@article{madison_tahir_broeck_phan_horn_sozzani_2024, title={Cell-material interactions in 3D bioprinted plant cells}, url={https://doi.org/10.1101/2024.01.30.578043}, DOI={10.1101/2024.01.30.578043}, abstractNote={Abstract3D bioprinting is an additive manufacturing technology with promise towards facilitating tissue engineering and single-cell investigations of cellular development and microenvironment responses. 3D bioprinting is still a new technology in the field of plant biology so its optimization with plant cells is still widely needed. Here, we present a study in which 3D bioprinting parameters, such as needle gauge, extrusion pressure, and scaffold type, were all tested in 3D bioprinted Tobacco BY-2 cells to evaluate how cell viability is responsive to each parameter. As a result, this study revealed an optimal range of extrusion pressures and needle gauges that resulted in an optimum cell viability. Furthermore, this study applied the identified optimal 3D bioprinting parameters to a different cell line,Arabidopsisroot protoplasts, and stress condition, phosphate starvation, to confirm that the identified parameters were optimal in a different species, cell type, and cellular microenvironment. This suggested that phosphate-starved bioprintedArabidopsiscells were less viable by 7 days, which was consistent with whole root phosphate starvation responses. As a result, the 3D bioprinter optimization yielded optimal cell viabilities in both BY-2 and Arabidopsis cells and facilitated an applied investigation into phosphate starvation stress.}, author={Madison, Imani and Tahir, Maimouna and Broeck, Lisa Van and Phan, Linh and Horn, Timothy and Sozzani, Rosangela}, year={2024}, month={Feb} }
 @article{morffy_broeck_miller_emenecker_bryant_lee_sageman-furnas_wilkinson_pathak_kotha_et al._2024, title={Identification of plant transcriptional activation domains}, url={https://doi.org/10.1038/s41586-024-07707-3}, DOI={10.1038/s41586-024-07707-3}, journal={Nature}, author={Morffy, Nicholas and Broeck, Lisa Van and Miller, Caelan and Emenecker, Ryan J. and Bryant, John A., Jr. and Lee, Tyler M. and Sageman-Furnas, Katelyn and Wilkinson, Edward G. and Pathak, Sunita and Kotha, Sanjana R. and et al.}, year={2024}, month={Aug} }
 @article{perez-sancho_broeck_garcia-caparros_sozzani_2024, title={Insights into multilevel spatial regulation within the root stem cell niche}, volume={86}, ISSN={["1879-0380"]}, url={https://doi.org/10.1016/j.gde.2024.102200}, DOI={10.1016/j.gde.2024.102200}, abstractNote={All differentiated root cells derive from stem cells spatially organized within the stem cell niche (SCN), a microenvironment located within the root tip. Here, we compiled recent advances in the understanding of how the SCN drives the establishment and maintenance of cell types. The quiescent center (QC) is widely recognized as the primary driver of cell fate determination, but it is recently considered a convergence center of multiple signals. Cell identity of the cortex endodermis initials is mainly driven by the regulatory feedback loops between transcription factors (TFs), acting as mobile signals between neighboring cells, including the QC. As exemplified in the vascular initials, the precise spatial expression of these regulatory TFs is connected with a dynamic hormonal interplay. Thus, stem cell maintenance and cell differentiation are regulated by a plethora of signals forming a complex, multilevel regulatory network. Integrating the transcriptional and post-translational regulations, protein–protein interactions, and mobile signals into models will be fundamental for the comprehensive understanding of SCN maintenance and differentiation.}, journal={CURRENT OPINION IN GENETICS & DEVELOPMENT}, author={Perez-Sancho, Jessica and Broeck, Lisa and Garcia-Caparros, Pedro and Sozzani, Rosangela}, year={2024}, month={Jun} }
 @inbook{madison_amin_song_sozzani_broeck_2023, title={A Data-Driven Signaling Network Inference Approach for Phosphoproteomics}, url={http://dx.doi.org/10.1007/978-1-0716-3327-4_27}, DOI={10.1007/978-1-0716-3327-4_27}, abstractNote={Proteins are rapidly and dynamically post-transcriptionally modified as cells respond to changes in their environment. For example, protein phosphorylation is mediated by kinases while dephosphorylation is mediated by phosphatases. Quantifying and predicting interactions between kinases, phosphatases, and target proteins over time will aid the study of signaling cascades under a variety of environmental conditions. Here, we describe methods to statistically analyze label-free phosphoproteomic data and infer posttranscriptional regulatory networks over time. We provide an R-based method that can be used to normalize and analyze label-free phosphoproteomic data using variance stabilizing normalization and a linear mixed model across multiple time points and conditions. We also provide a method to infer regulator-target interactions over time using a discretization scheme followed by dynamic Bayesian modeling computations to validate our conclusions. Overall, this pipeline is designed to perform functional analyses and predictions of phosphoproteomic signaling cascades.}, booktitle={Methods in Molecular Biology}, author={Madison, Imani and Amin, Fin and Song, Kuncheng and Sozzani, Rosangela and Broeck, Lisa Van}, year={2023} }
 @article{van den broeck_bhosale_song_fonseca de lima_ashley_zhu_zhu_van de cotte_neyt_ortiz_et al._2023, title={Functional annotation of proteins for signaling network inference in non-model species}, volume={14}, ISSN={2041-1723}, url={http://dx.doi.org/10.1038/s41467-023-40365-z}, DOI={10.1038/s41467-023-40365-z}, abstractNote={AbstractMolecular biology aims to understand cellular responses and regulatory dynamics in complex biological systems. However, these studies remain challenging in non-model species due to poor functional annotation of regulatory proteins. To overcome this limitation, we develop a multi-layer neural network that determines protein functionality directly from the protein sequence. We annotate kinases and phosphatases in Glycine max. We use the functional annotations from our neural network, Bayesian inference principles, and high resolution phosphoproteomics to infer phosphorylation signaling cascades in soybean exposed to cold, and identify Glyma.10G173000 (TOI5) and Glyma.19G007300 (TOT3) as key temperature regulators. Importantly, the signaling cascade inference does not rely upon known kinase motifs or interaction data, enabling de novo identification of kinase-substrate interactions. Conclusively, our neural network shows generalization and scalability, as such we extend our predictions to Oryza sativa, Zea mays, Sorghum bicolor, and Triticum aestivum. Taken together, we develop a signaling inference approach for non-model species leveraging our predicted kinases and phosphatases.}, number={1}, journal={Nature Communications}, publisher={Springer Science and Business Media LLC}, author={Van den Broeck, Lisa and Bhosale, Dinesh Kiran and Song, Kuncheng and Fonseca de Lima, Cássio Flavio and Ashley, Michael and Zhu, Tingting and Zhu, Shanshuo and Van De Cotte, Brigitte and Neyt, Pia and Ortiz, Anna C. and et al.}, year={2023}, month={Aug} }
 @misc{amin_van den broeck_de smet_locke_sozzani_2023, title={Optimal Brain Dissection in Dense Autoencoders: Towards Determining Feature Importance in -Omics Data}, url={http://dx.doi.org/10.1109/bip60195.2023.10379275}, DOI={10.1109/BIP60195.2023.10379275}, abstractNote={Recently, there has been increased interest in ma-chine learning explainability. Understanding the complex relationship between input features of a model and their respective outputs is of increased relevance, especially in biological science. In this paper, we introduce Optimal Brain Dissection (OBD), an innovative methodology designed to examine the importance of first-layer connections in a biology-inspired autoencoder. We incorporated regulator-target interactions within the first autoencoder layer, representing biological regulatory networks, and identified their importance to the reconstruction error, a critical aspect in navigating the complexity of high-dimensional omics data. Through a combination of pruning techniques and counterfactual reasoning, OBD offers a method to quantify feature importance, factoring in both weight magnitude and time-to-laziness. To implement this method, we propose a Dense Autoencoder (DAE) architecture, aiming for increased efficiency and reduced computation. Tailored for omics data, the DAE employs skip concatenations and circumvents non-existent target-target interactions. Our approach aims to understand the relative importance of connections for autoencoder performance, a critical step towards better counter-factual reasoning for neural networks.}, journal={2023 IEEE 5th International Conference on BioInspired Processing (BIP)}, publisher={IEEE}, author={Amin, Fin and Van den Broeck, Lisa and De Smet, Ive and Locke, Anna M. and Sozzani, Rossangela}, year={2023}, month={Nov} }
 @article{madison_gillan_peace_gabrieli_broeck_jones_sozzani_2023, title={Phosphate starvation: response mechanisms and solutions}, volume={8}, ISSN={["1460-2431"]}, url={https://doi.org/10.1093/jxb/erad326}, DOI={10.1093/jxb/erad326}, abstractNote={Abstract
               Phosphorus is essential to plant growth and agricultural crop yields, yet the challenges associated with phosphorus fertilization in agriculture, such as aquatic runoff pollution and poor phosphorus bioavailability, are increasingly difficult to manage. Comprehensively understanding the dynamics of phosphorus uptake and signaling mechanisms will inform the development of strategies to address these issues. This review describes regulatory mechanisms used by specific tissues in the root apical meristem to sense and take up phosphate from the rhizosphere. The major regulatory mechanisms and related hormone crosstalk underpinning phosphate starvation responses, cellular phosphate homeostasis, and plant adaptations to phosphate starvation are also discussed, along with an overview of the major mechanism of plant systemic phosphate starvation responses. Finally, this review discusses recent promising genetic engineering strategies for improving crop phosphorus use and computational approaches that may help further design strategies for improved plant phosphate acquisition. The mechanisms and approaches presented include a wide variety of species including not only Arabidopsis but also crop species such as Oryza sativa (rice), Glycine max (soybean), and Triticum aestivum (wheat) to address both general and species-specific mechanisms and strategies. The aspects of phosphorus deficiency responses and recently employed strategies of improving phosphate acquisition that are detailed in this review may provide insights into the mechanisms or phenotypes that may be targeted in efforts to improve crop phosphorus content and plant growth in low phosphorus soils.}, journal={JOURNAL OF EXPERIMENTAL BOTANY}, author={Madison, Imani and Gillan, Lydia and Peace, Jasmine and Gabrieli, Flavio and Broeck, Lisa and Jones, Jacob L. and Sozzani, Rosangela}, editor={Ort, DonaldEditor}, year={2023}, month={Aug} }
 @inproceedings{mahatma_broeck_morffy_staller_strader_sozzani_2023, title={Prediction and functional characterization of transcriptional activation domains}, url={https://doi.org/10.1109/CISS56502.2023.10089768}, DOI={10.1109/CISS56502.2023.10089768}, abstractNote={Gene expression is induced by transcription factors (TFs) through their activation domains (ADs). However, ADs are unconserved, intrinsically disordered sequences without a secondary structure, making it challenging to recognize and predict these regions and limiting our ability to identify TFs. Here, we address this challenge by leveraging a neural network approach to systematically predict ADs. As input for our neural network, we used computed properties for amino acid (AA) side chain and secondary structure, rather than relying on the raw sequence. Moreover, to shed light on the features learned by our neural network and greatly increase interpretability, we computed the input properties most important for an accurate prediction. Our findings further highlight the importance of aromatic and negatively charged AA and reveal the importance of unknown AA properties. Taking advantage of these most important features, we used an unsupervised learning approach to classify the ADs into 10 subclasses, which can further be explored for AA specificity and AD functionality. Overall, our pipeline, relying on supervised and unsupervised machine learning, shed light on the non-linear properties of ADs.}, author={Mahatma, Saloni and Broeck, Lisa Van and Morffy, Nicholas and Staller, Max V and Strader, Lucia C and Sozzani, Rosangela}, year={2023}, month={Mar} }
 @article{gaudinier_broeck_moreno-risueño_rodriguez-medina_sozzani_brady_2023, title={Quantitative Modeling of the Short-Term Response to Nitrogen Availability that Coordinates Early Events in Lateral Root Initiation}, url={https://doi.org/10.1101/2023.12.05.570292}, DOI={10.1101/2023.12.05.570292}, abstractNote={AbstractNitrogen (N) is an essential macronutrient and its bioavailability plays a major role in how plant development is tuned to environmental nutrient status. To find novel factors in early root system architecture responses to N conditions, we performedArabidopsis thalianaroot transcriptome profiling of a short-term time course in limiting and sufficient N conditions. Using this data, we inferred transcriptional regulatory networks in each condition, which revealed the N-condition specific responses of jasmonate regulation; transcriptional factor (TF) ERF107 plays a more generalized role in lateral root development while TF LBD13 is specific to N-limiting conditions. Further, we used a single cell LR cell-type specific transcriptome dataset to model and analyze the roles of TFs LBD13, ERF107, and PDF2 in early stages of LR development. Linking the N time course transcriptomics, LR mutant phenotypes, and cell-type specific single cell profiling, these approaches provide multiple lines of evidence to find and test the roles of TFs that are involved in early root patterning responses to N conditions.}, author={Gaudinier, Allison and Broeck, Lisa Van and Moreno-Risueño, Miguel and Rodriguez-Medina, Joel and Sozzani, Rosangela and Brady, Siobhan M.}, year={2023}, month={Dec} }
 @article{beretta_franchini_din_lacchini_broeck_sozzani_orozco-arroyo_caporali_adam_jouannic_et al._2023, title={The ALOG family members OsG1L1 and OsG1L2 regulate inflorescence branching in rice}, volume={4}, ISSN={["1365-313X"]}, url={https://doi.org/10.1111/tpj.16229}, DOI={10.1111/tpj.16229}, abstractNote={SUMMARYThe architecture of the rice inflorescence is an important determinant of crop yield. The length of the inflorescence and the number of branches are among the key factors determining the number of spikelets, and thus grains, that a plant will develop. In particular, the timing of the identity transition from indeterminate branch meristem to determinate spikelet meristem governs the complexity of the inflorescence. In this context, the ALOG gene TAWAWA1 (TAW1) has been shown to delay the transition to determinate spikelet development in Oryza sativa (rice). Recently, by combining precise laser microdissection of inflorescence meristems with RNA‐seq, we observed that two ALOG genes, OsG1‐like 1 (OsG1L1) and OsG1L2, have expression profiles similar to that of TAW1. Here, we report that osg1l1 and osg1l2 loss‐of‐function CRISPR mutants have similar phenotypes to the phenotype of the previously published taw1 mutant, suggesting that these genes might act on related pathways during inflorescence development. Transcriptome analysis of the osg1l2 mutant suggested interactions of OsG1L2 with other known inflorescence architecture regulators and the data sets were used for the construction of a gene regulatory network (GRN), proposing interactions among genes potentially involved in controlling inflorescence development in rice. In this GRN, we selected the homeodomain‐leucine zipper transcription factor encoding the gene OsHOX14 for further characterization. The spatiotemporal expression profiling and phenotypical analysis of CRISPR loss‐of‐function mutants of OsHOX14 suggests that the proposed GRN indeed serves as a valuable resource for the identification of new proteins involved in rice inflorescence development.}, journal={PLANT JOURNAL}, author={Beretta, Veronica M. and Franchini, Emanuela and Din, Israr Ud and Lacchini, Elia and Broeck, Lisa and Sozzani, Rosangela and Orozco-Arroyo, Gregorio and Caporali, Elisabetta and Adam, Helene and Jouannic, Stefan and et al.}, year={2023}, month={Apr} }
 @article{broeck_schwartz_krishnamoorthy_tahir_spurney_madison_melvin_gobble_nguyen_peters_et al._2022, title={Establishing a reproducible approach to study cellular functions of plant cells with 3D bioprinting}, url={https://doi.org/10.1126/sciadv.abp9906}, DOI={10.1126/sciadv.abp9906}, abstractNote={Capturing cell-to-cell signals in a three-dimensional (3D) environment is key to studying cellular functions. A major challenge in the current culturing methods is the lack of accurately capturing multicellular 3D environments. In this study, we established a framework for 3D bioprinting plant cells to study cell viability, cell division, and cell identity. We established long-term cell viability for bioprinted Arabidopsis and soybean cells. To analyze the generated large image datasets, we developed a high-throughput image analysis pipeline. Furthermore, we showed the cell cycle reentry of bioprinted cells for which the timing coincides with the induction of core cell cycle genes and regeneration-related genes, ultimately leading to microcallus formation. Last, the identity of bioprinted Arabidopsis root cells expressing endodermal markers was maintained for longer periods. The framework established here paves the way for a general use of 3D bioprinting for studying cellular reprogramming and cell cycle reentry toward tissue regeneration.}, journal={Science Advances}, author={Broeck, Lisa Van and Schwartz, Michael F. and Krishnamoorthy, Srikumar and Tahir, Maimouna Abderamane and Spurney, Ryan J. and Madison, Imani and Melvin, Charles and Gobble, Mariah and Nguyen, Thomas and Peters, Rachel and et al.}, year={2022}, month={Oct} }
 @inbook{broeck_gobble_sozzani_2022, title={Quantifying Intercellular Movement and Protein Stoichiometry for Computational Modeling}, url={http://dx.doi.org/10.1007/978-1-0716-2132-5_25}, DOI={10.1007/978-1-0716-2132-5_25}, abstractNote={Analyzing protein movement dynamics and their regulation has shown to be important in the study of cell fate decisions. Such analyses can be performed with scanning fluorescence correlation spectroscopy (scanning FCS), a versatile imaging methodology that has been applied in the animal kingdom and recently adapted to the plant kingdom. Specifically, scanning FCS allows for qualitatively capturing protein movement across barriers, such as the active transport through plasmodesmata, the analysis of protein movement rates, and the quantification of the stoichiometry of protein complexes, composed of one or more different proteins. Importantly, the quantifiable data generated with scanning FCS can be used to inform computational models, enhancing model simulations of in vivo events, such as cell fate decisions, during plant development.}, booktitle={Methods in Molecular Biology}, author={Broeck, Lisa Van and Gobble, Mariah and Sozzani, Rosangela}, year={2022} }
 @article{broeck_spurney_fisher_schwartz_clark_nguyen_madison_gobble_long_sozzani_2021, title={A hybrid model connecting regulatory interactions with stem cell divisions in the root}, volume={2}, url={https://doi.org/10.1017/qpb.2021.1}, DOI={10.1017/qpb.2021.1}, abstractNote={Abstract
	  Stem cells give rise to the entirety of cells within an organ. Maintaining stem cell identity and coordinately regulating stem cell divisions is crucial for proper development. In plants, mobile proteins, such as WUSCHEL-RELATED HOMEOBOX 5 (WOX5) and SHORTROOT (SHR), regulate divisions in the root stem cell niche. However, how these proteins coordinately function to establish systemic behaviour is not well understood. We propose a non-cell autonomous role for WOX5 in the cortex endodermis initial (CEI) and identify a regulator, ANGUSTIFOLIA (AN3)/GRF-INTERACTING FACTOR 1, that coordinates CEI divisions. Here, we show with a multi-scale hybrid model integrating ordinary differential equations (ODEs) and agent-based modeling that quiescent center (QC) and CEI divisions have different dynamics. Specifically, by combining continuous models to describe regulatory networks and agent-based rules, we model systemic behaviour, which led us to predict cell-type-specific expression dynamics of SHR, SCARECROW, WOX5, AN3 and CYCLIND6;1, and experimentally validate CEI cell divisions. Conclusively, our results show an interdependency between CEI and QC divisions.}, journal={Quantitative Plant Biology}, publisher={Cambridge University Press (CUP)}, author={Broeck, Lisa Van and Spurney, Ryan J. and Fisher, Adam P. and Schwartz, Michael and Clark, Natalie M. and Nguyen, Thomas T. and Madison, Imani and Gobble, Mariah and Long, Terri and Sozzani, Rosangela}, year={2021} }
 @article{kim_van den broeck_karre_choi_christensen_wang_jo_cho_balint‐kurti_2021, title={Analysis of the transcriptomic, metabolomic, and gene regulatory responses to
            <i>Puccinia sorghi
            in maize}, volume={22}, ISSN={1464-6722 1364-3703}, url={http://dx.doi.org/10.1111/mpp.13040}, DOI={10.1111/mpp.13040}, abstractNote={AbstractCommon rust, caused by Puccinia sorghi, is a widespread and destructive disease of maize. The Rp1‐D gene confers resistance to the P. sorghi IN2 isolate, mediating a hypersensitive cell death response (HR). To identify differentially expressed genes (DEGs) and metabolites associated with the compatible (susceptible) interaction and with Rp1‐D‐mediated resistance in maize, we performed transcriptomics and targeted metabolome analyses of P. sorghi IN2‐infected leaves from the near‐isogenic lines H95 and H95:Rp1‐D, which differed for the presence of Rp1‐D. We observed up‐regulation of genes involved in the defence response and secondary metabolism, including the phenylpropanoid, flavonoid, and terpenoid pathways. Metabolome analyses confirmed that intermediates from several transcriptionally up‐regulated pathways accumulated during the defence response. We identified a common response in H95:Rp1‐D and H95 with an additional H95:Rp1‐D‐specific resistance response observed at early time points at both transcriptional and metabolic levels. To better understand the mechanisms underlying Rp1‐D‐mediated resistance, we inferred gene regulatory networks occurring in response to P. sorghi infection. A number of transcription factors including WRKY53, BHLH124, NKD1, BZIP84, and MYB100 were identified as potentially important signalling hubs in the resistance‐specific response. Overall, this study provides a novel and multifaceted understanding of the maize susceptible and resistance‐specific responses to P. sorghi.}, number={4}, journal={Molecular Plant Pathology}, publisher={Wiley}, author={Kim, Saet‐Byul and Van den Broeck, Lisa and Karre, Shailesh and Choi, Hoseong and Christensen, Shawn A. and Wang, Guan‐Feng and Jo, Yeonhwa and Cho, Won Kyong and Balint‐Kurti, Peter}, year={2021}, month={Feb}, pages={465–479} }
 @misc{schwartz_peters_hunt_abdul-matin_broeck_sozzani_2021, title={Divide and Conquer: The Initiation and Proliferation of Meristems}, volume={40}, ISSN={["1549-7836"]}, url={http://dx.doi.org/10.1080/07352689.2021.1915228}, DOI={10.1080/07352689.2021.1915228}, abstractNote={Abstract In contrast to animals, which complete organogenesis early in their development, plants continuously produce organs, and structures throughout their entire lifecycle. Plants achieve the continuous growth of organs through the initiation and maintenance of meristems that populate the plant body. Plants contain two apical meristems, one at the shoot and one root, to produce the lateral organs of the shoot and the cell files of the root, respectively. Additional meristems within the plant produce branches while others produce the cell types within the vasculature system. Throughout development, plants must balance producing organs and maintaining their meristems, which requires tightly controlled regulations. This review focuses on the various plant meristems, how cells within these meristems maintain their identity, and particularly the molecular players that regulate stem cell maintenance. In addition, we summarize cell types which share molecular features with meristems, but do not follow the same rules regarding maintenance, including pericycle and rachis founder cells. Together, these populations of cells contribute to the entire organogenesis of plants.}, number={2}, journal={CRITICAL REVIEWS IN PLANT SCIENCES}, publisher={Informa UK Limited}, author={Schwartz, Michael F. and Peters, Rachel and Hunt, Aitch M. and Abdul-Matin, Abdul-Khaliq and Broeck, Lisa and Sozzani, Rosangela}, year={2021}, month={Mar}, pages={147–156} }
 @article{thomas_broeck_spurney_sozzani_frank_2022, title={Gene regulatory networks for compatible versus incompatible grafts identify a role for SlWOX4 during junction formation}, volume={34}, ISSN={["1532-298X"]}, url={https://doi.org/10.1093/plcell/koab246}, DOI={10.1093/plcell/koab246}, abstractNote={Abstract
               Grafting has been adopted for a wide range of crops to enhance productivity and resilience; for example, grafting of Solanaceous crops couples disease-resistant rootstocks with scions that produce high-quality fruit. However, incompatibility severely limits the application of grafting and graft incompatibility remains poorly understood. In grafts, immediate incompatibility results in rapid death, but delayed incompatibility can take months or even years to manifest, creating a significant economic burden for perennial crop production. To gain insight into the genetic mechanisms underlying this phenomenon, we developed a model system using heterografting of tomato (Solanum lycopersicum) and pepper (Capsicum annuum). These grafted plants express signs of anatomical junction failure within the first week of grafting. By generating a detailed timeline for junction formation, we were able to pinpoint the cellular basis for this delayed incompatibility. Furthermore, we inferred gene regulatory networks for compatible self-grafts and incompatible heterografts based on these key anatomical events, which predict core regulators for grafting. Finally, we examined the role of vascular development in graft formation and uncovered SlWOX4 as a potential regulator of graft compatibility. Following this predicted regulator up with functional analysis, we show that Slwox4 homografts fail to form xylem bridges across the junction, demonstrating that indeed, SlWOX4 is essential for vascular reconnection during grafting, and may function as an early indicator of graft failure.}, number={1}, journal={PLANT CELL}, publisher={Oxford University Press (OUP)}, author={Thomas, Hannah and Broeck, Lisa and Spurney, Ryan and Sozzani, Rosangela and Frank, Margaret}, year={2022}, month={Jan}, pages={535–556} }
 @article{krishnamoorthy_schwartz_broeck_hunt_horn_sozzani_2021, title={Tissue Regeneration with Hydrogel Encapsulation: A Review of Developments in Plants and Animals}, url={https://doi.org/10.34133/2021/9890319}, DOI={10.34133/2021/9890319}, abstractNote={
            Hydrogel encapsulation has been widely utilized in the study of fundamental cellular mechanisms and has been shown to provide a better representation of the complex
            in vivo
            microenvironment in natural biological conditions of mammalian cells. In this review, we provide a background into the adoption of hydrogel encapsulation methods in the study of mammalian cells, highlight some key findings that may aid with the adoption of similar methods for the study of plant cells, including the potential challenges and considerations, and discuss key findings of studies that have utilized these methods in plant sciences.
          }, journal={BioDesign Research}, author={Krishnamoorthy, Srikumar and Schwartz, Michael F. and Broeck, Lisa Van and Hunt, Aitch and Horn, Timothy J. and Sozzani, Rosangela}, year={2021}, month={Jan} }
 @article{doydora_gatiboni_grieger_hesterberg_jones_mclamore_peters_sozzani_van den broeck_duckworth_2020, title={Accessing Legacy Phosphorus in Soils}, volume={4}, ISSN={2571-8789}, url={http://dx.doi.org/10.3390/soilsystems4040074}, DOI={10.3390/soilsystems4040074}, abstractNote={Repeated applications of phosphorus (P) fertilizers result in the buildup of P in soil (commonly known as legacy P), a large fraction of which is not immediately available for plant use. Long-term applications and accumulations of soil P is an inefficient use of dwindling P supplies and can result in nutrient runoff, often leading to eutrophication of water bodies. Although soil legacy P is problematic in some regards, it conversely may serve as a source of P for crop use and could potentially decrease dependence on external P fertilizer inputs. This paper reviews the (1) current knowledge on the occurrence and bioaccessibility of different chemical forms of P in soil, (2) legacy P transformations with mineral and organic fertilizer applications in relation to their potential bioaccessibility, and (3) approaches and associated challenges for accessing native soil P that could be used to harness soil legacy P for crop production. We highlight how the occurrence and potential bioaccessibility of different forms of soil inorganic and organic P vary depending on soil properties, such as soil pH and organic matter content. We also found that accumulation of inorganic legacy P forms changes more than organic P species with fertilizer applications and cessations. We also discuss progress and challenges with current approaches for accessing native soil P that could be used for accessing legacy P, including natural and genetically modified plant-based strategies, the use of P-solubilizing microorganisms, and immobilized organic P-hydrolyzing enzymes. It is foreseeable that accessing legacy P will require multidisciplinary approaches to address these limitations.}, number={4}, journal={Soil Systems}, publisher={MDPI AG}, author={Doydora, Sarah and Gatiboni, Luciano and Grieger, Khara and Hesterberg, Dean and Jones, Jacob L. and McLamore, Eric S. and Peters, Rachel and Sozzani, Rosangela and Van den Broeck, Lisa and Duckworth, Owen W.}, year={2020}, month={Dec}, pages={74} }
 @article{broeck_spurney_fisher_schwartz_clark_nguyen_madison_gobble_long_sozzani_2020, title={Exchange of molecular and cellular information: a hybrid model that integrates stem cell divisions and key regulatory interactions}, url={https://doi.org/10.1101/2020.11.30.404426}, DOI={10.1101/2020.11.30.404426}, abstractNote={AbstractStem cells give rise to the entirety of cells within an organ. Maintaining stem cell identity and coordinately regulating stem cell divisions is crucial for proper development. In plants, mobile proteins, such as WOX5 and SHR, regulate divisions in the root stem cell niche (SCN). However, how these proteins coordinately function to establish systemic behavior is not well understood. We propose a non-cell autonomous role for WOX5 in the CEI and identify a regulator, AN3/GIF1, that coordinates CEI divisions. Here we show with a multiscale hybrid model integrating ODEs and agent-based modeling that QC and CEI divisions have different dynamics. Specifically, by combining continuous models to describe regulatory networks and agent-based rules, we model systemic behavior, which led us to predict cell-type-specific expression dynamics of SHR, SCR, WOX5, AN3, and CYCD6;1, and experimentally validate CEI cell divisions. Conclusively, our results show an interdependency between CEI and QC divisions.Thumbnail image}, author={Broeck, Lisa Van and Spurney, Ryan J. and Fisher, Adam P. and Schwartz, Michael and Clark, Natalie M. and Nguyen, Thomas T. and Madison, Imani and Gobble, Mariah and Long, Terri and Sozzani, Rosangela}, year={2020}, month={Dec} }
 @article{van den broeck_gordon_inzé_williams_sozzani_2020, title={Gene Regulatory Network Inference: Connecting Plant Biology and Mathematical Modeling}, volume={11}, ISSN={1664-8021}, url={http://dx.doi.org/10.3389/fgene.2020.00457}, DOI={10.3389/fgene.2020.00457}, abstractNote={Plant responses to environmental and intrinsic signals are tightly controlled by multiple transcription factors (TFs). These TFs and their regulatory connections form gene regulatory networks (GRNs), which provide a blueprint of the transcriptional regulations underlying plant development and environmental responses. This review provides examples of experimental methodologies commonly used to identify regulatory interactions and generate GRNs. Additionally, this review describes network inference techniques that leverage gene expression data to predict regulatory interactions. These computational and experimental methodologies yield complex networks that can identify new regulatory interactions, driving novel hypotheses. Biological properties that contribute to the complexity of GRNs are also described in this review. These include network topology, network size, transient binding of TFs to DNA, and competition between multiple upstream regulators. Finally, this review highlights the potential of machine learning approaches to leverage gene expression data to predict phenotypic outputs.}, journal={Frontiers in Genetics}, publisher={Frontiers Media SA}, author={Van den Broeck, Lisa and Gordon, Max and Inzé, Dirk and Williams, Cranos and Sozzani, Rosangela}, year={2020}, month={May} }
 @article{clark_van den broeck_guichard_stager_tanner_blilou_grossmann_iyer-pascuzzi_maizel_sparks_et al._2020, title={Novel Imaging Modalities Shedding Light on Plant Biology: Start Small and Grow Big}, volume={71}, ISSN={1543-5008 1545-2123}, url={http://dx.doi.org/10.1146/annurev-arplant-050718-100038}, DOI={10.1146/annurev-arplant-050718-100038}, abstractNote={ The acquisition of quantitative information on plant development across a range of temporal and spatial scales is essential to understand the mechanisms of plant growth. Recent years have shown the emergence of imaging methodologies that enable the capture and analysis of plant growth, from the dynamics of molecules within cells to the measurement of morphometricand physiological traits in field-grown plants. In some instances, these imaging methods can be parallelized across multiple samples to increase throughput. When high throughput is combined with high temporal and spatial resolution, the resulting image-derived data sets could be combined with molecular large-scale data sets to enable unprecedented systems-level computational modeling. Such image-driven functional genomics studies may be expected to appear at an accelerating rate in the near future given the early success of the foundational efforts reviewed here. We present new imaging modalities and review how they have enabled a better understanding of plant growth from the microscopic to the macroscopic scale. }, number={1}, journal={Annual Review of Plant Biology}, publisher={Annual Reviews}, author={Clark, Natalie M. and Van den Broeck, Lisa and Guichard, Marjorie and Stager, Adam and Tanner, Herbert G. and Blilou, Ikram and Grossmann, Guido and Iyer-Pascuzzi, Anjali S. and Maizel, Alexis and Sparks, Erin E. and et al.}, year={2020}, month={Apr}, pages={789–816} }
 @article{clark_fisher_berckmans_van den broeck_nelson_nguyen_bustillo-avendaño_zebell_moreno-risueno_simon_et al._2020, title={Protein complex stoichiometry and expression dynamics of transcription factors modulate stem cell division}, volume={117}, ISSN={0027-8424 1091-6490}, url={http://dx.doi.org/10.1073/pnas.2002166117}, DOI={10.1073/pnas.2002166117}, abstractNote={
            Stem cells divide and differentiate to form all of the specialized cell types in a multicellular organism. In the
            Arabidopsis
            root, stem cells are maintained in an undifferentiated state by a less mitotically active population of cells called the quiescent center (QC). Determining how the QC regulates the surrounding stem cell initials, or what makes the QC fundamentally different from the actively dividing initials, is important for understanding how stem cell divisions are maintained. Here we gained insight into the differences between the QC and the cortex endodermis initials (CEI) by studying the mobile transcription factor SHORTROOT (SHR) and its binding partner SCARECROW (SCR). We constructed an ordinary differential equation model of SHR and SCR in the QC and CEI which incorporated the stoichiometry of the SHR-SCR complex as well as upstream transcriptional regulation of SHR and SCR. Our model prediction, coupled with experimental validation, showed that high levels of the SHR-SCR complex are associated with more CEI division but less QC division. Furthermore, our model prediction allowed us to propose the putative upstream SHR regulators SEUSS and WUSCHEL-RELATED HOMEOBOX 5 and to experimentally validate their roles in QC and CEI division. In addition, our model established the timing of QC and CEI division and suggests that SHR repression of QC division depends on formation of the SHR homodimer. Thus, our results support that SHR-SCR protein complex stoichiometry and regulation of SHR transcription modulate the division timing of two different specialized cell types in the root stem cell niche.
          }, number={26}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Clark, Natalie M. and Fisher, Adam P. and Berckmans, Barbara and Van den Broeck, Lisa and Nelson, Emily C. and Nguyen, Thomas T. and Bustillo-Avendaño, Estefano and Zebell, Sophia G. and Moreno-Risueno, Miguel A. and Simon, Rüdiger and et al.}, year={2020}, month={Jun}, pages={15332–15342} }
 @article{spurney_broeck_clark_fisher_balaguer_sozzani_2020, title={tuxnet: a simple interface to process RNA sequencing data and infer gene regulatory networks}, volume={101}, ISSN={["1365-313X"]}, url={https://doi.org/10.1111/tpj.14558}, DOI={10.1111/tpj.14558}, abstractNote={SummaryPredicting gene regulatory networks (GRNs) from expression profiles is a common approach for identifying important biological regulators. Despite the increased use of inference methods, existing computational approaches often do not integrate RNA‐sequencing data analysis, are not automated or are restricted to users with bioinformatics backgrounds. To address these limitations, we developed tuxnet, a user‐friendly platform that can process raw RNA‐sequencing data from any organism with an existing reference genome using a modified tuxedo pipeline (hisat 2 + cufflinks package) and infer GRNs from these processed data. tuxnet is implemented as a graphical user interface and can mine gene regulations, either by applying a dynamic Bayesian network (DBN) inference algorithm, genist, or a regression tree‐based pipeline, rtp‐star. We obtained time‐course expression data of a PERIANTHIA (PAN) inducible line and inferred a GRN using genist to illustrate the use of tuxnet while gaining insight into the regulations downstream of the Arabidopsis root stem cell regulator PAN. Using rtp‐star, we inferred the network of ATHB13, a downstream gene of PAN, for which we obtained wild‐type and mutant expression profiles. Additionally, we generated two networks using temporal data from developmental leaf data and spatial data from root cell‐type data to highlight the use of tuxnet to form new testable hypotheses from previously explored data. Our case studies feature the versatility of tuxnet when using different types of gene expression data to infer networks and its accessibility as a pipeline for non‐bioinformaticians to analyze transcriptome data, predict causal regulations, assess network topology and identify key regulators.}, number={3}, journal={PLANT JOURNAL}, author={Spurney, Ryan J. and Broeck, Lisa and Clark, Natalie M. and Fisher, Adam P. and Balaguer, Maria A. de Luis and Sozzani, Rosangela}, year={2020}, month={Feb}, pages={716–730} }
 @article{n_broeck l_s_cotte b_m_k_d_i_2018, title={Early mannitol-triggered changes in the Arabidopsis leaf (phospho)proteome reveal growth regulators.}, volume={8}, url={http://europepmc.org/abstract/med/30010984}, DOI={10.1093/jxb/ery261}, abstractNote={Drought is one of the most detrimental environmental stresses to which plants are exposed. Especially mild drought is relevant to agriculture and significantly affects plant growth and development. In plant research, mannitol is often used to mimic drought stress and study the underlying responses. In growing leaf tissue of plants exposed to mannitol-induced stress, a highly-interconnected gene regulatory network is induced. However, early signaling and associated protein phosphorylation events that likely precede part of these transcriptional changes are largely unknown. Here, we performed a full proteome and phosphoproteome analysis on growing leaf tissue of Arabidopsis plants exposed to mild mannitol-induced stress and captured the fast (within the first half hour) events associated with this stress. Based on this in-depth data analysis, 167 and 172 differentially regulated proteins and phosphorylated sites were found back, respectively. Additionally, we identified H(+)-ATPASE 2 (AHA2) and CYSTEINE-RICH REPEAT SECRETORY PROTEIN 38 (CRRSP38) as novel regulators of shoot growth under osmotic stress. Highlight We captured early changes in the Arabidopsis leaf proteome and phosphoproteome upon mild mannitol stress and identified AHA2 and CRRSP38 as novel regulators of shoot growth under osmotic stress}, journal={Journal of experimental botany}, author={N, Nikonorova and Broeck L, Van and S, Zhu and Cotte B and M, Dubois and K, Gevaert and D, Inzé and I, De Smet}, year={2018}, month={Aug} }
 @article{dubois_broeck l van_inzé_2018, title={The Pivotal Role of Ethylene in Plant Growth.}, volume={4}, url={http://europepmc.org/abstract/med/29428350}, DOI={10.1016/j.tplants.2018.01.003}, abstractNote={An increasing number of transcriptome studies in plants exposed to biotic or abiotic stress highlight a role for ethylene under a broad range of stresses. The role of ethylene under stress is dual: it regulates a defense response, mostly in full-grown leaves, and a growth response in young leaves. In young leaves, ethylene and the downstream ERFs emerge as central regulators of leaf growth inhibition, orchestrating both cell division and cell expansion. The knowledge of ethylene-mediated growth inhibition can be successfully implemented in crops to improve plant growth and stress tolerance. Being continuously exposed to variable environmental conditions, plants produce phytohormones to react quickly and specifically to these changes. The phytohormone ethylene is produced in response to multiple stresses. While the role of ethylene in defense responses to pathogens is widely recognized, recent studies in arabidopsis and crop species highlight an emerging key role for ethylene in the regulation of organ growth and yield under abiotic stress. Molecular connections between ethylene and growth-regulatory pathways have been uncovered, and altering the expression of ethylene response factors (ERFs) provides a new strategy for targeted ethylene-response engineering. Crops with optimized ethylene responses show improved growth in the field, opening new windows for future crop improvement. This review focuses on how ethylene regulates shoot growth, with an emphasis on leaves. Being continuously exposed to variable environmental conditions, plants produce phytohormones to react quickly and specifically to these changes. The phytohormone ethylene is produced in response to multiple stresses. While the role of ethylene in defense responses to pathogens is widely recognized, recent studies in arabidopsis and crop species highlight an emerging key role for ethylene in the regulation of organ growth and yield under abiotic stress. Molecular connections between ethylene and growth-regulatory pathways have been uncovered, and altering the expression of ethylene response factors (ERFs) provides a new strategy for targeted ethylene-response engineering. Crops with optimized ethylene responses show improved growth in the field, opening new windows for future crop improvement. This review focuses on how ethylene regulates shoot growth, with an emphasis on leaves. The sessility of plants is undoubtedly their most disadvantageous feature compared to other living organisms, and implies that their survival can be threatened by environmental perturbations. However, plants have developed fascinating mechanisms enabling rapid detection of changing conditions accompanied by highly complex molecular responses, resulting in remarkable phenotypic plasticity. During the vegetative growth stage, one tightly controlled process is plant growth. Under favorable conditions, root and shoot growth is crucial to enable continuous nutrient uptake and energy production through photosynthesis, respectively. Leaf growth, for example, is controlled by no less than six different cellular mechanisms, including precise orchestration of the switch between cell division, that drives the growth of very young leaf primordia, and cell expansion and differentiation (reviewed in [1Gonzalez N. et al.Leaf size control: complex coordination of cell division and expansion.Trends Plant Sci. 2012; 17: 332-340Abstract Full Text Full Text PDF PubMed Scopus (182) Google Scholar]). By contrast, sustaining growth under unfavorable conditions could be detrimental. For example, growth under drought stress would increase the evaporative surface of the plant, rendering the plant even more susceptible. Plants thus constantly evaluate whether the environmental signals are favorable for growth or not, and redirect their resources either for growth or for stress defense. At the physiological level, the integration of environmental signals into proper phenotypic responses is orchestrated by phytohormones. Ethylene, the smallest phytohormone with the simple C2H4 structure, is gaseous and therefore enables plant-to-plant communication. Since its discovery around one century ago, the multiple facets of this hormone as a signaling molecule have fascinated scientists, and this led to the unraveling of its biosynthesis and signaling (Box 1 and Figure 1), and the identification of its various functions: regulation of leaf development, senescence, fruit ripening, stimulation of germination, etc. Importantly, ethylene is produced in response to multiple environmental stresses (Figure 1), both abiotic and biotic, suggesting that it acts as a bridge between a changing environment and developmental adaptation. The abiotic stress conditions that trigger ethylene synthesis include submergence, heat, shade, exposure to heavy metals and high salt, low nutrient availability, and water deficiency [2Skirycz A. et al.Pause-and-stop: the effects of osmotic stress on cell proliferation during early leaf development in Arabidopsis and a role for ethylene signaling in cell cycle arrest.Plant Cell. 2011; 23: 1876-1888Crossref PubMed Scopus (0) Google Scholar, 3Thao N.P. et al.Role of ethylene and its cross talk with other signaling molecules in plant responses to heavy metal stress.Plant Physiol. 2015; 169: 73-84Crossref PubMed Scopus (23) Google Scholar, 4Zhang M. et al.The regulatory roles of ethylene and reactive oxygen species (ROS) in plant salt stress responses.Plant Mol. Biol. 2016; 91: 651-659Crossref PubMed Scopus (11) Google Scholar, 5Dubois M. et al.Time of day determines Arabidopsis transcriptome and growth dynamics under mild drought.Plant Cell Environ. 2017; 40: 180-189Crossref PubMed Scopus (3) Google Scholar, 6Savada R.P. et al.Heat stress differentially modifies ethylene biosynthesis and signaling in pea floral and fruit tissues.Plant Mol. Biol. 2017; 95: 313-331Crossref PubMed Scopus (0) Google Scholar].Box 1Recent Advances in Ethylene Biosynthesis and SignalingThe ethylene biosynthesis pathway consists of a simple, three-step process: methionine is converted into S-adenosyl methionine (SAM; see Glossary), which is further converted by ACC-synthases (ACS) to ACC, the direct precursor of ethylene (Figure 1). Recycling of methylthioadenosine enables rapid ethylene biosynthesis when necessary [85Sauter M. et al.Methionine salvage and S-adenosylmethionine: essential links between sulfur, ethylene and polyamine biosynthesis.Biochem. J. 2013; 451: 145-154Crossref PubMed Scopus (90) Google Scholar]. Because the conversion from ACC to ethylene is an exothermic reaction that only requires oxygen, ethylene biosynthesis is regulated at the level of ACS enzymes, which are also under post-translational control: they can be phosphorylated before ubiquitin-mediated protein degradation by, for instance, ETO1 and CUL3 [86Thomann A. et al.Arabidopsis CULLIN3 genes regulate primary root growth and patterning by ethylene-dependent and -independent mechanisms.PLoS Genet. 2009; 5e1000328Crossref PubMed Scopus (0) Google Scholar, 87Yoon G.M. New insights into the protein turnover regulation in ethylene biosynthesis.Mol. Cells. 2015; 38: 597-603Crossref PubMed Google Scholar]. ACS induction and activation are responsive to environmental factors that trigger ethylene accumulation. As such, ACS genes are transcriptionally induced by drought [5Dubois M. et al.Time of day determines Arabidopsis transcriptome and growth dynamics under mild drought.Plant Cell Environ. 2017; 40: 180-189Crossref PubMed Scopus (3) Google Scholar] and by shade, under the control of PIF4 [58Nomoto Y. et al.Circadian clock- and PIF4-controlled plant growth: a coincidence mechanism directly integrates a hormone signaling network into the photoperiodic control of plant architectures in Arabidopsis thaliana.Plant Cell Physiol. 2012; 53: 1950-1964Crossref PubMed Scopus (52) Google Scholar]. ACS2 and ACS6 are post-translationally activated through phosphorylation by a MAPK-phosphorylation cascade involving MKK9 and MPK3/6 [88Xu J. Zhang S. Regulation of ethylene biosynthesis and signaling by protein kinases and phosphatases.Mol. Plant. 2014; 7: 939-942Abstract Full Text Full Text PDF Scopus (0) Google Scholar]. ACC levels are also regulated by conjugation and release from conjugates such as malonyl- or jasmonyl-ACC [89Van de Poel B. Van Der Straeten D. 1-Aminocyclopropane-1-carboxylic acid (ACC) in plants: more than just the precursor of ethylene!.Front. Plant Sci. 2014; 5: 640Crossref PubMed Scopus (35) Google Scholar]. The soluble ethylene precursor ACC can be taken up by the amino acid transporter LHT1 and further transported through the plant via the xylem (Figure 1) [90Shin K. et al.Genetic identification of ACC-RESISTANT2 reveals involvement of LYSINE HISTIDINE TRANSPORTER1 in the uptake of 1-aminocyclopropane-1-carboxylic acid in Arabidopsis thaliana.Plant Cell Physiol. 2015; 56: 572-582Crossref PubMed Scopus (15) Google Scholar].In the destination organ, ethylene triggers a signaling cascade initiated by ethylene receptors in the ER and Golgi membrane: ERS1 (ETHYLENE RESPONSE SENSOR 1), ERS2, ETR1 (ETHYLENE RESISTANCE 1), ETR2 and EIN4 (ETHYLENE INSENSITIVE 4). These receptors are active in the absence of ethylene, and their activity can be controlled by complex formation with RTE1 (REVERSION TO ETHYLENE SENSITIVITY) and ARGOS proteins: these are positive regulators of the ethylene receptors, and thus are negative regulators of ethylene sensitivity [11Rai M.I. et al.The ARGOS gene family functions in a negative feedback loop to desensitize plants to ethylene.BMC Plant Biol. 2015; 15: 157Crossref PubMed Scopus (12) Google Scholar, 91Resnick J.S. et al.REVERSION-TO-ETHYLENE SENSITIVITY1, a conserved gene that regulates ethylene receptor function in Arabidopsis.Proc. Natl. Acad. Sci. U. S. A. 2006; 103: 7917-7922Crossref PubMed Scopus (114) Google Scholar, 92Shi J. et al.Maize and Arabidopsis ARGOS proteins interact with ethylene receptor signaling complex, supporting a regulatory role for ARGOS in ethylene signal transduction.Plant Physiol. 2016; 171: 2783-2797Crossref PubMed Scopus (14) Google Scholar]. In the absence of ethylene, active receptors subsequently bind to and thereby activate the CTR1 protein [93Lacey R.F. Binder B.M. How plants sense ethylene gas – the ethylene receptors.J. Inorg. Biochem. 2014; 133: 58-62Crossref PubMed Scopus (12) Google Scholar]. The levels of the receptors are regulated by ethylene and CTR1: slightly increasing ethylene levels stimulate the transcription of the receptors and stabilization of CTR1, whereas higher ethylene levels push the receptor/CTR1 towards proteasome-mediated degradation [94Shakeel S.N. et al.Ethylene regulates levels of ethylene receptor/CTR1 signaling complexes in Arabidopsis thaliana.J. Biol. Chem. 2015; 290: 12415-12424Crossref PubMed Scopus (15) Google Scholar]. CTR1 is a kinase that represses EIN2, an ER-located membrane protein. When this repression is released in the presence of ethylene, EIN2 is dephosphorylated and cleaved, releasing a C-terminal fragment that either moves to P-bodies or to the nucleus [95Li W. et al.EIN2-directed translational regulation of ethylene signaling in Arabidopsis.Cell. 2015; 163: 670-683Abstract Full Text Full Text PDF PubMed Scopus (66) Google Scholar, 96Merchante C. et al.Gene-specific translation regulation mediated by the hormone-signaling molecule EIN2.Cell. 2015; 163: 684-697Abstract Full Text Full Text PDF PubMed Scopus (67) Google Scholar]. The downstream mode of action of the EIN2 fragment has long been a mystery, but recent studies have shown that it is involved in gene-specific regulation of translation [95Li W. et al.EIN2-directed translational regulation of ethylene signaling in Arabidopsis.Cell. 2015; 163: 670-683Abstract Full Text Full Text PDF PubMed Scopus (66) Google Scholar, 96Merchante C. et al.Gene-specific translation regulation mediated by the hormone-signaling molecule EIN2.Cell. 2015; 163: 684-697Abstract Full Text Full Text PDF PubMed Scopus (67) Google Scholar]. The EIN2 fragment binds to the 3'-untranslated regions (3'-UTRs) of EBF1 and EBF2 transcripts, thereby repressing their translation. EBF1 and EBF2 are two central F-box proteins that target the primary ethylene-responsive TFs EIN3 and EIN3-LIKE 1 (EIL1) for protein degradation in the absence of ethylene [97Guo H. Ecker J.R. Plant responses to ethylene gas are mediated by SCFEBF1/EBF2-dependent proteolysis of EIN3 transcription factor.Cell. 2003; 115: 667-677Abstract Full Text Full Text PDF PubMed Scopus (495) Google Scholar, 98Potuschak T. et al.EIN3-dependent regulation of plant ethylene hormone signaling by two Arabidopsis F box proteins: EBF1 and EBF2.Cell. 2003; 115: 679-689Abstract Full Text Full Text PDF PubMed Scopus (420) Google Scholar]. In the presence of ethylene, EIN3 and EIL1 induce the expression of numerous secondary transcription factors (TFs), the ERFs [99Nakano T. et al.Identification of genes of the plant-specific transcription-factor families cooperatively regulated by ethylene and jasmonate in Arabidopsis thaliana.J. Plant Res. 2006; 119: 407-413Crossref PubMed Scopus (0) Google Scholar]. The activity of some ERFs has been reported to be increased by phosphorylation through the MPK3/6-cascade that also regulates ethylene biosynthesis, providing dual-level regulation of the ERF-mediated response [24Meng X. et al.Phosphorylation of an ERF transcription factor by Arabidopsis MPK3/MPK6 regulates plant defense gene induction and fungal resistance.Plant Cell. 2013; 25: 1126-1142Crossref PubMed Scopus (143) Google Scholar, 100Yoo S.-D. Sheen J. MAPK signaling in plant hormone ethylene signal transduction.Plant Signal. Behav. 2008; 3: 848-849Crossref PubMed Google Scholar]. The ethylene biosynthesis pathway consists of a simple, three-step process: methionine is converted into S-adenosyl methionine (SAM; see Glossary), which is further converted by ACC-synthases (ACS) to ACC, the direct precursor of ethylene (Figure 1). Recycling of methylthioadenosine enables rapid ethylene biosynthesis when necessary [85Sauter M. et al.Methionine salvage and S-adenosylmethionine: essential links between sulfur, ethylene and polyamine biosynthesis.Biochem. J. 2013; 451: 145-154Crossref PubMed Scopus (90) Google Scholar]. Because the conversion from ACC to ethylene is an exothermic reaction that only requires oxygen, ethylene biosynthesis is regulated at the level of ACS enzymes, which are also under post-translational control: they can be phosphorylated before ubiquitin-mediated protein degradation by, for instance, ETO1 and CUL3 [86Thomann A. et al.Arabidopsis CULLIN3 genes regulate primary root growth and patterning by ethylene-dependent and -independent mechanisms.PLoS Genet. 2009; 5e1000328Crossref PubMed Scopus (0) Google Scholar, 87Yoon G.M. New insights into the protein turnover regulation in ethylene biosynthesis.Mol. Cells. 2015; 38: 597-603Crossref PubMed Google Scholar]. ACS induction and activation are responsive to environmental factors that trigger ethylene accumulation. As such, ACS genes are transcriptionally induced by drought [5Dubois M. et al.Time of day determines Arabidopsis transcriptome and growth dynamics under mild drought.Plant Cell Environ. 2017; 40: 180-189Crossref PubMed Scopus (3) Google Scholar] and by shade, under the control of PIF4 [58Nomoto Y. et al.Circadian clock- and PIF4-controlled plant growth: a coincidence mechanism directly integrates a hormone signaling network into the photoperiodic control of plant architectures in Arabidopsis thaliana.Plant Cell Physiol. 2012; 53: 1950-1964Crossref PubMed Scopus (52) Google Scholar]. ACS2 and ACS6 are post-translationally activated through phosphorylation by a MAPK-phosphorylation cascade involving MKK9 and MPK3/6 [88Xu J. Zhang S. Regulation of ethylene biosynthesis and signaling by protein kinases and phosphatases.Mol. Plant. 2014; 7: 939-942Abstract Full Text Full Text PDF Scopus (0) Google Scholar]. ACC levels are also regulated by conjugation and release from conjugates such as malonyl- or jasmonyl-ACC [89Van de Poel B. Van Der Straeten D. 1-Aminocyclopropane-1-carboxylic acid (ACC) in plants: more than just the precursor of ethylene!.Front. Plant Sci. 2014; 5: 640Crossref PubMed Scopus (35) Google Scholar]. The soluble ethylene precursor ACC can be taken up by the amino acid transporter LHT1 and further transported through the plant via the xylem (Figure 1) [90Shin K. et al.Genetic identification of ACC-RESISTANT2 reveals involvement of LYSINE HISTIDINE TRANSPORTER1 in the uptake of 1-aminocyclopropane-1-carboxylic acid in Arabidopsis thaliana.Plant Cell Physiol. 2015; 56: 572-582Crossref PubMed Scopus (15) Google Scholar]. In the destination organ, ethylene triggers a signaling cascade initiated by ethylene receptors in the ER and Golgi membrane: ERS1 (ETHYLENE RESPONSE SENSOR 1), ERS2, ETR1 (ETHYLENE RESISTANCE 1), ETR2 and EIN4 (ETHYLENE INSENSITIVE 4). These receptors are active in the absence of ethylene, and their activity can be controlled by complex formation with RTE1 (REVERSION TO ETHYLENE SENSITIVITY) and ARGOS proteins: these are positive regulators of the ethylene receptors, and thus are negative regulators of ethylene sensitivity [11Rai M.I. et al.The ARGOS gene family functions in a negative feedback loop to desensitize plants to ethylene.BMC Plant Biol. 2015; 15: 157Crossref PubMed Scopus (12) Google Scholar, 91Resnick J.S. et al.REVERSION-TO-ETHYLENE SENSITIVITY1, a conserved gene that regulates ethylene receptor function in Arabidopsis.Proc. Natl. Acad. Sci. U. S. A. 2006; 103: 7917-7922Crossref PubMed Scopus (114) Google Scholar, 92Shi J. et al.Maize and Arabidopsis ARGOS proteins interact with ethylene receptor signaling complex, supporting a regulatory role for ARGOS in ethylene signal transduction.Plant Physiol. 2016; 171: 2783-2797Crossref PubMed Scopus (14) Google Scholar]. In the absence of ethylene, active receptors subsequently bind to and thereby activate the CTR1 protein [93Lacey R.F. Binder B.M. How plants sense ethylene gas – the ethylene receptors.J. Inorg. Biochem. 2014; 133: 58-62Crossref PubMed Scopus (12) Google Scholar]. The levels of the receptors are regulated by ethylene and CTR1: slightly increasing ethylene levels stimulate the transcription of the receptors and stabilization of CTR1, whereas higher ethylene levels push the receptor/CTR1 towards proteasome-mediated degradation [94Shakeel S.N. et al.Ethylene regulates levels of ethylene receptor/CTR1 signaling complexes in Arabidopsis thaliana.J. Biol. Chem. 2015; 290: 12415-12424Crossref PubMed Scopus (15) Google Scholar]. CTR1 is a kinase that represses EIN2, an ER-located membrane protein. When this repression is released in the presence of ethylene, EIN2 is dephosphorylated and cleaved, releasing a C-terminal fragment that either moves to P-bodies or to the nucleus [95Li W. et al.EIN2-directed translational regulation of ethylene signaling in Arabidopsis.Cell. 2015; 163: 670-683Abstract Full Text Full Text PDF PubMed Scopus (66) Google Scholar, 96Merchante C. et al.Gene-specific translation regulation mediated by the hormone-signaling molecule EIN2.Cell. 2015; 163: 684-697Abstract Full Text Full Text PDF PubMed Scopus (67) Google Scholar]. The downstream mode of action of the EIN2 fragment has long been a mystery, but recent studies have shown that it is involved in gene-specific regulation of translation [95Li W. et al.EIN2-directed translational regulation of ethylene signaling in Arabidopsis.Cell. 2015; 163: 670-683Abstract Full Text Full Text PDF PubMed Scopus (66) Google Scholar, 96Merchante C. et al.Gene-specific translation regulation mediated by the hormone-signaling molecule EIN2.Cell. 2015; 163: 684-697Abstract Full Text Full Text PDF PubMed Scopus (67) Google Scholar]. The EIN2 fragment binds to the 3'-untranslated regions (3'-UTRs) of EBF1 and EBF2 transcripts, thereby repressing their translation. EBF1 and EBF2 are two central F-box proteins that target the primary ethylene-responsive TFs EIN3 and EIN3-LIKE 1 (EIL1) for protein degradation in the absence of ethylene [97Guo H. Ecker J.R. Plant responses to ethylene gas are mediated by SCFEBF1/EBF2-dependent proteolysis of EIN3 transcription factor.Cell. 2003; 115: 667-677Abstract Full Text Full Text PDF PubMed Scopus (495) Google Scholar, 98Potuschak T. et al.EIN3-dependent regulation of plant ethylene hormone signaling by two Arabidopsis F box proteins: EBF1 and EBF2.Cell. 2003; 115: 679-689Abstract Full Text Full Text PDF PubMed Scopus (420) Google Scholar]. In the presence of ethylene, EIN3 and EIL1 induce the expression of numerous secondary transcription factors (TFs), the ERFs [99Nakano T. et al.Identification of genes of the plant-specific transcription-factor families cooperatively regulated by ethylene and jasmonate in Arabidopsis thaliana.J. Plant Res. 2006; 119: 407-413Crossref PubMed Scopus (0) Google Scholar]. The activity of some ERFs has been reported to be increased by phosphorylation through the MPK3/6-cascade that also regulates ethylene biosynthesis, providing dual-level regulation of the ERF-mediated response [24Meng X. et al.Phosphorylation of an ERF transcription factor by Arabidopsis MPK3/MPK6 regulates plant defense gene induction and fungal resistance.Plant Cell. 2013; 25: 1126-1142Crossref PubMed Scopus (143) Google Scholar, 100Yoo S.-D. Sheen J. MAPK signaling in plant hormone ethylene signal transduction.Plant Signal. Behav. 2008; 3: 848-849Crossref PubMed Google Scholar]. Arabidopsis (Arabidopsis thaliana) plants overproducing ethylene are generally dwarfed, and plant growth is reduced by exposure to ethylene [7Burg S.P. Burg E.A. Ethylene formation in pea seedlings; its relation to the inhibition of bud growth caused by indole-3-acetic acid.Plant Physiol. 1968; 43: 1069-1074Crossref PubMed Google Scholar, 8Vogel J.P. et al.Recessive and dominant mutations in the ethylene biosynthetic gene ACS5 of Arabidopsis confer cytokinin insensitivity and ethylene overproduction, respectively.Proc. Natl. Acad. Sci. U. S. A. 1998; 95: 4766-4771Crossref PubMed Scopus (0) Google Scholar, 9Qu X. et al.A strong constitutive ethylene-response phenotype conferred on Arabidopsis plants containing null mutations in the ethylene receptors ETR1 and ERS1.BMC Plant Biol. 2007; 7: 3Crossref PubMed Scopus (0) Google Scholar]. Consequently, when the positive regulators of the ethylene signaling pathway (Box 1 and Figure 1) are mutated, plants are generally found to have larger rosettes with larger leaves in comparison to control plants. Increased growth has, for example, been observed upon mutation the endoplasmic reticulum (ER)- anchored protein EIN2 [10Feng G. et al.The Arabidopsis EIN2 restricts organ growth by retarding cell expansion.Plant Signal. Behav. 2015; 10e1017169Crossref PubMed Scopus (2) Google Scholar]. Conversely, mutants of negative regulators of ethylene signaling, such as the receptors ETR1 and ERS1 (Box 1), show a growth decrease [9Qu X. et al.A strong constitutive ethylene-response phenotype conferred on Arabidopsis plants containing null mutations in the ethylene receptors ETR1 and ERS1.BMC Plant Biol. 2007; 7: 3Crossref PubMed Scopus (0) Google Scholar]. Accordingly, overexpression of the negative regulators ARGOS or ARGOS-LIKE (ARL) stimulates leaf growth in arabidopsis [11Rai M.I. et al.The ARGOS gene family functions in a negative feedback loop to desensitize plants to ethylene.BMC Plant Biol. 2015; 15: 157Crossref PubMed Scopus (12) Google Scholar, 12Shi J. et al.Overexpression of ARGOS genes modifies plant sensitivity to ethylene, leading to improved drought tolerance in both Arabidopsis and maize.Plant Physiol. 2015; 169: 266-282Crossref PubMed Scopus (43) Google Scholar]. Moreover, plant lines in which the ethylene sensitivity is reduced, or treatments reducing sensitivity to ethylene, cause larger leaves. For instance, plants overexpressing NEIP2 or TCTP, genes encoding proteins interacting with the Nicotiana tabacum ethylene receptor, show decreased ethylene sensitivity but improved growth [13Cao Y.-R. et al.Tobacco ankyrin protein NEIP2 interacts with ethylene receptor NTHK1 and regulates plant growth and stress responses.Plant Cell Physiol. 2015; 56: 803-818Crossref PubMed Scopus (8) Google Scholar, 14Tao J.-J. et al.Tobacco translationally controlled tumor protein interacts with ethylene receptor tobacco histidine kinase1 and enhances plant growth through promotion of cell proliferation.Plant Physiol. 2015; 169: 96-114Crossref PubMed Scopus (18) Google Scholar]. Similarly, Pseudomonas frederiksbergensis, a soil bacterium that reduces plant sensitivity to ethylene, promotes the growth of red pepper plants [15Chatterjee P. et al.Beneficial soil bacterium Pseudomonas frederiksbergensis OS261 augments salt tolerance and promotes red pepper plant growth.Front. Plant Sci. 2017; 8: 705Crossref PubMed Scopus (0) Google Scholar]. Finally, some rhizosphere bacteria that promote plant growth do so by expressing ACC-DEAMINASE, decreasing the levels of 1-aminocyclopropane-1-carboxylic acid (ACC) in plants exposed to stress, and this has a positive effect on growth [16Chen L. et al.The rhizobacterium Variovorax paradoxus 5C-2, containing ACC deaminase, promotes growth and development of Arabidopsis thaliana via an ethylene-dependent pathway.J. Exp. Bot. 2013; 64: 1565-1573Crossref PubMed Scopus (30) Google Scholar]. Exceptionally, ethylene has been reported to stimulate leaf growth. In the presence of very low ethylene concentrations, Poa alpina and Poa compressa show increased leaf elongation rates [17Fiorani F. et al.Ethylene emission and responsiveness to applied ethylene vary among Poa species that inherently differ in leaf elongation rates.Plant Physiol. 2002; 129: 1382-1390Crossref PubMed Scopus (0) Google Scholar], and also the primary leaves of sunflower (Helianthus annuus) are enlarged [18Lee S.H. Reid D.M. The role of endogenous ethylene in the expansion of Helianthus annuus leaves.Can. J. Bot. 1997; 75: 501-508Crossref PubMed Google Scholar]. However, the opposite effect was observed as soon as ethylene levels are increased to concentrations higher than this low growth-promoting optimum. This general negative correlation between ethylene sensitivity and leaf growth has led to the classification of ethylene as a growth-repressing hormone. In plants, where growth mainly occurs post-embryonically through well-orchestrated cell divisions, the progression through the cell cycle is tightly governed by more than 70 core cell-cycle proteins (reviewed in [19Polyn S. et al.Cell cycle entry, maintenance, and exit during plant development.Curr. Opin. Plant Biol. 2015; 23: 1-7Crossref PubMed Scopus (46) Google Scholar]). Controlled by endogenous cues and environmental signals, cell-cycle progression and regulation vary depending on the plant organ, and the effect of ethylene is similarly organ-dependent. For instance, during the early development of the apical hook, ethylene participates in stimulating cell divisions, although its contribution is not crucial for curving of the apical hook [20Raz V. Koornneef M. Cell division activity during apical hook development.Plant Physiol. 2001; 125: 219-226Crossref PubMed Scopus (0) Google Scholar]. Moreover, ethylene and the downstream transcription factors (TFs) ERF018 and ERF109 promote cell division during vasculature development in arabidopsis stems [21Etchells J.P. et al.Plant vascular cell division is maintained by an interaction between PXY and ethylene signalling.PLoS Genet. 2012; 8e1002997Crossref PubMed Scopus (0) Google Scholar]. Thus, in these specific developmental contexts, ethylene can have a positive effect on cell division. In leaves of plants exposed to environmental stress, ethylene appears to have a negative effect on the cell cycle. When plants are exposed to less than 10 h of osmotic stress, ethylene mediates a temporary and reversible stop of the cell cycle. This is likely to occur through the inactivation of the CDKA by phosphorylation, possibly through the MPK3/6 pathway but independently from EIN3/EIL1 (Figure2) [2Skirycz A. et al.Pause-and-stop: the effects of osmotic stress on cell proliferation during early leaf development in Arabidopsis and a role for ethylene signaling in cell cycle arrest.Plant Cell. 2011; 23: 1876-1888Crossref PubMed Scopus (0) Google Scholar]. Moreover, at least four mechanisms in leaves link ethylene to the exit of cell division and a shift to endoreduplication and differentiation. First, accumulation of ethylene and induction of the BOLITA TF (an ERF, Table 1) triggers the activation of type II TEOSINTE BRANCHED 1/CYCLOIDEA/PCF (TCP) genes (Figure 2) [22Marsch-Martinez N. et al.BOLITA, an Arabidopsis AP2/ERF-like transcription factor that affects cell expansion and proliferation/differentiation pathways.Plant Mol. Biol. 2006; 62: 825-843Crossref PubMed Scopus (48) Google Scholar]. These TCP proteins bind to the promoter of RETINOBLASTOMA RELATED 1 (RBR1), and the encoded protein phosphorylates E2Fa and thus represses the transcription of the E2F target genes, thereby inhibiting progression into the S-phase and cell division. Second, ethylene induces the expression of ERF5 and ERF6, two closely related TFs, in actively growing leaves of plants exposed to stress [2Skirycz A. et al.Pause-and-stop: the effects of osmotic stress on cell proliferation during early leaf development in Arabidopsis and a role for ethylene signaling in cell cycle arrest.Plant Cell. 2011; 23: 1876-1888Crossref PubMed Scopus (0) Google Scholar, 23Dubois M. et al.ETHYLENE RESPONSE FACTOR6 acts as a central regulator of leaf growth under water-limiting conditions in Arabidopsis.Plant Physiol. 2013; 162: 319-332Crossref PubMed Scopus (97) Google Scholar, 24Meng X. et al.Phosphorylation of an ERF transcription factor by Arabidopsis MPK3/MPK6 regulates pl}, journal={Trends in plant science}, author={Dubois, M and Broeck L Van and Inzé, D}, year={2018}, month={Apr} }
 @article{broeck_dubois_vermeersch_storme_matsui_inzé_2017, title={From network to phenotype: the dynamic wiring of an Arabidopsis transcriptional network induced by osmotic stress}, volume={13}, url={https://doi.org/10.15252/msb.20177840}, DOI={10.15252/msb.20177840}, abstractNote={Plants have established different mechanisms to cope with environmental fluctuations and accordingly fine‐tune their growth and development through the regulation of complex molecular networks. It is largely unknown how the network architectures change and what the key regulators in stress responses and plant growth are. Here, we investigated a complex, highly interconnected network of 20 Arabidopsis transcription factors (TFs) at the basis of leaf growth inhibition upon mild osmotic stress. We tracked the dynamic behavior of the stress‐responsive TFs over time, showing the rapid induction following stress treatment, specifically in growing leaves. The connections between the TFs were uncovered using inducible overexpression lines and were validated with transient expression assays. This study resulted in the identification of a core network, composed of ERF6, ERF8, ERF9, ERF59, and ERF98, which is responsible for most transcriptional connections. The analyses highlight the biological function of this core network in environmental adaptation and its redundancy. Finally, a phenotypic analysis of loss‐of‐function and gain‐of‐function lines of the transcription factors established multiple connections between the stress‐responsive network and leaf growth.}, number={12}, journal={Molecular Systems Biology}, publisher={EMBO}, author={Broeck, Lisa Van and Dubois, Marieke and Vermeersch, Mattias and Storme, Veronique and Matsui, Minami and Inzé, Dirk}, year={2017}, month={Dec}, pages={961} }
 @article{ralfl34 regulates formative cell divisions in arabidopsis pericycle during lateral root initiation._2016, volume={8}, url={http://europepmc.org/abstract/med/27521602}, DOI={10.1093/jxb/erw281}, abstractNote={Highlight We describe the role of RALFL34 during early events in lateral root development, and demonstrate its specific importance in orchestrating formative cell divisions in the pericycle.}, journal={Journal of experimental botany}, year={2016}, month={Aug} }
 @article{time of day determines arabidopsis transcriptome and growth dynamics under mild drought._2017, volume={2}, url={http://europepmc.org/abstract/med/27479938}, DOI={10.1111/pce.12809}, abstractNote={AbstractDrought stress is a major problem for agriculture worldwide, causing significant yield losses. Plants have developed highly flexible mechanisms to deal with drought, including organ‐ and developmental stage‐specific responses. In young leaves, growth is repressed as an active mechanism to save water and energy, increasing the chances of survival but decreasing yield. Despite its importance, the molecular basis for this growth inhibition is largely unknown. Here, we present a novel approach to explore early molecular mechanisms controlling Arabidopsis leaf growth inhibition following mild drought. We found that growth and transcriptome responses to drought are highly dynamic. Growth was only repressed by drought during the day, and our evidence suggests that this may be due to gating by the circadian clock. Similarly, time of day strongly affected the extent, specificity, and in certain cases even direction of drought‐induced changes in gene expression. These findings underscore the importance of taking into account diurnal patterns to understand stress responses, as only a small core of drought‐responsive genes are affected by drought at all times of the day. Finally, we leveraged our high‐resolution data to demonstrate that phenotypic and transcriptome responses can be matched to identify putative novel regulators of growth under mild drought.}, journal={Plant, cell & environment}, year={2017}, month={Feb} }
 @article{the ethylene response factors erf6 and erf11 antagonistically regulate mannitol-induced growth inhibition in arabidopsis._2015, volume={9}, url={http://europepmc.org/abstract/med/25995327}, DOI={10.1104/pp.15.00335}, abstractNote={A negative feedback loop involving two Ethylene Response Factors fine-tunes growth inhibition and stress tolerance activation under mannitol-induced stress. Leaf growth is a tightly regulated and complex process, which responds in a dynamic manner to changing environmental conditions, but the mechanisms that reduce growth under adverse conditions are rather poorly understood. We previously identified a growth inhibitory pathway regulating leaf growth upon exposure to a low concentration of mannitol and characterized the ETHYLENE RESPONSE FACTOR (ERF)/APETALA2 transcription factor ERF6 as a central activator of both leaf growth inhibition and induction of stress tolerance genes. Here, we describe the role of the transcriptional repressor ERF11 in relation to the ERF6-mediated stress response in Arabidopsis (Arabidopsis thaliana). Using inducible overexpression lines, we show that ERF6 induces the expression of ERF11. ERF11 in turn molecularly counteracts the action of ERF6 and represses at least some of the ERF6-induced genes by directly competing for the target gene promoters. As a phenotypical consequence of the ERF6-ERF11 antagonism, the extreme dwarfism caused by ERF6 overexpression is suppressed by overexpression of ERF11. Together, our data demonstrate that dynamic mechanisms exist to fine-tune the stress response and that ERF11 counteracts ERF6 to maintain a balance between plant growth and stress defense.}, journal={Plant physiology}, year={2015}, month={Sep} }