Constructing the metabolic and regulatory pathways in germinating rice seeds through proteomic approach

Abstract

Construction of metabolic and regulatory pathways from proteomic data can contextualize the large-scale data within the overall physiological scheme of an organism. It is an efficient way to predict metabolic phenotype or regulatory style. We did protein profiling in the germinating rice seeds through 1-DE via LC MS/MS proteomic shotgun strategy. In total, 673 proteins were identified, and could be sorted into 14 functional groups. The largest group was metabolism related. The metabolic proteins were integrated into different metabolic pathways to show the style of reserves mobilization and precursor preparation during the germination. Analysis of the regulatory proteins indicated that regulation of redox homeostasis and gene expression also play important roles for the rice seed germination. Although transcription is unnecessary for the germination, it could ensure the rapidity and uniformity of germination. On the contrary, translation with the stored mRNA is required for the germination. This study will help us to further understand the metabolic style, regulation of redox homeostasis, and gene expression during rice seed germination.

Transcriptomic changes during tuber dormancy release process revealed by RNA sequencing in potato

“…As a dynamic process, dormancy release impacted numerous physiological processes including carbohydrate metabolism, protein metabolism, lipid metabolism, transport process, phytohormone metabolism, stress response and redox regulation, cell organization, development, second metabolism and cell wall metabolism, these common metabolic processes involved in plant seeds dormancy release were confirmed in earlier publications (Pawłowski, 2007(Pawłowski, , 2010Sreenivasulu et al, 2008;He et al, 2011;Yu et al, 2014). Therefore, the differentially expressed genes identified by RNA-seq during tuber dormancy release could be discussed with other plant models.…”

“…4), suggesting anaerobic respiration might help to provide supplementary ATPs when oxygen deficiency during tuber dormancy breaking. Therefore, the observed energy metabolism in potato tuber was resembled in the germination of tree and cereal seeds (Pawłowski, 2010;He et al, 2011).…”

“…4), indicating tuber lipid degradation may lead to energy release by peroxisomes and supply of carbon resources for the production of sucrose to the bud out growth. The existence of these lipids degradation enzymes might help to mobilize the stocking lipids during the rice seed germination (He et al, 2011). In addition, striking differences found by PageMan enrichment in the high levels of lipid metabolism were associated with lipid synthesis (Fig.…”

“…Energy metabolism is one of the most important factors associated with various seed dormancy breaking (Zhang et al, 2004;Yang et al, 2007;Pawłowski, 2010;He et al, 2011). The starch, protein and lipid mobilization during tuber dormancy breaking and sprouting are expected to supply substrates and energy for biological processes.…”

An Arabidopsis ATP-Dependent, DEAD-Box RNA Helicase Loses Activity upon IsoAsp Formation but Is Restored by PROTEIN ISOASPARTYL METHYLTRANSFERASE

“…From these and other data (Rajjou et al, 2004(Rajjou et al, , 2008(Rajjou et al, , 2012Kimura and Nambara, 2010;An and Lin, 2011;He et al, 2011;Kushwaha et al, 2012), it has been hypothesized that the proteins of the translational machinery could be viewed as an Achilles heel of orthodox seed longevity (Kushwaha et al, 2013) and may be a major target requiring protection and PIMT-mediated repair in organisms capable of entering a period of quiescence. One such target of rPIMT1 was PLANT RNA HELICASE75 (PRH75), a presumptive ATP-dependent, DEAD-box, RNA helicase (EC 3.6.4.13) targeted to the nucleolus and presumably involved in translation by assisting ribosome maturation (Lorkovic et al, 1997(Lorkovic et al, , 2004.…”