@article{20187,
  abstract     = {Very long-chain fatty acids (VLCFAs), being constituents of different types of lipids, are critical factors in plant development, presumably due to their impact on the endomembrane system. The VLCFAs are synthesized in the endoplasmic reticulum by a heterotetrameric enzymatic complex including β-ketoacyl CoA reductase 1 (KCR1), whose mutant is lethal. Here, we describe the ectopic shoot meristems (esm) mutant, a viable kcr1 allele presumably affecting surface properties of the KCR1 protein. This kcr1-2 mutant shows reduced fatty acyl elongation that impacts VLCFAs. The kcr1-2 plants show severe defects during different stages of development, which all correlate with defects in polar localization and subcellular trafficking of PIN auxin transporters and resulting asymmetric auxin distribution. Detailed analysis of KCR1 expression and patterning defects in kcr1-2 suggests that KCR1 plays a role in delineating boundaries around meristematic and specialized differentiating tissues, including root and shoot meristems, initiating lateral roots, lateral root primordia, and trichomes. In these contexts, KCR1-produced VLCFAs may act in a non-cell-autonomous manner. Viable kcr1-2 represents a useful tool to study VLCFA roles in plant development and highlights VLCFAs as critical developmental factors at the interface of cell polarity and tissue development.},
  author       = {Babic, David and Abualia, Rashed and Fiedler, Lukas and Qi, Linlin and Tellier, Frédérique and Smoljan, Adrijana and Rakusova, Hana and Valošek, Petr and Han, Huibin and Benková, Eva and Faure, Jean Denis and Friml, Jiří},
  issn         = {1365-313X},
  journal      = {Plant Journal},
  number       = {3},
  publisher    = {Wiley},
  title        = {{Biosynthesis of very long-chain fatty acids is required for Arabidopsis auxin-mediated embryonic and post-embryonic development}},
  doi          = {10.1111/tpj.70396},
  volume       = {123},
  year         = {2025},
}

@phdthesis{20362,
  abstract     = {Arabidopsis embryo has long served as a model system for understanding how plant body 
patterning and axis establishment arise. Previous work established that auxin flows, directed 
by polar transport and reinforced by local biosynthesis, underpin axes formation, while recent 
studies suggest that maternal tissue, membrane composition and surface receptor signaling add 
further regulatory layers. In this thesis, we dissect the layers of auxin-mediated processes which 
guide plant embryonic and post-embryonic development. We review methodological advances 
that allow the embryo to be imaged and studied. These tools offer exciting venues for future 
addressing of outstanding research questions. Furthermore, we dissect the contribution of 
maternal auxin for early embryo patterning. Targeted auxin scavenging in the integuments 
lowers the hormone reaching the proembryo, destabilizes PIN7 in the suspensor and weakens 
the initial apical maximum. The resulting deficit dampens downstream embryonic auxin 
biosynthesis, as well as auxin flow towards the root pole, indicating that maternally provided 
auxin controls auxin flows in the embryos on a larger scale than previously understood. 
Intriguingly, we uncover a prolonged maternal effect mediated by the receptor-like kinases 
TMK1 and TMK4. Reciprocal crosses and transgene analyses hint that these genes could be 
preferentially maternally-derived in both embryos and seedlings. Loss of maternal TMK 
activity arrests embryos, affects seedling development and persists into adult growth, 
suggesting that maternal effect could shape development beyond fertilization and early 
embryogenesis. Finally, we describe the role of very-long-chain fatty acids and membrane 
composition on PIN proteins and their auxin-induced relocalization. Disruption in this lipid 
metabolism triggers widespread patterning errors. 
Together, these results reposition early plant patterning as a hierarchical cascade that begins 
with maternal auxin, gets amplified by auxin transport and biosynthesis, potentially modulated 
by maternal receptor signaling and could ultimately be gated by the biophysical properties of 
the membrane. By integrating auxin supply, genetic imprinting and lipid-dependent trafficking 
into a single narrative, this thesis helps shifting the approach of viewing the embryo as an 
autonomous unit to regarding it as a dynamic system, continuously sculpted by its maternal 
context.},
  author       = {Babic, David},
  issn         = {2663-337X},
  pages        = {116},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Mechanisms of auxin-mediated early embryogenesis in Arabidopsis thaliana}},
  doi          = {10.15479/AT-ISTA-20362},
  year         = {2025},
}

@phdthesis{20364,
  abstract     = {Auxin is a central regulator of plant growth and development, orchestrating processes from 
embryogenesis to senescence through a complex network of biosynthesis, transport, and 
signaling pathways.  
In Arabidopsis thaliana, canonical nuclear auxin signaling is mediated by the TIR1/AFB 
receptors, which promote degradation of AUX/IAA repressors to enable ARF transcription 
factors-driven transcriptional reprogramming. Parallel to this well-established nuclear 
mechanism, auxin also triggers rapid, non-transcriptional responses. In particular, at the cell 
surface, most notably through ABP1 and TMKs. Despite decades of research, the integration 
of these pathways and their links to fundamental cellular processes remains not fully 
understood.  
In this study, we uncover a new role for TIR1/AFB signaling in rapidly activating 
macroautophagy during developmental reprogramming. Auxin induces autophagy via 
TIR1/AFB adenylate cyclase activity, linking auxin perception to cAMP production and 
transcriptional activation of autophagy machinery. Autophagy-deficient mutants exhibit 
delayed meristem differentiation, impaired lateral root progression, and reduced shoot 
organogenesis, demonstrating its necessity for timely developmental transitions. 
We also revisit the ABP1-TMK1 cell-surface auxin perception complex, providing 
biochemical and mass photometry evidence for auxin-dependent complex formation. We show 
that ABP1-TMK1 triggers an ultrafast global phosphorylation response targeting ~1000 
proteins, including the auxin transporter PIN2, and Rho-of-plants (ROP) GTPases regulators. 
This pathway directly regulates PIN2 phosphorylation, for gravitropism and auxin dependent 
ROP activation. 
These findings establish an integrated framework in which nuclear TIR1/AFB signaling and 
cell-surface ABP1-TMK signaling act in parallel to synchronize gene expression, cytoplasmic 
remodelling, and transporter regulation, thereby ensuring robust developmental plasticity in 
Arabidopsis thaliana. },
  author       = {Giannini, Caterina},
  issn         = {2663-337X},
  keywords     = {Auxin Signaling, Plant Development},
  pages        = {151},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Nuclear and cell surface auxin signaling in A. thaliana developmental transitions}},
  doi          = {10.15479/AT-ISTA-20364},
  year         = {2025},
}

@unpublished{19399,
  abstract     = {Phytohormone auxin and its directional transport mediate much of the remarkably plastic development of higher plants. Positive feedback between auxin signaling and transport is a key prerequisite for (i) self-organizing processes including vascular tissue formation and (ii) directional growth responses such as gravitropism. Here we identify a mechanism, by which auxin signaling directly targets PIN auxin transporters. Via the cell-surface ABP1-TMK1 receptor module, auxin rapidly induces phosphorylation and thus stabilization of PIN2. Following gravistimulation, initial auxin asymmetry activates autophosphorylation of the TMK1 kinase. This induces TMK1 interaction with and phosphorylation of PIN2, stabilizing PIN2 at the lower root side, thus reinforcing asymmetric auxin flow for root bending. Upstream of TMK1 in this regulation, ABP1 acts redundantly with the root-expressed ABP1-LIKE auxin receptor ABL3. Such positive feedback between cell-surface auxin signaling and PIN-mediated polar auxin transport is fundamental for robust root gravitropism and presumably also for other self-organizing developmental phenomena.},
  author       = {Rodriguez Solovey, Lesia and Fiedler, Lukas and Zou, Minxia and Giannini, Caterina and Monzer, Aline and Vladimirtsev, Dmitrii and Randuch, Marek and Yu, Yongfan and Gelová, Zuzana and Verstraeten, Inge and Hajny, Jakub and Chen, Meng and Tan, Shutang and Hörmayer, Lukas and Li, Lanxin and Marques-Bueno, Maria Mar and Quddoos, Zainab and Molnar, Gergely and Xu, Tongda and Kulich, Ivan and Jaillais, Yvon and Friml, Jiří},
  booktitle    = {bioRxiv},
  title        = {{ABP1/ABL3-TMK1 cell-surface auxin signaling directly targets PIN2-mediated auxin fluxes for root gravitropism}},
  doi          = {10.1101/2022.11.30.518503},
  year         = {2025},
}

@phdthesis{19478,
  abstract     = {Auxin is one of the most important phytohormones, playing a crucial role in plant growth and 
development. Genetic studies in Arabidopsis have identified core components of auxin 
signalling and established the classical transcriptional regulation mechanism. This classical 
paradigm recognizes TRANSPORT INHIBITOR RESPONSE 1 (TIR1)/AUXIN 
SIGNALLING F-BOX (AFB) proteins as auxin receptors possessing E3 ubiquitin ligase 
activity. Auxin functions as a "molecular glue" enhancing TIR1/AFB-Aux/IAA 
(AUXIN/INDOLE-3-ACETIC ACID) inhibitor interactions, leading to Aux/IAAs’ 
ubiquitination and degradation. This process releases AUXIN RESPONSE FACTORs (ARFs) 
from repression, enabling transcriptional activation of auxin-responsive genes. Notably, the 
discovery of adenylate cyclase (AC) activity in TIR1/AFBs, catalysing cAMP production from 
ATP, presents novel transcriptional regulatory possibilities, though cAMP's mechanistic role 
in auxin signalling remains unclear. Beyond transcriptional regulation (slow response) a non
transcriptional pathway (rapid response) mediated by AFB1 also exists, as auxin triggers rapid 
root growth inhibition within 30 seconds. How TIR1 and AFB1, with their distinct subcellular 
localizations, differentially regulate transcriptional and non-transcriptional processes remains 
unclear. To address these two key questions, this study conducted the following investigations.  
TIR1 and AFB1 display distinct subcellular localization patterns, with AFB1 specifically 
mediating auxin-induced rapid root growth inhibition. To examine whether subcellular 
localization differences contribute to functional divergence between TIR1 and AFB1, we 
utilized microfluidic systems combined with genetic complementation assays. Nuclear export 
signal-fused TIR1 failed to rescue the rapid response defects observed in afb1 mutants. In 
contrast, nuclear localization signal-fused AFB1 exhibited dual functional deficiencies: it 
neither restored the rapid response impairment in afb1 mutants nor compensated for 
transcriptional regulation defects in tir1 mutants which limitation stemmed from AFB1's 
intrinsic incapacity to assemble functional SCF complexes. These results collectively establish 
that the functional specialization of TIR1 and AFB1 is governed by both their subcellular 
compartmentalization and inherent biochemical characteristics. 
The mechanism by which cAMP derived from the auxin receptor TIR1/AFB modulates 
transcriptional regulation remains undefined. To address this, we genetically dissociated TIR1 
AC activity from its E3 ubiquitin ligase function to investigate cAMP's signalling role. AC
inactivating mutations preserved TIR1-mediated Aux/IAAs’ degradation but abolished ARF
i 
dependent transcriptional activation. tir1afb2 mutants expressing AC-deficient TIR1 variants 
failed to restore transcriptional responses. Crucially, compartmentalized cAMP accumulation 
within Aux/IAA - ARF complexes vicinity triggered auxin signalling independently of both 
auxin perception and Aux/IAAs’ degradation, confirming its secondary messenger identity. 
Further mechanistic analysis demonstrated cAMP directly interact with ARF. cAMP 
directly promotes ARF dissociation from Aux/IAA repressors and enhances ARF 
homodimerization. Genetic complementation assays revealed that ARF mutants lacking 
conserved cAMP-binding motifs exhibited partial functional recovery, providing direct 
evidence for cAMP-ARF physical interaction during signal propagation. 
These findings collectively challenge the established model of auxin signalling and define 
a novel TIR1-cAMP-ARF regulatory axis, substantially advancing our comprehension of 
auxin-mediated physiological regulation. },
  author       = {Chen, Huihuang},
  issn         = {2663-337X},
  pages        = {118},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{The cAMP second messenger in auxin signalling}},
  doi          = {10.15479/AT-ISTA-19478},
  year         = {2025},
}

@article{19421,
  abstract     = {The phytohormone auxin (Aux) is a principal endogenous developmental signal in plants. It mediates transcriptional reprogramming by a well-established canonical signalling mechanism. TIR1/AFB auxin receptors are F-box subunits of an ubiquitin ligase complex; after auxin perception, they associate with Aux/IAA transcriptional repressors and ubiquitinate them for degradation, thus enabling the activation of auxin response factor (ARF) transcription factors1,2,3. Here we revise this paradigm by showing that without TIR1 adenylate cyclase (AC) activity4, auxin-induced degradation of Aux/IAAs is not sufficient to mediate the transcriptional auxin response. Abolishing the TIR1 AC activity does not affect auxin-induced degradation of Aux/IAAs but renders TIR1 non-functional in mediating transcriptional reprogramming and auxin-regulated development, including shoot, root, root hair growth and lateral root formation. Transgenic plants show that local cAMP production in the vicinity of the Aux/IAA–ARF complex by unrelated AC enzymes bypasses the need for auxin perception and is sufficient to induce ARF-mediated transcription. These discoveries revise the canonical model of auxin signalling and establish TIR1/AFB-produced cAMP as a second messenger essential for transcriptional reprograming.},
  author       = {Chen, Huihuang and Qi, Linlin and Zou, Minxia and Lu, Mengting and Kwiatkowski, M and Pei, Yuanrong and Jaworski, K and Friml, Jiří},
  issn         = {1476-4687},
  journal      = {Nature},
  pages        = {1011--1016},
  publisher    = {Springer Nature},
  title        = {{TIR1-produced cAMP as a second messenger in transcriptional auxin signalling}},
  doi          = {10.1038/s41586-025-08669-w},
  volume       = {640},
  year         = {2025},
}

@article{17141,
  abstract     = {The TIR1/AFB–Aux/IAA–ARF canonical auxin signaling pathway is widely accepted to (de)active transcriptional regulation, thus controlling auxin-associated developmental processes. However, the theme of a rapid auxin response has emerged since the 2018 Auxins and Cytokinin in Plant Development conference. To date, a few signaling components have been identified to mediate both slow and rapid auxin responses, which unveils the complexity of auxin signaling.},
  author       = {Zhang, Zilin and Chen, Huihuang and Peng, Shuaiying and Han, Huibin},
  issn         = {0022-0957},
  journal      = {Journal of Experimental Botany},
  number       = {18},
  publisher    = {Oxford University Press},
  title        = {{Slow and rapid auxin responses in Arabidopsis}},
  doi          = {10.1093/jxb/erae246},
  volume       = {75},
  year         = {2024},
}

@unpublished{18689,
  abstract     = {Multiplexed fluorescence microscopy imaging is widely used in biomedical applications. However, simultaneous imaging of multiple fluorophores can result in spectral leaks and overlapping, which greatly degrades image quality and subsequent analysis. Existing popular spectral unmixing methods are mainly based on computational intensive linear models and the performance is heavily dependent on the reference spectra, which may greatly preclude its further applications. In this paper, we propose a deep learning-based blindly spectral unmixing method, termed AutoUnmix, to imitate the physical spectral mixing process. A tranfer learning framework is further devised to allow our AutoUnmix adapting to a variety of imaging systems without retraining the network. Our proposed method has demonstrated real-time unmixing capabilities, surpassing existing methods by up to 100-fold in terms of unmixing speed. We further validate the reconstruction performance on both synthetic datasets and biological samples. The unmixing results of AutoUnmix achieve a highest SSIM of 0.99 in both three- and four-color imaging, with nearly up to 20% higher than other popular unmixing methods. Due to the desirable property of data independency and superior blind unmixing performance, we believe AutoUnmix is a powerful tool to study the interaction process of different organelles labeled by multiple fluorophores.},
  author       = {Gallei, Michelle C and Truckenbrodt, Sven M and Kreuzinger, Caroline and Inumella, Syamala and Vistunou, Vitali and Sommer, Christoph M and Tavakoli, Mojtaba and Agudelo Duenas, Nathalie and Vorlaufer, Jakob and Jahr, Wiebke and Randuch, Marek and Johnson, Alexander J and Benková, Eva and Friml, Jiří and Danzl, Johann G},
  booktitle    = {bioRxiv},
  title        = {{Super-resolution expansion microscopy in plant roots}},
  doi          = {10.1101/2024.02.21.581330},
  year         = {2024},
}

@article{14251,
  abstract     = {The phytohormone auxin and its directional transport through tissues play a fundamental role in development of higher plants. This polar auxin transport predominantly relies on PIN-FORMED (PIN) auxin exporters. Hence, PIN polarization is crucial for development, but its evolution during the rise of morphological complexity in land plants remains unclear. Here, we performed a cross-species investigation by observing the trafficking and localization of endogenous and exogenous PINs in two bryophytes, Physcomitrium patens and Marchantia polymorpha, and in the flowering plant Arabidopsis thaliana. We confirmed that the GFP fusion did not compromise the auxin export function of all examined PINs by using radioactive auxin export assay and by observing the phenotypic changes in transgenic bryophytes. Endogenous PINs polarize to filamentous apices, while exogenous Arabidopsis PINs distribute symmetrically on the membrane in both bryophytes. In Arabidopsis root epidermis, bryophytic PINs show no defined polarity. Pharmacological interference revealed a strong cytoskeleton dependence of bryophytic but not Arabidopsis PIN polarization. The divergence of PIN polarization and trafficking is also observed within the bryophyte clade and between tissues of individual species. These results collectively reveal a divergence of PIN trafficking and polarity mechanisms throughout land plant evolution and a co-evolution of PIN sequence-based and cell-based polarity mechanisms.},
  author       = {Tang, Han and Lu, KJ and Zhang, Y and Cheng, YL and Tu, SL and Friml, Jiří},
  issn         = {2590-3462},
  journal      = {Plant Communications},
  number       = {1},
  publisher    = {Elsevier},
  title        = {{Divergence of trafficking and polarization mechanisms for PIN auxin transporters during land plant evolution}},
  doi          = {10.1016/j.xplc.2023.100669},
  volume       = {5},
  year         = {2024},
}

@article{14447,
  abstract     = {Auxin belongs among major phytohormones and governs multiple aspects of plant growth and development. The establishment of auxin concentration gradients, determines, among other processes, plant organ positioning and growth responses to environmental stimuli.
Herein we report the synthesis of new NBD- or DNS-labelled IAA derivatives and the elucidation of their biological activity, fluorescence properties and subcellular accumulation patterns in planta. These novel compounds did not show auxin-like activity, but instead antagonized physiological auxin effects. The DNS-labelled derivatives FL5 and FL6 showed strong anti-auxin activity in roots and hypocotyls, which also occurred at the level of gene transcription as confirmed by quantitative PCR analysis. The auxin antagonism of our derivatives was further demonstrated in vitro using an SPR-based binding assay. The NBD-labelled compound FL4 with the best fluorescence properties proved to be unsuitable to study auxin accumulation patterns in planta. On the other hand, the strongest anti-auxin activity possessing compounds FL5 and FL6 could be useful to study binding mechanisms to auxin receptors and for manipulations of auxin-regulated processes.},
  author       = {Bieleszová, Kristýna and Hladík, Pavel and Kubala, Martin and Napier, Richard and Brunoni, Federica and Gelová, Zuzana and Fiedler, Lukas and Kulich, Ivan and Strnad, Miroslav and Doležal, Karel and Novák, Ondřej and Friml, Jiří and Žukauskaitė, Asta},
  issn         = {1573-5087},
  journal      = {Plant Growth Regulation},
  pages        = {589--602},
  publisher    = {Springer Nature},
  title        = {{New fluorescent auxin derivatives: Anti-auxin activity and accumulation patterns in Arabidopsis thaliana}},
  doi          = {10.1007/s10725-023-01083-0},
  volume       = {102},
  year         = {2024},
}

@article{17048,
  abstract     = {A key mechanism employed by plants to adapt to salinity stress involves maintaining ion homeostasis via the actions of ion transporters. While the function of cation transporters in maintaining ion homeostasis in plants has been extensively studied, little is known about the roles of their anion counterparts in this process. Here, we describe a mechanism of salt adaptation in plants. We characterized the chloride channel (CLC) gene AtCLCf, whose expression is regulated by WRKY transcription factor under salt stress in Arabidopsis thaliana. Loss-of-function atclcf seedlings show increased sensitivity to salt, whereas AtCLCf overexpression confers enhanced resistance to salt stress. Salt stress induces the translocation of GFP-AtCLCf fusion protein to the plasma membrane (PM). Blocking AtCLCf translocation using the exocytosis inhibitor brefeldin-A or mutating the small GTPase gene AtRABA1b/BEX5 (RAS GENES FROM RAT BRAINA1b homolog) increases salt sensitivity in plants. Electrophysiology and liposome-based assays confirm the Cl−/H+ antiport function of AtCLCf. Therefore, we have uncovered a mechanism of plant adaptation to salt stress involving the NaCl-induced translocation of AtCLCf to the PM, thus facilitating Cl− removal at the roots, and increasing the plant’s salinity tolerance.},
  author       = {Rajappa, Sivamathini and Krishnamurthy, Pannaga and Huang, Hua and Yu, Dejie and Friml, Jiří and Xu, Jian and Kumar, Prakash P.},
  issn         = {2041-1723},
  journal      = {Nature Communications},
  publisher    = {Springer Nature},
  title        = {{The translocation of a chloride channel from the Golgi to the plasma membrane helps plants adapt to salt stress}},
  doi          = {10.1038/s41467-024-48234-z},
  volume       = {15},
  year         = {2024},
}

@misc{22776,
  author       = {Du, Yunlong},
  publisher    = {Repository},
  title        = {{SeRrbJ609}},
  doi          = {10.6084/m9.figshare.25448191},
  year         = {2024},
}

@article{17103,
  abstract     = {Phytoalexin sakuranetin functions in resistance against rice blast. However, the mechanisms underlying the effects of sakuranetin remains elusive. Here, we report that rice lines expressing resistance (R) genes were found to contain high levels of sakuranetin, which correlates with attenuated endocytic trafficking of plasma membrane (PM) proteins. Exogenous and endogenous sakuranetin attenuates the endocytosis of various PM proteins and the fungal effector PWL2. Moreover, accumulation of the avirulence protein AvrCO39, resulting from uptake into rice cells by Magnaporthe oryzae, was reduced following treatment with sakuranetin. Pharmacological manipulation of clathrin-mediated endocytic (CME) suggests that this pathway is targeted by sakuranetin. Indeed, attenuation of CME by sakuranetin is sufficient to convey resistance against rice blast. Our data reveals a mechanism of rice against M. oryzae by increasing sakuranetin levels and repressing the CME of pathogen effectors, which is distinct from the action of many R genes that mainly function by modulating transcription.},
  author       = {Jiang, Lihui and Zhang, Xiaoyan and Zhao, Yiting and Zhu, Haiyan and Fu, Qijing and Lu, Xinqi and Huang, Wuying and Yang, Xinyue and Zhou, Xuan and Wu, Lixia and Yang, Ao and He, Xie and Dong, Man and Peng, Ziai and Yang, Jing and Guo, Liwei and Wen, Jiancheng and Huang, Huichuan and Xie, Yong and Zhu, Shusheng and Li, Chengyun and He, Xiahong and Zhu, Youyong and Friml, Jiří and Du, Yunlong},
  issn         = {2041-1723},
  journal      = {Nature Communications},
  publisher    = {Springer Nature},
  title        = {{Phytoalexin sakuranetin attenuates endocytosis and enhances resistance to rice blast}},
  doi          = {10.1038/s41467-024-47746-y},
  volume       = {15},
  year         = {2024},
}

@article{15033,
  abstract     = {The GNOM (GN) Guanine nucleotide Exchange Factor for ARF small GTPases (ARF-GEF) is among the best studied trafficking regulators in plants, playing crucial and unique developmental roles in patterning and polarity. The current models place GN at the Golgi apparatus (GA), where it mediates secretion/recycling, and at the plasma membrane (PM) presumably contributing to clathrin-mediated endocytosis (CME). The mechanistic basis of the developmental function of GN, distinct from the other ARF-GEFs including its closest homologue GNOM-LIKE1 (GNL1), remains elusive. Insights from this study largely extend the current notions of GN function. We show that GN, but not GNL1, localizes to the cell periphery at long-lived structures distinct from clathrin-coated pits, while CME and secretion proceed normally in <jats:italic>gn</jats:italic> knockouts. The functional GN mutant variant GN<jats:sup>fewerroots</jats:sup>, absent from the GA, suggests that the cell periphery is the major site of GN action responsible for its developmental function. Following inhibition by Brefeldin A, GN, but not GNL1, relocates to the PM likely on exocytic vesicles, suggesting selective molecular associations en route to the cell periphery. A study of GN-GNL1 chimeric ARF-GEFs indicates that all GN domains contribute to the specific GN function in a partially redundant manner. Together, this study offers significant steps toward the elucidation of the mechanism underlying unique cellular and development functions of GNOM.},
  author       = {Adamowski, Maciek and Matijevic, Ivana and Friml, Jiří},
  issn         = {2050-084X},
  journal      = {eLife},
  keywords     = {General Immunology and Microbiology, General Biochemistry, Genetics and Molecular Biology, General Medicine, General Neuroscience},
  publisher    = {eLife Sciences Publications},
  title        = {{Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery}},
  doi          = {10.7554/elife.68993},
  volume       = {13},
  year         = {2024},
}

@article{14826,
  abstract     = {The plant-signaling molecule auxin triggers fast and slow cellular responses across land plants and algae. The nuclear auxin pathway mediates gene expression and controls growth and development in land plants, but this pathway is absent from algal sister groups. Several components of rapid responses have been identified in Arabidopsis, but it is unknown if these are part of a conserved mechanism. We recently identified a fast, proteome-wide phosphorylation response to auxin. Here, we show that this response occurs across 5 land plant and algal species and converges on a core group of shared targets. We found conserved rapid physiological responses to auxin in the same species and identified rapidly accelerated fibrosarcoma (RAF)-like protein kinases as central mediators of auxin-triggered phosphorylation across species. Genetic analysis connects this kinase to both auxin-triggered protein phosphorylation and rapid cellular response, thus identifying an ancient mechanism for fast auxin responses in the green lineage.},
  author       = {Kuhn, Andre and Roosjen, Mark and Mutte, Sumanth and Dubey, Shiv Mani and Carrillo Carrasco, Vanessa Polet and Boeren, Sjef and Monzer, Aline and Koehorst, Jasper and Kohchi, Takayuki and Nishihama, Ryuichi and Fendrych, Matyas and Sprakel, Joris and Friml, Jiří and Weijers, Dolf},
  issn         = {1097-4172},
  journal      = {Cell},
  keywords     = {General Biochemistry, Genetics and Molecular Biology},
  number       = {1},
  pages        = {130--148.e17},
  publisher    = {Elsevier},
  title        = {{RAF-like protein kinases mediate a deeply conserved, rapid auxin response}},
  doi          = {10.1016/j.cell.2023.11.021},
  volume       = {187},
  year         = {2024},
}

@article{15319,
  abstract     = {Exocyst component of 70-kDa (EXO70) proteins are constituents of the exocyst complex implicated in vesicle tethering during exocytosis. MILDEW RESISTANCE LOCUS O (MLO) proteins are plant-specific calcium channels and some MLO isoforms enable fungal powdery mildew pathogenesis. We here detected an unexpected phenotypic overlap of Arabidopsis thaliana exo70H4 and mlo2 mlo6 mlo12 triple mutant plants regarding the biogenesis of leaf trichome secondary cell walls. Biochemical and Fourier transform infrared spectroscopic analyses corroborated deficiencies in the composition of trichome cell walls in these mutants. Transgenic lines expressing fluorophore-tagged EXO70H4 and MLO exhibited extensive colocalization of these proteins. Furthermore, mCherry-EXO70H4 mislocalized in trichomes of the mlo triple mutant and, vice versa, MLO6-GFP mislocalized in trichomes of the exo70H4 mutant. Expression of GFP-marked PMR4 callose synthase, a known cargo of EXO70H4-dependent exocytosis, revealed reduced cell wall delivery of GFP-PMR4 in trichomes of mlo triple mutant plants. In vivo protein–protein interaction assays in plant and yeast cells uncovered isoform-preferential interactions between EXO70.2 subfamily members and MLO proteins. Finally, exo70H4 and mlo6 mutants, when combined, showed synergistically enhanced resistance to powdery mildew attack. Taken together, our data point to an isoform-specific interplay of EXO70 and MLO proteins in the modulation of trichome cell wall biogenesis and powdery mildew susceptibility.},
  author       = {Huebbers, Jan W. and Caldarescu, George A. and Kubátová, Zdeňka and Sabol, Peter and Levecque, Sophie C.J. and Kuhn, Hannah and Kulich, Ivan and Reinstädler, Anja and Büttgen, Kim and Manga-Robles, Alba and Mélida, Hugo and Pauly, Markus and Panstruga, Ralph and Žárský, Viktor},
  issn         = {1532-298X},
  journal      = {Plant Cell},
  number       = {4},
  pages        = {1007--1035},
  publisher    = {Oxford University Press},
  title        = {{Interplay of EXO70 and MLO proteins modulates trichome cell wall composition and susceptibility to powdery mildew}},
  doi          = {10.1093/plcell/koad319},
  volume       = {36},
  year         = {2024},
}

@article{17436,
  abstract     = {The auxin signaling molecule controls a variety of growth and developmental processes in land plants. Auxin regulates gene expression through a nuclear auxin signaling pathway (NAP) consisting of the ubiquitin ligase auxin receptor TIR1/AFB, its Aux/IAA degradation substrate, and DNA-binding ARF transcription factors. Although extensive qualitative understanding of the pathway and its interactions has been obtained, mostly by studying the flowering plant Arabidopsis thaliana, it remains unknown how these translate to quantitative system behavior in vivo, a problem that is confounded by the large NAP gene families in most species. Here, we used the minimal NAP of the liverwort Marchantia polymorpha to quantitatively map NAP protein accumulation and dynamics in vivo through the use of knockin fluorescent fusion proteins. Beyond revealing the dynamic native accumulation profile of the entire NAP protein network, we discovered that the two central ARFs, MpARF1 and MpARF2, are proteasomally degraded. This auxin-independent degradation tunes ARF protein stoichiometry to favor gene activation, thereby reprogramming auxin response during the developmental progression. Thus, quantitative analysis of the entire NAP has enabled us to identify ARF degradation and the stoichiometries of activator and repressor ARFs as a potential mechanism for controlling gemma germination.},
  author       = {Das, Shubhajit and De Roij, Martijn and Bellows, Simon and Alvarez, Melissa Dipp and Mutte, Sumanth and Kohlen, Wouter and Farcot, Etienne and Weijers, Dolf and Borst, Jan Willem},
  issn         = {2590-3462},
  journal      = {Plant Communications},
  number       = {11},
  publisher    = {Elsevier},
  title        = {{Quantitative imaging reveals the role of MpARF proteasomal degradation during gemma germination}},
  doi          = {10.1016/j.xplc.2024.101039},
  volume       = {5},
  year         = {2024},
}

@article{18465,
  abstract     = {The phytohormone auxin is polarly transported in plants by PIN-FORMED (PIN) transporters and controls virtually all growth and developmental processes. Canonical PINs possess a long, largely disordered cytosolic loop. Auxin transport by canonical PINs is activated by loop phosphorylation by certain kinases. The structure of the PIN transmembrane domains was recently determined, their transport properties remained poorly characterized, and the role of the loop in the transport process was unclear. Here, we determined the quantitative kinetic parameters of auxin transport mediated by Arabidopsis PINs to mathematically model auxin distribution in roots and to test these predictions in vivo. Using chimeras between transmembrane and loop domains of different PINs, we demonstrate a strong correlation between transport parameters and physiological output, indicating that the loop domain is not only required to activate PIN-mediated auxin transport, but it has an additional role in the transport process by a currently unknown mechanism.},
  author       = {Janacek, DP and Kolb, M and Schulz, L and Mergner, J and Kuster, B and Glanc, Matous and Friml, Jiří and Ten Tusscher, K and Schwechheimer, C and Hammes, UZ},
  issn         = {1878-1551},
  journal      = {Developmental Cell},
  number       = {14},
  pages        = {S1534--5807(24)00569--0},
  publisher    = {Elsevier},
  title        = {{Transport properties of canonical PIN-FORMED proteins from Arabidopsis and the role of the loop domain in auxin transport}},
  doi          = {10.1016/j.devcel.2024.09.020},
  volume       = {59},
  year         = {2024},
}

@article{18582,
  abstract     = {Identification of PIN exporters for auxin, the major coordinative signal in plants, some 25 years ago, signifies a landmark in our understanding of plant-specific mechanisms underlying development and adaptation. Auxin is directionally transported throughout the plant body; a unique feature already envisioned by Darwin and solidified by PINs’ discovery and characterization. The PIN-based auxin distribution network with its complex regulations of PIN expression, localization and activity turned out to underlie a remarkable multitude of developmental processes and represents means to integrate endogenous and environmental signals. Given the recent anniversary, we here summarize past and current developments in this exciting field.},
  author       = {Luschnig, Christian and Friml, Jiří},
  issn         = {2041-1723},
  journal      = {Nature Communications},
  publisher    = {Springer Nature},
  title        = {{Over 25 years of decrypting PIN-mediated plant development}},
  doi          = {10.1038/s41467-024-54240-y},
  volume       = {15},
  year         = {2024},
}

@article{15251,
  abstract     = {Brassinosteroids are steroidal phytohormones that regulate plant development and physiology, including adaptation to environmental stresses. Brassinosteroids are synthesized in the cell interior but bind receptors at the cell surface, necessitating a yet to be identified export mechanism. Here, we show that a member of the ATP-binding cassette (ABC) transporter superfamily, ABCB19, functions as a brassinosteroid exporter. We present its structure in both the substrate-unbound and the brassinosteroid-bound states. Bioactive brassinosteroids are potent activators of ABCB19 ATP hydrolysis activity, and transport assays showed that ABCB19 transports brassinosteroids. In Arabidopsis thaliana, ABCB19 and its close homolog, ABCB1, positively regulate brassinosteroid responses. Our results uncover an elusive export mechanism for bioactive brassinosteroids that is tightly coordinated with brassinosteroid signaling.},
  author       = {Ying, Wei and Wang, Yaowei and Wei, Hong and Luo, Yongming and Ma, Qian and Zhu, Heyuan and Janssens, Hilde and Vukašinović, Nemanja and Kvasnica, Miroslav and Winne, Johan M. and Gao, Yongxiang and Tan, Shutang and Friml, Jiří and Liu, Xin and Russinova, Eugenia and Sun, Linfeng},
  issn         = {1095-9203},
  journal      = {Science},
  number       = {6689},
  pages        = {eadj4591},
  publisher    = {American Association for the Advancement of Science},
  title        = {{Structure and function of the Arabidopsis ABC transporter ABCB19 in brassinosteroid export}},
  doi          = {10.1126/science.adj4591},
  volume       = {383},
  year         = {2024},
}