[{"page":"10 - 19","volume":250,"oa":1,"_id":"1410","title":"Phosphatidylinositol 4-phosphate 5-kinases 1 and 2 are involved in the regulation of vacuole morphology during Arabidopsis thaliana pollen development","date_updated":"2025-09-18T14:29:16Z","department":[{"_id":"JiFr"}],"scopus_import":"1","abstract":[{"text":"The pollen grains arise after meiosis of pollen mother cells within the anthers. A series of complex structural changes follows, generating mature pollen grains capable of performing the double fertilization of the female megasporophyte. Several signaling molecules, including hormones and lipids, have been involved in the regulation and appropriate control of pollen development. Phosphatidylinositol 4-phophate 5-kinases (PIP5K), which catalyze the biosynthesis of the phosphoinositide PtdIns(4,5)P2, are important for tip polar growth of root hairs and pollen tubes, embryo development, vegetative plant growth, and responses to the environment. Here, we report a role of PIP5Ks during microgametogenesis. PIP5K1 and PIP5K2 are expressed during early stages of pollen development and their transcriptional activity respond to auxin in pollen grains. Early male gametophytic lethality to certain grade was observed in both pip5k1-/- and pip5k2-/- single mutants. The number of pip5k mutant alleles is directly related to the frequency of aborted pollen grains suggesting the two genes are involved in the same function. Indeed PIP5K1 and PIP5K2 are functionally redundant since homozygous double mutants did not render viable pollen grains. The loss of function of PIP5K1 and PIP5K2results in defects in vacuole morphology in pollen at the later stages and epidermal root cells. Our results show that PIP5K1, PIP5K2 and phosphoinositide signaling are important cues for early developmental stages and vacuole formation during microgametogenesis.","lang":"eng"}],"file":[{"date_created":"2019-04-17T07:41:57Z","relation":"main_file","file_id":"6331","date_updated":"2020-07-14T12:44:53Z","file_size":4338545,"checksum":"ca08de036e6ddc81e6f760e0ccdebd3f","file_name":"2016_PlantScience_Ugalde.pdf","content_type":"application/pdf","access_level":"open_access","creator":"dernst"}],"intvolume":" 250","month":"09","has_accepted_license":"1","year":"2016","pmid":1,"isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","quality_controlled":"1","publisher":"Elsevier","file_date_updated":"2020-07-14T12:44:53Z","pubrep_id":"1005","external_id":{"pmid":["27457979"],"isi":["000381545000002"]},"oa_version":"Submitted Version","acknowledgement":"the Odysseus Program of the Research Foundation-Flanders [G091608] to JF.","publist_id":"5797","ddc":["581"],"author":[{"last_name":"Ugalde","first_name":"José","full_name":"Ugalde, José"},{"full_name":"Rodríguez Furlán, Cecilia","first_name":"Cecilia","last_name":"Rodríguez Furlán"},{"first_name":"Riet","full_name":"De Rycke, Riet","last_name":"De Rycke"},{"last_name":"Norambuena","full_name":"Norambuena, Lorena","first_name":"Lorena"},{"full_name":"Friml, Jirí","first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"},{"full_name":"León, Gabriel","first_name":"Gabriel","last_name":"León"},{"first_name":"Ricardo","full_name":"Tejos, Ricardo","last_name":"Tejos"}],"date_created":"2018-12-11T11:51:51Z","day":"01","date_published":"2016-09-01T00:00:00Z","status":"public","citation":{"ama":"Ugalde J, Rodríguez Furlán C, De Rycke R, et al. Phosphatidylinositol 4-phosphate 5-kinases 1 and 2 are involved in the regulation of vacuole morphology during Arabidopsis thaliana pollen development. Plant Science. 2016;250:10-19. doi:10.1016/j.plantsci.2016.05.014","ista":"Ugalde J, Rodríguez Furlán C, De Rycke R, Norambuena L, Friml J, León G, Tejos R. 2016. Phosphatidylinositol 4-phosphate 5-kinases 1 and 2 are involved in the regulation of vacuole morphology during Arabidopsis thaliana pollen development. Plant Science. 250, 10–19.","mla":"Ugalde, José, et al. “Phosphatidylinositol 4-Phosphate 5-Kinases 1 and 2 Are Involved in the Regulation of Vacuole Morphology during Arabidopsis Thaliana Pollen Development.” Plant Science, vol. 250, Elsevier, 2016, pp. 10–19, doi:10.1016/j.plantsci.2016.05.014.","ieee":"J. Ugalde et al., “Phosphatidylinositol 4-phosphate 5-kinases 1 and 2 are involved in the regulation of vacuole morphology during Arabidopsis thaliana pollen development,” Plant Science, vol. 250. Elsevier, pp. 10–19, 2016.","apa":"Ugalde, J., Rodríguez Furlán, C., De Rycke, R., Norambuena, L., Friml, J., León, G., & Tejos, R. (2016). Phosphatidylinositol 4-phosphate 5-kinases 1 and 2 are involved in the regulation of vacuole morphology during Arabidopsis thaliana pollen development. Plant Science. Elsevier. https://doi.org/10.1016/j.plantsci.2016.05.014","short":"J. Ugalde, C. Rodríguez Furlán, R. De Rycke, L. Norambuena, J. Friml, G. León, R. Tejos, Plant Science 250 (2016) 10–19.","chicago":"Ugalde, José, Cecilia Rodríguez Furlán, Riet De Rycke, Lorena Norambuena, Jiří Friml, Gabriel León, and Ricardo Tejos. “Phosphatidylinositol 4-Phosphate 5-Kinases 1 and 2 Are Involved in the Regulation of Vacuole Morphology during Arabidopsis Thaliana Pollen Development.” Plant Science. Elsevier, 2016. https://doi.org/10.1016/j.plantsci.2016.05.014."},"article_processing_charge":"No","language":[{"iso":"eng"}],"type":"journal_article","doi":"10.1016/j.plantsci.2016.05.014","publication":"Plant Science","publication_status":"published"},{"scopus_import":"1","file":[{"relation":"main_file","date_created":"2018-12-12T10:13:32Z","file_id":"5016","date_updated":"2020-07-14T12:44:53Z","file_size":3828383,"checksum":"23522ced3508ffe7a4f247c4230e6493","file_name":"IST-2018-1004-v1+1_Simon_NewPhytol_2016_proof.pdf","content_type":"application/pdf","access_level":"open_access","creator":"system"}],"abstract":[{"lang":"eng","text":"Plant development mediated by the phytohormone auxin depends on tightly controlled cellular auxin levels at its target tissue that are largely established by intercellular and intracellular auxin transport mediated by PIN auxin transporters. Among the eight members of the Arabidopsis PIN family, PIN6 is the least characterized candidate. In this study we generated functional, fluorescent protein-tagged PIN6 proteins and performed comprehensive analysis of their subcellular localization and also performed a detailed functional characterization of PIN6 and its developmental roles. The localization study of PIN6 revealed a dual localization at the plasma membrane (PM) and endoplasmic reticulum (ER). Transport and metabolic profiling assays in cultured cells and Arabidopsis strongly suggest that PIN6 mediates both auxin transport across the PM and intracellular auxin homeostasis, including the regulation of free auxin and auxin conjugates levels. As evidenced by the loss- and gain-of-function analysis, the complex function of PIN6 in auxin transport and homeostasis is required for auxin distribution during lateral and adventitious root organogenesis and for progression of these developmental processes. These results illustrate a unique position of PIN6 within the family of PIN auxin transporters and further add complexity to the developmentally crucial process of auxin transport."}],"has_accepted_license":"1","month":"07","intvolume":" 211","page":"65 - 74","oa":1,"volume":211,"date_updated":"2025-09-18T14:23:21Z","department":[{"_id":"JiFr"}],"_id":"1417","title":"PIN6 auxin transporter at endoplasmic reticulum and plasma membrane mediates auxin homeostasis and organogenesis in Arabidopsis","pubrep_id":"1004","external_id":{"isi":["000379212800008"]},"acknowledgement":"This work was supported by the European Research Council (project ERC-2011-StG-20101109-PSDP, project CEITEC (CZ.1.05/1.1.00/02.0068) and the Czech Science Foundation GACR (project no. 13-4063 7S to J.F.)","oa_version":"Submitted Version","isi":1,"year":"2016","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","quality_controlled":"1","file_date_updated":"2020-07-14T12:44:53Z","publisher":"Wiley-Blackwell","day":"01","issue":"1","date_published":"2016-07-01T00:00:00Z","publist_id":"5790","ddc":["581"],"author":[{"orcid":"0000-0002-1998-6741","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","last_name":"Simon","full_name":"Simon, Sibu","first_name":"Sibu"},{"first_name":"Petr","full_name":"Skůpa, Petr","last_name":"Skůpa"},{"last_name":"Viaene","first_name":"Tom","full_name":"Viaene, Tom"},{"last_name":"Zwiewka","full_name":"Zwiewka, Marta","first_name":"Marta"},{"last_name":"Tejos","first_name":"Ricardo","full_name":"Tejos, Ricardo"},{"last_name":"Klíma","full_name":"Klíma, Petr","first_name":"Petr"},{"full_name":"Čarná, Mária","first_name":"Mária","last_name":"Čarná"},{"last_name":"Rolčík","full_name":"Rolčík, Jakub","first_name":"Jakub"},{"last_name":"De Rycke","first_name":"Riet","full_name":"De Rycke, Riet"},{"full_name":"Moreno, Ignacio","first_name":"Ignacio","last_name":"Moreno"},{"full_name":"Dobrev, Petre","first_name":"Petre","last_name":"Dobrev"},{"last_name":"Orellana","first_name":"Ariel","full_name":"Orellana, Ariel"},{"first_name":"Eva","full_name":"Zažímalová, Eva","last_name":"Zažímalová"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jirí","first_name":"Jirí"}],"corr_author":"1","date_created":"2018-12-11T11:51:54Z","publication":"New Phytologist","publication_status":"published","status":"public","article_processing_charge":"No","citation":{"short":"S. Simon, P. Skůpa, T. Viaene, M. Zwiewka, R. Tejos, P. Klíma, M. Čarná, J. Rolčík, R. De Rycke, I. Moreno, P. Dobrev, A. Orellana, E. Zažímalová, J. Friml, New Phytologist 211 (2016) 65–74.","chicago":"Simon, Sibu, Petr Skůpa, Tom Viaene, Marta Zwiewka, Ricardo Tejos, Petr Klíma, Mária Čarná, et al. “PIN6 Auxin Transporter at Endoplasmic Reticulum and Plasma Membrane Mediates Auxin Homeostasis and Organogenesis in Arabidopsis.” New Phytologist. Wiley-Blackwell, 2016. https://doi.org/10.1111/nph.14019.","ieee":"S. Simon et al., “PIN6 auxin transporter at endoplasmic reticulum and plasma membrane mediates auxin homeostasis and organogenesis in Arabidopsis,” New Phytologist, vol. 211, no. 1. Wiley-Blackwell, pp. 65–74, 2016.","apa":"Simon, S., Skůpa, P., Viaene, T., Zwiewka, M., Tejos, R., Klíma, P., … Friml, J. (2016). PIN6 auxin transporter at endoplasmic reticulum and plasma membrane mediates auxin homeostasis and organogenesis in Arabidopsis. New Phytologist. Wiley-Blackwell. https://doi.org/10.1111/nph.14019","ista":"Simon S, Skůpa P, Viaene T, Zwiewka M, Tejos R, Klíma P, Čarná M, Rolčík J, De Rycke R, Moreno I, Dobrev P, Orellana A, Zažímalová E, Friml J. 2016. PIN6 auxin transporter at endoplasmic reticulum and plasma membrane mediates auxin homeostasis and organogenesis in Arabidopsis. New Phytologist. 211(1), 65–74.","mla":"Simon, Sibu, et al. “PIN6 Auxin Transporter at Endoplasmic Reticulum and Plasma Membrane Mediates Auxin Homeostasis and Organogenesis in Arabidopsis.” New Phytologist, vol. 211, no. 1, Wiley-Blackwell, 2016, pp. 65–74, doi:10.1111/nph.14019.","ama":"Simon S, Skůpa P, Viaene T, et al. PIN6 auxin transporter at endoplasmic reticulum and plasma membrane mediates auxin homeostasis and organogenesis in Arabidopsis. New Phytologist. 2016;211(1):65-74. doi:10.1111/nph.14019"},"language":[{"iso":"eng"}],"doi":"10.1111/nph.14019","type":"journal_article"},{"date_published":"2016-02-01T00:00:00Z","issue":"2","day":"01","date_created":"2018-12-11T11:52:17Z","author":[{"last_name":"Adibi","full_name":"Adibi, Milad","first_name":"Milad"},{"id":"2E46069C-F248-11E8-B48F-1D18A9856A87","last_name":"Yoshida","full_name":"Yoshida, Saiko","first_name":"Saiko"},{"first_name":"Dolf","full_name":"Weijers, Dolf","last_name":"Weijers"},{"first_name":"Christian","full_name":"Fleck, Christian","last_name":"Fleck"}],"ddc":["570"],"publist_id":"5711","publication_status":"published","publication":"PLoS One","type":"journal_article","doi":"10.1371/journal.pone.0147830","citation":{"ama":"Adibi M, Yoshida S, Weijers D, Fleck C. Centering the organizing center in the Arabidopsis thaliana shoot apical meristem by a combination of cytokinin signaling and self-organization. PLoS One. 2016;11(2). doi:10.1371/journal.pone.0147830","mla":"Adibi, Milad, et al. “Centering the Organizing Center in the Arabidopsis Thaliana Shoot Apical Meristem by a Combination of Cytokinin Signaling and Self-Organization.” PLoS One, vol. 11, no. 2, e0147830, Public Library of Science, 2016, doi:10.1371/journal.pone.0147830.","ista":"Adibi M, Yoshida S, Weijers D, Fleck C. 2016. Centering the organizing center in the Arabidopsis thaliana shoot apical meristem by a combination of cytokinin signaling and self-organization. PLoS One. 11(2), e0147830.","apa":"Adibi, M., Yoshida, S., Weijers, D., & Fleck, C. (2016). Centering the organizing center in the Arabidopsis thaliana shoot apical meristem by a combination of cytokinin signaling and self-organization. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0147830","ieee":"M. Adibi, S. Yoshida, D. Weijers, and C. Fleck, “Centering the organizing center in the Arabidopsis thaliana shoot apical meristem by a combination of cytokinin signaling and self-organization,” PLoS One, vol. 11, no. 2. Public Library of Science, 2016.","chicago":"Adibi, Milad, Saiko Yoshida, Dolf Weijers, and Christian Fleck. “Centering the Organizing Center in the Arabidopsis Thaliana Shoot Apical Meristem by a Combination of Cytokinin Signaling and Self-Organization.” PLoS One. Public Library of Science, 2016. https://doi.org/10.1371/journal.pone.0147830.","short":"M. Adibi, S. Yoshida, D. Weijers, C. Fleck, PLoS One 11 (2016)."},"article_processing_charge":"No","language":[{"iso":"eng"}],"status":"public","intvolume":" 11","month":"02","has_accepted_license":"1","abstract":[{"lang":"eng","text":"Plants have the ability to continously generate new organs by maintaining populations of stem cells throught their lives. The shoot apical meristem (SAM) provides a stable environment for the maintenance of stem cells. All cells inside the SAM divide, yet boundaries and patterns are maintained. Experimental evidence indicates that patterning is independent of cell lineage, thus a dynamic self-regulatory mechanism is required. A pivotal role in the organization of the SAM is played by the WUSCHEL gene (WUS). An important question in this regard is that how WUS expression is positioned in the SAM via a cell-lineage independent signaling mechanism. In this study we demonstrate via mathematical modeling that a combination of an inhibitor of the Cytokinin (CK) receptor, Arabidopsis histidine kinase 4 (AHK4) and two morphogens originating from the top cell layer, can plausibly account for the cell lineage-independent centering of WUS expression within SAM. Furthermore, our laser ablation and microsurgical experiments support the hypothesis that patterning in SAM occurs at the level of CK reception and signaling. The model suggests that the interplay between CK signaling, WUS/CLV feedback loop and boundary signals can account for positioning of the WUS expression, and provides directions for further experimental investigation."}],"file":[{"access_level":"open_access","content_type":"application/pdf","creator":"system","file_name":"IST-2016-521-v1+1_journal.pone.0147830.PDF","checksum":"6066146e527335030f83aa5924ab72a6","file_size":4297148,"relation":"main_file","date_created":"2018-12-12T10:14:16Z","date_updated":"2020-07-14T12:44:57Z","file_id":"5066"}],"article_number":"e0147830","scopus_import":"1","title":"Centering the organizing center in the Arabidopsis thaliana shoot apical meristem by a combination of cytokinin signaling and self-organization","_id":"1482","department":[{"_id":"JiFr"}],"date_updated":"2025-09-18T11:35:51Z","volume":11,"oa":1,"oa_version":"Published Version","acknowledgement":"We thank J. Traas, B. Müller and V. Reddy for providing seed materials and Y. Deb for advice regarding the laser ablation experiments. We specially thank Thomas Laux for stimulating discussions and support in the initial phase of this project.","external_id":{"isi":["000370054100011"]},"pubrep_id":"521","file_date_updated":"2020-07-14T12:44:57Z","publisher":"Public Library of Science","quality_controlled":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"year":"2016","isi":1},{"external_id":{"isi":["000376807500004"]},"pubrep_id":"1002","acknowledgement":"We thank Maciek Adamowski for helpful discussions and Qiang Zhu and Israel Ausin for critical reading of the manuscript. We sincerely apologize to colleagues whose work we could not include owing to space limitations.","oa_version":"Submitted Version","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"year":"2016","file_date_updated":"2020-07-14T12:44:57Z","publisher":"Cell Press","quality_controlled":"1","scopus_import":"1","has_accepted_license":"1","month":"06","article_type":"review","intvolume":" 26","file":[{"file_size":2329117,"date_updated":"2020-07-14T12:44:57Z","file_id":"5155","relation":"main_file","date_created":"2018-12-12T10:15:34Z","creator":"system","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2018-1002-v1+1_Chen_TICB_2016_proofs.pdf","checksum":"b229e5bb4676ec3e27b7b9ea603b3a63"}],"page":"409 - 419","oa":1,"volume":26,"date_updated":"2025-09-18T11:35:11Z","department":[{"_id":"JiFr"}],"title":"Environmental and endogenous control of cortical microtubule orientation","_id":"1484","publication":"Trends in Cell Biology","publication_status":"published","language":[{"iso":"eng"}],"citation":{"ista":"Chen X, Wu S, Liu Z, Friml J. 2016. Environmental and endogenous control of cortical microtubule orientation. Trends in Cell Biology. 26(6), 409–419.","mla":"Chen, Xu, et al. “Environmental and Endogenous Control of Cortical Microtubule Orientation.” Trends in Cell Biology, vol. 26, no. 6, Cell Press, 2016, pp. 409–19, doi:10.1016/j.tcb.2016.02.003.","ama":"Chen X, Wu S, Liu Z, Friml J. Environmental and endogenous control of cortical microtubule orientation. Trends in Cell Biology. 2016;26(6):409-419. doi:10.1016/j.tcb.2016.02.003","short":"X. Chen, S. Wu, Z. Liu, J. Friml, Trends in Cell Biology 26 (2016) 409–419.","chicago":"Chen, Xu, Shuang Wu, Zengyu Liu, and Jiří Friml. “Environmental and Endogenous Control of Cortical Microtubule Orientation.” Trends in Cell Biology. Cell Press, 2016. https://doi.org/10.1016/j.tcb.2016.02.003.","ieee":"X. Chen, S. Wu, Z. Liu, and J. Friml, “Environmental and endogenous control of cortical microtubule orientation,” Trends in Cell Biology, vol. 26, no. 6. Cell Press, pp. 409–419, 2016.","apa":"Chen, X., Wu, S., Liu, Z., & Friml, J. (2016). Environmental and endogenous control of cortical microtubule orientation. Trends in Cell Biology. Cell Press. https://doi.org/10.1016/j.tcb.2016.02.003"},"article_processing_charge":"No","status":"public","doi":"10.1016/j.tcb.2016.02.003","type":"journal_article","day":"01","date_published":"2016-06-01T00:00:00Z","issue":"6","ddc":["581"],"publist_id":"5704","date_created":"2018-12-11T11:52:17Z","author":[{"id":"4E5ADCAA-F248-11E8-B48F-1D18A9856A87","last_name":"Chen","full_name":"Chen, Xu","first_name":"Xu"},{"last_name":"Wu","first_name":"Shuang","full_name":"Wu, Shuang"},{"full_name":"Liu, Zengyu","first_name":"Zengyu","last_name":"Liu"},{"full_name":"Friml, Jiřĺ","first_name":"Jiřĺ","last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}]},{"external_id":{"isi":["000376482300015"]},"pubrep_id":"1001","acknowledgement":"European Social Fund (CZ.1.07/2.3.00/20.0043) and the Czech Science Foundation GAČR (GA13-40637S) to JF. ","oa_version":"Preprint","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"year":"2016","publisher":"Springer","file_date_updated":"2020-07-14T12:45:08Z","quality_controlled":"1","scopus_import":"1","month":"06","has_accepted_license":"1","intvolume":" 35","file":[{"relation":"main_file","date_created":"2018-12-12T10:08:34Z","file_id":"4695","date_updated":"2020-07-14T12:45:08Z","file_size":5637591,"checksum":"0dc6a300cde6536ceedd2bcdd2060efb","file_name":"IST-2018-1001-v1+1_Zemova_JPlantGrowthRegul_2016_proofs.pdf","content_type":"application/pdf","access_level":"open_access","creator":"system"}],"abstract":[{"text":"The plant hormone auxin (indole-3-acetic acid) is a major regulator of plant growth and development including embryo and root patterning, lateral organ formation and growth responses to environmental stimuli. Auxin is directionally transported from cell to cell by the action of specific auxin influx [AUXIN-RESISTANT1 (AUX1)] and efflux [PIN-FORMED (PIN)] transport regulators, whose polar, subcellular localizations are aligned with the direction of the auxin flow. Auxin itself regulates its own transport by modulation of the expression and subcellular localization of the auxin transporters. Increased auxin levels promote the transcription of PIN2 and AUX1 genes as well as stabilize PIN proteins at the plasma membrane, whereas prolonged auxin exposure increases the turnover of PIN proteins and their degradation in the vacuole. In this study, we applied a forward genetic approach, to identify molecular components playing a role in the auxin-mediated degradation. We generated EMS-mutagenized Arabidopsis PIN2::PIN2:GFP, AUX1::AUX1:YFP eir1aux1 populations and designed a screen for mutants with persistently strong fluorescent signals of the tagged PIN2 and AUX1 after prolonged treatment with the synthetic auxin 2,4-dichlorophenoxyacetic acid (2,4-D). This approach yielded novel auxin degradation mutants defective in trafficking and degradation of PIN2 and AUX1 proteins and established a role for auxin-mediated degradation in plant development.","lang":"eng"}],"oa":1,"page":"465 - 476","volume":35,"department":[{"_id":"JiFr"}],"date_updated":"2025-09-18T10:51:26Z","_id":"1641","title":"A forward genetic screen for new regulators of auxin mediated degradation of auxin transport proteins in Arabidopsis thaliana","publication":"Journal of Plant Growth Regulation","publication_status":"published","citation":{"short":"R. Zemová, M. Zwiewka, A. Bielach, H. Robert, J. Friml, Journal of Plant Growth Regulation 35 (2016) 465–476.","chicago":"Zemová, Radka, Marta Zwiewka, Agnieszka Bielach, Hélène Robert, and Jiří Friml. “A Forward Genetic Screen for New Regulators of Auxin Mediated Degradation of Auxin Transport Proteins in Arabidopsis Thaliana.” Journal of Plant Growth Regulation. Springer, 2016. https://doi.org/10.1007/s00344-015-9553-2.","ieee":"R. Zemová, M. Zwiewka, A. Bielach, H. Robert, and J. Friml, “A forward genetic screen for new regulators of auxin mediated degradation of auxin transport proteins in Arabidopsis thaliana,” Journal of Plant Growth Regulation, vol. 35, no. 2. Springer, pp. 465–476, 2016.","apa":"Zemová, R., Zwiewka, M., Bielach, A., Robert, H., & Friml, J. (2016). A forward genetic screen for new regulators of auxin mediated degradation of auxin transport proteins in Arabidopsis thaliana. Journal of Plant Growth Regulation. Springer. https://doi.org/10.1007/s00344-015-9553-2","ista":"Zemová R, Zwiewka M, Bielach A, Robert H, Friml J. 2016. A forward genetic screen for new regulators of auxin mediated degradation of auxin transport proteins in Arabidopsis thaliana. Journal of Plant Growth Regulation. 35(2), 465–476.","mla":"Zemová, Radka, et al. “A Forward Genetic Screen for New Regulators of Auxin Mediated Degradation of Auxin Transport Proteins in Arabidopsis Thaliana.” Journal of Plant Growth Regulation, vol. 35, no. 2, Springer, 2016, pp. 465–76, doi:10.1007/s00344-015-9553-2.","ama":"Zemová R, Zwiewka M, Bielach A, Robert H, Friml J. A forward genetic screen for new regulators of auxin mediated degradation of auxin transport proteins in Arabidopsis thaliana. Journal of Plant Growth Regulation. 2016;35(2):465-476. doi:10.1007/s00344-015-9553-2"},"language":[{"iso":"eng"}],"article_processing_charge":"No","status":"public","doi":"10.1007/s00344-015-9553-2","type":"journal_article","day":"01","date_published":"2016-06-01T00:00:00Z","issue":"2","ddc":["581"],"publist_id":"5512","date_created":"2018-12-11T11:53:12Z","corr_author":"1","author":[{"first_name":"Radka","full_name":"Zemová, Radka","last_name":"Zemová"},{"full_name":"Zwiewka, Marta","first_name":"Marta","last_name":"Zwiewka"},{"full_name":"Bielach, Agnieszka","first_name":"Agnieszka","last_name":"Bielach"},{"last_name":"Robert","full_name":"Robert, Hélène","first_name":"Hélène"},{"first_name":"Jirí","full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","last_name":"Friml"}]},{"date_created":"2018-12-11T11:46:53Z","author":[{"last_name":"Liu","first_name":"Zhijun","full_name":"Liu, Zhijun"},{"first_name":"Nan","full_name":"Yang, Nan","last_name":"Yang"},{"last_name":"Lv","full_name":"Lv, Yanting","first_name":"Yanting"},{"first_name":"Lixia","full_name":"Pan, Lixia","last_name":"Pan"},{"first_name":"Shuo","full_name":"Lv, Shuo","last_name":"Lv"},{"full_name":"Han, Huibin","first_name":"Huibin","id":"31435098-F248-11E8-B48F-1D18A9856A87","last_name":"Han"},{"last_name":"Wang","first_name":"Guodong","full_name":"Wang, Guodong"}],"publist_id":"7308","date_published":"2016-06-02T00:00:00Z","issue":"6","day":"02","doi":"10.1080/15592324.2016.1191734","type":"journal_article","citation":{"ieee":"Z. Liu et al., “The CLE gene family in Populus trichocarpa,” Plant Signaling & Behavior, vol. 11, no. 6. Taylor & Francis, 2016.","apa":"Liu, Z., Yang, N., Lv, Y., Pan, L., Lv, S., Han, H., & Wang, G. (2016). The CLE gene family in Populus trichocarpa. Plant Signaling & Behavior. Taylor & Francis. https://doi.org/10.1080/15592324.2016.1191734","short":"Z. Liu, N. Yang, Y. Lv, L. Pan, S. Lv, H. Han, G. Wang, Plant Signaling & Behavior 11 (2016).","chicago":"Liu, Zhijun, Nan Yang, Yanting Lv, Lixia Pan, Shuo Lv, Huibin Han, and Guodong Wang. “The CLE Gene Family in Populus Trichocarpa.” Plant Signaling & Behavior. Taylor & Francis, 2016. https://doi.org/10.1080/15592324.2016.1191734.","ama":"Liu Z, Yang N, Lv Y, et al. The CLE gene family in Populus trichocarpa. Plant Signaling & Behavior. 2016;11(6). doi:10.1080/15592324.2016.1191734","ista":"Liu Z, Yang N, Lv Y, Pan L, Lv S, Han H, Wang G. 2016. The CLE gene family in Populus trichocarpa. Plant Signaling & Behavior. 11(6), e1191734.","mla":"Liu, Zhijun, et al. “The CLE Gene Family in Populus Trichocarpa.” Plant Signaling & Behavior, vol. 11, no. 6, e1191734, Taylor & Francis, 2016, doi:10.1080/15592324.2016.1191734."},"language":[{"iso":"eng"}],"article_processing_charge":"No","status":"public","publication_status":"published","publication":"Plant Signaling & Behavior","department":[{"_id":"JiFr"}],"date_updated":"2025-09-22T14:21:19Z","title":"The CLE gene family in Populus trichocarpa","_id":"510","oa":1,"volume":11,"month":"06","intvolume":" 11","abstract":[{"text":"The CLE (CLAVATA3/Embryo Surrounding Region-related) peptides are small secreted signaling peptides that are primarily involved in the regulation of stem cell homeostasis in different plant meristems. Particularly, the characterization of the CLE41-PXY/TDR signaling pathway has greatly advanced our understanding on the potential roles of CLE peptides in vascular development and wood formation. Nevertheless, our knowledge on this gene family in a tree species is limited. In a recent study, we reported on a systematically investigation of the CLE gene family in Populus trichocarpa . The potential roles of PtCLE genes were studied by comparative analysis and transcriptional pro fi ling. Among fi fty PtCLE members, many PtCLE proteins share identical CLE motifs or contain the same CLE motif as that of AtCLEs, while PtCLE genes exhibited either comparable or distinct expression patterns comparing to their Arabidopsis counterparts. These fi ndings indicate the existence of both functional conservation and functional divergence between PtCLEs and their AtCLE orthologues. Our results provide valuable resources for future functional investigations of these critical signaling molecules in woody plants. ","lang":"eng"}],"article_number":"e1191734","scopus_import":"1","publisher":"Taylor & Francis","quality_controlled":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"year":"2016","acknowledgement":"We are grateful to Dr. Long (Laboratoire de Reproduction et Developpement des Plantes,CNRS,INRA,ENSLyon,UCBL,Universite de Lyon,France)for critical reading of the article. Work in our group is supported by the National Natural Science Foundation of China (31271575; 31200902), the Fundamental Research Funds for the Central Univ ersities (GK201103005), the Specialized Research Fund for the Doctoral Program of Higher Education from the Ministry of Education of China (20120202120009), the Scientific Research Foundation for the Returned Overseas Chinese Scholars, State Education Ministry, and the Natural Science Basic Research Plan in Shaanxi Province of China (2014JM3064). ","oa_version":"Submitted Version","external_id":{"isi":["000378740600025"]},"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4973754/"}]},{"publication":"Cell Discovery","ec_funded":1,"publication_status":"published","language":[{"iso":"eng"}],"article_processing_charge":"No","citation":{"apa":"Łangowski, Ł., Wabnik, K. T., Li, H., Vanneste, S., Naramoto, S., Tanaka, H., & Friml, J. (2016). Cellular mechanisms for cargo delivery and polarity maintenance at different polar domains in plant cells. Cell Discovery. Nature Publishing Group. https://doi.org/10.1038/celldisc.2016.18","ieee":"Ł. Łangowski et al., “Cellular mechanisms for cargo delivery and polarity maintenance at different polar domains in plant cells,” Cell Discovery, vol. 2. Nature Publishing Group, 2016.","chicago":"Łangowski, Łukasz, Krzysztof T Wabnik, Hongjiang Li, Steffen Vanneste, Satoshi Naramoto, Hirokazu Tanaka, and Jiří Friml. “Cellular Mechanisms for Cargo Delivery and Polarity Maintenance at Different Polar Domains in Plant Cells.” Cell Discovery. Nature Publishing Group, 2016. https://doi.org/10.1038/celldisc.2016.18.","short":"Ł. Łangowski, K.T. Wabnik, H. Li, S. Vanneste, S. Naramoto, H. Tanaka, J. Friml, Cell Discovery 2 (2016).","ama":"Łangowski Ł, Wabnik KT, Li H, et al. Cellular mechanisms for cargo delivery and polarity maintenance at different polar domains in plant cells. Cell Discovery. 2016;2. doi:10.1038/celldisc.2016.18","mla":"Łangowski, Łukasz, et al. “Cellular Mechanisms for Cargo Delivery and Polarity Maintenance at Different Polar Domains in Plant Cells.” Cell Discovery, vol. 2, 16018, Nature Publishing Group, 2016, doi:10.1038/celldisc.2016.18.","ista":"Łangowski Ł, Wabnik KT, Li H, Vanneste S, Naramoto S, Tanaka H, Friml J. 2016. Cellular mechanisms for cargo delivery and polarity maintenance at different polar domains in plant cells. Cell Discovery. 2, 16018."},"status":"public","doi":"10.1038/celldisc.2016.18","type":"journal_article","day":"19","date_published":"2016-07-19T00:00:00Z","ddc":["580"],"publist_id":"6299","date_created":"2018-12-11T11:50:02Z","author":[{"full_name":"Łangowski, Łukasz","first_name":"Łukasz","last_name":"Łangowski"},{"full_name":"Wabnik, Krzysztof T","first_name":"Krzysztof T","last_name":"Wabnik","id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7263-0560"},{"id":"33CA54A6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5039-9660","last_name":"Li","first_name":"Hongjiang","full_name":"Li, Hongjiang"},{"first_name":"Steffen","full_name":"Vanneste, Steffen","last_name":"Vanneste"},{"last_name":"Naramoto","first_name":"Satoshi","full_name":"Naramoto, Satoshi"},{"full_name":"Tanaka, Hirokazu","first_name":"Hirokazu","last_name":"Tanaka"},{"first_name":"Jirí","full_name":"Friml, Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"}],"external_id":{"isi":["000414797400001"]},"pubrep_id":"757","acknowledgement":"We thank Bonnie Bartel, Jenny Russinova and Niko Geldner\r\nfor sharing published material, Martine de Cock and Annick\r\nBleys for help in preparing the manuscript. This work was\r\nsupported by the European Research Council (project\r\nERC-2011-StG-20101109-PSDP); Czech Science Foundation\r\nGAČR (GA13-40637S); project CEITEC—Central European\r\nInstitute of Technology (CZ.1.05/1.1.00/02.0068). SV is a\r\npostdoctoral fellow of the Research Foundation-Flanders.\r\nSN is a Project Assistant Professor supported by the Japanese\r\nSociety for the Promotion of Science (JSPS; 30612022 to SN),\r\nthe NC-CARP project of the Ministry of Education, Culture,\r\nSports, Science and Technology in Japan to SN.","oa_version":"Published Version","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"year":"2016","file_date_updated":"2018-12-12T10:13:33Z","publisher":"Nature Publishing Group","quality_controlled":"1","scopus_import":"1","article_number":"16018","month":"07","has_accepted_license":"1","intvolume":" 2","file":[{"creator":"system","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2017-757-v1+1_celldisc201618.pdf","file_size":5261671,"date_updated":"2018-12-12T10:13:33Z","file_id":"5017","date_created":"2018-12-12T10:13:33Z","relation":"main_file"}],"abstract":[{"text":"The asymmetric localization of proteins in the plasma membrane domains of eukaryotic cells is a fundamental manifestation of cell polarity that is central to multicellular organization and developmental patterning. In plants, the mechanisms underlying the polar localization of cargo proteins are still largely unknown and appear to be fundamentally distinct from those operating in mammals. Here, we present a systematic, quantitative comparative analysis of the polar delivery and subcellular localization of proteins that characterize distinct polar plasma membrane domains in plant cells. The combination of microscopic analyses and computational modeling revealed a mechanistic framework common to diverse polar cargos and underlying the establishment and maintenance of apical, basal, and lateral polar domains in plant cells. This mechanism depends on the polar secretion, constitutive endocytic recycling, and restricted lateral diffusion of cargos within the plasma membrane. Moreover, our observations suggest that polar cargo distribution involves the individual protein potential to form clusters within the plasma membrane and interact with the extracellular matrix. Our observations provide insights into the shared cellular mechanisms of polar cargo delivery and polarity maintenance in plant cells.","lang":"eng"}],"project":[{"call_identifier":"FP7","grant_number":"282300","name":"Polarity and subcellular dynamics in plants","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"oa":1,"volume":2,"date_updated":"2025-09-22T14:19:46Z","department":[{"_id":"EvBe"},{"_id":"JiFr"}],"_id":"1081","title":"Cellular mechanisms for cargo delivery and polarity maintenance at different polar domains in plant cells"},{"oa_version":"Submitted Version","external_id":{"isi":["000364407200001"],"pmid":["27250258"]},"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4905525/","open_access":"1"}],"publisher":"Nature Publishing Group","quality_controlled":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"pmid":1,"year":"2015","month":"07","intvolume":" 1","article_type":"original","abstract":[{"lang":"eng","text":"In plants, vacuolar H+-ATPase (V-ATPase) activity acidifies both the trans-Golgi network/early endosome (TGN/EE) and the vacuole. This dual V-ATPase function has impeded our understanding of how the pH homeostasis within the plant TGN/EE controls exo- and endocytosis. Here, we show that the weak V-ATPase mutant deetiolated3 (det3) displayed a pH increase in the TGN/EE, but not in the vacuole, strongly impairing secretion and recycling of the brassinosteroid receptor and the cellulose synthase complexes to the plasma membrane, in contrast to mutants lacking tonoplast-localized V-ATPase activity only. The brassinosteroid insensitivity and the cellulose deficiency defects in det3 were tightly correlated with reduced Golgi and TGN/EE motility. Thus, our results provide strong evidence that acidification of the TGN/EE, but not of the vacuole, is indispensable for functional secretion and recycling in plants."}],"article_number":"15094","scopus_import":"1","department":[{"_id":"JiFr"}],"date_updated":"2025-09-29T11:04:05Z","_id":"1383","title":"V-ATPase activity in the TGN/EE is required for exocytosis and recycling in Arabidopsis","oa":1,"volume":1,"publication_status":"published","publication":"Nature Plants","doi":"10.1038/nplants.2015.94","type":"journal_article","language":[{"iso":"eng"}],"citation":{"ieee":"L. Yu et al., “V-ATPase activity in the TGN/EE is required for exocytosis and recycling in Arabidopsis,” Nature Plants, vol. 1, no. 7. Nature Publishing Group, 2015.","apa":"Yu, L., Scholl, S., Doering, A., Yi, Z., Irani, N., Di Rubbo, S., … Russinova, E. (2015). V-ATPase activity in the TGN/EE is required for exocytosis and recycling in Arabidopsis. Nature Plants. Nature Publishing Group. https://doi.org/10.1038/nplants.2015.94","short":"L. Yu, S. Scholl, A. Doering, Z. Yi, N. Irani, S. Di Rubbo, L. Neumetzler, P. Krishnamoorthy, I. Van Houtte, E. Mylle, V. Bischoff, S. Vernhettes, J. Winne, J. Friml, Y. Stierhof, K. Schumacher, S. Persson, E. Russinova, Nature Plants 1 (2015).","chicago":"Yu, Luo, Stefan Scholl, Anett Doering, Zhang Yi, Niloufer Irani, Simone Di Rubbo, Lutz Neumetzler, et al. “V-ATPase Activity in the TGN/EE Is Required for Exocytosis and Recycling in Arabidopsis.” Nature Plants. Nature Publishing Group, 2015. https://doi.org/10.1038/nplants.2015.94.","ama":"Yu L, Scholl S, Doering A, et al. V-ATPase activity in the TGN/EE is required for exocytosis and recycling in Arabidopsis. Nature Plants. 2015;1(7). doi:10.1038/nplants.2015.94","ista":"Yu L, Scholl S, Doering A, Yi Z, Irani N, Di Rubbo S, Neumetzler L, Krishnamoorthy P, Van Houtte I, Mylle E, Bischoff V, Vernhettes S, Winne J, Friml J, Stierhof Y, Schumacher K, Persson S, Russinova E. 2015. V-ATPase activity in the TGN/EE is required for exocytosis and recycling in Arabidopsis. Nature Plants. 1(7), 15094.","mla":"Yu, Luo, et al. “V-ATPase Activity in the TGN/EE Is Required for Exocytosis and Recycling in Arabidopsis.” Nature Plants, vol. 1, no. 7, 15094, Nature Publishing Group, 2015, doi:10.1038/nplants.2015.94."},"article_processing_charge":"No","status":"public","date_published":"2015-07-06T00:00:00Z","issue":"7","day":"06","date_created":"2018-12-11T11:51:42Z","author":[{"last_name":"Yu","full_name":"Yu, Luo","first_name":"Luo"},{"full_name":"Scholl, Stefan","first_name":"Stefan","last_name":"Scholl"},{"full_name":"Doering, Anett","first_name":"Anett","last_name":"Doering"},{"last_name":"Yi","first_name":"Zhang","full_name":"Yi, Zhang"},{"first_name":"Niloufer","full_name":"Irani, Niloufer","last_name":"Irani"},{"last_name":"Di Rubbo","full_name":"Di Rubbo, Simone","first_name":"Simone"},{"first_name":"Lutz","full_name":"Neumetzler, Lutz","last_name":"Neumetzler"},{"last_name":"Krishnamoorthy","first_name":"Praveen","full_name":"Krishnamoorthy, Praveen"},{"last_name":"Van Houtte","full_name":"Van Houtte, Isabelle","first_name":"Isabelle"},{"last_name":"Mylle","first_name":"Evelien","full_name":"Mylle, Evelien"},{"last_name":"Bischoff","first_name":"Volker","full_name":"Bischoff, Volker"},{"full_name":"Vernhettes, Samantha","first_name":"Samantha","last_name":"Vernhettes"},{"full_name":"Winne, Johan","first_name":"Johan","last_name":"Winne"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí","full_name":"Friml, Jirí"},{"first_name":"York","full_name":"Stierhof, York","last_name":"Stierhof"},{"last_name":"Schumacher","full_name":"Schumacher, Karin","first_name":"Karin"},{"first_name":"Staffan","full_name":"Persson, Staffan","last_name":"Persson"},{"full_name":"Russinova, Eugenia","first_name":"Eugenia","last_name":"Russinova"}],"publist_id":"5827"},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","publisher":"F1000 Research","file_date_updated":"2020-07-14T12:44:59Z","pubrep_id":"497","acknowledgement":"This work was supported by ERC Independent Research grant (ERC-2011-StG-20101109-PSDP to JF). JM internship was supported by the grant “Action Austria – Slovakia”.\r\nData associated with the article are available under the terms of the Creative Commons Zero \"No rights reserved\" data waiver (CC0 1.0 Public domain dedication). \r\n\r\nData availability: \r\nF1000Research: Dataset 1. Dataset 1, 10.5256/f1000research.7143.d104552\r\n\r\nF1000Research: Dataset 2. Dataset 2, 10.5256/f1000research.7143.d104553\r\n\r\nF1000Research: Dataset 3. Dataset 3, 10.5256/f1000research.7143.d104554","oa_version":"Published Version","volume":4,"oa":1,"project":[{"call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300"}],"department":[{"_id":"JiFr"},{"_id":"ToBo"}],"date_updated":"2025-04-15T07:48:03Z","title":"Embryo-lethal phenotypes in early abp1 mutants are due to disruption of the neighboring BSM gene","_id":"1509","scopus_import":"1","file":[{"file_size":4414248,"relation":"main_file","date_created":"2018-12-12T10:16:12Z","file_id":"5198","date_updated":"2020-07-14T12:44:59Z","content_type":"application/pdf","access_level":"open_access","creator":"system","checksum":"8beae5cbe988e1060265ae7de2ee8306","file_name":"IST-2016-497-v1+1_10.12688_f1000research.7143.1_20151102.pdf"}],"abstract":[{"lang":"eng","text":"The Auxin Binding Protein1 (ABP1) has been identified based on its ability to bind auxin with high affinity and studied for a long time as a prime candidate for the extracellular auxin receptor responsible for mediating in particular the fast non-transcriptional auxin responses. However, the contradiction between the embryo-lethal phenotypes of the originally described Arabidopsis T-DNA insertional knock-out alleles (abp1-1 and abp1-1s) and the wild type-like phenotypes of other recently described loss-of-function alleles (abp1-c1 and abp1-TD1) questions the biological importance of ABP1 and relevance of the previous genetic studies. Here we show that there is no hidden copy of the ABP1 gene in the Arabidopsis genome but the embryo-lethal phenotypes of abp1-1 and abp1-1s alleles are very similar to the knock-out phenotypes of the neighboring gene, BELAYA SMERT (BSM). Furthermore, the allelic complementation test between bsm and abp1 alleles shows that the embryo-lethality in the abp1-1 and abp1-1s alleles is caused by the off-target disruption of the BSM locus by the T-DNA insertions. This clarifies the controversy of different phenotypes among published abp1 knock-out alleles and asks for reflections on the developmental role of ABP1."}],"month":"10","has_accepted_license":"1","intvolume":" 4","status":"public","citation":{"chicago":"Michalko, Jaroslav, Marta Lukacisinova, Mark Tobias Bollenbach, and Jiří Friml. “Embryo-Lethal Phenotypes in Early Abp1 Mutants Are Due to Disruption of the Neighboring BSM Gene.” F1000 Research . F1000 Research, 2015. https://doi.org/10.12688/f1000research.7143.1.","short":"J. Michalko, M. Lukacisinova, M.T. Bollenbach, J. Friml, F1000 Research 4 (2015).","apa":"Michalko, J., Lukacisinova, M., Bollenbach, M. T., & Friml, J. (2015). Embryo-lethal phenotypes in early abp1 mutants are due to disruption of the neighboring BSM gene. F1000 Research . F1000 Research. https://doi.org/10.12688/f1000research.7143.1","ieee":"J. Michalko, M. Lukacisinova, M. T. Bollenbach, and J. Friml, “Embryo-lethal phenotypes in early abp1 mutants are due to disruption of the neighboring BSM gene,” F1000 Research , vol. 4. F1000 Research, 2015.","mla":"Michalko, Jaroslav, et al. “Embryo-Lethal Phenotypes in Early Abp1 Mutants Are Due to Disruption of the Neighboring BSM Gene.” F1000 Research , vol. 4, F1000 Research, 2015, doi:10.12688/f1000research.7143.1.","ista":"Michalko J, Lukacisinova M, Bollenbach MT, Friml J. 2015. Embryo-lethal phenotypes in early abp1 mutants are due to disruption of the neighboring BSM gene. F1000 Research . 4.","ama":"Michalko J, Lukacisinova M, Bollenbach MT, Friml J. Embryo-lethal phenotypes in early abp1 mutants are due to disruption of the neighboring BSM gene. F1000 Research . 2015;4. doi:10.12688/f1000research.7143.1"},"language":[{"iso":"eng"}],"article_processing_charge":"No","doi":"10.12688/f1000research.7143.1","type":"journal_article","ec_funded":1,"publication":"F1000 Research ","publication_status":"published","publist_id":"5668","ddc":["570"],"author":[{"last_name":"Michalko","id":"483727CA-F248-11E8-B48F-1D18A9856A87","full_name":"Michalko, Jaroslav","first_name":"Jaroslav"},{"id":"4342E402-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2519-8004","last_name":"Dravecka","full_name":"Dravecka, Marta","first_name":"Marta"},{"first_name":"Tobias","full_name":"Bollenbach, Tobias","last_name":"Bollenbach","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4398-476X"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí","first_name":"Jirí"}],"date_created":"2018-12-11T11:52:26Z","corr_author":"1","day":"01","date_published":"2015-10-01T00:00:00Z"},{"day":"01","issue":"3","date_published":"2015-03-01T00:00:00Z","publication_identifier":{"issn":["1445-4408"]},"publist_id":"5639","author":[{"full_name":"Yang, Huaiyu","first_name":"Huaiyu","last_name":"Yang"},{"first_name":"Jenny","full_name":"Von Der Fecht Bartenbach, Jenny","last_name":"Von Der Fecht Bartenbach"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jirí","full_name":"Friml, Jirí"},{"last_name":"Lohmann","full_name":"Lohmann, Jan","first_name":"Jan"},{"last_name":"Neuhäuser","full_name":"Neuhäuser, Benjamin","first_name":"Benjamin"},{"last_name":"Ludewig","first_name":"Uwe","full_name":"Ludewig, Uwe"}],"date_created":"2018-12-11T11:52:34Z","publication":"Functional Plant Biology","publication_status":"published","status":"public","article_processing_charge":"No","citation":{"ama":"Yang H, Von Der Fecht Bartenbach J, Friml J, Lohmann J, Neuhäuser B, Ludewig U. Auxin-modulated root growth inhibition in Arabidopsis thaliana seedlings with ammonium as the sole nitrogen source. Functional Plant Biology. 2015;42(3):239-251. doi:10.1071/FP14171","ista":"Yang H, Von Der Fecht Bartenbach J, Friml J, Lohmann J, Neuhäuser B, Ludewig U. 2015. Auxin-modulated root growth inhibition in Arabidopsis thaliana seedlings with ammonium as the sole nitrogen source. Functional Plant Biology. 42(3), 239–251.","mla":"Yang, Huaiyu, et al. “Auxin-Modulated Root Growth Inhibition in Arabidopsis Thaliana Seedlings with Ammonium as the Sole Nitrogen Source.” Functional Plant Biology, vol. 42, no. 3, CSIRO, 2015, pp. 239–51, doi:10.1071/FP14171.","ieee":"H. Yang, J. Von Der Fecht Bartenbach, J. Friml, J. Lohmann, B. Neuhäuser, and U. Ludewig, “Auxin-modulated root growth inhibition in Arabidopsis thaliana seedlings with ammonium as the sole nitrogen source,” Functional Plant Biology, vol. 42, no. 3. CSIRO, pp. 239–251, 2015.","apa":"Yang, H., Von Der Fecht Bartenbach, J., Friml, J., Lohmann, J., Neuhäuser, B., & Ludewig, U. (2015). Auxin-modulated root growth inhibition in Arabidopsis thaliana seedlings with ammonium as the sole nitrogen source. Functional Plant Biology. CSIRO. https://doi.org/10.1071/FP14171","short":"H. Yang, J. Von Der Fecht Bartenbach, J. Friml, J. Lohmann, B. Neuhäuser, U. Ludewig, Functional Plant Biology 42 (2015) 239–251.","chicago":"Yang, Huaiyu, Jenny Von Der Fecht Bartenbach, Jiří Friml, Jan Lohmann, Benjamin Neuhäuser, and Uwe Ludewig. “Auxin-Modulated Root Growth Inhibition in Arabidopsis Thaliana Seedlings with Ammonium as the Sole Nitrogen Source.” Functional Plant Biology. CSIRO, 2015. https://doi.org/10.1071/FP14171."},"language":[{"iso":"eng"}],"doi":"10.1071/FP14171","type":"journal_article","scopus_import":"1","abstract":[{"lang":"eng","text":"Ammonium is the major nitrogen source in some plant ecosystems but is toxic at high concentrations, especially when available as the exclusive nitrogen source. Ammonium stress rapidly leads to various metabolic and hormonal imbalances that ultimately inhibit root and shoot growth in many plant species, including Arabidopsis thaliana (L.) Heynh. To identify molecular and genetic factors involved in seedling survival with prolonged exclusive NH4+ nutrition, a transcriptomic analysis with microarrays was used. Substantial transcriptional differences were most pronounced in (NH4)2SO4-grown seedlings, compared with plants grown on KNO3 or NH4NO3. Consistent with previous physiological analyses, major differences in the expression modules of photosynthesis-related genes, an altered mitochondrial metabolism, differential expression of the primary NH4+ assimilation, alteration of transporter gene expression and crucial changes in cell wall biosynthesis were found. A major difference in plant hormone responses, particularly of auxin but not cytokinin, was striking. The activity of the DR5::GUS reporter revealed a dramatically decreased auxin response in (NH4)2SO4-grown primary roots. The impaired root growth on (NH4)2SO4 was partially rescued by exogenous auxin or in specific mutants in the auxin pathway. The data suggest that NH4+-induced nutritional and metabolic imbalances can be partially overcome by elevated auxin levels."}],"month":"03","intvolume":" 42","article_type":"original","volume":42,"page":"239 - 251","department":[{"_id":"JiFr"}],"date_updated":"2025-09-23T07:59:44Z","title":"Auxin-modulated root growth inhibition in Arabidopsis thaliana seedlings with ammonium as the sole nitrogen source","_id":"1532","external_id":{"isi":["000349635900003"],"pmid":["32480670"]},"oa_version":"None","pmid":1,"isi":1,"year":"2015","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","quality_controlled":"1","publisher":"CSIRO"},{"date_published":"2015-11-18T00:00:00Z","day":"18","date_created":"2018-12-11T11:52:34Z","author":[{"first_name":"Hongzhe","full_name":"Wang, Hongzhe","last_name":"Wang"},{"last_name":"Yang","full_name":"Yang, Kezhen","first_name":"Kezhen"},{"last_name":"Zou","first_name":"Junjie","full_name":"Zou, Junjie"},{"last_name":"Zhu","full_name":"Zhu, Lingling","first_name":"Lingling"},{"first_name":"Zidian","full_name":"Xie, Zidian","last_name":"Xie"},{"last_name":"Morita","full_name":"Morita, Miyoterao","first_name":"Miyoterao"},{"last_name":"Tasaka","first_name":"Masao","full_name":"Tasaka, Masao"},{"first_name":"Jirí","full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","last_name":"Friml"},{"last_name":"Grotewold","first_name":"Erich","full_name":"Grotewold, Erich"},{"last_name":"Beeckman","full_name":"Beeckman, Tom","first_name":"Tom"},{"full_name":"Vanneste, Steffen","first_name":"Steffen","last_name":"Vanneste"},{"last_name":"Sack","first_name":"Fred","full_name":"Sack, Fred"},{"last_name":"Le","first_name":"Jie","full_name":"Le, Jie"}],"ddc":["570"],"publist_id":"5637","publication_status":"published","publication":"Nature Communications","ec_funded":1,"type":"journal_article","doi":"10.1038/ncomms9822","article_processing_charge":"No","citation":{"ieee":"H. Wang et al., “Transcriptional regulation of PIN genes by FOUR LIPS and MYB88 during Arabidopsis root gravitropism,” Nature Communications, vol. 6. Nature Publishing Group, 2015.","apa":"Wang, H., Yang, K., Zou, J., Zhu, L., Xie, Z., Morita, M., … Le, J. (2015). Transcriptional regulation of PIN genes by FOUR LIPS and MYB88 during Arabidopsis root gravitropism. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms9822","short":"H. Wang, K. Yang, J. Zou, L. Zhu, Z. Xie, M. Morita, M. Tasaka, J. Friml, E. Grotewold, T. Beeckman, S. Vanneste, F. Sack, J. Le, Nature Communications 6 (2015).","chicago":"Wang, Hongzhe, Kezhen Yang, Junjie Zou, Lingling Zhu, Zidian Xie, Miyoterao Morita, Masao Tasaka, et al. “Transcriptional Regulation of PIN Genes by FOUR LIPS and MYB88 during Arabidopsis Root Gravitropism.” Nature Communications. Nature Publishing Group, 2015. https://doi.org/10.1038/ncomms9822.","ama":"Wang H, Yang K, Zou J, et al. Transcriptional regulation of PIN genes by FOUR LIPS and MYB88 during Arabidopsis root gravitropism. Nature Communications. 2015;6. doi:10.1038/ncomms9822","ista":"Wang H, Yang K, Zou J, Zhu L, Xie Z, Morita M, Tasaka M, Friml J, Grotewold E, Beeckman T, Vanneste S, Sack F, Le J. 2015. Transcriptional regulation of PIN genes by FOUR LIPS and MYB88 during Arabidopsis root gravitropism. Nature Communications. 6, 8822.","mla":"Wang, Hongzhe, et al. “Transcriptional Regulation of PIN Genes by FOUR LIPS and MYB88 during Arabidopsis Root Gravitropism.” Nature Communications, vol. 6, 8822, Nature Publishing Group, 2015, doi:10.1038/ncomms9822."},"language":[{"iso":"eng"}],"status":"public","intvolume":" 6","month":"11","has_accepted_license":"1","abstract":[{"text":"PIN proteins are auxin export carriers that direct intercellular auxin flow and in turn regulate many aspects of plant growth and development including responses to environmental changes. The Arabidopsis R2R3-MYB transcription factor FOUR LIPS (FLP) and its paralogue MYB88 regulate terminal divisions during stomatal development, as well as female reproductive development and stress responses. Here we show that FLP and MYB88 act redundantly but differentially in regulating the transcription of PIN3 and PIN7 in gravity-sensing cells of primary and lateral roots. On the one hand, FLP is involved in responses to gravity stimulation in primary roots, whereas on the other, FLP and MYB88 function complementarily in establishing the gravitropic set-point angles of lateral roots. Our results support a model in which FLP and MYB88 expression specifically determines the temporal-spatial patterns of PIN3 and PIN7 transcription that are closely associated with their preferential functions during root responses to gravity.","lang":"eng"}],"file":[{"file_size":1852268,"date_created":"2018-12-12T10:17:07Z","relation":"main_file","file_id":"5259","date_updated":"2020-07-14T12:45:01Z","content_type":"application/pdf","access_level":"open_access","creator":"system","checksum":"3c06735fc7cd7e482ca830cbd26001bf","file_name":"IST-2016-485-v1+1_ncomms9822.pdf"}],"article_number":"8822","scopus_import":"1","_id":"1534","title":"Transcriptional regulation of PIN genes by FOUR LIPS and MYB88 during Arabidopsis root gravitropism","department":[{"_id":"JiFr"}],"date_updated":"2025-09-23T14:55:59Z","project":[{"name":"Polarity and subcellular dynamics in plants","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300","call_identifier":"FP7"}],"oa":1,"volume":6,"oa_version":"Published Version","external_id":{"isi":["000366295500008"]},"pubrep_id":"485","publisher":"Nature Publishing Group","file_date_updated":"2020-07-14T12:45:01Z","quality_controlled":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"year":"2015","isi":1},{"abstract":[{"lang":"eng","text":"Strigolactones, first discovered as germination stimulants for parasitic weeds [1], are carotenoid-derived phytohormones that play major roles in inhibiting lateral bud outgrowth and promoting plant-mycorrhizal symbiosis [2-4]. Furthermore, strigolactones are involved in the regulation of lateral and adventitious root development, root cell division [5, 6], secondary growth [7], and leaf senescence [8]. Recently, we discovered the strigolactone transporter Petunia axillaris PLEIOTROPIC DRUG RESISTANCE 1 (PaPDR1), which is required for efficient mycorrhizal colonization and inhibition of lateral bud outgrowth [9]. However, how strigolactones are transported through the plant remained unknown. Here we show that PaPDR1 exhibits a cell-type-specific asymmetric localization in different root tissues. In root tips, PaPDR1 is co-expressed with the strigolactone biosynthetic gene DAD1 (CCD8), and it is localized at the apical membrane of root hypodermal cells, presumably mediating the shootward transport of strigolactone. Above the root tip, in the hypodermal passage cells that form gates for the entry of mycorrhizal fungi, PaPDR1 is present in the outer-lateral membrane, compatible with its postulated function as strigolactone exporter from root to soil. Transport studies are in line with our localization studies since (1) a papdr1 mutant displays impaired transport of strigolactones out of the root tip to the shoot as well as into the rhizosphere and (2) DAD1 expression and PIN1/PIN2 levels change in plants deregulated for PDR1 expression, suggestive of variations in endogenous strigolactone contents. In conclusion, our results indicate that the polar localizations of PaPDR1 mediate directional shootward strigolactone transport as well as localized exudation into the soil."}],"month":"02","intvolume":" 25","scopus_import":"1","department":[{"_id":"JiFr"}],"date_updated":"2025-09-23T07:57:02Z","title":"Asymmetric localizations of the ABC transporter PaPDR1 trace paths of directional strigolactone transport","_id":"1536","volume":25,"page":"647 - 655","acknowledgement":"This work was funded by a grant of the Swiss National Foundation to E.M.\r\nWe thank Dr. José María Mateos (University of Zurich) for providing us with the vibratome, Prof. Dolf Weijers (Wageningen University, the Netherlands) for shipping us his set of ligation-independent cloning vectors, Prof. Bruno Humbel (University of Lausanne) for suggestions on GFP-PDR1 detection, and Dr. Undine Krügel (University of Zurich) and Prof. Michal Jasinski (Polish Academy of Science) for hints on protein quantification.","oa_version":"None","external_id":{"isi":["000350708800029"]},"quality_controlled":"1","publisher":"Cell Press","isi":1,"year":"2015","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","issue":"5","date_published":"2015-02-12T00:00:00Z","day":"12","author":[{"last_name":"Sasse","full_name":"Sasse, Joëlle","first_name":"Joëlle"},{"full_name":"Simon, Sibu","first_name":"Sibu","last_name":"Simon","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1998-6741"},{"last_name":"Gübeli","first_name":"Christian","full_name":"Gübeli, Christian"},{"full_name":"Liu, Guowei","first_name":"Guowei","last_name":"Liu"},{"last_name":"Cheng","full_name":"Cheng, Xi","first_name":"Xi"},{"first_name":"Jirí","full_name":"Friml, Jirí","last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Harro","full_name":"Bouwmeester, Harro","last_name":"Bouwmeester"},{"last_name":"Martinoia","first_name":"Enrico","full_name":"Martinoia, Enrico"},{"first_name":"Lorenzo","full_name":"Borghi, Lorenzo","last_name":"Borghi"}],"date_created":"2018-12-11T11:52:35Z","publist_id":"5635","publication_status":"published","publication":"Current Biology","doi":"10.1016/j.cub.2015.01.015","type":"journal_article","status":"public","language":[{"iso":"eng"}],"citation":{"short":"J. Sasse, S. Simon, C. Gübeli, G. Liu, X. Cheng, J. Friml, H. Bouwmeester, E. Martinoia, L. Borghi, Current Biology 25 (2015) 647–655.","chicago":"Sasse, Joëlle, Sibu Simon, Christian Gübeli, Guowei Liu, Xi Cheng, Jiří Friml, Harro Bouwmeester, Enrico Martinoia, and Lorenzo Borghi. “Asymmetric Localizations of the ABC Transporter PaPDR1 Trace Paths of Directional Strigolactone Transport.” Current Biology. Cell Press, 2015. https://doi.org/10.1016/j.cub.2015.01.015.","ieee":"J. Sasse et al., “Asymmetric localizations of the ABC transporter PaPDR1 trace paths of directional strigolactone transport,” Current Biology, vol. 25, no. 5. Cell Press, pp. 647–655, 2015.","apa":"Sasse, J., Simon, S., Gübeli, C., Liu, G., Cheng, X., Friml, J., … Borghi, L. (2015). Asymmetric localizations of the ABC transporter PaPDR1 trace paths of directional strigolactone transport. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2015.01.015","ista":"Sasse J, Simon S, Gübeli C, Liu G, Cheng X, Friml J, Bouwmeester H, Martinoia E, Borghi L. 2015. Asymmetric localizations of the ABC transporter PaPDR1 trace paths of directional strigolactone transport. Current Biology. 25(5), 647–655.","mla":"Sasse, Joëlle, et al. “Asymmetric Localizations of the ABC Transporter PaPDR1 Trace Paths of Directional Strigolactone Transport.” Current Biology, vol. 25, no. 5, Cell Press, 2015, pp. 647–55, doi:10.1016/j.cub.2015.01.015.","ama":"Sasse J, Simon S, Gübeli C, et al. Asymmetric localizations of the ABC transporter PaPDR1 trace paths of directional strigolactone transport. Current Biology. 2015;25(5):647-655. doi:10.1016/j.cub.2015.01.015"},"article_processing_charge":"No"},{"day":"01","scopus_import":"1","date_published":"2015-12-01T00:00:00Z","month":"12","intvolume":" 169","abstract":[{"text":"A plethora of diverse programmed cell death (PCD) processes has been described in living organisms. In animals and plants, different forms of PCD play crucial roles in development, immunity, and responses to the environment. While the molecular control of some animal PCD forms such as apoptosis is known in great detail, we still know comparatively little about the regulation of the diverse types of plant PCD. In part, this deficiency in molecular understanding is caused by the lack of reliable reporters to detect PCD processes. Here, we addressed this issue by using a combination of bioinformatics approaches to identify commonly regulated genes during diverse plant PCD processes in Arabidopsis (Arabidopsis thaliana). Our results indicate that the transcriptional signatures of developmentally controlled cell death are largely distinct from the ones associated with environmentally induced cell death. Moreover, different cases of developmental PCD share a set of cell death-associated genes. Most of these genes are evolutionary conserved within the green plant lineage, arguing for an evolutionary conserved core machinery of developmental PCD. Based on this information, we established an array of specific promoter-reporter lines for developmental PCD in Arabidopsis. These PCD indicators represent a powerful resource that can be used in addition to established morphological and biochemical methods to detect and analyze PCD processes in vivo and in planta.","lang":"eng"}],"issue":"4","volume":169,"page":"2684 - 2699","publist_id":"5628","date_created":"2018-12-11T11:52:38Z","author":[{"last_name":"Olvera Carrillo","full_name":"Olvera Carrillo, Yadira","first_name":"Yadira"},{"last_name":"Van Bel","first_name":"Michiel","full_name":"Van Bel, Michiel"},{"full_name":"Van Hautegem, Tom","first_name":"Tom","last_name":"Van Hautegem"},{"first_name":"Matyas","full_name":"Fendrych, Matyas","last_name":"Fendrych","id":"43905548-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9767-8699"},{"last_name":"Huysmans","full_name":"Huysmans, Marlies","first_name":"Marlies"},{"last_name":"Šimášková","full_name":"Šimášková, Mária","first_name":"Mária"},{"full_name":"Van Durme, Matthias","first_name":"Matthias","last_name":"Van Durme"},{"full_name":"Buscaill, Pierre","first_name":"Pierre","last_name":"Buscaill"},{"first_name":"Susana","full_name":"Rivas, Susana","last_name":"Rivas"},{"first_name":"Núria","full_name":"Coll, Núria","last_name":"Coll"},{"first_name":"Frederik","full_name":"Coppens, Frederik","last_name":"Coppens"},{"full_name":"Maere, Steven","first_name":"Steven","last_name":"Maere"},{"first_name":"Moritz","full_name":"Nowack, Moritz","last_name":"Nowack"}],"date_updated":"2025-09-22T14:28:43Z","department":[{"_id":"JiFr"}],"_id":"1543","title":"A conserved core of programmed cell death indicator genes discriminates developmentally and environmentally induced programmed cell death in plants","publication":"Plant Physiology","external_id":{"isi":["000368472700025"]},"publication_status":"published","oa_version":"None","article_processing_charge":"No","citation":{"ama":"Olvera Carrillo Y, Van Bel M, Van Hautegem T, et al. A conserved core of programmed cell death indicator genes discriminates developmentally and environmentally induced programmed cell death in plants. Plant Physiology. 2015;169(4):2684-2699. doi:10.1104/pp.15.00769","ista":"Olvera Carrillo Y, Van Bel M, Van Hautegem T, Fendrych M, Huysmans M, Šimášková M, Van Durme M, Buscaill P, Rivas S, Coll N, Coppens F, Maere S, Nowack M. 2015. A conserved core of programmed cell death indicator genes discriminates developmentally and environmentally induced programmed cell death in plants. Plant Physiology. 169(4), 2684–2699.","mla":"Olvera Carrillo, Yadira, et al. “A Conserved Core of Programmed Cell Death Indicator Genes Discriminates Developmentally and Environmentally Induced Programmed Cell Death in Plants.” Plant Physiology, vol. 169, no. 4, American Society of Plant Biologists, 2015, pp. 2684–99, doi:10.1104/pp.15.00769.","ieee":"Y. Olvera Carrillo et al., “A conserved core of programmed cell death indicator genes discriminates developmentally and environmentally induced programmed cell death in plants,” Plant Physiology, vol. 169, no. 4. American Society of Plant Biologists, pp. 2684–2699, 2015.","apa":"Olvera Carrillo, Y., Van Bel, M., Van Hautegem, T., Fendrych, M., Huysmans, M., Šimášková, M., … Nowack, M. (2015). A conserved core of programmed cell death indicator genes discriminates developmentally and environmentally induced programmed cell death in plants. Plant Physiology. American Society of Plant Biologists. https://doi.org/10.1104/pp.15.00769","short":"Y. Olvera Carrillo, M. Van Bel, T. Van Hautegem, M. Fendrych, M. Huysmans, M. Šimášková, M. Van Durme, P. Buscaill, S. Rivas, N. Coll, F. Coppens, S. Maere, M. Nowack, Plant Physiology 169 (2015) 2684–2699.","chicago":"Olvera Carrillo, Yadira, Michiel Van Bel, Tom Van Hautegem, Matyas Fendrych, Marlies Huysmans, Mária Šimášková, Matthias Van Durme, et al. “A Conserved Core of Programmed Cell Death Indicator Genes Discriminates Developmentally and Environmentally Induced Programmed Cell Death in Plants.” Plant Physiology. American Society of Plant Biologists, 2015. https://doi.org/10.1104/pp.15.00769."},"language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","status":"public","isi":1,"year":"2015","doi":"10.1104/pp.15.00769","type":"journal_article","publisher":"American Society of Plant Biologists"},{"citation":{"ama":"Liao C, Smet W, Brunoud G, Yoshida S, Vernoux T, Weijers D. Reporters for sensitive and quantitative measurement of auxin response. Nature Methods. 2015;12(3):207-210. doi:10.1038/nmeth.3279","ista":"Liao C, Smet W, Brunoud G, Yoshida S, Vernoux T, Weijers D. 2015. Reporters for sensitive and quantitative measurement of auxin response. Nature Methods. 12(3), 207–210.","mla":"Liao, Cheyang, et al. “Reporters for Sensitive and Quantitative Measurement of Auxin Response.” Nature Methods, vol. 12, no. 3, Nature Publishing Group, 2015, pp. 207–10, doi:10.1038/nmeth.3279.","ieee":"C. Liao, W. Smet, G. Brunoud, S. Yoshida, T. Vernoux, and D. Weijers, “Reporters for sensitive and quantitative measurement of auxin response,” Nature Methods, vol. 12, no. 3. Nature Publishing Group, pp. 207–210, 2015.","apa":"Liao, C., Smet, W., Brunoud, G., Yoshida, S., Vernoux, T., & Weijers, D. (2015). Reporters for sensitive and quantitative measurement of auxin response. Nature Methods. Nature Publishing Group. https://doi.org/10.1038/nmeth.3279","short":"C. Liao, W. Smet, G. Brunoud, S. Yoshida, T. Vernoux, D. Weijers, Nature Methods 12 (2015) 207–210.","chicago":"Liao, Cheyang, Wouter Smet, Géraldine Brunoud, Saiko Yoshida, Teva Vernoux, and Dolf Weijers. “Reporters for Sensitive and Quantitative Measurement of Auxin Response.” Nature Methods. Nature Publishing Group, 2015. https://doi.org/10.1038/nmeth.3279."},"article_processing_charge":"No","language":[{"iso":"eng"}],"status":"public","doi":"10.1038/nmeth.3279","type":"journal_article","publication":"Nature Methods","publication_status":"published","publist_id":"5617","date_created":"2018-12-11T11:52:41Z","author":[{"full_name":"Liao, Cheyang","first_name":"Cheyang","last_name":"Liao"},{"last_name":"Smet","first_name":"Wouter","full_name":"Smet, Wouter"},{"last_name":"Brunoud","full_name":"Brunoud, Géraldine","first_name":"Géraldine"},{"id":"2E46069C-F248-11E8-B48F-1D18A9856A87","last_name":"Yoshida","full_name":"Yoshida, Saiko","first_name":"Saiko"},{"last_name":"Vernoux","full_name":"Vernoux, Teva","first_name":"Teva"},{"last_name":"Weijers","first_name":"Dolf","full_name":"Weijers, Dolf"}],"day":"26","date_published":"2015-02-26T00:00:00Z","issue":"3","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"pmid":1,"year":"2015","publisher":"Nature Publishing Group","quality_controlled":"1","external_id":{"isi":["000350670300017"],"pmid":["25643149"]},"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4344836/"}],"oa_version":"Submitted Version","page":"207 - 210","volume":12,"oa":1,"department":[{"_id":"JiFr"}],"date_updated":"2025-09-23T10:34:32Z","title":"Reporters for sensitive and quantitative measurement of auxin response","_id":"1554","scopus_import":"1","month":"02","intvolume":" 12","abstract":[{"text":"The visualization of hormonal signaling input and output is key to understanding how multicellular development is regulated. The plant signaling molecule auxin triggers many growth and developmental responses, but current tools lack the sensitivity or precision to visualize these. We developed a set of fluorescent reporters that allow sensitive and semiquantitative readout of auxin responses at cellular resolution in Arabidopsis thaliana. These generic tools are suitable for any transformable plant species.","lang":"eng"}]},{"external_id":{"isi":["000359687400017"]},"pubrep_id":"480","oa_version":"Published Version","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"year":"2015","publisher":"Oxford University Press","file_date_updated":"2020-07-14T12:45:02Z","quality_controlled":"1","scopus_import":"1","month":"08","has_accepted_license":"1","intvolume":" 66","file":[{"file_id":"5051","date_updated":"2020-07-14T12:45:02Z","relation":"main_file","date_created":"2018-12-12T10:14:02Z","file_size":7753043,"checksum":"257919be0ce3d306185d3891ad7acf39","file_name":"IST-2016-480-v1+1_J._Exp._Bot.-2015-Jia-4631-42.pdf","creator":"system","content_type":"application/pdf","access_level":"open_access"}],"abstract":[{"lang":"eng","text":"The elongator complex subunit 2 (ELP2) protein, one subunit of an evolutionarily conserved histone acetyltransferase complex, has been shown to participate in leaf patterning, plant immune and abiotic stress responses in Arabidopsis thaliana. Here, its role in root development was explored. Compared to the wild type, the elp2 mutant exhibited an accelerated differentiation of its root stem cells and cell division was more active in its quiescent centre (QC). The key transcription factors responsible for maintaining root stem cell and QC identity, such as AP2 transcription factors PLT1 (PLETHORA1) and PLT2 (PLETHORA2), GRAS transcription factors such as SCR (SCARECROW) and SHR (SHORT ROOT) and WUSCHEL-RELATED HOMEOBOX5 transcription factor WOX5, were all strongly down-regulated in the mutant. On the other hand, expression of the G2/M transition activator CYCB1 was substantially induced in elp2. The auxin efflux transporters PIN1 and PIN2 showed decreased protein levels and PIN1 also displayed mild polarity alterations in elp2, which resulted in a reduced auxin content in the root tip. Either the acetylation or methylation level of each of these genes differed between the mutant and the wild type, suggesting that the ELP2 regulation of root development involves the epigenetic modification of a range of transcription factors and other developmental regulators."}],"page":"4631 - 4642","oa":1,"volume":66,"department":[{"_id":"JiFr"}],"date_updated":"2025-09-23T13:42:27Z","_id":"1556","title":"The Arabidopsis thaliana elongator complex subunit 2 epigenetically affects root development","publication":"Journal of Experimental Botany","publication_status":"published","language":[{"iso":"eng"}],"article_processing_charge":"No","citation":{"ista":"Jia Y, Tian H, Li H, Yu Q, Wang L, Friml J, Ding Z. 2015. The Arabidopsis thaliana elongator complex subunit 2 epigenetically affects root development. Journal of Experimental Botany. 66(15), 4631–4642.","mla":"Jia, Yuebin, et al. “The Arabidopsis Thaliana Elongator Complex Subunit 2 Epigenetically Affects Root Development.” Journal of Experimental Botany, vol. 66, no. 15, Oxford University Press, 2015, pp. 4631–42, doi:10.1093/jxb/erv230.","ama":"Jia Y, Tian H, Li H, et al. The Arabidopsis thaliana elongator complex subunit 2 epigenetically affects root development. Journal of Experimental Botany. 2015;66(15):4631-4642. doi:10.1093/jxb/erv230","short":"Y. Jia, H. Tian, H. Li, Q. Yu, L. Wang, J. Friml, Z. Ding, Journal of Experimental Botany 66 (2015) 4631–4642.","chicago":"Jia, Yuebin, Huiyu Tian, Hongjiang Li, Qianqian Yu, Lei Wang, Jiří Friml, and Zhaojun Ding. “The Arabidopsis Thaliana Elongator Complex Subunit 2 Epigenetically Affects Root Development.” Journal of Experimental Botany. Oxford University Press, 2015. https://doi.org/10.1093/jxb/erv230.","ieee":"Y. Jia et al., “The Arabidopsis thaliana elongator complex subunit 2 epigenetically affects root development,” Journal of Experimental Botany, vol. 66, no. 15. Oxford University Press, pp. 4631–4642, 2015.","apa":"Jia, Y., Tian, H., Li, H., Yu, Q., Wang, L., Friml, J., & Ding, Z. (2015). The Arabidopsis thaliana elongator complex subunit 2 epigenetically affects root development. Journal of Experimental Botany. Oxford University Press. https://doi.org/10.1093/jxb/erv230"},"status":"public","doi":"10.1093/jxb/erv230","type":"journal_article","day":"01","date_published":"2015-08-01T00:00:00Z","issue":"15","ddc":["570"],"publist_id":"5615","date_created":"2018-12-11T11:52:42Z","author":[{"last_name":"Jia","first_name":"Yuebin","full_name":"Jia, Yuebin"},{"full_name":"Tian, Huiyu","first_name":"Huiyu","last_name":"Tian"},{"first_name":"Hongjiang","full_name":"Li, Hongjiang","orcid":"0000-0001-5039-9660","id":"33CA54A6-F248-11E8-B48F-1D18A9856A87","last_name":"Li"},{"last_name":"Yu","full_name":"Yu, Qianqian","first_name":"Qianqian"},{"full_name":"Wang, Lei","first_name":"Lei","last_name":"Wang"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jirí","first_name":"Jirí"},{"last_name":"Ding","full_name":"Ding, Zhaojun","first_name":"Zhaojun"}]},{"oa_version":"None","external_id":{"isi":["000351697100012"]},"quality_controlled":"1","publisher":"Company of Biologists","isi":1,"year":"2015","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","abstract":[{"text":"CyclophilinAis a conserved peptidyl-prolyl cis-trans isomerase (PPIase) best known as the cellular receptor of the immunosuppressant cyclosporine A. Despite significant effort, evidence of developmental functions of cyclophilin A in non-plant systems has remained obscure. Mutations in a tomato (Solanum lycopersicum) cyclophilin A ortholog, DIAGEOTROPICA (DGT), have been shown to abolish the organogenesis of lateral roots; however, a mechanistic explanation of the phenotype is lacking. Here, we show that the dgt mutant lacks auxin maxima relevant to priming and specification of lateral root founder cells. DGT is expressed in shoot and root, and localizes to both the nucleus and cytoplasm during lateral root organogenesis. Mutation of ENTIRE/ IAA9, a member of the auxin-responsive Aux/IAA protein family of transcriptional repressors, partially restores the inability of dgt to initiate lateral root primordia but not the primordia outgrowth. By comparison, grafting of a wild-type scion restores the process of lateral root formation, consistent with participation of a mobile signal. Antibodies do not detect movement of the DGT protein into the dgt rootstock; however, experiments with radiolabeled auxin and an auxin-specific microelectrode demonstrate abnormal auxin fluxes. Functional studies of DGT in heterologous yeast and tobacco-leaf auxin-transport systems demonstrate that DGT negatively regulates PIN-FORMED (PIN) auxin efflux transporters by affecting their plasma membrane localization. Studies in tomato support complex effects of the dgt mutation on PIN expression level, expression domain and plasma membrane localization. Our data demonstrate that DGT regulates auxin transport in lateral root formation.","lang":"eng"}],"month":"02","intvolume":" 142","scopus_import":"1","date_updated":"2025-09-23T13:49:06Z","department":[{"_id":"JiFr"}],"title":"The cyclophilin a DIAGEOTROPICA gene affects auxin transport in both root and shoot to control lateral root formation","_id":"1558","page":"712 - 721","volume":142,"publication_status":"published","publication":"Development","doi":"10.1242/dev.113225","type":"journal_article","status":"public","article_processing_charge":"No","language":[{"iso":"eng"}],"citation":{"chicago":"Ivanchenko, Maria, Jinsheng Zhu, Bangjun Wang, Eva Medvecka, Yunlong Du, Elisa Azzarello, Stefano Mancuso, et al. “The Cyclophilin a DIAGEOTROPICA Gene Affects Auxin Transport in Both Root and Shoot to Control Lateral Root Formation.” Development. Company of Biologists, 2015. https://doi.org/10.1242/dev.113225.","short":"M. Ivanchenko, J. Zhu, B. Wang, E. Medvecka, Y. Du, E. Azzarello, S. Mancuso, M. Megraw, S. Filichkin, J. Dubrovsky, J. Friml, M. Geisler, Development 142 (2015) 712–721.","apa":"Ivanchenko, M., Zhu, J., Wang, B., Medvecka, E., Du, Y., Azzarello, E., … Geisler, M. (2015). The cyclophilin a DIAGEOTROPICA gene affects auxin transport in both root and shoot to control lateral root formation. Development. Company of Biologists. https://doi.org/10.1242/dev.113225","ieee":"M. Ivanchenko et al., “The cyclophilin a DIAGEOTROPICA gene affects auxin transport in both root and shoot to control lateral root formation,” Development, vol. 142, no. 4. Company of Biologists, pp. 712–721, 2015.","mla":"Ivanchenko, Maria, et al. “The Cyclophilin a DIAGEOTROPICA Gene Affects Auxin Transport in Both Root and Shoot to Control Lateral Root Formation.” Development, vol. 142, no. 4, Company of Biologists, 2015, pp. 712–21, doi:10.1242/dev.113225.","ista":"Ivanchenko M, Zhu J, Wang B, Medvecka E, Du Y, Azzarello E, Mancuso S, Megraw M, Filichkin S, Dubrovsky J, Friml J, Geisler M. 2015. The cyclophilin a DIAGEOTROPICA gene affects auxin transport in both root and shoot to control lateral root formation. Development. 142(4), 712–721.","ama":"Ivanchenko M, Zhu J, Wang B, et al. The cyclophilin a DIAGEOTROPICA gene affects auxin transport in both root and shoot to control lateral root formation. Development. 2015;142(4):712-721. doi:10.1242/dev.113225"},"issue":"4","date_published":"2015-02-15T00:00:00Z","day":"15","author":[{"last_name":"Ivanchenko","first_name":"Maria","full_name":"Ivanchenko, Maria"},{"first_name":"Jinsheng","full_name":"Zhu, Jinsheng","last_name":"Zhu"},{"full_name":"Wang, Bangjun","first_name":"Bangjun","last_name":"Wang"},{"full_name":"Medvecka, Eva","first_name":"Eva","id":"298814E2-F248-11E8-B48F-1D18A9856A87","last_name":"Medvecka"},{"last_name":"Du","full_name":"Du, Yunlong","first_name":"Yunlong"},{"full_name":"Azzarello, Elisa","first_name":"Elisa","last_name":"Azzarello"},{"last_name":"Mancuso","first_name":"Stefano","full_name":"Mancuso, Stefano"},{"full_name":"Megraw, Molly","first_name":"Molly","last_name":"Megraw"},{"last_name":"Filichkin","full_name":"Filichkin, Sergei","first_name":"Sergei"},{"full_name":"Dubrovsky, Joseph","first_name":"Joseph","last_name":"Dubrovsky"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí","first_name":"Jirí"},{"last_name":"Geisler","full_name":"Geisler, Markus","first_name":"Markus"}],"date_created":"2018-12-11T11:52:42Z","publist_id":"5613"},{"abstract":[{"lang":"eng","text":"The plant hormone auxin is a key regulator of plant growth and development. Auxin levels are sensed and interpreted by distinct receptor systems that activate a broad range of cellular responses. The Auxin-Binding Protein1 (ABP1) that has been identified based on its ability to bind auxin with high affinity is a prime candidate for the extracellular receptor responsible for mediating a range of auxin effects, in particular, the fast non-transcriptional ones. Contradictory genetic studies suggested prominent or no importance of ABP1 in many developmental processes. However, how crucial the role of auxin binding to ABP1 is for its functions has not been addressed. Here, we show that the auxin-binding pocket of ABP1 is essential for its gain-of-function cellular and developmental roles. In total, 16 different abp1 mutants were prepared that possessed substitutions in the metal core or in the hydrophobic amino acids of the auxin-binding pocket as well as neutral mutations. Their analysis revealed that an intact auxin-binding pocket is a prerequisite for ABP1 to activate downstream components of the ABP1 signalling pathway, such as Rho of Plants (ROPs) and to mediate the clathrin association with membranes for endocytosis regulation. In planta analyses demonstrated the importance of the auxin binding pocket for all known ABP1-mediated postembryonic developmental processes, including morphology of leaf epidermal cells, root growth and root meristem activity, and vascular tissue differentiation. Taken together, these findings suggest that auxin binding to ABP1 is central to its function, supporting the role of ABP1 as auxin receptor."}],"month":"08","intvolume":" 66","article_type":"original","scopus_import":"1","department":[{"_id":"JiFr"},{"_id":"EM-Fac"}],"date_updated":"2025-09-23T07:59:07Z","title":"Auxin-binding pocket of ABP1 is crucial for its gain-of-function cellular and developmental roles","_id":"1562","page":"5055 - 5065","volume":66,"project":[{"grant_number":"282300","name":"Polarity and subcellular dynamics in plants","_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"acknowledgement":"This work was supported by ERC Independent Research grant (ERC-2011-StG- 20101109-PSDP to JF); the European Social Fund and the state budget of the Czech Republic [the project ‘Employment of Newly Graduated Doctors of Science for Scientific Excellence’ (CZ.1.07/2.3.00/30.0009) to TN]; the Czech Science Foundation (GACR) [project 13-40637S to JF].","oa_version":"None","external_id":{"isi":["000359688300017"]},"quality_controlled":"1","publisher":"Oxford University Press","isi":1,"year":"2015","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","issue":"16","date_published":"2015-08-01T00:00:00Z","day":"01","author":[{"full_name":"Grones, Peter","first_name":"Peter","id":"399876EC-F248-11E8-B48F-1D18A9856A87","last_name":"Grones"},{"full_name":"Chen, Xu","first_name":"Xu","last_name":"Chen","id":"4E5ADCAA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Simon, Sibu","first_name":"Sibu","last_name":"Simon","orcid":"0000-0002-1998-6741","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kaufmann","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9735-5315","first_name":"Walter","full_name":"Kaufmann, Walter"},{"first_name":"Riet","full_name":"De Rycke, Riet","last_name":"De Rycke"},{"full_name":"Nodzyński, Tomasz","first_name":"Tomasz","last_name":"Nodzyński"},{"last_name":"Zažímalová","full_name":"Zažímalová, Eva","first_name":"Eva"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí","first_name":"Jirí"}],"corr_author":"1","date_created":"2018-12-11T11:52:44Z","publist_id":"5609","publication_status":"published","ec_funded":1,"publication":"Journal of Experimental Botany","doi":"10.1093/jxb/erv177","type":"journal_article","status":"public","article_processing_charge":"No","language":[{"iso":"eng"}],"citation":{"ista":"Grones P, Chen X, Simon S, Kaufmann W, De Rycke R, Nodzyński T, Zažímalová E, Friml J. 2015. Auxin-binding pocket of ABP1 is crucial for its gain-of-function cellular and developmental roles. Journal of Experimental Botany. 66(16), 5055–5065.","mla":"Grones, Peter, et al. “Auxin-Binding Pocket of ABP1 Is Crucial for Its Gain-of-Function Cellular and Developmental Roles.” Journal of Experimental Botany, vol. 66, no. 16, Oxford University Press, 2015, pp. 5055–65, doi:10.1093/jxb/erv177.","ama":"Grones P, Chen X, Simon S, et al. Auxin-binding pocket of ABP1 is crucial for its gain-of-function cellular and developmental roles. Journal of Experimental Botany. 2015;66(16):5055-5065. doi:10.1093/jxb/erv177","short":"P. Grones, X. Chen, S. Simon, W. Kaufmann, R. De Rycke, T. Nodzyński, E. Zažímalová, J. Friml, Journal of Experimental Botany 66 (2015) 5055–5065.","chicago":"Grones, Peter, Xu Chen, Sibu Simon, Walter Kaufmann, Riet De Rycke, Tomasz Nodzyński, Eva Zažímalová, and Jiří Friml. “Auxin-Binding Pocket of ABP1 Is Crucial for Its Gain-of-Function Cellular and Developmental Roles.” Journal of Experimental Botany. Oxford University Press, 2015. https://doi.org/10.1093/jxb/erv177.","ieee":"P. Grones et al., “Auxin-binding pocket of ABP1 is crucial for its gain-of-function cellular and developmental roles,” Journal of Experimental Botany, vol. 66, no. 16. Oxford University Press, pp. 5055–5065, 2015.","apa":"Grones, P., Chen, X., Simon, S., Kaufmann, W., De Rycke, R., Nodzyński, T., … Friml, J. (2015). Auxin-binding pocket of ABP1 is crucial for its gain-of-function cellular and developmental roles. Journal of Experimental Botany. Oxford University Press. https://doi.org/10.1093/jxb/erv177"}},{"article_processing_charge":"No","citation":{"mla":"Doyle, Siamsa, et al. “An Early Secretory Pathway Mediated by Gnom-like 1 and Gnom Is Essential for Basal Polarity Establishment in Arabidopsis Thaliana.” PNAS, vol. 112, no. 7, National Academy of Sciences, 2015, pp. E806–15, doi:10.1073/pnas.1424856112.","ista":"Doyle S, Haegera A, Vain T, Rigala A, Viotti C, Łangowskaa M, Maa Q, Friml J, Raikhel N, Hickse G, Robert S. 2015. An early secretory pathway mediated by gnom-like 1 and gnom is essential for basal polarity establishment in Arabidopsis thaliana. PNAS. 112(7), E806–E815.","ama":"Doyle S, Haegera A, Vain T, et al. An early secretory pathway mediated by gnom-like 1 and gnom is essential for basal polarity establishment in Arabidopsis thaliana. PNAS. 2015;112(7):E806-E815. doi:10.1073/pnas.1424856112","chicago":"Doyle, Siamsa, Ash Haegera, Thomas Vain, Adeline Rigala, Corrado Viotti, Małgorzata Łangowskaa, Qian Maa, et al. “An Early Secretory Pathway Mediated by Gnom-like 1 and Gnom Is Essential for Basal Polarity Establishment in Arabidopsis Thaliana.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1424856112.","short":"S. Doyle, A. Haegera, T. Vain, A. Rigala, C. Viotti, M. Łangowskaa, Q. Maa, J. Friml, N. Raikhel, G. Hickse, S. Robert, PNAS 112 (2015) E806–E815.","apa":"Doyle, S., Haegera, A., Vain, T., Rigala, A., Viotti, C., Łangowskaa, M., … Robert, S. (2015). An early secretory pathway mediated by gnom-like 1 and gnom is essential for basal polarity establishment in Arabidopsis thaliana. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1424856112","ieee":"S. Doyle et al., “An early secretory pathway mediated by gnom-like 1 and gnom is essential for basal polarity establishment in Arabidopsis thaliana,” PNAS, vol. 112, no. 7. National Academy of Sciences, pp. E806–E815, 2015."},"language":[{"iso":"eng"}],"status":"public","doi":"10.1073/pnas.1424856112","type":"journal_article","publication":"PNAS","ec_funded":1,"publication_status":"published","ddc":["580"],"publist_id":"5602","date_created":"2018-12-11T11:52:46Z","author":[{"first_name":"Siamsa","full_name":"Doyle, Siamsa","last_name":"Doyle"},{"last_name":"Haegera","full_name":"Haegera, Ash","first_name":"Ash"},{"last_name":"Vain","first_name":"Thomas","full_name":"Vain, Thomas"},{"first_name":"Adeline","full_name":"Rigala, Adeline","last_name":"Rigala"},{"last_name":"Viotti","first_name":"Corrado","full_name":"Viotti, Corrado"},{"full_name":"Łangowskaa, Małgorzata","first_name":"Małgorzata","last_name":"Łangowskaa"},{"full_name":"Maa, Qian","first_name":"Qian","last_name":"Maa"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jirí","first_name":"Jirí"},{"full_name":"Raikhel, Natasha","first_name":"Natasha","last_name":"Raikhel"},{"first_name":"Glenn","full_name":"Hickse, Glenn","last_name":"Hickse"},{"last_name":"Robert","first_name":"Stéphanie","full_name":"Robert, Stéphanie"}],"day":"17","date_published":"2015-02-17T00:00:00Z","issue":"7","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"year":"2015","publisher":"National Academy of Sciences","quality_controlled":"1","external_id":{"isi":["000349446000025"]},"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4343110/","open_access":"1"}],"acknowledgement":"This work was supported by Vetenskapsrådet and Vinnova (Verket för Innovationssystemet) (S.M.D., T.V., M.Ł., and S.R.), Knut och Alice Wallenbergs Stiftelse (S.M.D., A.R., and C.V.), Kempestiftelserna (A.H. and Q.M.), Carl Tryggers Stiftelse för Vetenskaplig Forskning (Q.M.), European Research Council Grant ERC-2011-StG-20101109-PSDP (to J.F.), US Department of Energy Grant DE-FG02-02ER15295 (to N.V.R.), and National Science Foundation Grant MCB-0817916 (to N.V.R. and G.R.H.). ","oa_version":"Published Version","project":[{"call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300"}],"page":"E806 - E815","oa":1,"volume":112,"department":[{"_id":"JiFr"}],"date_updated":"2026-06-18T17:48:36Z","title":"An early secretory pathway mediated by gnom-like 1 and gnom is essential for basal polarity establishment in Arabidopsis thaliana","_id":"1569","scopus_import":"1","month":"02","intvolume":" 112","abstract":[{"lang":"eng","text":"Spatial regulation of the plant hormone indole-3-acetic acid (IAA, or auxin) is essential for plant development. Auxin gradient establishment is mediated by polarly localized auxin transporters, including PIN-FORMED (PIN) proteins. Their localization and abundance at the plasma membrane are tightly regulated by endomembrane machinery, especially the endocytic and recycling pathways mediated by the ADP ribosylation factor guanine nucleotide exchange factor (ARF-GEF) GNOM. We assessed the role of the early secretory pathway in establishing PIN1 polarity in Arabidopsis thaliana by pharmacological and genetic approaches. We identified the compound endosidin 8 (ES8), which selectively interferes with PIN1 basal polarity without altering the polarity of apical proteins. ES8 alters the auxin distribution pattern in the root and induces a strong developmental phenotype, including reduced root length. The ARF-GEF- defective mutants gnom-like 1 ( gnl1-1) and gnom ( van7) are significantly resistant to ES8. The compound does not affect recycling or vacuolar trafficking of PIN1 but leads to its intracellular accumulation, resulting in loss of PIN1 basal polarity at the plasma membrane. Our data confirm a role for GNOM in endoplasmic reticulum (ER) - Golgi trafficking and reveal that a GNL1/GNOM-mediated early secretory pathway selectively regulates PIN1 basal polarity establishment in a manner essential for normal plant development."}]},{"publication_status":"published","publication":"Nature Communications","type":"journal_article","doi":"10.1038/ncomms9821","status":"public","language":[{"iso":"eng"}],"citation":{"apa":"Chen, Q., Liu, Y., Maere, S., Lee, E., Van Isterdael, G., Xie, Z., … Vanneste, S. (2015). A coherent transcriptional feed-forward motif model for mediating auxin-sensitive PIN3 expression during lateral root development. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms9821","ieee":"Q. Chen et al., “A coherent transcriptional feed-forward motif model for mediating auxin-sensitive PIN3 expression during lateral root development,” Nature Communications, vol. 6. Nature Publishing Group, 2015.","chicago":"Chen, Qian, Yang Liu, Steven Maere, Eunkyoung Lee, Gert Van Isterdael, Zidian Xie, Wei Xuan, et al. “A Coherent Transcriptional Feed-Forward Motif Model for Mediating Auxin-Sensitive PIN3 Expression during Lateral Root Development.” Nature Communications. Nature Publishing Group, 2015. https://doi.org/10.1038/ncomms9821.","short":"Q. Chen, Y. Liu, S. Maere, E. Lee, G. Van Isterdael, Z. Xie, W. Xuan, J. Lucas, V. Vassileva, S. Kitakura, P. Marhavý, K.T. Wabnik, N. Geldner, E. Benková, J. Le, H. Fukaki, E. Grotewold, C. Li, J. Friml, F. Sack, T. Beeckman, S. Vanneste, Nature Communications 6 (2015).","ama":"Chen Q, Liu Y, Maere S, et al. A coherent transcriptional feed-forward motif model for mediating auxin-sensitive PIN3 expression during lateral root development. Nature Communications. 2015;6. doi:10.1038/ncomms9821","mla":"Chen, Qian, et al. “A Coherent Transcriptional Feed-Forward Motif Model for Mediating Auxin-Sensitive PIN3 Expression during Lateral Root Development.” Nature Communications, vol. 6, 8821, Nature Publishing Group, 2015, doi:10.1038/ncomms9821.","ista":"Chen Q, Liu Y, Maere S, Lee E, Van Isterdael G, Xie Z, Xuan W, Lucas J, Vassileva V, Kitakura S, Marhavý P, Wabnik KT, Geldner N, Benková E, Le J, Fukaki H, Grotewold E, Li C, Friml J, Sack F, Beeckman T, Vanneste S. 2015. A coherent transcriptional feed-forward motif model for mediating auxin-sensitive PIN3 expression during lateral root development. Nature Communications. 6, 8821."},"article_processing_charge":"No","date_published":"2015-11-18T00:00:00Z","day":"18","author":[{"full_name":"Chen, Qian","first_name":"Qian","last_name":"Chen"},{"first_name":"Yang","full_name":"Liu, Yang","last_name":"Liu"},{"last_name":"Maere","first_name":"Steven","full_name":"Maere, Steven"},{"last_name":"Lee","full_name":"Lee, Eunkyoung","first_name":"Eunkyoung"},{"last_name":"Van Isterdael","first_name":"Gert","full_name":"Van Isterdael, Gert"},{"full_name":"Xie, Zidian","first_name":"Zidian","last_name":"Xie"},{"last_name":"Xuan","full_name":"Xuan, Wei","first_name":"Wei"},{"last_name":"Lucas","first_name":"Jessica","full_name":"Lucas, Jessica"},{"last_name":"Vassileva","full_name":"Vassileva, Valya","first_name":"Valya"},{"full_name":"Kitakura, Saeko","first_name":"Saeko","last_name":"Kitakura"},{"last_name":"Marhavy","orcid":"0000-0001-5227-5741","id":"3F45B078-F248-11E8-B48F-1D18A9856A87","full_name":"Marhavy, Peter","first_name":"Peter"},{"id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7263-0560","last_name":"Wabnik","full_name":"Wabnik, Krzysztof T","first_name":"Krzysztof T"},{"full_name":"Geldner, Niko","first_name":"Niko","last_name":"Geldner"},{"first_name":"Eva","full_name":"Benková, Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","last_name":"Benková"},{"full_name":"Le, Jie","first_name":"Jie","last_name":"Le"},{"full_name":"Fukaki, Hidehiro","first_name":"Hidehiro","last_name":"Fukaki"},{"last_name":"Grotewold","full_name":"Grotewold, Erich","first_name":"Erich"},{"first_name":"Chuanyou","full_name":"Li, Chuanyou","last_name":"Li"},{"last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","first_name":"Jirí"},{"last_name":"Sack","full_name":"Sack, Fred","first_name":"Fred"},{"full_name":"Beeckman, Tom","first_name":"Tom","last_name":"Beeckman"},{"last_name":"Vanneste","first_name":"Steffen","full_name":"Vanneste, Steffen"}],"date_created":"2018-12-11T11:52:48Z","publist_id":"5597","ddc":["580"],"oa_version":"Published Version","acknowledgement":"of the European Research Council (project ERC-2011-StG-20101109-PSDP) (to J.F.), a FEBS long-term fellowship (to P.M.) ","pubrep_id":"477","external_id":{"isi":["000366295500007"]},"quality_controlled":"1","publisher":"Nature Publishing Group","file_date_updated":"2020-07-14T12:45:02Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"year":"2015","isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","abstract":[{"text":"Multiple plant developmental processes, such as lateral root development, depend on auxin distribution patterns that are in part generated by the PIN-formed family of auxin-efflux transporters. Here we propose that AUXIN RESPONSE FACTOR7 (ARF7) and the ARF7-regulated FOUR LIPS/MYB124 (FLP) transcription factors jointly form a coherent feed-forward motif that mediates the auxin-responsive PIN3 transcription in planta to steer the early steps of lateral root formation. This regulatory mechanism might endow the PIN3 circuitry with a temporal 'memory' of auxin stimuli, potentially maintaining and enhancing the robustness of the auxin flux directionality during lateral root development. The cooperative action between canonical auxin signalling and other transcription factors might constitute a general mechanism by which transcriptional auxin-sensitivity can be regulated at a tissue-specific level.","lang":"eng"}],"file":[{"file_name":"IST-2016-477-v1+1_ncomms9821.pdf","checksum":"8ff5c108899b548806e1cb7a302fe76d","creator":"system","access_level":"open_access","content_type":"application/pdf","date_updated":"2020-07-14T12:45:02Z","file_id":"5085","relation":"main_file","date_created":"2018-12-12T10:14:32Z","file_size":1701815}],"intvolume":" 6","has_accepted_license":"1","month":"11","article_number":"8821","scopus_import":"1","_id":"1574","title":"A coherent transcriptional feed-forward motif model for mediating auxin-sensitive PIN3 expression during lateral root development","date_updated":"2025-09-22T14:28:09Z","department":[{"_id":"EvBe"},{"_id":"JiFr"}],"oa":1,"volume":6},{"oa_version":"Submitted Version","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4330589/","open_access":"1"}],"external_id":{"isi":["000350764700007"],"pmid":["25604445"]},"quality_controlled":"1","publisher":"American Society of Plant Biologists","pmid":1,"isi":1,"year":"2015","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","abstract":[{"text":"Auxin participates in a multitude of developmental processes, as well as responses to environmental cues. Compared with other plant hormones, auxin exhibits a unique property, as it undergoes directional, cell-to-cell transport facilitated by plasma membrane-localized transport proteins. Among them, a prominent role has been ascribed to the PIN family of auxin efflux facilitators. PIN proteins direct polar auxin transport on account of their asymmetric subcellular localizations. In this review, we provide an overview of the multiple developmental roles of PIN proteins, including the atypical endoplasmic reticulum-localized members of the family, and look at the family from an evolutionary perspective. Next, we cover the cell biological and molecular aspects of PIN function, in particular the establishment of their polar subcellular localization. Hormonal and environmental inputs into the regulation of PIN action are summarized as well.","lang":"eng"}],"month":"01","intvolume":" 27","scopus_import":"1","date_updated":"2026-04-08T14:20:44Z","department":[{"_id":"JiFr"}],"title":"PIN-dependent auxin transport: Action, regulation, and evolution","_id":"1591","page":"20 - 32","oa":1,"volume":27,"publication_status":"published","publication":"Plant Cell","doi":"10.1105/tpc.114.134874","type":"journal_article","status":"public","article_processing_charge":"No","citation":{"short":"M. Adamowski, J. Friml, Plant Cell 27 (2015) 20–32.","chicago":"Adamowski, Maciek, and Jiří Friml. “PIN-Dependent Auxin Transport: Action, Regulation, and Evolution.” Plant Cell. American Society of Plant Biologists, 2015. https://doi.org/10.1105/tpc.114.134874.","ieee":"M. Adamowski and J. Friml, “PIN-dependent auxin transport: Action, regulation, and evolution,” Plant Cell, vol. 27, no. 1. American Society of Plant Biologists, pp. 20–32, 2015.","apa":"Adamowski, M., & Friml, J. (2015). PIN-dependent auxin transport: Action, regulation, and evolution. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.114.134874","ista":"Adamowski M, Friml J. 2015. PIN-dependent auxin transport: Action, regulation, and evolution. Plant Cell. 27(1), 20–32.","mla":"Adamowski, Maciek, and Jiří Friml. “PIN-Dependent Auxin Transport: Action, Regulation, and Evolution.” Plant Cell, vol. 27, no. 1, American Society of Plant Biologists, 2015, pp. 20–32, doi:10.1105/tpc.114.134874.","ama":"Adamowski M, Friml J. PIN-dependent auxin transport: Action, regulation, and evolution. Plant Cell. 2015;27(1):20-32. doi:10.1105/tpc.114.134874"},"language":[{"iso":"eng"}],"issue":"1","date_published":"2015-01-20T00:00:00Z","day":"20","author":[{"full_name":"Adamowski, Maciek","first_name":"Maciek","last_name":"Adamowski","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6463-5257"},{"first_name":"Jirí","full_name":"Friml, Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"}],"date_created":"2018-12-11T11:52:54Z","corr_author":"1","related_material":{"record":[{"status":"public","id":"938","relation":"dissertation_contains"}]},"publist_id":"5580"}]