On the Extent of Tyrosine Phosphorylation in Chloroplasts

Detection of the Arabidopsis Proteome and Its Post-translational Modifications and the Nature of the Unobserved (Dark) Proteome in PeptideAtlas

This study describes a new release of the Arabidopsis thaliana PeptideAtlas proteomics resource (build 2023-10) providing protein sequence coverage, matched mass spectrometry (MS) spectra, selected post-translational modifications (PTMs), and metadata. 70 million MS/MS spectra were matched to the Araport11 annotation, identifying ∼0.6 million unique peptides and 18,267 proteins at the highest confidence level and 3396 lower confidence proteins, together representing 78.6% of the predicted proteome. Additional identified proteins not predicted in Araport11 should be considered for the next Arabidopsis genome annotation. This release identified 5198 phosphorylated proteins, 668 ubiquitinated proteins, 3050 N-terminally acetylated proteins, and 864 lysine-acetylated proteins and mapped their PTM sites. MS support was lacking for 21.4% (5896 proteins) of the predicted Araport11 proteome: the "dark" proteome. This dark proteome is highly enriched for E3 ligases, transcription factors, and for certain (e.g., CLE, IDA, PSY) but not other (e.g., THIONIN, CAP) signaling peptides families. A machine learning model trained on RNA expression data and protein properties predicts the probability that proteins will be detected. The model aids in discovery of proteins with short half-life (e.g., SIG1,3 and ERF-VII TFs) and for developing strategies to identify the missing proteins. PeptideAtlas is linked to TAIR, tracks in JBrowse, and several other community proteomics resources.

Mass Spectrometry-Based Identification of Phospho-Tyr in Plant Proteomics

O-Phosphorylation (phosphorylation of the hydroxyl-group of S, T, and Y residues) is among the first described and most thoroughly studied posttranslational modification (PTM). Y-Phosphorylation, catalyzed by Y-kinases, is a key step in both signal transduction and regulation of enzymatic activity in mammalian systems. Canonical Y-kinase sequences are absent from plant genomes/kinomes, often leading to the assumption that plant cells lack O-phospho-l-tyrosine (pY). However, recent improvements in sample preparation, coupled with advances in instrument sensitivity and accessibility, have led to results that unequivocally disproved this assumption. Identification of hundreds of pY-peptides/proteins, followed by validation using genomic, molecular, and biochemical approaches, implies previously unappreciated roles for this "animal PTM" in plants. Herein, we review extant results from studies of pY in plants and propose a strategy for preparation and analysis of pY-peptides that will allow a depth of coverage of the plant pY-proteome comparable to that achieved in mammalian systems.

Phospho-mutant activity assays provide evidence for alternative phospho-regulation pathways of the transcription factor FER-LIKE IRON DEFICIENCY-INDUCED TRANSCRIPTION FACTOR

The key basic helix-loop-helix (bHLH) transcription factor in iron (Fe) uptake, FER-LIKE IRON DEFICIENCY-INDUCED TRANSCRIPTION FACTOR (FIT), is controlled by multiple signaling pathways, important to adjust Fe acquisition to growth and environmental constraints. FIT protein exists in active and inactive protein pools, and phosphorylation of serine Ser272 in the C-terminus, a regulatory domain of FIT, provides a trigger for FIT activation. Here, we use phospho-mutant activity assays and study phospho-mimicking and phospho-dead mutations of three additional predicted phosphorylation sites, namely at Ser221 and at tyrosines Tyr238 and Tyr278, besides Ser 272. Phospho-mutations at these sites affect FIT activities in yeast, plant, and mammalian cells. The diverse array of cellular phenotypes is seen at the level of cellular localization, nuclear mobility, homodimerization, and dimerization with the FIT-activating partner bHLH039, promoter transactivation, and protein stability. Phospho-mimicking Tyr mutations of FIT disturb fit mutant plant complementation. Taken together, we provide evidence that FIT is activated through Ser and deactivated through Tyr site phosphorylation. We therefore propose that FIT activity is regulated by alternative phosphorylation pathways.

Phytotoxic metabolites produced by Verticillium dahliae Kleb. in olive wilting: a chemical and spectroscopic approach for their molecular characterisation

Most of the symptoms associated with Verticillium wilt disease in olive cultivation are due to complexes excreted by Verticillium dahliae. In this study chemical and physico-chemical techniques were combined to investigate how the molecular structure of phytotoxins isolated from two pathotypes of Verticillium dahliae, defoliating, D, and non-defoliating, ND, grown on two different media, Verticillium-dahliae-Medium (VdM) and Simulated Xylem-fluid-Medium (SXM), can affect their aggressiveness. Data obtained highlight important structural differences, both in term of elemental composition and in functional groups distribution. Such peculiarities strongly affect their solubility, resulted higher for the phytotoxins from D pathotype. This property likely induces serious modifications of the conformational state of the proteinaceous component, making tyrosine residues accessible to the phosphate ion. A phosphorylation mechanism would thus be promoted, that is going to interfere with the function of the involved proteins in intracellular signalling networks, likely by altering its role in modulating the plant's response.

A Framework to Investigate Peroxisomal Protein Phosphorylation in Arabidopsis

Peroxisomes perform essential roles in a range of cellular processes, highlighted by lipid metabolism, reactive species detoxification, and response to a variety of stimuli. The ability of peroxisomes to grow, divide, respond to changing cellular needs, interact with other organelles, and adjust their proteome as required, suggest that, like other organelles, their specialized roles are highly regulated. Similar to most other cellular processes, there is an emerging role for protein phosphorylation to regulate these events. In this review, we establish a knowledge framework of key players that control protein phosphorylation events in the plant peroxisome (i.e., the protein kinases and phosphatases), and highlight a vastly expanded set of (phospho)substrates.

Protein Kinases and Phosphatases of the Plastid and Their Potential Role in Starch Metabolism

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.

MSE for Label-Free Absolute Protein Quantification in Complex Proteomes

Label-free peptide quantification is a promising approach for the large-scale characterization of proteome dynamics at low cost. Here, we describe a method for absolute label-free quantification using an untargeted approach for peptide fragmentation referred to as MSE. We show that spiked external standards provide sufficient accuracy for the quantification of proteins in complex samples resulting in similar protein quantification results as spectral counting. As an advantage, label-free quantification also works for small numbers of samples whereas spectral counting requires large datasets to result in a similar robustness. The sensitivity of protein identification increases significantly when ion mobility separation is included in addition to the standard LC-MS setup in the analysis workflow. Ion mobility decreases sample complexity and serves as an additional separation criterion to align a parent ion with its product ions after MSE fragmentation. As a drawback, quantification of high abundance proteins becomes inaccurate because of detector saturation. We describe here a suitable workflow to achieve good sensitivity for protein quantification and give initial guidance on data interpretation. To achieve good identification and quantification accuracy, the protein amount loaded onto the column should not exceed 400-600 ng. In a dynamic range window of 3-4 orders of magnitude, robust quantification can be obtained with complex samples comprising up to 2000-3000 proteins.

A Cautionary Tale on the Inclusion of Variable Posttranslational Modifications in Database-Dependent Searches of Mass Spectrometry Data

Mass spectrometry-based proteomics allows in principle the identification of unknown target proteins of posttranslational modifications and the sites of attachment. Including a variety of posttranslational modifications in database-dependent searches of high-throughput mass spectrometry data holds the promise to gain spectrum assignments to modified peptides, thereby increasing the number of assigned spectra, and to identify potentially interesting modification events. However, these potential benefits come for the price of an increased search space, which can lead to reduced scores, increased score thresholds, and erroneous peptide spectrum matches. We have assessed here the advantages and disadvantages of including the variable posttranslational modifications methionine oxidation, protein N-terminal acetylation, cysteine carbamidomethylation, transformation of N-terminal glutamine to pyroglutamic acid (Gln→pyro-Glu), and deamidation of asparagine and glutamine. Based on calculations of local false discovery rates and comparisons to known features of the respective modifications, we recommend for searches of samples that were not enriched for specific posttranslational modifications to only include methionine oxidation, protein N-terminal acetylation, and peptide N-terminal Gln→pyro-Glu as variable modifications. The principle of the validation strategy adopted here can also be applied for assessing the inclusion of posttranslational modifications for differently prepared samples, or for additional modifications. In addition, we have reassessed the special properties of the ubiquitin footprint, which is the remainder of ubiquitin moieties attached to lysines after tryptic digest. We show here that the ubiquitin footprint often breaks off as neutral loss and that it can be distinguished from dicarbamidomethylation events.

Identification of STN7/STN8 kinase targets reveals connections between electron transport, metabolism and gene expression

The thylakoid-associated kinases STN7 and STN8 are involved in short- and long-term acclimation of photosynthetic electron transport to changing light conditions. Here we report the identification of STN7/STN8 in vivo targets that connect photosynthetic electron transport with metabolism and gene expression. Comparative phosphoproteomics with the stn7 and stn8 single and double mutants identified two proteases, one RNA-binding protein, a ribosomal protein, the large subunit of Rubisco and a ferredoxin-NADP reductase as targets for the thylakoid-associated kinases. Phosphorylation of three of the above proteins can be partially complemented by STN8 in the stn7 single mutant, albeit at lower efficiency, while phosphorylation of the remaining three proteins strictly depends on STN7. The properties of the STN7-dependent phosphorylation site are similar to those of phosphorylated light-harvesting complex proteins entailing glycine or another small hydrophobic amino acid in the -1 position. Our analysis uncovers the STN7/STN8 kinases as mediators between photosynthetic electron transport, its immediate downstream sinks and long-term adaptation processes affecting metabolite accumulation and gene expression.

An evolutionary view on thylakoid protein phosphorylation uncovers novel phosphorylation hotspots with potential functional implications

The regulation of photosynthetic light reactions by reversible protein phosphorylation is well established today, but functional studies have so far mostly been restricted to processes affecting light-harvesting complex II and the core proteins of photosystem II. Virtually no functional data are available on regulatory effects at the other photosynthetic complexes despite the identification of multiple phosphorylation sites. Therefore we summarize the available data from 50 published phospho-proteomics studies covering the main complexes involved in photosynthetic light reactions in the 'green lineage' (i.e. green algae and land plants) as well as its cyanobacterial counterparts. In addition, we performed an extensive orthologue search for the major photosynthetic thylakoid proteins in 41 sequenced genomes and generated sequence alignments to survey the phylogenetic distribution of phosphorylation sites and their evolutionary conservation from green algae to higher plants. We observed a number of uncharacterized phosphorylation hotspots at photosystem I and the ATP synthase with potential functional relevance as well as an unexpected divergence of phosphosites. Although technical limitations might account for a number of those differences, we think that many of these phosphosites have important functions. This is particularly important for mono- and dicot plants, where these sites might be involved in regulatory processes such as stress acclimation.

Phosphorylation of plastoglobular proteins in Arabidopsis thaliana

Plastoglobules (PGs) are plastid lipid-protein particles with a small specialized proteome and metabolome. Among the 30 core PG proteins are six proteins of the ancient ABC1 atypical kinase (ABC1K) family and their locations in an Arabidopsis mRNA-based co-expression network suggested central regulatory roles. To identify candidate ABC1K targets and a possible ABC1K hierarchical phosphorylation network within the chloroplast PG proteome, we searched Arabidopsis phosphoproteomics data from publicly available sources. Evaluation of underlying spectra and/or associated information was challenging for a variety of reasons, but supported pSer sites and a few pThr sites in nine PG proteins, including five FIBRILLINS. PG phosphorylation motifs are discussed in the context of possible responsible kinases. The challenges of collection and evaluation of published Arabidopsis phosphorylation data are discussed, illustrating the importance of deposition of all mass spectrometry data in well-organized repositories such as PRIDE and ProteomeXchange. This study provides a starting point for experimental testing of phosho-sites in PG proteins and also suggests that phosphoproteomics studies specifically designed toward the PG proteome and its ABC1K are needed to understand phosphorylation networks in these specialized particles.

Protein phosphorylation in chloroplasts - a survey of phosphorylation targets

The development of new software tools, improved mass spectrometry equipment, a suite of optimized scan types, and better-quality phosphopeptide affinity capture have paved the way for an explosion of mass spectrometry data on phosphopeptides. Because phosphoproteomics achieves good sensitivity, most studies use complete cell extracts for phosphopeptide enrichment and identification without prior enrichment of proteins or subcellular compartments. As a consequence, the phosphoproteome of cell organelles often comes as a by-product from large-scale studies and is commonly assembled from these in meta-analyses. This review aims at providing some guidance on the limitations of meta-analyses that combine data from analyses with different scopes, reports on the current status of knowledge on chloroplast phosphorylation targets, provides initial insights into phosphorylation site conservation in different plant species, and highlights emerging information on the integration of gene expression with metabolism and photosynthesis by means of protein phosphorylation.

Posttranslational Protein Modifications in Plant Metabolism

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.