Label-Free Quantitative Proteome Analysis Reveals the Underlying Mechanisms of Grain Nuclear Proteins Involved in Wheat Water-Deficit Response

Abstract

In this study, we performed the first nuclear proteome analysis of wheat developing grains under water deficit by using a label-free based quantitative proteomic approach. In total, we identified 625 unique proteins as differentially accumulated proteins (DAPs), of which 398 DAPs were predicted to be localized in nucleus. Under water deficit, 146 DAPs were up-regulated and mainly involved in the stress response and oxidation-reduction process, while 252 were down-regulated and mainly participated in translation, the cellular amino metabolic process, and the oxidation-reduction process. The cis-acting elements analysis of the key nuclear DAPs encoding genes demonstrated that most of these genes contained the same cis-acting elements in the promoter region, mainly including ABRE involved in abscisic acid response, antioxidant response element, MYB responsive to drought regulation and MYC responsive to early drought. The cis-acting elements related to environmental stress and hormones response were relatively abundant. The transcription expression profiling of the nuclear up-regulated DAPs encoding genes under different organs, developmental stages and abiotic stresses was further detected by RNA-seq and Real-time quantitative polymerase chain reaction, and more than 50% of these genes showed consistency between transcription and translation expression. Finally, we proposed a putative synergistic responsive network of wheat nuclear proteome to water deficit, revealing the underlying mechanisms of wheat grain nuclear proteome in response to water deficit.

Genome-wide identification of wheat ABC1K gene family and functional dissection of TaABC1K3 and TaABC1K6 involved in drought tolerance

“…TPM was used for RNA-seq data and the data was normalized. TBtools was used for heatmap construction and cluster analysis according to Li et al (2021) .…”

“…The cis-acting element identification and RNA-seq expression analysis of TaABC1K genes According to Li et al (2021), 1,500 bp promoter region from the TaABC1K gene initiation codon was downloaded from the Ensembl Plant database, and the number and type of the cis-acting elements were analyzed by PlantCARE online website 8 based on Rombauts et al (1999). The publicly Chinese Spring (CS) wheat RNA-seq database was used to analyze RNA-seq data of TaABC1K encoding genes from the expVIP website.…”

Wheat Proteomics for Abiotic Stress Tolerance and Root System Architecture: Current Status and Future Prospects

“…Additionally, advanced label-free techniques can identify a range of proteins including low abundance proteins, at a lower cost, and more quick analysis than labeled techniques [ 185 , 186 ]. It also offers subcellular (e.g., chloroplast, grain nucleus) protein identification [ 72 , 187 ]. Furthermore, the genes encoding key DEPs can be used in marker-assisted breeding or genome-editing approaches for wheat RSA and stress tolerance improvement [ 72 ].…”