@article{ma_ca2_2025,
	title = {Ca2+ waves and ethylene/{JA} crosstalk orchestrate wound responses in {Arabidopsis} roots},
	volume = {26},
	issn = {1469-221X},
	url = {https://www.embopress.org/doi/full/10.1038/s44319-025-00471-z},
	doi = {10.1038/s44319-025-00471-z},
	abstract = {Wounding triggers complex and multi-faceted responses in plants. Among these, calcium (Ca2+) waves serve as an immediate and localized response to strong stimuli, such as nematode infection or laser ablation. Here, we investigate the propagation patterns of Ca2+ waves induced by laser ablation and observe that glutamate-receptor-like channels (GLR3.3/GLR3.6), the stretch-activated anion channel MSL10, and the mechanosensitive Ca2+-permeable channels MCA1/MCA2 influence this process. These channels contribute to ethylene-associated signaling pathways, potentially through the WRKY33-ACS6 regulatory network. Furthermore, our findings show that ACC/ethylene signaling modulates Ca2+ wave propagation following laser ablation. Ethylene perception and synthesis at the site of damage regulate the local jasmonate response, which displays tissue-specific patterns upon laser ablation. Overall, our data provide new insights into the molecular and cellular processes underlying plant responses to localized damage, highlighting the roles of specific ion channels and hormone signaling pathways in shaping these responses in Arabidopsis roots.},
	number = {12},
	urldate = {2025-06-27},
	journal = {EMBO reports},
	author = {Ma, Xuemin and Hasan, M Shamim and Anjam, Muhammad Shahzad and Mahmud, Sakil and Bhattacharyya, Sabarna and Vothknecht, Ute C and Mendy, Badou and Grundler, Florian M W and Marhavý, Peter},
	month = jun,
	year = {2025},
	note = {Num Pages: 3203
Publisher: John Wiley \& Sons, Ltd},
	keywords = {Ca2+ Wave, Ethylene, Jasmonate, Laser Ablation},
	pages = {3187--3203},
}

Wounding triggers complex and multi-faceted responses in plants. Among these, calcium (Ca2+) waves serve as an immediate and localized response to strong stimuli, such as nematode infection or laser ablation. Here, we investigate the propagation patterns of Ca2+ waves induced by laser ablation and observe that glutamate-receptor-like channels (GLR3.3/GLR3.6), the stretch-activated anion channel MSL10, and the mechanosensitive Ca2+-permeable channels MCA1/MCA2 influence this process. These channels contribute to ethylene-associated signaling pathways, potentially through the WRKY33-ACS6 regulatory network. Furthermore, our findings show that ACC/ethylene signaling modulates Ca2+ wave propagation following laser ablation. Ethylene perception and synthesis at the site of damage regulate the local jasmonate response, which displays tissue-specific patterns upon laser ablation. Overall, our data provide new insights into the molecular and cellular processes underlying plant responses to localized damage, highlighting the roles of specific ion channels and hormone signaling pathways in shaping these responses in Arabidopsis roots.

@article{di_fino_cellular_2025,
	title = {Cellular damage triggers mechano-chemical control of cell wall dynamics and patterned cell divisions in plant healing},
	volume = {60},
	issn = {1534-5807},
	url = {https://www.sciencedirect.com/science/article/pii/S1534580724007718},
	doi = {10.1016/j.devcel.2024.12.032},
	abstract = {Reactivation of cell division is crucial for the regeneration of damaged tissues, which is a fundamental process across all multicellular organisms. However, the mechanisms underlying the activation of cell division in plants during regeneration remain poorly understood. Here, we show that single-cell endodermal ablation generates a transient change in the local mechanical pressure on neighboring pericycle cells to activate patterned cell division that is crucial for tissue regeneration in Arabidopsis roots. Moreover, we provide strong evidence that this process relies on the phytohormone ethylene. Thus, our results highlight a previously unrecognized role of mechano-chemical control in patterned cell division during regeneration in plants.},
	number = {10},
	urldate = {2025-05-23},
	journal = {Developmental Cell},
	author = {Di Fino, Luciano Martín and Anjam, Muhammad Shahzad and Besten, Maarten and Mentzelopoulou, Andriani and Papadakis, Vassilis and Zahid, Nageena and Baez, Luis Alonso and Trozzi, Nicola and Majda, Mateusz and Ma, Xuemin and Hamann, Thorsten and Sprakel, Joris and Moschou, Panagiotis N. and Smith, Richard S. and Marhavý, Peter},
	month = may,
	year = {2025},
	keywords = {cell division, cell wall, ethylene, mechanobiology, pectin, regeneration, single-cell laser ablation, xylem-pole-pericycle},
	pages = {1411--1422.e6},
}

Reactivation of cell division is crucial for the regeneration of damaged tissues, which is a fundamental process across all multicellular organisms. However, the mechanisms underlying the activation of cell division in plants during regeneration remain poorly understood. Here, we show that single-cell endodermal ablation generates a transient change in the local mechanical pressure on neighboring pericycle cells to activate patterned cell division that is crucial for tissue regeneration in Arabidopsis roots. Moreover, we provide strong evidence that this process relies on the phytohormone ethylene. Thus, our results highlight a previously unrecognized role of mechano-chemical control in patterned cell division during regeneration in plants.

@article{mazumdar_damage_2025,
	title = {Damage activates \textit{{EXG1}} and \textit{{RLP44}} to suppress vascular differentiation during regeneration in \textit{{Arabidopsis}}},
	volume = {6},
	issn = {2590-3462},
	url = {https://www.sciencedirect.com/science/article/pii/S2590346225000185},
	doi = {10.1016/j.xplc.2025.101256},
	abstract = {Plants possess remarkable regenerative abilities to form de novo vasculature after damage and in response to pathogens that invade and withdraw nutrients. To identify common factors that affect vascular formation upon stress, we searched for Arabidopsis thaliana genes differentially expressed upon Agrobacterium infection, nematode infection, and plant grafting. One such gene is cell wall-related and highly induced by all three stresses, which we named ENHANCED XYLEM AND GRAFTING1 (EXG1), since its mutations promote ectopic xylem formation in a vascular cell induction system and enhance graft formation. Further observations revealed that exg1 mutants show inhibited cambium development and callus formation but enhanced tissue attachment, syncytium size, phloem reconnection, and xylem formation. Given that brassinosteroids also promote xylem differentiation, we analyzed brassinosteroid-related genes and found that mutations in RLP44 encoding a receptor-like protein cause similar regeneration-related phenotypes as mutations in EXG1. Like EXG1, RLP44 expression is also induced by grafting and wounding. Mutations in EXG1 and RLP44 affect the expression of many genes in common, including those related to cell walls and genes important for vascular regeneration. Our results suggest that EXG1 integrates information from wounding or pathogen stress and functions with RLP44 to suppress vascular differentiation during regeneration and healing.},
	number = {4},
	urldate = {2025-04-22},
	journal = {Plant Communications},
	author = {Mazumdar, Shamik and Augstein, Frauke and Zhang, Ai and Musseau, Constance and Anjam, Muhammad Shahzad and Marhavy, Peter and Melnyk, Charles W.},
	month = apr,
	year = {2025},
	keywords = {Cell wall, Grafting, Regeneration, Stress, Wounding, Xylem, cell wall, grafting, regeneration, stress, wounding, xylem},
	pages = {101256},
}

Plants possess remarkable regenerative abilities to form de novo vasculature after damage and in response to pathogens that invade and withdraw nutrients. To identify common factors that affect vascular formation upon stress, we searched for Arabidopsis thaliana genes differentially expressed upon Agrobacterium infection, nematode infection, and plant grafting. One such gene is cell wall-related and highly induced by all three stresses, which we named ENHANCED XYLEM AND GRAFTING1 (EXG1), since its mutations promote ectopic xylem formation in a vascular cell induction system and enhance graft formation. Further observations revealed that exg1 mutants show inhibited cambium development and callus formation but enhanced tissue attachment, syncytium size, phloem reconnection, and xylem formation. Given that brassinosteroids also promote xylem differentiation, we analyzed brassinosteroid-related genes and found that mutations in RLP44 encoding a receptor-like protein cause similar regeneration-related phenotypes as mutations in EXG1. Like EXG1, RLP44 expression is also induced by grafting and wounding. Mutations in EXG1 and RLP44 affect the expression of many genes in common, including those related to cell walls and genes important for vascular regeneration. Our results suggest that EXG1 integrates information from wounding or pathogen stress and functions with RLP44 to suppress vascular differentiation during regeneration and healing.

@article{baral_typhon_2025,
	title = {{TYPHON} proteins are {RAB}-dependent mediators of the trans-{Golgi} network secretory pathway},
	volume = {37},
	issn = {1040-4651},
	url = {https://doi.org/10.1093/plcell/koae280},
	doi = {10.1093/plcell/koae280},
	abstract = {The trans-Golgi network (TGN), a key compartment in endomembrane trafficking, participates in both secretion to and endocytosis from the plasma membrane. Consequently, the TGN plays a key role in plant growth and development. Understanding how proteins are sorted for secretion or endocytic recycling at the TGN is critical for elucidating mechanisms of plant development. We previously showed that the protein ECHIDNA is essential for phytohormonal control of hypocotyl bending because it mediates secretion of cell wall components and the auxin influx carrier AUXIN RESISTANT 1 (AUX1) from the TGN. Despite the critical role of ECHIDNA in TGN-mediated trafficking, its mode of action remains unknown in Arabidopsis (Arabidopsis thaliana). We therefore performed a suppressor screen on the ech mutant. Here, we report the identification of TGN-localized TYPHON 1 (TPN1) and TPN2 proteins. A single amino acid change in either TPN protein causes dominant suppression of the ech mutant's defects in growth and AUX1 secretion, while also restoring wild-type (WT)-like ethylene-responsive hypocotyl bending. Importantly, genetic and cell biological evidence shows that TPN1 acts through RAS-ASSOCIATED BINDING H1b (RABH1b), a TGN-localized RAB-GTPase. These results provide insights into ECHIDNA-mediated secretory trafficking of cell wall and auxin carriers at the TGN, as well as its role in controlling plant growth.},
	number = {1},
	urldate = {2025-01-20},
	journal = {The Plant Cell},
	author = {Baral, Anirban and Gendre, Delphine and Aryal, Bibek and Fougère, Louise and Di Fino, Luciano Martin and Ohori, Chihiro and Sztojka, Bernadette and Uemura, Tomohiro and Ueda, Takashi and Marhavý, Peter and Boutté, Yohann and Bhalerao, Rishikesh P},
	month = jan,
	year = {2025},
	pages = {koae280},
}

The trans-Golgi network (TGN), a key compartment in endomembrane trafficking, participates in both secretion to and endocytosis from the plasma membrane. Consequently, the TGN plays a key role in plant growth and development. Understanding how proteins are sorted for secretion or endocytic recycling at the TGN is critical for elucidating mechanisms of plant development. We previously showed that the protein ECHIDNA is essential for phytohormonal control of hypocotyl bending because it mediates secretion of cell wall components and the auxin influx carrier AUXIN RESISTANT 1 (AUX1) from the TGN. Despite the critical role of ECHIDNA in TGN-mediated trafficking, its mode of action remains unknown in Arabidopsis (Arabidopsis thaliana). We therefore performed a suppressor screen on the ech mutant. Here, we report the identification of TGN-localized TYPHON 1 (TPN1) and TPN2 proteins. A single amino acid change in either TPN protein causes dominant suppression of the ech mutant's defects in growth and AUX1 secretion, while also restoring wild-type (WT)-like ethylene-responsive hypocotyl bending. Importantly, genetic and cell biological evidence shows that TPN1 acts through RAS-ASSOCIATED BINDING H1b (RABH1b), a TGN-localized RAB-GTPase. These results provide insights into ECHIDNA-mediated secretory trafficking of cell wall and auxin carriers at the TGN, as well as its role in controlling plant growth.

@article{liu_proxitome-rna-capture_2024,
	title = {A proxitome-{RNA}-capture approach reveals that processing bodies repress coregulated hub genes},
	volume = {36},
	issn = {1040-4651},
	url = {https://doi.org/10.1093/plcell/koad288},
	doi = {10.1093/plcell/koad288},
	abstract = {Cellular condensates are usually ribonucleoprotein assemblies with liquid- or solid-like properties. Because these subcellular structures lack a delineating membrane, determining their compositions is difficult. Here we describe a proximity-biotinylation approach for capturing the RNAs of the condensates known as processing bodies (PBs) in Arabidopsis (Arabidopsis thaliana). By combining this approach with RNA detection, in silico, and high-resolution imaging approaches, we studied PBs under normal conditions and heat stress. PBs showed a much more dynamic RNA composition than the total transcriptome. RNAs involved in cell wall development and regeneration, plant hormonal signaling, secondary metabolism/defense, and RNA metabolism were enriched in PBs. RNA-binding proteins and the liquidity of PBs modulated RNA recruitment, while RNAs were frequently recruited together with their encoded proteins. In PBs, RNAs follow distinct fates: in small liquid-like PBs, RNAs get degraded while in more solid-like larger ones, they are stored. PB properties can be regulated by the actin-polymerizing SCAR (suppressor of the cyclic AMP)-WAVE (WASP family verprolin homologous) complex. SCAR/WAVE modulates the shuttling of RNAs between PBs and the translational machinery, thereby adjusting ethylene signaling. In summary, we provide an approach to identify RNAs in condensates that allowed us to reveal a mechanism for regulating RNA fate.},
	number = {3},
	urldate = {2024-03-01},
	journal = {The Plant Cell},
	author = {Liu, Chen and Mentzelopoulou, Andriani and Hatzianestis, Ioannis H and Tzagkarakis, Epameinondas and Skaltsogiannis, Vasileios and Ma, Xuemin and Michalopoulou, Vassiliki A and Romero-Campero, Francisco J and Romero-Losada, Ana B and Sarris, Panagiotis F and Marhavy, Peter and Bölter, Bettina and Kanterakis, Alexandros and Gutierrez-Beltran, Emilio and Moschou, Panagiotis N},
	month = mar,
	year = {2024},
	pages = {559--584},
}

Cellular condensates are usually ribonucleoprotein assemblies with liquid- or solid-like properties. Because these subcellular structures lack a delineating membrane, determining their compositions is difficult. Here we describe a proximity-biotinylation approach for capturing the RNAs of the condensates known as processing bodies (PBs) in Arabidopsis (Arabidopsis thaliana). By combining this approach with RNA detection, in silico, and high-resolution imaging approaches, we studied PBs under normal conditions and heat stress. PBs showed a much more dynamic RNA composition than the total transcriptome. RNAs involved in cell wall development and regeneration, plant hormonal signaling, secondary metabolism/defense, and RNA metabolism were enriched in PBs. RNA-binding proteins and the liquidity of PBs modulated RNA recruitment, while RNAs were frequently recruited together with their encoded proteins. In PBs, RNAs follow distinct fates: in small liquid-like PBs, RNAs get degraded while in more solid-like larger ones, they are stored. PB properties can be regulated by the actin-polymerizing SCAR (suppressor of the cyclic AMP)-WAVE (WASP family verprolin homologous) complex. SCAR/WAVE modulates the shuttling of RNAs between PBs and the translational machinery, thereby adjusting ethylene signaling. In summary, we provide an approach to identify RNAs in condensates that allowed us to reveal a mechanism for regulating RNA fate.

@article{hasan_redox_2024,
	title = {Redox signalling in plant–nematode interactions: {Insights} into molecular crosstalk and defense mechanisms},
	volume = {47},
	copyright = {© 2024 John Wiley \& Sons Ltd.},
	issn = {1365-3040},
	shorttitle = {Redox signalling in plant–nematode interactions},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/pce.14925},
	doi = {10.1111/pce.14925},
	abstract = {Plant–parasitic nematodes, specifically cyst nematodes (CNs) and root-knot nematodes (RKNs), pose significant threats to global agriculture, leading to substantial crop losses. Both CNs and RKNs induce permanent feeding sites in the root of their host plants, which then serve as their only source of nutrients throughout their lifecycle. Plants deploy reactive oxygen species (ROS) as a primary defense mechanism against nematode invasion. Notably, both CNs and RKNs have evolved sophisticated strategies to manipulate the host's redox environment to their advantage, with each employing distinct tactics to combat ROS. In this review, we have focused on the role of ROS and its scavenging network in interactions between host plants and CNs and RKNs. Overall, this review emphasizes the complex interplay between plant defense mechanism, redox signalling and nematode survival tactics, suggesting potential avenues for developing innovative nematode management strategies in agriculture.},
	language = {en},
	number = {8},
	urldate = {2024-07-19},
	journal = {Plant, Cell \& Environment},
	author = {Hasan, M. Shamim and Lin, Ching-Jung and Marhavy, Peter and Kyndt, Tina and Siddique, Shahid},
	year = {2024},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/pce.14925},
	keywords = {ROS, antioxidants, cyst nematodes, effectors, root-knot nematodes},
	pages = {2811--2820},
}

Plant–parasitic nematodes, specifically cyst nematodes (CNs) and root-knot nematodes (RKNs), pose significant threats to global agriculture, leading to substantial crop losses. Both CNs and RKNs induce permanent feeding sites in the root of their host plants, which then serve as their only source of nutrients throughout their lifecycle. Plants deploy reactive oxygen species (ROS) as a primary defense mechanism against nematode invasion. Notably, both CNs and RKNs have evolved sophisticated strategies to manipulate the host's redox environment to their advantage, with each employing distinct tactics to combat ROS. In this review, we have focused on the role of ROS and its scavenging network in interactions between host plants and CNs and RKNs. Overall, this review emphasizes the complex interplay between plant defense mechanism, redox signalling and nematode survival tactics, suggesting potential avenues for developing innovative nematode management strategies in agriculture.

@article{guerreiro_unveiling_2023,
	title = {Unveiling the intricate mechanisms of plant defense},
	volume = {1},
	issn = {2813-821X},
	url = {https://www.frontiersin.org/articles/10.3389/fphgy.2023.1285373},
	doi = {10.3389/fphgy.2023.1285373},
	abstract = {Plants may lack mobility, but they are not defenseless against the constant threats posed by pathogens and pests. Pattern Recognition Receptors (PRRs), which are located on the plasma membrane, enable plants to effectively recognize intruders. These receptors function by sensing elicitors or fragments of the cell wall that arise from damage. Recent studies underscore the significance of maintaining cell wall integrity in the coordination of defense mechanisms following the detection of parasitism. Pathogen invasion often triggers alterations in cell wall structure, which leads to the release of molecules like β-glucans and oligogalacturonides. These small molecules are then recognized by PRRs, which stimulate downstream signaling pathways that involve both receptor-like kinases and calcium-dependent signaling. Here, we present the latest insights into plant signaling that play a vital role in immunity: the maintenance of cell wall integrity; the intricate interplay between receptor-like kinases; and the involvement of calcium ions. The goal of the review is to provide readers with a deeper understanding of the intricate mechanisms underlying plant defense strategies.},
	urldate = {2024-02-08},
	journal = {Frontiers in Plant Physiology},
	author = {Guerreiro, Julie and Marhavý, Peter},
	year = {2023},
}

Plants may lack mobility, but they are not defenseless against the constant threats posed by pathogens and pests. Pattern Recognition Receptors (PRRs), which are located on the plasma membrane, enable plants to effectively recognize intruders. These receptors function by sensing elicitors or fragments of the cell wall that arise from damage. Recent studies underscore the significance of maintaining cell wall integrity in the coordination of defense mechanisms following the detection of parasitism. Pathogen invasion often triggers alterations in cell wall structure, which leads to the release of molecules like β-glucans and oligogalacturonides. These small molecules are then recognized by PRRs, which stimulate downstream signaling pathways that involve both receptor-like kinases and calcium-dependent signaling. Here, we present the latest insights into plant signaling that play a vital role in immunity: the maintenance of cell wall integrity; the intricate interplay between receptor-like kinases; and the involvement of calcium ions. The goal of the review is to provide readers with a deeper understanding of the intricate mechanisms underlying plant defense strategies.

@article{kolbeck_casp_2022,
	title = {{CASP} microdomain formation requires cross cell wall stabilization of domains and non-cell autonomous action of {LOTR1}},
	volume = {11},
	issn = {2050-084X},
	url = {https://doi.org/10.7554/eLife.69602},
	doi = {10/gpjfdm},
	abstract = {Efficient uptake of nutrients in both animal and plant cells requires tissue-spanning diffusion barriers separating inner tissues from the outer lumen/soil. However, we poorly understand how such contiguous three-dimensional superstructures are formed in plants. Here, we show that correct establishment of the plant Casparian Strip (CS) network relies on local neighbor communication. We show that positioning of Casparian Strip membrane domains (CSDs) is tightly coordinated between neighbors in wild-type and that restriction of domain formation involves the putative extracellular protease LOTR1. Impaired domain restriction in lotr1 leads to fully functional CSDs at ectopic positions, forming ‘half strips’. LOTR1 action in the endodermis requires its expression in the stele. LOTR1 endodermal expression cannot complement, while cortex expression causes a dominant-negative phenotype. Our findings establish LOTR1 as a crucial player in CSD positioning acting in a directional, non-cell-autonomous manner to restrict and coordinate CS positioning.},
	urldate = {2022-02-17},
	journal = {eLife},
	author = {Kolbeck, Andreas and Marhavý, Peter and De Bellis, Damien and Li, Baohai and Kamiya, Takehiro and Fujiwara, Toru and Kalmbach, Lothar and Geldner, Niko},
	editor = {Benitez-Alfonso, Yoselin and Kleine-Vehn, Jürgen and Jallais, Yvon and Somssich, Marc},
	month = jan,
	year = {2022},
	keywords = {arabidopsis, casparian strip, endodermis, microdomains, neprosin, network},
	pages = {e69602},
}

Efficient uptake of nutrients in both animal and plant cells requires tissue-spanning diffusion barriers separating inner tissues from the outer lumen/soil. However, we poorly understand how such contiguous three-dimensional superstructures are formed in plants. Here, we show that correct establishment of the plant Casparian Strip (CS) network relies on local neighbor communication. We show that positioning of Casparian Strip membrane domains (CSDs) is tightly coordinated between neighbors in wild-type and that restriction of domain formation involves the putative extracellular protease LOTR1. Impaired domain restriction in lotr1 leads to fully functional CSDs at ectopic positions, forming ‘half strips’. LOTR1 action in the endodermis requires its expression in the stele. LOTR1 endodermal expression cannot complement, while cortex expression causes a dominant-negative phenotype. Our findings establish LOTR1 as a crucial player in CSD positioning acting in a directional, non-cell-autonomous manner to restrict and coordinate CS positioning.

@article{de_bellis_extracellular_2022,
	title = {Extracellular vesiculo-tubular structures associated with suberin deposition in plant cell walls},
	volume = {13},
	copyright = {2022 The Author(s)},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/s41467-022-29110-0},
	doi = {10.1038/s41467-022-29110-0},
	abstract = {Suberin is a fundamental plant biopolymer, found in protective tissues, such as seed coats, exodermis and endodermis of roots. Suberin is deposited in most suberizing cells in the form of lamellae just outside of the plasma membrane, below the primary cell wall. How monomeric suberin precursors, thought to be synthesized at the endoplasmic reticulum, are transported outside of the cell, for polymerization into suberin lamellae has remained obscure. Using electron-microscopy, we observed large numbers of extracellular vesiculo-tubular structures (EVs) to accumulate specifically in suberizing cells, in both chemically and cryo-fixed samples. EV presence correlates perfectly with root suberization and we could block suberin deposition and vesicle accumulation by affecting early, as well as late steps in the secretory pathway. Whereas many previous reports have described EVs in the context of biotic interactions, our results suggest a developmental role for extracellular vesicles in the formation of a major cell wall polymer.},
	language = {en},
	number = {1},
	urldate = {2024-02-08},
	journal = {Nature Communications},
	author = {De Bellis, Damien and Kalmbach, Lothar and Marhavý, Peter and Daraspe, Jean and Geldner, Niko and Barberon, Marie},
	month = mar,
	year = {2022},
	note = {Number: 1
Publisher: Nature Publishing Group},
	keywords = {Plant cell biology, Plant development},
	pages = {1489},
}

Suberin is a fundamental plant biopolymer, found in protective tissues, such as seed coats, exodermis and endodermis of roots. Suberin is deposited in most suberizing cells in the form of lamellae just outside of the plasma membrane, below the primary cell wall. How monomeric suberin precursors, thought to be synthesized at the endoplasmic reticulum, are transported outside of the cell, for polymerization into suberin lamellae has remained obscure. Using electron-microscopy, we observed large numbers of extracellular vesiculo-tubular structures (EVs) to accumulate specifically in suberizing cells, in both chemically and cryo-fixed samples. EV presence correlates perfectly with root suberization and we could block suberin deposition and vesicle accumulation by affecting early, as well as late steps in the secretory pathway. Whereas many previous reports have described EVs in the context of biotic interactions, our results suggest a developmental role for extracellular vesicles in the formation of a major cell wall polymer.

@incollection{anjam_rna_2022,
	address = {New York, NY},
	series = {Methods in {Molecular} {Biology}},
	title = {{RNA} {Isolation} from {Nematode}-{Induced} {Feeding} {Sites} in {Arabidopsis} {RootsRoots} {Using} {Laser} {Capture} {Microdissection}},
	isbn = {978-1-07-162297-1},
	url = {https://doi.org/10.1007/978-1-0716-2297-1_22},
	abstract = {Nematodes are diverse multicellular organisms that are most abundantly found in the soil. Most nematodes are free-living and feed on a range of organisms. Based on their feeding habits, soil nematodes can be classified into four groups: bacterial, omnivorous, fungal, and plant-feeding. Plant-parasitic nematodes (PPNs) are a serious threat to global food security, causing substantial losses to the agricultural sector. Root-knot and cyst nematodes are the most important of PPNs, significantly limiting the yield of commercial crops such as sugar beet, mustard, and cauliflower. The life cycle of these nematodes consists of four molting stages (J1–J4) that precede adulthood. Nonetheless, only second-stage juveniles (J2), which hatch from eggs, are infective worms that can parasitize the host’s roots. The freshly hatched juveniles (J2) of beet cyst nematode, Heterodera schachtii, establish a permanent feeding site inside the roots of the host plant. A cocktail of proteinaceous secretions is injected into a selected cell which later develops into a syncytium via local cell wall dissolution of several hundred neighboring cells. The formation of syncytium is accompanied by massive transcriptional, metabolic, and proteomic changes inside the host tissues. It creates a metabolic sink in which solutes are translocated to feed the nematodes throughout their life cycle. Deciphering the molecular signaling cascades during syncytium establishment is thus essential in studying the plant-nematode interactions and ensuring sustainability in agricultural practices. However, isolating RNA, protein, and metabolites from syncytial cells remains challenging. Extensive use of laser capture microdissection (LCM) in animal and human tissues has shown this approach to be a powerful technique for isolating a single cell from complex tissues. Here, we describe a simplified protocol for Arabidopsis-Heterodera schachtii infection assays, which is routinely applied in several plant-nematode laboratories. Next, we provide a detailed protocol for isolating high-quality RNA from syncytial cells induced by Heterodera schachtii in the roots of Arabidopsis thaliana plants.},
	language = {en},
	urldate = {2022-04-29},
	booktitle = {Environmental {Responses} in {Plants}: {Methods} and {Protocols}},
	publisher = {Springer US},
	author = {Anjam, Muhammad Shahzad and Siddique, Shahid and Marhavý, Peter},
	editor = {Duque, Paula and Szakonyi, Dóra},
	year = {2022},
	keywords = {Arabidopsis root dissection, Laser capture dissection, Plant-nematode infection, RNA extraction, Syncytial cell isolation},
	pages = {313--324},
}

Nematodes are diverse multicellular organisms that are most abundantly found in the soil. Most nematodes are free-living and feed on a range of organisms. Based on their feeding habits, soil nematodes can be classified into four groups: bacterial, omnivorous, fungal, and plant-feeding. Plant-parasitic nematodes (PPNs) are a serious threat to global food security, causing substantial losses to the agricultural sector. Root-knot and cyst nematodes are the most important of PPNs, significantly limiting the yield of commercial crops such as sugar beet, mustard, and cauliflower. The life cycle of these nematodes consists of four molting stages (J1–J4) that precede adulthood. Nonetheless, only second-stage juveniles (J2), which hatch from eggs, are infective worms that can parasitize the host’s roots. The freshly hatched juveniles (J2) of beet cyst nematode, Heterodera schachtii, establish a permanent feeding site inside the roots of the host plant. A cocktail of proteinaceous secretions is injected into a selected cell which later develops into a syncytium via local cell wall dissolution of several hundred neighboring cells. The formation of syncytium is accompanied by massive transcriptional, metabolic, and proteomic changes inside the host tissues. It creates a metabolic sink in which solutes are translocated to feed the nematodes throughout their life cycle. Deciphering the molecular signaling cascades during syncytium establishment is thus essential in studying the plant-nematode interactions and ensuring sustainability in agricultural practices. However, isolating RNA, protein, and metabolites from syncytial cells remains challenging. Extensive use of laser capture microdissection (LCM) in animal and human tissues has shown this approach to be a powerful technique for isolating a single cell from complex tissues. Here, we describe a simplified protocol for Arabidopsis-Heterodera schachtii infection assays, which is routinely applied in several plant-nematode laboratories. Next, we provide a detailed protocol for isolating high-quality RNA from syncytial cells induced by Heterodera schachtii in the roots of Arabidopsis thaliana plants.

@article{otvos_pickle_2021,
	title = {Pickle {Recruits} {Retinoblastoma} {Related} 1 to {Control} {Lateral} {Root} {Formation} in {Arabidopsis}},
	volume = {22},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	url = {https://www.mdpi.com/1422-0067/22/8/3862},
	doi = {10.3390/ijms22083862},
	abstract = {Lateral root (LR) formation is an example of a plant post-embryonic organogenesis event. LRs are issued from non-dividing cells entering consecutive steps of formative divisions, proliferation and elongation. The chromatin remodeling protein PICKLE (PKL) negatively regulates auxin-mediated LR formation through a mechanism that is not yet known. Here we show that PKL interacts with RETINOBLASTOMA-RELATED 1 (RBR1) to repress the LATERAL ORGAN BOUNDARIES-DOMAIN 16 (LBD16) promoter activity. Since LBD16 function is required for the formative division of LR founder cells, repression mediated by the PKL–RBR1 complex negatively regulates formative division and LR formation. Inhibition of LR formation by PKL–RBR1 is counteracted by auxin, indicating that, in addition to auxin-mediated transcriptional responses, the fine-tuned process of LR formation is also controlled at the chromatin level in an auxin-signaling dependent manner.},
	language = {en},
	number = {8},
	urldate = {2021-07-01},
	journal = {International Journal of Molecular Sciences},
	author = {Ötvös, Krisztina and Miskolczi, Pál and Marhavý, Peter and Cruz-Ramírez, Alfredo and Benková, Eva and Robert, Stéphanie and Bakó, László},
	month = jan,
	year = {2021},
	keywords = {\textit{de novo} organogenesis, auxin signaling, chromatin remodeling},
	pages = {3862},
}

Lateral root (LR) formation is an example of a plant post-embryonic organogenesis event. LRs are issued from non-dividing cells entering consecutive steps of formative divisions, proliferation and elongation. The chromatin remodeling protein PICKLE (PKL) negatively regulates auxin-mediated LR formation through a mechanism that is not yet known. Here we show that PKL interacts with RETINOBLASTOMA-RELATED 1 (RBR1) to repress the LATERAL ORGAN BOUNDARIES-DOMAIN 16 (LBD16) promoter activity. Since LBD16 function is required for the formative division of LR founder cells, repression mediated by the PKL–RBR1 complex negatively regulates formative division and LR formation. Inhibition of LR formation by PKL–RBR1 is counteracted by auxin, indicating that, in addition to auxin-mediated transcriptional responses, the fine-tuned process of LR formation is also controlled at the chromatin level in an auxin-signaling dependent manner.

@article{zhou_co-incidence_2020,
	title = {Co-incidence of {Damage} and {Microbial} {Patterns} {Controls} {Localized} {Immune} {Responses} in {Roots}},
	volume = {180},
	issn = {00928674},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S009286742030060X},
	doi = {10.1016/j.cell.2020.01.013},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {Cell},
	author = {Zhou, Feng and Emonet, Aurélia and Dénervaud Tendon, Valérie and Marhavý, Peter and Wu, Dousheng and Lahaye, Thomas and Geldner, Niko},
	month = feb,
	year = {2020},
	pages = {440--453.e18},
}

@article{kubiasova_cytokinin_2020,
	title = {Cytokinin fluoroprobe reveals multiple sites of cytokinin perception at plasma membrane and endoplasmic reticulum},
	volume = {11},
	issn = {2041-1723},
	url = {http://www.nature.com/articles/s41467-020-17949-0},
	doi = {10.1038/s41467-020-17949-0},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Nature Communications},
	author = {Kubiasová, Karolina and Montesinos, Juan Carlos and Šamajová, Olga and Nisler, Jaroslav and Mik, Václav and Semerádová, Hana and Plíhalová, Lucie and Novák, Ondřej and Marhavý, Peter and Cavallari, Nicola and Zalabák, David and Berka, Karel and Doležal, Karel and Galuszka, Petr and Šamaj, Jozef and Strnad, Miroslav and Benková, Eva and Plíhal, Ondřej and Spíchal, Lukáš},
	month = dec,
	year = {2020},
	pages = {4285},
}

@article{fujita_schengen_2020,
	title = {{SCHENGEN} receptor module drives localized {ROS} production and lignification in plant roots},
	volume = {39},
	issn = {0261-4189},
	url = {https://www.embopress.org/doi/full/10.15252/embj.2019103894},
	doi = {10/gjct3x},
	abstract = {Abstract Production of reactive oxygen species (ROS) by NADPH oxidases (NOXs) impacts many processes in animals and plants, and many plant receptor pathways involve rapid, NOX-dependent increases of ROS. Yet, their general reactivity has made it challenging to pinpoint the precise role and immediate molecular action of ROS. A well-understood ROS action in plants is to provide the co-substrate for lignin peroxidases in the cell wall. Lignin can be deposited with exquisite spatial control, but the underlying mechanisms have remained elusive. Here, we establish a kinase signaling relay that exerts direct, spatial control over ROS production and lignification within the cell wall. We show that polar localization of a single kinase component is crucial for pathway function. Our data indicate that an intersection of more broadly localized components allows for micrometer-scale precision of lignification and that this system is triggered through initiation of ROS production as a critical peroxidase co-substrate.},
	number = {9},
	urldate = {2021-06-21},
	journal = {The EMBO Journal},
	author = {Fujita, Satoshi and De Bellis, Damien and Edel, Kai H and Köster, Philipp and Andersen, Tonni Grube and Schmid-Siegert, Emanuel and Dénervaud Tendon, Valérie and Pfister, Alexandre and Marhavý, Peter and Ursache, Robertas and Doblas, Verónica G and Barberon, Marie and Daraspe, Jean and Creff, Audrey and Ingram, Gwyneth and Kudla, Jörg and Geldner, Niko},
	month = may,
	year = {2020},
	note = {Publisher: John Wiley \& Sons, Ltd},
	keywords = {Casparian strips, extracellular diffusion barriers, lignin, localized ROS production, polarized signaling},
	pages = {e103894},
}

Abstract Production of reactive oxygen species (ROS) by NADPH oxidases (NOXs) impacts many processes in animals and plants, and many plant receptor pathways involve rapid, NOX-dependent increases of ROS. Yet, their general reactivity has made it challenging to pinpoint the precise role and immediate molecular action of ROS. A well-understood ROS action in plants is to provide the co-substrate for lignin peroxidases in the cell wall. Lignin can be deposited with exquisite spatial control, but the underlying mechanisms have remained elusive. Here, we establish a kinase signaling relay that exerts direct, spatial control over ROS production and lignification within the cell wall. We show that polar localization of a single kinase component is crucial for pathway function. Our data indicate that an intersection of more broadly localized components allows for micrometer-scale precision of lignification and that this system is triggered through initiation of ROS production as a critical peroxidase co-substrate.

@article{yoshida_soseki-based_2019,
	title = {A {SOSEKI}-based coordinate system interprets global polarity cues in {Arabidopsis}},
	volume = {5},
	issn = {2055-0278},
	url = {http://www.nature.com/articles/s41477-019-0363-6},
	doi = {10/gfvgd3},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {Nature Plants},
	author = {Yoshida, Saiko and van der Schuren, Alja and van Dop, Maritza and van Galen, Luc and Saiga, Shunsuke and Adibi, Milad and Möller, Barbara and ten Hove, Colette A. and Marhavý, Peter and Smith, Richard and Friml, Jiri and Weijers, Dolf},
	month = feb,
	year = {2019},
	pages = {160--166},
}

@article{marhava_re-activation_2019,
	title = {Re-activation of {Stem} {Cell} {Pathways} for {Pattern} {Restoration} in {Plant} {Wound} {Healing}},
	volume = {177},
	issn = {00928674},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0092867419304015},
	doi = {10/gfz9tc},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {Cell},
	author = {Marhava, Petra and Hoermayer, Lukas and Yoshida, Saiko and Marhavý, Peter and Benková, Eva and Friml, Jiří},
	month = may,
	year = {2019},
	pages = {957--969.e13},
}

@article{holbein_root_2019,
	title = {Root endodermal barrier system contributes to defence against plant‐parasitic cyst and root‐knot nematodes},
	volume = {100},
	issn = {0960-7412, 1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.14459},
	doi = {10.1111/tpj.14459},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {The Plant Journal},
	author = {Holbein, Julia and Franke, Rochus B. and Marhavý, Peter and Fujita, Satoshi and Górecka, Mirosława and Sobczak, Mirosław and Geldner, Niko and Schreiber, Lukas and Grundler, Florian M. W. and Siddique, Shahid},
	month = oct,
	year = {2019},
	pages = {221--236},
}

@article{marhavy_singlecell_2019,
	title = {Single‐cell damage elicits regional, nematode‐restricting ethylene responses in roots},
	volume = {38},
	issn = {0261-4189, 1460-2075},
	url = {https://onlinelibrary.wiley.com/doi/10.15252/embj.2018100972},
	doi = {10/gf2hvf},
	language = {en},
	number = {10},
	urldate = {2021-06-07},
	journal = {The EMBO Journal},
	author = {Marhavý, Peter and Kurenda, Andrzej and Siddique, Shahid and Dénervaud Tendon, Valerie and Zhou, Feng and Holbein, Julia and Hasan, M Shamim and Grundler, Florian MW and Farmer, Edward E and Geldner, Niko},
	month = may,
	year = {2019},
}

@article{ursache_protocol_2018,
	title = {A protocol for combining fluorescent proteins with histological stains for diverse cell wall components},
	volume = {93},
	issn = {0960-7412, 1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.13784},
	doi = {10/gkf56d},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {The Plant Journal},
	author = {Ursache, Robertas and Andersen, Tonni Grube and Marhavý, Peter and Geldner, Niko},
	month = jan,
	year = {2018},
	pages = {399--412},
}

@article{drapek_minimum_2018,
	title = {Minimum requirements for changing and maintaining endodermis cell identity in the {Arabidopsis} root},
	volume = {4},
	issn = {2055-0278},
	url = {http://www.nature.com/articles/s41477-018-0213-y},
	doi = {10/gd9kpt},
	language = {en},
	number = {8},
	urldate = {2021-06-07},
	journal = {Nature Plants},
	author = {Drapek, Colleen and Sparks, Erin E. and Marhavý, Peter and Taylor, Isaiah and Andersen, Tonni G. and Hennacy, Jessica H. and Geldner, Niko and Benfey, Philip N.},
	month = aug,
	year = {2018},
	pages = {586--595},
}

@article{marhavy_targeted_2016,
	title = {Targeted cell elimination reveals an auxin-guided biphasic mode of lateral root initiation},
	volume = {30},
	issn = {0890-9369, 1549-5477},
	url = {http://genesdev.cshlp.org/lookup/doi/10.1101/gad.276964.115},
	doi = {10.1101/gad.276964.115},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {Genes \& Development},
	author = {Marhavý, Peter and Montesinos, Juan Carlos and Abuzeineh, Anas and Van Damme, Daniel and Vermeer, Joop E.M. and Duclercq, Jerôme and Rakusová, Hana and Nováková, Petra and Friml, Jiři and Geldner, Niko and Benková, Eva},
	month = feb,
	year = {2016},
	keywords = {auxin, lateral root organogenesis, mechanical forces, meristem proliferation activity},
	pages = {471--483},
}

@article{chen_coherent_2015,
	title = {A coherent transcriptional feed-forward motif model for mediating auxin-sensitive {PIN3} expression during lateral root development},
	volume = {6},
	issn = {2041-1723 (Electronic) 2041-1723 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26578065},
	doi = {10.1038/ncomms9821},
	abstract = {Multiple plant developmental processes, such as lateral root development, depend on auxin distribution patterns that are in part generated by the PIN-formed family of auxin-efflux transporters. Here we propose that AUXIN RESPONSE FACTOR7 (ARF7) and the ARF7-regulated FOUR LIPS/MYB124 (FLP) transcription factors jointly form a coherent feed-forward motif that mediates the auxin-responsive PIN3 transcription in planta to steer the early steps of lateral root formation. This regulatory mechanism might endow the PIN3 circuitry with a temporal 'memory' of auxin stimuli, potentially maintaining and enhancing the robustness of the auxin flux directionality during lateral root development. The cooperative action between canonical auxin signalling and other transcription factors might constitute a general mechanism by which transcriptional auxin-sensitivity can be regulated at a tissue-specific level.},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Nat Commun},
	author = {Chen, Q. and Liu, Y. and Maere, S. and Lee, E. and Van Isterdael, G. and Xie, Z. and Xuan, W. and Lucas, J. and Vassileva, V. and Kitakura, S. and Marhavý, P. and Wabnik, K. and Geldner, N. and Benkova, E. and Le, J. and Fukaki, H. and Grotewold, E. and Li, C. and Friml, J. and Sack, F. and Beeckman, T. and Vanneste, S.},
	month = nov,
	year = {2015},
	keywords = {*Gene Expression Regulation, Plant, Arabidopsis Proteins/*genetics/metabolism, Arabidopsis/*genetics/growth \& development, Chromatin Immunoprecipitation, Feedback, Physiological, Glucuronidase/metabolism, Organisms, Genetically Modified, Plant Roots/*growth \& development/metabolism, RNA, Messenger/*metabolism, Reverse Transcriptase Polymerase Chain Reaction, Signal Transduction, Transcription Factors/*genetics/metabolism, Transcription, Genetic},
	pages = {8821},
}

Multiple plant developmental processes, such as lateral root development, depend on auxin distribution patterns that are in part generated by the PIN-formed family of auxin-efflux transporters. Here we propose that AUXIN RESPONSE FACTOR7 (ARF7) and the ARF7-regulated FOUR LIPS/MYB124 (FLP) transcription factors jointly form a coherent feed-forward motif that mediates the auxin-responsive PIN3 transcription in planta to steer the early steps of lateral root formation. This regulatory mechanism might endow the PIN3 circuitry with a temporal 'memory' of auxin stimuli, potentially maintaining and enhancing the robustness of the auxin flux directionality during lateral root development. The cooperative action between canonical auxin signalling and other transcription factors might constitute a general mechanism by which transcriptional auxin-sensitivity can be regulated at a tissue-specific level.

@article{simaskova_cytokinin_2015,
	title = {Cytokinin response factors regulate {PIN}-{FORMED} auxin transporters},
	volume = {6},
	issn = {2041-1723 (Electronic) 2041-1723 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26541513},
	doi = {10.1038/ncomms9717},
	abstract = {Auxin and cytokinin are key endogenous regulators of plant development. Although cytokinin-mediated modulation of auxin distribution is a developmentally crucial hormonal interaction, its molecular basis is largely unknown. Here we show a direct regulatory link between cytokinin signalling and the auxin transport machinery uncovering a mechanistic framework for cytokinin-auxin cross-talk. We show that the CYTOKININ RESPONSE FACTORS (CRFs), transcription factors downstream of cytokinin perception, transcriptionally control genes encoding PIN-FORMED (PIN) auxin transporters at a specific PIN CYTOKININ RESPONSE ELEMENT (PCRE) domain. Removal of this cis-regulatory element effectively uncouples PIN transcription from the CRF-mediated cytokinin regulation and attenuates plant cytokinin sensitivity. We propose that CRFs represent a missing cross-talk component that fine-tunes auxin transport capacity downstream of cytokinin signalling to control plant development.},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Nat Commun},
	author = {Simaskova, M. and O'Brien, J. A. and Khan, M. and Van Noorden, G. and Otvos, K. and Vieten, A. and De Clercq, I. and Van Haperen, J. M. A. and Cuesta, C. and Hoyerova, K. and Vanneste, S. and Marhavý, P. and Wabnik, K. and Van Breusegem, F. and Nowack, M. and Murphy, A. and Friml, J. and Weijers, D. and Beeckman, T. and Benkova, E.},
	month = nov,
	year = {2015},
	note = {Edition: 2015/11/07},
	keywords = {Arabidopsis, Arabidopsis Proteins/*genetics/metabolism, Chromatin Immunoprecipitation, Cytokinins/*metabolism, Gene Expression Regulation, Plant, Green Fluorescent Proteins, Indoleacetic Acids/*metabolism, Membrane Transport Proteins/*genetics/metabolism, Microscopy, Confocal, Plant Roots/metabolism, Plants, Genetically Modified, Real-Time Polymerase Chain Reaction, Response Elements, Signal Transduction, Transcription Factors/*genetics/metabolism},
	pages = {8717},
}

Auxin and cytokinin are key endogenous regulators of plant development. Although cytokinin-mediated modulation of auxin distribution is a developmentally crucial hormonal interaction, its molecular basis is largely unknown. Here we show a direct regulatory link between cytokinin signalling and the auxin transport machinery uncovering a mechanistic framework for cytokinin-auxin cross-talk. We show that the CYTOKININ RESPONSE FACTORS (CRFs), transcription factors downstream of cytokinin perception, transcriptionally control genes encoding PIN-FORMED (PIN) auxin transporters at a specific PIN CYTOKININ RESPONSE ELEMENT (PCRE) domain. Removal of this cis-regulatory element effectively uncouples PIN transcription from the CRF-mediated cytokinin regulation and attenuates plant cytokinin sensitivity. We propose that CRFs represent a missing cross-talk component that fine-tunes auxin transport capacity downstream of cytokinin signalling to control plant development.

@article{marhavy_real-time_2015,
	title = {Real-time {Analysis} of {Lateral} {Root} {Organogenesis} in {Arabidopsis}},
	volume = {5},
	issn = {2331-8325},
	url = {http://www.bio-protocol.org/e1446},
	doi = {10/ggsz3x},
	language = {en},
	number = {8},
	urldate = {2021-06-07},
	journal = {BIO-PROTOCOL},
	author = {Marhavý, Peter and Benkova, Eva},
	year = {2015},
}

@article{marhavy_cytokinin_2014,
	title = {Cytokinin {Controls} {Polarity} of {PIN1}-{Dependent} {Auxin} {Transport} during {Lateral} {Root} {Organogenesis}},
	volume = {24},
	issn = {09609822},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0960982214004023},
	doi = {10/f52zbg},
	language = {en},
	number = {9},
	urldate = {2021-06-08},
	journal = {Current Biology},
	author = {Marhavý, Peter and Duclercq, Jérôme and Weller, Benjamin and Feraru, Elena and Bielach, Agnieszka and Offringa, Remko and Friml, Jiří and Schwechheimer, Claus and Murphy, Angus and Benková, Eva},
	month = may,
	year = {2014},
	pages = {1031--1037},
}

@article{rosquete_auxin_2013,
	title = {An {Auxin} {Transport} {Mechanism} {Restricts} {Positive} {Orthogravitropism} in {Lateral} {Roots}},
	volume = {23},
	issn = {09609822},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0960982213003667},
	doi = {10/f4w5br},
	language = {en},
	number = {9},
	urldate = {2021-06-08},
	journal = {Current Biology},
	author = {Rosquete, Michel Ruiz and von Wangenheim, Daniel and Marhavý, Peter and Barbez, Elke and Stelzer, Ernst H.K. and Benková, Eva and Maizel, Alexis and Kleine-Vehn, Jürgen},
	month = may,
	year = {2013},
	pages = {817--822},
}

@article{pollier_protein_2013,
	title = {The protein quality control system manages plant defence compound synthesis},
	volume = {504},
	issn = {1476-4687},
	doi = {10/f5jcsn},
	abstract = {Jasmonates are ubiquitous oxylipin-derived phytohormones that are essential in the regulation of many development, growth and defence processes. Across the plant kingdom, jasmonates act as elicitors of the production of bioactive secondary metabolites that serve in defence against attackers. Knowledge of the conserved jasmonate perception and early signalling machineries is increasing, but the downstream mechanisms that regulate defence metabolism remain largely unknown. Here we show that, in the legume Medicago truncatula, jasmonate recruits the endoplasmic-reticulum-associated degradation (ERAD) quality control system to manage the production of triterpene saponins, widespread bioactive compounds that share a biogenic origin with sterols. An ERAD-type RING membrane-anchor E3 ubiquitin ligase is co-expressed with saponin synthesis enzymes to control the activity of 3-hydroxy-3-methylglutaryl-CoA reductase (HMGR), the rate-limiting enzyme in the supply of the ubiquitous terpene precursor isopentenyl diphosphate. Thus, unrestrained bioactive saponin accumulation is prevented and plant development and integrity secured. This control apparatus is equivalent to the ERAD system that regulates sterol synthesis in yeasts and mammals but that uses distinct E3 ubiquitin ligases, of the HMGR degradation 1 (HRD1) type, to direct destruction of HMGR. Hence, the general principles for the management of sterol and triterpene saponin biosynthesis are conserved across eukaryotes but can be controlled by divergent regulatory cues.},
	language = {eng},
	number = {7478},
	journal = {Nature},
	author = {Pollier, Jacob and Moses, Tessa and González-Guzmán, Miguel and De Geyter, Nathan and Lippens, Saskia and Vanden Bossche, Robin and Marhavý, Peter and Kremer, Anna and Morreel, Kris and Guérin, Christopher J. and Tava, Aldo and Oleszek, Wieslaw and Thevelein, Johan M. and Campos, Narciso and Goormachtig, Sofie and Goossens, Alain},
	month = dec,
	year = {2013},
	pmid = {24213631},
	keywords = {Cells, Cultured, Endoplasmic Reticulum-Associated Degradation, Gene Expression Profiling, Gene Expression Regulation, Plant, Gene Silencing, Genetic Complementation Test, Medicago truncatula, Microscopy, Electron, Scanning, Molecular Sequence Data, Mutation, Plant Growth Regulators, Plant Roots, Saccharomyces cerevisiae, Saponins, Signal Transduction, Ubiquitin-Protein Ligases},
	pages = {148--152},
}

Jasmonates are ubiquitous oxylipin-derived phytohormones that are essential in the regulation of many development, growth and defence processes. Across the plant kingdom, jasmonates act as elicitors of the production of bioactive secondary metabolites that serve in defence against attackers. Knowledge of the conserved jasmonate perception and early signalling machineries is increasing, but the downstream mechanisms that regulate defence metabolism remain largely unknown. Here we show that, in the legume Medicago truncatula, jasmonate recruits the endoplasmic-reticulum-associated degradation (ERAD) quality control system to manage the production of triterpene saponins, widespread bioactive compounds that share a biogenic origin with sterols. An ERAD-type RING membrane-anchor E3 ubiquitin ligase is co-expressed with saponin synthesis enzymes to control the activity of 3-hydroxy-3-methylglutaryl-CoA reductase (HMGR), the rate-limiting enzyme in the supply of the ubiquitous terpene precursor isopentenyl diphosphate. Thus, unrestrained bioactive saponin accumulation is prevented and plant development and integrity secured. This control apparatus is equivalent to the ERAD system that regulates sterol synthesis in yeasts and mammals but that uses distinct E3 ubiquitin ligases, of the HMGR degradation 1 (HRD1) type, to direct destruction of HMGR. Hence, the general principles for the management of sterol and triterpene saponin biosynthesis are conserved across eukaryotes but can be controlled by divergent regulatory cues.

@article{marhavy_auxin_2012,
	title = {Auxin reflux between the endodermis and pericycle promotes lateral root initiation},
	volume = {32},
	issn = {0261-4189, 1460-2075},
	url = {http://emboj.embopress.org/cgi/doi/10.1038/emboj.2012.303},
	doi = {10/gkgdj3},
	number = {1},
	urldate = {2021-06-08},
	journal = {The EMBO Journal},
	author = {Marhavý, Peter and Vanstraelen, Marleen and De Rybel, Bert and Zhaojun, Ding and Bennett, Malcolm J and Beeckman, Tom and Benková, Eva},
	month = nov,
	year = {2012},
	pages = {149--158},
}

@article{bielach_genetic_2012,
	title = {Genetic approach towards the identification of auxin–cytokinin crosstalk components involved in root development},
	volume = {367},
	url = {https://royalsocietypublishing.org/doi/10.1098/rstb.2011.0233},
	doi = {10/f32frv},
	abstract = {Phytohormones are important plant growth regulators that control many developmental processes, such as cell division, cell differentiation, organogenesis and morphogenesis. They regulate a multitude of apparently unrelated physiological processes, often with overlapping roles, and they mutually modulate their effects. These features imply important synergistic and antagonistic interactions between the various plant hormones. Auxin and cytokinin are central hormones involved in the regulation of plant growth and development, including processes determining root architecture, such as root pole establishment during early embryogenesis, root meristem maintenance and lateral root organogenesis. Thus, to control root development both pathways put special demands on the mechanisms that balance their activities and mediate their interactions. Here, we summarize recent knowledge on the role of auxin and cytokinin in the regulation of root architecture with special focus on lateral root organogenesis, discuss the latest findings on the molecular mechanisms of their interactions, and present forward genetic screen as a tool to identify novel molecular components of the auxin and cytokinin crosstalk.},
	number = {1595},
	urldate = {2021-06-08},
	journal = {Philosophical Transactions of the Royal Society B: Biological Sciences},
	author = {Bielach, Agnieszka and Duclercq, Jérôme and Marhavý, Peter and Benková, Eva},
	month = jun,
	year = {2012},
	note = {Publisher: Royal Society},
	pages = {1469--1478},
}

Phytohormones are important plant growth regulators that control many developmental processes, such as cell division, cell differentiation, organogenesis and morphogenesis. They regulate a multitude of apparently unrelated physiological processes, often with overlapping roles, and they mutually modulate their effects. These features imply important synergistic and antagonistic interactions between the various plant hormones. Auxin and cytokinin are central hormones involved in the regulation of plant growth and development, including processes determining root architecture, such as root pole establishment during early embryogenesis, root meristem maintenance and lateral root organogenesis. Thus, to control root development both pathways put special demands on the mechanisms that balance their activities and mediate their interactions. Here, we summarize recent knowledge on the role of auxin and cytokinin in the regulation of root architecture with special focus on lateral root organogenesis, discuss the latest findings on the molecular mechanisms of their interactions, and present forward genetic screen as a tool to identify novel molecular components of the auxin and cytokinin crosstalk.

@article{bielach_spatiotemporal_2012,
	title = {Spatiotemporal {Regulation} of {Lateral} {Root} {Organogenesis} in \textit{{Arabidopsis}} by {Cytokinin}},
	volume = {24},
	issn = {1040-4651, 1532-298X},
	url = {https://academic.oup.com/plcell/article/24/10/3967-3981/6101532},
	doi = {10/f4ffx8},
	language = {en},
	number = {10},
	urldate = {2021-06-08},
	journal = {The Plant Cell},
	author = {Bielach, Agnieszka and Podlešáková, Kateřina and Marhavý, Peter and Duclercq, Jérôme and Cuesta, Candela and Müller, Bruno and Grunewald, Wim and Tarkowski, Petr and Benková, Eva},
	month = oct,
	year = {2012},
	pages = {3967--3981},
}

@article{marhavy_cytokinin_2011,
	title = {Cytokinin {Modulates} {Endocytic} {Trafficking} of {PIN1} {Auxin} {Efflux} {Carrier} to {Control} {Plant} {Organogenesis}},
	volume = {21},
	issn = {15345807},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1534580711003522},
	doi = {10/bz65s4},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {Developmental Cell},
	author = {Marhavý, Peter and Bielach, Agnieszka and Abas, Lindy and Abuzeineh, Anas and Duclercq, Jerome and Tanaka, Hirokazu and Pařezová, Markéta and Petrášek, Jan and Friml, Jiří and Kleine-Vehn, Jürgen and Benková, Eva},
	month = oct,
	year = {2011},
	pages = {796--804},
}

@article{zadnikova_role_2010,
	title = {Role of {PIN}-mediated auxin efflux in apical hook development of \textit{{Arabidopsis} thaliana}},
	volume = {137},
	issn = {1477-9129, 0950-1991},
	url = {https://journals.biologists.com/dev/article/137/4/607/44209/Role-of-PIN-mediated-auxin-efflux-in-apical-hook},
	doi = {10/cs9rb3},
	abstract = {The apical hook of dark-grown Arabidopsis seedlings is a simple structure that develops soon after germination to protect the meristem tissues during emergence through the soil and that opens upon exposure to light. Differential growth at the apical hook proceeds in three sequential steps that are regulated by multiple hormones, principally auxin and ethylene. We show that the progress of the apical hook through these developmental phases depends on the dynamic, asymmetric distribution of auxin, which is regulated by auxin efflux carriers of the PIN family. Several PIN proteins exhibited specific, partially overlapping spatial and temporal expression patterns, and their subcellular localization suggested auxin fluxes during hook development. Genetic manipulation of individual PIN activities interfered with different stages of hook development, implying that specific combinations of PIN genes are required for progress of the apical hook through the developmental phases. Furthermore, ethylene might modulate apical hook development by prolonging the formation phase and strongly suppressing the maintenance phase. This ethylene effect is in part mediated by regulation of PIN-dependent auxin efflux and auxin signaling.},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {Development},
	author = {Žádníková, Petra and Petrášek, Jan and Marhavý, Peter and Raz, Vered and Vandenbussche, Filip and Ding, Zhaojun and Schwarzerová, Kateřina and Morita, Miyo T. and Tasaka, Masao and Hejátko, Jan and Van Der Straeten, Dominique and Friml, Jiří and Benková, Eva},
	month = feb,
	year = {2010},
	pages = {607--617},
}

The apical hook of dark-grown Arabidopsis seedlings is a simple structure that develops soon after germination to protect the meristem tissues during emergence through the soil and that opens upon exposure to light. Differential growth at the apical hook proceeds in three sequential steps that are regulated by multiple hormones, principally auxin and ethylene. We show that the progress of the apical hook through these developmental phases depends on the dynamic, asymmetric distribution of auxin, which is regulated by auxin efflux carriers of the PIN family. Several PIN proteins exhibited specific, partially overlapping spatial and temporal expression patterns, and their subcellular localization suggested auxin fluxes during hook development. Genetic manipulation of individual PIN activities interfered with different stages of hook development, implying that specific combinations of PIN genes are required for progress of the apical hook through the developmental phases. Furthermore, ethylene might modulate apical hook development by prolonging the formation phase and strongly suppressing the maintenance phase. This ethylene effect is in part mediated by regulation of PIN-dependent auxin efflux and auxin signaling.