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Abstract
Phospho-proteomic studies have confirmed that phosphorylation is a common mechanism to regulate protein function in the chloroplast, including the enzymes of starch metabolism. In addition to the photosynthetic machinery protein kinases (STN7 and STN8) and their cognate protein phosphatases PPH1 (TAP38) and PBCP, multiple other protein kinases and phosphatases have now been localized to the chloroplast. Here, we build a framework for understanding protein kinases and phosphatases, their regulation, and potential roles in starch metabolism. We also catalog mapped phosphorylation sites on proteins of chloroplast starch metabolism to illustrate the potential and mostly unknown roles of protein phosphorylation in the regulation of starch biology.
Highlights
Mass spectrometry, and quantitative mass spectrometry, has further established the prevalence of protein covalent modifications as a mechanism to control protein function (Baginsky and Gruissem, 2009; Grabsztunowicz et al, 2017; Hartl et al, 2017)
The first notable feature of this table is that most starch machinery proteins are phospho-proteins, and most are phosphorylated at multiple sites, including chloroplast transit peptides, with phosphorylation predominantly on serine and threonine residues [we have removed several potential phospho-tyrosines based on Lu et al (2015b) and Baginsky (2016)]
Protein phosphorylation is prevalent in the plastid and clearly the starch machinery is controlled in this fashion-typically at multiple sites and with multiple protein kinases suggesting multiple factors/conditions feed into regulating these enzymes
Summary
Quantitative mass spectrometry, has further established the prevalence of protein covalent modifications as a mechanism to control protein function (Baginsky and Gruissem, 2009; Grabsztunowicz et al, 2017; Hartl et al, 2017). Given the abundance of protein phosphorylation in prokaryotes it is no surprise that an organelle derived from prokaryotes (plastids) has many events controlled by this process Consistent with this are the growing proteomic datasets that demonstrate widespread protein phosphorylation in the chloroplast. Our analysis here of the starch metabolic machinery utilized the entire PhosPhAt 4.0 dataset with all tyrosine phosphorylation sites removed (for reasons stated above). This information (Supplementary Table 1) should be regarded as a start point for a study and all sites should be confirmed by additional research. With the inventory being near completion we can start to utilize phospho-proteomic data and mapped sites on starch metabolic enzymes to tease out potential protein kinase/phosphatase substrates using genetics and biochemistry utilizing this list of players. Several enzymes are marked ‘none’ to indicate they have yet to be shown to be phospho-proteins, but this may only reflect the depth of the studies, tissue used, metabolic conditions, or workflow (for instance, granule bound enzymes could be lost in a first step of a phospho-proteomic workflow)
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