Integrative proteomics and phosphoproteomics reveals phosphorylation networks involved in the maintenance and expression of embryogenic competence in sugarcane callus

Xavier, Lucas Rodrigues; Almeida, Felipe Astolpho; Pinto, Vitor Batista; Passamani, Lucas Zanchetta; Santa–Catarina, Claudete; Filho, Gonçalo Apolinário de Souza; Mooney, Brian; Thelen, Jay J.; Silveira, Vanildo

doi:10.1016/j.jplph.2021.153587

Cited by 4 publications

(3 citation statements)

References 68 publications

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“…The increase in the accumulation of histone deacetylase HDT1 (evm.model.supercontig_5.85, orthologous to AtHD2C) protein was accumulated throughout the induction of the embryogenic callus (Supplementary Table S1). Studies in sugarcane have shown that histone deacetylase 1, belonging to the HDAC family, is also involved in the differentiation of somatic embryos, interacting with corepressors such as TOPLESS to modulate protein post-translational regulation during somatic embryo differentiation [20]. Thus, the temporal analysis of the data in the present study suggests that histone acetylation/methylation is regulated at early stages of callus formation and acquisition of competence in C. papaya embryogenic callus.…”

Section: Acquisition Of Embryogenic Competence In Somatic Cells Invol...supporting

confidence: 52%

“…Phosphorylation is a post-translational modification involved in fine tuning the interactions, localization, activity, and shape of proteins. Several proteins with regulatory roles are phosphorylated at specific tyrosine, threonine, and serine residues in embryogenic calli and differentiating somatic embryos [20,23]. Our data reveal the accumulation of two serine/threonine-protein phosphatase PP2A-2 catalytic subunit (evm.model.supercontig_13.7 and evm.model.supercontig_1.195, orthologous to AtPP2A-2 and AtPP2A-3, respectively) and two serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A beta isoforms (evm.model.supercontig_13.7 and evm.model.supercontig_1.195, both orthologous to AtPP2AA2) throughout embryogenic callus induction and their predicted interaction with 14-3-3 proteins (Table 1) (Figure 4).…”

Section: Acquisition Of Embryogenic Competence In Somatic Cells Invol...mentioning

confidence: 99%

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Time-Dependent Proteomic Signatures Associated with Embryogenic Callus Induction in Carica papaya L.

Xavier,

Corrêa,

da Paschoa

et al. 2023

Plants

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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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Section: Acquisition Of Embryogenic Competence In Somatic Cells Invol...supporting

confidence: 52%

Section: Acquisition Of Embryogenic Competence In Somatic Cells Invol...mentioning

confidence: 99%

Time-Dependent Proteomic Signatures Associated with Embryogenic Callus Induction in Carica papaya L.

Xavier,

Corrêa,

da Paschoa

et al. 2023

Plants

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“…SOM is repressed at the transcriptional level upon light exposure [72]. Moreover, the phosphorylation of LUH has recently been reported in sugarcane callus and is associated with embryogenic competency [74]. SOM and LUH dephosphorylation at the early stages of imbibition might be a new mechanism to control their stability and/or their biological activity.…”

Section: Discussionmentioning

confidence: 97%

Dynamics of Protein Phosphorylation during Arabidopsis Seed Germination

Baudouin

Puyaubert

Meimoun

et al. 2022

IJMS

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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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Plant proteomics: From the molecular basis of biological processes to a systems biology perspective

Bykova

Rampitsch

Igamberdiev

2023

Journal of Plant Physiology

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Integrative proteomics and phosphoproteomics reveals phosphorylation networks involved in the maintenance and expression of embryogenic competence in sugarcane callus

Cited by 4 publications

References 68 publications

Time-Dependent Proteomic Signatures Associated with Embryogenic Callus Induction in Carica papaya L.

Time-Dependent Proteomic Signatures Associated with Embryogenic Callus Induction in Carica papaya L.

Dynamics of Protein Phosphorylation during Arabidopsis Seed Germination

Plant proteomics: From the molecular basis of biological processes to a systems biology perspective

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