root formation. Root growth inhibition from phosphate (Pi) deficiency is triggered by iron-stimulated, apoplastic reactive oxygen species generation and cell wall modifications, which impair cell-to-cell communication and meristem maintenance. These processes require LOW PHOSPHATE RESPONSE1 (LPR1), a cell wall-targeted ferroxidase, and PHOSPHATE DEFICIENCY RESPONSE2 (PDR2), the single endoplasmic reticulum (ER)-resident P5-type ATPase (AtP5A), which is thought to control LPR1 secretion or activity. Autophagy is a conserved process involving the vacuolar degradation of cellular components. While the function of autophagy is well established under nutrient starvation (C, N, or S), it remains to be explored under Pi deprivation. Because AtP5A/PDR2 likely functions in the ER stress response, we analyzed the effect of Pi limitation on autophagy. Our comparative study of mutants defective in the local Pi deficiency response, ER stress response, and autophagy demonstrated that ER stress-dependent autophagy is rapidly activated as part of the developmental root response to Pi limitation and requires the genetic PDR2-LPR1 module. We conclude that Pi-dependent activation of autophagy in the root apex is a consequence of local Pi sensing and the associated ER stress response, rather than a means for systemic recycling of the macronutrient.} } @INBOOK{IPB-31, author = {Möller, B. and Bürstenbinder, K. and}, title = {{2019 IEEE 16th International Symposium on Biomedical Imaging (ISBI 2019)}}, year = {2019}, pages = {199-203}, chapter = {{Semi-Automatic Cell Segmentation from Noisy Image Data for Quantification of Microtubule Organization on Single Cell Level}}, doi = {10.1109/ISBI.2019.8759145}, abstract = {The structure of the microtubule cytoskeleton provides valuable information related to morphogenesis of cells. The cytoskeleton organizes into diverse patterns that vary in cells of different types and tissues, but also within a single tissue. To assess differences in cytoskeleton organization methods are needed that quantify cytoskeleton patterns within a complete cell and which are suitable for large data sets. A major bottleneck in most approaches, however, is a lack of techniques for automatic extraction of cell contours. Here, we present a semi-automatic pipeline for cell segmentation and quantification of microtubule organization. Automatic methods are applied to extract major parts of the contours and a handy image editor is provided to manually add missing information efficiently. Experimental results prove that our approach yields high-quality contour data with minimal user intervention and serves a suitable basis for subsequent quantitative studies.} } @INBOOK{IPB-30, author = {Möller, B. and Zergiebel, L. and Bürstenbinder, K. and}, title = {{Plant Cell Morphogenesis}}, year = {2019}, pages = {151-171}, chapter = {{Quantitative and Comparative Analysis of Global Patterns of (Microtubule) Cytoskeleton Organization with CytoskeletonAnalyzer2D}}, journal = {Methods Mol. Biol.}, editor = {Cvrčková, F. \& Žárský, V., eds.}, doi = {10.1007/978-1-4939-9469-4_10}, volume = {1992}, abstract = {The microtubule cytoskeleton plays important roles in cell morphogenesis. To investigate the mechanisms of cytoskeletal organization, for example, during growth or development, in genetic studies, or in response to environmental stimuli, image analysis tools for quantitative assessment are needed. Here, we present a method for texture measure-based quantification and comparative analysis of global microtubule cytoskeleton patterns and subsequent visualization of output data. In contrast to other approaches that focus on the extraction of individual cytoskeletal fibers and analysis of their orientation relative to the growth axis, CytoskeletonAnalyzer2D quantifies cytoskeletal organization based on the analysis of local binary patterns. CytoskeletonAnalyzer2D thus is particularly well suited to study cytoskeletal organization in cells where individual fibers are difficult to extract or which lack a clearly defined growth axis, such as leaf epidermal pavement cells. The tool is available as ImageJ plugin and can be combined with publicly available software and tools, such as R and Cytoscape, to visualize similarity networks of cytoskeletal patterns.} } @INBOOK{IPB-29, author = {Möller, B. and Poeschl, Y. and Klemm, S. and Bürstenbinder, K. and}, title = {{Plant Cell Morphogenesis}}, year = {2019}, pages = {329-349}, chapter = {{Morphological Analysis of Leaf Epidermis Pavement Cells with PaCeQuant}}, journal = {Methods Mol. Biol.}, editor = {Cvrčková, F. \& Žárský, V., eds.}, doi = {10.1007/978-1-4939-9469-4_22}, volume = {1992}, abstract = {Morphological analysis of cell shapes requires segmentation of cell contours from input images and subsequent extraction of meaningful shape descriptors that provide the basis for qualitative and quantitative assessment of shape characteristics. Here, we describe the publicly available ImageJ plugin PaCeQuant and its associated R package PaCeQuantAna, which provides a pipeline for fully automatic segmentation, feature extraction, statistical analysis, and graphical visualization of cell shape properties. PaCeQuant is specifically well suited for analysis of jigsaw puzzle-like leaf epidermis pavement cells from 2D input images and supports the quantification of global, contour-based, skeleton-based, and pavement cell-specific shape descriptors.} } @Article{IPB-2532, author = {Mitra, D. and Kumari, P. and Quegwer, J. and Klemm, S. and Möller, B. and Poeschl, Y. and Pflug, P. and Stamm, G. and Abel, S. and Bürstenbinder, K. and}, title = {{Microtubule-associated protein IQ67 DOMAIN5 regulates interdigitation of leaf pavement cells in Arabidopsis thaliana}}, year = {2018}, journal = {bioRxiv}, doi = {10.1101/268466}, abstract = {Plant microtubules form a highly dynamic intracellular network with important roles for regulating cell division, cell proliferation and cell morphology. Its organization and dynamics are coordinated by various microtubule-associated proteins (MAPs) that integrate environmental and developmental stimuli to fine-tune and adjust cytoskeletal arrays. IQ67 DOMAIN (IQD) proteins recently emerged as a class of plant-specific MAPs with largely unknown functions. Here, using a reverse genetics approach, we characterize Arabidopsis IQD5 in terms of its expression domains, subcellular localization and biological functions. We show that IQD5 is expressed mostly in vegetative tissues, where it localizes to cortical microtubule arrays. Our phenotypic analysis of iqd5 loss-of-function lines reveals functions of IQD5 in pavement cell (PC) shape morphogenesis, as indicated by reduced interdigitation of neighboring cells in the leaf epidermis of iqd5 mutants. Histochemical analysis of cell wall composition further suggests reduced rates of cellulose deposition in anticlinal cell walls, which correlate with reduced asymmetric expansion. Lastly, we provide evidence for IQD5-dependent recruitment of calmodulin calcium sensors to cortical microtubule arrays. Our work thus identifies IQD5 as a novel player in PC shape regulation, and, for the first time, links calcium signaling to developmental processes that regulate multi-polar growth in PCs.} } @Article{IPB-793, author = {Ibañez, C. and Delker, C. and Martinez, C. and Bürstenbinder, K. and Janitza, P. and Lippmann, R. and Ludwig, W. and Sun, H. and James, G. V. and Klecker, M. and Grossjohann, A. and Schneeberger, K. and Prat, S. and Quint, M. and}, title = {{Brassinosteroids Dominate Hormonal Regulation of Plant Thermomorphogenesis via BZR1}}, year = {2018}, pages = {303-310.e3}, journal = {Curr. Biol.}, doi = {10.1016/j.cub.2017.11.077}, volume = {28}, abstract = {Thermomorphogenesis is defined as the suite of morphological changes that together are likely to contribute to adaptive growth acclimation to usually elevated ambient temperature [1, 2]. While many details of warmth-induced signal transduction are still elusive, parallels to light signaling recently became obvious (reviewed in [3]). It involves photoreceptors that can also sense changes in ambient temperature [3, 4, 5] and act, for example, by repressing protein activity of the central integrator of temperature information PHYTOCHROME-INTERACTING FACTOR 4 (PIF4 [6]). In addition, PIF4 transcript accumulation is tightly controlled by the evening complex member EARLY FLOWERING 3 [7, 8]. According to the current understanding, PIF4 activates growth-promoting genes directly but also via inducing auxin biosynthesis and signaling, resulting in cell elongation. Based on a mutagenesis screen in the model plant Arabidopsis thaliana for mutants with defects in temperature-induced hypocotyl elongation, we show here that both PIF4 and auxin function depend on brassinosteroids. Genetic and pharmacological analyses place brassinosteroids downstream of PIF4 and auxin. We found that brassinosteroids act via the transcription factor BRASSINAZOLE RESISTANT 1 (BZR1), which accumulates in the nucleus at high temperature, where it induces expression of growth-promoting genes. Furthermore, we show that at elevated temperature BZR1 binds to the promoter of PIF4, inducing its expression. These findings suggest that BZR1 functions in an amplifying feedforward loop involved in PIF4 activation. Although numerous negative regulators of PIF4 have been described, we identify BZR1 here as a true temperature-dependent positive regulator of PIF4, acting as a major growth coordinator.} } @Article{IPB-784, author = {Gantner, J. and Ordon, J. and Ilse, T. and Kretschmer, C. and Gruetzner, R. and Löfke, C. and Dagdas, Y. and Bürstenbinder, K. and Marillonnet, S. and Stuttmann, J. and}, title = {{Peripheral infrastructure vectors and an extended set of plant parts for the Modular Cloning system}}, year = {2018}, pages = {e0197185}, journal = {PLOS ONE}, doi = {10.1371/journal.pone.0197185}, volume = {13}, abstract = {Standardized DNA assembly strategies facilitate the generation of multigene constructs from collections of building blocks in plant synthetic biology. A common syntax for hierarchical DNA assembly following the Golden Gate principle employing Type IIs restriction endonucleases was recently developed, and underlies the Modular Cloning and GoldenBraid systems. In these systems, transcriptional units and/or multigene constructs are assembled from libraries of standardized building blocks, also referred to as phytobricks, in several hierarchical levels and by iterative Golden Gate reactions. Here, a toolkit containing further modules for the novel DNA assembly standards was developed. Intended for use with Modular Cloning, most modules are also compatible with GoldenBraid. Firstly, a collection of approximately 80 additional phytobricks is provided, comprising e.g. modules for inducible expression systems, promoters or epitope tags. Furthermore, DNA modules were developed for connecting Modular Cloning and Gateway cloning, either for toggling between systems or for standardized Gateway destination vector assembly. Finally, first instances of a “peripheral infrastructure” around Modular Cloning are presented: While available toolkits are designed for the assembly of plant transformation constructs, vectors were created to also use coding sequence-containing phytobricks directly in yeast two hybrid interaction or bacterial infection assays. The presented material will further enhance versatility of hierarchical DNA assembly strategies.} } @Article{IPB-868, author = {Bürstenbinder, K. and Möller, B. and Plötner, R. and Stamm, G. and Hause, G. and Mitra, D. and Abel, S. and}, title = {{The IQD Family of Calmodulin-Binding Proteins Links Calcium Signaling to Microtubules, Membrane Subdomains, and the Nucleus}}, year = {2017}, pages = {1692-1708}, journal = {Plant Physiol.}, doi = {10.1104/pp.16.01743}, volume = {173}, abstract = {Calcium (Ca2\+) signaling and dynamic reorganization of the cytoskeleton are essential processes for the coordination and control of plant cell shape and cell growth. Calmodulin (CaM) and closely related calmodulin-like (CML) polypeptides are principal sensors of Ca2\+ signals. CaM/CMLs decode and relay information encrypted by the second messenger via differential interactions with a wide spectrum of targets to modulate their diverse biochemical activities. The plant-specific IQ67 DOMAIN (IQD) family emerged as possibly the largest class of CaM-interacting proteins with undefined molecular functions and biological roles. Here, we show that the 33 members of the IQD family in Arabidopsis (Arabidopsis thaliana) differentially localize, using green fluorescent protein (GFP)-tagged proteins, to multiple and distinct subcellular sites, including microtubule (MT) arrays, plasma membrane subdomains, and nuclear compartments. Intriguingly, the various IQD-specific localization patterns coincide with the subcellular patterns of IQD-dependent recruitment of CaM, suggesting that the diverse IQD members sequester Ca2\+-CaM signaling modules to specific subcellular sites for precise regulation of Ca2\+-dependent processes. Because MT localization is a hallmark of most IQD family members, we quantitatively analyzed GFP-labeled MT arrays in Nicotiana benthamiana cells transiently expressing GFP-IQD fusions and observed IQD-specific MT patterns, which point to a role of IQDs in MT organization and dynamics. Indeed, stable overexpression of select IQD proteins in Arabidopsis altered cellular MT orientation, cell shape, and organ morphology. Because IQDs share biochemical properties with scaffold proteins, we propose that IQD families provide an assortment of platform proteins for integrating CaM-dependent Ca2\+ signaling at multiple cellular sites to regulate cell function, shape, and growth.} } @Article{IPB-867, author = {Bürstenbinder, K. and Mitra, D. and Quegwer, J. and}, title = {{Functions of IQD proteins as hubs in cellular calcium and auxin signaling: A toolbox for shape formation and tissue-specification in plants?}}, year = {2017}, pages = {e1331198}, journal = {Plant Signal Behav.}, doi = {10.1080/15592324.2017.1331198}, volume = {12}, abstract = {Calcium (Ca2\+) ions play pivotal roles as second messengers in intracellular signal transduction, and coordinate many biological processes. Changes in intracellular Ca2\+ levels are perceived by Ca2\+ sensors such as calmodulin (CaM) and CaM-like (CML) proteins, which transduce Ca2\+ signals into cellular responses by regulation of diverse target proteins. Insights into molecular functions of CaM targets are thus essential to understand the molecular and cellular basis of Ca2\+ signaling. During the last decade, IQ67-domain (IQD) proteins emerged as the largest class of CaM targets in plants with mostly unknown functions. In the March issue of Plant Physiology, we presented the first comprehensive characterization of the 33-membered IQD family in Arabidopsis thaliana. We showed, by analysis of the subcellular localization of translational green fluorescent protein (GFP) fusion proteins, that most IQD members label microtubules (MTs), and additionally often localize to the cell nucleus or to membranes, where they recruit CaM Ca2\+ sensors. Important functions at MTs are supported by altered MT organization and plant growth in IQD gain-of-function lines. Because IQD proteins share structural hallmarks of scaffold proteins, we propose roles of IQDs in the assembly of macromolecular complexes to orchestrate Ca2\+ CaM signaling from membranes to the nucleus. Interestingly, expression of several IQDs is regulated by auxin, which suggests functions of IQDs as hubs in cellular auxin and calcium signaling to regulate plant growth and development.} } @Article{IPB-914, author = {Möller, B. and Poeschl, Y. and Plötner, R. and Bürstenbinder, K. and}, title = {{PaCeQuant: A Tool for High-Throughput Quantification of Pavement Cell Shape Characteristics}}, year = {2017}, pages = {998-1017}, journal = {Plant Physiol.}, doi = {10.1104/pp.17.00961}, volume = {175}, abstract = {Pavement cells (PCs) are the most frequently occurring cell type in the leaf epidermis and play important roles in leaf growth and function. In many plant species, PCs form highly complex jigsaw-puzzle-shaped cells with interlocking lobes. Understanding of their development is of high interest for plant science research because of their importance for leaf growth and hence for plant fitness and crop yield. Studies of PC development, however, are limited, because robust methods are lacking that enable automatic segmentation and quantification of PC shape parameters suitable to reflect their cellular complexity. Here, we present our new ImageJ-based tool, PaCeQuant, which provides a fully automatic image analysis workflow for PC shape quantification. PaCeQuant automatically detects cell boundaries of PCs from confocal input images and enables manual correction of automatic segmentation results or direct import of manually segmented cells. PaCeQuant simultaneously extracts 27 shape features that include global, contour-based, skeleton-based, and PC-specific object descriptors. In addition, we included a method for classification and analysis of lobes at two-cell junctions and three-cell junctions, respectively. We provide an R script for graphical visualization and statistical analysis. We validated PaCeQuant by extensive comparative analysis to manual segmentation and existing quantification tools and demonstrated its usability to analyze PC shape characteristics during development and between different genotypes. PaCeQuant thus provides a platform for robust, efficient, and reproducible quantitative analysis of PC shape characteristics that can easily be applied to study PC development in large data sets.} } @Article{IPB-1136, author = {Müller, J. and Toev, T. and Heisters, M. and Teller, J. and Moore, K. and Hause, G. and Dinesh, D. and Bürstenbinder, K. and Abel, S. and}, title = {{Iron-Dependent Callose Deposition Adjusts Root Meristem Maintenance to Phosphate Availability}}, year = {2015}, pages = {216-230}, journal = {Dev. Cell}, doi = {10.1016/j.devcel.2015.02.007}, volume = {33}, abstract = {Plant root development is informed by numerous edaphic cues. Phosphate (Pi) availability impacts the root system architecture by adjusting meristem activity. However, the sensory mechanisms monitoring external Pi status are elusive. Two functionally interacting Arabidopsis genes, LPR1 (ferroxidase) and PDR2 (P5-type ATPase), are key players in root Pi sensing, which is modified by iron (Fe) availability. We show that the LPR1-PDR2 module facilitates, upon Pi limitation, cell-specific apoplastic Fe and callose deposition in the meristem and elongation zone of primary roots. Expression of cell-wall-targeted LPR1 determines the sites of Fe accumulation as well as callose production, which interferes with symplastic communication in the stem cell niche, as demonstrated by impaired SHORT-ROOT movement. Antagonistic interactions of Pi and Fe availability control primary root growth via meristem-specific callose formation, likely triggered by LPR1-dependent redox signaling. Our results link callose-regulated cell-to-cell signaling in root meristems to the perception of an abiotic cue.} } @Article{IPB-1281, author = {Ziegler, J. and Qwegwer, J. and Schubert, M. and Erickson, J. L. and Schattat, M. and Bürstenbinder, K. and Grubb, C. D. and Abel, S. and}, title = {{Simultaneous analysis of apolar phytohormones and 1-aminocyclopropan-1-carboxylic acid by high performance liquid chromatography/electrospray negative ion tandem mass spectrometry via 9-fluorenylmethoxycarbonyl chloride derivatization}}, year = {2014}, pages = {102-109}, journal = {J. Chromatogr. A}, doi = {10.1016/j.chroma.2014.08.029}, volume = {1362}, abstract = {A strategy to detect and quantify the polar ethylene precursor 1-aminocyclopropan-1-carboxylic acid (ACC) along with the more apolar phytohormones abscisic acid (ABA), indole-3-acetic acid (IAA), jasmonic acid (JA), jasmonic acid-isoleucine conjugate (JA-Ile), 12-oxo-phytodienoic acid (OPDA), trans-zeatin, and trans-zeatin 9-riboside using a single extraction is presented. Solid phase resins commonly employed for extraction of phytohormones do not allow the recovery of ACC. We circumvent this problem by attaching an apolar group to ACC via derivatization with the amino group specific reagent 9-fluorenylmethoxycarbonyl chloride (Fmoc-Cl). Derivatization in the methanolic crude extract does not modify other phytohormones. The derivatized ACC could be purified and detected together with the more apolar phytohormones using common solid phase extraction resins and reverse phase HPLC/electrospray negative ion tandem mass spectrometry. The limit of detection was in the low nanomolar range for all phytohormones, a sensitivity sufficient to accurately determine the phytohormone levels from less than 50 mg (fresh weight) of Arabidopsis thaliana and Nicotiana benthamiana tissues. Comparison with previously published phytohormone levels and the reported changes in phytohormone levels after stress treatments confirmed the accuracy of the method.} } @Article{IPB-1295, author = {Bürstenbinder, K. and Savchenko, T. and Müller, J. and Adamson, A. W. and Stamm, G. and Kwong, R. and Zipp, B. J. and Dinesh, D. C. and Abel, S. and}, title = {{Arabidopsis Calmodulin-binding Protein IQ67-Domain 1 Localizes to Microtubules and Interacts with Kinesin Light Chain-related Protein-1}}, year = {2013}, pages = {1871-1882}, journal = {J. Biol. Chem.}, doi = {10.1074/jbc.M112.396200}, volume = {288}, abstract = {Calcium (Ca2\+) is a key second messenger in eukaryotes and regulates diverse cellular processes, most notably via calmodulin (CaM). In Arabidopsis thaliana, IQD1 (IQ67 domain 1) is the founding member of the IQD family of putative CaM targets. The 33 predicted IQD proteins share a conserved domain of 67 amino acids that is characterized by a unique arrangement of multiple CaM recruitment motifs, including so-called IQ motifs. Whereas IQD1 has been implicated in the regulation of defense metabolism, the biochemical functions of IQD proteins remain to be elucidated. In this study we show that IQD1 binds to multiple Arabidopsis CaM and CaM-like (CML) proteins in vitro and in yeast two-hybrid interaction assays. CaM overlay assays revealed moderate affinity of IQD1 to CaM2 (Kd ∼ 0.6 μm). Deletion mapping of IQD1 demonstrated the importance of the IQ67 domain for CaM2 binding in vitro, which is corroborated by interaction of the shortest IQD member, IQD20, with Arabidopsis CaM/CMLs in yeast. A genetic screen of a cDNA library identified Arabidopsis kinesin light chain-related protein-1 (KLCR1) as an IQD1 interactor. The subcellular localization of GFP-tagged IQD1 proteins to microtubules and the cell nucleus in transiently and stably transformed plant tissues (tobacco leaves and Arabidopsis seedlings) suggests direct interaction of IQD1 and KLCR1 in planta that is supported by GFP∼IQD1-dependent recruitment of RFP∼KLCR1 and RFP∼CaM2 to microtubules. Collectively, the prospect arises that IQD1 and related proteins provide Ca2\+/CaM-regulated scaffolds for facilitating cellular transport of specific cargo along microtubular tracks via kinesin motor proteins.} } @Article{IPB-1284, author = {Abel, S. and Bürstenbinder, K. and Müller, J. and}, title = {{The emerging function of IQD proteins as scaffolds in cellular signaling and trafficking}}, year = {2013}, pages = {e24369}, journal = {Plant Signal Behav.}, doi = {10.4161/psb.24369}, volume = {8}, abstract = {Calcium (Ca2+) signaling modules are essential for adjusting plant growth and performance to environmental constraints. Differential interactions between sensors of Ca2+ dynamics and their molecular targets are at the center of the transduction process. Calmodulin (CaM) and CaM-like (CML) proteins are principal Ca2+-sensors in plants that govern the activities of numerous downstream proteins with regulatory properties. The families of IQ67-Domain (IQD) proteins are a large class of plant-specific CaM/CML-targets (e.g., 33 members in A. thaliana) which share a unique domain of multiple varied CaM retention motifs in tandem orientation. Genetic studies in Arabidopsis and tomato revealed first roles for IQD proteins related to basal defense response and plant development. Molecular, biochemical and histochemical analysis of Arabidopsis IQD1 demonstrated association with microtubules as well as targeting to the cell nucleus and nucleolus. In vivo binding to CaM and kinesin light chain-related protein-1 (KLCR1) suggests a Ca2+-regulated scaffolding function of IQD1 in kinesin motor-dependent transport of multiprotein complexes. Furthermore, because IQD1 interacts in vitro with single-stranded nucleic acids, the prospect arises that IQD1 and other IQD family members facilitate cellular RNA localization as one mechanism to control and fine-tune gene expression and protein sorting.} }