Abstract
BackgroundProteins are the workforce of the cell and their phosphorylation status tailors specific responses efficiently. One of the main challenges of phosphoproteomic approaches is to deconvolute biological processes that specifically respond to an experimental query from a list of phosphoproteins. Comparison of the frequency distribution of GO (Gene Ontology) terms in a given phosphoproteome set with that observed in the genome reference set (GenRS) is the most widely used tool to infer biological significance. Yet, this comparison assumes that GO term distribution between the phosphoproteome and the genome are identical. However, this hypothesis has not been tested due to the lack of a comprehensive phosphoproteome database.ResultsIn this study, we test this hypothesis by constructing three phosphoproteome databases in Arabidopsis thaliana: one based in experimental data (ExpRS), another based in in silico phosphorylation protein prediction (PredRS) and a third that is the union of both (UnRS). Our results show that the three phosphoproteome reference sets show default enrichment of several GO terms compared to GenRS, indicating that GO term distribution in the phosphoproteomes does not match that of the genome. Moreover, these differences overshadow the identification of GO terms that are specifically enriched in a particular condition. To overcome this limitation, we present an additional comparison of the sample of interest with UnRS to uncover GO terms specifically enriched in a particular phosphoproteome experiment. Using this strategy, we found that mRNA splicing and cytoplasmic microtubule compounds are important processes specifically enriched in the phosphoproteome of dark-grown Arabidopsis seedlings.ConclusionsThis study provides a novel strategy to uncover GO specific terms in phosphoproteome data of Arabidopsis that could be applied to any other organism. We also highlight the importance of specific phosphorylation pathways that take place during dark-grown Arabidopsis development.
Highlights
Proteins are the workforce of the cell and their phosphorylation status tailors specific responses efficiently
Our results show that Gene Ontology (GO) term distributions for the phosphoproteomes of reference are different from the genome in the three ontologies (BP, molecular functions (MF) and cellular components (CC)), revealing that enriched GO terms in a phosphoproteome sample would be systemically enriched in phosphorylation experiments independently of the phosphoproteome sample background, overshading those GO terms specific to a sample of interest
We used two representative computational tools, MusiteDeep and PhosPhAt, that have been shown to have a good performance with high specificity and sensitivity [14]
Summary
Proteins are the workforce of the cell and their phosphorylation status tailors specific responses efficiently. Comparison of the frequency distribution of GO (Gene Ontology) terms in a given phosphoproteome set with that observed in the genome reference set (GenRS) is the most widely used tool to infer biological significance. This comparison assumes that GO term distribution between the phosphoproteome and the genome are identical. Changes in post-translational modifications (PTM) enable the fast modulation of protein function in response to endogenous or environmental cues, a requirement to the crucial changes in gene expression that ensures cell adaptation. In Arabidopsis, the role of protein phosphorylation in regulating cellular processes is supported by the identification of numerous protein kinases and phosphatases in the genome [8]. Because of the stimuli-dependent nature of protein phosphorylation, a comprehensive mapping of the Arabidopsis phosphoproteome has been technically challenging
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
