iTRAQ-based comparative proteomic analysis provides insights into somatic embryogenesis in Gossypium hirsutum L.

Abstract

Key messageiTRAQ based proteomic identified key proteins and provided new insights into the molecular mechanisms underlying somatic embryogenesis in cotton.AbstractSomatic embryogenesis, which involves cell dedifferentiation and redifferentiation, has been used as a model system for understanding molecular events of plant embryo development in vitro. In this study, we performed comparative proteomics analysis using samples of non-embryogenic callus (NEC), embryogenic callus (EC) and somatic embryo (SE) using the isobaric tags for relative and absolute quantitation (iTRAQ) technology. In total, 5892 proteins were identified amongst the three samples. The majority of these proteins (93.4%) were found to have catalytic activity, binding activity, transporter activity or structural molecular activity. Of these proteins, 1024 and 858 were differentially expressed in NEC versus EC and EC versus SE, respectively. Compared to NEC, EC had 452 and 572 down- and up-regulated proteins, respectively, and compared to EC, SE had 647 and 221 down- and up-regulated proteins, respectively. KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis indicated that genetic information transmission, plant hormone transduction, glycolysis, fatty acid biosynthesis and metabolism, galactose metabolism were the top pathways involved in somatic embryogenesis. Our proteomics results not only confirmed our previous transcriptomic results on the role of the polyamine metabolic pathways and stress responses in cotton somatic embryogenesis, but identified key proteins important for cotton somatic embryogenesis and provided new insights into the molecular mechanisms underlying somatic embryogenesis in cotton.

Advanced Proteomic Approaches to Elucidate Somatic Embryogenesis

“…AAA cv. Grand Naine, and Z. mays ( Ge et al, 2017 ; Kumaravel et al, 2017 ; Zhu et al, 2018 ). Those proteins include indole-3-pyruvate monooxygenase protein YUCCA3, an enzyme of the auxin biosynthesis, in Musa spp.…”

“…AAA cv. Grand Naine that is more abundant in EC ( Kumaravel et al, 2017 ), and an IAA-conjugate hydrolase GH3 that is more abundant in both EC and late SE stages in Z. mays and G. hirsutum ( Ge et al, 2017 ; Zhu et al, 2018 ). GH3 collectively may result in an increase in IAA ( Zhao et al, 2001 ).…”

“…AAA cv. Grand Naine and cytokinin trans-hydroxylase are upregulated in the EC of Z. mays ( Ge et al, 2017 ; Kumaravel et al, 2017 ), cytokinin receptors CRE1 and B-ARR are more abundant in EC, and histidine phosphotransfer protein is upregulated in SE in G. hirsutum ( Zhu et al, 2018 ), factors that are required for the cytokinin response ( Mason et al, 2005 ). Phospholipase A1, 12-oxophytodienoic acid reductase, acyl-CoA oxidase, and enoyl-CoA hydratase/3-hydroxyacyl-CoA dehydrogenase are more abundant in EC at the II stage ( Ge et al, 2017 ).…”

Global scale transcriptome analysis reveals differentially expressed genes involve in early somatic embryogenesis in Dimocarpus longan Lour.

“…The fatty acid composition rapidly changed during SE in Daucus carota [57], and Gossypium hirsutum [33]. In our study, a total of 35 fatty acid biosynthesis related genes were differently expressed during SE (Additional file 7: Extracellular protein encoding genes effect on the transition from NEC to EC It had been reported that extracellular protein germins and germin-like (GLPs), Arabinogalactan proteins (AGPs), chitinases (CHIs), lipid transfer proteins (LTPs) and glycoprotein were critical to SE, and can be served as protein marker during early SE [58].…”

“…Meanwhile, the comparative proteome analysis during SE also characterized numerous proteins that associated with SE in many plant species, such as Maize [28], Papaya [29], Cacao [30], Sugarcane [31], Musa. spp [32], and Gossypium hirsutum [33]. The transcriptome and proteome analysis of plant SE revealed several molecular regulation mechanisms of SE, and a large number of potential key factors of embryogenesis.…”