Background
Nutrient dynamics in storage organs is a complex developmental process that requires coordinated interactions of environmental, biochemical, and genetic factors. It correlates with metabolically programmed progressive differentiation of genetically distinct compartments in seed. Nutrient signals and metabolic adaptations determine differentiation pattern and transition from maternally-controlled embryonic growth to maturation under filial regulation. Although sink organ developmental events have been identified, our understanding of transcriptional, translational, post-translational and metabolic regulation of reserve synthesis, accumulation and utilization is limited.
Method
Chickpea seeds were collected at different developmental stages (7-60 DAF) and germination stage. RNA-seq was performed using Illumina Hi-seq 2000 paired-end sequencing technology. Proteome and phosphoproteome were developed using 2-DE and subsequent Pro-Q Diamond staining. Further, TiO2 based phosphopeptide enrichment was done followed by identification of phosphoproteins using TripleTOF mass spectrometer. Integrated global network was built using cytoscaape. Furthermore, qRT-PCR analysis was performed to validate the omics datasets.
Results
To understand nutrient dynamics during embryonic and cotyledonary photoheterotrophic transition to mature and germinating autotrophic seeds, an integrated transcriptomics, proteomics and phosphoproteomics study in six sequential seed developmental stages in chickpea was performed. Differential gene expression analysis led to the identification of 6582 nutrient-associated transcripts predominantly involved in primary metabolism in synthesis phase, while downregulation of these pathways characterise the accumulation phase. Resume of central metabolism was observed in nutrient utilization phase. MS/MS analyses identified 175 and 78 nutrient-associated proteins/phosphoproteins (NAPs/NAPPs) related to metabolism, storage and biogenesis, and protein turnover. Identification of site-specific phosphorylation of amino acids indicated their possible effect in nutrient dynamics. Network analyses identified three significant modules centered around HSP70, vicilin, chalcone synthase and SBP65.
Conclusions
Our study identified several potentially interesting nutrient-associated transcripts and proteoforms of biological significance. Altogether, these findings demonstrate that nutrient signals act as metabolic and differentiation determinant governing storage organ reprogramming.