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Proteomic approach during the induction of somatic embryo-genesis in Coffea canephora

ABSTRACT: This research seeks to contribute to our understanding of the primary cellular pathways involved in the induction of SE in C. canephora. The process of our model consists of two stages: 1) preconditioning in MS medium with auxin (NAA) and cytokinin (KIN); and 2) induction in Yasuda liquid medium added with cytokinin (BA). Therefore, in this study, we analyzed different days of the SE induction process using shotgun label-free quantitative proteomics. 1630 proteins were found among different sampling days of the process, of which, the majority were up-accumulated during the induction stage. We found that some of the most enriched pathways during the process were the biosynthesis of amino acids and secondary metabolites. Eighteen proteins were found related to auxin homeostasis and two to cytokinin metabolism, such as ABC, BIG, ILR, LOG, and ARR, among others. Ten proteins and transcription factors related to SE were also identified, like SERK1, SKP1, nuclear transcription factor Y, MADS-box and calreticulin,; and 19 related to other processes of plant development, among which the 14-3-3 and PP2A proteins stand out.

INSTRUMENT(S): Orbitrap Fusion

ORGANISM(S): Coffea Canephora

TISSUE(S): Leaf

SUBMITTER: ANA QUINTANA

LAB HEAD: Victor Manuel Loyola Vargas

PROVIDER: PXD047172 | Pride | 2024-01-26

REPOSITORIES: pride

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Proteomic Approach during the Induction of Somatic Embryogenesis in Coffea canephora.

Quintana-Escobar Ana Odetth AO Bojórquez-Velázquez Esaú E Ruiz-May Eliel E Loyola-Vargas Víctor Manuel VM

Plants (Basel, Switzerland) 20231207 24

Plant growth regulators (PGR) are essential for somatic embryogenesis (SE) in different species, and Coffea canephora is no exception. In our study model, previously, we have been able to elucidate the participation of various genes involved in SE by using different strategies; however, until now, we have not used a proteomic approach. This research seeks to contribute to understanding the primary cellular pathways involved in developing SE in C. canephora. The process of our model ...[more]

PMID: 38140424

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Project description:Somatic embryogenesis (SE) exemplifies the unique developmental plasticity of plant cells. The regulatory processes, including epigenetic modifications controlling embryogenic reprogramming of cell transcriptome, have just started to be revealed. To identify the genes of histone acetylation-regulated expression in SE, we analyzed global transcriptomes of Arabidopsis explants undergoing embryogenic induction in response to treatment with histone deacetylase inhibitor, trichostatin A (TSA). The TSA-induced and auxin (2,4-dichlorophenoxyacetic acid; 2,4-D)-induced transcriptomes were compared. RNA-seq results revealed the similarities of the TSA- and auxin-induced transcriptomic responses that involve extensive deregulation, mostly repression, of the majority of genes. Within the differentially expressed genes (DEGs), we identified the master regulators (transcription factors TF) of SE, genes involved in biosynthesis, signaling, and polar transport of auxin and NITRILASE-encoding genes of the function in indole-3-acetic acid (IAA) biosynthesis. TSA-upregulated TF genes of essential functions in auxin-induced SE, included LEC1/LEC2, FUS3, AGL15, MYB118, PHB, PHV, PLTs, and WUS/WOXs. The TSA-induced transcriptome revealed also extensive upregulation of stress-related genes, including those related to stress hormone biosynthesis. In line with transcriptomic data, TSA-induced explants accumulated salicylic acid (SA) and abscisic acid (ABA), suggesting the role of histone acetylation (Hac) in regulating stress hormone-related responses during SE induction. Since mostly the adaxial side of cotyledon explant contributes to SE induction, we also identified organ polarity-related genes responding to TSA treatment, including AIL7/PLT7, RGE1, LBD18, 40, HB32, CBF1, and ULT2. Analysis of the relevant mutants supported the role of polarity-related genes in SE induction. The study results provide a step forward in deciphering the epigenetic network controlling embryogenic transition in somatic cells of plants.

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Dataset Information

Proteomic approach during the induction of somatic embryo-genesis in Coffea canephora

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Publications

Proteomic Approach during the Induction of Somatic Embryogenesis in <i>Coffea canephora</i>.

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