--- _id: '10719' abstract: - lang: eng text: Auxin, one of the first identified and most widely studied phytohormones, has been and will remain a hot topic in plant biology. After more than a century of passionate exploration, the mysteries of its synthesis, transport, signaling, and metabolism have largely been unlocked. Due to the rapid development of new technologies, new methods, and new genetic materials, the study of auxin has entered the fast lane over the past 30 years. Here, we highlight advances in understanding auxin signaling, including auxin perception, rapid auxin responses, TRANSPORT INHIBITOR RESPONSE 1 and AUXIN SIGNALING F-boxes (TIR1/AFBs)-mediated transcriptional and non-transcriptional branches, and the epigenetic regulation of auxin signaling. We also focus on feedback inhibition mechanisms that prevent the over-amplification of auxin signals. In addition, we cover the TRANSMEMBRANE KINASEs (TMKs)-mediated non-canonical signaling, which converges with TIR1/AFBs-mediated transcriptional regulation to coordinate plant growth and development. The identification of additional auxin signaling components and their regulation will continue to open new avenues of research in this field, leading to an increasingly deeper, more comprehensive understanding of how auxin signals are interpreted at the cellular level to regulate plant growth and development. acknowledgement: "This research was financially supported by the National Natural Science Foundation of China and the Israel Science Foundation (NSFC-ISF; 32061143005), National Natural Science Foundation of China (32000225), Natural Science Foundation of Shandong Province (ZR2020QC036), and China Postdoctoral Science Foundation (2020M682165).\r\n" article_processing_charge: No article_type: review author: - first_name: Z full_name: Yu, Z last_name: Yu - first_name: F full_name: Zhang, F last_name: Zhang - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Z full_name: Ding, Z last_name: Ding citation: ama: 'Yu Z, Zhang F, Friml J, Ding Z. Auxin signaling: Research advances over the past 30 years. Journal of Integrative Plant Biology. 2022;64(2):371-392. doi:10.1111/jipb.13225' apa: 'Yu, Z., Zhang, F., Friml, J., & Ding, Z. (2022). Auxin signaling: Research advances over the past 30 years. Journal of Integrative Plant Biology. Wiley. https://doi.org/10.1111/jipb.13225' chicago: 'Yu, Z, F Zhang, Jiří Friml, and Z Ding. “Auxin Signaling: Research Advances over the Past 30 Years.” Journal of Integrative Plant Biology. Wiley, 2022. https://doi.org/10.1111/jipb.13225.' ieee: 'Z. Yu, F. Zhang, J. Friml, and Z. Ding, “Auxin signaling: Research advances over the past 30 years,” Journal of Integrative Plant Biology, vol. 64, no. 2. Wiley, pp. 371–392, 2022.' ista: 'Yu Z, Zhang F, Friml J, Ding Z. 2022. Auxin signaling: Research advances over the past 30 years. Journal of Integrative Plant Biology. 64(2), 371–392.' mla: 'Yu, Z., et al. “Auxin Signaling: Research Advances over the Past 30 Years.” Journal of Integrative Plant Biology, vol. 64, no. 2, Wiley, 2022, pp. 371–92, doi:10.1111/jipb.13225.' short: Z. Yu, F. Zhang, J. Friml, Z. Ding, Journal of Integrative Plant Biology 64 (2022) 371–392. date_created: 2022-02-03T09:52:59Z date_published: 2022-02-01T00:00:00Z date_updated: 2023-08-02T14:08:30Z day: '01' department: - _id: JiFr doi: 10.1111/jipb.13225 external_id: isi: - '000761281200011' pmid: - '35018726' intvolume: ' 64' isi: 1 issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1111/jipb.13225 month: '02' oa: 1 oa_version: Published Version page: 371-392 pmid: 1 publication: Journal of Integrative Plant Biology publication_identifier: eissn: - 1744-7909 issn: - 1672-9072 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: 'Auxin signaling: Research advances over the past 30 years' type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 64 year: '2022' ... --- _id: '10768' abstract: - lang: eng text: Among the most fascinated properties of the plant hormone auxin is its ability to promote formation of its own directional transport routes. These gradually narrowing auxin channels form from the auxin source toward the sink and involve coordinated, collective polarization of individual cells. Once established, the channels provide positional information, along which new vascular strands form, for example, during organogenesis, regeneration, or leave venation. The main prerequisite of this still mysterious auxin canalization mechanism is a feedback between auxin signaling and its directional transport. This is manifested by auxin-induced re-arrangements of polar, subcellular localization of PIN-FORMED (PIN) auxin exporters. Immanent open questions relate to how position of auxin source and sink as well as tissue context are sensed and translated into tissue polarization and how cells communicate to polarize coordinately. Recently, identification of the first molecular players opens new avenues into molecular studies of this intriguing example of self-organizing plant development. acknowledgement: The authors apologize to those researchers whose work was not cited. In addition, exciting topics such as PIN polarization in context of phyllotaxis, shoot branching and termination of gravitropic bending, or role of additional auxin transporters could not have been included owing to lack of space. This work was supported by the Czech Science Foundation GAČR (GA18-26981S). The authors also acknowledge the EMBO for supporting J.H. with a long-term fellowship (ALTF217-2021). article_number: '102174' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Jakub full_name: Hajny, Jakub id: 4800CC20-F248-11E8-B48F-1D18A9856A87 last_name: Hajny orcid: 0000-0003-2140-7195 - first_name: Shutang full_name: Tan, Shutang id: 2DE75584-F248-11E8-B48F-1D18A9856A87 last_name: Tan orcid: 0000-0002-0471-8285 - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: 'Hajny J, Tan S, Friml J. Auxin canalization: From speculative models toward molecular players. Current Opinion in Plant Biology. 2022;65(2). doi:10.1016/j.pbi.2022.102174' apa: 'Hajny, J., Tan, S., & Friml, J. (2022). Auxin canalization: From speculative models toward molecular players. Current Opinion in Plant Biology. Elsevier. https://doi.org/10.1016/j.pbi.2022.102174' chicago: 'Hajny, Jakub, Shutang Tan, and Jiří Friml. “Auxin Canalization: From Speculative Models toward Molecular Players.” Current Opinion in Plant Biology. Elsevier, 2022. https://doi.org/10.1016/j.pbi.2022.102174.' ieee: 'J. Hajny, S. Tan, and J. Friml, “Auxin canalization: From speculative models toward molecular players,” Current Opinion in Plant Biology, vol. 65, no. 2. Elsevier, 2022.' ista: 'Hajny J, Tan S, Friml J. 2022. Auxin canalization: From speculative models toward molecular players. Current Opinion in Plant Biology. 65(2), 102174.' mla: 'Hajny, Jakub, et al. “Auxin Canalization: From Speculative Models toward Molecular Players.” Current Opinion in Plant Biology, vol. 65, no. 2, 102174, Elsevier, 2022, doi:10.1016/j.pbi.2022.102174.' short: J. Hajny, S. Tan, J. Friml, Current Opinion in Plant Biology 65 (2022). date_created: 2022-02-20T23:01:32Z date_published: 2022-02-01T00:00:00Z date_updated: 2023-08-02T14:29:12Z day: '01' ddc: - '580' department: - _id: JiFr doi: 10.1016/j.pbi.2022.102174 external_id: isi: - '000758724700004' pmid: - '35123880' file: - access_level: open_access checksum: f1ee02b6fb4200934eeb31fa69120885 content_type: application/pdf creator: dernst date_created: 2022-03-10T13:34:09Z date_updated: 2022-03-10T13:34:09Z file_id: '10844' file_name: 2022_CurrentOpPlantBiology_Hajny.pdf file_size: 820322 relation: main_file success: 1 file_date_updated: 2022-03-10T13:34:09Z has_accepted_license: '1' intvolume: ' 65' isi: 1 issue: '2' language: - iso: eng month: '02' oa: 1 oa_version: Published 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: 'Auxin canalization: From speculative models toward molecular players' 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: 65 year: '2022' ... --- _id: '10841' abstract: - lang: eng text: In eukaryotes, clathrin-coated vesicles (CCVs) facilitate the internalization of material from the cell surface as well as the movement of cargo in post-Golgi trafficking pathways. This diversity of functions is partially provided by multiple monomeric and multimeric clathrin adaptor complexes that provide compartment and cargo selectivity. The adaptor-protein assembly polypeptide-1 (AP-1) complex operates as part of the secretory pathway at the trans-Golgi network (TGN), while the AP-2 complex and the TPLATE complex jointly operate at the plasma membrane to execute clathrin-mediated endocytosis. Key to our further understanding of clathrin-mediated trafficking in plants will be the comprehensive identification and characterization of the network of evolutionarily conserved and plant-specific core and accessory machinery involved in the formation and targeting of CCVs. To facilitate these studies, we have analyzed the proteome of enriched TGN/early endosome-derived and endocytic CCVs isolated from dividing and expanding suspension-cultured Arabidopsis (Arabidopsis thaliana) cells. Tandem mass spectrometry analysis results were validated by differential chemical labeling experiments to identify proteins co-enriching with CCVs. Proteins enriched in CCVs included previously characterized CCV components and cargos such as the vacuolar sorting receptors in addition to conserved and plant-specific components whose function in clathrin-mediated trafficking has not been previously defined. Notably, in addition to AP-1 and AP-2, all subunits of the AP-4 complex, but not AP-3 or AP-5, were found to be in high abundance in the CCV proteome. The association of AP-4 with suspension-cultured Arabidopsis CCVs is further supported via additional biochemical data. acknowledged_ssus: - _id: EM-Fac acknowledgement: 'The authors would like to acknowledge the VIB Proteomics Core Facility (VIB-UGent Center for Medical Biotechnology in Ghent, Belgium) and the Research Technology Support Facility Proteomics Core (Michigan State University in East Lansing, Michigan) for sample analysis, as well as the University of Wisconsin Biotechnology Center Mass Spectrometry Core Facility (Madison, WI) for help with data processing. Additionally, we are grateful to Sue Weintraub (UT Health San Antonio) and Sydney Thomas (UW- Madison) for assistance with data analysis. This research was supported by grants to S.Y.B. from the National Science Foundation (Nos. 1121998 and 1614915) and a Vilas Associate Award (University of Wisconsin, Madison, Graduate School); to J.P. from the National Natural Science Foundation of China (Nos. 91754104, 31820103008, and 31670283); to I.H. from the National Research Foundation of Korea (No. 2019R1A2B5B03099982). This research was also supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Electron microscopy Facility (EMF). A.J. is supported by funding from the Austrian Science Fund (FWF): I3630B25 to J.F. A.H. is supported by funding from the National Science Foundation (NSF IOS Nos. 1025837 and 1147032).' article_processing_charge: No article_type: original author: - first_name: DA full_name: Dahhan, DA last_name: Dahhan - first_name: GD full_name: Reynolds, GD last_name: Reynolds - first_name: JJ full_name: Cárdenas, JJ last_name: Cárdenas - first_name: D full_name: Eeckhout, D last_name: Eeckhout - 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: K full_name: Yperman, K last_name: Yperman - first_name: Walter full_name: Kaufmann, Walter id: 3F99E422-F248-11E8-B48F-1D18A9856A87 last_name: Kaufmann orcid: 0000-0001-9735-5315 - first_name: N full_name: Vang, N last_name: Vang - first_name: X full_name: Yan, X last_name: Yan - first_name: I full_name: Hwang, I last_name: Hwang - first_name: A full_name: Heese, A last_name: Heese - first_name: G full_name: De Jaeger, G last_name: De Jaeger - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: D full_name: Van Damme, D last_name: Van Damme - first_name: J full_name: Pan, J last_name: Pan - first_name: SY full_name: Bednarek, SY last_name: Bednarek citation: ama: Dahhan D, Reynolds G, Cárdenas J, et al. Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components. Plant Cell. 2022;34(6):2150-2173. doi:10.1093/plcell/koac071 apa: Dahhan, D., Reynolds, G., Cárdenas, J., Eeckhout, D., Johnson, A. J., Yperman, K., … Bednarek, S. (2022). Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components. Plant Cell. Oxford Academic. https://doi.org/10.1093/plcell/koac071 chicago: Dahhan, DA, GD Reynolds, JJ Cárdenas, D Eeckhout, Alexander J Johnson, K Yperman, Walter Kaufmann, et al. “Proteomic Characterization of Isolated Arabidopsis Clathrin-Coated Vesicles Reveals Evolutionarily Conserved and Plant-Specific Components.” Plant Cell. Oxford Academic, 2022. https://doi.org/10.1093/plcell/koac071. ieee: D. Dahhan et al., “Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components,” Plant Cell, vol. 34, no. 6. Oxford Academic, pp. 2150–2173, 2022. ista: Dahhan D, Reynolds G, Cárdenas J, Eeckhout D, Johnson AJ, Yperman K, Kaufmann W, Vang N, Yan X, Hwang I, Heese A, De Jaeger G, Friml J, Van Damme D, Pan J, Bednarek S. 2022. Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components. Plant Cell. 34(6), 2150–2173. mla: Dahhan, DA, et al. “Proteomic Characterization of Isolated Arabidopsis Clathrin-Coated Vesicles Reveals Evolutionarily Conserved and Plant-Specific Components.” Plant Cell, vol. 34, no. 6, Oxford Academic, 2022, pp. 2150–73, doi:10.1093/plcell/koac071. short: D. Dahhan, G. Reynolds, J. Cárdenas, D. Eeckhout, A.J. Johnson, K. Yperman, W. Kaufmann, N. Vang, X. Yan, I. Hwang, A. Heese, G. De Jaeger, J. Friml, D. Van Damme, J. Pan, S. Bednarek, Plant Cell 34 (2022) 2150–2173. date_created: 2022-03-08T13:47:51Z date_published: 2022-06-01T00:00:00Z date_updated: 2023-08-02T14:46:48Z day: '01' department: - _id: JiFr - _id: EM-Fac doi: 10.1093/plcell/koac071 external_id: isi: - '000767438800001' pmid: - '35218346' intvolume: ' 34' isi: 1 issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1101/2021.09.16.460678 month: '06' oa: 1 oa_version: Preprint page: 2150-2173 pmid: 1 project: - _id: 26538374-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I03630 name: Molecular mechanisms of endocytic cargo recognition in plants publication: Plant Cell publication_identifier: eissn: - 1532-298x issn: - 1040-4651 publication_status: published publisher: Oxford Academic quality_controlled: '1' scopus_import: '1' status: public title: Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 34 year: '2022' ... --- _id: '10888' abstract: - lang: eng text: Despite the growing interest in using chemical genetics in plant research, small molecule target identification remains a major challenge. The cellular thermal shift assay coupled with high-resolution mass spectrometry (CETSA MS) that monitors changes in the thermal stability of proteins caused by their interactions with small molecules, other proteins, or posttranslational modifications, allows the discovery of drug targets or the study of protein–metabolite and protein–protein interactions mainly in mammalian cells. To showcase the applicability of this method in plants, we applied CETSA MS to intact Arabidopsis thaliana cells and identified the thermal proteome of the plant-specific glycogen synthase kinase 3 (GSK3) inhibitor, bikinin. A comparison between the thermal and the phosphoproteomes of bikinin revealed the auxin efflux carrier PIN-FORMED1 (PIN1) as a substrate of the Arabidopsis GSK3s that negatively regulate the brassinosteroid signaling. We established that PIN1 phosphorylation by the GSK3s is essential for maintaining its intracellular polarity that is required for auxin-mediated regulation of vascular patterning in the leaf, thus revealing cross-talk between brassinosteroid and auxin signaling. acknowledgement: "We thank Yanhai Yin for providing the anti-BES1 antibody, Johan Winne and Brenda Callebaut for synthesizing bikinin, Yuki Kondo and Hiroo Fukuda for published materials, Tomasz Nodzy\x03nski for useful advice, and Martine De Cock for help in preparing the manuscript. This\r\nwork was supported by the China Scholarship Council for predoctoral (Q.L. and X.X.) and postdoctoral (Y.Z.) fellowships; the Agency for Innovation by Science and Technology for a predoctoral fellowship (W.D.); the Research Foundation-Flanders, Projects G009018N and G002121N (E.R.); and the VIB TechWatch Fund (E.R.)." article_number: e2118220119 article_processing_charge: No article_type: original author: - first_name: Qing full_name: Lu, Qing last_name: Lu - first_name: Yonghong full_name: Zhang, Yonghong last_name: Zhang - first_name: Joakim full_name: Hellner, Joakim last_name: Hellner - first_name: Caterina full_name: Giannini, Caterina id: e3fdddd5-f6e0-11ea-865d-ca99ee6367f4 last_name: Giannini - first_name: Xiangyu full_name: Xu, Xiangyu last_name: Xu - first_name: Jarne full_name: Pauwels, Jarne last_name: Pauwels - first_name: Qian full_name: Ma, Qian last_name: Ma - first_name: Wim full_name: Dejonghe, Wim last_name: Dejonghe - first_name: Huibin full_name: Han, Huibin id: 31435098-F248-11E8-B48F-1D18A9856A87 last_name: Han - first_name: Brigitte full_name: Van De Cotte, Brigitte last_name: Van De Cotte - first_name: Francis full_name: Impens, Francis last_name: Impens - first_name: Kris full_name: Gevaert, Kris last_name: Gevaert - first_name: Ive full_name: De Smet, Ive last_name: De Smet - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Daniel Martinez full_name: Molina, Daniel Martinez last_name: Molina - first_name: Eugenia full_name: Russinova, Eugenia last_name: Russinova citation: ama: Lu Q, Zhang Y, Hellner J, et al. Proteome-wide cellular thermal shift assay reveals unexpected cross-talk between brassinosteroid and auxin signaling. Proceedings of the National Academy of Sciences of the United States of America. 2022;119(11). doi:10.1073/pnas.2118220119 apa: Lu, Q., Zhang, Y., Hellner, J., Giannini, C., Xu, X., Pauwels, J., … Russinova, E. (2022). Proteome-wide cellular thermal shift assay reveals unexpected cross-talk between brassinosteroid and auxin signaling. Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2118220119 chicago: Lu, Qing, Yonghong Zhang, Joakim Hellner, Caterina Giannini, Xiangyu Xu, Jarne Pauwels, Qian Ma, et al. “Proteome-Wide Cellular Thermal Shift Assay Reveals Unexpected Cross-Talk between Brassinosteroid and Auxin Signaling.” Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences, 2022. https://doi.org/10.1073/pnas.2118220119. ieee: Q. Lu et al., “Proteome-wide cellular thermal shift assay reveals unexpected cross-talk between brassinosteroid and auxin signaling,” Proceedings of the National Academy of Sciences of the United States of America, vol. 119, no. 11. Proceedings of the National Academy of Sciences, 2022. ista: Lu Q, Zhang Y, Hellner J, Giannini C, Xu X, Pauwels J, Ma Q, Dejonghe W, Han H, Van De Cotte B, Impens F, Gevaert K, De Smet I, Friml J, Molina DM, Russinova E. 2022. Proteome-wide cellular thermal shift assay reveals unexpected cross-talk between brassinosteroid and auxin signaling. Proceedings of the National Academy of Sciences of the United States of America. 119(11), e2118220119. mla: Lu, Qing, et al. “Proteome-Wide Cellular Thermal Shift Assay Reveals Unexpected Cross-Talk between Brassinosteroid and Auxin Signaling.” Proceedings of the National Academy of Sciences of the United States of America, vol. 119, no. 11, e2118220119, Proceedings of the National Academy of Sciences, 2022, doi:10.1073/pnas.2118220119. short: Q. Lu, Y. Zhang, J. Hellner, C. Giannini, X. Xu, J. Pauwels, Q. Ma, W. Dejonghe, H. Han, B. Van De Cotte, F. Impens, K. Gevaert, I. De Smet, J. Friml, D.M. Molina, E. Russinova, Proceedings of the National Academy of Sciences of the United States of America 119 (2022). date_created: 2022-03-20T23:01:39Z date_published: 2022-03-07T00:00:00Z date_updated: 2023-08-03T06:06:27Z day: '07' ddc: - '580' department: - _id: JiFr doi: 10.1073/pnas.2118220119 external_id: isi: - '000771756300008' pmid: - '35254915' file: - access_level: open_access checksum: 83e0fea7919570d0b519b41193342571 content_type: application/pdf creator: dernst date_created: 2022-03-21T09:19:47Z date_updated: 2022-03-21T09:19:47Z file_id: '10910' file_name: 2022_PNAS_Lu.pdf file_size: 2169534 relation: main_file success: 1 file_date_updated: 2022-03-21T09:19:47Z has_accepted_license: '1' intvolume: ' 119' isi: 1 issue: '11' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ month: '03' oa: 1 oa_version: Published Version pmid: 1 publication: Proceedings of the National Academy of Sciences of the United States of America publication_identifier: eissn: - 1091-6490 publication_status: published publisher: Proceedings of the National Academy of Sciences quality_controlled: '1' scopus_import: '1' status: public title: Proteome-wide cellular thermal shift assay reveals unexpected cross-talk between brassinosteroid and auxin signaling 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 119 year: '2022' ... --- _id: '11589' abstract: - lang: eng text: Calcium-dependent protein kinases (CPK) are key components of a wide array of signaling pathways, translating stress and nutrient signaling into the modulation of cellular processes such as ion transport and transcription. However, not much is known about CPKs in endomembrane trafficking. Here, we screened for CPKs that impact on root growth and gravitropism, by overexpressing constitutively active forms of CPKs under the control of an inducible promoter in Arabidopsis thaliana. We found that inducible overexpression of an constitutive active CPK30 (CA-CPK30) resulted in a loss of root gravitropism and ectopic auxin accumulation in the root tip. Immunolocalization revealed that CA-CPK30 roots have reduced PIN protein levels, PIN1 polarity defects and impaired Brefeldin A (BFA)-sensitive trafficking. Moreover, FM4-64 uptake was reduced, indicative of a defect in endocytosis. The effects on BFA-sensitive trafficking were not specific to PINs, as BFA could not induce aggregation of ARF1- and CHC-labeled endosomes in CA-CPK30. Interestingly, the interference with BFA-body formation, could be reverted by increasing the extracellular pH, indicating a pH-dependence of this CA-CPK30 effect. Altogether, our data reveal an important role for CPK30 in root growth regulation and endomembrane trafficking in Arabidopsis thaliana. acknowledgement: "RW and JC predoctoral fellows that were supported by the Chinese Science Counsil. The IPS2 benefits from the support of the LabEx Saclay Plant Sciences-SPS (ANR-10-LABX-0040-SPS).\r\nWe thank Jen Sheen for establishing and generously sharing the CKP family clone sets, and for providing useful feedback on the manuscript." article_number: '862398' article_processing_charge: No article_type: original author: - first_name: Ren full_name: Wang, Ren last_name: Wang - first_name: Ellie full_name: Himschoot, Ellie last_name: Himschoot - first_name: Jian full_name: Chen, Jian last_name: Chen - first_name: Marie full_name: Boudsocq, Marie last_name: Boudsocq - first_name: Danny full_name: Geelen, Danny last_name: Geelen - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Tom full_name: Beeckman, Tom last_name: Beeckman - first_name: Steffen full_name: Vanneste, Steffen last_name: Vanneste citation: ama: Wang R, Himschoot E, Chen J, et al. Constitutive active CPK30 interferes with root growth and endomembrane trafficking in Arabidopsis thaliana. Frontiers in Plant Science. 2022;13. doi:10.3389/fpls.2022.862398 apa: Wang, R., Himschoot, E., Chen, J., Boudsocq, M., Geelen, D., Friml, J., … Vanneste, S. (2022). Constitutive active CPK30 interferes with root growth and endomembrane trafficking in Arabidopsis thaliana. Frontiers in Plant Science. Frontiers. https://doi.org/10.3389/fpls.2022.862398 chicago: Wang, Ren, Ellie Himschoot, Jian Chen, Marie Boudsocq, Danny Geelen, Jiří Friml, Tom Beeckman, and Steffen Vanneste. “Constitutive Active CPK30 Interferes with Root Growth and Endomembrane Trafficking in Arabidopsis Thaliana.” Frontiers in Plant Science. Frontiers, 2022. https://doi.org/10.3389/fpls.2022.862398. ieee: R. Wang et al., “Constitutive active CPK30 interferes with root growth and endomembrane trafficking in Arabidopsis thaliana,” Frontiers in Plant Science, vol. 13. Frontiers, 2022. ista: Wang R, Himschoot E, Chen J, Boudsocq M, Geelen D, Friml J, Beeckman T, Vanneste S. 2022. Constitutive active CPK30 interferes with root growth and endomembrane trafficking in Arabidopsis thaliana. Frontiers in Plant Science. 13, 862398. mla: Wang, Ren, et al. “Constitutive Active CPK30 Interferes with Root Growth and Endomembrane Trafficking in Arabidopsis Thaliana.” Frontiers in Plant Science, vol. 13, 862398, Frontiers, 2022, doi:10.3389/fpls.2022.862398. short: R. Wang, E. Himschoot, J. Chen, M. Boudsocq, D. Geelen, J. Friml, T. Beeckman, S. Vanneste, Frontiers in Plant Science 13 (2022). date_created: 2022-07-17T22:01:54Z date_published: 2022-06-16T00:00:00Z date_updated: 2023-08-03T12:01:47Z day: '16' ddc: - '580' department: - _id: JiFr doi: 10.3389/fpls.2022.862398 external_id: isi: - '000819250500001' pmid: - '35783951' file: - access_level: open_access checksum: 95313515637c0f84de591d204375d764 content_type: application/pdf creator: dernst date_created: 2022-07-18T08:05:15Z date_updated: 2022-07-18T08:05:15Z file_id: '11596' file_name: 2022_FrontiersPlantScience_Wang.pdf file_size: 5040638 relation: main_file success: 1 file_date_updated: 2022-07-18T08:05:15Z has_accepted_license: '1' intvolume: ' 13' isi: 1 language: - iso: eng month: '06' oa: 1 oa_version: Published Version pmid: 1 publication: Frontiers in Plant Science publication_identifier: eissn: - 1664-462X publication_status: published publisher: Frontiers quality_controlled: '1' related_material: link: - relation: erratum url: https://doi.org/10.3389/fpls.2022.1100792 scopus_import: '1' status: public title: Constitutive active CPK30 interferes with root growth and endomembrane trafficking in Arabidopsis thaliana 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: 13 year: '2022' ... --- _id: '11723' abstract: - lang: eng text: Plant cell growth responds rapidly to various stimuli, adapting architecture to environmental changes. Two major endogenous signals regulating growth are the phytohormone auxin and the secreted peptides rapid alkalinization factors (RALFs). Both trigger very rapid cellular responses and also exert long-term effects [Du et al., Annu. Rev. Plant Biol. 71, 379–402 (2020); Blackburn et al., Plant Physiol. 182, 1657–1666 (2020)]. However, the way, in which these distinct signaling pathways converge to regulate growth, remains unknown. Here, using vertical confocal microscopy combined with a microfluidic chip, we addressed the mechanism of RALF action on growth. We observed correlation between RALF1-induced rapid Arabidopsis thaliana root growth inhibition and apoplast alkalinization during the initial phase of the response, and revealed that RALF1 reversibly inhibits primary root growth through apoplast alkalinization faster than within 1 min. This rapid apoplast alkalinization was the result of RALF1-induced net H+ influx and was mediated by the receptor FERONIA (FER). Furthermore, we investigated the cross-talk between RALF1 and the auxin signaling pathways during root growth regulation. The results showed that RALF-FER signaling triggered auxin signaling with a delay of approximately 1 h by up-regulating auxin biosynthesis, thus contributing to sustained RALF1-induced growth inhibition. This biphasic RALF1 action on growth allows plants to respond rapidly to environmental stimuli and also reprogram growth and development in the long term. acknowledgement: We thank Sarah M. Assmann, Kris Vissenberg, and Nadine Paris for kindly sharing seeds; Matyáš Fendrych for initiating this project and providing constant support; Lukas Fiedler for revising the manuscript; and Huibin Han and Arseny Savin for contributing to genotyping. This work was supported by the Austrian Science Fund (FWF) I 3630-B25 (to J.F.) and the Doctoral Fellowship Progrmme of the Austrian Academy of Sciences (to L.L.) We also acknowledge Taif University Researchers Supporting Project TURSP-HC2021/02 and funding “Plants as a tool for sustainable global development (no. CZ.02.1.01/0.0/0.0/16_019/0000827).” article_number: e2121058119 article_processing_charge: No article_type: original author: - first_name: Lanxin full_name: Li, Lanxin id: 367EF8FA-F248-11E8-B48F-1D18A9856A87 last_name: Li orcid: 0000-0002-5607-272X - first_name: Huihuang full_name: Chen, Huihuang id: 83c96512-15b2-11ec-abd3-b7eede36184f last_name: Chen - first_name: Saqer S. full_name: Alotaibi, Saqer S. last_name: Alotaibi - first_name: Aleš full_name: Pěnčík, Aleš last_name: Pěnčík - first_name: Maciek full_name: Adamowski, Maciek id: 45F536D2-F248-11E8-B48F-1D18A9856A87 last_name: Adamowski orcid: 0000-0001-6463-5257 - first_name: Ondřej full_name: Novák, Ondřej last_name: Novák - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Li L, Chen H, Alotaibi SS, et al. RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis. Proceedings of the National Academy of Sciences. 2022;119(31). doi:10.1073/pnas.2121058119 apa: Li, L., Chen, H., Alotaibi, S. S., Pěnčík, A., Adamowski, M., Novák, O., & Friml, J. (2022). RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2121058119 chicago: Li, Lanxin, Huihuang Chen, Saqer S. Alotaibi, Aleš Pěnčík, Maciek Adamowski, Ondřej Novák, and Jiří Friml. “RALF1 Peptide Triggers Biphasic Root Growth Inhibition Upstream of Auxin Biosynthesis.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2022. https://doi.org/10.1073/pnas.2121058119. ieee: L. Li et al., “RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis,” Proceedings of the National Academy of Sciences, vol. 119, no. 31. Proceedings of the National Academy of Sciences, 2022. ista: Li L, Chen H, Alotaibi SS, Pěnčík A, Adamowski M, Novák O, Friml J. 2022. RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis. Proceedings of the National Academy of Sciences. 119(31), e2121058119. mla: Li, Lanxin, et al. “RALF1 Peptide Triggers Biphasic Root Growth Inhibition Upstream of Auxin Biosynthesis.” Proceedings of the National Academy of Sciences, vol. 119, no. 31, e2121058119, Proceedings of the National Academy of Sciences, 2022, doi:10.1073/pnas.2121058119. short: L. Li, H. Chen, S.S. Alotaibi, A. Pěnčík, M. Adamowski, O. Novák, J. Friml, Proceedings of the National Academy of Sciences 119 (2022). date_created: 2022-08-04T20:06:49Z date_published: 2022-07-25T00:00:00Z date_updated: 2023-08-03T12:43:53Z day: '25' ddc: - '580' department: - _id: GradSch - _id: JiFr doi: 10.1073/pnas.2121058119 external_id: isi: - '000881496900002' pmid: - '35878023' file: - access_level: open_access checksum: ae6f19b0d9efba6687f9e4dc1bab1d6e content_type: application/pdf creator: dernst date_created: 2022-08-08T07:42:09Z date_updated: 2022-08-08T07:42:09Z file_id: '11747' file_name: 2022_PNAS_Li.pdf file_size: 2506262 relation: main_file success: 1 file_date_updated: 2022-08-08T07:42:09Z has_accepted_license: '1' intvolume: ' 119' isi: 1 issue: '31' keyword: - Multidisciplinary language: - iso: eng month: '07' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 26538374-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I03630 name: Molecular mechanisms of endocytic cargo recognition in plants - _id: 26B4D67E-B435-11E9-9278-68D0E5697425 grant_number: '25351' name: 'A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root' publication: Proceedings of the National Academy of Sciences publication_identifier: eissn: - 1091-6490 issn: - 0027-8424 publication_status: published publisher: Proceedings of the National Academy of Sciences quality_controlled: '1' scopus_import: '1' status: public title: RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 119 year: '2022' ... --- _id: '12053' abstract: - lang: eng text: Strigolactones (SLs) are a class of phytohormones that regulate plant shoot branching and adventitious root development. However, little is known regarding the role of SLs in controlling the behavior of the smallest unit of the organism, the single cell. Here, taking advantage of a classic single-cell model offered by the cotton (Gossypium hirsutum) fiber cell, we show that SLs, whose biosynthesis is fine-tuned by gibberellins (GAs), positively regulate cell elongation and cell wall thickness by promoting the biosynthesis of very-long-chain fatty acids (VLCFAs) and cellulose, respectively. Furthermore, we identified two layers of transcription factors (TFs) involved in the hierarchical regulation of this GA-SL crosstalk. The top-layer TF GROWTH-REGULATING FACTOR 4 (GhGRF4) directly activates expression of the SL biosynthetic gene DWARF27 (D27) to increase SL accumulation in fiber cells and GAs induce GhGRF4 expression. SLs induce the expression of four second-layer TF genes (GhNAC100-2, GhBLH51, GhGT2, and GhB9SHZ1), which transmit SL signals downstream to two ketoacyl-CoA synthase genes (KCS) and three cellulose synthase (CesA) genes by directly activating their transcription. Finally, the KCS and CesA enzymes catalyze the biosynthesis of very long chain fatty acids and cellulose, respectively, to regulate development of high-grade cotton fibers. In addition to providing a theoretical basis for cotton fiber improvement, our results shed light on SL signaling in plant development at the single-cell level. acknowledgement: This work was supported by the National Natural Science Foundation of China (32070549), Shaanxi Youth Entrusted Talent Program (20190205), Fundamental Research Funds for the Central Universities (GK202002005 and GK202201017), Young Elite Scientists Sponsorship Program by China Association for Science and Technology (CAST) (2019-2021QNRC001), State Key Laboratory of Cotton Biology Open Fund (CB2020A12 and CB2021A21) and FWF Stand-alone Project (P29988). article_processing_charge: No article_type: original author: - first_name: Z full_name: Tian, Z last_name: Tian - first_name: Yuzhou full_name: Zhang, Yuzhou id: 3B6137F2-F248-11E8-B48F-1D18A9856A87 last_name: Zhang orcid: 0000-0003-2627-6956 - first_name: L full_name: Zhu, L last_name: Zhu - first_name: B full_name: Jiang, B last_name: Jiang - first_name: H full_name: Wang, H last_name: Wang - first_name: R full_name: Gao, R last_name: Gao - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: G full_name: Xiao, G last_name: Xiao citation: ama: Tian Z, Zhang Y, Zhu L, et al. Strigolactones act downstream of gibberellins to regulate fiber cell elongation and cell wall thickness in cotton (Gossypium hirsutum). The Plant Cell. 2022;34(12):4816-4839. doi:10.1093/plcell/koac270 apa: Tian, Z., Zhang, Y., Zhu, L., Jiang, B., Wang, H., Gao, R., … Xiao, G. (2022). Strigolactones act downstream of gibberellins to regulate fiber cell elongation and cell wall thickness in cotton (Gossypium hirsutum). The Plant Cell. Oxford University Press. https://doi.org/10.1093/plcell/koac270 chicago: Tian, Z, Yuzhou Zhang, L Zhu, B Jiang, H Wang, R Gao, Jiří Friml, and G Xiao. “Strigolactones Act Downstream of Gibberellins to Regulate Fiber Cell Elongation and Cell Wall Thickness in Cotton (Gossypium Hirsutum).” The Plant Cell. Oxford University Press, 2022. https://doi.org/10.1093/plcell/koac270. ieee: Z. Tian et al., “Strigolactones act downstream of gibberellins to regulate fiber cell elongation and cell wall thickness in cotton (Gossypium hirsutum),” The Plant Cell, vol. 34, no. 12. Oxford University Press, pp. 4816–4839, 2022. ista: Tian Z, Zhang Y, Zhu L, Jiang B, Wang H, Gao R, Friml J, Xiao G. 2022. Strigolactones act downstream of gibberellins to regulate fiber cell elongation and cell wall thickness in cotton (Gossypium hirsutum). The Plant Cell. 34(12), 4816–4839. mla: Tian, Z., et al. “Strigolactones Act Downstream of Gibberellins to Regulate Fiber Cell Elongation and Cell Wall Thickness in Cotton (Gossypium Hirsutum).” The Plant Cell, vol. 34, no. 12, Oxford University Press, 2022, pp. 4816–39, doi:10.1093/plcell/koac270. short: Z. Tian, Y. Zhang, L. Zhu, B. Jiang, H. Wang, R. Gao, J. Friml, G. Xiao, The Plant Cell 34 (2022) 4816–4839. date_created: 2022-09-07T14:19:39Z date_published: 2022-12-01T00:00:00Z date_updated: 2023-08-03T13:41:06Z day: '01' ddc: - '580' department: - _id: JiFr doi: 10.1093/plcell/koac270 external_id: isi: - '000852753000001' pmid: - '36040191' file: - access_level: open_access checksum: 1c606d9545f29dfca15235f69ad27b58 content_type: application/pdf creator: dernst date_created: 2023-01-20T08:29:12Z date_updated: 2023-01-20T08:29:12Z file_id: '12318' file_name: 2022_PlantCell_Tian.pdf file_size: 3282540 relation: main_file success: 1 file_date_updated: 2023-01-20T08:29:12Z has_accepted_license: '1' intvolume: ' 34' isi: 1 issue: '12' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: 4816-4839 pmid: 1 project: - _id: 262EF96E-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P29988 name: RNA-directed DNA methylation in plant development publication: The Plant Cell publication_identifier: eissn: - 1532-298X issn: - 1040-4651 publication_status: published publisher: Oxford University Press quality_controlled: '1' related_material: link: - relation: erratum url: https://doi.org/10.1093/plcell/koac342 scopus_import: '1' status: public title: Strigolactones act downstream of gibberellins to regulate fiber cell elongation and cell wall thickness in cotton (Gossypium hirsutum) 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 34 year: '2022' ... --- _id: '12052' abstract: - lang: eng text: Directionality in the intercellular transport of the plant hormone auxin is determined by polar plasma membrane localization of PIN-FORMED (PIN) auxin transport proteins. However, apart from PIN phosphorylation at conserved motifs, no further determinants explicitly controlling polar PIN sorting decisions have been identified. Here we present Arabidopsis WAVY GROWTH 3 (WAV3) and closely related RING-finger E3 ubiquitin ligases, whose loss-of-function mutants show a striking apical-to-basal polarity switch in PIN2 localization in root meristem cells. WAV3 E3 ligases function as essential determinants for PIN polarity, acting independently from PINOID/WAG-dependent PIN phosphorylation. They antagonize ectopic deposition of de novo synthesized PIN proteins already immediately following completion of cell division, presumably via preventing PIN sorting into basal, ARF GEF-mediated trafficking. Our findings reveal an involvement of E3 ligases in the selective targeting of apically localized PINs in higher plants. acknowledgement: We would like to thank Tatsuo Sakai, Marcus Heisler, Toru Fujiwara, Lucia Strader, Christian Hardtke, Malcolm Bennett, Claus Schwechheimer, Gerd Jürgens and Remko Offringa for sharing published materials and Alba Grau Gimeno for support. We are greatly indebted to Bert de Rybel for supporting N.K. and M.G. to work on the final stages of manuscript preparation as postdocs in his laboratory. A full-length SOR1 cDNA clone (J090099M14) was obtained from the National Agriculture and Food Research Organization (NARO, Japan). Support by the Multiscale Imaging Core Facility at the BOKU is greatly acknowledged. This work has been supported by grants from the Austrian Science Fund (FWF P25931-B16; P31493-B25 to Christian Luschnig; I3630-B25 to Jiří Friml; P30850-B32 to Barbara Korbei) and from the Swiss National Funds (31003A-165877/1 to Markus Geisler) and the European Union’s Horizon 2020 research and innovation program (Marie Skłodowska-Curie grant agreement No 885979 to Matouš Glanc). article_number: '5147' article_processing_charge: No article_type: original author: - first_name: N full_name: Konstantinova, N last_name: Konstantinova - first_name: Lukas full_name: Hörmayer, Lukas id: 2EEE7A2A-F248-11E8-B48F-1D18A9856A87 last_name: Hörmayer - first_name: Matous full_name: Glanc, Matous id: 1AE1EA24-02D0-11E9-9BAA-DAF4881429F2 last_name: Glanc orcid: 0000-0003-0619-7783 - first_name: R full_name: Keshkeih, R last_name: Keshkeih - first_name: Shutang full_name: Tan, Shutang id: 2DE75584-F248-11E8-B48F-1D18A9856A87 last_name: Tan orcid: 0000-0002-0471-8285 - first_name: M full_name: Di Donato, M last_name: Di Donato - first_name: K full_name: Retzer, K last_name: Retzer - first_name: J full_name: Moulinier-Anzola, J last_name: Moulinier-Anzola - first_name: M full_name: Schwihla, M last_name: Schwihla - first_name: B full_name: Korbei, B last_name: Korbei - first_name: M full_name: Geisler, M last_name: Geisler - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: C full_name: Luschnig, C last_name: Luschnig citation: ama: Konstantinova N, Hörmayer L, Glanc M, et al. WAVY GROWTH Arabidopsis E3 ubiquitin ligases affect apical PIN sorting decisions. Nature Communications. 2022;13. doi:10.1038/s41467-022-32888-8 apa: Konstantinova, N., Hörmayer, L., Glanc, M., Keshkeih, R., Tan, S., Di Donato, M., … Luschnig, C. (2022). WAVY GROWTH Arabidopsis E3 ubiquitin ligases affect apical PIN sorting decisions. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-022-32888-8 chicago: Konstantinova, N, Lukas Hörmayer, Matous Glanc, R Keshkeih, Shutang Tan, M Di Donato, K Retzer, et al. “WAVY GROWTH Arabidopsis E3 Ubiquitin Ligases Affect Apical PIN Sorting Decisions.” Nature Communications. Springer Nature, 2022. https://doi.org/10.1038/s41467-022-32888-8. ieee: N. Konstantinova et al., “WAVY GROWTH Arabidopsis E3 ubiquitin ligases affect apical PIN sorting decisions,” Nature Communications, vol. 13. Springer Nature, 2022. ista: Konstantinova N, Hörmayer L, Glanc M, Keshkeih R, Tan S, Di Donato M, Retzer K, Moulinier-Anzola J, Schwihla M, Korbei B, Geisler M, Friml J, Luschnig C. 2022. WAVY GROWTH Arabidopsis E3 ubiquitin ligases affect apical PIN sorting decisions. Nature Communications. 13, 5147. mla: Konstantinova, N., et al. “WAVY GROWTH Arabidopsis E3 Ubiquitin Ligases Affect Apical PIN Sorting Decisions.” Nature Communications, vol. 13, 5147, Springer Nature, 2022, doi:10.1038/s41467-022-32888-8. short: N. Konstantinova, L. Hörmayer, M. Glanc, R. Keshkeih, S. Tan, M. Di Donato, K. Retzer, J. Moulinier-Anzola, M. Schwihla, B. Korbei, M. Geisler, J. Friml, C. Luschnig, Nature Communications 13 (2022). date_created: 2022-09-07T14:19:26Z date_published: 2022-09-01T00:00:00Z date_updated: 2023-08-03T13:40:32Z day: '01' ddc: - '580' department: - _id: JiFr doi: 10.1038/s41467-022-32888-8 external_id: isi: - '000848744900004' pmid: - '36050482' file: - access_level: open_access checksum: 43336758c89cd6c045839089af070afe content_type: application/pdf creator: dernst date_created: 2022-09-08T07:46:16Z date_updated: 2022-09-08T07:46:16Z file_id: '12063' file_name: 2022_NatureCommunications_Konstantinova.pdf file_size: 6678579 relation: main_file success: 1 file_date_updated: 2022-09-08T07:46:16Z has_accepted_license: '1' intvolume: ' 13' isi: 1 language: - iso: eng month: '09' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 26538374-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I03630 name: Molecular mechanisms of endocytic cargo recognition in plants publication: Nature Communications publication_identifier: issn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - relation: erratum url: https://doi.org/10.1038/s41467-022-33198-9 status: public title: WAVY GROWTH Arabidopsis E3 ubiquitin ligases affect apical PIN sorting decisions 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: 13 year: '2022' ... --- _id: '12054' abstract: - lang: eng text: 'Polar auxin transport is unique to plants and coordinates their growth and development1,2. The PIN-FORMED (PIN) auxin transporters exhibit highly asymmetrical localizations at the plasma membrane and drive polar auxin transport3,4; however, their structures and transport mechanisms remain largely unknown. Here, we report three inward-facing conformation structures of Arabidopsis thaliana PIN1: the apo state, bound to the natural auxin indole-3-acetic acid (IAA), and in complex with the polar auxin transport inhibitor N-1-naphthylphthalamic acid (NPA). The transmembrane domain of PIN1 shares a conserved NhaA fold5. In the substrate-bound structure, IAA is coordinated by both hydrophobic stacking and hydrogen bonding. NPA competes with IAA for the same site at the intracellular pocket, but with a much higher affinity. These findings inform our understanding of the substrate recognition and transport mechanisms of PINs and set up a framework for future research on directional auxin transport, one of the most crucial processes underlying plant development.' acknowledgement: We thank the Cryo-EM Center of the University of Science and Technology of China (USTC) and the Center for Biological Imaging (CBI), Institute of Biophysics, Chinese Academy of Science, for the EM facility support; we thank B. Zhu, X. Huang and all the other staff members for their technical support on cryo-EM data collection. We thank J. Ren for his technical support with the transport assays and M. Seeger for providing the sybody libraries. This work was supported by the Strategic Priority Research Program of Chinese Academy of Sciences (XDB 37020204 to D.L. and XDB37020103 to Linfeng Sun), National Natural Science Foundation of China (82151215 and 31870726 to D.L., 31900885 to X.L., and 31870732 to Linfeng Sun), Natural Science Foundation of Anhui Province (2008085MC90 to X.L. and 2008085J15 to Linfeng Sun), the Fundamental Research Funds for the Central Universities (WK9100000031 to Linfeng Sun), and the USTC Research Funds of the Double First-Class Initiative (YD9100002004 to Linfeng Sun). Linfeng Sun is supported by an Outstanding Young Scholar Award from the Qiu Shi Science and Technologies Foundation, and a Young Scholar Award from the Cyrus Tang Foundation. article_processing_charge: No article_type: original author: - first_name: Z full_name: Yang, Z last_name: Yang - first_name: J full_name: Xia, J last_name: Xia - first_name: J full_name: Hong, J last_name: Hong - first_name: C full_name: Zhang, C last_name: Zhang - first_name: H full_name: Wei, H last_name: Wei - first_name: W full_name: Ying, W last_name: Ying - first_name: C full_name: Sun, C last_name: Sun - first_name: L full_name: Sun, L last_name: Sun - first_name: Y full_name: Mao, Y last_name: Mao - first_name: Y full_name: Gao, Y last_name: Gao - first_name: S full_name: Tan, S last_name: Tan - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: D full_name: Li, D last_name: Li - first_name: X full_name: Liu, X last_name: Liu - first_name: L full_name: Sun, L last_name: Sun citation: ama: Yang Z, Xia J, Hong J, et al. Structural insights into auxin recognition and efflux by Arabidopsis PIN1. Nature. 2022;609(7927):611-615. doi:10.1038/s41586-022-05143-9 apa: Yang, Z., Xia, J., Hong, J., Zhang, C., Wei, H., Ying, W., … Sun, L. (2022). Structural insights into auxin recognition and efflux by Arabidopsis PIN1. Nature. Springer Nature. https://doi.org/10.1038/s41586-022-05143-9 chicago: Yang, Z, J Xia, J Hong, C Zhang, H Wei, W Ying, C Sun, et al. “Structural Insights into Auxin Recognition and Efflux by Arabidopsis PIN1.” Nature. Springer Nature, 2022. https://doi.org/10.1038/s41586-022-05143-9. ieee: Z. Yang et al., “Structural insights into auxin recognition and efflux by Arabidopsis PIN1,” Nature, vol. 609, no. 7927. Springer Nature, pp. 611–615, 2022. ista: Yang Z, Xia J, Hong J, Zhang C, Wei H, Ying W, Sun C, Sun L, Mao Y, Gao Y, Tan S, Friml J, Li D, Liu X, Sun L. 2022. Structural insights into auxin recognition and efflux by Arabidopsis PIN1. Nature. 609(7927), 611–615. mla: Yang, Z., et al. “Structural Insights into Auxin Recognition and Efflux by Arabidopsis PIN1.” Nature, vol. 609, no. 7927, Springer Nature, 2022, pp. 611–15, doi:10.1038/s41586-022-05143-9. short: Z. Yang, J. Xia, J. Hong, C. Zhang, H. Wei, W. Ying, C. Sun, L. Sun, Y. Mao, Y. Gao, S. Tan, J. Friml, D. Li, X. Liu, L. Sun, Nature 609 (2022) 611–615. date_created: 2022-09-07T14:19:52Z date_published: 2022-08-02T00:00:00Z date_updated: 2023-08-03T13:41:44Z day: '02' ddc: - '580' department: - _id: JiFr doi: 10.1038/s41586-022-05143-9 external_id: isi: - '000848082900002' pmid: - '35917925' file: - access_level: open_access checksum: 3136a585f8e1c7e73b5e1418b3d01898 content_type: application/pdf creator: dernst date_created: 2022-09-08T08:02:54Z date_updated: 2022-09-08T08:02:54Z file_id: '12064' file_name: 2022_Nature_Yang.pdf file_size: 32344580 relation: main_file success: 1 file_date_updated: 2022-09-08T08:02:54Z has_accepted_license: '1' intvolume: ' 609' isi: 1 issue: '7927' language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: 611-615 pmid: 1 publication: Nature publication_identifier: eissn: - 1476-4687 issn: - 0028-0836 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Structural insights into auxin recognition and efflux by Arabidopsis PIN1 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: 609 year: '2022' ... --- _id: '12121' abstract: - lang: eng text: Autophagosomes are double-membraned vesicles that traffic harmful or unwanted cellular macromolecules to the vacuole for recycling. Although autophagosome biogenesis has been extensively studied, autophagosome maturation, i.e., delivery and fusion with the vacuole, remains largely unknown in plants. Here, we have identified an autophagy adaptor, CFS1, that directly interacts with the autophagosome marker ATG8 and localizes on both membranes of the autophagosome. Autophagosomes form normally in Arabidopsis thaliana cfs1 mutants, but their delivery to the vacuole is disrupted. CFS1’s function is evolutionarily conserved in plants, as it also localizes to the autophagosomes and plays a role in autophagic flux in the liverwort Marchantia polymorpha. CFS1 regulates autophagic flux by bridging autophagosomes with the multivesicular body-localized ESCRT-I component VPS23A, leading to the formation of amphisomes. Similar to CFS1-ATG8 interaction, disrupting the CFS1-VPS23A interaction blocks autophagic flux and renders plants sensitive to nitrogen starvation. Altogether, our results reveal a conserved vacuolar sorting hub that regulates autophagic flux in plants. acknowledgement: "We thank Suayip Ustün, Karin Schumacher, Erika Isono, Gerd Juergens, Takashi Ueda, Daniel Hofius, and Liwen Jiang for sharing published materials.\r\nWe acknowledge funding from Austrian Academy of Sciences, Austrian Science Fund (FWF, P 32355, P 34944), Austrian Science Fund (FWF-SFB F79), Vienna Science and Technology\r\nFund (WWTF, LS17-047) to Y. Dagdas; Austrian Academy of Sciences DOC Fellowship to J. Zhao, Marie Curie VIP2 Fellowship to J.C. De La Concepcion and M. Clavel; Hong Kong Research Grant Council (GRF14121019, 14113921, AoE/M-05/12, C4002-17G) to B.-H. Kang. We thank Vienna Biocenter Core Facilities (VBCF) Protein Chemistry, Biooptics, Plant Sciences, Molecular Biology, and Protein Technologies. We thank J. Matthew Watson\r\nand members of the Dagdas lab for the critical reading and editing of the manuscript." article_number: e202203139 article_processing_charge: No article_type: original author: - first_name: Jierui full_name: Zhao, Jierui last_name: Zhao - first_name: Mai Thu full_name: Bui, Mai Thu last_name: Bui - first_name: Juncai full_name: Ma, Juncai last_name: Ma - first_name: Fabian full_name: Künzl, Fabian last_name: Künzl - first_name: Lorenzo full_name: Picchianti, Lorenzo last_name: Picchianti - first_name: Juan Carlos full_name: De La Concepcion, Juan Carlos last_name: De La Concepcion - first_name: Yixuan full_name: Chen, Yixuan last_name: Chen - first_name: Sofia full_name: Petsangouraki, Sofia last_name: Petsangouraki - first_name: Azadeh full_name: Mohseni, Azadeh last_name: Mohseni - first_name: Marta full_name: García-Leon, Marta last_name: García-Leon - first_name: Marta Salas full_name: Gomez, Marta Salas last_name: Gomez - first_name: Caterina full_name: Giannini, Caterina id: e3fdddd5-f6e0-11ea-865d-ca99ee6367f4 last_name: Giannini - first_name: Dubois full_name: Gwennogan, Dubois last_name: Gwennogan - first_name: Roksolana full_name: Kobylinska, Roksolana last_name: Kobylinska - first_name: Marion full_name: Clavel, Marion last_name: Clavel - first_name: Swen full_name: Schellmann, Swen last_name: Schellmann - first_name: Yvon full_name: Jaillais, Yvon last_name: Jaillais - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Byung-Ho full_name: Kang, Byung-Ho last_name: Kang - first_name: Yasin full_name: Dagdas, Yasin last_name: Dagdas citation: ama: Zhao J, Bui MT, Ma J, et al. Plant autophagosomes mature into amphisomes prior to their delivery to the central vacuole. Journal of Cell Biology. 2022;221(12). doi:10.1083/jcb.202203139 apa: Zhao, J., Bui, M. T., Ma, J., Künzl, F., Picchianti, L., De La Concepcion, J. C., … Dagdas, Y. (2022). Plant autophagosomes mature into amphisomes prior to their delivery to the central vacuole. Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.202203139 chicago: Zhao, Jierui, Mai Thu Bui, Juncai Ma, Fabian Künzl, Lorenzo Picchianti, Juan Carlos De La Concepcion, Yixuan Chen, et al. “Plant Autophagosomes Mature into Amphisomes Prior to Their Delivery to the Central Vacuole.” Journal of Cell Biology. Rockefeller University Press, 2022. https://doi.org/10.1083/jcb.202203139. ieee: J. Zhao et al., “Plant autophagosomes mature into amphisomes prior to their delivery to the central vacuole,” Journal of Cell Biology, vol. 221, no. 12. Rockefeller University Press, 2022. ista: Zhao J, Bui MT, Ma J, Künzl F, Picchianti L, De La Concepcion JC, Chen Y, Petsangouraki S, Mohseni A, García-Leon M, Gomez MS, Giannini C, Gwennogan D, Kobylinska R, Clavel M, Schellmann S, Jaillais Y, Friml J, Kang B-H, Dagdas Y. 2022. Plant autophagosomes mature into amphisomes prior to their delivery to the central vacuole. Journal of Cell Biology. 221(12), e202203139. mla: Zhao, Jierui, et al. “Plant Autophagosomes Mature into Amphisomes Prior to Their Delivery to the Central Vacuole.” Journal of Cell Biology, vol. 221, no. 12, e202203139, Rockefeller University Press, 2022, doi:10.1083/jcb.202203139. short: J. Zhao, M.T. Bui, J. Ma, F. Künzl, L. Picchianti, J.C. De La Concepcion, Y. Chen, S. Petsangouraki, A. Mohseni, M. García-Leon, M.S. Gomez, C. Giannini, D. Gwennogan, R. Kobylinska, M. Clavel, S. Schellmann, Y. Jaillais, J. Friml, B.-H. Kang, Y. Dagdas, Journal of Cell Biology 221 (2022). date_created: 2023-01-12T11:57:10Z date_published: 2022-12-01T00:00:00Z date_updated: 2023-08-03T14:20:15Z day: '01' ddc: - '580' department: - _id: JiFr doi: 10.1083/jcb.202203139 external_id: isi: - '000932958800001' pmid: - '36260289' file: - access_level: open_access checksum: 050b5cc4b25e6b94fe3e3cbfe0f5c06b content_type: application/pdf creator: dernst date_created: 2023-01-23T10:30:11Z date_updated: 2023-01-23T10:30:11Z file_id: '12342' file_name: 2022_JCB_Zhao.pdf file_size: 10365777 relation: main_file success: 1 file_date_updated: 2023-01-23T10:30:11Z has_accepted_license: '1' intvolume: ' 221' isi: 1 issue: '12' keyword: - Cell Biology language: - iso: eng month: '12' oa: 1 oa_version: Published Version pmid: 1 publication: Journal of Cell Biology publication_identifier: eissn: - 1540-8140 issn: - 0021-9525 publication_status: published publisher: Rockefeller University Press quality_controlled: '1' scopus_import: '1' status: public title: Plant autophagosomes mature into amphisomes prior to their delivery to the central vacuole 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: 221 year: '2022' ... --- _id: '12130' abstract: - lang: eng text: Germline determination is essential for species survival and evolution in multicellular organisms. In most flowering plants, formation of the female germline is initiated with specification of one megaspore mother cell (MMC) in each ovule; however, the molecular mechanism underlying this key event remains unclear. Here we report that spatially restricted auxin signaling promotes MMC fate in Arabidopsis. Our results show that the microRNA160 (miR160) targeted gene ARF17 (AUXIN RESPONSE FACTOR17) is required for promoting MMC specification by genetically interacting with the SPL/NZZ (SPOROCYTELESS/NOZZLE) gene. Alterations of auxin signaling cause formation of supernumerary MMCs in an ARF17- and SPL/NZZ-dependent manner. Furthermore, miR160 and ARF17 are indispensable for attaining a normal auxin maximum at the ovule apex via modulating the expression domain of PIN1 (PIN-FORMED1) auxin transporter. Our findings elucidate the mechanism by which auxin signaling promotes the acquisition of female germline cell fate in plants. acknowledgement: "We thank A. Cheung,W. Lukowitz, V.Walbot, D.Weijers, and R. Yadegari for critically reading the manuscript; E. Xiong and G. Zhang for preparing some experiments, T. Schuck, J. Gonnering, and P. Engevold for plant care, the Arabidopsis Biological Resource Center (ABRC) for ARF10,ARF16, ARF17, EMS1,MIR160a BAC clones and cDNAs, the SALK_090804 seed, T. Nakagawa for pGBW vectors, Y. Zhao for the YUC1 cDNA, Q. Chen for the pHEE401E vector, R. Yadegari for pAT5G01860::n1GFP, pAT5G45980:n1GFP, pAT5G50490::n1GFP, pAT5G56200:n1GFP vectors, and D.Weijers for the pGreenII KAN SV40-3×GFP and R2D2 vectors, W. Yang for the splmutant, Y. Qin for the pKNU::KNU-VENUS vector and seed, G. Tang for the STTM160/160-48 vector, and L. Colombo for pPIN1::PIN1-GFP spl and pin1-5 seeds. This work was supported by the US National Science Foundation (NSF)-Israel Binational Science Foundation (BSF) research grant to D.Z. (IOS-1322796) and T.A. (2012756). D.Z. also\r\ngratefully acknowledges supports of the Shaw Scientist Award from the Greater Milwaukee Foundation, USDA National Institute of Food and Agriculture (NIFA, 2022-67013-36294), the UWM Discovery and Innovation Grant, the Bradley Catalyst Award from the UWM Research\r\nFoundation, and WiSys and UW System Applied Research Funding Programs." article_number: '6960' article_processing_charge: No article_type: original author: - first_name: Jian full_name: Huang, Jian last_name: Huang - first_name: Lei full_name: Zhao, Lei last_name: Zhao - first_name: Shikha full_name: Malik, Shikha last_name: Malik - first_name: Benjamin R. full_name: Gentile, Benjamin R. last_name: Gentile - first_name: Va full_name: Xiong, Va last_name: Xiong - first_name: Tzahi full_name: Arazi, Tzahi last_name: Arazi - first_name: Heather A. full_name: Owen, Heather A. last_name: Owen - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Dazhong full_name: Zhao, Dazhong last_name: Zhao citation: ama: Huang J, Zhao L, Malik S, et al. Specification of female germline by microRNA orchestrated auxin signaling in Arabidopsis. Nature Communications. 2022;13. doi:10.1038/s41467-022-34723-6 apa: Huang, J., Zhao, L., Malik, S., Gentile, B. R., Xiong, V., Arazi, T., … Zhao, D. (2022). Specification of female germline by microRNA orchestrated auxin signaling in Arabidopsis. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-022-34723-6 chicago: Huang, Jian, Lei Zhao, Shikha Malik, Benjamin R. Gentile, Va Xiong, Tzahi Arazi, Heather A. Owen, Jiří Friml, and Dazhong Zhao. “Specification of Female Germline by MicroRNA Orchestrated Auxin Signaling in Arabidopsis.” Nature Communications. Springer Nature, 2022. https://doi.org/10.1038/s41467-022-34723-6. ieee: J. Huang et al., “Specification of female germline by microRNA orchestrated auxin signaling in Arabidopsis,” Nature Communications, vol. 13. Springer Nature, 2022. ista: Huang J, Zhao L, Malik S, Gentile BR, Xiong V, Arazi T, Owen HA, Friml J, Zhao D. 2022. Specification of female germline by microRNA orchestrated auxin signaling in Arabidopsis. Nature Communications. 13, 6960. mla: Huang, Jian, et al. “Specification of Female Germline by MicroRNA Orchestrated Auxin Signaling in Arabidopsis.” Nature Communications, vol. 13, 6960, Springer Nature, 2022, doi:10.1038/s41467-022-34723-6. short: J. Huang, L. Zhao, S. Malik, B.R. Gentile, V. Xiong, T. Arazi, H.A. Owen, J. Friml, D. Zhao, Nature Communications 13 (2022). date_created: 2023-01-12T12:02:41Z date_published: 2022-11-15T00:00:00Z date_updated: 2023-08-04T08:52:01Z day: '15' ddc: - '580' department: - _id: JiFr doi: 10.1038/s41467-022-34723-6 external_id: isi: - '000884426700001' pmid: - '36379956' file: - access_level: open_access checksum: 233922a7b9507d9d48591e6799e4526e content_type: application/pdf creator: dernst date_created: 2023-01-23T11:17:33Z date_updated: 2023-01-23T11:17:33Z file_id: '12346' file_name: 2022_NatureCommunications_Huang.pdf file_size: 3375249 relation: main_file success: 1 file_date_updated: 2023-01-23T11:17:33Z has_accepted_license: '1' intvolume: ' 13' isi: 1 keyword: - General Physics and Astronomy - General Biochemistry - Genetics and Molecular Biology - General Chemistry - Multidisciplinary language: - iso: eng month: '11' oa: 1 oa_version: Published Version pmid: 1 publication: Nature Communications publication_identifier: issn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Specification of female germline by microRNA orchestrated auxin signaling 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 13 year: '2022' ... --- _id: '12239' abstract: - lang: eng text: Biological systems are the sum of their dynamic three-dimensional (3D) parts. Therefore, it is critical to study biological structures in 3D and at high resolution to gain insights into their physiological functions. Electron microscopy of metal replicas of unroofed cells and isolated organelles has been a key technique to visualize intracellular structures at nanometer resolution. However, many of these methods require specialized equipment and personnel to complete them. Here, we present novel accessible methods to analyze biological structures in unroofed cells and biochemically isolated organelles in 3D and at nanometer resolution, focusing on Arabidopsis clathrin-coated vesicles (CCVs). While CCVs are essential trafficking organelles, their detailed structural information is lacking due to their poor preservation when observed via classical electron microscopy protocols experiments. First, we establish a method to visualize CCVs in unroofed cells using scanning transmission electron microscopy tomography, providing sufficient resolution to define the clathrin coat arrangements. Critically, the samples are prepared directly on electron microscopy grids, removing the requirement to use extremely corrosive acids, thereby enabling the use of this method in any electron microscopy lab. Secondly, we demonstrate that this standardized sample preparation allows the direct comparison of isolated CCV samples with those visualized in cells. Finally, to facilitate the high-throughput and robust screening of metal replicated samples, we provide a deep learning analysis method to screen the “pseudo 3D” morphologies of CCVs imaged with 2D modalities. Collectively, our work establishes accessible ways to examine the 3D structure of biological samples and provide novel insights into the structure of plant CCVs. acknowledged_ssus: - _id: EM-Fac - _id: LifeSc - _id: Bio acknowledgement: A.J. is supported by funding from the Austrian Science Fund I3630B25 (to J.F.). This research was supported by the Scientific Service Units of Institute of Science and Technology Austria (ISTA) through resources provided by the Electron Microscopy Facility, Lab Support Facility, and the Imaging and Optics Facility. We acknowledge Prof. David Robinson (Heidelberg) and Prof. Jan Traas (Lyon) for making us aware of previously published classical on-grid preparation methods. No conflict of interest declared. article_processing_charge: Yes (via OA deal) article_type: original author: - 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: Walter full_name: Kaufmann, Walter id: 3F99E422-F248-11E8-B48F-1D18A9856A87 last_name: Kaufmann orcid: 0000-0001-9735-5315 - 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: Tommaso full_name: Costanzo, Tommaso id: D93824F4-D9BA-11E9-BB12-F207E6697425 last_name: Costanzo orcid: 0000-0001-9732-3815 - first_name: Dana A. full_name: Dahhan, Dana A. last_name: Dahhan - first_name: Sebastian Y. full_name: Bednarek, Sebastian Y. last_name: Bednarek - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Johnson AJ, Kaufmann W, Sommer CM, et al. Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution. Molecular Plant. 2022;15(10):1533-1542. doi:10.1016/j.molp.2022.09.003 apa: Johnson, A. J., Kaufmann, W., Sommer, C. M., Costanzo, T., Dahhan, D. A., Bednarek, S. Y., & Friml, J. (2022). Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution. Molecular Plant. Elsevier. https://doi.org/10.1016/j.molp.2022.09.003 chicago: Johnson, Alexander J, Walter Kaufmann, Christoph M Sommer, Tommaso Costanzo, Dana A. Dahhan, Sebastian Y. Bednarek, and Jiří Friml. “Three-Dimensional Visualization of Planta Clathrin-Coated Vesicles at Ultrastructural Resolution.” Molecular Plant. Elsevier, 2022. https://doi.org/10.1016/j.molp.2022.09.003. ieee: A. J. Johnson et al., “Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution,” Molecular Plant, vol. 15, no. 10. Elsevier, pp. 1533–1542, 2022. ista: Johnson AJ, Kaufmann W, Sommer CM, Costanzo T, Dahhan DA, Bednarek SY, Friml J. 2022. Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution. Molecular Plant. 15(10), 1533–1542. mla: Johnson, Alexander J., et al. “Three-Dimensional Visualization of Planta Clathrin-Coated Vesicles at Ultrastructural Resolution.” Molecular Plant, vol. 15, no. 10, Elsevier, 2022, pp. 1533–42, doi:10.1016/j.molp.2022.09.003. short: A.J. Johnson, W. Kaufmann, C.M. Sommer, T. Costanzo, D.A. Dahhan, S.Y. Bednarek, J. Friml, Molecular Plant 15 (2022) 1533–1542. date_created: 2023-01-16T09:51:49Z date_published: 2022-10-03T00:00:00Z date_updated: 2023-08-04T09:39:24Z day: '03' ddc: - '580' department: - _id: JiFr - _id: EM-Fac - _id: Bio doi: 10.1016/j.molp.2022.09.003 external_id: isi: - '000882769800009' pmid: - '36081349' file: - access_level: open_access checksum: 04d5c12490052d03e4dc4412338a43dd content_type: application/pdf creator: dernst date_created: 2023-01-30T07:46:51Z date_updated: 2023-01-30T07:46:51Z file_id: '12435' file_name: 2022_MolecularPlant_Johnson.pdf file_size: 2307251 relation: main_file success: 1 file_date_updated: 2023-01-30T07:46:51Z has_accepted_license: '1' intvolume: ' 15' isi: 1 issue: '10' keyword: - Plant Science - Molecular Biology language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: 1533-1542 pmid: 1 project: - _id: 26538374-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I03630 name: Molecular mechanisms of endocytic cargo recognition in plants publication: Molecular Plant publication_identifier: issn: - 1674-2052 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution 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: 15 year: '2022' ... --- _id: '11489' abstract: - lang: eng text: Much of plant development depends on cell-to-cell redistribution of the plant hormone auxin, which is facilitated by the plasma membrane (PM) localized PIN FORMED (PIN) proteins. Auxin export activity, developmental roles, subcellular trafficking, and polarity of PINs have been well studied, but their structure remains elusive besides a rough outline that they contain two groups of 5 alpha-helices connected by a large hydrophilic loop (HL). Here, we focus on the PIN1 HL as we could produce it in sufficient quantities for biochemical investigations to provide insights into its secondary structure. Circular dichroism (CD) studies revealed its nature as an intrinsically disordered protein (IDP), manifested by the increase of structure content upon thermal melting. Consistent with IDPs serving as interaction platforms, PIN1 loops homodimerize. PIN1 HL cytoplasmic overexpression in Arabidopsis disrupts early endocytic trafficking of PIN1 and PIN2 and causes defects in the cotyledon vasculature formation. In summary, we demonstrate that PIN1 HL has an intrinsically disordered nature, which must be considered to gain further structural insights. Some secondary structures may form transiently during pairing with known and yet-to-be-discovered interactors. acknowledgement: 'We thank Charo del Genio from Coventry University and Richard Napier from the University of Warwick for helpful discussion concerning protein modeling and inspiration concerning CD spectroscopy, respectively. We thank Jan Hejatko for sharing the published AHP2 construct. We also thank Josef Houser from the core facility BIC CEITEC for valuable assistance, discussions, and ideas relating to CD. We acknowledge the: Core Facility CELLIM of CEITEC supported by the Czech-BioImaging large RI project (LM2018129 funded by MEYS CR), part of the Euro-BioImaging (www.eurobioimaging.eu accessed on 1 January 2016) ALM and medical imaging Node (Brno, CZ), CF Biomolecular Interactions and Crystallization of CIISB, Instruct-CZ Centre, supported by MEYS CR (LM2018127) and European Regional Development Fund-Project “UP CIISB“ (No. CZ.02.1.01/0.0/0.0/18_046/0015974) for their support with obtaining scientific data presented in this paper; Plant Sciences Core Facility of CEITEC Masaryk University for technical support. Open Access Funding by the Austrian Science Fund (FWF).' article_processing_charge: Yes article_type: original author: - first_name: V full_name: Bilanovičová, V last_name: Bilanovičová - first_name: N full_name: Rýdza, N last_name: Rýdza - first_name: L full_name: Koczka, L last_name: Koczka - first_name: M full_name: Hess, M last_name: Hess - first_name: E full_name: Feraru, E last_name: Feraru - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: T full_name: Nodzyński, T last_name: Nodzyński citation: ama: Bilanovičová V, Rýdza N, Koczka L, et al. The hydrophilic loop of Arabidopsis PIN1 auxin efflux carrier harbors hallmarks of an intrinsically disordered protein. International Journal of Molecular Sciences. 2022;23(11):6352. doi:10.3390/ijms23116352 apa: Bilanovičová, V., Rýdza, N., Koczka, L., Hess, M., Feraru, E., Friml, J., & Nodzyński, T. (2022). The hydrophilic loop of Arabidopsis PIN1 auxin efflux carrier harbors hallmarks of an intrinsically disordered protein. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms23116352 chicago: Bilanovičová, V, N Rýdza, L Koczka, M Hess, E Feraru, Jiří Friml, and T Nodzyński. “The Hydrophilic Loop of Arabidopsis PIN1 Auxin Efflux Carrier Harbors Hallmarks of an Intrinsically Disordered Protein.” International Journal of Molecular Sciences. MDPI, 2022. https://doi.org/10.3390/ijms23116352. ieee: V. Bilanovičová et al., “The hydrophilic loop of Arabidopsis PIN1 auxin efflux carrier harbors hallmarks of an intrinsically disordered protein,” International Journal of Molecular Sciences, vol. 23, no. 11. MDPI, p. 6352, 2022. ista: Bilanovičová V, Rýdza N, Koczka L, Hess M, Feraru E, Friml J, Nodzyński T. 2022. The hydrophilic loop of Arabidopsis PIN1 auxin efflux carrier harbors hallmarks of an intrinsically disordered protein. International Journal of Molecular Sciences. 23(11), 6352. mla: Bilanovičová, V., et al. “The Hydrophilic Loop of Arabidopsis PIN1 Auxin Efflux Carrier Harbors Hallmarks of an Intrinsically Disordered Protein.” International Journal of Molecular Sciences, vol. 23, no. 11, MDPI, 2022, p. 6352, doi:10.3390/ijms23116352. short: V. Bilanovičová, N. Rýdza, L. Koczka, M. Hess, E. Feraru, J. Friml, T. Nodzyński, International Journal of Molecular Sciences 23 (2022) 6352. date_created: 2022-07-05T15:14:34Z date_published: 2022-06-06T00:00:00Z date_updated: 2023-08-09T10:13:57Z day: '06' ddc: - '570' department: - _id: JiFr doi: 10.3390/ijms23116352 external_id: isi: - '000808733300001' pmid: - '35683031' file: - access_level: open_access checksum: e997a57a928ec9d51fad8ce824a05935 content_type: application/pdf creator: cchlebak date_created: 2022-07-06T07:36:59Z date_updated: 2022-07-06T07:36:59Z file_id: '11492' file_name: 2022_IntJMolSci_Bilanovicova.pdf file_size: 2324542 relation: main_file success: 1 file_date_updated: 2022-07-06T07:36:59Z has_accepted_license: '1' intvolume: ' 23' isi: 1 issue: '11' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: '6352' pmid: 1 project: - _id: 262EF96E-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P29988 name: RNA-directed DNA methylation in plant development publication: International Journal of Molecular Sciences publication_identifier: issn: - 1422-0067 publication_status: published publisher: MDPI quality_controlled: '1' status: public title: The hydrophilic loop of Arabidopsis PIN1 auxin efflux carrier harbors hallmarks of an intrinsically disordered protein 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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 23 year: '2022' ... --- _id: '12144' abstract: - lang: eng text: The phytohormone auxin is the major coordinative signal in plant development1, mediating transcriptional reprogramming by a well-established canonical signalling pathway. TRANSPORT INHIBITOR RESPONSE 1 (TIR1)/AUXIN-SIGNALING F-BOX (AFB) auxin receptors are F-box subunits of ubiquitin ligase complexes. In response to auxin, they associate with Aux/IAA transcriptional repressors and target them for degradation via ubiquitination2,3. Here we identify adenylate cyclase (AC) activity as an additional function of TIR1/AFB receptors across land plants. Auxin, together with Aux/IAAs, stimulates cAMP production. Three separate mutations in the AC motif of the TIR1 C-terminal region, all of which abolish the AC activity, each render TIR1 ineffective in mediating gravitropism and sustained auxin-induced root growth inhibition, and also affect auxin-induced transcriptional regulation. These results highlight the importance of TIR1/AFB AC activity in canonical auxin signalling. They also identify a unique phytohormone receptor cassette combining F-box and AC motifs, and the role of cAMP as a second messenger in plants. acknowledged_ssus: - _id: LifeSc - _id: Bio acknowledgement: This research was supported by the Lab Support Facility (LSF) and the Imaging and Optics Facility (IOF) of IST Austria. We thank C. Gehring for suggestions and advice; and K. U. Torii and G. Stacey for seeds and plasmids. This project was funded by a European Research Council Advanced Grant (ETAP-742985). M.F.K. and R.N. acknowledge the support of the EU MSCA-IF project CrysPINs (792329). M.K. was supported by the project POWR.03.05.00-00-Z302/17 Universitas Copernicana Thoruniensis in Futuro–IDS “Academia Copernicana”. CIDG acknowledges support from UKRI under Future Leaders Fellowship grant number MR/T020652/1. article_processing_charge: No 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: Mateusz full_name: Kwiatkowski, Mateusz last_name: Kwiatkowski - first_name: Huihuang full_name: Chen, Huihuang id: 83c96512-15b2-11ec-abd3-b7eede36184f last_name: Chen - first_name: Lukas full_name: Hörmayer, Lukas id: 2EEE7A2A-F248-11E8-B48F-1D18A9856A87 last_name: Hörmayer orcid: 0000-0001-8295-2926 - first_name: Scott A full_name: Sinclair, Scott A id: 2D99FE6A-F248-11E8-B48F-1D18A9856A87 last_name: Sinclair orcid: 0000-0002-4566-0593 - first_name: Minxia full_name: Zou, Minxia id: 5c243f41-03f3-11ec-841c-96faf48a7ef9 last_name: Zou - first_name: Charo I. full_name: del Genio, Charo I. last_name: del Genio - first_name: Martin F. full_name: Kubeš, Martin F. last_name: Kubeš - first_name: Richard full_name: Napier, Richard last_name: Napier - first_name: Krzysztof full_name: Jaworski, Krzysztof last_name: Jaworski - 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, Kwiatkowski M, Chen H, et al. Adenylate cyclase activity of TIR1/AFB auxin receptors in plants. Nature. 2022;611(7934):133-138. doi:10.1038/s41586-022-05369-7 apa: Qi, L., Kwiatkowski, M., Chen, H., Hörmayer, L., Sinclair, S. A., Zou, M., … Friml, J. (2022). Adenylate cyclase activity of TIR1/AFB auxin receptors in plants. Nature. Springer Nature. https://doi.org/10.1038/s41586-022-05369-7 chicago: Qi, Linlin, Mateusz Kwiatkowski, Huihuang Chen, Lukas Hörmayer, Scott A Sinclair, Minxia Zou, Charo I. del Genio, et al. “Adenylate Cyclase Activity of TIR1/AFB Auxin Receptors in Plants.” Nature. Springer Nature, 2022. https://doi.org/10.1038/s41586-022-05369-7. ieee: L. Qi et al., “Adenylate cyclase activity of TIR1/AFB auxin receptors in plants,” Nature, vol. 611, no. 7934. Springer Nature, pp. 133–138, 2022. ista: Qi L, Kwiatkowski M, Chen H, Hörmayer L, Sinclair SA, Zou M, del Genio CI, Kubeš MF, Napier R, Jaworski K, Friml J. 2022. Adenylate cyclase activity of TIR1/AFB auxin receptors in plants. Nature. 611(7934), 133–138. mla: Qi, Linlin, et al. “Adenylate Cyclase Activity of TIR1/AFB Auxin Receptors in Plants.” Nature, vol. 611, no. 7934, Springer Nature, 2022, pp. 133–38, doi:10.1038/s41586-022-05369-7. short: L. Qi, M. Kwiatkowski, H. Chen, L. Hörmayer, S.A. Sinclair, M. Zou, C.I. del Genio, M.F. Kubeš, R. Napier, K. Jaworski, J. Friml, Nature 611 (2022) 133–138. date_created: 2023-01-12T12:06:05Z date_published: 2022-11-03T00:00:00Z date_updated: 2023-10-03T11:04:53Z day: '03' department: - _id: JiFr doi: 10.1038/s41586-022-05369-7 ec_funded: 1 external_id: isi: - '000875061600013' pmid: - '36289340' intvolume: ' 611' isi: 1 issue: '7934' language: - iso: eng main_file_link: - open_access: '1' url: http://wrap.warwick.ac.uk/168325/1/WRAP-denylate-cyclase-activity-TIR1-AFB-auxin-receptors-root-growth-22.pdf month: '11' oa: 1 oa_version: Submitted Version page: 133-138 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 publication: Nature publication_identifier: eissn: - 1476-4687 issn: - 0028-0836 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Adenylate cyclase activity of TIR1/AFB auxin receptors in plants type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 611 year: '2022' ... --- _id: '12120' abstract: - lang: eng text: Plant root architecture flexibly adapts to changing nitrate (NO3−) availability in the soil; however, the underlying molecular mechanism of this adaptive development remains under-studied. To explore the regulation of NO3−-mediated root growth, we screened for low-nitrate-resistant mutant (lonr) and identified mutants that were defective in the NAC transcription factor NAC075 (lonr1) as being less sensitive to low NO3− in terms of primary root growth. We show that NAC075 is a mobile transcription factor relocating from the root stele tissues to the endodermis based on NO3− availability. Under low-NO3− availability, the kinase CBL-interacting protein kinase 1 (CIPK1) is activated, and it phosphorylates NAC075, restricting its movement from the stele, which leads to the transcriptional regulation of downstream target WRKY53, consequently leading to adapted root architecture. Our work thus identifies an adaptive mechanism involving translocation of transcription factor based on nutrient availability and leading to cell-specific reprogramming of plant root growth. acknowledgement: The authors are grateful to Jörg Kudla, Ying Miao, Yu Zheng, Gang Li, and Jun Zheng for providing published materials and to Wenkun Zhou and Caifu Jiang for helpful discussions. This work was supported by grants from the National Key Research and Development Program of China (2021YFF1000500), the National Natural Science Foundation of China (32170265 and 32022007), the Beijing Municipal Natural Science Foundation (5192011), and the Chinese Universities Scientific Fund (2022TC153). article_processing_charge: No article_type: original author: - first_name: Huixin full_name: Xiao, Huixin last_name: Xiao - first_name: Yumei full_name: Hu, Yumei last_name: Hu - first_name: Yaping full_name: Wang, Yaping last_name: Wang - first_name: Jinkui full_name: Cheng, Jinkui last_name: Cheng - first_name: Jinyi full_name: Wang, Jinyi last_name: Wang - first_name: Guojingwei full_name: Chen, Guojingwei last_name: Chen - first_name: Qian full_name: Li, Qian last_name: Li - first_name: Shuwei full_name: Wang, Shuwei last_name: Wang - first_name: Yalu full_name: Wang, Yalu last_name: Wang - first_name: Shao-Shuai full_name: Wang, Shao-Shuai last_name: Wang - first_name: Yi full_name: Wang, Yi last_name: Wang - first_name: Wei full_name: Xuan, Wei last_name: Xuan - first_name: Zhen full_name: Li, Zhen last_name: Li - first_name: Yan full_name: Guo, Yan last_name: Guo - first_name: Zhizhong full_name: Gong, Zhizhong last_name: Gong - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Jing full_name: Zhang, Jing last_name: Zhang citation: ama: Xiao H, Hu Y, Wang Y, et al. Nitrate availability controls translocation of the transcription factor NAC075 for cell-type-specific reprogramming of root growth. Developmental Cell. 2022;57(23):2638-2651.e6. doi:10.1016/j.devcel.2022.11.006 apa: Xiao, H., Hu, Y., Wang, Y., Cheng, J., Wang, J., Chen, G., … Zhang, J. (2022). Nitrate availability controls translocation of the transcription factor NAC075 for cell-type-specific reprogramming of root growth. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2022.11.006 chicago: Xiao, Huixin, Yumei Hu, Yaping Wang, Jinkui Cheng, Jinyi Wang, Guojingwei Chen, Qian Li, et al. “Nitrate Availability Controls Translocation of the Transcription Factor NAC075 for Cell-Type-Specific Reprogramming of Root Growth.” Developmental Cell. Elsevier, 2022. https://doi.org/10.1016/j.devcel.2022.11.006. ieee: H. Xiao et al., “Nitrate availability controls translocation of the transcription factor NAC075 for cell-type-specific reprogramming of root growth,” Developmental Cell, vol. 57, no. 23. Elsevier, p. 2638–2651.e6, 2022. ista: Xiao H, Hu Y, Wang Y, Cheng J, Wang J, Chen G, Li Q, Wang S, Wang Y, Wang S-S, Wang Y, Xuan W, Li Z, Guo Y, Gong Z, Friml J, Zhang J. 2022. Nitrate availability controls translocation of the transcription factor NAC075 for cell-type-specific reprogramming of root growth. Developmental Cell. 57(23), 2638–2651.e6. mla: Xiao, Huixin, et al. “Nitrate Availability Controls Translocation of the Transcription Factor NAC075 for Cell-Type-Specific Reprogramming of Root Growth.” Developmental Cell, vol. 57, no. 23, Elsevier, 2022, p. 2638–2651.e6, doi:10.1016/j.devcel.2022.11.006. short: H. Xiao, Y. Hu, Y. Wang, J. Cheng, J. Wang, G. Chen, Q. Li, S. Wang, Y. Wang, S.-S. Wang, Y. Wang, W. Xuan, Z. Li, Y. Guo, Z. Gong, J. Friml, J. Zhang, Developmental Cell 57 (2022) 2638–2651.e6. date_created: 2023-01-12T11:57:00Z date_published: 2022-12-05T00:00:00Z date_updated: 2023-10-04T08:23:20Z day: '05' department: - _id: JiFr doi: 10.1016/j.devcel.2022.11.006 external_id: isi: - '000919603800005' pmid: - '36473460' intvolume: ' 57' isi: 1 issue: '23' keyword: - Developmental Biology - Cell Biology - General Biochemistry - Genetics and Molecular Biology - Molecular Biology language: - iso: eng month: '12' oa_version: None page: 2638-2651.e6 pmid: 1 publication: Developmental Cell publication_identifier: issn: - 1534-5807 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Nitrate availability controls translocation of the transcription factor NAC075 for cell-type-specific reprogramming of root growth type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 57 year: '2022' ... --- _id: '12291' abstract: - lang: eng text: The phytohormone auxin triggers transcriptional reprogramming through a well-characterized perception machinery in the nucleus. By contrast, mechanisms that underlie fast effects of auxin, such as the regulation of ion fluxes, rapid phosphorylation of proteins or auxin feedback on its transport, remain unclear1,2,3. Whether auxin-binding protein 1 (ABP1) is an auxin receptor has been a source of debate for decades1,4. Here we show that a fraction of Arabidopsis thaliana ABP1 is secreted and binds auxin specifically at an acidic pH that is typical of the apoplast. ABP1 and its plasma-membrane-localized partner, transmembrane kinase 1 (TMK1), are required for the auxin-induced ultrafast global phospho-response and for downstream processes that include the activation of H+-ATPase and accelerated cytoplasmic streaming. abp1 and tmk mutants cannot establish auxin-transporting channels and show defective auxin-induced vasculature formation and regeneration. An ABP1(M2X) variant that lacks the capacity to bind auxin is unable to complement these defects in abp1 mutants. These data indicate that ABP1 is the auxin receptor for TMK1-based cell-surface signalling, which mediates the global phospho-response and auxin canalization. acknowledged_ssus: - _id: Bio - _id: EM-Fac - _id: LifeSc acknowledgement: We acknowledge K. Kubiasová for excellent technical assistance, J. Neuhold, A. Lehner and A. Sedivy for technical assistance with protein production and purification at Vienna Biocenter Core Facilities; Creoptix for performing GCI; and the Bioimaging, Electron Microscopy and Life Science Facilities at ISTA, the Plant Sciences Core Facility of CEITEC Masaryk University, the Core Facility CELLIM (MEYS CR, LM2018129 Czech-BioImaging) and J. Sprakel for their assistance. J.F. is grateful to R. Napier for many insightful suggestions and support. We thank all past and present members of the Friml group for their support and for other contributions to this effort to clarify the controversial role of ABP1 over the past seven years. The project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 742985 to J.F. and 833867 to D.W.); the Austrian Science Fund (FWF; P29988 to J.F.); the Netherlands Organization for Scientific Research (NWO; VICI grant 865.14.001 to D.W. and VENI grant VI.Veni.212.003 to A.K.); the Ministry of Education, Science and Technological Development of the Republic of Serbia (contract no. 451-03-68/2022-14/200053 to B.D.Ž.); and the MEXT/JSPS KAKENHI to K.T. (20K06685) and T.K. (20H05687 and 20H05910). article_processing_charge: No article_type: original author: - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - 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: Zuzana full_name: Gelová, Zuzana id: 0AE74790-0E0B-11E9-ABC7-1ACFE5697425 last_name: Gelová orcid: 0000-0003-4783-1752 - 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: Ewa full_name: Mazur, Ewa last_name: Mazur - first_name: Aline full_name: Monzer, Aline id: 2DB5D88C-D7B3-11E9-B8FD-7907E6697425 last_name: Monzer - first_name: Lesia full_name: Rodriguez Solovey, Lesia id: 3922B506-F248-11E8-B48F-1D18A9856A87 last_name: Rodriguez Solovey orcid: 0000-0002-7244-7237 - first_name: Mark full_name: Roosjen, Mark last_name: Roosjen - first_name: Inge full_name: Verstraeten, Inge id: 362BF7FE-F248-11E8-B48F-1D18A9856A87 last_name: Verstraeten orcid: 0000-0001-7241-2328 - first_name: Branka D. full_name: Živanović, Branka D. last_name: Živanović - first_name: Minxia full_name: Zou, Minxia id: 5c243f41-03f3-11ec-841c-96faf48a7ef9 last_name: Zou - first_name: Lukas full_name: Fiedler, Lukas id: 7c417475-8972-11ed-ae7b-8b674ca26986 last_name: Fiedler - first_name: Caterina full_name: Giannini, Caterina id: e3fdddd5-f6e0-11ea-865d-ca99ee6367f4 last_name: Giannini - first_name: Peter full_name: Grones, Peter last_name: Grones - first_name: Mónika full_name: Hrtyan, Mónika id: 45A71A74-F248-11E8-B48F-1D18A9856A87 last_name: Hrtyan - first_name: Walter full_name: Kaufmann, Walter id: 3F99E422-F248-11E8-B48F-1D18A9856A87 last_name: Kaufmann orcid: 0000-0001-9735-5315 - first_name: Andre full_name: Kuhn, Andre last_name: Kuhn - first_name: Madhumitha full_name: Narasimhan, Madhumitha id: 44BF24D0-F248-11E8-B48F-1D18A9856A87 last_name: Narasimhan orcid: 0000-0002-8600-0671 - first_name: Marek full_name: Randuch, Marek id: 6ac4636d-15b2-11ec-abd3-fb8df79972ae last_name: Randuch - first_name: Nikola full_name: Rýdza, Nikola last_name: Rýdza - first_name: Koji full_name: Takahashi, Koji last_name: Takahashi - first_name: Shutang full_name: Tan, Shutang id: 2DE75584-F248-11E8-B48F-1D18A9856A87 last_name: Tan orcid: 0000-0002-0471-8285 - first_name: Anastasiia full_name: Teplova, Anastasiia id: e3736151-106c-11ec-b916-c2558e2762c6 last_name: Teplova - first_name: Toshinori full_name: Kinoshita, Toshinori last_name: Kinoshita - first_name: Dolf full_name: Weijers, Dolf last_name: Weijers - first_name: Hana full_name: Rakusová, Hana last_name: Rakusová citation: ama: Friml J, Gallei MC, Gelová Z, et al. ABP1–TMK auxin perception for global phosphorylation and auxin canalization. Nature. 2022;609(7927):575-581. doi:10.1038/s41586-022-05187-x apa: Friml, J., Gallei, M. C., Gelová, Z., Johnson, A. J., Mazur, E., Monzer, A., … Rakusová, H. (2022). ABP1–TMK auxin perception for global phosphorylation and auxin canalization. Nature. Springer Nature. https://doi.org/10.1038/s41586-022-05187-x chicago: Friml, Jiří, Michelle C Gallei, Zuzana Gelová, Alexander J Johnson, Ewa Mazur, Aline Monzer, Lesia Rodriguez Solovey, et al. “ABP1–TMK Auxin Perception for Global Phosphorylation and Auxin Canalization.” Nature. Springer Nature, 2022. https://doi.org/10.1038/s41586-022-05187-x. ieee: J. Friml et al., “ABP1–TMK auxin perception for global phosphorylation and auxin canalization,” Nature, vol. 609, no. 7927. Springer Nature, pp. 575–581, 2022. ista: Friml J, Gallei MC, Gelová Z, Johnson AJ, Mazur E, Monzer A, Rodriguez Solovey L, Roosjen M, Verstraeten I, Živanović BD, Zou M, Fiedler L, Giannini C, Grones P, Hrtyan M, Kaufmann W, Kuhn A, Narasimhan M, Randuch M, Rýdza N, Takahashi K, Tan S, Teplova A, Kinoshita T, Weijers D, Rakusová H. 2022. ABP1–TMK auxin perception for global phosphorylation and auxin canalization. Nature. 609(7927), 575–581. mla: Friml, Jiří, et al. “ABP1–TMK Auxin Perception for Global Phosphorylation and Auxin Canalization.” Nature, vol. 609, no. 7927, Springer Nature, 2022, pp. 575–81, doi:10.1038/s41586-022-05187-x. short: J. Friml, M.C. Gallei, Z. Gelová, A.J. Johnson, E. Mazur, A. Monzer, L. Rodriguez Solovey, M. Roosjen, I. Verstraeten, B.D. Živanović, M. Zou, L. Fiedler, C. Giannini, P. Grones, M. Hrtyan, W. Kaufmann, A. Kuhn, M. Narasimhan, M. Randuch, N. Rýdza, K. Takahashi, S. Tan, A. Teplova, T. Kinoshita, D. Weijers, H. Rakusová, Nature 609 (2022) 575–581. date_created: 2023-01-16T10:04:48Z date_published: 2022-09-15T00:00:00Z date_updated: 2023-11-07T08:16:09Z day: '15' ddc: - '580' department: - _id: JiFr - _id: GradSch - _id: EvBe - _id: EM-Fac doi: 10.1038/s41586-022-05187-x ec_funded: 1 external_id: isi: - '000851357500002' pmid: - '36071161' file: - access_level: open_access checksum: a6055c606aefb900bf62ae3e7d15f921 content_type: application/pdf creator: amally date_created: 2023-11-02T17:12:37Z date_updated: 2023-11-02T17:12:37Z file_id: '14483' file_name: Friml Nature 2022_merged.pdf file_size: 79774945 relation: main_file success: 1 file_date_updated: 2023-11-02T17:12:37Z has_accepted_license: '1' intvolume: ' 609' isi: 1 issue: '7927' language: - iso: eng month: '09' oa: 1 oa_version: Submitted Version page: 575-581 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: Nature publication_identifier: eissn: - 1476-4687 issn: - 0028-0836 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: ABP1–TMK auxin perception for global phosphorylation and auxin canalization type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 609 year: '2022' ... --- _id: '11626' abstract: - lang: eng text: Plant growth and development is well known to be both, flexible and dynamic. The high capacity for post-embryonic organ formation and tissue regeneration requires tightly regulated intercellular communication and coordinated tissue polarization. One of the most important drivers for patterning and polarity in plant development is the phytohormone auxin. Auxin has the unique characteristic to establish polarized channels for its own active directional cell to cell transport. This fascinating phenomenon is called auxin canalization. Those auxin transport channels are characterized by the expression and polar, subcellular localization of PIN auxin efflux carriers. PIN proteins have the ability to dynamically change their localization and auxin itself can affect this by interfering with trafficking. Most of the underlying molecular mechanisms of canalization still remain enigmatic. What is known so far is that canonical auxin signaling is indispensable but also other non-canonical signaling components are thought to play a role. In order to shed light into the mysteries auf auxin canalization this study revisits the branches of auxin signaling in detail. Further a new auxin analogue, PISA, is developed which triggers auxin-like responses but does not directly activate canonical transcriptional auxin signaling. We revisit the direct auxin effect on PIN trafficking where we found that, contradictory to previous observations, auxin is very specifically promoting endocytosis of PIN2 but has no overall effect on endocytosis. Further, we evaluate which cellular processes related to PIN subcellular dynamics are involved in the establishment of auxin conducting channels and the formation of vascular tissue. We are re-evaluating the function of AUXIN BINDING PROTEIN 1 (ABP1) and provide a comprehensive picture about its developmental phneotypes and involvement in auxin signaling and canalization. Lastly, we are focusing on the crosstalk between the hormone strigolactone (SL) and auxin and found that SL is interfering with essentially all processes involved in auxin canalization in a non-transcriptional manner. Lastly we identify a new way of SL perception and signaling which is emanating from mitochondria, is independent of canonical SL signaling and is modulating primary root growth. alternative_title: - ISTA Thesis 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 citation: ama: Gallei MC. Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana. 2022. doi:10.15479/at:ista:11626 apa: Gallei, M. C. (2022). Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11626 chicago: Gallei, Michelle C. “Auxin and Strigolactone Non-Canonical Signaling Regulating Development in Arabidopsis Thaliana.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11626. ieee: M. C. Gallei, “Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana,” Institute of Science and Technology Austria, 2022. ista: Gallei MC. 2022. Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana. Institute of Science and Technology Austria. mla: Gallei, Michelle C. Auxin and Strigolactone Non-Canonical Signaling Regulating Development in Arabidopsis Thaliana. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11626. short: M.C. Gallei, Auxin and Strigolactone Non-Canonical Signaling Regulating Development in Arabidopsis Thaliana, Institute of Science and Technology Austria, 2022. date_created: 2022-07-20T11:21:53Z date_published: 2022-07-20T00:00:00Z date_updated: 2023-11-07T08:20:13Z day: '20' ddc: - '575' degree_awarded: PhD department: - _id: GradSch - _id: JiFr doi: 10.15479/at:ista:11626 ec_funded: 1 file: - access_level: open_access checksum: bd7ac35403cf5b4b2607287d2a104b3a content_type: application/pdf creator: mgallei date_created: 2022-07-25T09:08:47Z date_updated: 2022-07-25T09:08:47Z file_id: '11645' file_name: Thesis_Gallei.pdf file_size: 9730864 relation: main_file - access_level: closed checksum: a9e54fe5471ba25dc13c2150c1b8ccbb content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: mgallei date_created: 2022-07-25T09:09:09Z date_updated: 2022-07-25T09:39:58Z file_id: '11646' file_name: Thesis_Gallei_source.docx file_size: 19560720 relation: source_file - access_level: closed checksum: 3994f7f20058941b5bb8a16886b21e71 content_type: application/pdf creator: mgallei date_created: 2022-07-25T09:09:32Z date_updated: 2022-07-25T09:39:58Z description: This is the print version of the thesis including the full appendix file_id: '11647' file_name: Thesis_Gallei_to_print.pdf file_size: 24542837 relation: source_file - access_level: open_access checksum: f24acd3c0d864f4c6676e8b0d7bfa76b content_type: application/pdf creator: mgallei date_created: 2022-07-25T11:48:45Z date_updated: 2022-07-25T11:48:45Z file_id: '11650' file_name: Thesis_Gallei_Appendix.pdf file_size: 15435966 relation: main_file file_date_updated: 2022-07-25T11:48:45Z has_accepted_license: '1' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: '248' project: - _id: 261099A6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742985' name: Tracing Evolution of Auxin Transport and Polarity in Plants publication_identifier: isbn: - 978-3-99078-019-0 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '8931' relation: part_of_dissertation status: public - id: '9287' relation: part_of_dissertation status: public - id: '7142' relation: part_of_dissertation status: public - id: '7465' relation: part_of_dissertation status: public - id: '8138' relation: part_of_dissertation status: public - id: '6260' relation: part_of_dissertation status: public - id: '10411' relation: part_of_dissertation status: public status: public supervisor: - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 - first_name: Eilon full_name: Shani, Eilon last_name: Shani title: Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2022' ... --- _id: '10411' abstract: - lang: eng text: The phytohormone auxin is the major growth regulator governing tropic responses including gravitropism. Auxin build-up at the lower side of stimulated shoots promotes cell expansion, whereas in roots it inhibits growth, leading to upward shoot bending and downward root bending, respectively. Yet it remains an enigma how the same signal can trigger such opposite cellular responses. In this review, we discuss several recent unexpected insights into the mechanisms underlying auxin regulation of growth, challenging several existing models. We focus on the divergent mechanisms of apoplastic pH regulation in shoots and roots revisiting the classical Acid Growth Theory and discuss coordinated involvement of multiple auxin signaling pathways. From this emerges a more comprehensive, updated picture how auxin regulates growth. acknowledgement: The authors thank Alexandra Mally for editing the text. This work was supported by the Austrian Science Fund (FWF) I 3630-B25 to Jiří Friml and the DOC Fellowship of the Austrian Academy of Sciences to Lanxin Li. All figures were created with BioRender.com. article_processing_charge: No article_type: original author: - first_name: Lanxin full_name: Li, Lanxin id: 367EF8FA-F248-11E8-B48F-1D18A9856A87 last_name: Li orcid: 0000-0002-5607-272X - 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: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: 'Li L, Gallei MC, Friml J. Bending to auxin: Fast acid growth for tropisms. Trends in Plant Science. 2022;27(5):440-449. doi:10.1016/j.tplants.2021.11.006' apa: 'Li, L., Gallei, M. C., & Friml, J. (2022). Bending to auxin: Fast acid growth for tropisms. Trends in Plant Science. Cell Press. https://doi.org/10.1016/j.tplants.2021.11.006' chicago: 'Li, Lanxin, Michelle C Gallei, and Jiří Friml. “Bending to Auxin: Fast Acid Growth for Tropisms.” Trends in Plant Science. Cell Press, 2022. https://doi.org/10.1016/j.tplants.2021.11.006.' ieee: 'L. Li, M. C. Gallei, and J. Friml, “Bending to auxin: Fast acid growth for tropisms,” Trends in Plant Science, vol. 27, no. 5. Cell Press, pp. 440–449, 2022.' ista: 'Li L, Gallei MC, Friml J. 2022. Bending to auxin: Fast acid growth for tropisms. Trends in Plant Science. 27(5), 440–449.' mla: 'Li, Lanxin, et al. “Bending to Auxin: Fast Acid Growth for Tropisms.” Trends in Plant Science, vol. 27, no. 5, Cell Press, 2022, pp. 440–49, doi:10.1016/j.tplants.2021.11.006.' short: L. Li, M.C. Gallei, J. Friml, Trends in Plant Science 27 (2022) 440–449. date_created: 2021-12-05T23:01:43Z date_published: 2022-05-01T00:00:00Z date_updated: 2023-11-07T08:20:14Z day: '01' ddc: - '580' department: - _id: JiFr doi: 10.1016/j.tplants.2021.11.006 external_id: isi: - '000793707900005' pmid: - '34848141' file: - access_level: open_access checksum: 3d94980ee1ff6bec100dd813f6a921a6 content_type: application/pdf creator: amally date_created: 2023-11-02T17:00:03Z date_updated: 2023-11-02T17:00:03Z file_id: '14480' file_name: Li Plants 2021_accepted.pdf file_size: 805779 relation: main_file success: 1 file_date_updated: 2023-11-02T17:00:03Z has_accepted_license: '1' intvolume: ' 27' isi: 1 issue: '5' language: - iso: eng month: '05' oa: 1 oa_version: Submitted Version page: 440-449 pmid: 1 project: - _id: 26538374-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I03630 name: Molecular mechanisms of endocytic cargo recognition in plants - _id: 26B4D67E-B435-11E9-9278-68D0E5697425 grant_number: '25351' name: 'A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root' publication: Trends in Plant Science publication_identifier: issn: - 1360-1385 publication_status: published publisher: Cell Press quality_controlled: '1' related_material: record: - id: '11626' relation: dissertation_contains status: public scopus_import: '1' status: public title: 'Bending to auxin: Fast acid growth for tropisms' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 27 year: '2022' ... --- _id: '13240' abstract: - lang: eng text: Ustilago maydis is a biotrophic phytopathogenic fungus that causes corn smut disease. As a well-established model system, U. maydis is genetically fully accessible with large omics datasets available and subject to various biological questions ranging from DNA-repair, RNA-transport, and protein secretion to disease biology. For many genetic approaches, tight control of transgene regulation is important. Here we established an optimised version of the Tetracycline-ON (TetON) system for U. maydis. We demonstrate the Tetracycline concentration-dependent expression of fluorescent protein transgenes and the system’s suitability for the induced expression of the toxic protein BCL2 Associated X-1 (Bax1). The Golden Gate compatible vector system contains a native minimal promoter from the mating factor a-1 encoding gene, mfa with ten copies of the tet-regulated operator (tetO) and a codon optimised Tet-repressor (tetR*) which is translationally fused to the native transcriptional corepressor Mql1 (UMAG_05501). The metabolism-independent transcriptional regulator system is functional both, in liquid culture as well as on solid media in the presence of the inducer and can become a useful tool for toxin-antitoxin studies, identification of antifungal proteins, and to study functions of toxic gene products in Ustilago maydis. acknowledgement: "The research leading to these results received funding from the European Research Council under the European Union’s Seventh Framework Programme ERC-2013-STG (grant agreement: 335691), the Austrian Science Fund (I 3033-B22), the Austrian Academy of Sciences, and the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany's Excellence Strategy EXC-2070-390732324 (PhenoRob) and DFG grant (DJ 64/5-1).\r\nWe would like to thank the GMI/IMBA/IMP core facilities for their excellent technical support. We would like to acknowledge Dr. Sinéad A. O’Sullivan from DZNE, University of Bonn for providing anti-GFP antibodies. The authors are thankful to the Excellence University of Bonn for providing infrastructure and instrumentation facilities at the INRES-Plant Pathology department." article_number: '1029114' article_processing_charge: Yes article_type: original author: - first_name: Kishor D. full_name: Ingole, Kishor D. last_name: Ingole - first_name: Nithya full_name: Nagarajan, Nithya last_name: Nagarajan - first_name: Simon full_name: Uhse, Simon last_name: Uhse - first_name: Caterina full_name: Giannini, Caterina id: e3fdddd5-f6e0-11ea-865d-ca99ee6367f4 last_name: Giannini - first_name: Armin full_name: Djamei, Armin last_name: Djamei citation: ama: Ingole KD, Nagarajan N, Uhse S, Giannini C, Djamei A. Tetracycline-controlled (TetON) gene expression system for the smut fungus Ustilago maydis. Frontiers in Fungal Biology. 2022;3. doi:10.3389/ffunb.2022.1029114 apa: Ingole, K. D., Nagarajan, N., Uhse, S., Giannini, C., & Djamei, A. (2022). Tetracycline-controlled (TetON) gene expression system for the smut fungus Ustilago maydis. Frontiers in Fungal Biology. Frontiers Media. https://doi.org/10.3389/ffunb.2022.1029114 chicago: Ingole, Kishor D., Nithya Nagarajan, Simon Uhse, Caterina Giannini, and Armin Djamei. “Tetracycline-Controlled (TetON) Gene Expression System for the Smut Fungus Ustilago Maydis.” Frontiers in Fungal Biology. Frontiers Media, 2022. https://doi.org/10.3389/ffunb.2022.1029114. ieee: K. D. Ingole, N. Nagarajan, S. Uhse, C. Giannini, and A. Djamei, “Tetracycline-controlled (TetON) gene expression system for the smut fungus Ustilago maydis,” Frontiers in Fungal Biology, vol. 3. Frontiers Media, 2022. ista: Ingole KD, Nagarajan N, Uhse S, Giannini C, Djamei A. 2022. Tetracycline-controlled (TetON) gene expression system for the smut fungus Ustilago maydis. Frontiers in Fungal Biology. 3, 1029114. mla: Ingole, Kishor D., et al. “Tetracycline-Controlled (TetON) Gene Expression System for the Smut Fungus Ustilago Maydis.” Frontiers in Fungal Biology, vol. 3, 1029114, Frontiers Media, 2022, doi:10.3389/ffunb.2022.1029114. short: K.D. Ingole, N. Nagarajan, S. Uhse, C. Giannini, A. Djamei, Frontiers in Fungal Biology 3 (2022). date_created: 2023-07-16T22:01:12Z date_published: 2022-10-19T00:00:00Z date_updated: 2024-03-06T14:01:57Z day: '19' ddc: - '579' department: - _id: JiFr doi: 10.3389/ffunb.2022.1029114 file: - access_level: open_access checksum: 2254e0119c0749d6f7237084fefcece6 content_type: application/pdf creator: dernst date_created: 2023-07-17T11:46:34Z date_updated: 2023-07-17T11:46:34Z file_id: '13242' file_name: 2023_FrontiersFungalBio_Ingole.pdf file_size: 27966699 relation: main_file success: 1 file_date_updated: 2023-07-17T11:46:34Z has_accepted_license: '1' intvolume: ' 3' language: - iso: eng month: '10' oa: 1 oa_version: Published Version publication: Frontiers in Fungal Biology publication_identifier: eissn: - 2673-6128 publication_status: published publisher: Frontiers Media quality_controlled: '1' scopus_import: '1' status: public title: Tetracycline-controlled (TetON) gene expression system for the smut fungus Ustilago maydis 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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 3 year: '2022' ... --- _id: '10267' abstract: - lang: eng text: Tropisms are among the most important growth responses for plant adaptation to the surrounding environment. One of the most common tropisms is root gravitropism. Root gravitropism enables the plant to anchor securely to the soil enabling the absorption of water and nutrients. Most of the knowledge related to the plant gravitropism has been acquired from the flowering plants, due to limited research in non-seed plants. Limited research on non-seed plants is due in large part to the lack of standard research methods. Here, we describe the experimental methods to evaluate gravitropism in representative non-seed plant species, including the non-vascular plant moss Physcomitrium patens, the early diverging extant vascular plant lycophyte Selaginella moellendorffii and fern Ceratopteris richardii. In addition, we introduce the methods used for statistical analysis of the root gravitropism in non-seed plant species. acknowledgement: The Ceratopteris richardii spores were obtained from the lab of Jo Ann Banks at Purdue University. This work was supported by funding from the European Union’s Horizon 2020 research and innovation program (ERC grant agreement number 742985), Austrian Science Fund (FWF, grant number I 3630-B25), IST Fellow program and DOC Fellowship of the Austrian Academy of Sciences. alternative_title: - Methods in Molecular Biology article_processing_charge: No author: - first_name: Yuzhou full_name: Zhang, Yuzhou id: 3B6137F2-F248-11E8-B48F-1D18A9856A87 last_name: Zhang orcid: 0000-0003-2627-6956 - first_name: Lanxin full_name: Li, Lanxin id: 367EF8FA-F248-11E8-B48F-1D18A9856A87 last_name: Li orcid: 0000-0002-5607-272X - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: 'Zhang Y, Li L, Friml J. Evaluation of gravitropism in non-seed plants. In: Blancaflor EB, ed. Plant Gravitropism. Vol 2368. MIMB. Springer Nature; 2021:43-51. doi:10.1007/978-1-0716-1677-2_2' apa: Zhang, Y., Li, L., & Friml, J. (2021). Evaluation of gravitropism in non-seed plants. In E. B. Blancaflor (Ed.), Plant Gravitropism (Vol. 2368, pp. 43–51). Springer Nature. https://doi.org/10.1007/978-1-0716-1677-2_2 chicago: Zhang, Yuzhou, Lanxin Li, and Jiří Friml. “Evaluation of Gravitropism in Non-Seed Plants.” In Plant Gravitropism, edited by Elison B Blancaflor, 2368:43–51. MIMB. Springer Nature, 2021. https://doi.org/10.1007/978-1-0716-1677-2_2. ieee: Y. Zhang, L. Li, and J. Friml, “Evaluation of gravitropism in non-seed plants,” in Plant Gravitropism, vol. 2368, E. B. Blancaflor, Ed. Springer Nature, 2021, pp. 43–51. ista: 'Zhang Y, Li L, Friml J. 2021.Evaluation of gravitropism in non-seed plants. In: Plant Gravitropism. Methods in Molecular Biology, vol. 2368, 43–51.' mla: Zhang, Yuzhou, et al. “Evaluation of Gravitropism in Non-Seed Plants.” Plant Gravitropism, edited by Elison B Blancaflor, vol. 2368, Springer Nature, 2021, pp. 43–51, doi:10.1007/978-1-0716-1677-2_2. short: Y. Zhang, L. Li, J. Friml, in:, E.B. Blancaflor (Ed.), Plant Gravitropism, Springer Nature, 2021, pp. 43–51. date_created: 2021-11-11T09:26:10Z date_published: 2021-10-14T00:00:00Z date_updated: 2022-08-26T09:13:00Z day: '14' department: - _id: JiFr doi: 10.1007/978-1-0716-1677-2_2 ec_funded: 1 editor: - first_name: Elison B full_name: Blancaflor, Elison B last_name: Blancaflor external_id: pmid: - '34647246' intvolume: ' 2368' language: - iso: eng month: '10' oa_version: None page: 43-51 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: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: 26538374-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I03630 name: Molecular mechanisms of endocytic cargo recognition in plants publication: Plant Gravitropism publication_identifier: eisbn: - 978-1-0716-1677-2 isbn: - 978-1-0716-1676-5 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' series_title: MIMB status: public title: Evaluation of gravitropism in non-seed plants type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2368 year: '2021' ...