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Xavier LR, Corrêa CCG, da Paschoa RP, Vieira KDS, Pacheco DDR, Gomes LDES, Duncan BC, da Conceição LDS, Pinto VB, Santa-Catarina C, Silveira V. Time-Dependent Proteomic Signatures Associated with Embryogenic Callus Induction in Carica papaya L. PLANTS (BASEL, SWITZERLAND) 2023; 12:3891. [PMID: 38005788 PMCID: PMC10675192 DOI: 10.3390/plants12223891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/09/2023] [Accepted: 11/15/2023] [Indexed: 11/26/2023]
Abstract
Sex segregation increases the cost of Carica papaya production through seed-based propagation. Therefore, in vitro techniques are an attractive option for clonal propagation, especially of hermaphroditic plants. Here, we performed a temporal analysis of the proteome of C. papaya calli aiming to identify the key players involved in embryogenic callus formation. Mature zygotic embryos used as explants were treated with 20 μM 2,4-dichlorophenoxyacetic acid to induce embryogenic callus. Total proteins were extracted from explants at 0 (zygotic embryo) and after 7, 14, and 21 days of induction. A total of 1407 proteins were identified using a bottom-up proteomic approach. The clustering analysis revealed four distinct patterns of protein accumulation throughout callus induction. Proteins related to seed maturation and storage are abundant in the explant before induction, decreasing as callus formation progresses. Carbohydrate and amino acid metabolisms, aerobic respiration, and protein catabolic processes were enriched throughout days of callus induction. Protein kinases associated with auxin responses, such as SKP1-like proteins 1B, accumulated in response to callus induction. Additionally, regulatory proteins, including histone deacetylase (HD2C) and argonaute 1 (AGO1), were more abundant at 7 days, suggesting their role in the acquisition of embryogenic competence. Predicted protein-protein networks revealed the regulatory role of proteins 14-3-3 accumulated during callus induction and the association of proteins involved in oxidative phosphorylation and hormone response. Our findings emphasize the modulation of the proteome during embryogenic callus initiation and identify regulatory proteins that might be involved in the activation of this process.
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Affiliation(s)
- Lucas Rodrigues Xavier
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes 28013-602, RJ, Brazil; (L.R.X.); (C.C.G.C.); (R.P.d.P.); (K.d.S.V.); (D.D.R.P.); (L.d.E.S.G.); (B.C.D.); (L.d.S.d.C.)
- Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes 28013-602, RJ, Brazil
| | - Caio Cezar Guedes Corrêa
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes 28013-602, RJ, Brazil; (L.R.X.); (C.C.G.C.); (R.P.d.P.); (K.d.S.V.); (D.D.R.P.); (L.d.E.S.G.); (B.C.D.); (L.d.S.d.C.)
- Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes 28013-602, RJ, Brazil
| | - Roberta Pena da Paschoa
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes 28013-602, RJ, Brazil; (L.R.X.); (C.C.G.C.); (R.P.d.P.); (K.d.S.V.); (D.D.R.P.); (L.d.E.S.G.); (B.C.D.); (L.d.S.d.C.)
- Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes 28013-602, RJ, Brazil
| | - Karina da Silva Vieira
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes 28013-602, RJ, Brazil; (L.R.X.); (C.C.G.C.); (R.P.d.P.); (K.d.S.V.); (D.D.R.P.); (L.d.E.S.G.); (B.C.D.); (L.d.S.d.C.)
- Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes 28013-602, RJ, Brazil
| | - Daniel Dastan Rezabala Pacheco
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes 28013-602, RJ, Brazil; (L.R.X.); (C.C.G.C.); (R.P.d.P.); (K.d.S.V.); (D.D.R.P.); (L.d.E.S.G.); (B.C.D.); (L.d.S.d.C.)
- Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes 28013-602, RJ, Brazil
| | - Lucas do Espirito Santo Gomes
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes 28013-602, RJ, Brazil; (L.R.X.); (C.C.G.C.); (R.P.d.P.); (K.d.S.V.); (D.D.R.P.); (L.d.E.S.G.); (B.C.D.); (L.d.S.d.C.)
- Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes 28013-602, RJ, Brazil
| | - Bárbara Cardoso Duncan
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes 28013-602, RJ, Brazil; (L.R.X.); (C.C.G.C.); (R.P.d.P.); (K.d.S.V.); (D.D.R.P.); (L.d.E.S.G.); (B.C.D.); (L.d.S.d.C.)
- Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes 28013-602, RJ, Brazil
| | - Laís dos Santos da Conceição
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes 28013-602, RJ, Brazil; (L.R.X.); (C.C.G.C.); (R.P.d.P.); (K.d.S.V.); (D.D.R.P.); (L.d.E.S.G.); (B.C.D.); (L.d.S.d.C.)
- Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes 28013-602, RJ, Brazil
| | - Vitor Batista Pinto
- Laboratório de Biologia Celular e Tecidual, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes 28013-602, RJ, Brazil; (V.B.P.); (C.S.-C.)
| | - Claudete Santa-Catarina
- Laboratório de Biologia Celular e Tecidual, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes 28013-602, RJ, Brazil; (V.B.P.); (C.S.-C.)
| | - Vanildo Silveira
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes 28013-602, RJ, Brazil; (L.R.X.); (C.C.G.C.); (R.P.d.P.); (K.d.S.V.); (D.D.R.P.); (L.d.E.S.G.); (B.C.D.); (L.d.S.d.C.)
- Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes 28013-602, RJ, Brazil
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Bykova NV, Rampitsch C, Igamberdiev AU. Plant proteomics: From the molecular basis of biological processes to a systems biology perspective. JOURNAL OF PLANT PHYSIOLOGY 2023; 280:153880. [PMID: 36455335 DOI: 10.1016/j.jplph.2022.153880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Affiliation(s)
- Natalia V Bykova
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, R6M 1Y5, Canada.
| | - Christof Rampitsch
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, R6M 1Y5, Canada.
| | - Abir U Igamberdiev
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, 45 Arctic Avenue, A1C 5S7, Canada.
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Baudouin E, Puyaubert J, Meimoun P, Blein-Nicolas M, Davanture M, Zivy M, Bailly C. Dynamics of Protein Phosphorylation during Arabidopsis Seed Germination. Int J Mol Sci 2022; 23:ijms23137059. [PMID: 35806063 PMCID: PMC9266807 DOI: 10.3390/ijms23137059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/16/2022] [Accepted: 06/22/2022] [Indexed: 11/16/2022] Open
Abstract
Seed germination is critical for early plantlet development and is tightly controlled by environmental factors. Nevertheless, the signaling networks underlying germination control remain elusive. In this study, the remodeling of Arabidopsis seed phosphoproteome during imbibition was investigated using stable isotope dimethyl labeling and nanoLC-MS/MS analysis. Freshly harvested seeds were imbibed under dark or constant light to restrict or promote germination, respectively. For each light regime, phosphoproteins were extracted and identified from dry and imbibed (6 h, 16 h, and 24 h) seeds. A large repertoire of 10,244 phosphopeptides from 2546 phosphoproteins, including 110 protein kinases and key regulators of seed germination such as Delay Of Germination 1 (DOG1), was established. Most phosphoproteins were only identified in dry seeds. Early imbibition led to a similar massive downregulation in dormant and non-dormant seeds. After 24 h, 411 phosphoproteins were specifically identified in non-dormant seeds. Gene ontology analyses revealed their involvement in RNA and protein metabolism, transport, and signaling. In addition, 489 phosphopeptides were quantified, and 234 exhibited up or downregulation during imbibition. Interaction networks and motif analyses revealed their association with potential signaling modules involved in germination control. Our study provides evidence of a major role of phosphosignaling in the regulation of Arabidopsis seed germination.
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Affiliation(s)
- Emmanuel Baudouin
- Laboratoire de Biologie du Développement, UMR 7622, Institut de Biologie Paris-Seine (IBPS), Sorbonne Université, CNRS, F-75005 Paris, France; (J.P.); (P.M.); (C.B.)
- Correspondence: ; Tel.: +33-1-44-27-59-87
| | - Juliette Puyaubert
- Laboratoire de Biologie du Développement, UMR 7622, Institut de Biologie Paris-Seine (IBPS), Sorbonne Université, CNRS, F-75005 Paris, France; (J.P.); (P.M.); (C.B.)
| | - Patrice Meimoun
- Laboratoire de Biologie du Développement, UMR 7622, Institut de Biologie Paris-Seine (IBPS), Sorbonne Université, CNRS, F-75005 Paris, France; (J.P.); (P.M.); (C.B.)
| | - Mélisande Blein-Nicolas
- PAPPSO, Génétique Quantitative et Evolution (GQE), Université Paris-Saclay, INRAE, CNRS, AgroParisTech, F-91190 Gif-sur-Yvette, France; (M.B.-N.); (M.D.); (M.Z.)
| | - Marlène Davanture
- PAPPSO, Génétique Quantitative et Evolution (GQE), Université Paris-Saclay, INRAE, CNRS, AgroParisTech, F-91190 Gif-sur-Yvette, France; (M.B.-N.); (M.D.); (M.Z.)
| | - Michel Zivy
- PAPPSO, Génétique Quantitative et Evolution (GQE), Université Paris-Saclay, INRAE, CNRS, AgroParisTech, F-91190 Gif-sur-Yvette, France; (M.B.-N.); (M.D.); (M.Z.)
| | - Christophe Bailly
- Laboratoire de Biologie du Développement, UMR 7622, Institut de Biologie Paris-Seine (IBPS), Sorbonne Université, CNRS, F-75005 Paris, France; (J.P.); (P.M.); (C.B.)
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