Abstract
Over the past decade, ample transcriptome data have been generated at different stages during seed germination; however, far less is known about protein synthesis during this important physiological process. Generally, the correlation between transcript levels and protein abundance is low, which strongly limits the use of transcriptome data to accurately estimate protein expression. Polysomal profiling has emerged as a tool to identify mRNAs that are actively translated. The association of the mRNA to the polysome, also referred to as translatome, provides a proxy for mRNA translation. In this study, the correlation between the changes in total mRNA, polysome-associated mRNA, and protein levels across seed germination was investigated. The direct correlation between polysomal mRNA and protein abundance at a single time-point during seed germination is low. However, once the polysomal mRNA of a time-point is compared to the proteome of the next time-point, the correlation is much higher. 35% of the investigated proteome has delayed changes at the protein level. Genes have been classified based on their delayed protein changes, and specific motifs in these genes have been identified. Moreover, mRNA and protein stability and mRNA length have been found as important predictors for changes in protein abundance. In conclusion, polysome association and/or dissociation predicts future changes in protein abundance in germinating seeds.
Highlights
The central dogma in molecular biology is that a gene is transcribed into a mRNA, which is further translated into a protein
The number of identified proteins is much lower than the number of transcripts identified in transcriptome and polysome analyses that were performed on exact the same samples, which resulted in 19,781 expressed genes (Bai et al, 2017)
Comparative analyses revealed that the proteins identified represent genes that are significantly higher expressed at both the mRNA and polysomal mRNA level compared to the total set of genes expressed in germinating seeds (Wilcoxon Rank Sum test, p-value < 0.0001; Figure 1A; Supplementary Figure S1)
Summary
The central dogma in molecular biology is that a gene is transcribed into a mRNA, which is further translated into a protein. Data produced by the high-throughput techniques, such as next-generation sequencing and mass spectrometry, have shown that there is a lack of correlation between mRNA levels and protein abundance levels (Chen et al, 2002; Nie et al, 2006; Haider and Pal, 2013). This lack of correlation might partly be hampered by the low throughput of protein analysis compared to the high-throughput transcriptome analysis. In this study, germinating seeds were used as a system to identify whether the translatome can be used to predict protein level changes
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