Abstract
BackgroundProtein content determines the state of cells. The variation in protein abundance is crucial when organisms are in the early stages of heat stress, but the reasons affecting their changes are largely unknown.ResultsWe quantified 47,535 mRNAs and 3742 proteins in the filling grains of wheat in two different thermal environments. The impact of mRNA abundance and sequence features involved in protein translation and degradation on protein expression was evaluated by regression analysis. Transcription, codon usage and amino acid frequency were the main drivers of changes in protein expression under heat stress, and their combined contribution explains 58.2 and 66.4% of the protein variation at 30 and 40 °C (20 °C as control), respectively. Transcription contributes more to alterations in protein content at 40 °C (31%) than at 30 °C (6%). Furthermore, the usage of codon AAG may be closely related to the rapid alteration of proteins under heat stress. The contributions of AAG were 24 and 13% at 30 and 40 °C, respectively.ConclusionIn this study, we analyzed the factors affecting the changes in protein expression in the early stage of heat stress and evaluated their influence.
Highlights
Protein content determines the state of cells
Quantification of the wheat grain transcriptome and proteome under short-term heat stress To understand how filling grain quickly adapts to temperature variations, wheat
1800 and 5551 were identified as differentially expressed transcripts (DETs; fold change > 2, p < 0.05, false discovery rate (FDR); Table S1) under two types of heat environments (30 and 40 °C; 20 °C served as the control)
Summary
Protein content determines the state of cells. The fluctuation of protein abundance determine the state of cells, and the elements that affect protein expression have been extensively studied in recent years [1,2,3,4]. Transcriptome sequencing is accurate and efficient, but due to the bottleneck of proteomics, it is incapable of quantifying a more comprehensive protein landscape. This discrepancy makes people usually use transcription to speculate about protein expression. Studies have shown that transcription is a weak proxy for protein abundance (R2, 0.2–0.4) in various species [5,6,7,8,9,10], especially in stressful environments (R2 < 0.09) [11,12,13]. In addition to the fact that protein synthesis fails to keep
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