[{"oa":1,"file_date_updated":"2025-12-30T07:28:09Z","_id":"19601","author":[{"first_name":"Martijn","last_name":"De Roij","full_name":"De Roij, Martijn"},{"first_name":"Jorge","full_name":"Hernández García, Jorge","last_name":"Hernández García"},{"full_name":"Das, Shubhajit","last_name":"Das","first_name":"Shubhajit","id":"b08969a4-f2a5-11ed-b6c4-ff0f10b7d0be"},{"last_name":"Borst","full_name":"Borst, Jan Willem","first_name":"Jan Willem"},{"full_name":"Weijers, Dolf","last_name":"Weijers","first_name":"Dolf"}],"has_accepted_license":"1","ddc":["580"],"publisher":"Springer Nature","publication_status":"published","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_type":"hybrid","day":"11","external_id":{"pmid":["40216983"]},"date_updated":"2025-12-30T07:28:49Z","page":"717-724","date_created":"2025-04-20T22:01:28Z","article_type":"letter_note","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"oa_version":"Published Version","file":[{"file_size":7062474,"date_updated":"2025-12-30T07:28:09Z","file_name":"2025_NaturePlants_deRoij.pdf","content_type":"application/pdf","success":1,"checksum":"8225c1899bb2f39f9a1707cc0697a052","relation":"main_file","date_created":"2025-12-30T07:28:09Z","creator":"dernst","file_id":"20882","access_level":"open_access"}],"OA_place":"publisher","citation":{"ama":"De Roij M, Hernández García J, Das S, Borst JW, Weijers D. ARF degradation defines a deeply conserved step in auxin response. <i>Nature Plants</i>. 2025;11:717-724. doi:<a href=\"https://doi.org/10.1038/s41477-025-01975-1\">10.1038/s41477-025-01975-1</a>","short":"M. De Roij, J. Hernández García, S. Das, J.W. Borst, D. Weijers, Nature Plants 11 (2025) 717–724.","ista":"De Roij M, Hernández García J, Das S, Borst JW, Weijers D. 2025. ARF degradation defines a deeply conserved step in auxin response. Nature Plants. 11, 717–724.","ieee":"M. De Roij, J. Hernández García, S. Das, J. W. Borst, and D. Weijers, “ARF degradation defines a deeply conserved step in auxin response,” <i>Nature Plants</i>, vol. 11. Springer Nature, pp. 717–724, 2025.","mla":"De Roij, Martijn, et al. “ARF Degradation Defines a Deeply Conserved Step in Auxin Response.” <i>Nature Plants</i>, vol. 11, Springer Nature, 2025, pp. 717–24, doi:<a href=\"https://doi.org/10.1038/s41477-025-01975-1\">10.1038/s41477-025-01975-1</a>.","apa":"De Roij, M., Hernández García, J., Das, S., Borst, J. W., &#38; Weijers, D. (2025). ARF degradation defines a deeply conserved step in auxin response. <i>Nature Plants</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41477-025-01975-1\">https://doi.org/10.1038/s41477-025-01975-1</a>","chicago":"De Roij, Martijn, Jorge Hernández García, Shubhajit Das, Jan Willem Borst, and Dolf Weijers. “ARF Degradation Defines a Deeply Conserved Step in Auxin Response.” <i>Nature Plants</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41477-025-01975-1\">https://doi.org/10.1038/s41477-025-01975-1</a>."},"status":"public","article_processing_charge":"Yes (in subscription journal)","volume":11,"abstract":[{"lang":"eng","text":"In land plants, the signalling molecule auxin profoundly controls growth and development, chiefly through a transcriptional response system. The auxin response is mediated by modulating the activity of DNA-binding auxin response factor (ARF) proteins. The concentrations and stoichiometry of the competing A- and B-class ARFs define cells’ capacity for auxin response. In the minimal auxin response system of the liverwort Marchantia polymorpha, both A- and B-ARFs are unstable, but the underlying mechanisms, developmental relevance and evolutionary history of this instability are unknown. Here we identify a minimal motif that is necessary for MpARF2 (B-class) degradation and show that it is critical for development and the auxin response. Through comparative analysis and motif swaps among all ARF classes in extant algae and land plants, we infer that the emergence of ARF instability probably occurred in the ancestor of the A- and B-ARF clades and, therefore, preceded or coincided with the origin of the auxin response system."}],"month":"04","department":[{"_id":"JiFr"}],"acknowledgement":"We thank S. Woudenberg, S. Valk and J. Rienstra for help and advice, A. Kuhn for comments on the paper and M. Prigge and M. Estelle for helpful discussions. This work was supported by a grant from Netherlands Organization for Scientific Research (NWO; OCENW.M20.031 to J.W.B.), a Marie Skłodowska-Curie Individual Fellowship (H2020-MSCA-IF-2020 contract number to J.H.G.) and a research grant from the Human Frontiers Research Program (HFSP; grant RGP0015/2022 to D.W.).","year":"2025","intvolume":"        11","title":"ARF degradation defines a deeply conserved step in auxin response","publication_identifier":{"eissn":["2055-0278"]},"pmid":1,"doi":"10.1038/s41477-025-01975-1","scopus_import":"1","publication":"Nature Plants","language":[{"iso":"eng"}],"date_published":"2025-04-11T00:00:00Z","type":"journal_article","license":"https://creativecommons.org/licenses/by/4.0/"},{"oa_version":"Published Version","file":[{"file_name":"2024_PlantCommunications_Das.pdf","file_size":4970540,"date_updated":"2025-01-09T12:25:32Z","content_type":"application/pdf","success":1,"checksum":"38cabc1042ac7fb70e6c4c510eba88fc","relation":"main_file","date_created":"2025-01-09T12:25:32Z","creator":"dernst","file_id":"18811","access_level":"open_access"}],"OA_place":"publisher","citation":{"ama":"Das S, De Roij M, Bellows S, et al. Quantitative imaging reveals the role of MpARF proteasomal degradation during gemma germination. <i>Plant Communications</i>. 2024;5(11). doi:<a href=\"https://doi.org/10.1016/j.xplc.2024.101039\">10.1016/j.xplc.2024.101039</a>","short":"S. Das, M. De Roij, S. Bellows, M.D. Alvarez, S. Mutte, W. Kohlen, E. Farcot, D. Weijers, J.W. Borst, Plant Communications 5 (2024).","mla":"Das, Shubhajit, et al. “Quantitative Imaging Reveals the Role of MpARF Proteasomal Degradation during Gemma Germination.” <i>Plant Communications</i>, vol. 5, no. 11, 101039, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.xplc.2024.101039\">10.1016/j.xplc.2024.101039</a>.","apa":"Das, S., De Roij, M., Bellows, S., Alvarez, M. D., Mutte, S., Kohlen, W., … Borst, J. W. (2024). Quantitative imaging reveals the role of MpARF proteasomal degradation during gemma germination. <i>Plant Communications</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.xplc.2024.101039\">https://doi.org/10.1016/j.xplc.2024.101039</a>","chicago":"Das, Shubhajit, Martijn De Roij, Simon Bellows, Melissa Dipp Alvarez, Sumanth Mutte, Wouter Kohlen, Etienne Farcot, Dolf Weijers, and Jan Willem Borst. “Quantitative Imaging Reveals the Role of MpARF Proteasomal Degradation during Gemma Germination.” <i>Plant Communications</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.xplc.2024.101039\">https://doi.org/10.1016/j.xplc.2024.101039</a>.","ista":"Das S, De Roij M, Bellows S, Alvarez MD, Mutte S, Kohlen W, Farcot E, Weijers D, Borst JW. 2024. Quantitative imaging reveals the role of MpARF proteasomal degradation during gemma germination. Plant Communications. 5(11), 101039.","ieee":"S. Das <i>et al.</i>, “Quantitative imaging reveals the role of MpARF proteasomal degradation during gemma germination,” <i>Plant Communications</i>, vol. 5, no. 11. Elsevier, 2024."},"date_created":"2024-08-18T22:01:04Z","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_processing_charge":"Yes","volume":5,"abstract":[{"lang":"eng","text":"The auxin signaling molecule controls a variety of growth and developmental processes in land plants. Auxin regulates gene expression through a nuclear auxin signaling pathway (NAP) consisting of the ubiquitin ligase auxin receptor TIR1/AFB, its Aux/IAA degradation substrate, and DNA-binding ARF transcription factors. Although extensive qualitative understanding of the pathway and its interactions has been obtained, mostly by studying the flowering plant Arabidopsis thaliana, it remains unknown how these translate to quantitative system behavior in vivo, a problem that is confounded by the large NAP gene families in most species. Here, we used the minimal NAP of the liverwort Marchantia polymorpha to quantitatively map NAP protein accumulation and dynamics in vivo through the use of knockin fluorescent fusion proteins. Beyond revealing the dynamic native accumulation profile of the entire NAP protein network, we discovered that the two central ARFs, MpARF1 and MpARF2, are proteasomally degraded. This auxin-independent degradation tunes ARF protein stoichiometry to favor gene activation, thereby reprogramming auxin response during the developmental progression. Thus, quantitative analysis of the entire NAP has enabled us to identify ARF degradation and the stoichiometries of activator and repressor ARFs as a potential mechanism for controlling gemma germination."}],"month":"11","department":[{"_id":"JiFr"}],"status":"public","title":"Quantitative imaging reveals the role of MpARF proteasomal degradation during gemma germination","pmid":1,"article_number":"101039","publication_identifier":{"eissn":["2590-3462"]},"issue":"11","acknowledgement":"We are grateful to Iris Nieuwland and Neri van Laar for experimental support. No conflict of interest declared.\r\nThis work was supported by the Netherlands Organisation for Scientific Research, the Netherlands (grants ALWOP.402 and OCENW.M20.031 to J.W.B.) and the Human Frontiers Research Program (grant RGP0015/2022 to D.W.).","year":"2024","intvolume":"         5","scopus_import":"1","language":[{"iso":"eng"}],"publication":"Plant Communications","date_published":"2024-11-11T00:00:00Z","type":"journal_article","doi":"10.1016/j.xplc.2024.101039","author":[{"last_name":"Das","full_name":"Das, Shubhajit","id":"b08969a4-f2a5-11ed-b6c4-ff0f10b7d0be","first_name":"Shubhajit"},{"last_name":"De Roij","full_name":"De Roij, Martijn","first_name":"Martijn"},{"first_name":"Simon","last_name":"Bellows","full_name":"Bellows, Simon"},{"full_name":"Alvarez, Melissa Dipp","last_name":"Alvarez","first_name":"Melissa Dipp"},{"first_name":"Sumanth","last_name":"Mutte","full_name":"Mutte, Sumanth"},{"first_name":"Wouter","full_name":"Kohlen, Wouter","last_name":"Kohlen"},{"first_name":"Etienne","last_name":"Farcot","full_name":"Farcot, Etienne"},{"full_name":"Weijers, Dolf","last_name":"Weijers","first_name":"Dolf"},{"full_name":"Borst, Jan Willem","last_name":"Borst","first_name":"Jan Willem"}],"_id":"17436","has_accepted_license":"1","ddc":["580"],"publisher":"Elsevier","oa":1,"file_date_updated":"2025-01-09T12:25:32Z","quality_controlled":"1","publication_status":"published","DOAJ_listed":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"11","external_id":{"pmid":["38988072"]},"OA_type":"gold","date_updated":"2025-01-09T12:26:55Z"}]