Update: Post-translational protein modifications in plant metabolism

Abstract

ORCID ID: 0000-0001-9536-0487 (K.J.v.W.).Posttranslational modifications (PTMs) of proteins greatly expand proteome diversity, increase functionality, and allow for rapid responses, all at relatively low costs for the cell. PTMs play key roles in plants through their impact on signaling, gene expression, protein stability and interactions, and enzyme kinetics. Following a brief discussion of the experimental and bioinformatics challenges of PTM identification, localization, and quantification (occupancy), a concise overview is provided of the major PTMs and their (potential) functional consequences in plants, with emphasis on plant metabolism. Classic examples that illustrate the regulation of plant metabolic enzymes and pathways by PTMs and their cross talk are summarized. Recent large-scale proteomics studies mapped many PTMs to a wide range of metabolic functions. Unraveling of the PTM code, i.e. a predictive understanding of the (combinatorial) consequences of PTMs, is needed to convert this growing wealth of data into an understanding of plant metabolic regulation.The primary amino acid sequence of proteins is defined by the translated mRNA, often followed by Nor C-terminal cleavages for preprocessing, maturation, and/or activation. Proteins can undergo further reversible or irreversible posttranslational modifications (PTMs) of specific amino acid residues. Proteins are directly responsible for the production of plant metabolites because they act as enzymes or as regulators of enzymes. Ultimately, most proteins in a plant cell can affect plant metabolism (e.g. through effects on plant gene expression, cell fate and development, structural support, transport, etc.). Many metabolic enzymes and their regulators undergo a variety of PTMs, possibly resulting in changes in oligomeric state, stabilization/degradation, and (de)activation (Huber and Hardin, 2004), and PTMs can facilitate the optimization of metabolic flux. However, the direct in vivo consequence of a PTM on a metabolic enzyme or pathway is frequently not very clear, in part because it requires measurements of input and output of the reactions, including flux through the enzyme or pathway. This Update will start out with a short overview on the major PTMs observed for each amino acid residue (Table I), followed by a brief discussion of techniques for the characterization of protein PTMs, including determination of the localization within proteins (i.e. the specific residues) and occupancy. Challenges in dealing with multiple PTMs per protein and cross talk between PTMs will be briefly outlined. We then describe the major physiological PTMs observed in plants as well as PTMs that are nonenzymatically induced during sample preparation (Table II). Finally, this Update is completed with a number of well-studied, classical examples of the regulation of plant metabolism by PTMs, in particular for enzymes in primary metabolism (Calvin cycle, glycolysis, and respiration) and the C4 shuttle accommodating photosynthesis in C4 plants (Table III). As will be ev...

The Plant PTM Viewer, a central resource exploring plant protein modifications. From site-seeing to protein function

“…Given the vast amount of characterized PTMs on plant proteins, an enormous challenge now posed is on their functional characterization. Recently, a community effort has been suggested that would collect and assemble all PTM data for plant proteomes to systematically determine possible functional implications for plant proteins and the biological processes they are involved in (Friso and van Wijk, 2015). Although some PTM databases (Minguez et al, 2015, Huang et al, 2016, 2018b) provide plant protein modifications, PTM data are still largely uncatalogued and hardly explored in an integrative manner.…”

Proteome Profile of Starch Granules Purified from Rice (Oryza sativa) Endosperm

“…Many reports have shown that metabolic pathway enzymes are subject to extensive posttranslational modifications such as acetylation [59–62]. In this study, we achieved significant coverage of the starch granule associated proteins with deep mass analysis, including GBSS 1, with up to 85.7% coverage of its protein sequence (S2 Table).…”

Discovering Lipid Droplet Proteins: From Seeds to Seedlings

“…In addition to identifying novel LD-associated proteins, the authors generated a valuable proteomics data set that will be useful for studying lipid storage and dynamics during seed development and seedling establishment. Many aspects of plant metabolism are now known to be extensively regulated via posttranslational mechanisms involving enzymes and/or their associated proteins rather than through regulation at the transcriptional level (Friso and van Wijk, 2015). As quantitative proteomics approaches continue to improve, these data sets will be instrumental in identifying key regulators of lipid metabolism and other plant metabolic pathways.…”