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Kwaśniewska K, Breathnach C, Fitzsimons C, Goslin K, Thomson B, Beegan J, Finocchio A, Prunet N, Ó’Maoiléidigh DS, Wellmer F. Expression of KNUCKLES in the Stem Cell Domain Is Required for Its Function in the Control of Floral Meristem Activity in Arabidopsis. Front Plant Sci 2021; 12:704351. [PMID: 34367223 PMCID: PMC8336581 DOI: 10.3389/fpls.2021.704351] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 06/24/2021] [Indexed: 05/27/2023]
Abstract
In the model plant Arabidopsis thaliana, the zinc-finger transcription factor KNUCKLES (KNU) plays an important role in the termination of floral meristem activity, a process that is crucial for preventing the overgrowth of flowers. The KNU gene is activated in floral meristems by the floral organ identity factor AGAMOUS (AG), and it has been shown that both AG and KNU act in floral meristem control by directly repressing the stem cell regulator WUSCHEL (WUS), which leads to a loss of stem cell activity. When we re-examined the expression pattern of KNU in floral meristems, we found that KNU is expressed throughout the center of floral meristems, which includes, but is considerably broader than the WUS expression domain. We therefore hypothesized that KNU may have additional functions in the control of floral meristem activity. To test this, we employed a gene perturbation approach and knocked down KNU activity at different times and in different domains of the floral meristem. In these experiments we found that early expression in the stem cell domain, which is characterized by the expression of the key meristem regulatory gene CLAVATA3 (CLV3), is crucial for the establishment of KNU expression. The results of additional genetic and molecular analyses suggest that KNU represses floral meristem activity to a large extent by acting on CLV3. Thus, KNU might need to suppress the expression of several meristem regulators to terminate floral meristem activity efficiently.
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Affiliation(s)
| | | | | | - Kevin Goslin
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Bennett Thomson
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Joseph Beegan
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Andrea Finocchio
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Nathanaël Prunet
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Diarmuid S. Ó’Maoiléidigh
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Frank Wellmer
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
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Goslin K, Zheng B, Serrano-Mislata A, Rae L, Ryan PT, Kwaśniewska K, Thomson B, Ó'Maoiléidigh DS, Madueño F, Wellmer F, Graciet E. Transcription Factor Interplay between LEAFY and APETALA1/CAULIFLOWER during Floral Initiation. Plant Physiol 2017; 174:1097-1109. [PMID: 28385730 PMCID: PMC5462026 DOI: 10.1104/pp.17.00098] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 04/05/2017] [Indexed: 05/21/2023]
Abstract
The transcription factors LEAFY (LFY) and APETALA1 (AP1), together with the AP1 paralog CAULIFLOWER (CAL), control the onset of flower development in a partially redundant manner. This redundancy is thought to be mediated, at least in part, through the regulation of a shared set of target genes. However, whether these genes are independently or cooperatively regulated by LFY and AP1/CAL is currently unknown. To better understand the regulatory relationship between LFY and AP1/CAL and to obtain deeper insights into the control of floral initiation, we monitored the activity of LFY in the absence of AP1/CAL function. We found that the regulation of several known LFY target genes is unaffected by AP1/CAL perturbation, while others appear to require AP1/CAL activity. Furthermore, we obtained evidence that LFY and AP1/CAL control the expression of some genes in an antagonistic manner. Notably, these include key regulators of floral initiation such as TERMINAL FLOWER1 (TFL1), which had been previously reported to be directly repressed by both LFY and AP1. We show here that TFL1 expression is suppressed by AP1 but promoted by LFY. We further demonstrate that LFY has an inhibitory effect on flower formation in the absence of AP1/CAL activity. We propose that LFY and AP1/CAL act as part of an incoherent feed-forward loop, a network motif where two interconnected pathways or transcription factors act in opposite directions on a target gene, to control the establishment of a stable developmental program for the formation of flowers.
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Affiliation(s)
- Kevin Goslin
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland (K.G., B.Z., L.R., P.T.R., K.K., B.T., D.S.Ó., F.W.)
- Department of Biology, National University of Ireland Maynooth, Maynooth, Ireland (K.G., E.G.); and
- Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV, Valencia, Spain (A.S.-M., F.M.)
| | - Beibei Zheng
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland (K.G., B.Z., L.R., P.T.R., K.K., B.T., D.S.Ó., F.W.)
- Department of Biology, National University of Ireland Maynooth, Maynooth, Ireland (K.G., E.G.); and
- Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV, Valencia, Spain (A.S.-M., F.M.)
| | - Antonio Serrano-Mislata
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland (K.G., B.Z., L.R., P.T.R., K.K., B.T., D.S.Ó., F.W.)
- Department of Biology, National University of Ireland Maynooth, Maynooth, Ireland (K.G., E.G.); and
- Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV, Valencia, Spain (A.S.-M., F.M.)
| | - Liina Rae
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland (K.G., B.Z., L.R., P.T.R., K.K., B.T., D.S.Ó., F.W.)
- Department of Biology, National University of Ireland Maynooth, Maynooth, Ireland (K.G., E.G.); and
- Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV, Valencia, Spain (A.S.-M., F.M.)
| | - Patrick T Ryan
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland (K.G., B.Z., L.R., P.T.R., K.K., B.T., D.S.Ó., F.W.)
- Department of Biology, National University of Ireland Maynooth, Maynooth, Ireland (K.G., E.G.); and
- Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV, Valencia, Spain (A.S.-M., F.M.)
| | - Kamila Kwaśniewska
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland (K.G., B.Z., L.R., P.T.R., K.K., B.T., D.S.Ó., F.W.)
- Department of Biology, National University of Ireland Maynooth, Maynooth, Ireland (K.G., E.G.); and
- Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV, Valencia, Spain (A.S.-M., F.M.)
| | - Bennett Thomson
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland (K.G., B.Z., L.R., P.T.R., K.K., B.T., D.S.Ó., F.W.)
- Department of Biology, National University of Ireland Maynooth, Maynooth, Ireland (K.G., E.G.); and
- Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV, Valencia, Spain (A.S.-M., F.M.)
| | - Diarmuid S Ó'Maoiléidigh
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland (K.G., B.Z., L.R., P.T.R., K.K., B.T., D.S.Ó., F.W.)
- Department of Biology, National University of Ireland Maynooth, Maynooth, Ireland (K.G., E.G.); and
- Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV, Valencia, Spain (A.S.-M., F.M.)
| | - Francisco Madueño
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland (K.G., B.Z., L.R., P.T.R., K.K., B.T., D.S.Ó., F.W.)
- Department of Biology, National University of Ireland Maynooth, Maynooth, Ireland (K.G., E.G.); and
- Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV, Valencia, Spain (A.S.-M., F.M.)
| | - Frank Wellmer
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland (K.G., B.Z., L.R., P.T.R., K.K., B.T., D.S.Ó., F.W.);
- Department of Biology, National University of Ireland Maynooth, Maynooth, Ireland (K.G., E.G.); and
- Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV, Valencia, Spain (A.S.-M., F.M.)
| | - Emmanuelle Graciet
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland (K.G., B.Z., L.R., P.T.R., K.K., B.T., D.S.Ó., F.W.)
- Department of Biology, National University of Ireland Maynooth, Maynooth, Ireland (K.G., E.G.); and
- Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV, Valencia, Spain (A.S.-M., F.M.)
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de Marchi R, Sorel M, Mooney B, Fudal I, Goslin K, Kwaśniewska K, Ryan PT, Pfalz M, Kroymann J, Pollmann S, Feechan A, Wellmer F, Rivas S, Graciet E. The N-end rule pathway regulates pathogen responses in plants. Sci Rep 2016; 6:26020. [PMID: 27173012 PMCID: PMC4865862 DOI: 10.1038/srep26020] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 04/27/2016] [Indexed: 12/24/2022] Open
Abstract
To efficiently counteract pathogens, plants rely on a complex set of immune responses that are tightly regulated to allow the timely activation, appropriate duration and adequate amplitude of defense programs. The coordination of the plant immune response is known to require the activity of the ubiquitin/proteasome system, which controls the stability of proteins in eukaryotes. Here, we demonstrate that the N-end rule pathway, a subset of the ubiquitin/proteasome system, regulates the defense against a wide range of bacterial and fungal pathogens in the model plant Arabidopsis thaliana. We show that this pathway positively regulates the biosynthesis of plant-defense metabolites such as glucosinolates, as well as the biosynthesis and response to the phytohormone jasmonic acid, which plays a key role in plant immunity. Our results also suggest that the arginylation branch of the N-end rule pathway regulates the timing and amplitude of the defense program against the model pathogen Pseudomonas syringae AvrRpm1.
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Affiliation(s)
- Rémi de Marchi
- Maynooth University, Department of Biology, Maynooth, Co. Kildare, Ireland.,LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Maud Sorel
- Maynooth University, Department of Biology, Maynooth, Co. Kildare, Ireland
| | - Brian Mooney
- Maynooth University, Department of Biology, Maynooth, Co. Kildare, Ireland
| | - Isabelle Fudal
- UMR BIOGER, INRA, AgroParisTech, Université Paris Saclay, 78850 Thiverval-Grignon, France
| | - Kevin Goslin
- Maynooth University, Department of Biology, Maynooth, Co. Kildare, Ireland
| | - Kamila Kwaśniewska
- Trinity College Dublin, Smurfit Institute of Genetics, Dublin 2, Ireland
| | - Patrick T Ryan
- Trinity College Dublin, Smurfit Institute of Genetics, Dublin 2, Ireland
| | - Marina Pfalz
- Ecologie Systématique Evolution, CNRS/Université Paris-Sud/AgroParisTech, Université Paris-Saclay, 91400 Orsay, France
| | - Juergen Kroymann
- Ecologie Systématique Evolution, CNRS/Université Paris-Sud/AgroParisTech, Université Paris-Saclay, 91400 Orsay, France
| | - Stephan Pollmann
- Centro de Biotecnología y Genómica de Plantas, U.P.M. - I.N.I.A., Parque Científico y Tecnológico de la U.P.M., Campus de Montegancedo, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Angela Feechan
- School of Agriculture &Food Science and UCD Earth Institute, College of Health and Agricultural Sciences, University College Dublin, Belfield, Dublin 4, Ireland
| | - Frank Wellmer
- Trinity College Dublin, Smurfit Institute of Genetics, Dublin 2, Ireland
| | - Susana Rivas
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Emmanuelle Graciet
- Maynooth University, Department of Biology, Maynooth, Co. Kildare, Ireland
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Ryan PT, Ó'Maoiléidigh DS, Drost HG, Kwaśniewska K, Gabel A, Grosse I, Graciet E, Quint M, Wellmer F. Patterns of gene expression during Arabidopsis flower development from the time of initiation to maturation. BMC Genomics 2015; 16:488. [PMID: 26126740 PMCID: PMC4488132 DOI: 10.1186/s12864-015-1699-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2015] [Accepted: 06/15/2015] [Indexed: 11/10/2022] Open
Abstract
Background The formation of flowers is one of the main model systems to elucidate the molecular mechanisms that control developmental processes in plants. Although several studies have explored gene expression during flower development in the model plant Arabidopsis thaliana on a genome-wide scale, a continuous series of expression data from the earliest floral stages until maturation has been lacking. Here, we used a floral induction system to close this information gap and to generate a reference dataset for stage-specific gene expression during flower formation. Results Using a floral induction system, we collected floral buds at 14 different stages from the time of initiation until maturation. Using whole-genome microarray analysis, we identified 7,405 genes that exhibit rapid expression changes during flower development. These genes comprise many known floral regulators and we found that the expression profiles for these regulators match their known expression patterns, thus validating the dataset. We analyzed groups of co-expressed genes for over-represented cellular and developmental functions through Gene Ontology analysis and found that they could be assigned specific patterns of activities, which are in agreement with the progression of flower development. Furthermore, by mapping binding sites of floral organ identity factors onto our dataset, we were able to identify gene groups that are likely predominantly under control of these transcriptional regulators. We further found that the distribution of paralogs among groups of co-expressed genes varies considerably, with genes expressed predominantly at early and intermediate stages of flower development showing the highest proportion of such genes. Conclusions Our results highlight and describe the dynamic expression changes undergone by a large number of genes during flower development. They further provide a comprehensive reference dataset for temporal gene expression during flower formation and we demonstrate that it can be used to integrate data from other genomics approaches such as genome-wide localization studies of transcription factor binding sites. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1699-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Patrick T Ryan
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Diarmuid S Ó'Maoiléidigh
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland.,Present address: Max Planck Institute for Plant Breeding Research, D-50829, Cologne, Germany
| | - Hajk-Georg Drost
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | | | - Alexander Gabel
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Ivo Grosse
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Emmanuelle Graciet
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland.,Department of Biology, National University of Ireland Maynooth, Maynooth, Ireland
| | - Marcel Quint
- Leibniz Institute of Plant Biochemistry, Department of Molecular Signal Processing, Halle (Saale), Germany.
| | - Frank Wellmer
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland.
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5
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Ó'Maoiléidigh DS, Thomson B, Raganelli A, Wuest SE, Ryan PT, Kwaśniewska K, Carles CC, Graciet E, Wellmer F. Gene network analysis of Arabidopsis thaliana flower development through dynamic gene perturbations. Plant J 2015; 83:344-358. [PMID: 25990192 DOI: 10.1111/tpj.12878] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Revised: 04/23/2015] [Accepted: 04/29/2015] [Indexed: 06/04/2023]
Abstract
Understanding how flowers develop from undifferentiated stem cells has occupied developmental biologists for decades. Key to unraveling this process is a detailed knowledge of the global regulatory hierarchies that control developmental transitions, cell differentiation and organ growth. These hierarchies may be deduced from gene perturbation experiments, which determine the effects on gene expression after specific disruption of a regulatory gene. Here, we tested experimental strategies for gene perturbation experiments during Arabidopsis thaliana flower development. We used artificial miRNAs (amiRNAs) to disrupt the functions of key floral regulators, and expressed them under the control of various inducible promoter systems that are widely used in the plant research community. To be able to perform genome-wide experiments with stage-specific resolution using the various inducible promoter systems for gene perturbation experiments, we also generated a series of floral induction systems that allow collection of hundreds of synchronized floral buds from a single plant. Based on our results, we propose strategies for performing dynamic gene perturbation experiments in flowers, and outline how they may be combined with versions of the floral induction system to dissect the gene regulatory network underlying flower development.
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Affiliation(s)
| | - Bennett Thomson
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Andrea Raganelli
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Samuel E Wuest
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Patrick T Ryan
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Kamila Kwaśniewska
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Cristel C Carles
- UMR 5168, Université Grenoble Alpes, F-38041, Grenoble, France
- UMR 5168, Centre National de la Recherche Scientifique, F-38054, Grenoble, France
- Laboratoire Physiologie Cellulaire et Végétale, Comissariat a l'Energie Atomique (CEA), Institut de Recherches en Technologies et Sciences pour le Vivant (iRTSV), F-38054, Grenoble, France
- Institut National de la Recherche Agronomique, F-38054, Grenoble, France
| | - Emmanuelle Graciet
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
- Department of Biology, National University of Ireland Maynooth, Maynooth, Ireland
| | - Frank Wellmer
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
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6
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Ó’Maoiléidigh DS, Wuest SE, Rae L, Raganelli A, Ryan PT, Kwaśniewska K, Das P, Lohan AJ, Loftus B, Graciet E, Wellmer F. Control of reproductive floral organ identity specification in Arabidopsis by the C function regulator AGAMOUS. Plant Cell 2013; 25:2482-503. [PMID: 23821642 PMCID: PMC3753378 DOI: 10.1105/tpc.113.113209] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Revised: 06/05/2013] [Accepted: 06/17/2013] [Indexed: 05/18/2023]
Abstract
The floral organ identity factor AGAMOUS (AG) is a key regulator of Arabidopsis thaliana flower development, where it is involved in the formation of the reproductive floral organs as well as in the control of meristem determinacy. To obtain insights into how AG specifies organ fate, we determined the genes and processes acting downstream of this C function regulator during early flower development and distinguished between direct and indirect effects. To this end, we combined genome-wide localization studies, gene perturbation experiments, and computational analyses. Our results demonstrate that AG controls flower development to a large extent by controlling the expression of other genes with regulatory functions, which are involved in mediating a plethora of different developmental processes. One aspect of this function is the suppression of the leaf development program in emerging floral primordia. Using trichome initiation as an example, we demonstrate that AG inhibits an important aspect of leaf development through the direct control of key regulatory genes. A comparison of the gene expression programs controlled by AG and the B function regulators APETALA3 and PISTILLATA, respectively, showed that while they control many developmental processes in conjunction, they also have marked antagonistic, as well as independent activities.
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Affiliation(s)
| | - Samuel E. Wuest
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Liina Rae
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Andrea Raganelli
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Patrick T. Ryan
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Kamila Kwaśniewska
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Pradeep Das
- École Normale Supérieure, 69364 Lyon, cedex 07, France
| | - Amanda J. Lohan
- Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Brendan Loftus
- Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Emmanuelle Graciet
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
- Address correspondence to
| | - Frank Wellmer
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
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