{"entity": "researcher", "timestamp": "2026-08-15T13:42:47.617Z", "family": "Nov\u00e1k", "given": "Ond\u0159ej", "initials": "O", "orcid": "0000-0003-3452-0154", "affiliations": ["Ume\u00e5 Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901 83, Ume\u00e5, Sweden.", "Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Sciences and Faculty of Science of Palack\u00fd University, CZ-78371, Olomouc, Czech Republic."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/8c19165acb9a4ff79dd96af7fccdc5f8.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/8c19165acb9a4ff79dd96af7fccdc5f8"}}, "publications": [{"entity": "publication", "iuid": "067b61d871b748229c2cf96c89adeaa7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/067b61d871b748229c2cf96c89adeaa7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/067b61d871b748229c2cf96c89adeaa7"}}, "title": "A suitable strategy to find IAA metabolism mutants.", "authors": [{"family": "Casanova-S\u00e1ez", "given": "Rub\u00e9n", "initials": "R", "orcid": "0000-0001-5683-7051", "researcher": {"href": "https://publications.scilifelab.se/researcher/17868bb801534bd794ef1f5d2815a531.json"}}, {"family": "P\u011bn\u010d\u00edk", "given": "Ale\u0161", "initials": "A", "orcid": "0000-0002-1314-2249", "researcher": {"href": "https://publications.scilifelab.se/researcher/b13dbbec35c441daa7ed84daa05cd6e7.json"}}, {"family": "Mu\u00f1oz-Viana", "given": "Rafael", "initials": "R", "orcid": "0000-0002-1363-6978", "researcher": {"href": "https://publications.scilifelab.se/researcher/1bd9a92a13fd4395aeae214b4930e55a.json"}}, {"family": "Brunoni", "given": "Federica", "initials": "F", "orcid": "0000-0003-1497-9419", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a28132c7a0e407da31e4d79698679c6.json"}}, {"family": "Pinto", "given": "Rui", "initials": "R", "orcid": "0000-0002-8527-4873", "researcher": {"href": "https://publications.scilifelab.se/researcher/58f5bd6ddde8458d927e78ef13efb67b.json"}}, {"family": "Nov\u00e1k", "given": "Ond\u0159ej", "initials": "O", "orcid": "0000-0003-3452-0154", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c19165acb9a4ff79dd96af7fccdc5f8.json"}}, {"family": "Ljung", "given": "Karin", "initials": "K", "orcid": "0000-0003-2901-189X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f91b1e1f90c24559b915ebcd265804a4.json"}}, {"family": "Mateo-Bonmat\u00ed", "given": "Eduardo", "initials": "E", "orcid": "0000-0002-2364-5173", "researcher": {"href": "https://publications.scilifelab.se/researcher/f1e96edf1a914d2f8ea8eb46c3ebacc4.json"}}], "type": "journal article", "published": "2025-03-21", "journal": {"title": "Physiol Plantarum", "issn": "1399-3054", "volume": "177", "issue": "2", "pages": "e70166", "issn-l": "0031-9317"}, "abstract": "Indole-3-acetic acid (IAA), the most common form of auxin, is involved in a great range of plant physiological processes. IAA is synthesized from the amino acid tryptophan and can be transported and inactivated in a myriad of ways. Despite intense research efforts, there are still dark corners in our comprehension of IAA metabolism and its interplays with other pathways. Genetic screens are a powerful tool for unbiasedly looking for new players in a given biological process. However, pleiotropism of auxin-related phenotypes and indirect effects make it necessary to incorporate additional screening steps to specifically find mutants affected in IAA homeostasis. We previously developed and validated a high-throughput methodology to simultaneously quantify IAA, key precursors, and inactive forms from as little as 10 mg of fresh tissue. We have carried out a genetic screening to identify mutants involved in IAA metabolism. Auxin reporters DR5pro:VENUS and 35Spro:DII-VENUS were EMS-mutagenized and subjected to a parallel morphological and reporter-signal pre-screen. We then obtained the auxin metabolite profile of 325 M3 selected lines and used multivariate data analysis to identify potential IAA-metabolism mutants. To test the screening design, we identified the causal mutations in three of the candidate lines by mapping-by-sequencing: dii365.3, dii571.1 and dr693. These carry new alleles of CYP83A1, MIAO, and SUPERROOT2, respectively, all of which have been previously involved in auxin homeostasis. Our results support the suitability of this approach to find new genes involved in IAA metabolism.", "doi": "10.1111/ppl.70166", "pmid": "40113441", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11925725"}], "notes": [], "created": "2025-11-18T12:07:26.876Z", "modified": "2025-11-18T12:07:27.054Z"}, {"entity": "publication", "iuid": "ce734f9ae7b5490b8f6022b18a7a3fc0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ce734f9ae7b5490b8f6022b18a7a3fc0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ce734f9ae7b5490b8f6022b18a7a3fc0"}}, "title": "In situ seasonal patterns of root auxin concentrations and meristem length in an arctic sedge.", "authors": [{"family": "Blume-Werry", "given": "Gesche", "initials": "G", "orcid": "0000-0003-0909-670X", "researcher": {"href": "https://publications.scilifelab.se/researcher/834dc85a0d9f4ab59572deab63e643a3.json"}}, {"family": "Semenchuk", "given": "Philipp", "initials": "P", "orcid": "0000-0002-1949-6427", "researcher": {"href": "https://publications.scilifelab.se/researcher/663ebd034e3f481fa7a569a83dd21e34.json"}}, {"family": "Ljung", "given": "Karin", "initials": "K", "orcid": "0000-0003-2901-189X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f91b1e1f90c24559b915ebcd265804a4.json"}}, {"family": "Milbau", "given": "Ann", "initials": "A", "orcid": "0000-0003-3555-8883", "researcher": {"href": "https://publications.scilifelab.se/researcher/9389bf5441d54064bfaee999117d752c.json"}}, {"family": "Novak", "given": "Ondrej", "initials": "O", "orcid": "0000-0003-3452-0154", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c19165acb9a4ff79dd96af7fccdc5f8.json"}}, {"family": "Olofsson", "given": "Johan", "initials": "J", "orcid": "0000-0002-6943-1218", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e9ecce51d244e0ab066f315aae8548d.json"}}, {"family": "Brunoni", "given": "Federica", "initials": "F", "orcid": "0000-0003-1497-9419", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a28132c7a0e407da31e4d79698679c6.json"}}], "type": "journal article", "published": "2024-05-00", "journal": {"title": "New Phytol.", "issn": "1469-8137", "volume": "242", "issue": "3", "pages": "988-999", "issn-l": "0028-646X"}, "abstract": "Seasonal dynamics of root growth play an important role in large-scale ecosystem processes; they are largely governed by growth regulatory compounds and influenced by environmental conditions. Yet, our knowledge about physiological drivers of root growth is mostly limited to laboratory-based studies on model plant species. We sampled root tips of Eriophorum vaginatum and analyzed their auxin concentrations and meristem lengths biweekly over a growing season in situ in a subarctic peatland, both in surface soil and at the permafrost thawfront. Auxin concentrations were almost five times higher in surface than in thawfront soils and increased over the season, especially at the thawfront. Surprisingly, meristem length showed an opposite pattern and was almost double in thawfront compared with surface soils. Meristem length increased from peak to late season in the surface soils but decreased at the thawfront. Our study of in situ seasonal dynamics in root physiological parameters illustrates the potential for physiological methods to be applied in ecological studies and emphasizes the importance of in situ measurements. The strong effect of root location and the unexpected opposite patterns of meristem length and auxin concentrations likely show that auxin actively governs root growth to ensure a high potential for nutrient uptake at the thawfront.", "doi": "10.1111/nph.19616", "pmid": "38375943", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [], "notes": [], "created": "2024-11-26T10:28:02.968Z", "modified": "2025-10-17T13:03:13.205Z"}, {"entity": "publication", "iuid": "a5f8668f28494e83a69d5f25e8db3fde", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a5f8668f28494e83a69d5f25e8db3fde.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a5f8668f28494e83a69d5f25e8db3fde"}}, "title": "Fluorescence-activated multi-organelle mapping of subcellular plant hormone distribution.", "authors": [{"family": "Skalick\u00fd", "given": "Vladim\u00edr", "initials": "V", "orcid": "0000-0001-5369-8906", "researcher": {"href": "https://publications.scilifelab.se/researcher/aa0883baaa234b1eb8f80b6b5dc2ac07.json"}}, {"family": "Antoniadi", "given": "Ioanna", "initials": "I", "orcid": "0000-0001-9053-2788", "researcher": {"href": "https://publications.scilifelab.se/researcher/60bcbb474ded4df08079520c92de49bf.json"}}, {"family": "P\u011bn\u010d\u00edk", "given": "Ale\u0161", "initials": "A", "orcid": "0000-0002-1314-2249", "researcher": {"href": "https://publications.scilifelab.se/researcher/b13dbbec35c441daa7ed84daa05cd6e7.json"}}, {"family": "Chamr\u00e1d", "given": "Ivo", "initials": "I", "orcid": "0000-0003-3812-6314", "researcher": {"href": "https://publications.scilifelab.se/researcher/83a3faec745445f0a9b0b0d2cd7538cb.json"}}, {"family": "Lenobel", "given": "Ren\u00e9", "initials": "R", "orcid": "0000-0001-7387-0056", "researcher": {"href": "https://publications.scilifelab.se/researcher/1283e2c432974d159fe2b24c4fa9f48f.json"}}, {"family": "Kube\u0161", "given": "Martin F", "initials": "MF", "orcid": "0000-0003-2182-4490", "researcher": {"href": "https://publications.scilifelab.se/researcher/e50ec82af0434dbd8b159dc6bbd7f1c6.json"}}, {"family": "Zatloukal", "given": "Marek", "initials": "M", "orcid": "0000-0001-9962-2798", "researcher": {"href": "https://publications.scilifelab.se/researcher/aa91c54a8d7e413b8bb581dae3a11556.json"}}, {"family": "\u017dukauskait\u0117", "given": "Asta", "initials": "A", "orcid": "0000-0001-6759-8789", "researcher": {"href": "https://publications.scilifelab.se/researcher/d2f55d830fe14a6db1f912a852666646.json"}}, {"family": "Strnad", "given": "Miroslav", "initials": "M", "orcid": "0000-0002-2806-794X", "researcher": {"href": "https://publications.scilifelab.se/researcher/141c6516a148415c8d089a5b2ce40f75.json"}}, {"family": "Ljung", "given": "Karin", "initials": "K", "orcid": "0000-0003-2901-189X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f91b1e1f90c24559b915ebcd265804a4.json"}}, {"family": "Nov\u00e1k", "given": "Ond\u0159ej", "initials": "O", "orcid": "0000-0003-3452-0154", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c19165acb9a4ff79dd96af7fccdc5f8.json"}}], "type": "journal article", "published": "2023-12-00", "journal": {"title": "Plant J.", "issn": "1365-313X", "volume": "116", "issue": "6", "pages": "1825-1841", "issn-l": "0960-7412"}, "abstract": "Auxins and cytokinins are two major families of phytohormones that control most aspects of plant growth, development and plasticity. Their distribution in plants has been described, but the importance of cell- and subcellular-type specific phytohormone homeostasis remains undefined. Herein, we revealed auxin and cytokinin distribution maps showing their different organelle-specific allocations within the Arabidopsis plant cell. To do so, we have developed Fluorescence-Activated multi-Organelle Sorting (FAmOS), an innovative subcellular fractionation technique based on flow cytometric principles. FAmOS allows the simultaneous sorting of four differently labelled organelles based on their individual light scatter and fluorescence parameters while ensuring hormone metabolic stability. Our data showed different subcellular distribution of auxin and cytokinins, revealing the formation of phytohormone gradients that have been suggested by the subcellular localization of auxin and cytokinin transporters, receptors and metabolic enzymes. Both hormones showed enrichment in vacuoles, while cytokinins were also accumulated in the endoplasmic reticulum.", "doi": "10.1111/tpj.16456", "pmid": "37682018", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [], "notes": [], "created": "2024-01-18T14:45:38.272Z", "modified": "2025-10-17T13:03:13.273Z"}, {"entity": "publication", "iuid": "f6d6d658e79a40398c7da028e8e5fd3f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f6d6d658e79a40398c7da028e8e5fd3f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f6d6d658e79a40398c7da028e8e5fd3f"}}, "title": "iP &amp; OEIP \u2013 Cytokinin Micro Application Modulates Root Development with High Spatial Resolution", "authors": [{"family": "Pa\u0159\u00edzkov\u00e1", "given": "Barbora", "initials": "B"}, {"family": "Antoniadi", "given": "Ioanna", "initials": "I", "orcid": "0000-0001-9053-2788", "researcher": {"href": "https://publications.scilifelab.se/researcher/60bcbb474ded4df08079520c92de49bf.json"}}, {"family": "Poxson", "given": "David J", "initials": "DJ", "orcid": "0000-0002-4246-8723", "researcher": {"href": "https://publications.scilifelab.se/researcher/b9282ef8814a48c5abd57f14bda5a140.json"}}, {"family": "Karady", "given": "Michal", "initials": "M", "orcid": "0000-0002-5603-706X", "researcher": {"href": "https://publications.scilifelab.se/researcher/114911ccd31849e1a7584b5a52e9eb14.json"}}, {"family": "Simon", "given": "Daniel T", "initials": "DT", "orcid": "0000-0002-2799-3490", "researcher": {"href": "https://publications.scilifelab.se/researcher/062af2c2b5e94ee5ae1ab5bb7c44b609.json"}}, {"family": "Zatloukal", "given": "Marek", "initials": "M", "orcid": "0000-0001-9962-2798", "researcher": {"href": "https://publications.scilifelab.se/researcher/aa91c54a8d7e413b8bb581dae3a11556.json"}}, {"family": "Strnad", "given": "Miroslav", "initials": "M", "orcid": "0000-0002-2806-794X", "researcher": {"href": "https://publications.scilifelab.se/researcher/141c6516a148415c8d089a5b2ce40f75.json"}}, {"family": "Dole\u017eal", "given": "Karel", "initials": "K", "orcid": "0000-0003-4938-0350", "researcher": {"href": "https://publications.scilifelab.se/researcher/f209cf1d8e5d4945b81bd9f01c2b2665.json"}}, {"family": "Nov\u00e1k", "given": "Ond\u0159ej", "initials": "O", "orcid": "0000-0003-3452-0154", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c19165acb9a4ff79dd96af7fccdc5f8.json"}}, {"family": "Ljung", "given": "Karin", "initials": "K", "orcid": "0000-0003-2901-189X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f91b1e1f90c24559b915ebcd265804a4.json"}}], "type": "journal-article", "published": "2022-10-00", "journal": {"title": "Adv Materials Technologies", "issn": "2365-709X", "volume": "7", "issue": "10", "pages": "2101664", "issn-l": null}, "abstract": null, "doi": "10.1002/admt.202101664", "pmid": null, "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [], "notes": [], "created": "2022-12-05T08:13:22.264Z", "modified": "2025-10-17T13:03:14.626Z"}, {"entity": "publication", "iuid": "5a695409066f48d7b8257d27f5949ea2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5a695409066f48d7b8257d27f5949ea2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5a695409066f48d7b8257d27f5949ea2"}}, "title": "Inactivation of the entire Arabidopsis group II GH3s confers tolerance to salinity and water deficit.", "authors": [{"family": "Casanova-S\u00e1ez", "given": "Rub\u00e9n", "initials": "R", "orcid": "0000-0001-5683-7051", "researcher": {"href": "https://publications.scilifelab.se/researcher/17868bb801534bd794ef1f5d2815a531.json"}}, {"family": "Mateo-Bonmat\u00ed", "given": "Eduardo", "initials": "E", "orcid": "0000-0002-2364-5173", "researcher": {"href": "https://publications.scilifelab.se/researcher/f1e96edf1a914d2f8ea8eb46c3ebacc4.json"}}, {"family": "\u0160imura", "given": "Jan", "initials": "J", "orcid": "0000-0002-1567-2278", "researcher": {"href": "https://publications.scilifelab.se/researcher/ac1674ad68434ab19f17056e7824c932.json"}}, {"family": "P\u011bn\u010d\u00edk", "given": "Ale\u0161", "initials": "A", "orcid": "0000-0002-1314-2249", "researcher": {"href": "https://publications.scilifelab.se/researcher/b13dbbec35c441daa7ed84daa05cd6e7.json"}}, {"family": "Nov\u00e1k", "given": "Ond\u0159ej", "initials": "O", "orcid": "0000-0003-3452-0154", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c19165acb9a4ff79dd96af7fccdc5f8.json"}}, {"family": "Staswick", "given": "Paul", "initials": "P", "orcid": "0000-0003-2798-0275", "researcher": {"href": "https://publications.scilifelab.se/researcher/4600c9bfb57f4146943a0fe71cde267b.json"}}, {"family": "Ljung", "given": "Karin", "initials": "K", "orcid": "0000-0003-2901-189X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f91b1e1f90c24559b915ebcd265804a4.json"}}], "type": "journal article", "published": "2022-07-00", "journal": {"title": "New Phytol.", "issn": "1469-8137", "volume": "235", "issue": "1", "pages": "263-275", "issn-l": "0028-646X"}, "abstract": "Indole-3-acetic acid (IAA) controls a plethora of developmental processes. Thus, regulation of its concentration is of great relevance for plant performance. Cellular IAA concentration depends on its transport, biosynthesis and the various pathways for IAA inactivation, including oxidation and conjugation. Group II members of the GRETCHEN HAGEN 3 (GH3) gene family code for acyl acid amido synthetases catalysing the conjugation of IAA to amino acids. However, the high degree of functional redundancy among them has hampered thorough analysis of their roles in plant development. In this work, we generated an Arabidopsis gh3.1,2,3,4,5,6,9,17 (gh3oct) mutant to knock out the group II GH3 pathway. The gh3oct plants had an elaborated root architecture, showed an increased tolerance to different osmotic stresses, including an IAA-dependent tolerance to salinity, and were more tolerant to water deficit. Indole-3-acetic acid metabolite quantification in gh3oct plants suggested the existence of additional GH3-like enzymes in IAA metabolism. Moreover, our data suggested that 2-oxindole-3-acetic acid production depends, at least in part, on the GH3 pathway. Targeted stress-hormone analysis further suggested involvement of abscisic acid in the differential response to salinity of gh3oct plants. Taken together, our data provide new insights into the roles of group II GH3s in IAA metabolism and hormone-regulated plant development.", "doi": "10.1111/nph.18114", "pmid": "35322877", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9322293"}], "notes": [], "created": "2022-12-05T08:06:56.189Z", "modified": "2025-10-17T13:03:14.842Z"}, {"entity": "publication", "iuid": "2638d2e84c7340918359a95f918c1bae", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2638d2e84c7340918359a95f918c1bae.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2638d2e84c7340918359a95f918c1bae"}}, "title": "Dynamics of Auxin and Cytokinin Metabolism during Early Root and Hypocotyl Growth in Theobroma cacao.", "authors": [{"family": "Mboene Noah", "given": "Alexandre", "initials": "A", "orcid": "0000-0002-8766-6467", "researcher": {"href": "https://publications.scilifelab.se/researcher/c0895fa148094bb48c5ece1124f5a8ab.json"}}, {"family": "Casanova-S\u00e1ez", "given": "Rub\u00e9n", "initials": "R", "orcid": "0000-0001-5683-7051", "researcher": {"href": "https://publications.scilifelab.se/researcher/17868bb801534bd794ef1f5d2815a531.json"}}, {"family": "Makondy Ango", "given": "Rolande Eugenie", "initials": "RE"}, {"family": "Antoniadi", "given": "Ioanna", "initials": "I"}, {"family": "Karady", "given": "Michal", "initials": "M"}, {"family": "Nov\u00e1k", "given": "Ond\u0159ej", "initials": "O", "orcid": "0000-0003-3452-0154", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c19165acb9a4ff79dd96af7fccdc5f8.json"}}, {"family": "Niemenak", "given": "Nicolas", "initials": "N"}, {"family": "Ljung", "given": "Karin", "initials": "K", "orcid": "0000-0003-2901-189X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f91b1e1f90c24559b915ebcd265804a4.json"}}], "type": "journal article", "published": "2021-05-12", "journal": {"title": "Plants (Basel)", "issn": "2223-7747", "volume": "10", "issue": "5", "issn-l": null}, "abstract": "The spatial location and timing of plant developmental events are largely regulated by the well balanced effects of auxin and cytokinin phytohormone interplay. Together with transport, localized metabolism regulates the concentration gradients of their bioactive forms, ultimately eliciting growth responses. In order to explore the dynamics of auxin and cytokinin metabolism during early seedling growth in Theobroma cacao (cacao), we have performed auxin and cytokinin metabolite profiling in hypocotyls and root developmental sections at different times by using ultra-high-performance liquid chromatography-electrospray tandem mass spectrometry (UHPLC-MS/MS). Our work provides quantitative characterization of auxin and cytokinin metabolites throughout early root and hypocotyl development and identifies common and distinctive features of auxin and cytokinin metabolism during cacao seedling development.", "doi": "10.3390/plants10050967", "pmid": "34066241", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pii", "key": "plants10050967"}, {"db": "pmc", "key": "PMC8151989"}], "notes": [], "created": "2021-12-09T13:29:28.551Z", "modified": "2025-10-17T13:03:16.113Z"}, {"entity": "publication", "iuid": "acb48c2531964cb4b5a8c73639e2f114", "links": {"self": {"href": "https://publications.scilifelab.se/publication/acb48c2531964cb4b5a8c73639e2f114.json"}, "display": {"href": "https://publications.scilifelab.se/publication/acb48c2531964cb4b5a8c73639e2f114"}}, "title": "Cell-surface receptors enable perception of extracellular cytokinins.", "authors": [{"family": "Antoniadi", "given": "Ioanna", "initials": "I", "orcid": "0000-0001-9053-2788", "researcher": {"href": "https://publications.scilifelab.se/researcher/60bcbb474ded4df08079520c92de49bf.json"}}, {"family": "Nov\u00e1k", "given": "Ond\u0159ej", "initials": "O", "orcid": "0000-0003-3452-0154", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c19165acb9a4ff79dd96af7fccdc5f8.json"}}, {"family": "Gelov\u00e1", "given": "Zuzana", "initials": "Z", "orcid": "0000-0003-4783-1752", "researcher": {"href": "https://publications.scilifelab.se/researcher/afc862721b52467aa092f0ecf9fc7bed.json"}}, {"family": "Johnson", "given": "Alexander", "initials": "A", "orcid": "0000-0002-2739-8843", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9414092144944429b428466733e6567.json"}}, {"family": "Pl\u00edhal", "given": "Ond\u0159ej", "initials": "O", "orcid": "0000-0003-0645-2019", "researcher": {"href": "https://publications.scilifelab.se/researcher/f42115be2a6b4268a3bf6f9200479f93.json"}}, {"family": "Simersk\u00fd", "given": "Radim", "initials": "R", "orcid": "0000-0002-4481-6680", "researcher": {"href": "https://publications.scilifelab.se/researcher/218c11787cf2467a98ab7d0c826de187.json"}}, {"family": "Mik", "given": "V\u00e1clav", "initials": "V", "orcid": "0000-0002-8515-3035", "researcher": {"href": "https://publications.scilifelab.se/researcher/51f69a95dba24bd793e708f0cdcc2ded.json"}}, {"family": "Vain", "given": "Thomas", "initials": "T"}, {"family": "Mateo-Bonmat\u00ed", "given": "Eduardo", "initials": "E", "orcid": "0000-0002-2364-5173", "researcher": {"href": "https://publications.scilifelab.se/researcher/f1e96edf1a914d2f8ea8eb46c3ebacc4.json"}}, {"family": "Karady", "given": "Michal", "initials": "M"}, {"family": "Pernisov\u00e1", "given": "Mark\u00e9ta", "initials": "M", "orcid": "0000-0002-5803-2879", "researcher": {"href": "https://publications.scilifelab.se/researcher/acc243598b74495999230f9b1b0da0be.json"}}, {"family": "Pla\u010dkov\u00e1", "given": "Lenka", "initials": "L"}, {"family": "Opassathian", "given": "Korawit", "initials": "K"}, {"family": "Hej\u00e1tko", "given": "Jan", "initials": "J"}, {"family": "Robert", "given": "St\u00e9phanie", "initials": "S", "orcid": "0000-0002-0013-3239", "researcher": {"href": "https://publications.scilifelab.se/researcher/74a96c43520f4c9c91e44be8a7d39e6c.json"}}, {"family": "Friml", "given": "Ji\u0159\u00ed", "initials": "J", "orcid": "0000-0002-8302-7596", "researcher": {"href": "https://publications.scilifelab.se/researcher/6e525fe6afc5490a86223e38be195cee.json"}}, {"family": "Dole\u017eal", "given": "Karel", "initials": "K", "orcid": "0000-0003-4938-0350", "researcher": {"href": "https://publications.scilifelab.se/researcher/f209cf1d8e5d4945b81bd9f01c2b2665.json"}}, {"family": "Ljung", "given": "Karin", "initials": "K", "orcid": "0000-0003-2901-189X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f91b1e1f90c24559b915ebcd265804a4.json"}}, {"family": "Turnbull", "given": "Colin", "initials": "C", "orcid": "0000-0001-6635-1418", "researcher": {"href": "https://publications.scilifelab.se/researcher/abd75adef49f4c789b69206cdb7e8cf0.json"}}], "type": "journal article", "published": "2020-08-27", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "11", "issue": "1", "pages": "4284", "issn-l": "2041-1723"}, "abstract": "Cytokinins are mobile multifunctional plant hormones with roles in development and stress resilience. Although their Histidine Kinase receptors are substantially localised to the endoplasmic reticulum, cellular sites of cytokinin perception and importance of spatially heterogeneous cytokinin distribution continue to be debated. Here we show that cytokinin perception by plasma membrane receptors is an effective additional path for cytokinin response. Readout from a Two Component Signalling cytokinin-specific reporter (TCSn::GFP) closely matches intracellular cytokinin content in roots, yet we also find cytokinins in extracellular fluid, potentially enabling action at the cell surface. Cytokinins covalently linked to beads that could not pass the plasma membrane increased expression of both TCSn::GFP and Cytokinin Response Factors. Super-resolution microscopy of GFP-labelled receptors and diminished TCSn::GFP response to immobilised cytokinins in cytokinin receptor mutants, further indicate that receptors can function at the cell surface. We argue that dual intracellular and surface locations may augment flexibility of cytokinin responses.", "doi": "10.1038/s41467-020-17700-9", "pmid": "32855409", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-020-17700-9"}, {"db": "pmc", "key": "PMC7453015"}], "notes": [], "created": "2020-12-11T11:56:05.497Z", "modified": "2025-10-17T13:03:16.685Z"}, {"entity": "publication", "iuid": "a758a54e14db475586eb19b410a7141a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a758a54e14db475586eb19b410a7141a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a758a54e14db475586eb19b410a7141a"}}, "title": "A role for the auxin precursor anthranilic acid in root gravitropism via regulation of PIN-FORMED protein polarity and relocalisation in Arabidopsis.", "authors": [{"family": "Doyle", "given": "Siamsa M", "initials": "SM", "orcid": "0000-0003-4889-3496", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a82fafd2ab34ff2bac338ce451bb4bb.json"}}, {"family": "Rigal", "given": "Adeline", "initials": "A"}, {"family": "Grones", "given": "Peter", "initials": "P", "orcid": "0000-0003-4132-4151", "researcher": {"href": "https://publications.scilifelab.se/researcher/20417b1485074106b74042617b5e2e59.json"}}, {"family": "Karady", "given": "Michal", "initials": "M", "orcid": "0000-0002-5603-706X", "researcher": {"href": "https://publications.scilifelab.se/researcher/114911ccd31849e1a7584b5a52e9eb14.json"}}, {"family": "Barange", "given": "Deepak K", "initials": "DK", "orcid": "0000-0003-1279-1068", "researcher": {"href": "https://publications.scilifelab.se/researcher/d00627926367423093b7e1645ee55ad1.json"}}, {"family": "Majda", "given": "Mateusz", "initials": "M", "orcid": "0000-0003-3405-2901", "researcher": {"href": "https://publications.scilifelab.se/researcher/582d7b364d4d4442a7f470e52ed031bc.json"}}, {"family": "Pa\u0159\u00edzkov\u00e1", "given": "Barbora", "initials": "B", "orcid": "0000-0002-8125-2271", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9dd3d0c062245a5b188e774955cd210.json"}}, {"family": "Karampelias", "given": "Michael", "initials": "M", "orcid": "0000-0002-2095-988X", "researcher": {"href": "https://publications.scilifelab.se/researcher/dbd70d20b66b4fb4a8d1308b2f54e2a2.json"}}, {"family": "Zwiewka", "given": "Marta", "initials": "M"}, {"family": "P\u011bn\u010d\u00edk", "given": "Ale\u0161", "initials": "A"}, {"family": "Almqvist", "given": "Fredrik", "initials": "F"}, {"family": "Ljung", "given": "Karin", "initials": "K", "orcid": "0000-0003-2901-189X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f91b1e1f90c24559b915ebcd265804a4.json"}}, {"family": "Nov\u00e1k", "given": "Ond\u0159ej", "initials": "O", "orcid": "0000-0003-3452-0154", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c19165acb9a4ff79dd96af7fccdc5f8.json"}}, {"family": "Robert", "given": "St\u00e9phanie", "initials": "S", "orcid": "0000-0002-0013-3239", "researcher": {"href": "https://publications.scilifelab.se/researcher/74a96c43520f4c9c91e44be8a7d39e6c.json"}}], "type": "journal article", "published": "2019-08-00", "journal": {"title": "New Phytol.", "issn": "1469-8137", "issn-l": "0028-646X", "volume": "223", "issue": "3", "pages": "1420-1432"}, "abstract": "distribution of auxin within plant tissues is of great importance for developmental plasticity, including root gravitropic growth. Auxin flow is directed by the subcellular polar distribution and dynamic relocalisation of auxin transporters such as the PIN-FORMED (PIN) efflux carriers, which can be influenced by the main natural plant auxin indole-3-acetic acid (IAA). Anthranilic acid (AA) is an important early precursor of IAA and previously published studies with AA analogues have suggested that AA may also regulate PIN localisation. Using Arabidopsis thaliana as a model species, we studied an AA-deficient mutant displaying agravitropic root growth, treated seedlings with AA and AA analogues and transformed lines to over-produce AA while inhibiting its conversion to downstream IAA precursors. We showed that AA rescues root gravitropic growth in the AA-deficient mutant at concentrations that do not rescue IAA levels. Overproduction of AA affects root gravitropism without affecting IAA levels. Treatments with, or deficiency in, AA result in defects in PIN polarity and gravistimulus-induced PIN relocalisation in root cells. Our results revealed a previously unknown role for AA in the regulation of PIN subcellular localisation and dynamics involved in root gravitropism, which is independent of its better known role in IAA biosynthesis.", "doi": "10.1111/nph.15877", "pmid": "31038751", "labels": {"Swedish Metabolomics Centre": "Service", "Chemical Biology Consortium Sweden": "Service"}, "xrefs": [], "notes": [], "created": "2020-01-07T15:52:13.037Z", "modified": "2025-10-17T13:04:28.531Z"}, {"entity": "publication", "iuid": "f59c91815d66466eba5b3ad85f9fe687", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f59c91815d66466eba5b3ad85f9fe687.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f59c91815d66466eba5b3ad85f9fe687"}}, "title": "Selective auxin agonists induce specific AUX/IAA protein degradation to modulate plant development.", "authors": [{"family": "Vain", "given": "Thomas", "initials": "T"}, {"family": "Raggi", "given": "Sara", "initials": "S", "orcid": "0000-0002-7925-5772", "researcher": {"href": "https://publications.scilifelab.se/researcher/b7f5c77f8e6e4904b5dd2d8241316589.json"}}, {"family": "Ferro", "given": "Noel", "initials": "N"}, {"family": "Barange", "given": "Deepak Kumar", "initials": "DK"}, {"family": "Kieffer", "given": "Martin", "initials": "M"}, {"family": "Ma", "given": "Qian", "initials": "Q"}, {"family": "Doyle", "given": "Siamsa M", "initials": "SM", "orcid": "0000-0003-4889-3496", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a82fafd2ab34ff2bac338ce451bb4bb.json"}}, {"family": "Thelander", "given": "Mattias", "initials": "M"}, {"family": "Pa\u0159\u00edzkov\u00e1", "given": "Barbora", "initials": "B", "orcid": "0000-0002-8125-2271", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9dd3d0c062245a5b188e774955cd210.json"}}, {"family": "Nov\u00e1k", "given": "Ond\u0159ej", "initials": "O", "orcid": "0000-0003-3452-0154", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c19165acb9a4ff79dd96af7fccdc5f8.json"}}, {"family": "Ismail", "given": "Alexandre", "initials": "A"}, {"family": "Enquist", "given": "Per-Anders", "initials": "P"}, {"family": "Rigal", "given": "Adeline", "initials": "A"}, {"family": "\u0141angowska", "given": "Ma\u0142gorzata", "initials": "M"}, {"family": "Ramans Harborough", "given": "Sigurd", "initials": "S"}, {"family": "Zhang", "given": "Yi", "initials": "Y"}, {"family": "Ljung", "given": "Karin", "initials": "K", "orcid": "0000-0003-2901-189X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f91b1e1f90c24559b915ebcd265804a4.json"}}, {"family": "Callis", "given": "Judy", "initials": "J"}, {"family": "Almqvist", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0504-4446", "researcher": {"href": "https://publications.scilifelab.se/researcher/6f8d848fccce44da9bcd4e79f7eae64c.json"}}, {"family": "Kepinski", "given": "Stefan", "initials": "S"}, {"family": "Estelle", "given": "Mark", "initials": "M"}, {"family": "Pauwels", "given": "Laurens", "initials": "L", "orcid": "0000-0002-0221-9052", "researcher": {"href": "https://publications.scilifelab.se/researcher/6cbb68c7a39a447d937693fede33a7c9.json"}}, {"family": "Robert", "given": "St\u00e9phanie", "initials": "S", "orcid": "0000-0002-0013-3239", "researcher": {"href": "https://publications.scilifelab.se/researcher/74a96c43520f4c9c91e44be8a7d39e6c.json"}}], "type": "journal article", "published": "2019-03-26", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "issn-l": "0027-8424", "volume": "116", "issue": "13", "pages": "6463-6472"}, "abstract": "Auxin phytohormones control most aspects of plant development through a complex and interconnected signaling network. In the presence of auxin, AUXIN/INDOLE-3-ACETIC ACID (AUX/IAA) transcriptional repressors are targeted for degradation by the SKP1-CULLIN1-F-BOX (SCF) ubiquitin-protein ligases containing TRANSPORT INHIBITOR RESISTANT 1/AUXIN SIGNALING F-BOX (TIR1/AFB). CULLIN1-neddylation is required for SCFTIR1/AFB functionality, as exemplified by mutants deficient in the NEDD8-activating enzyme subunit AUXIN-RESISTANT 1 (AXR1). Here, we report a chemical biology screen that identifies small molecules requiring AXR1 to modulate plant development. We selected four molecules of interest, RubNeddin 1 to 4 (RN1 to -4), among which RN3 and RN4 trigger selective auxin responses at transcriptional, biochemical, and morphological levels. This selective activity is explained by their ability to consistently promote the interaction between TIR1 and a specific subset of AUX/IAA proteins, stimulating the degradation of particular AUX/IAA combinations. Finally, we performed a genetic screen using RN4, the RN with the greatest potential for dissecting auxin perception, which revealed that the chromatin remodeling ATPase BRAHMA is implicated in auxin-mediated apical hook development. These results demonstrate the power of selective auxin agonists to dissect auxin perception for plant developmental functions, as well as offering opportunities to discover new molecular players involved in auxin responses.", "doi": "10.1073/pnas.1809037116", "pmid": "30850516", "labels": {"Swedish Metabolomics Centre": "Service", "Chemical Biology Consortium Sweden": "Collaborative"}, "xrefs": [{"db": "pii", "key": "1809037116"}, {"db": "pmc", "key": "PMC6442611"}], "notes": [], "created": "2019-06-17T08:28:28.156Z", "modified": "2025-10-17T13:04:28.584Z"}, {"entity": "publication", "iuid": "a712e24f08954aeba5fb0176ef569efa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a712e24f08954aeba5fb0176ef569efa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a712e24f08954aeba5fb0176ef569efa"}}, "title": "Plant Hormonomics: Multiple Phytohormone Profiling by Targeted Metabolomics", "authors": [{"family": "\u0160imura", "given": "Jan", "initials": "J"}, {"family": "Antoniadi", "given": "Ioanna", "initials": "I", "orcid": "0000-0001-9053-2788", "researcher": {"href": "https://publications.scilifelab.se/researcher/60bcbb474ded4df08079520c92de49bf.json"}}, {"family": "\u0160irok\u00e1", "given": "Jitka", "initials": "J"}, {"family": "Tarkowsk\u00e1", "given": "Danu\u00a1e", "initials": "D"}, {"family": "Strnad", "given": "Miroslav", "initials": "M", "orcid": "0000-0002-2806-794X", "researcher": {"href": "https://publications.scilifelab.se/researcher/141c6516a148415c8d089a5b2ce40f75.json"}}, {"family": "Ljung", "given": "Karin", "initials": "K", "orcid": "0000-0003-2901-189X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f91b1e1f90c24559b915ebcd265804a4.json"}}, {"family": "Nov\u00e1k", "given": "Ond\u0159ej", "initials": "O", "orcid": "0000-0003-3452-0154", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c19165acb9a4ff79dd96af7fccdc5f8.json"}}], "type": "journal-article", "published": "2018-06-13", "journal": {"title": "Plant Physiol.", "issn": "1532-2548", "volume": "177", "issue": "2", "pages": "476-489", "issn-l": "0032-0889"}, "abstract": "Phytohormones are physiologically important small molecules that play essential roles in intricate signaling networks that regulate diverse processes in plants. We present a method for the simultaneous targeted profiling of 101 phytohormone-related analytes from minute amounts of fresh plant material (less than 20 mg). Rapid and nonselective extraction, fast one-step sample purification, and extremely sensitive ultra-high-performance liquid chromatography-tandem mass spectrometry enable concurrent quantification of the main phytohormone classes: cytokinins, auxins, brassinosteroids, gibberellins, jasmonates, salicylates, and abscisates. We validated this hormonomic approach in salt-stressed and control Arabidopsis ( Arabidopsis thaliana) seedlings, quantifying a total of 43 endogenous compounds in both root and shoot samples. Subsequent multivariate statistical data processing and cross-validation with transcriptomic data highlighted the main hormone metabolites involved in plant adaptation to salt stress.", "doi": "10.1104/pp.18.00293", "pmid": "29703867", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pii", "key": "pp.18.00293"}, {"db": "pmc", "key": "PMC6001343"}], "notes": [], "created": "2019-01-10T11:27:29.867Z", "modified": "2025-10-17T13:03:18.115Z"}, {"entity": "publication", "iuid": "dad2c2d54faa4a46a778b12fa7f53f4a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dad2c2d54faa4a46a778b12fa7f53f4a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dad2c2d54faa4a46a778b12fa7f53f4a"}}, "title": "Ultra-rapid auxin metabolite profiling for high-throughput mutant screening in Arabidopsis.", "authors": [{"family": "Penc\u00edk", "given": "Ale\u0161", "initials": "A"}, {"family": "Casanova-S\u00e1ez", "given": "Rub\u00e9n", "initials": "R"}, {"family": "Pilarov\u00e1", "given": "Veronika", "initials": "V"}, {"family": "\u017dukauskaite", "given": "Asta", "initials": "A"}, {"family": "Pinto", "given": "Rui", "initials": "R"}, {"family": "Micol", "given": "Jos\u00e9 Luis", "initials": "JL", "orcid": "0000-0002-0396-1750", "researcher": {"href": "https://publications.scilifelab.se/researcher/f9fed6e5b83447ea8954d666f0f2c1a1.json"}}, {"family": "Ljung", "given": "Karin", "initials": "K", "orcid": "0000-0003-2901-189X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f91b1e1f90c24559b915ebcd265804a4.json"}}, {"family": "Nov\u00e1k", "given": "Ondrej", "initials": "O", "orcid": "0000-0003-3452-0154", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c19165acb9a4ff79dd96af7fccdc5f8.json"}}], "type": "journal article", "published": "2018-04-27", "journal": {"title": "J. Exp. Bot.", "issn": "1460-2431", "volume": "69", "issue": "10", "pages": "2569-2579", "issn-l": "0022-0957"}, "abstract": "Auxin (indole-3-acetic acid, IAA) plays fundamental roles as a signalling molecule during numerous plant growth and development processes. The formation of local auxin gradients and auxin maxima/minima, which is very important for these processes, is regulated by auxin metabolism (biosynthesis, degradation, and conjugation) as well as transport. When studying auxin metabolism pathways it is crucial to combine data obtained from genetic investigations with the identification and quantification of individual metabolites. Thus, to facilitate efforts to elucidate auxin metabolism and its roles in plants, we have developed a high-throughput method for simultaneously quantifying IAA and its key metabolites in minute samples (<10 mg FW) of Arabidopsis thaliana tissues by in-tip micro solid-phase extraction and fast LC-tandem MS. As a proof of concept, we applied the method to a collection of Arabidopsis mutant lines and identified lines with altered IAA metabolite profiles using multivariate data analysis. Finally, we explored the correlation between IAA metabolite profiles and IAA-related phenotypes. The developed rapid analysis of large numbers of samples (>100 samples d-1) is a valuable tool to screen for novel regulators of auxin metabolism and homeostasis among large collections of genotypes.", "doi": "10.1093/jxb/ery084", "pmid": "29514302", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pii", "key": "4919650"}, {"db": "pmc", "key": "PMC5920284"}], "notes": [], "created": "2019-01-10T11:22:35.140Z", "modified": "2025-10-17T13:03:18.202Z"}, {"entity": "publication", "iuid": "4f6a27020d4e4cc8a66101b05df1d17e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4f6a27020d4e4cc8a66101b05df1d17e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4f6a27020d4e4cc8a66101b05df1d17e"}}, "title": "Auxin minimum triggers the developmental switch from cell division to cell differentiation in the Arabidopsis root.", "authors": [{"family": "Di Mambro", "given": "Riccardo", "initials": "R", "orcid": "0000-0002-1243-7395", "researcher": {"href": "https://publications.scilifelab.se/researcher/e06682ddf24e45648d08dc1db5a272d5.json"}}, {"family": "De Ruvo", "given": "Micol", "initials": "M"}, {"family": "Pacifici", "given": "Elena", "initials": "E"}, {"family": "Salvi", "given": "Elena", "initials": "E"}, {"family": "Sozzani", "given": "Rosangela", "initials": "R"}, {"family": "Benfey", "given": "Philip N", "initials": "PN"}, {"family": "Busch", "given": "Wolfgang", "initials": "W", "orcid": "0000-0003-2042-7290", "researcher": {"href": "https://publications.scilifelab.se/researcher/690f19002a5e49aea937eb9025827fae.json"}}, {"family": "Novak", "given": "Ondrej", "initials": "O", "orcid": "0000-0003-3452-0154", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c19165acb9a4ff79dd96af7fccdc5f8.json"}}, {"family": "Ljung", "given": "Karin", "initials": "K", "orcid": "0000-0003-2901-189X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f91b1e1f90c24559b915ebcd265804a4.json"}}, {"family": "Di Paola", "given": "Luisa", "initials": "L"}, {"family": "Mar\u00e9e", "given": "Athanasius F M", "initials": "AFM"}, {"family": "Costantino", "given": "Paolo", "initials": "P"}, {"family": "Grieneisen", "given": "Ver\u00f4nica A", "initials": "VA"}, {"family": "Sabatini", "given": "Sabrina", "initials": "S"}], "type": "journal article", "published": "2017-09-05", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "volume": "114", "issue": "36", "pages": "E7641-E7649", "issn-l": "0027-8424"}, "abstract": "In multicellular organisms, a stringent control of the transition between cell division and differentiation is crucial for correct tissue and organ development. In the Arabidopsis root, the boundary between dividing and differentiating cells is positioned by the antagonistic interaction of the hormones auxin and cytokinin. Cytokinin affects polar auxin transport, but how this impacts the positional information required to establish this tissue boundary, is still unknown. By combining computational modeling with molecular genetics, we show that boundary formation is dependent on cytokinin's control on auxin polar transport and degradation. The regulation of both processes shapes the auxin profile in a well-defined auxin minimum. This auxin minimum positions the boundary between dividing and differentiating cells, acting as a trigger for this developmental transition, thus controlling meristem size.", "doi": "10.1073/pnas.1705833114", "pmid": "28831001", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pii", "key": "1705833114"}, {"db": "pmc", "key": "PMC5594665"}], "notes": [], "created": "2018-01-09T12:29:37.442Z", "modified": "2025-10-17T13:03:18.557Z"}, {"entity": "publication", "iuid": "8ca9d3a01c9b4aa4aad6efb812f5ba28", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8ca9d3a01c9b4aa4aad6efb812f5ba28.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8ca9d3a01c9b4aa4aad6efb812f5ba28"}}, "title": "The PLETHORA Gene Regulatory Network Guides Growth and Cell Differentiation in Arabidopsis Roots.", "authors": [{"family": "Santuari", "given": "Luca", "initials": "L", "orcid": "0000-0001-8784-2507", "researcher": {"href": "https://publications.scilifelab.se/researcher/e9873001033642d48aef68099cea4b28.json"}}, {"family": "Sanchez-Perez", "given": "Gabino F", "initials": "GF"}, {"family": "Luijten", "given": "Marijn", "initials": "M", "orcid": "0000-0003-4476-0987", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd8beb86add6485690c7d3fd6a66f5ab.json"}}, {"family": "Rutjens", "given": "Bas", "initials": "B"}, {"family": "Terpstra", "given": "Inez", "initials": "I", "orcid": "0000-0002-3085-2533", "researcher": {"href": "https://publications.scilifelab.se/researcher/d7372f690ad8428a85deb4834b5cb8ed.json"}}, {"family": "Berke", "given": "Lidija", "initials": "L", "orcid": "0000-0003-3842-9462", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c33790b7a3a40a3b45086fe1bbcb316.json"}}, {"family": "Gorte", "given": "Maartje", "initials": "M"}, {"family": "Prasad", "given": "Kalika", "initials": "K"}, {"family": "Bao", "given": "Dongping", "initials": "D"}, {"family": "Timmermans-Hereijgers", "given": "Johanna L P M", "initials": "JL"}, {"family": "Maeo", "given": "Kenichiro", "initials": "K"}, {"family": "Nakamura", "given": "Kenzo", "initials": "K"}, {"family": "Shimotohno", "given": "Akie", "initials": "A"}, {"family": "Pencik", "given": "Ales", "initials": "A"}, {"family": "Novak", "given": "Ondrej", "initials": "O", "orcid": "0000-0003-3452-0154", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c19165acb9a4ff79dd96af7fccdc5f8.json"}}, {"family": "Ljung", "given": "Karin", "initials": "K", "orcid": "0000-0003-2901-189X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f91b1e1f90c24559b915ebcd265804a4.json"}}, {"family": "van Heesch", "given": "Sebastiaan", "initials": "S"}, {"family": "de Bruijn", "given": "Ewart", "initials": "E"}, {"family": "Cuppen", "given": "Edwin", "initials": "E"}, {"family": "Willemsen", "given": "Viola", "initials": "V"}, {"family": "M\u00e4h\u00f6nen", "given": "Ari Pekka", "initials": "AP", "orcid": "0000-0001-6051-866X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8baabc2415814b679cd23908454a8c6a.json"}}, {"family": "Lukowitz", "given": "Wolfgang", "initials": "W", "orcid": "0000-0002-5864-7240", "researcher": {"href": "https://publications.scilifelab.se/researcher/5858790eda7f4f7795bcaadcc9667ba8.json"}}, {"family": "Snel", "given": "Berend", "initials": "B", "orcid": "0000-0002-5804-8547", "researcher": {"href": "https://publications.scilifelab.se/researcher/7064025c1e924c41b09fd25e6ab96d28.json"}}, {"family": "de Ridder", "given": "Dick", "initials": "D", "orcid": "0000-0002-4944-4310", "researcher": {"href": "https://publications.scilifelab.se/researcher/939d2f487c5349fb957fba649ee74a17.json"}}, {"family": "Scheres", "given": "Ben", "initials": "B", "orcid": "0000-0001-5400-9578", "researcher": {"href": "https://publications.scilifelab.se/researcher/708f108f17634ddd9ed3b72bd767fd43.json"}}, {"family": "Heidstra", "given": "Renze", "initials": "R", "orcid": "0000-0001-9032-5770", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e22a935f6ad48ca8262087dfc928cea.json"}}], "type": "journal article", "published": "2016-12-00", "journal": {"title": "Plant Cell", "issn": "1532-298X", "volume": "28", "issue": "12", "pages": "2937-2951", "issn-l": "1040-4651"}, "abstract": "Organ formation in animals and plants relies on precise control of cell state transitions to turn stem cell daughters into fully differentiated cells. In plants, cells cannot rearrange due to shared cell walls. Thus, differentiation progression and the accompanying cell expansion must be tightly coordinated across tissues. PLETHORA (PLT) transcription factor gradients are unique in their ability to guide the progression of cell differentiation at different positions in the growing Arabidopsis thaliana root, which contrasts with well-described transcription factor gradients in animals specifying distinct cell fates within an essentially static context. To understand the output of the PLT gradient, we studied the gene set transcriptionally controlled by PLTs. Our work reveals how the PLT gradient can regulate cell state by region-specific induction of cell proliferation genes and repression of differentiation. Moreover, PLT targets include major patterning genes and autoregulatory feedback components, enforcing their role as master regulators of organ development.", "doi": "10.1105/tpc.16.00656", "pmid": "27920338", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC5240741"}, {"db": "pii", "key": "tpc.16.00656"}], "notes": [], "created": "2023-04-12T14:14:49.191Z", "modified": "2025-10-17T13:03:19.206Z"}, {"entity": "publication", "iuid": "bffdc421008341a591e5c8e562205455", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bffdc421008341a591e5c8e562205455.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bffdc421008341a591e5c8e562205455"}}, "title": "The Allelochemical MDCA Inhibits Lignification and Affects Auxin Homeostasis.", "authors": [{"family": "Steenackers", "given": "Ward", "initials": "W"}, {"family": "Cesarino", "given": "Igor", "initials": "I", "orcid": "0000-0002-6789-2432", "researcher": {"href": "https://publications.scilifelab.se/researcher/cdb44fbb92af48ff92d2854f4bd95a3b.json"}}, {"family": "Kl\u00edma", "given": "Petr", "initials": "P", "orcid": "0000-0001-5678-2919", "researcher": {"href": "https://publications.scilifelab.se/researcher/449675d45ea64435a73a60bdf76d3d20.json"}}, {"family": "Quareshy", "given": "Mussa", "initials": "M", "orcid": "0000-0001-8115-9803", "researcher": {"href": "https://publications.scilifelab.se/researcher/8b7ecbb5893d4c1ba2d96087ff89cf70.json"}}, {"family": "Vanholme", "given": "Ruben", "initials": "R", "orcid": "0000-0001-5848-3138", "researcher": {"href": "https://publications.scilifelab.se/researcher/ab4700dc00c84477b42b04f800342121.json"}}, {"family": "Corneillie", "given": "Sander", "initials": "S"}, {"family": "Kumpf", "given": "Robert Peter", "initials": "RP", "orcid": "0000-0002-4046-6935", "researcher": {"href": "https://publications.scilifelab.se/researcher/89a9f19855fe4a719fb69cc7b613764d.json"}}, {"family": "Van de Wouwer", "given": "Dorien", "initials": "D"}, {"family": "Ljung", "given": "Karin", "initials": "K", "orcid": "0000-0003-2901-189X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f91b1e1f90c24559b915ebcd265804a4.json"}}, {"family": "Goeminne", "given": "Geert", "initials": "G", "orcid": "0000-0002-0337-2999", "researcher": {"href": "https://publications.scilifelab.se/researcher/de05b07d3b044577a9e606d19c3004fd.json"}}, {"family": "Nov\u00e1k", "given": "Ond\u0159ej", "initials": "O", "orcid": "0000-0003-3452-0154", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c19165acb9a4ff79dd96af7fccdc5f8.json"}}, {"family": "Za\u017e\u00edmalov\u00e1", "given": "Eva", "initials": "E"}, {"family": "Napier", "given": "Richard", "initials": "R", "orcid": "0000-0002-0605-518X", "researcher": {"href": "https://publications.scilifelab.se/researcher/45b807545a9f46ad90011b850dfb1328.json"}}, {"family": "Boerjan", "given": "Wout", "initials": "W", "orcid": "0000-0003-1495-510X", "researcher": {"href": "https://publications.scilifelab.se/researcher/c8215f848a3047669e8896145e8db4b5.json"}}, {"family": "Vanholme", "given": "Bartel", "initials": "B", "orcid": "0000-0002-7214-7170", "researcher": {"href": "https://publications.scilifelab.se/researcher/ef6569a7a1814aa5acd9099d26e4b786.json"}}], "type": "journal article", "published": "2016-10-00", "journal": {"title": "Plant Physiol.", "issn": "1532-2548", "volume": "172", "issue": "2", "pages": "874-888", "issn-l": "0032-0889"}, "abstract": "The phenylpropanoid 3,4-(methylenedioxy)cinnamic acid (MDCA) is a plant-derived compound first extracted from roots of Asparagus officinalis and further characterized as an allelochemical. Later on, MDCA was identified as an efficient inhibitor of 4-COUMARATE-CoA LIGASE (4CL), a key enzyme of the general phenylpropanoid pathway. By blocking 4CL, MDCA affects the biosynthesis of many important metabolites, which might explain its phytotoxicity. To decipher the molecular basis of the allelochemical activity of MDCA, we evaluated the effect of this compound on Arabidopsis thaliana seedlings. Metabolic profiling revealed that MDCA is converted in planta into piperonylic acid (PA), an inhibitor of CINNAMATE-4-HYDROXYLASE (C4H), the enzyme directly upstream of 4CL. The inhibition of C4H was also reflected in the phenolic profile of MDCA-treated plants. Treatment of in vitro grown plants resulted in an inhibition of primary root growth and a proliferation of lateral and adventitious roots. These observed growth defects were not the consequence of lignin perturbation, but rather the result of disturbing auxin homeostasis. Based on DII-VENUS quantification and direct measurement of cellular auxin transport, we concluded that MDCA disturbs auxin gradients by interfering with auxin efflux. In addition, mass spectrometry was used to show that MDCA triggers auxin biosynthesis, conjugation, and catabolism. A similar shift in auxin homeostasis was found in the c4h mutant ref3-2, indicating that MDCA triggers a cross talk between the phenylpropanoid and auxin biosynthetic pathways independent from the observed auxin efflux inhibition. Altogether, our data provide, to our knowledge, a novel molecular explanation for the phytotoxic properties of MDCA.", "doi": "10.1104/pp.15.01972", "pmid": "27506238", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC5047068"}, {"db": "pii", "key": "pp.15.01972"}], "notes": [], "created": "2023-04-12T14:14:52.688Z", "modified": "2025-10-17T13:03:19.381Z"}, {"entity": "publication", "iuid": "3c25f8896fae4f55bf8ac8986e241e3d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3c25f8896fae4f55bf8ac8986e241e3d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3c25f8896fae4f55bf8ac8986e241e3d"}}, "title": "Dynamic regulation of auxin oxidase and conjugating enzymes AtDAO1 and GH3 modulates auxin homeostasis.", "authors": [{"family": "Mellor", "given": "Nathan", "initials": "N"}, {"family": "Band", "given": "Leah R", "initials": "LR"}, {"family": "P\u011bn\u010d\u00edk", "given": "Ale\u0161", "initials": "A"}, {"family": "Nov\u00e1k", "given": "Ond\u0159ej", "initials": "O", "orcid": "0000-0003-3452-0154", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c19165acb9a4ff79dd96af7fccdc5f8.json"}}, {"family": "Rashed", "given": "Afaf", "initials": "A"}, {"family": "Holman", "given": "Tara", "initials": "T"}, {"family": "Wilson", "given": "Michael H", "initials": "MH"}, {"family": "Vo\u00df", "given": "Ute", "initials": "U"}, {"family": "Bishopp", "given": "Anthony", "initials": "A"}, {"family": "King", "given": "John R", "initials": "JR"}, {"family": "Ljung", "given": "Karin", "initials": "K", "orcid": "0000-0003-2901-189X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f91b1e1f90c24559b915ebcd265804a4.json"}}, {"family": "Bennett", "given": "Malcolm J", "initials": "MJ", "orcid": "0000-0003-0475-390X", "researcher": {"href": "https://publications.scilifelab.se/researcher/76e4df838f034767afdcc563e61ed0b4.json"}}, {"family": "Owen", "given": "Markus R", "initials": "MR", "orcid": "0000-0002-3028-9138", "researcher": {"href": "https://publications.scilifelab.se/researcher/01f389f3cd9247868abffe574470d6ff.json"}}], "type": "journal article", "published": "2016-09-27", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "volume": "113", "issue": "39", "pages": "11022-11027", "issn-l": "0027-8424"}, "abstract": "The hormone auxin is a key regulator of plant growth and development, and great progress has been made understanding auxin transport and signaling. Here, we show that auxin metabolism and homeostasis are also regulated in a complex manner. The principal auxin degradation pathways in Arabidopsis include oxidation by Arabidopsis thaliana gene DIOXYGENASE FOR AUXIN OXIDATION 1/2 (AtDAO1/2) and conjugation by Gretchen Hagen3s (GH3s). Metabolic profiling of dao1-1 root tissues revealed a 50% decrease in the oxidation product 2-oxoindole-3-acetic acid (oxIAA) and increases in the conjugated forms indole-3-acetic acid aspartic acid (IAA-Asp) and indole-3-acetic acid glutamic acid (IAA-Glu) of 438- and 240-fold, respectively, whereas auxin remains close to the WT. By fitting parameter values to a mathematical model of these metabolic pathways, we show that, in addition to reduced oxidation, both auxin biosynthesis and conjugation are increased in dao1-1 Transcripts of AtDAO1 and GH3 genes increase in response to auxin over different timescales and concentration ranges. Including this regulation of AtDAO1 and GH3 in an extended model reveals that auxin oxidation is more important for auxin homoeostasis at lower hormone concentrations, whereas auxin conjugation is most significant at high auxin levels. Finally, embedding our homeostasis model in a multicellular simulation to assess the spatial effect of the dao1-1 mutant shows that auxin increases in outer root tissues in agreement with the dao1-1 mutant root hair phenotype. We conclude that auxin homeostasis is dependent on AtDAO1, acting in concert with GH3, to maintain auxin at optimal levels for plant growth and development.", "doi": "10.1073/pnas.1604458113", "pmid": "27651495", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC5047161"}, {"db": "pii", "key": "1604458113"}], "notes": [], "created": "2023-04-12T14:14:41.884Z", "modified": "2025-10-17T13:03:19.435Z"}]}