--- DOAJ_listed: '1' _id: '17048' abstract: - lang: eng text: 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. acknowledgement: The authors thank Drs. Akihiko Nakano and Tomohiro Uemura (RIKEN and Ochanomizu University, Japan) for providing plant material (seeds of GFP-RABA1bQ72L GFP-RABA1bS27N), Dr. Prakash Arumugam (SIFBI, A*STAR, Singapore) for providing the yeast strains used in this study, and Dr. Jobichen Chacko for help with homology model building. We thank Prof. Elliot Meyerowitz (Caltech) and Dr. On Sun Lau (NUS) for critical reading of our manuscript. The National University of Singapore provided partial financial support as grant number A−8000149-03-00, and PhD research scholarship to S.R. article_number: '3978' article_processing_charge: Yes article_type: original author: - first_name: Sivamathini full_name: Rajappa, Sivamathini last_name: Rajappa - first_name: Pannaga full_name: Krishnamurthy, Pannaga last_name: Krishnamurthy - first_name: Hua full_name: Huang, Hua last_name: Huang - first_name: Dejie full_name: Yu, Dejie last_name: Yu - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Jian full_name: Xu, Jian last_name: Xu - first_name: Prakash P. full_name: Kumar, Prakash P. last_name: Kumar citation: ama: Rajappa S, Krishnamurthy P, Huang H, et al. The translocation of a chloride channel from the Golgi to the plasma membrane helps plants adapt to salt stress. Nature Communications. 2024;15. doi:10.1038/s41467-024-48234-z apa: Rajappa, S., Krishnamurthy, P., Huang, H., Yu, D., Friml, J., Xu, J., & Kumar, P. P. (2024). The translocation of a chloride channel from the Golgi to the plasma membrane helps plants adapt to salt stress. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-024-48234-z chicago: Rajappa, Sivamathini, Pannaga Krishnamurthy, Hua Huang, Dejie Yu, Jiří Friml, Jian Xu, and Prakash P. Kumar. “The Translocation of a Chloride Channel from the Golgi to the Plasma Membrane Helps Plants Adapt to Salt Stress.” Nature Communications. Springer Nature, 2024. https://doi.org/10.1038/s41467-024-48234-z. ieee: S. Rajappa et al., “The translocation of a chloride channel from the Golgi to the plasma membrane helps plants adapt to salt stress,” Nature Communications, vol. 15. Springer Nature, 2024. ista: Rajappa S, Krishnamurthy P, Huang H, Yu D, Friml J, Xu J, Kumar PP. 2024. The translocation of a chloride channel from the Golgi to the plasma membrane helps plants adapt to salt stress. Nature Communications. 15, 3978. mla: Rajappa, Sivamathini, et al. “The Translocation of a Chloride Channel from the Golgi to the Plasma Membrane Helps Plants Adapt to Salt Stress.” Nature Communications, vol. 15, 3978, Springer Nature, 2024, doi:10.1038/s41467-024-48234-z. short: S. Rajappa, P. Krishnamurthy, H. Huang, D. Yu, J. Friml, J. Xu, P.P. Kumar, Nature Communications 15 (2024). date_created: 2024-05-26T22:00:57Z date_published: 2024-05-10T00:00:00Z date_updated: 2025-09-08T07:37:29Z day: '10' ddc: - '580' department: - _id: JiFr doi: 10.1038/s41467-024-48234-z external_id: isi: - '001221549300004' pmid: - '38729926' file: - access_level: open_access checksum: 79aacbe31cf7626b78da062b1339bdb0 content_type: application/pdf creator: dernst date_created: 2024-05-27T07:43:46Z date_updated: 2024-05-27T07:43:46Z file_id: '17056' file_name: 2024_NatureComm_Rajappa.pdf file_size: 20961818 relation: main_file success: 1 file_date_updated: 2024-05-27T07:43:46Z has_accepted_license: '1' intvolume: ' 15' isi: 1 language: - iso: eng license: https://creativecommons.org/licenses/by/4.0/ month: '05' oa: 1 oa_version: Published Version pmid: 1 publication: Nature Communications publication_identifier: eissn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: The translocation of a chloride channel from the Golgi to the plasma membrane helps plants adapt to salt stress tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 15 year: '2024' ... --- OA_place: publisher OA_type: hybrid _id: '17141' abstract: - lang: eng text: 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. acknowledgement: "We thank other lab members for their critical comments on this manuscript. We also thank the editor and reviewers for their constructive comments to improve our manuscript. We apologize to authors whose important work we could not include due to space limitations.\r\nThis work is supported by funding from Jiangxi Agricultural University (9232308314) and the Science and Technology Department of Jiangxi Province (20223BCJ25037) to HBH, and the Science and Technology Department of Jiangxi Province (20202ACB215002) to SYP." article_number: erae246 article_processing_charge: No article_type: original author: - first_name: Zilin full_name: Zhang, Zilin last_name: Zhang - first_name: Huihuang full_name: Chen, Huihuang id: 83c96512-15b2-11ec-abd3-b7eede36184f last_name: Chen - first_name: Shuaiying full_name: Peng, Shuaiying last_name: Peng - first_name: Huibin full_name: Han, Huibin last_name: Han citation: ama: Zhang Z, Chen H, Peng S, Han H. Slow and rapid auxin responses in Arabidopsis. Journal of Experimental Botany. 2024;75(18). doi:10.1093/jxb/erae246 apa: Zhang, Z., Chen, H., Peng, S., & Han, H. (2024). Slow and rapid auxin responses in Arabidopsis. Journal of Experimental Botany. Oxford University Press. https://doi.org/10.1093/jxb/erae246 chicago: Zhang, Zilin, Huihuang Chen, Shuaiying Peng, and Huibin Han. “Slow and Rapid Auxin Responses in Arabidopsis.” Journal of Experimental Botany. Oxford University Press, 2024. https://doi.org/10.1093/jxb/erae246. ieee: Z. Zhang, H. Chen, S. Peng, and H. Han, “Slow and rapid auxin responses in Arabidopsis,” Journal of Experimental Botany, vol. 75, no. 18. Oxford University Press, 2024. ista: Zhang Z, Chen H, Peng S, Han H. 2024. Slow and rapid auxin responses in Arabidopsis. Journal of Experimental Botany. 75(18), erae246. mla: Zhang, Zilin, et al. “Slow and Rapid Auxin Responses in Arabidopsis.” Journal of Experimental Botany, vol. 75, no. 18, erae246, Oxford University Press, 2024, doi:10.1093/jxb/erae246. short: Z. Zhang, H. Chen, S. Peng, H. Han, Journal of Experimental Botany 75 (2024). date_created: 2024-06-15T19:50:15Z date_published: 2024-09-27T00:00:00Z date_updated: 2025-09-08T07:57:50Z day: '27' ddc: - '580' department: - _id: GradSch - _id: JiFr doi: 10.1093/jxb/erae246 external_id: isi: - '001270051200001' pmid: - '38794966' file: - access_level: open_access checksum: 91b9435ed0f6640809c7588df19abf2f content_type: application/pdf creator: dernst date_created: 2025-01-02T10:26:22Z date_updated: 2025-01-02T10:26:22Z file_id: '18720' file_name: 2024_JourExperimentalBotany_Zhang.pdf file_size: 763097 relation: main_file success: 1 file_date_updated: 2025-01-02T10:26:22Z has_accepted_license: '1' intvolume: ' 75' isi: 1 issue: '18' language: - iso: eng month: '09' oa: 1 oa_version: Published Version pmid: 1 publication: Journal of Experimental Botany publication_identifier: issn: - 0022-0957 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: Slow and rapid auxin responses in Arabidopsis tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 75 year: '2024' ... --- OA_place: publisher OA_type: hybrid _id: '18465' abstract: - lang: eng text: 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. acknowledgement: This work was funded by DFG3468/6-1, DFG3468/6-3, and SFB924 to U.Z.H. We thank Angela Alkofer and Helene Prunkl for excellent technical assistance and Xenopus maintenance. Christian Luschnig is acknowledged for sharing unpublished results and valuable discussions. article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: DP full_name: Janacek, DP last_name: Janacek - first_name: M full_name: Kolb, M last_name: Kolb - first_name: L full_name: Schulz, L last_name: Schulz - first_name: J full_name: Mergner, J last_name: Mergner - first_name: B full_name: Kuster, B last_name: Kuster - first_name: Matous full_name: Glanc, Matous id: 1AE1EA24-02D0-11E9-9BAA-DAF4881429F2 last_name: Glanc orcid: 0000-0003-0619-7783 - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: K full_name: Ten Tusscher, K last_name: Ten Tusscher - first_name: C full_name: Schwechheimer, C last_name: Schwechheimer - first_name: UZ full_name: Hammes, UZ last_name: Hammes citation: ama: Janacek D, Kolb M, Schulz L, et al. Transport properties of canonical PIN-FORMED proteins from Arabidopsis and the role of the loop domain in auxin transport. Developmental Cell. 2024;59(14):S1534-5807(24)00569-0. doi:10.1016/j.devcel.2024.09.020 apa: Janacek, D., Kolb, M., Schulz, L., Mergner, J., Kuster, B., Glanc, M., … Hammes, U. (2024). Transport properties of canonical PIN-FORMED proteins from Arabidopsis and the role of the loop domain in auxin transport. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2024.09.020 chicago: Janacek, DP, M Kolb, L Schulz, J Mergner, B Kuster, Matous Glanc, Jiří Friml, K Ten Tusscher, C Schwechheimer, and UZ Hammes. “Transport Properties of Canonical PIN-FORMED Proteins from Arabidopsis and the Role of the Loop Domain in Auxin Transport.” Developmental Cell. Elsevier, 2024. https://doi.org/10.1016/j.devcel.2024.09.020. ieee: D. Janacek et al., “Transport properties of canonical PIN-FORMED proteins from Arabidopsis and the role of the loop domain in auxin transport,” Developmental Cell, vol. 59, no. 14. Elsevier, pp. S1534-5807(24)00569–0, 2024. ista: Janacek D, Kolb M, Schulz L, Mergner J, Kuster B, Glanc M, Friml J, Ten Tusscher K, Schwechheimer C, Hammes U. 2024. Transport properties of canonical PIN-FORMED proteins from Arabidopsis and the role of the loop domain in auxin transport. Developmental Cell. 59(14), S1534-5807(24)00569–0. mla: Janacek, DP, et al. “Transport Properties of Canonical PIN-FORMED Proteins from Arabidopsis and the Role of the Loop Domain in Auxin Transport.” Developmental Cell, vol. 59, no. 14, Elsevier, 2024, pp. S1534-5807(24)00569-0, doi:10.1016/j.devcel.2024.09.020. short: D. Janacek, M. Kolb, L. Schulz, J. Mergner, B. Kuster, M. Glanc, J. Friml, K. Ten Tusscher, C. Schwechheimer, U. Hammes, Developmental Cell 59 (2024) S1534-5807(24)00569–0. date_created: 2024-10-23T08:41:27Z date_published: 2024-12-16T00:00:00Z date_updated: 2025-09-08T14:33:17Z day: '16' ddc: - '570' department: - _id: JiFr doi: 10.1016/j.devcel.2024.09.020 external_id: isi: - '001390774300001' pmid: - '39413780' file: - access_level: open_access checksum: 34423ee9fb4e30334f3572eddf1da2ae content_type: application/pdf creator: dernst date_created: 2025-01-13T09:20:15Z date_updated: 2025-01-13T09:20:15Z file_id: '18835' file_name: 2024_DevelopmentalCell_Janacek.pdf file_size: 3675955 relation: main_file success: 1 file_date_updated: 2025-01-13T09:20:15Z has_accepted_license: '1' intvolume: ' 59' isi: 1 issue: '14' language: - iso: eng license: https://creativecommons.org/licenses/by-nc/4.0/ month: '12' oa: 1 oa_version: Published Version page: S1534-5807(24)00569-0 pmid: 1 publication: Developmental Cell publication_identifier: eissn: - 1878-1551 issn: - 1534-5807 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Transport properties of canonical PIN-FORMED proteins from Arabidopsis and the role of the loop domain in auxin transport tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 59 year: '2024' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '18582' abstract: - lang: eng text: 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. acknowledgement: We gratefully acknowledge Leo Gälweiler for authorizing his PIN1 story. We would like to thank Yuanrong Pei for invaluable help with preparing figures. Work in the lab of C.L. is supported by grants from the Austrian Science Fund (PAT 8419423) and by the Gesellschaft für Forschungsförderung Niederösterreich m.b.H. (FTI19-008). The lab of J.F. is supported by the Austrian Science Fund (I 6123-B and P 37051-B). article_number: '9904' article_processing_charge: Yes article_type: original author: - first_name: Christian full_name: Luschnig, Christian last_name: Luschnig - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Luschnig C, Friml J. Over 25 years of decrypting PIN-mediated plant development. Nature Communications. 2024;15. doi:10.1038/s41467-024-54240-y apa: Luschnig, C., & Friml, J. (2024). Over 25 years of decrypting PIN-mediated plant development. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-024-54240-y chicago: Luschnig, Christian, and Jiří Friml. “Over 25 Years of Decrypting PIN-Mediated Plant Development.” Nature Communications. Springer Nature, 2024. https://doi.org/10.1038/s41467-024-54240-y. ieee: C. Luschnig and J. Friml, “Over 25 years of decrypting PIN-mediated plant development,” Nature Communications, vol. 15. Springer Nature, 2024. ista: Luschnig C, Friml J. 2024. Over 25 years of decrypting PIN-mediated plant development. Nature Communications. 15, 9904. mla: Luschnig, Christian, and Jiří Friml. “Over 25 Years of Decrypting PIN-Mediated Plant Development.” Nature Communications, vol. 15, 9904, Springer Nature, 2024, doi:10.1038/s41467-024-54240-y. short: C. Luschnig, J. Friml, Nature Communications 15 (2024). corr_author: '1' date_created: 2024-11-24T23:01:48Z date_published: 2024-12-01T00:00:00Z date_updated: 2025-09-08T14:53:48Z day: '01' ddc: - '580' department: - _id: JiFr doi: 10.1038/s41467-024-54240-y external_id: isi: - '001356232600004' pmid: - '39548100' file: - access_level: open_access checksum: 3a31af06f52100d287f1e9d9c2aa1d40 content_type: application/pdf creator: dernst date_created: 2024-12-03T14:10:54Z date_updated: 2024-12-03T14:10:54Z file_id: '18615' file_name: 2024_NatureComm_Luschnig.pdf file_size: 1426555 relation: main_file success: 1 file_date_updated: 2024-12-03T14:10:54Z has_accepted_license: '1' intvolume: ' 15' isi: 1 language: - iso: eng month: '12' oa: 1 oa_version: Published Version pmid: 1 project: - _id: bd76d395-d553-11ed-ba76-f678c14f9033 grant_number: I06123 name: Peptide receptors for auxin canalization in Arabidopsis - _id: 7bcece63-9f16-11ee-852c-ae94e099eeb6 grant_number: P37051 name: Guanylate cyclase activity of TIR1/AFBs auxin receptors publication: Nature Communications publication_identifier: eissn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Over 25 years of decrypting PIN-mediated plant development tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 15 year: '2024' ... --- OA_place: publisher OA_type: hybrid _id: '18596' abstract: - lang: eng text: Hormone perception and signaling pathways have a fundamental regulatory function in the physiological processes of plants. Cytokinins, a class of plant hormones, regulate cell division and meristem maintenance. The cytokinin signaling pathway is well established in the model plant Arabidopsis thaliana. Several negative feedback mechanisms, tightly controlling cytokinin signaling output, have been described previously. In this study, we identified a new feedback mechanism executed through alternative splicing of the cytokinin receptor AHK4/CRE1. A novel splicing variant named CRE1int7 results from seventh intron retention, introducing a premature termination codon in the transcript. We showed that CRE1int7 is translated in planta into a truncated receptor lacking the C-terminal receiver domain essential for signal transduction. CRE1int7 can bind cytokinin but cannot activate the downstream cascade. We present a novel negative feedback mechanism of the cytokinin signaling pathway, facilitated by a decoy receptor that can inactivate canonical cytokinin receptors via dimerization and compete with them for ligand binding. Ensuring proper plant growth and development requires precise control of the cytokinin signaling pathway at several levels. CRE1int7 represents a so-far unknown mechanism for fine-tuning the cytokinin signaling pathway in Arabidopsis. acknowledged_ssus: - _id: Bio - _id: LifeSc acknowledgement: We dedicate this paper to the deceased Petr Galuszka for his inspiration and support of our project. We thank Prof. Peter Hedden for constructive criticism of the manuscript and English editing. No conflict of interest is declared. article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Michaela full_name: Králová, Michaela last_name: Králová - first_name: Ivona full_name: Kubalová, Ivona last_name: Kubalová - first_name: Jakub full_name: Hajný, Jakub last_name: Hajný - first_name: Karolina full_name: Kubiasova, Karolina id: 946011F4-3E71-11EA-860B-C7A73DDC885E last_name: Kubiasova orcid: 0000-0001-5630-9419 - first_name: Karolína full_name: Vagaská, Karolína last_name: Vagaská - first_name: Zengxiang full_name: Ge, Zengxiang id: f43371a3-09ff-11eb-8013-bd0c6a2f6de8 last_name: Ge orcid: 0000-0001-9381-3577 - first_name: Michelle C full_name: Gallei, Michelle C id: 35A03822-F248-11E8-B48F-1D18A9856A87 last_name: Gallei orcid: 0000-0003-1286-7368 - first_name: Hana full_name: Semerádová, Hana id: 42FE702E-F248-11E8-B48F-1D18A9856A87 last_name: Semerádová - first_name: Anna full_name: Kuchařová, Anna last_name: Kuchařová - first_name: Martin full_name: Hönig, Martin last_name: Hönig - first_name: Aline full_name: Monzer, Aline id: 2DB5D88C-D7B3-11E9-B8FD-7907E6697425 last_name: Monzer - first_name: Martin full_name: Kovačik, Martin last_name: Kovačik - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Ondřej full_name: Novák, Ondřej last_name: Novák - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 - first_name: Yoshihisa full_name: Ikeda, Yoshihisa last_name: Ikeda - first_name: David full_name: Zalabák, David last_name: Zalabák citation: ama: Králová M, Kubalová I, Hajný J, et al. A decoy receptor derived from alternative splicing fine-tunes cytokinin signaling in Arabidopsis. Molecular Plant. 2024;17(12):1850-1865. doi:10.1016/j.molp.2024.11.001 apa: Králová, M., Kubalová, I., Hajný, J., Kubiasova, K., Vagaská, K., Ge, Z., … Zalabák, D. (2024). A decoy receptor derived from alternative splicing fine-tunes cytokinin signaling in Arabidopsis. Molecular Plant. Elsevier. https://doi.org/10.1016/j.molp.2024.11.001 chicago: Králová, Michaela, Ivona Kubalová, Jakub Hajný, Karolina Kubiasova, Karolína Vagaská, Zengxiang Ge, Michelle C Gallei, et al. “A Decoy Receptor Derived from Alternative Splicing Fine-Tunes Cytokinin Signaling in Arabidopsis.” Molecular Plant. Elsevier, 2024. https://doi.org/10.1016/j.molp.2024.11.001. ieee: M. Králová et al., “A decoy receptor derived from alternative splicing fine-tunes cytokinin signaling in Arabidopsis,” Molecular Plant, vol. 17, no. 12. Elsevier, pp. 1850–1865, 2024. ista: Králová M, Kubalová I, Hajný J, Kubiasova K, Vagaská K, Ge Z, Gallei MC, Semerádová H, Kuchařová A, Hönig M, Monzer A, Kovačik M, Friml J, Novák O, Benková E, Ikeda Y, Zalabák D. 2024. A decoy receptor derived from alternative splicing fine-tunes cytokinin signaling in Arabidopsis. Molecular Plant. 17(12), 1850–1865. mla: Králová, Michaela, et al. “A Decoy Receptor Derived from Alternative Splicing Fine-Tunes Cytokinin Signaling in Arabidopsis.” Molecular Plant, vol. 17, no. 12, Elsevier, 2024, pp. 1850–65, doi:10.1016/j.molp.2024.11.001. short: M. Králová, I. Kubalová, J. Hajný, K. Kubiasova, K. Vagaská, Z. Ge, M.C. Gallei, H. Semerádová, A. Kuchařová, M. Hönig, A. Monzer, M. Kovačik, J. Friml, O. Novák, E. Benková, Y. Ikeda, D. Zalabák, Molecular Plant 17 (2024) 1850–1865. date_created: 2024-11-28T11:13:35Z date_published: 2024-12-02T00:00:00Z date_updated: 2025-09-08T14:46:45Z day: '02' ddc: - '580' department: - _id: JiFr - _id: EvBe doi: 10.1016/j.molp.2024.11.001 external_id: isi: - '001373778300001' pmid: - '39501563' file: - access_level: open_access checksum: a11feea4b1677df76b632eca04bfc1dd content_type: application/pdf creator: dernst date_created: 2024-12-03T11:08:09Z date_updated: 2024-12-03T11:08:09Z file_id: '18612' file_name: 2024_MolecularPlant_Kralova.pdf file_size: 3308945 relation: main_file success: 1 file_date_updated: 2024-12-03T11:08:09Z has_accepted_license: '1' intvolume: ' 17' isi: 1 issue: '12' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ month: '12' oa: 1 oa_version: Published Version page: 1850-1865 pmid: 1 publication: Molecular Plant publication_identifier: issn: - 1674-2052 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: A decoy receptor derived from alternative splicing fine-tunes cytokinin signaling in Arabidopsis tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 17 year: '2024' ... --- OA_place: repository OA_type: green _id: '17377' abstract: - lang: eng text: "Lateral root (LR) formation, that is vital for plant development, is one of many auxin-modulated processes, but the underlying regulatory mechanism is not yet fully known. Recently, \r\nGonzález-García et al. discovered the BiAux compound and showed that it is involved in LR development via regulating specific auxin coreceptors." acknowledgement: "This work was supported by funding from the National Science Centre, Poland, under the OPUS call in the Weave program and the Austrian Science Fund, Austria project (FWF)/OPUS – Peptide receptor complexes for auxin canalization and regeneration in Arabidopsis (grant \r\n2021/43/I/NZ1/01835) to E.M., and grant I 6123-B to J.F." article_processing_charge: No article_type: original author: - first_name: Barbara full_name: Wójcikowska, Barbara last_name: Wójcikowska - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Ewa full_name: Mazur, Ewa last_name: Mazur citation: ama: Wójcikowska B, Friml J, Mazur E. BiAux, a newly discovered compound triggering auxin signaling. Trends in Plant Science. 2024;29(12):1279-1281. doi:10.1016/j.tplants.2024.07.008 apa: Wójcikowska, B., Friml, J., & Mazur, E. (2024). BiAux, a newly discovered compound triggering auxin signaling. Trends in Plant Science. Elsevier. https://doi.org/10.1016/j.tplants.2024.07.008 chicago: Wójcikowska, Barbara, Jiří Friml, and Ewa Mazur. “BiAux, a Newly Discovered Compound Triggering Auxin Signaling.” Trends in Plant Science. Elsevier, 2024. https://doi.org/10.1016/j.tplants.2024.07.008. ieee: B. Wójcikowska, J. Friml, and E. Mazur, “BiAux, a newly discovered compound triggering auxin signaling,” Trends in Plant Science, vol. 29, no. 12. Elsevier, pp. 1279–1281, 2024. ista: Wójcikowska B, Friml J, Mazur E. 2024. BiAux, a newly discovered compound triggering auxin signaling. Trends in Plant Science. 29(12), 1279–1281. mla: Wójcikowska, Barbara, et al. “BiAux, a Newly Discovered Compound Triggering Auxin Signaling.” Trends in Plant Science, vol. 29, no. 12, Elsevier, 2024, pp. 1279–81, doi:10.1016/j.tplants.2024.07.008. short: B. Wójcikowska, J. Friml, E. Mazur, Trends in Plant Science 29 (2024) 1279–1281. corr_author: '1' date_created: 2024-08-04T22:01:22Z date_published: 2024-12-01T00:00:00Z date_updated: 2025-11-24T15:13:16Z day: '01' ddc: - '580' department: - _id: JiFr doi: 10.1016/j.tplants.2024.07.008 external_id: isi: - '001375335200001' pmid: - '39079770' file: - access_level: open_access checksum: 89a83fe25b9ec1aad8e22d134a342c09 content_type: application/pdf creator: dernst date_created: 2025-11-24T15:12:50Z date_updated: 2025-11-24T15:12:50Z file_id: '20691' file_name: 2024_TrendsPlantScience_Wojcikowska_submittedversion.pdf file_size: 277636 relation: main_file success: 1 file_date_updated: 2025-11-24T15:12:50Z has_accepted_license: '1' intvolume: ' 29' isi: 1 issue: '12' language: - iso: eng month: '12' oa: 1 oa_version: Submitted Version page: 1279-1281 pmid: 1 project: - _id: bd76d395-d553-11ed-ba76-f678c14f9033 grant_number: I06123 name: Peptide receptors for auxin canalization in Arabidopsis publication: Trends in Plant Science publication_identifier: issn: - 1360-1385 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: BiAux, a newly discovered compound triggering auxin signaling type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 29 year: '2024' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '17436' abstract: - lang: eng text: 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. acknowledgement: "We are grateful to Iris Nieuwland and Neri van Laar for experimental support. No conflict of interest declared.\r\nThis work was supported by the Netherlands Organisation for Scientific Research, the Netherlands (grants ALWOP.402 and OCENW.M20.031 to J.W.B.) and the Human Frontiers Research Program (grant RGP0015/2022 to D.W.)." article_number: '101039' article_processing_charge: Yes article_type: original author: - first_name: Shubhajit full_name: Das, Shubhajit id: b08969a4-f2a5-11ed-b6c4-ff0f10b7d0be last_name: Das - first_name: Martijn full_name: De Roij, Martijn last_name: De Roij - first_name: Simon full_name: Bellows, Simon last_name: Bellows - first_name: Melissa Dipp full_name: Alvarez, Melissa Dipp last_name: Alvarez - first_name: Sumanth full_name: Mutte, Sumanth last_name: Mutte - first_name: Wouter full_name: Kohlen, Wouter last_name: Kohlen - first_name: Etienne full_name: Farcot, Etienne last_name: Farcot - first_name: Dolf full_name: Weijers, Dolf last_name: Weijers - first_name: Jan Willem full_name: Borst, Jan Willem last_name: Borst citation: ama: Das S, De Roij M, Bellows S, et al. Quantitative imaging reveals the role of MpARF proteasomal degradation during gemma germination. Plant Communications. 2024;5(11). doi:10.1016/j.xplc.2024.101039 apa: Das, S., De Roij, M., Bellows, S., Alvarez, M. D., Mutte, S., Kohlen, W., … Borst, J. W. (2024). Quantitative imaging reveals the role of MpARF proteasomal degradation during gemma germination. Plant Communications. Elsevier. https://doi.org/10.1016/j.xplc.2024.101039 chicago: Das, Shubhajit, Martijn De Roij, Simon Bellows, Melissa Dipp Alvarez, Sumanth Mutte, Wouter Kohlen, Etienne Farcot, Dolf Weijers, and Jan Willem Borst. “Quantitative Imaging Reveals the Role of MpARF Proteasomal Degradation during Gemma Germination.” Plant Communications. Elsevier, 2024. https://doi.org/10.1016/j.xplc.2024.101039. ieee: S. Das et al., “Quantitative imaging reveals the role of MpARF proteasomal degradation during gemma germination,” Plant Communications, vol. 5, no. 11. Elsevier, 2024. ista: Das S, De Roij M, Bellows S, Alvarez MD, Mutte S, Kohlen W, Farcot E, Weijers D, Borst JW. 2024. Quantitative imaging reveals the role of MpARF proteasomal degradation during gemma germination. Plant Communications. 5(11), 101039. mla: Das, Shubhajit, et al. “Quantitative Imaging Reveals the Role of MpARF Proteasomal Degradation during Gemma Germination.” Plant Communications, vol. 5, no. 11, 101039, Elsevier, 2024, doi:10.1016/j.xplc.2024.101039. short: S. Das, M. De Roij, S. Bellows, M.D. Alvarez, S. Mutte, W. Kohlen, E. Farcot, D. Weijers, J.W. Borst, Plant Communications 5 (2024). date_created: 2024-08-18T22:01:04Z date_published: 2024-11-11T00:00:00Z date_updated: 2025-01-09T12:26:55Z day: '11' ddc: - '580' department: - _id: JiFr doi: 10.1016/j.xplc.2024.101039 external_id: pmid: - '38988072' file: - access_level: open_access checksum: 38cabc1042ac7fb70e6c4c510eba88fc content_type: application/pdf creator: dernst date_created: 2025-01-09T12:25:32Z date_updated: 2025-01-09T12:25:32Z file_id: '18811' file_name: 2024_PlantCommunications_Das.pdf file_size: 4970540 relation: main_file success: 1 file_date_updated: 2025-01-09T12:25:32Z has_accepted_license: '1' intvolume: ' 5' issue: '11' language: - iso: eng month: '11' oa: 1 oa_version: Published Version pmid: 1 publication: Plant Communications publication_identifier: eissn: - 2590-3462 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Quantitative imaging reveals the role of MpARF proteasomal degradation during gemma germination tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 5 year: '2024' ... --- OA_place: publisher OA_type: gold _id: '18073' abstract: - lang: eng text: Conserved signaling cascades monitor protein-folding homeostasis to ensure proper cellular function. One of the evolutionary conserved key players is IRE1, which maintains endoplasmic reticulum (ER) homeostasis through the unfolded protein response (UPR). Upon accumulation of misfolded proteins in the ER, IRE1 forms clusters on the ER membrane to initiate UPR signaling. What regulates IRE1 cluster formation is not fully understood. Here, we show that the ER lumenal domain (LD) of human IRE1α forms biomolecular condensates in vitro. IRE1α LD condensates were stabilized both by binding to unfolded polypeptides as well as by tethering to model membranes, suggesting their role in assembling IRE1α into signaling-competent stable clusters. Molecular dynamics simulations indicated that weak multivalent interactions drive IRE1α LD clustering. Mutagenesis experiments identified disordered regions in IRE1α LD to control its clustering in vitro and in cells. Importantly, dysregulated clustering of IRE1α mutants led to defects in IRE1α signaling. Our results revealed that disordered regions in IRE1α LD control its clustering and suggest their role as a common strategy in regulating protein assembly on membranes. acknowledgement: We thank late Thomas Peterbauer at the Max Perutz Labs Biooptics Light Microscopy Facility for his help and support. We are grateful to Kitti Csalyi and Thomas Sauer at Max Perutz Labs Biooptics FACS facility for their help. We thank Grzegorz Scibisz and Sertan Atilla for their support with the expression and purification of mCherry-IRE1α LD-10His. We are grateful to Aleksandra S Anisimova with her help in the generation of stable cell lines and the statistical analyses of the data. We thank Venja Vieweger for her help with the characterization of the WLLI and D123P IRE1 mutants in cells. We are thankful to Monika Kubickova for the help with the AUC experiments. We acknowledge CF BIC of CIISB, Instruct-CZ Centre, supported by MEYS CR (LM2023042)) and European Regional Development Fund-Project, UP CIISB“ (No. CZ.02.1.01/0.0/0.0/18_046/0015974). We thank the members of the Karagöz lab for the critical reading and editing of the manuscript. We are thankful to our colleagues Diego Acosta-Alvear, Vladislav Belyy, Jirka Peschek, Yasin Dagdas, Javier Martinez, Sascha Martens and Alwin Köhler for their invaluable input on the manuscript. We are grateful to Life Science Editors, especially Katrina Woolcock for her useful edits and comments on the manuscript. We acknowledge funding from Austrian Science Fund (FWF-SFB F79 and FWF-W 1261) to GEK. PK acknowledges the support of the Max Perutz PhD fellowship. GAV is funded by Stand-Alone grants (P30231-B, P30415-B, P36572), Special Research Grant (SFB grant F79), and Doctoral School grant (DK grant W1261) from the Austrian Science Fund (FWF). ES and RC acknowledge support and funding by the Frankfurt Institute of Advanced Studies, the LOEWE Center for Multiscale Modelling in Life Sciences of the state of Hesse, the Collaborative Research Center 1507 “Membrane-associated Protein Assemblies, Machineries, and Supercomplexes” (Project ID 450648163), and the International Max Planck Research School on Cellular Biophysics (to RC), the Center for Scientific Computing of the Goethe University and the Jülich Supercomputing Centre for computational resources and support. article_processing_charge: Yes article_type: original author: - first_name: Paulina full_name: Kettel, Paulina last_name: Kettel - first_name: Laura full_name: Marosits, Laura last_name: Marosits - first_name: Elena full_name: Spinetti, Elena last_name: Spinetti - first_name: Michael full_name: Rechberger, Michael last_name: Rechberger - first_name: Caterina full_name: Giannini, Caterina id: e3fdddd5-f6e0-11ea-865d-ca99ee6367f4 last_name: Giannini - first_name: Philipp full_name: Radler, Philipp id: 40136C2A-F248-11E8-B48F-1D18A9856A87 last_name: Radler orcid: '0000-0001-9198-2182 ' - first_name: Isabell full_name: Niedermoser, Isabell last_name: Niedermoser - first_name: Irmgard full_name: Fischer, Irmgard last_name: Fischer - first_name: Gijs A. full_name: Versteeg, Gijs A. last_name: Versteeg - first_name: Martin full_name: Loose, Martin id: 462D4284-F248-11E8-B48F-1D18A9856A87 last_name: Loose orcid: 0000-0001-7309-9724 - first_name: Roberto full_name: Covino, Roberto last_name: Covino - first_name: G. Elif full_name: Karagöz, G. Elif last_name: Karagöz citation: ama: Kettel P, Marosits L, Spinetti E, et al. Disordered regions in the IRE1α ER lumenal domain mediate its stress-induced clustering. EMBO Journal. 2024;43(20):4668-4698. doi:10.1038/s44318-024-00207-0 apa: Kettel, P., Marosits, L., Spinetti, E., Rechberger, M., Giannini, C., Radler, P., … Karagöz, G. E. (2024). Disordered regions in the IRE1α ER lumenal domain mediate its stress-induced clustering. EMBO Journal. Embo Press. https://doi.org/10.1038/s44318-024-00207-0 chicago: Kettel, Paulina, Laura Marosits, Elena Spinetti, Michael Rechberger, Caterina Giannini, Philipp Radler, Isabell Niedermoser, et al. “Disordered Regions in the IRE1α ER Lumenal Domain Mediate Its Stress-Induced Clustering.” EMBO Journal. Embo Press, 2024. https://doi.org/10.1038/s44318-024-00207-0. ieee: P. Kettel et al., “Disordered regions in the IRE1α ER lumenal domain mediate its stress-induced clustering,” EMBO Journal, vol. 43, no. 20. Embo Press, pp. 4668–4698, 2024. ista: Kettel P, Marosits L, Spinetti E, Rechberger M, Giannini C, Radler P, Niedermoser I, Fischer I, Versteeg GA, Loose M, Covino R, Karagöz GE. 2024. Disordered regions in the IRE1α ER lumenal domain mediate its stress-induced clustering. EMBO Journal. 43(20), 4668–4698. mla: Kettel, Paulina, et al. “Disordered Regions in the IRE1α ER Lumenal Domain Mediate Its Stress-Induced Clustering.” EMBO Journal, vol. 43, no. 20, Embo Press, 2024, pp. 4668–98, doi:10.1038/s44318-024-00207-0. short: P. Kettel, L. Marosits, E. Spinetti, M. Rechberger, C. Giannini, P. Radler, I. Niedermoser, I. Fischer, G.A. Versteeg, M. Loose, R. Covino, G.E. Karagöz, EMBO Journal 43 (2024) 4668–4698. date_created: 2024-09-15T22:01:42Z date_published: 2024-10-15T00:00:00Z date_updated: 2025-09-08T09:22:11Z day: '15' ddc: - '570' department: - _id: MaLo - _id: JiFr doi: 10.1038/s44318-024-00207-0 external_id: isi: - '001306286100002' pmid: - '39232130' file: - access_level: open_access checksum: 04f4df1a561083f2846676442fc4eb3c content_type: application/pdf creator: dernst date_created: 2025-01-13T08:43:20Z date_updated: 2025-01-13T08:43:20Z file_id: '18827' file_name: 2024_Embo_Kettel.pdf file_size: 10080854 relation: main_file success: 1 file_date_updated: 2025-01-13T08:43:20Z has_accepted_license: '1' intvolume: ' 43' isi: 1 issue: '20' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: 4668-4698 pmid: 1 publication: EMBO Journal publication_identifier: eissn: - 1460-2075 issn: - 0261-4189 publication_status: published publisher: Embo Press quality_controlled: '1' scopus_import: '1' status: public title: Disordered regions in the IRE1α ER lumenal domain mediate its stress-induced clustering tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 43 year: '2024' ... --- OA_type: closed access _id: '18311' abstract: - lang: eng text: Local wound signaling in plants informs the surrounding tissues about an injury and initiates the regeneration process. In a recent paper published in Cell, Yang and colleagues show the involvement of a single Pep family member from tomato in wound signaling and how exogenous application of this regeneration factor enhances transformation efficiency in crops. article_processing_charge: No article_type: original author: - first_name: Lukas full_name: Hörmayer, Lukas id: 2EEE7A2A-F248-11E8-B48F-1D18A9856A87 last_name: Hörmayer orcid: 0000-0001-8295-2926 - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: 'Hörmayer L, Friml J. Feeling the danger: Local wound signaling in plants. Cell Research. 2024;34:761-762. doi:10.1038/s41422-024-01035-x' apa: 'Hörmayer, L., & Friml, J. (2024). Feeling the danger: Local wound signaling in plants. Cell Research. Springer Nature. https://doi.org/10.1038/s41422-024-01035-x' chicago: 'Hörmayer, Lukas, and Jiří Friml. “Feeling the Danger: Local Wound Signaling in Plants.” Cell Research. Springer Nature, 2024. https://doi.org/10.1038/s41422-024-01035-x.' ieee: 'L. Hörmayer and J. Friml, “Feeling the danger: Local wound signaling in plants,” Cell Research, vol. 34. Springer Nature, pp. 761–762, 2024.' ista: 'Hörmayer L, Friml J. 2024. Feeling the danger: Local wound signaling in plants. Cell Research. 34, 761–762.' mla: 'Hörmayer, Lukas, and Jiří Friml. “Feeling the Danger: Local Wound Signaling in Plants.” Cell Research, vol. 34, Springer Nature, 2024, pp. 761–62, doi:10.1038/s41422-024-01035-x.' short: L. Hörmayer, J. Friml, Cell Research 34 (2024) 761–762. corr_author: '1' date_created: 2024-10-13T22:01:51Z date_published: 2024-11-01T00:00:00Z date_updated: 2025-09-08T09:57:18Z day: '01' department: - _id: JiFr doi: 10.1038/s41422-024-01035-x external_id: isi: - '001326684200001' pmid: - '39354142' intvolume: ' 34' isi: 1 language: - iso: eng month: '11' oa_version: None page: 761-762 pmid: 1 publication: Cell Research publication_identifier: eissn: - 1748-7838 issn: - 1001-0602 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: 'Feeling the danger: Local wound signaling in plants' type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 34 year: '2024' ... --- OA_place: repository _id: '18689' abstract: - lang: eng text: 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. acknowledged_ssus: - _id: Bio - _id: LifeSc - _id: M-Shop - _id: E-Lib acknowledgement: "We gratefully acknowledge support by the Scientific Service Units at ISTA, including the Imaging and Optics and Lab Support facilities and the mechanical workshop and Library. We thank Philipp Velicky for STED microscope alignment.\r\n\r\nThis project has received funding from the Austrian Science Fund (FWF): I 3630-B25 (J.G.D) and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 742985, J.F.). It has also received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385. S.T. has received funding as an ISTplus Fellow from the European Union’s Horizon 2020 Research and Innovation Programme under Marie Skłodowska-Curie grant agreement no. 754411 and from an EMBO Long-Term Fellowship (grant number ALTF 679-2018). It has further received funding from the Austrian Science Fund (FWF) grant DK W1232 (M.T, N.A-D., J.G.D). W.J. received funding via a Human Frontier Science Program postdoctoral fellowship LT000557/2018.\r\n\r\nThe funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript." article_processing_charge: No author: - first_name: Michelle C full_name: Gallei, Michelle C id: 35A03822-F248-11E8-B48F-1D18A9856A87 last_name: Gallei orcid: 0000-0003-1286-7368 - first_name: Sven M full_name: Truckenbrodt, Sven M id: 45812BD4-F248-11E8-B48F-1D18A9856A87 last_name: Truckenbrodt - first_name: Caroline full_name: Kreuzinger, Caroline id: 382077BA-F248-11E8-B48F-1D18A9856A87 last_name: Kreuzinger - first_name: Syamala full_name: Inumella, Syamala id: F8660870-D756-11E9-98C5-34DFE5697425 last_name: Inumella orcid: 0009-0002-5890-120X - first_name: Vitali full_name: Vistunou, Vitali id: 7e146587-8972-11ed-ae7b-d7a32ea86a81 last_name: Vistunou - first_name: Christoph M full_name: Sommer, Christoph M id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87 last_name: Sommer orcid: 0000-0003-1216-9105 - first_name: Mojtaba full_name: Tavakoli, Mojtaba id: 3A0A06F4-F248-11E8-B48F-1D18A9856A87 last_name: Tavakoli orcid: 0000-0002-7667-6854 - first_name: Nathalie full_name: Agudelo Duenas, Nathalie id: 40E7F008-F248-11E8-B48F-1D18A9856A87 last_name: Agudelo Duenas - first_name: Jakob full_name: Vorlaufer, Jakob id: 937696FA-C996-11E9-8C7C-CF13E6697425 last_name: Vorlaufer orcid: 0009-0000-7590-3501 - first_name: Wiebke full_name: Jahr, Wiebke id: 425C1CE8-F248-11E8-B48F-1D18A9856A87 last_name: Jahr orcid: 0000-0003-0201-2315 - first_name: Marek full_name: Randuch, Marek id: 6ac4636d-15b2-11ec-abd3-fb8df79972ae last_name: Randuch - first_name: Alexander J full_name: Johnson, Alexander J id: 46A62C3A-F248-11E8-B48F-1D18A9856A87 last_name: Johnson orcid: 0000-0002-2739-8843 - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Johann G full_name: Danzl, Johann G id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87 last_name: Danzl orcid: 0000-0001-8559-3973 citation: ama: Gallei MC, Truckenbrodt SM, Kreuzinger C, et al. Super-resolution expansion microscopy in plant roots. bioRxiv. doi:10.1101/2024.02.21.581330 apa: Gallei, M. C., Truckenbrodt, S. M., Kreuzinger, C., Inumella, S., Vistunou, V., Sommer, C. M., … Danzl, J. G. (n.d.). Super-resolution expansion microscopy in plant roots. bioRxiv. https://doi.org/10.1101/2024.02.21.581330 chicago: Gallei, Michelle C, Sven M Truckenbrodt, Caroline Kreuzinger, Syamala Inumella, Vitali Vistunou, Christoph M Sommer, Mojtaba Tavakoli, et al. “Super-Resolution Expansion Microscopy in Plant Roots.” BioRxiv, n.d. https://doi.org/10.1101/2024.02.21.581330. ieee: M. C. Gallei et al., “Super-resolution expansion microscopy in plant roots,” bioRxiv. . ista: Gallei MC, Truckenbrodt SM, Kreuzinger C, Inumella S, Vistunou V, Sommer CM, Tavakoli M, Agudelo Duenas N, Vorlaufer J, Jahr W, Randuch M, Johnson AJ, Benková E, Friml J, Danzl JG. Super-resolution expansion microscopy in plant roots. bioRxiv, 10.1101/2024.02.21.581330. mla: Gallei, Michelle C., et al. “Super-Resolution Expansion Microscopy in Plant Roots.” BioRxiv, doi:10.1101/2024.02.21.581330. short: M.C. Gallei, S.M. Truckenbrodt, C. Kreuzinger, S. Inumella, V. Vistunou, C.M. Sommer, M. Tavakoli, N. Agudelo Duenas, J. Vorlaufer, W. Jahr, M. Randuch, A.J. Johnson, E. Benková, J. Friml, J.G. Danzl, BioRxiv (n.d.). corr_author: '1' date_created: 2024-12-19T12:28:00Z date_published: 2024-02-21T00:00:00Z date_updated: 2026-07-28T08:33:52Z day: '21' department: - _id: EvBe - _id: JoDa - _id: JiFr doi: 10.1101/2024.02.21.581330 ec_funded: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1101/2024.02.21.581330 month: '02' oa: 1 oa_version: Preprint project: - _id: 261099A6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742985' name: Tracing Evolution of Auxin Transport and Polarity in Plants - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships - _id: 26AA4EF2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: W1232-B24 name: Molecular Drug Targets - _id: 269B5B22-B435-11E9-9278-68D0E5697425 grant_number: ALTF 679-2018 name: UltraX - achieving sub-nanometer resolution in light microscopy using iterative X10 microscopy in combination with nanobodies and STED publication: bioRxiv publication_status: draft related_material: record: - id: '19003' relation: later_version status: public - id: '18681' relation: dissertation_contains status: public status: public title: Super-resolution expansion microscopy in plant roots tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2024' ... --- _id: '14826' abstract: - lang: eng text: 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. acknowledgement: 'We are grateful to Asuka Shitaku and Eri Koide for generating and sharing the Marchantia PRAF-mCitrine line and Peng-Cheng Wang for sharing the Arabidopsis raf mutant. We are grateful to our team members for discussions and helpful advice. This work was supported by funding from the Netherlands Organization for Scientific Research (NWO): VICI grant 865.14.001 and ENW-KLEIN OCENW.KLEIN.027 grants to D.W.; VENI grant VI.VENI.212.003 to A.K.; the European Research Council AdG DIRNDL (contract number 833867) to D.W.; CoG CATCH to J.S.; StG CELLONGATE (contract 803048) to M.F.; and AdG ETAP (contract 742985) to J.F.; MEXT KAKENHI grant number JP19H05675 to T.K.; JSPS KAKENHI grant number JP20H03275 to R.N.; Takeda Science Foundation to R.N.; and the Austrian Science Fund (FWF, P29988) to J.F.' article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Andre full_name: Kuhn, Andre last_name: Kuhn - first_name: Mark full_name: Roosjen, Mark last_name: Roosjen - first_name: Sumanth full_name: Mutte, Sumanth last_name: Mutte - first_name: Shiv Mani full_name: Dubey, Shiv Mani last_name: Dubey - first_name: Vanessa Polet full_name: Carrillo Carrasco, Vanessa Polet last_name: Carrillo Carrasco - first_name: Sjef full_name: Boeren, Sjef last_name: Boeren - first_name: Aline full_name: Monzer, Aline id: 2DB5D88C-D7B3-11E9-B8FD-7907E6697425 last_name: Monzer - first_name: Jasper full_name: Koehorst, Jasper last_name: Koehorst - first_name: Takayuki full_name: Kohchi, Takayuki last_name: Kohchi - first_name: Ryuichi full_name: Nishihama, Ryuichi last_name: Nishihama - first_name: Matyas full_name: Fendrych, Matyas id: 43905548-F248-11E8-B48F-1D18A9856A87 last_name: Fendrych orcid: 0000-0002-9767-8699 - first_name: Joris full_name: Sprakel, Joris last_name: Sprakel - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Dolf full_name: Weijers, Dolf last_name: Weijers citation: ama: Kuhn A, Roosjen M, Mutte S, et al. RAF-like protein kinases mediate a deeply conserved, rapid auxin response. Cell. 2024;187(1):130-148.e17. doi:10.1016/j.cell.2023.11.021 apa: Kuhn, A., Roosjen, M., Mutte, S., Dubey, S. M., Carrillo Carrasco, V. P., Boeren, S., … Weijers, D. (2024). RAF-like protein kinases mediate a deeply conserved, rapid auxin response. Cell. Elsevier. https://doi.org/10.1016/j.cell.2023.11.021 chicago: Kuhn, Andre, Mark Roosjen, Sumanth Mutte, Shiv Mani Dubey, Vanessa Polet Carrillo Carrasco, Sjef Boeren, Aline Monzer, et al. “RAF-like Protein Kinases Mediate a Deeply Conserved, Rapid Auxin Response.” Cell. Elsevier, 2024. https://doi.org/10.1016/j.cell.2023.11.021. ieee: A. Kuhn et al., “RAF-like protein kinases mediate a deeply conserved, rapid auxin response,” Cell, vol. 187, no. 1. Elsevier, p. 130–148.e17, 2024. ista: Kuhn A, Roosjen M, Mutte S, Dubey SM, Carrillo Carrasco VP, Boeren S, Monzer A, Koehorst J, Kohchi T, Nishihama R, Fendrych M, Sprakel J, Friml J, Weijers D. 2024. RAF-like protein kinases mediate a deeply conserved, rapid auxin response. Cell. 187(1), 130–148.e17. mla: Kuhn, Andre, et al. “RAF-like Protein Kinases Mediate a Deeply Conserved, Rapid Auxin Response.” Cell, vol. 187, no. 1, Elsevier, 2024, p. 130–148.e17, doi:10.1016/j.cell.2023.11.021. short: A. Kuhn, M. Roosjen, S. Mutte, S.M. Dubey, V.P. Carrillo Carrasco, S. Boeren, A. Monzer, J. Koehorst, T. Kohchi, R. Nishihama, M. Fendrych, J. Sprakel, J. Friml, D. Weijers, Cell 187 (2024) 130–148.e17. date_created: 2024-01-17T12:45:40Z date_published: 2024-01-04T00:00:00Z date_updated: 2026-08-14T09:33:45Z day: '04' ddc: - '580' department: - _id: JiFr doi: 10.1016/j.cell.2023.11.021 ec_funded: 1 external_id: isi: - '001152705700001' pmid: - '38128538' file: - access_level: open_access checksum: 06fd236a9ee0b46ccb05f44695bfc34b content_type: application/pdf creator: dernst date_created: 2024-01-22T13:41:41Z date_updated: 2024-01-22T13:41:41Z file_id: '14874' file_name: 2024_Cell_Kuhn.pdf file_size: 13194060 relation: main_file success: 1 file_date_updated: 2024-01-22T13:41:41Z has_accepted_license: '1' intvolume: ' 187' isi: 1 issue: '1' keyword: - General Biochemistry - Genetics and Molecular Biology language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 130-148.e17 pmid: 1 project: - _id: 261099A6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742985' name: Tracing Evolution of Auxin Transport and Polarity in Plants - _id: 262EF96E-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P29988 name: RNA-directed DNA methylation in plant development publication: Cell publication_identifier: eissn: - 1097-4172 issn: - 0092-8674 publication_status: published publisher: Elsevier quality_controlled: '1' related_material: record: - id: '19395' relation: dissertation_contains status: public scopus_import: '1' status: public title: RAF-like protein kinases mediate a deeply conserved, rapid auxin response tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 187 year: '2024' ... --- DOAJ_listed: '1' _id: '17103' abstract: - lang: eng text: 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. acknowledgement: We thank Professor Jianqiang Wu (Kunming Institute of Botany, Chinese Academy of Sciences) for his generous support with the sakuranetin measurement. We thank International Rice Research Institute (IRRI) for provision of the rice NILs. We thank Professor Zhongkai Zhang (Yunnan Academy of Agricultural Sciences) for his generous support with subcellular structure observation of rice roots. We thank Professor Barbara Valent (Kansas State University) for her generously provision of the plasmid containing the PWL2 gene. We thank Professor Zuhua He (Chinese Academy of Sciences) for the gift of the transgenic rice line expressing the Pigm gene, OsNPR1-RNAi mutant line and ROD1-overexpression rice line. We thank Professor Yinong Yang (The Pennsylvania State University) for provision of the rice line NahG. We thank Professor Muyuan Zhu (Zhejiang University) for provision of the transgenic plants overexpressing miR393a. We thank Professor Zhengge Zhu (Hebei Normal University) for provision of the rice line overexpressing OsPIN3t-GFP. We thank Professor Yanhua Qi (Zhejiang University) for provision of the arf12 mutant line. Thanks also go to Professor Jean-Benoit Morel (Plant Health Institute of Montpellier) for provision of the fungus M. oryzae strain Guy11 (AvrCo39-mRFP). This work was supported by grants from the National Natural Science Foundation of China (Grant Nos. 32260085, 31460453, 31660501, 31860064, 31760500 and 31901870), the Major Special Program for Scientific Research, Education Department of Yunnan Province (Grant No. ZD2015005). The project was also sponsored by SRF for ROCS, SEM (Grant No. [2013] 1792), the Key Projects of Applied Basic Research Plan of Yunnan Province (Grant No. 2017FA018, 202301AS070082), the Major Science and Technology Project in Yunnan Province (202102AE090042, 202202AE090036 and 202102AE090017), the Young and Middle-Aged Academic and Technical Leaders Reserve Talent Program in Yunnan Province (202205AC160076), the China Postdoctoral Science Foundation (2019M653849XB) and the National Key Research and Development Program of China (2023YFE0107500). article_number: '3437' article_processing_charge: Yes article_type: original author: - first_name: Lihui full_name: Jiang, Lihui last_name: Jiang - first_name: Xiaoyan full_name: Zhang, Xiaoyan last_name: Zhang - first_name: Yiting full_name: Zhao, Yiting last_name: Zhao - first_name: Haiyan full_name: Zhu, Haiyan last_name: Zhu - first_name: Qijing full_name: Fu, Qijing last_name: Fu - first_name: Xinqi full_name: Lu, Xinqi last_name: Lu - first_name: Wuying full_name: Huang, Wuying last_name: Huang - first_name: Xinyue full_name: Yang, Xinyue last_name: Yang - first_name: Xuan full_name: Zhou, Xuan last_name: Zhou - first_name: Lixia full_name: Wu, Lixia last_name: Wu - first_name: Ao full_name: Yang, Ao last_name: Yang - first_name: Xie full_name: He, Xie last_name: He - first_name: Man full_name: Dong, Man last_name: Dong - first_name: Ziai full_name: Peng, Ziai last_name: Peng - first_name: Jing full_name: Yang, Jing last_name: Yang - first_name: Liwei full_name: Guo, Liwei last_name: Guo - first_name: Jiancheng full_name: Wen, Jiancheng last_name: Wen - first_name: Huichuan full_name: Huang, Huichuan last_name: Huang - first_name: Yong full_name: Xie, Yong last_name: Xie - first_name: Shusheng full_name: Zhu, Shusheng last_name: Zhu - first_name: Chengyun full_name: Li, Chengyun last_name: Li - first_name: Xiahong full_name: He, Xiahong last_name: He - first_name: Youyong full_name: Zhu, Youyong last_name: Zhu - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Yunlong full_name: Du, Yunlong last_name: Du citation: ama: Jiang L, Zhang X, Zhao Y, et al. Phytoalexin sakuranetin attenuates endocytosis and enhances resistance to rice blast. Nature Communications. 2024;15. doi:10.1038/s41467-024-47746-y apa: Jiang, L., Zhang, X., Zhao, Y., Zhu, H., Fu, Q., Lu, X., … Du, Y. (2024). Phytoalexin sakuranetin attenuates endocytosis and enhances resistance to rice blast. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-024-47746-y chicago: Jiang, Lihui, Xiaoyan Zhang, Yiting Zhao, Haiyan Zhu, Qijing Fu, Xinqi Lu, Wuying Huang, et al. “Phytoalexin Sakuranetin Attenuates Endocytosis and Enhances Resistance to Rice Blast.” Nature Communications. Springer Nature, 2024. https://doi.org/10.1038/s41467-024-47746-y. ieee: L. Jiang et al., “Phytoalexin sakuranetin attenuates endocytosis and enhances resistance to rice blast,” Nature Communications, vol. 15. Springer Nature, 2024. ista: Jiang L, Zhang X, Zhao Y, Zhu H, Fu Q, Lu X, Huang W, Yang X, Zhou X, Wu L, Yang A, He X, Dong M, Peng Z, Yang J, Guo L, Wen J, Huang H, Xie Y, Zhu S, Li C, He X, Zhu Y, Friml J, Du Y. 2024. Phytoalexin sakuranetin attenuates endocytosis and enhances resistance to rice blast. Nature Communications. 15, 3437. mla: Jiang, Lihui, et al. “Phytoalexin Sakuranetin Attenuates Endocytosis and Enhances Resistance to Rice Blast.” Nature Communications, vol. 15, 3437, Springer Nature, 2024, doi:10.1038/s41467-024-47746-y. short: L. Jiang, X. Zhang, Y. Zhao, H. Zhu, Q. Fu, X. Lu, W. Huang, X. Yang, X. Zhou, L. Wu, A. Yang, X. He, M. Dong, Z. Peng, J. Yang, L. Guo, J. Wen, H. Huang, Y. Xie, S. Zhu, C. Li, X. He, Y. Zhu, J. Friml, Y. Du, Nature Communications 15 (2024). date_created: 2024-06-03T08:54:50Z date_published: 2024-04-23T00:00:00Z date_updated: 2026-09-03T09:18:44Z day: '23' ddc: - '580' department: - _id: JiFr doi: 10.1038/s41467-024-47746-y external_id: isi: - '001207290500013' pmid: - '38653755' file: - access_level: open_access checksum: 80cb2f2c538e81064f4836b54bc313ca content_type: application/pdf creator: dernst date_created: 2024-06-03T12:05:10Z date_updated: 2024-06-03T12:05:10Z file_id: '17110' file_name: 2024_NatureComm_Jiang.pdf file_size: 8013695 relation: main_file success: 1 file_date_updated: 2024-06-03T12:05:10Z has_accepted_license: '1' intvolume: ' 15' isi: 1 language: - iso: eng month: '04' oa: 1 oa_version: Published Version pmid: 1 publication: Nature Communications publication_identifier: eissn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '22776' relation: used_in_publication status: public scopus_import: '1' status: public title: Phytoalexin sakuranetin attenuates endocytosis and enhances resistance to rice blast tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 15 year: '2024' ... --- OA_place: repository OA_type: green _id: '22776' article_processing_charge: No author: - first_name: Yunlong full_name: Du, Yunlong last_name: Du citation: ama: Du Y. SeRrbJ609. 2024. doi:10.6084/m9.figshare.25448191 apa: Du, Y. (2024). SeRrbJ609. Repository. https://doi.org/10.6084/m9.figshare.25448191 chicago: Du, Yunlong. “SeRrbJ609.” Repository, 2024. https://doi.org/10.6084/m9.figshare.25448191. ieee: Y. Du, “SeRrbJ609.” Repository, 2024. ista: Du Y. 2024. SeRrbJ609, Repository, 10.6084/m9.figshare.25448191. mla: Du, Yunlong. SeRrbJ609. Repository, 2024, doi:10.6084/m9.figshare.25448191. short: Y. Du, (2024). date_created: 2026-09-03T09:17:46Z date_published: 2024-03-21T00:00:00Z date_updated: 2026-09-03T09:18:44Z day: '21' ddc: - '580' department: - _id: JiFr doi: 10.6084/m9.figshare.25448191 main_file_link: - open_access: '1' url: https://doi.org/10.6084/m9.figshare.25448191 month: '03' oa: 1 oa_version: None publisher: Repository related_material: record: - id: '17103' relation: research_data status: public status: public title: SeRrbJ609 type: research_data_reference user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 year: '2024' ... --- _id: '18063' abstract: - lang: eng text: The developmental plasticity of the root system plays an essential role in the adaptation of plants to the environment. Among many other signals, auxin and its directional, intercellular transport are critical in regulating root growth and development. In particular, the PIN-FORMED2 (PIN2) auxin exporter acts as a key regulator of root gravitropic growth. Multiple regulators have been reported to be involved in PIN2-mediated root growth; however, our information remains incomplete. Here, we identified ROWY Bro1-domain proteins as important regulators of PIN2 sorting control. Genetic analysis revealed that Arabidopsis rowy1 single mutants and higher-order rowy1 rowy2 rowy3 triple mutants presented a wavy root growth phenotype. Cell biological experiments revealed that ROWY1 and PIN2 colocalized to the apical side of the plasma membrane in the root epidermis and that ROWYs are required for correct PM targeting of PIN2. In addition, ROWYs also affected PIN3 protein abundance in the stele, suggesting the potential involvement of additional PIN transporters as well as other proteins. A global transcriptome analysis revealed that ROWY genes are involved in the Fe2+ availability perception pathway. This work establishes ROWYs as important novel regulators of root gravitropic growth by connecting micronutrient availability to the proper subcellular targeting of PIN auxin transporters. acknowledgement: We thank Drs. Erika Isono (University of Constance), Grégory Vert (University of Toulouse), and Liwen Jiang (The Chinese University of Hong Kong) for kindly sharing published Arabidopsis lines; Dr. Yuzhou Zhang (ISTA) for help with molecular cloning, and Drs. Melinda Abas (BOKU), Eugenia Russinova (Ghent University), and Zhaojun Ding (Shandong University) for valuable discussions. This work was supported by grants to S.T. from the National Natural Science Foundation of China (32321001), the USTC Research Funds of the Double First-Class Initiative (YD9100002016), the Research Funds from the Center for Advanced Interdisciplinary Science and Biomedicine of IHM, the Division of Life Sciences and Medicine, the University of Science and Technology of China (QYPY20220012), the Fundamental Research Funds for the Central Universities (WK9100000021), and start-up funding from the University of Science and Technology of China and the Chinese Academy of Sciences (GG9100007007, KY9100000026, KY9100000051, and KJ2070000079). J.S. was supported by the National Natural Science Foundation of China (31970181 and 32170342). J.F. was supported by Austrian Science Fund (FWF; projects I6123 and P37051-B). article_number: '1085' article_processing_charge: Yes article_type: original author: - first_name: Yakun full_name: Peng, Yakun last_name: Peng - first_name: Kangkang full_name: Ji, Kangkang last_name: Ji - first_name: Yanbo full_name: Mao, Yanbo last_name: Mao - first_name: Yiqun full_name: Wang, Yiqun id: 82F537F2-B517-11E9-84D7-6433E6697425 last_name: Wang - first_name: Barbara full_name: Korbei, Barbara last_name: Korbei - first_name: Christian full_name: Luschnig, Christian last_name: Luschnig - first_name: Jinbo full_name: Shen, Jinbo last_name: Shen - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Shutang full_name: Tan, Shutang id: 2DE75584-F248-11E8-B48F-1D18A9856A87 last_name: Tan orcid: 0000-0002-0471-8285 citation: ama: Peng Y, Ji K, Mao Y, et al. Polarly localized Bro1 domain proteins regulate PIN-FORMED abundance and root gravitropic growth in Arabidopsis. Communications Biology. 2024;7. doi:10.1038/s42003-024-06747-9 apa: Peng, Y., Ji, K., Mao, Y., Wang, Y., Korbei, B., Luschnig, C., … Tan, S. (2024). Polarly localized Bro1 domain proteins regulate PIN-FORMED abundance and root gravitropic growth in Arabidopsis. Communications Biology. Springer Nature. https://doi.org/10.1038/s42003-024-06747-9 chicago: Peng, Yakun, Kangkang Ji, Yanbo Mao, Yiqun Wang, Barbara Korbei, Christian Luschnig, Jinbo Shen, Eva Benková, Jiří Friml, and Shutang Tan. “Polarly Localized Bro1 Domain Proteins Regulate PIN-FORMED Abundance and Root Gravitropic Growth in Arabidopsis.” Communications Biology. Springer Nature, 2024. https://doi.org/10.1038/s42003-024-06747-9. ieee: Y. Peng et al., “Polarly localized Bro1 domain proteins regulate PIN-FORMED abundance and root gravitropic growth in Arabidopsis,” Communications Biology, vol. 7. Springer Nature, 2024. ista: Peng Y, Ji K, Mao Y, Wang Y, Korbei B, Luschnig C, Shen J, Benková E, Friml J, Tan S. 2024. Polarly localized Bro1 domain proteins regulate PIN-FORMED abundance and root gravitropic growth in Arabidopsis. Communications Biology. 7, 1085. mla: Peng, Yakun, et al. “Polarly Localized Bro1 Domain Proteins Regulate PIN-FORMED Abundance and Root Gravitropic Growth in Arabidopsis.” Communications Biology, vol. 7, 1085, Springer Nature, 2024, doi:10.1038/s42003-024-06747-9. short: Y. Peng, K. Ji, Y. Mao, Y. Wang, B. Korbei, C. Luschnig, J. Shen, E. Benková, J. Friml, S. Tan, Communications Biology 7 (2024). date_created: 2024-09-15T22:01:38Z date_published: 2024-09-04T00:00:00Z date_updated: 2026-09-04T22:30:04Z day: '04' ddc: - '570' department: - _id: EvBe - _id: JiFr doi: 10.1038/s42003-024-06747-9 external_id: isi: - '001306499600002' pmid: - '39232040' file: - access_level: open_access checksum: 7d66af41c90e73d1b8a375eb652a9561 content_type: application/pdf creator: dernst date_created: 2024-09-17T09:44:29Z date_updated: 2024-09-17T09:44:29Z file_id: '18084' file_name: 2024_CommBiology_Peng.pdf file_size: 7718758 relation: main_file success: 1 file_date_updated: 2024-09-17T09:44:29Z has_accepted_license: '1' intvolume: ' 7' isi: 1 language: - iso: eng month: '09' oa: 1 oa_version: Published Version pmid: 1 project: - _id: bd76d395-d553-11ed-ba76-f678c14f9033 grant_number: I06123 name: Peptide receptors for auxin canalization in Arabidopsis - _id: 7bcece63-9f16-11ee-852c-ae94e099eeb6 grant_number: P37051 name: Guanylate cyclase activity of TIR1/AFBs auxin receptors publication: Communications Biology publication_identifier: eissn: - 2399-3642 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '20117' relation: dissertation_contains status: public scopus_import: '1' status: public title: Polarly localized Bro1 domain proteins regulate PIN-FORMED abundance and root gravitropic growth in Arabidopsis tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 7 year: '2024' ... --- _id: '12543' abstract: - lang: eng text: Treating sick group members is a hallmark of collective disease defence in vertebrates and invertebrates alike. Despite substantial effects on pathogen fitness and epidemiology, it is still largely unknown how pathogens react to the selection pressure imposed by care intervention. Using social insects and pathogenic fungi, we here performed a serial passage experiment in the presence or absence of colony members, which provide social immunity by grooming off infectious spores from exposed individuals. We found specific effects on pathogen diversity, virulence and transmission. Under selection of social immunity, pathogens invested into higher spore production, but spores were less virulent. Notably, they also elicited a lower grooming response in colony members, compared with spores from the individual host selection lines. Chemical spore analysis suggested that the spores from social selection lines escaped the caregivers’ detection by containing lower levels of ergosterol, a key fungal membrane component. Experimental application of chemically pure ergosterol indeed induced sanitary grooming, supporting its role as a microbe-associated cue triggering host social immunity against fungal pathogens. By reducing this detection cue, pathogens were able to evade the otherwise very effective collective disease defences of their social hosts. acknowledged_ssus: - _id: LifeSc acknowledgement: We thank B. M. Steinwender, N. V. Meyling and J. Eilenberg for the fungal strains; J. Anaya-Rojas for statistical advice; the Social Immunity team at ISTA for ant collection and experimental help, in particular H. Leitner, and the ISTA Lab Support Facility for general laboratory support; D. Ebert, H. Schulenburg and J. Heinze for continued project discussion; and M. Sixt, R. Roemhild and the Social Immunity team for comments on the manuscript. The study was funded by the German Research Foundation (CR118/3-1) within the Framework of the Priority Program SPP 1399, and the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Programme (No. 771402; EPIDEMICSonCHIP), both to S.C. article_processing_charge: No article_type: original author: - first_name: Miriam full_name: Stock, Miriam id: 42462816-F248-11E8-B48F-1D18A9856A87 last_name: Stock - first_name: Barbara full_name: Milutinovic, Barbara id: 2CDC32B8-F248-11E8-B48F-1D18A9856A87 last_name: Milutinovic orcid: 0000-0002-8214-4758 - first_name: Michaela full_name: Hönigsberger, Michaela id: 953894f3-25bd-11ec-8556-f70a9d38ef60 last_name: Hönigsberger - first_name: Anna V full_name: Grasse, Anna V id: 406F989C-F248-11E8-B48F-1D18A9856A87 last_name: Grasse - first_name: Florian full_name: Wiesenhofer, Florian id: 39523C54-F248-11E8-B48F-1D18A9856A87 last_name: Wiesenhofer - first_name: Niklas full_name: Kampleitner, Niklas id: 2AC57FAC-F248-11E8-B48F-1D18A9856A87 last_name: Kampleitner - first_name: Madhumitha full_name: Narasimhan, Madhumitha id: 44BF24D0-F248-11E8-B48F-1D18A9856A87 last_name: Narasimhan orcid: 0000-0002-8600-0671 - first_name: Thomas full_name: Schmitt, Thomas last_name: Schmitt - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 citation: ama: Stock M, Milutinovic B, Hönigsberger M, et al. Pathogen evasion of social immunity. Nature Ecology and Evolution. 2023;7:450-460. doi:10.1038/s41559-023-01981-6 apa: Stock, M., Milutinovic, B., Hönigsberger, M., Grasse, A. V., Wiesenhofer, F., Kampleitner, N., … Cremer, S. (2023). Pathogen evasion of social immunity. Nature Ecology and Evolution. Springer Nature. https://doi.org/10.1038/s41559-023-01981-6 chicago: Stock, Miriam, Barbara Milutinovic, Michaela Hönigsberger, Anna V Grasse, Florian Wiesenhofer, Niklas Kampleitner, Madhumitha Narasimhan, Thomas Schmitt, and Sylvia Cremer. “Pathogen Evasion of Social Immunity.” Nature Ecology and Evolution. Springer Nature, 2023. https://doi.org/10.1038/s41559-023-01981-6. ieee: M. Stock et al., “Pathogen evasion of social immunity,” Nature Ecology and Evolution, vol. 7. Springer Nature, pp. 450–460, 2023. ista: Stock M, Milutinovic B, Hönigsberger M, Grasse AV, Wiesenhofer F, Kampleitner N, Narasimhan M, Schmitt T, Cremer S. 2023. Pathogen evasion of social immunity. Nature Ecology and Evolution. 7, 450–460. mla: Stock, Miriam, et al. “Pathogen Evasion of Social Immunity.” Nature Ecology and Evolution, vol. 7, Springer Nature, 2023, pp. 450–60, doi:10.1038/s41559-023-01981-6. short: M. Stock, B. Milutinovic, M. Hönigsberger, A.V. Grasse, F. Wiesenhofer, N. Kampleitner, M. Narasimhan, T. Schmitt, S. Cremer, Nature Ecology and Evolution 7 (2023) 450–460. corr_author: '1' date_created: 2023-02-12T23:00:59Z date_published: 2023-03-01T00:00:00Z date_updated: 2025-04-14T07:47:53Z day: '01' ddc: - '570' department: - _id: SyCr - _id: LifeSc - _id: JiFr doi: 10.1038/s41559-023-01981-6 ec_funded: 1 external_id: isi: - '000924572800001' pmid: - '36732670' file: - access_level: open_access checksum: 8244f4650a0e7aeea488d1bcd4a31702 content_type: application/pdf creator: dernst date_created: 2023-08-16T11:54:59Z date_updated: 2023-08-16T11:54:59Z file_id: '14069' file_name: 2023_NatureEcoEvo_Stock.pdf file_size: 1600499 relation: main_file success: 1 file_date_updated: 2023-08-16T11:54:59Z has_accepted_license: '1' intvolume: ' 7' isi: 1 language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: 450-460 pmid: 1 project: - _id: 2649B4DE-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '771402' name: Epidemics in ant societies on a chip - _id: 25DAF0B2-B435-11E9-9278-68D0E5697425 grant_number: CR-118/3-1 name: Host-Parasite Coevolution publication: Nature Ecology and Evolution publication_identifier: eissn: - 2397-334X publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - description: News on ISTA website relation: press_release url: https://ista.ac.at/en/news/how-sneaky-germs-hide-from-ants/ scopus_import: '1' status: public title: Pathogen evasion of social immunity tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 7 year: '2023' ... --- OA_place: publisher OA_type: free access _id: '12878' abstract: - lang: eng text: Salicylic acid (SA) plays important roles in different aspects of plant development, including root growth, where auxin is also a major player by means of its asymmetric distribution. However, the mechanism underlying the effect of SA on the development of rice roots remains poorly understood. Here, we show that SA inhibits rice root growth by interfering with auxin transport associated with the OsPIN3t- and clathrin-mediated gene regulatory network (GRN). SA inhibits root growth as well as Brefeldin A-sensitive trafficking through a non-canonical SA signaling mechanism. Transcriptome analysis of rice seedlings treated with SA revealed that the OsPIN3t auxin transporter is at the center of a GRN involving the coat protein clathrin. The root growth and endocytic trafficking in both the pin3t and clathrin heavy chain mutants were SA insensitivity. SA inhibitory effect on the endocytosis of OsPIN3t was dependent on clathrin; however, the root growth and endocytic trafficking mediated by tyrphostin A23 (TyrA23) were independent of the pin3t mutant under SA treatment. These data reveal that SA affects rice root growth through the convergence of transcriptional and non-SA signaling mechanisms involving OsPIN3t-mediated auxin transport and clathrin-mediated trafficking as key components. acknowledgement: The authors thank Professor Jianqiang Wu (Kunming Institute of Botany, Chinese Academy of Sciences) for support with phytohormone measurement. Thanks also go to Professor Pieter. B. F. Ouwerkerk (Leiden University) and Professor Jean-Benoit Morel (Plant Health Institute of Montpellier) for provision of the rice lines NB-7B-70 and NB-7B-76 and wild-type NB-61-WT, Professor Zuhua He (Chinese Academy of Sciences) for provision of the rice OsNPR1-RNAi mutant, and Professor Yinong Yang (The Pennsylvania State University) for provision of the rice line NahG. This work was supported by grants from the National Natural Science Foundation of China (Grant Nos. 32260085, 31460453, 31660501, 31860064, 31970609, 31801792 and 31960554), the Key Projects of the Applied Basic Research Plan of Yunnan Province (202301AS070082), the Major Special Program for Scientific Research, Education Department of Yunnan Province (Grant No. ZD2015005), the Start-up fund from Xishuangbanna Tropical Botanical Garden, and ‘Top Talents Program in Science and Technology’ from Yunnan Province, the SRF for ROCS, SEM (Grant No. [2013] 1792), and the Major Science and Technology Project in Yunnan Province (202102AE090042 and 202202AE090036); and the young and middle-aged academic and technical leaders reserve talent program in Yunnan Province (202205AC160076). article_processing_charge: No article_type: original author: - first_name: Lihui full_name: Jiang, Lihui last_name: Jiang - first_name: Baolin full_name: Yao, Baolin last_name: Yao - first_name: Xiaoyan full_name: Zhang, Xiaoyan last_name: Zhang - first_name: Lixia full_name: Wu, Lixia last_name: Wu - first_name: Qijing full_name: Fu, Qijing last_name: Fu - first_name: Yiting full_name: Zhao, Yiting last_name: Zhao - first_name: Yuxin full_name: Cao, Yuxin last_name: Cao - first_name: Ruomeng full_name: Zhu, Ruomeng last_name: Zhu - first_name: Xinqi full_name: Lu, Xinqi last_name: Lu - first_name: Wuying full_name: Huang, Wuying last_name: Huang - first_name: Jianping full_name: Zhao, Jianping last_name: Zhao - first_name: Kuixiu full_name: Li, Kuixiu last_name: Li - first_name: Shuanglu full_name: Zhao, Shuanglu last_name: Zhao - first_name: Li full_name: Han, Li last_name: Han - first_name: Xuan full_name: Zhou, Xuan last_name: Zhou - first_name: Chongyu full_name: Luo, Chongyu last_name: Luo - first_name: Haiyan full_name: Zhu, Haiyan last_name: Zhu - first_name: Jing full_name: Yang, Jing last_name: Yang - first_name: Huichuan full_name: Huang, Huichuan last_name: Huang - first_name: Zhengge full_name: Zhu, Zhengge last_name: Zhu - first_name: Xiahong full_name: He, Xiahong last_name: He - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Zhongkai full_name: Zhang, Zhongkai last_name: Zhang - first_name: Changning full_name: Liu, Changning last_name: Liu - first_name: Yunlong full_name: Du, Yunlong last_name: Du citation: ama: Jiang L, Yao B, Zhang X, et al. Salicylic acid inhibits rice endocytic protein trafficking mediated by OsPIN3t and clathrin to affect root growth. Plant Journal. 2023;115(1):155-174. doi:10.1111/tpj.16218 apa: Jiang, L., Yao, B., Zhang, X., Wu, L., Fu, Q., Zhao, Y., … Du, Y. (2023). Salicylic acid inhibits rice endocytic protein trafficking mediated by OsPIN3t and clathrin to affect root growth. Plant Journal. Wiley. https://doi.org/10.1111/tpj.16218 chicago: Jiang, Lihui, Baolin Yao, Xiaoyan Zhang, Lixia Wu, Qijing Fu, Yiting Zhao, Yuxin Cao, et al. “Salicylic Acid Inhibits Rice Endocytic Protein Trafficking Mediated by OsPIN3t and Clathrin to Affect Root Growth.” Plant Journal. Wiley, 2023. https://doi.org/10.1111/tpj.16218. ieee: L. Jiang et al., “Salicylic acid inhibits rice endocytic protein trafficking mediated by OsPIN3t and clathrin to affect root growth,” Plant Journal, vol. 115, no. 1. Wiley, pp. 155–174, 2023. ista: Jiang L, Yao B, Zhang X, Wu L, Fu Q, Zhao Y, Cao Y, Zhu R, Lu X, Huang W, Zhao J, Li K, Zhao S, Han L, Zhou X, Luo C, Zhu H, Yang J, Huang H, Zhu Z, He X, Friml J, Zhang Z, Liu C, Du Y. 2023. Salicylic acid inhibits rice endocytic protein trafficking mediated by OsPIN3t and clathrin to affect root growth. Plant Journal. 115(1), 155–174. mla: Jiang, Lihui, et al. “Salicylic Acid Inhibits Rice Endocytic Protein Trafficking Mediated by OsPIN3t and Clathrin to Affect Root Growth.” Plant Journal, vol. 115, no. 1, Wiley, 2023, pp. 155–74, doi:10.1111/tpj.16218. short: L. Jiang, B. Yao, X. Zhang, L. Wu, Q. Fu, Y. Zhao, Y. Cao, R. Zhu, X. Lu, W. Huang, J. Zhao, K. Li, S. Zhao, L. Han, X. Zhou, C. Luo, H. Zhu, J. Yang, H. Huang, Z. Zhu, X. He, J. Friml, Z. Zhang, C. Liu, Y. Du, Plant Journal 115 (2023) 155–174. date_created: 2023-04-30T22:01:06Z date_published: 2023-07-01T00:00:00Z date_updated: 2026-06-18T17:29:30Z day: '01' ddc: - '580' department: - _id: JiFr doi: 10.1111/tpj.16218 external_id: isi: - '000971861400001' pmid: - '37025008 ' intvolume: ' 115' isi: 1 issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1111/tpj.16218 month: '07' oa: 1 oa_version: Published Version page: 155-174 pmid: 1 publication: Plant Journal publication_identifier: eissn: - 1365-313X issn: - 0960-7412 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Salicylic acid inhibits rice endocytic protein trafficking mediated by OsPIN3t and clathrin to affect root growth type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 115 year: '2023' ... --- _id: '13213' abstract: - lang: eng text: The primary cell wall is a fundamental plant constituent that is flexible but sufficiently rigid to support the plant cell shape. Although many studies have demonstrated that reactive oxygen species (ROS) serve as important signaling messengers to modify the cell wall structure and affect cellular growth, the regulatory mechanism underlying the spatial-temporal regulation of ROS activity for cell wall maintenance remains largely unclear. Here, we demonstrate the role of the Arabidopsis (Arabidopsis thaliana) multicopper oxidase-like protein skewed 5 (SKU5) and its homolog SKU5-similar 1 (SKS1) in root cell wall formation through modulating ROS homeostasis. Loss of SKU5 and SKS1 function resulted in aberrant division planes, protruding cell walls, ectopic deposition of iron, and reduced nicotinamide adeninedinucleotide phosphate (NADPH) oxidase-dependent ROS overproduction in the root epidermis–cortex and cortex–endodermis junctions. A decrease in ROS level or inhibition of NADPH oxidase activity rescued the cell wall defects of sku5 sks1 double mutants. SKU5 and SKS1 proteins were activated by iron treatment, and iron over-accumulated in the walls between the root epidermis and cortex cell layers of sku5 sks1. The glycosylphosphatidylinositol-anchored motif was crucial for membrane association and functionality of SKU5 and SKS1. Overall, our results identified SKU5 and SKS1 as regulators of ROS at the cell surface for regulation of cell wall structure and root cell growth. acknowledgement: We thank Dong liu for offering iron staining technique; ZhiChang Chen and Zhenbiao Yang for discussion; Dandan Zheng for earlier attempt; Liwen Jiang and Dingquan Huang for initial tests of the TEM experiment; John C. Sedbrook for a donation of sku5 and pSKU5::SKU5-GFP seeds; Catherine Perrot-Rechenmann and Ke Zhou for the donation of sks1, sks2, and sku5 sks1 seeds; Zengyu Liu and Zhongquan Lin for live-imaging microscopy assistance. We are grateful to Can Peng, and Xixia Li for helping with sample preparation, and taking TEM images, at the Center for Biological Imaging (CBI), Institute of Biophysics, Chinese Academy of Science. article_processing_charge: No article_type: original author: - first_name: C full_name: Chen, C last_name: Chen - first_name: Y full_name: Zhang, Y last_name: Zhang - first_name: J full_name: Cai, J last_name: Cai - first_name: Y full_name: Qiu, Y last_name: Qiu - first_name: L full_name: Li, L last_name: Li - first_name: C full_name: Gao, C last_name: Gao - first_name: Y full_name: Gao, Y last_name: Gao - first_name: M full_name: Ke, M last_name: Ke - first_name: S full_name: Wu, S last_name: Wu - first_name: C full_name: Wei, C last_name: Wei - first_name: J full_name: Chen, J last_name: Chen - first_name: T full_name: Xu, T last_name: Xu - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: J full_name: Wang, J last_name: Wang - first_name: R full_name: Li, R last_name: Li - first_name: D full_name: Chao, D last_name: Chao - first_name: B full_name: Zhang, B last_name: Zhang - first_name: X full_name: Chen, X last_name: Chen - first_name: Z full_name: Gao, Z last_name: Gao citation: ama: Chen C, Zhang Y, Cai J, et al. Multi-copper oxidases SKU5 and SKS1 coordinate cell wall formation using apoplastic redox-based reactions in roots. Plant Physiology. 2023;192(3):2243-2260. doi:10.1093/plphys/kiad207 apa: Chen, C., Zhang, Y., Cai, J., Qiu, Y., Li, L., Gao, C., … Gao, Z. (2023). Multi-copper oxidases SKU5 and SKS1 coordinate cell wall formation using apoplastic redox-based reactions in roots. Plant Physiology. American Society of Plant Biologists. https://doi.org/10.1093/plphys/kiad207 chicago: Chen, C, Y Zhang, J Cai, Y Qiu, L Li, C Gao, Y Gao, et al. “Multi-Copper Oxidases SKU5 and SKS1 Coordinate Cell Wall Formation Using Apoplastic Redox-Based Reactions in Roots.” Plant Physiology. American Society of Plant Biologists, 2023. https://doi.org/10.1093/plphys/kiad207. ieee: C. Chen et al., “Multi-copper oxidases SKU5 and SKS1 coordinate cell wall formation using apoplastic redox-based reactions in roots,” Plant Physiology, vol. 192, no. 3. American Society of Plant Biologists, pp. 2243–2260, 2023. ista: Chen C, Zhang Y, Cai J, Qiu Y, Li L, Gao C, Gao Y, Ke M, Wu S, Wei C, Chen J, Xu T, Friml J, Wang J, Li R, Chao D, Zhang B, Chen X, Gao Z. 2023. Multi-copper oxidases SKU5 and SKS1 coordinate cell wall formation using apoplastic redox-based reactions in roots. Plant Physiology. 192(3), 2243–2260. mla: Chen, C., et al. “Multi-Copper Oxidases SKU5 and SKS1 Coordinate Cell Wall Formation Using Apoplastic Redox-Based Reactions in Roots.” Plant Physiology, vol. 192, no. 3, American Society of Plant Biologists, 2023, pp. 2243–60, doi:10.1093/plphys/kiad207. short: C. Chen, Y. Zhang, J. Cai, Y. Qiu, L. Li, C. Gao, Y. Gao, M. Ke, S. Wu, C. Wei, J. Chen, T. Xu, J. Friml, J. Wang, R. Li, D. Chao, B. Zhang, X. Chen, Z. Gao, Plant Physiology 192 (2023) 2243–2260. date_created: 2023-07-12T07:32:58Z date_published: 2023-07-01T00:00:00Z date_updated: 2024-10-21T06:01:27Z day: '01' ddc: - '575' department: - _id: JiFr doi: 10.1093/plphys/kiad207 external_id: isi: - '000971795800001' pmid: - '37010107' file: - access_level: open_access checksum: 5492e1d18ac3eaf202633d210fa0fb75 content_type: application/pdf creator: cchlebak date_created: 2023-07-13T13:26:33Z date_updated: 2023-07-13T13:26:33Z file_id: '13220' file_name: 2023_PlantPhys_Chen.pdf file_size: 2076977 relation: main_file success: 1 file_date_updated: 2023-07-13T13:26:33Z has_accepted_license: '1' intvolume: ' 192' isi: 1 issue: '3' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 2243-2260 pmid: 1 publication: Plant Physiology publication_identifier: eissn: - 1532-2548 issn: - 0032-0889 publication_status: published publisher: American Society of Plant Biologists quality_controlled: '1' scopus_import: '1' status: public title: Multi-copper oxidases SKU5 and SKS1 coordinate cell wall formation using apoplastic redox-based reactions in roots tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 192 year: '2023' ... --- _id: '13266' abstract: - lang: eng text: The 3′,5′-cyclic adenosine monophosphate (cAMP) is a versatile second messenger in many mammalian signaling pathways. However, its role in plants remains not well-recognized. Recent discovery of adenylate cyclase (AC) activity for transport inhibitor response 1/auxin-signaling F-box proteins (TIR1/AFB) auxin receptors and the demonstration of its importance for canonical auxin signaling put plant cAMP research back into spotlight. This insight briefly summarizes the well-established cAMP signaling pathways in mammalian cells and describes the turbulent and controversial history of plant cAMP research highlighting the major progress and the unresolved points. We also briefly review the current paradigm of auxin signaling to provide a background for the discussion on the AC activity of TIR1/AFB auxin receptors and its potential role in transcriptional auxin signaling as well as impact of these discoveries on plant cAMP research in general. acknowledgement: 'We gratefully acknowledge our brave colleagues, whose excellent efforts kept the plant cAMP research going in the last two decades. The authors were financially supported by the Austrian Science Fund (FWF): I 6123 and P 37051-B.' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Linlin full_name: Qi, Linlin id: 44B04502-A9ED-11E9-B6FC-583AE6697425 last_name: Qi orcid: 0000-0001-5187-8401 - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Qi L, Friml J. Tale of cAMP as a second messenger in auxin signaling and beyond. New Phytologist. 2023;240(2):489-495. doi:10.1111/nph.19123 apa: Qi, L., & Friml, J. (2023). Tale of cAMP as a second messenger in auxin signaling and beyond. New Phytologist. Wiley. https://doi.org/10.1111/nph.19123 chicago: Qi, Linlin, and Jiří Friml. “Tale of CAMP as a Second Messenger in Auxin Signaling and Beyond.” New Phytologist. Wiley, 2023. https://doi.org/10.1111/nph.19123. ieee: L. Qi and J. Friml, “Tale of cAMP as a second messenger in auxin signaling and beyond,” New Phytologist, vol. 240, no. 2. Wiley, pp. 489–495, 2023. ista: Qi L, Friml J. 2023. Tale of cAMP as a second messenger in auxin signaling and beyond. New Phytologist. 240(2), 489–495. mla: Qi, Linlin, and Jiří Friml. “Tale of CAMP as a Second Messenger in Auxin Signaling and Beyond.” New Phytologist, vol. 240, no. 2, Wiley, 2023, pp. 489–95, doi:10.1111/nph.19123. short: L. Qi, J. Friml, New Phytologist 240 (2023) 489–495. corr_author: '1' date_created: 2023-07-23T22:01:13Z date_published: 2023-10-01T00:00:00Z date_updated: 2024-10-22T12:50:00Z day: '01' ddc: - '580' department: - _id: JiFr doi: 10.1111/nph.19123 external_id: isi: - '001026321500001' pmid: - '37434303' file: - access_level: open_access checksum: 6d9bbd45b8e7bb3ceee2586d447bacb2 content_type: application/pdf creator: dernst date_created: 2024-01-29T11:21:43Z date_updated: 2024-01-29T11:21:43Z file_id: '14898' file_name: 2023_NewPhytologist_Qi.pdf file_size: 974464 relation: main_file success: 1 file_date_updated: 2024-01-29T11:21:43Z has_accepted_license: '1' intvolume: ' 240' isi: 1 issue: '2' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: 489-495 pmid: 1 project: - _id: bd76d395-d553-11ed-ba76-f678c14f9033 grant_number: I06123 name: Peptide receptors for auxin canalization in Arabidopsis - _id: 7bcece63-9f16-11ee-852c-ae94e099eeb6 grant_number: P37051 name: Guanylate cyclase activity of TIR1/AFBs auxin receptors publication: New Phytologist publication_identifier: eissn: - 1469-8137 issn: - 0028-646X publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Tale of cAMP as a second messenger in auxin signaling and beyond tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 240 year: '2023' ... --- _id: '14313' abstract: - lang: eng text: To respond to auxin, the chief orchestrator of their multicellularity, plants evolved multiple receptor systems and signal transduction cascades. Despite decades of research, however, we are still lacking a satisfactory synthesis of various auxin signaling mechanisms. The chief discrepancy and historical controversy of the field is that of rapid and slow auxin effects on plant physiology and development. How is it possible that ions begin to trickle across the plasma membrane as soon as auxin enters the cell, even though the best-characterized transcriptional auxin pathway can take effect only after tens of minutes? Recently, unexpected progress has been made in understanding this and other unknowns of auxin signaling. We provide a perspective on these exciting developments and concepts whose general applicability might have ramifications beyond auxin signaling. acknowledgement: The opening quote is not intended to reflect any political views of the authors. The authors by no means endorse the rhetoric of Donald Rumsfeld or the 2003 invasion of Iraq by the United States. Nevertheless, Rumsfeld's quote led to both public and academic debates on the concept of known and unknown unknowns, which can be applied to the recent unexpected developments in the auxin signaling field. We thank Linlin Qi and Huihuang Chen for their suggestions on figure presentation and inspiring discussions of TIR1/AFB signaling. Finally, we thank Aroosa Hussain for discussion of Greek mythology. article_number: '102443' article_processing_charge: No article_type: review author: - first_name: Lukas full_name: Fiedler, Lukas id: 7c417475-8972-11ed-ae7b-8b674ca26986 last_name: Fiedler - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: 'Fiedler L, Friml J. Rapid auxin signaling: Unknowns old and new. Current Opinion in Plant Biology. 2023;75(10). doi:10.1016/j.pbi.2023.102443' apa: 'Fiedler, L., & Friml, J. (2023). Rapid auxin signaling: Unknowns old and new. Current Opinion in Plant Biology. Elsevier. https://doi.org/10.1016/j.pbi.2023.102443' chicago: 'Fiedler, Lukas, and Jiří Friml. “Rapid Auxin Signaling: Unknowns Old and New.” Current Opinion in Plant Biology. Elsevier, 2023. https://doi.org/10.1016/j.pbi.2023.102443.' ieee: 'L. Fiedler and J. Friml, “Rapid auxin signaling: Unknowns old and new,” Current Opinion in Plant Biology, vol. 75, no. 10. Elsevier, 2023.' ista: 'Fiedler L, Friml J. 2023. Rapid auxin signaling: Unknowns old and new. Current Opinion in Plant Biology. 75(10), 102443.' mla: 'Fiedler, Lukas, and Jiří Friml. “Rapid Auxin Signaling: Unknowns Old and New.” Current Opinion in Plant Biology, vol. 75, no. 10, 102443, Elsevier, 2023, doi:10.1016/j.pbi.2023.102443.' short: L. Fiedler, J. Friml, Current Opinion in Plant Biology 75 (2023). corr_author: '1' date_created: 2023-09-10T22:01:11Z date_published: 2023-10-01T00:00:00Z date_updated: 2025-09-09T12:54:16Z day: '01' ddc: - '580' department: - _id: JiFr doi: 10.1016/j.pbi.2023.102443 external_id: isi: - '001080095300001' pmid: - '37666097' file: - access_level: open_access checksum: 1c476c3414d2dfb0c85db0cb6cfd8a28 content_type: application/pdf creator: amally date_created: 2023-11-02T17:03:20Z date_updated: 2023-11-02T17:03:20Z file_id: '14482' file_name: Fiedler CurrOpinOlantBiol 2023_revised.pdf file_size: 737872 relation: main_file success: 1 file_date_updated: 2023-11-02T17:03:20Z has_accepted_license: '1' intvolume: ' 75' isi: 1 issue: '10' language: - iso: eng month: '10' oa: 1 oa_version: Submitted Version pmid: 1 publication: Current Opinion in Plant Biology publication_identifier: issn: - 1369-5266 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: 'Rapid auxin signaling: Unknowns old and new' type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 75 year: '2023' ... --- _id: '14339' abstract: - lang: eng text: Lateral roots are typically maintained at non-vertical angles with respect to gravity. These gravitropic setpoint angles are intriguing because their maintenance requires that roots are able to effect growth response both with and against the gravity vector, a phenomenon previously attributed to gravitropism acting against an antigravitropic offset mechanism. Here we show how the components mediating gravitropism in the vertical primary root—PINs and phosphatases acting upon them—are reconfigured in their regulation such that lateral root growth at a range of angles can be maintained. We show that the ability of Arabidopsis lateral roots to bend both downward and upward requires the generation of auxin asymmetries and is driven by angle-dependent variation in downward gravitropic auxin flux acting against angle-independent upward, antigravitropic flux. Further, we demonstrate a symmetry in auxin distribution in lateral roots at gravitropic setpoint angle that can be traced back to a net, balanced polarization of PIN3 and PIN7 auxin transporters in the columella. These auxin fluxes are shifted by altering PIN protein phosphoregulation in the columella, either by introducing PIN3 phosphovariant versions or via manipulation of levels of the phosphatase subunit PP2A/RCN1. Finally, we show that auxin, in addition to driving lateral root directional growth, acts within the lateral root columella to induce more vertical growth by increasing RCN1 levels, causing a downward shift in PIN3 localization, thereby diminishing the magnitude of the upward, antigravitropic auxin flux. acknowledgement: We thank D. Weijers, C. Schwechheimer and R. Offringa for generous sharing of published and unpublished materials and P. Masson for advice on the use of the ARL2 promoter. We are grateful to M. Del Bianco and O. Leyser for critical reading of the manuscript. This work was supported by the BBSRC (grants BB/N010124/1 and BB/R000859/1 to S.K.), the Gatsby Charitable Foundation and the Leverhulme Trust (RPG-2018-137 to S.K.). article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: S full_name: Roychoudhry, S last_name: Roychoudhry - first_name: K full_name: Sageman-Furnas, K last_name: Sageman-Furnas - first_name: C full_name: Wolverton, C last_name: Wolverton - first_name: Peter full_name: Grones, Peter id: 399876EC-F248-11E8-B48F-1D18A9856A87 last_name: Grones - first_name: Shutang full_name: Tan, Shutang id: 2DE75584-F248-11E8-B48F-1D18A9856A87 last_name: Tan orcid: 0000-0002-0471-8285 - first_name: Gergely full_name: Molnar, Gergely id: 34F1AF46-F248-11E8-B48F-1D18A9856A87 last_name: Molnar - first_name: M full_name: De Angelis, M last_name: De Angelis - first_name: HL full_name: Goodman, HL last_name: Goodman - first_name: N full_name: Capstaff, N last_name: Capstaff - first_name: Lloyd full_name: JPB, Lloyd last_name: JPB - first_name: J full_name: Mullen, J last_name: Mullen - first_name: R full_name: Hangarter, R last_name: Hangarter - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: S full_name: Kepinski, S last_name: Kepinski citation: ama: Roychoudhry S, Sageman-Furnas K, Wolverton C, et al. Antigravitropic PIN polarization maintains non-vertical growth in lateral roots. Nature Plants. 2023;9:1500-1513. doi:10.1038/s41477-023-01478-x apa: Roychoudhry, S., Sageman-Furnas, K., Wolverton, C., Grones, P., Tan, S., Molnar, G., … Kepinski, S. (2023). Antigravitropic PIN polarization maintains non-vertical growth in lateral roots. Nature Plants. Springer Nature. https://doi.org/10.1038/s41477-023-01478-x chicago: Roychoudhry, S, K Sageman-Furnas, C Wolverton, Peter Grones, Shutang Tan, Gergely Molnar, M De Angelis, et al. “Antigravitropic PIN Polarization Maintains Non-Vertical Growth in Lateral Roots.” Nature Plants. Springer Nature, 2023. https://doi.org/10.1038/s41477-023-01478-x. ieee: S. Roychoudhry et al., “Antigravitropic PIN polarization maintains non-vertical growth in lateral roots,” Nature Plants, vol. 9. Springer Nature, pp. 1500–1513, 2023. ista: Roychoudhry S, Sageman-Furnas K, Wolverton C, Grones P, Tan S, Molnar G, De Angelis M, Goodman H, Capstaff N, JPB L, Mullen J, Hangarter R, Friml J, Kepinski S. 2023. Antigravitropic PIN polarization maintains non-vertical growth in lateral roots. Nature Plants. 9, 1500–1513. mla: Roychoudhry, S., et al. “Antigravitropic PIN Polarization Maintains Non-Vertical Growth in Lateral Roots.” Nature Plants, vol. 9, Springer Nature, 2023, pp. 1500–13, doi:10.1038/s41477-023-01478-x. short: S. Roychoudhry, K. Sageman-Furnas, C. Wolverton, P. Grones, S. Tan, G. Molnar, M. De Angelis, H. Goodman, N. Capstaff, L. JPB, J. Mullen, R. Hangarter, J. Friml, S. Kepinski, Nature Plants 9 (2023) 1500–1513. date_created: 2023-09-15T09:56:01Z date_published: 2023-09-01T00:00:00Z date_updated: 2024-10-21T06:01:33Z day: '01' ddc: - '580' department: - _id: JiFr doi: 10.1038/s41477-023-01478-x external_id: isi: - '001069238800014' pmid: - '37666965' file: - access_level: open_access checksum: 3d6d5d5abb937c14a5f6f0afba3b8624 content_type: application/pdf creator: dernst date_created: 2023-09-20T10:51:31Z date_updated: 2023-09-20T10:51:31Z file_id: '14351' file_name: 2023_NaturePlants_Roychoudhry.pdf file_size: 9647103 relation: main_file success: 1 file_date_updated: 2023-09-20T10:51:31Z has_accepted_license: '1' intvolume: ' 9' isi: 1 language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: 1500-1513 pmid: 1 publication: Nature Plants publication_identifier: issn: - 2055-0278 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Antigravitropic PIN polarization maintains non-vertical growth in lateral roots tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2023' ...