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Du C, Liu M, Yan Y, Guo X, Cao X, Jiao Y, Zheng J, Ma Y, Xie Y, Li H, Yang C, Gao C, Zhao Q, Zhang Z. The U-box E3 ubiquitin ligase PUB35 negatively regulates ABA signaling through AFP1-mediated degradation of ABI5. THE PLANT CELL 2024; 36:3277-3297. [PMID: 38924024 PMCID: PMC11371175 DOI: 10.1093/plcell/koae194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 06/04/2024] [Accepted: 06/19/2024] [Indexed: 06/28/2024]
Abstract
Abscisic acid (ABA) signaling is crucial for plant responses to various abiotic stresses. The Arabidopsis (Arabidopsis thaliana) transcription factor ABA INSENSITIVE 5 (ABI5) is a central regulator of ABA signaling. ABI5 BINDING PROTEIN 1 (AFP1) interacts with ABI5 and facilitates its 26S-proteasome-mediated degradation, although the detailed mechanism has remained unclear. Here, we report that an ABA-responsive U-box E3 ubiquitin ligase, PLANT U-BOX 35 (PUB35), physically interacts with AFP1 and ABI5. PUB35 directly ubiquitinated ABI5 in a bacterially reconstituted ubiquitination system and promoted ABI5 protein degradation in vivo. ABI5 degradation was enhanced by AFP1 in response to ABA treatment. Phosphorylation of the T201 and T206 residues in ABI5 disrupted the ABI5-AFP1 interaction and affected the ABI5-PUB35 interaction and PUB35-mediated degradation of ABI5 in vivo. Genetic analysis of seed germination and seedling growth showed that pub35 mutants were hypersensitive to ABA as well as to salinity and osmotic stresses, whereas PUB35 overexpression lines were hyposensitive. Moreover, abi5 was epistatic to pub35, whereas the pub35-2 afp1-1 double mutant showed a similar ABA response to the two single mutants. Together, our results reveal a PUB35-AFP1 module involved in fine-tuning ABA signaling through ubiquitination and 26S-proteasome-mediated degradation of ABI5 during seed germination and seedling growth.
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Affiliation(s)
- Chang Du
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Meng Liu
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Yujie Yan
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Xiaoyu Guo
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Xiuping Cao
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Yuzhe Jiao
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Jiexuan Zheng
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Yanchun Ma
- College of Life Sciences, Liaocheng University, Liaocheng, 252000, Shandong, China
| | - Yuting Xie
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Hongbo Li
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Chengwei Yang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Caiji Gao
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Qingzhen Zhao
- College of Life Sciences, Liaocheng University, Liaocheng, 252000, Shandong, China
| | - Zhonghui Zhang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China
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Vittozzi Y, Krüger T, Majee A, Née G, Wenkel S. ABI5 binding proteins: key players in coordinating plant growth and development. TRENDS IN PLANT SCIENCE 2024; 29:1006-1017. [PMID: 38584080 DOI: 10.1016/j.tplants.2024.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 03/05/2024] [Accepted: 03/11/2024] [Indexed: 04/09/2024]
Abstract
During the course of terrestrial evolution, plants have developed complex networks that involve the coordination of phytohormone signalling pathways in order to adapt to an ever-changing environment. Transcription factors coordinate these responses by engaging in different protein complexes and exerting both positive and negative effects. ABA INSENSITIVE 5 (ABI5) binding proteins (AFPs), which are closely related to NOVEL INTERACTOR OF JAZ (NINJA)-like proteins, are known for their fundamental role in plants' morphological and physiological growth. Recent studies have shown that AFPs regulate several hormone-signalling pathways, including abscisic acid (ABA) and gibberellic acid (GA). Here, we review the genetic control of AFPs and their crosstalk with plant hormone signalling, and discuss the contributions of AFPs to plants' growth and development.
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Affiliation(s)
- Ylenia Vittozzi
- University of Copenhagen, Department of Plant & Environmental Sciences, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark; NovoCrops Centre, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
| | - Thorben Krüger
- University of Münster, Institut für Biologie und Biotechnologie der Pflanzen, Schlossplatz 4, 48149 Münster, Germany
| | - Adity Majee
- Umeå Plant Science Centre, Umeå University, Linnaeus väg 6, 907 36 Umeå, Sweden
| | - Guillaume Née
- University of Münster, Institut für Biologie und Biotechnologie der Pflanzen, Schlossplatz 4, 48149 Münster, Germany.
| | - Stephan Wenkel
- University of Copenhagen, Department of Plant & Environmental Sciences, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark; NovoCrops Centre, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark; Umeå Plant Science Centre, Umeå University, Linnaeus väg 6, 907 36 Umeå, Sweden.
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Omelyanchuk NA, Lavrekha VV, Bogomolov AG, Dolgikh VA, Sidorenko AD, Zemlyanskaya EV. Computational Reconstruction of the Transcription Factor Regulatory Network Induced by Auxin in Arabidopsis thaliana L. PLANTS (BASEL, SWITZERLAND) 2024; 13:1905. [PMID: 39065433 PMCID: PMC11280061 DOI: 10.3390/plants13141905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Revised: 07/05/2024] [Accepted: 07/06/2024] [Indexed: 07/28/2024]
Abstract
In plant hormone signaling, transcription factor regulatory networks (TFRNs), which link the master transcription factors to the biological processes under their control, remain insufficiently characterized despite their crucial function. Here, we identify a TFRN involved in the response to the key plant hormone auxin and define its impact on auxin-driven biological processes. To reconstruct the TFRN, we developed a three-step procedure, which is based on the integrated analysis of differentially expressed gene lists and a representative collection of transcription factor binding profiles. Its implementation is available as a part of the CisCross web server. With the new method, we distinguished two transcription factor subnetworks. The first operates before auxin treatment and is switched off upon hormone application, the second is switched on by the hormone. Moreover, we characterized the functioning of the auxin-regulated TFRN in control of chlorophyll and lignin biosynthesis, abscisic acid signaling, and ribosome biogenesis.
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Affiliation(s)
- Nadya A. Omelyanchuk
- Department of Systems Biology, Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (N.A.O.); (V.V.L.); (A.G.B.); (V.A.D.); (A.D.S.)
| | - Viktoriya V. Lavrekha
- Department of Systems Biology, Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (N.A.O.); (V.V.L.); (A.G.B.); (V.A.D.); (A.D.S.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Anton G. Bogomolov
- Department of Systems Biology, Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (N.A.O.); (V.V.L.); (A.G.B.); (V.A.D.); (A.D.S.)
| | - Vladislav A. Dolgikh
- Department of Systems Biology, Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (N.A.O.); (V.V.L.); (A.G.B.); (V.A.D.); (A.D.S.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Aleksandra D. Sidorenko
- Department of Systems Biology, Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (N.A.O.); (V.V.L.); (A.G.B.); (V.A.D.); (A.D.S.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Elena V. Zemlyanskaya
- Department of Systems Biology, Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (N.A.O.); (V.V.L.); (A.G.B.); (V.A.D.); (A.D.S.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
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Smolikova G, Krylova E, Petřík I, Vilis P, Vikhorev A, Strygina K, Strnad M, Frolov A, Khlestkina E, Medvedev S. Involvement of Abscisic Acid in Transition of Pea ( Pisum sativum L.) Seeds from Germination to Post-Germination Stages. PLANTS (BASEL, SWITZERLAND) 2024; 13:206. [PMID: 38256760 PMCID: PMC10819913 DOI: 10.3390/plants13020206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 12/30/2023] [Accepted: 01/07/2024] [Indexed: 01/24/2024]
Abstract
The transition from seed to seedling represents a critical developmental step in the life cycle of higher plants, dramatically affecting plant ontogenesis and stress tolerance. The release from dormancy to acquiring germination ability is defined by a balance of phytohormones, with the substantial contribution of abscisic acid (ABA), which inhibits germination. We studied the embryonic axis of Pisum sativum L. before and after radicle protrusion. Our previous work compared RNA sequencing-based transcriptomics in the embryonic axis isolated before and after radicle protrusion. The current study aims to analyze ABA-dependent gene regulation during the transition of the embryonic axis from the germination to post-germination stages. First, we determined the levels of abscisates (ABA, phaseic acid, dihydrophaseic acid, and neo-phaseic acid) using ultra-high-performance liquid chromatography-tandem mass spectrometry. Second, we made a detailed annotation of ABA-associated genes using RNA sequencing-based transcriptome profiling. Finally, we analyzed the DNA methylation patterns in the promoters of the PsABI3, PsABI4, and PsABI5 genes. We showed that changes in the abscisate profile are characterized by the accumulation of ABA catabolites, and the ABA-related gene profile is accompanied by the upregulation of genes controlling seedling development and the downregulation of genes controlling water deprivation. The expression of ABI3, ABI4, and ABI5, which encode crucial transcription factors during late maturation, was downregulated by more than 20-fold, and their promoters exhibited high levels of methylation already at the late germination stage. Thus, although ABA remains important, other regulators seems to be involved in the transition from seed to seedling.
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Affiliation(s)
- Galina Smolikova
- Department of Plant Physiology and Biochemistry, St. Petersburg State University, 199034 St. Petersburg, Russia; (E.K.); (S.M.)
| | - Ekaterina Krylova
- Department of Plant Physiology and Biochemistry, St. Petersburg State University, 199034 St. Petersburg, Russia; (E.K.); (S.M.)
- Federal Research Center N.I. Vavilov All-Russian Institute of Plant Genetic Resources, 190000 St. Petersburg, Russia;
| | - Ivan Petřík
- Laboratory of Growth Regulators, The Czech Academy of Sciences, Institute of Experimental Botany & Palacky University, Faculty of Science, Slechtitelu 27, CZ-78371 Olomouc, Czech Republic; (I.P.); (M.S.)
| | - Polina Vilis
- Department of Plant Physiology and Biochemistry, St. Petersburg State University, 199034 St. Petersburg, Russia; (E.K.); (S.M.)
| | - Aleksander Vikhorev
- School of Advanced Engineering Studies, Novosibirsk State University, 630090 Novosibirsk, Russia
| | | | - Miroslav Strnad
- Laboratory of Growth Regulators, The Czech Academy of Sciences, Institute of Experimental Botany & Palacky University, Faculty of Science, Slechtitelu 27, CZ-78371 Olomouc, Czech Republic; (I.P.); (M.S.)
| | - Andrej Frolov
- Laboratory of Analytical Biochemistry and Biotechnology, K.A. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, 127276 Moscow, Russia;
| | - Elena Khlestkina
- Federal Research Center N.I. Vavilov All-Russian Institute of Plant Genetic Resources, 190000 St. Petersburg, Russia;
| | - Sergei Medvedev
- Department of Plant Physiology and Biochemistry, St. Petersburg State University, 199034 St. Petersburg, Russia; (E.K.); (S.M.)
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Bizouerne E, Ly Vu J, Ly Vu B, Diouf I, Bitton F, Causse M, Verdier J, Buitink J, Leprince O. Genetic Variability in Seed Longevity and Germination Traits in a Tomato MAGIC Population in Contrasting Environments. PLANTS (BASEL, SWITZERLAND) 2023; 12:3632. [PMID: 37896095 PMCID: PMC10610530 DOI: 10.3390/plants12203632] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 10/18/2023] [Accepted: 10/19/2023] [Indexed: 10/29/2023]
Abstract
The stable production of high vigorous seeds is pivotal to crop yield. Also, a high longevity is essential to avoid progressive loss of seed vigour during storage. Both seed traits are strongly influenced by the environment during seed development. Here, we investigated the impact of heat stress (HS) during fruit ripening on tomato seed lifespan during storage at moderate relative humidity, speed (t50) and homogeneity of germination, using a MAGIC population that was produced under optimal and HS conditions. A plasticity index was used to assess the extent of the impact of HS for each trait. HS reduced the average longevity and germination homogeneity by 50% within the parents and MAGIC population. However, there was a high genetic variability in the seed response to heat stress. A total of 39 QTLs were identified, including six longevity QTLs for seeds from control (3) and HS (3) conditions, and six plasticity QTLs for longevity, with only one overlapping with a longevity QTL under HS. Four out of the six longevity QTL co-located with t50 QTL, revealing hotspots for seed quality traits. Twenty-one QTLs with intervals below 3 cM were analyzed using previous transcriptome and gene network data to propose candidate genes for seed vigour and longevity traits.
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Affiliation(s)
- Elise Bizouerne
- Institut Agro, INRAE, University Angers, IRHS, SFR QUASAV, 49000 Angers, France; (E.B.); (J.L.V.); (B.L.V.); (J.V.); (J.B.)
| | - Joseph Ly Vu
- Institut Agro, INRAE, University Angers, IRHS, SFR QUASAV, 49000 Angers, France; (E.B.); (J.L.V.); (B.L.V.); (J.V.); (J.B.)
| | - Benoît Ly Vu
- Institut Agro, INRAE, University Angers, IRHS, SFR QUASAV, 49000 Angers, France; (E.B.); (J.L.V.); (B.L.V.); (J.V.); (J.B.)
| | - Isidore Diouf
- Génétique et Amélioration des Fruits et Légumes, Centre de Recherche PACA, INRAE, UR1052, CS60094, 84143 Avignon, France (F.B.); (M.C.)
| | - Frédérique Bitton
- Génétique et Amélioration des Fruits et Légumes, Centre de Recherche PACA, INRAE, UR1052, CS60094, 84143 Avignon, France (F.B.); (M.C.)
| | - Mathilde Causse
- Génétique et Amélioration des Fruits et Légumes, Centre de Recherche PACA, INRAE, UR1052, CS60094, 84143 Avignon, France (F.B.); (M.C.)
| | - Jérôme Verdier
- Institut Agro, INRAE, University Angers, IRHS, SFR QUASAV, 49000 Angers, France; (E.B.); (J.L.V.); (B.L.V.); (J.V.); (J.B.)
| | - Julia Buitink
- Institut Agro, INRAE, University Angers, IRHS, SFR QUASAV, 49000 Angers, France; (E.B.); (J.L.V.); (B.L.V.); (J.V.); (J.B.)
| | - Olivier Leprince
- Institut Agro, INRAE, University Angers, IRHS, SFR QUASAV, 49000 Angers, France; (E.B.); (J.L.V.); (B.L.V.); (J.V.); (J.B.)
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