1
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Li T, Wang Y, Natran A, Zhang Y, Wang H, Du K, Qin P, Yuan H, Chen W, Tu B, Inzé D, Dubois M. C-TERMINAL DOMAIN PHOSPHATASE-LIKE 3 contributes to GA-mediated growth and flowering by interaction with DELLA proteins. New Phytol 2024. [PMID: 38594216 DOI: 10.1111/nph.19742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 03/14/2024] [Indexed: 04/11/2024]
Abstract
Gibberellic acid (GA) plays a central role in many plant developmental processes and is crucial for crop improvement. DELLA proteins, the core suppressors in the GA signaling pathway, are degraded by GA via the 26S proteasomal pathway to release the GA response. However, little is known about the phosphorylation-mediated regulation of DELLA proteins. In this study, we combined GA response assays with protein-protein interaction analysis to infer the connection between Arabidopsis thaliana DELLAs and the C-TERMINAL DOMAIN PHOSPHATASE-LIKE 3 (CPL3), a phosphatase involved in the dephosphorylation of RNA polymerase II. We show that CPL3 directly interacts with DELLA proteins and promotes DELLA protein stability by inhibiting its degradation by the 26S proteasome. Consequently, CPL3 negatively modulates multiple GA-mediated processes of plant development, including hypocotyl elongation, flowering time, and anthocyanin accumulation. Taken together, our findings demonstrate that CPL3 serves as a novel regulator that could improve DELLA stability and thereby participate in GA signaling transduction.
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Affiliation(s)
- Ting Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, 611130, Chengdu, China
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Gent, Belgium
- Center for Plant Systems Biology, VIB, 9052, Gent, Belgium
| | - Yongqin Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, 611130, Chengdu, China
| | - Annelore Natran
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Gent, Belgium
- Center for Plant Systems Biology, VIB, 9052, Gent, Belgium
| | - Yi Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, 611130, Chengdu, China
| | - Hao Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 611130, Chengdu, Sichuan, China
| | - Kangxi Du
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 611130, Chengdu, Sichuan, China
| | - Peng Qin
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 611130, Chengdu, Sichuan, China
| | - Hua Yuan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, 611130, Chengdu, China
| | - Weilan Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 611130, Chengdu, Sichuan, China
| | - Bin Tu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 611130, Chengdu, Sichuan, China
| | - Dirk Inzé
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Gent, Belgium
- Center for Plant Systems Biology, VIB, 9052, Gent, Belgium
| | - Marieke Dubois
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Gent, Belgium
- Center for Plant Systems Biology, VIB, 9052, Gent, Belgium
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2
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Wu T, Natran A, Prost L, Aydogdu E, Van de Peer Y, Bafort Q. Studying Whole-Genome Duplication Using Experimental Evolution of Spirodela polyrhiza. Methods Mol Biol 2023; 2545:373-390. [PMID: 36720823 DOI: 10.1007/978-1-0716-2561-3_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
In this chapter, we present the use of Spirodela polyrhiza in experiments designed to study the evolutionary impact of whole-genome duplication (WGD). We shortly introduce this duckweed species and explain why it is a suitable model for experimental evolution. Subsequently, we discuss the most relevant steps and methods in the design of a ploidy-related duckweed experiment. These steps include strain selection, ploidy determination, different methods of making polyploid duckweeds, replication, culturing conditions, preservation, and the ways to quantify phenotypic and transcriptomic change.
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Affiliation(s)
- Tian Wu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Annelore Natran
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Lucas Prost
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, VIB, Ghent, Belgium
- Department of Biology, Ghent University, Ghent, Belgium
| | - Eylem Aydogdu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Quinten Bafort
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
- VIB Center for Plant Systems Biology, VIB, Ghent, Belgium.
- Department of Biology, Ghent University, Ghent, Belgium.
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3
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Bafort Q, Wu T, Natran A, De Clerck O, Van de Peer Y. The immediate effects of polyploidization of Spirodela polyrhiza change in a strain-specific way along environmental gradients. Evol Lett 2023; 7:37-47. [PMID: 37065435 PMCID: PMC10091501 DOI: 10.1093/evlett/qrac003] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 11/15/2022] [Accepted: 12/20/2022] [Indexed: 02/04/2023] Open
Abstract
Abstract
The immediate effects of plant polyploidization are well characterized and it is generally accepted that these morphological, physiological, developmental, and phenological changes contribute to polyploid establishment. Studies on the environmental dependence of the immediate effects of whole-genome duplication (WGD) are, however, scarce but suggest that these immediate effects are altered by stressful conditions. As polyploid establishment seems to be associated with environmental disturbance, the relationship between ploidy-induced phenotypical changes and environmental conditions is highly relevant. Here, we use a common garden experiment on the greater duckweed Spirodela polyrhiza to test whether the immediate effects of WGD can facilitate the establishment of tetraploid duckweed along gradients of two environmental stressors. Because successful polyploid establishment often depends on recurrent polyploidization events, we include four genetically diverse strains and assess whether these immediate effects are strain-specific. We find evidence that WGD can indeed confer a fitness advantage under stressful conditions and that the environment affects ploidy-induced changes in fitness and trait reaction norms in a strain-specific way.
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Affiliation(s)
- Quinten Bafort
- Department of Biology, Ghent University , Ghent , Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University and VIB-UGent Center for Plant Systems Biology , Ghent , Belgium
| | - Tian Wu
- Department of Plant Biotechnology and Bioinformatics, Ghent University and VIB-UGent Center for Plant Systems Biology , Ghent , Belgium
| | - Annelore Natran
- Department of Plant Biotechnology and Bioinformatics, Ghent University and VIB-UGent Center for Plant Systems Biology , Ghent , Belgium
| | | | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University and VIB-UGent Center for Plant Systems Biology , Ghent , Belgium
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University , Nanjing , China
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria , Pretoria , South Africa
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4
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Vanhaeren H, Chen Y, Vermeersch M, De Milde L, De Vleeschhauwer V, Natran A, Persiau G, Eeckhout D, De Jaeger G, Gevaert K, Inzé D. UBP12 and UBP13 negatively regulate the activity of the ubiquitin-dependent peptidases DA1, DAR1 and DAR2. eLife 2020; 9:52276. [PMID: 32209225 PMCID: PMC7141810 DOI: 10.7554/elife.52276] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 03/24/2020] [Indexed: 12/20/2022] Open
Abstract
Protein ubiquitination is a very diverse post-translational modification leading to protein degradation or delocalization, or altering protein activity. In Arabidopsis thaliana, two E3 ligases, BIG BROTHER (BB) and DA2, activate the latent peptidases DA1, DAR1 and DAR2 by mono-ubiquitination at multiple sites. Subsequently, these activated peptidases destabilize various positive growth regulators. Here, we show that two ubiquitin-specific proteases, UBP12 and UBP13, deubiquitinate DA1, DAR1 and DAR2, hence reducing their peptidase activity. Overexpression of UBP12 or UBP13 strongly decreased leaf size and cell area, and resulted in lower ploidy levels. Mutants in which UBP12 and UBP13 were downregulated produced smaller leaves that contained fewer and smaller cells. Remarkably, neither UBP12 nor UBP13 were found to be cleavage substrates of the activated DA1. Our results therefore suggest that UBP12 and UBP13 work upstream of DA1, DAR1 and DAR2 to restrict their protease activity and hence fine-tune plant growth and development.
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Affiliation(s)
- Hannes Vanhaeren
- VIB Center for Plant Systems Biology, Technologiepark, Zwijnaarde, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark, Zwijnaarde, Belgium.,VIB Center for Medical Biotechnology, Albert Baertsoenkaai, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Albert Baertsoenkaai, Ghent, Belgium
| | - Ying Chen
- VIB Center for Plant Systems Biology, Technologiepark, Zwijnaarde, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark, Zwijnaarde, Belgium
| | - Mattias Vermeersch
- VIB Center for Plant Systems Biology, Technologiepark, Zwijnaarde, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark, Zwijnaarde, Belgium
| | - Liesbeth De Milde
- VIB Center for Plant Systems Biology, Technologiepark, Zwijnaarde, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark, Zwijnaarde, Belgium
| | - Valerie De Vleeschhauwer
- VIB Center for Plant Systems Biology, Technologiepark, Zwijnaarde, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark, Zwijnaarde, Belgium
| | - Annelore Natran
- VIB Center for Plant Systems Biology, Technologiepark, Zwijnaarde, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark, Zwijnaarde, Belgium
| | - Geert Persiau
- VIB Center for Plant Systems Biology, Technologiepark, Zwijnaarde, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark, Zwijnaarde, Belgium
| | - Dominique Eeckhout
- VIB Center for Plant Systems Biology, Technologiepark, Zwijnaarde, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark, Zwijnaarde, Belgium
| | - Geert De Jaeger
- VIB Center for Plant Systems Biology, Technologiepark, Zwijnaarde, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark, Zwijnaarde, Belgium
| | - Kris Gevaert
- VIB Center for Medical Biotechnology, Albert Baertsoenkaai, Ghent, Belgium
| | - Dirk Inzé
- VIB Center for Plant Systems Biology, Technologiepark, Zwijnaarde, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark, Zwijnaarde, Belgium
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5
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Li T, Natran A, Chen Y, Vercruysse J, Wang K, Gonzalez N, Dubois M, Inzé D. A genetics screen highlights emerging roles for CPL3, RST1 and URT1 in RNA metabolism and silencing. Nat Plants 2019; 5:539-550. [PMID: 31076735 DOI: 10.1038/s41477-019-0419-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 03/28/2019] [Indexed: 05/19/2023]
Abstract
Post-transcriptional gene silencing (PTGS) is a major mechanism regulating gene expression in higher eukaryotes. To identify novel players in PTGS, a forward genetics screen was performed on an Arabidopsis thaliana line overexpressing a strong growth-repressive gene, ETHYLENE RESPONSE FACTOR6 (ERF6). We identified six independent ethyl-methanesulfonate mutants rescuing the dwarfism of ERF6-overexpressing plants as a result of transgene silencing. Among the causative genes, ETHYLENE-INSENSITIVE5, SUPERKILLER2 and HASTY1 have previously been reported to inhibit PTGS. Notably, the three other causative genes have not, to date, been related to PTGS: UTP:RNA-URIDYLYLTRANSFERASE1 (URT1), C-TERMINAL DOMAIN PHOSPHATASE-LIKE3 (CPL3) and RESURRECTION1 (RST1). We show that these genes may participate in protecting the 3' end of transgene transcripts. We present a model in which URT1, CPL3 and RST1 are classified as PTGS suppressors, as compromisation of these genes provokes the accumulation of aberrant transcripts which, in turn, trigger the production of small interfering RNAs, initiating RNA silencing.
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Affiliation(s)
- Ting Li
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Annelore Natran
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Yanjun Chen
- College of Life Science, Wuhan University, Wuhan, China
| | - Jasmien Vercruysse
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Kun Wang
- College of Life Science, Wuhan University, Wuhan, China
| | - Nathalie Gonzalez
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- INRA, Université de Bordeaux, Villenave d'Ornon, France
| | - Marieke Dubois
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Dirk Inzé
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
- VIB Center for Plant Systems Biology, Ghent, Belgium.
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6
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Baekelandt A, Pauwels L, Wang Z, Li N, De Milde L, Natran A, Vermeersch M, Li Y, Goossens A, Inzé D, Gonzalez N. Arabidopsis Leaf Flatness Is Regulated by PPD2 and NINJA through Repression of CYCLIN D3 Genes. Plant Physiol 2018; 178:217-232. [PMID: 29991485 PMCID: PMC6130026 DOI: 10.1104/pp.18.00327] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 06/28/2018] [Indexed: 05/18/2023]
Abstract
In Arabidopsis (Arabidopsis thaliana), reduced expression of the transcriptional regulator PEAPOD2 (PPD2) results in propeller-like rosettes with enlarged and dome-shaped leaves. However, the molecular and cellular processes underlying this peculiar phenotype remain elusive. Here, we studied the interaction between PPD2 and NOVEL INTERACTOR OF JAZ (NINJA) and demonstrated that ninja loss-of-function plants produce rosettes with dome-shaped leaves similar to those of ppd mutants but without the increase in size. We showed that ninja mutants have a convex-shaped primary cell cycle arrest front, putatively leading to excessive cell division in the central leaf blade region. Furthermore, ppd and ninja mutants have a similar increase in the expression of CYCLIN D3;2 (CYCD3;2), and ectopic overexpression of CYCD3;2 phenocopies the ppd and ninja rosette and leaf shape phenotypes without affecting the size. Our results reveal a pivotal contribution of NINJA in leaf development, in addition to its well-studied function in jasmonate signaling, and imply a new function for D3-type cyclins in, at least partially, uncoupling the size and shape phenotypes of ppd leaves.
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Affiliation(s)
- Alexandra Baekelandt
- Ghent University, Department of Plant Biotechnology and Bioinformatics, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052 Ghent, Belgium
| | - Laurens Pauwels
- Ghent University, Department of Plant Biotechnology and Bioinformatics, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052 Ghent, Belgium
| | - Zhibiao Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Na Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Liesbeth De Milde
- Ghent University, Department of Plant Biotechnology and Bioinformatics, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052 Ghent, Belgium
| | - Annelore Natran
- Ghent University, Department of Plant Biotechnology and Bioinformatics, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052 Ghent, Belgium
| | - Mattias Vermeersch
- Ghent University, Department of Plant Biotechnology and Bioinformatics, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052 Ghent, Belgium
| | - Yunhai Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Alain Goossens
- Ghent University, Department of Plant Biotechnology and Bioinformatics, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052 Ghent, Belgium
| | - Dirk Inzé
- Ghent University, Department of Plant Biotechnology and Bioinformatics, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052 Ghent, Belgium
| | - Nathalie Gonzalez
- Ghent University, Department of Plant Biotechnology and Bioinformatics, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052 Ghent, Belgium
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