Phosphoproteomics perspective on plant signal transduction and tyrosine phosphorylation

Mithoe, Sharon C; Menke, Frank L.H.

doi:10.1016/j.phytochem.2010.12.009

Cited by 43 publications

(30 citation statements)

References 84 publications

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“…Bioinformatics analysis of the Arabidopsis genome identified 57 candidate DSKs (Rudrabhatla et al, 2006), three putative tyrosine kinases, and 625 tyrosine kinase-like kinases (Martin et al, 2009). In plants, tyrosine phosphorylation was initially deemed insignificant, but large-scale phosphoproteomics in Arabidopsis revealed that tyrosine phosphorylation is widespread (Sugiyama et al, 2008;Nakagami et al, 2010Nakagami et al, , 2012Ghelis, 2011;Mithoe and Menke, 2011;Oh et al, 2012bOh et al, , 2012c. Our meta-analysis emphasizes that detection of tyrosine phosphorylation largely depends on proteomics and/or mass spectrometric workflows.…”

Section: Tyrosine Phosphorylationmentioning

confidence: 89%

Meta-Analysis of Arabidopsis thaliana Phospho-Proteomics Data Reveals Compartmentalization of Phosphorylation Motifs

et al. 2014

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ORCID ID: 0000-0001-9536-0487 (K.J.v.W.)Protein (de)phosphorylation plays an important role in plants. To provide a robust foundation for subcellular phosphorylation signaling network analysis and kinase-substrate relationships, we performed a meta-analysis of 27 published and unpublished in-house mass spectrometry-based phospho-proteome data sets for Arabidopsis thaliana covering a range of processes, (non)photosynthetic tissue types, and cell cultures. This resulted in an assembly of 60,366 phospho-peptides matching to 8141 nonredundant proteins. Filtering the data for quality and consistency generated a set of medium and a set of high confidence phospho-proteins and their assigned phospho-sites. The relation between single and multiphosphorylated peptides is discussed. The distribution of p-proteins across cellular functions and subcellular compartments was determined and showed overrepresentation of protein kinases. Extensive differences in frequency of pY were found between individual studies due to proteomics and mass spectrometry workflows. Interestingly, pY was underrepresented in peroxisomes but overrepresented in mitochondria. Using motif-finding algorithms motif-x and MMFPh at high stringency, we identified compartmentalization of phosphorylation motifs likely reflecting localized kinase activity. The filtering of the data assembly improved signal/noise ratio for such motifs. Identified motifs were linked to kinases through (bioinformatic) enrichment analysis. This study also provides insight into the challenges/pitfalls of using large-scale phospho-proteomic data sets to nonexperts.

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Section: Tyrosine Phosphorylationmentioning

confidence: 89%

Meta-Analysis of Arabidopsis thaliana Phospho-Proteomics Data Reveals Compartmentalization of Phosphorylation Motifs

et al. 2014

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“…The first replica contained a total of 1756 quantified phosphopeptides, and the second replica contained 2319 quantified phosphopeptides, with an overlap of 57% (1007 peptides, supplemental Table 2). The two combined datasets represent one of the largest available Arabidopsis quantitative phosphoproteomic datasets to date (10,39). We compared our phosphopeptides to all experimental phosphopeptides in the PhosPhAt 4.0 database (39).…”

Section: Modification Of the Lris For Proteomics-auxin-inducedmentioning

confidence: 99%

Quantitative Phosphoproteomics after Auxin-stimulated Lateral Root Induction Identifies an SNX1 Protein Phosphorylation Site Required for Growth

Zhang

Zhou

Berke

et al. 2013

Molecular & Cellular Proteomics

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Protein phosphorylation is instrumental to early signaling events. Studying system-wide phosphorylation in relation to processes under investigation requires a quantitative proteomics approach. In Arabidopsis, auxin application can induce pericycle cell divisions and lateral root formation. Initiation of lateral root formation requires transcriptional reprogramming following auxin-mediated degradation of transcriptional repressors. The immediate early signaling events prior to this derepression are virtually uncharacterized. To identify the signal molecules responding to auxin application, we used a lateral root-inducible system that was previously developed to trigger synchronous division of pericycle cells. To identify and quantify the early signaling events following this induction, we combined 15 N-based metabolic labeling and phosphopeptide enrichment and applied a mass spectrometry-based approach. In total, 3068 phosphopeptides were identified from auxin-treated root tissue. This root proteome dataset contains largely phosphopeptides not previously reported and represents one of the largest quantitative phosphoprotein datasets from Arabidopsis to date. Key proteins responding to auxin treatment included the multidrug resistance-like and PIN2 auxin carriers, AUXIN RESPONSE FACTOR2 (ARF2), SUPPRESSOR OF AUXIN RESISTANCE 3 (SAR3), and SORTING NEXIN1 (SNX1). Mutational analysis of serine 16 of SNX1 showed that over-

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“…On the contrary, other studies reported a phosphotyrosine content comparable to the animal phosphoproteomes, such as 85:10.7: 4.3 (46), and 82.7:13.1:4.2 (47) in Arabidopsis cell cultures, and 84.8:12.3:2.9 in a rice cell culture (47). From the differing contents of phosphotyrosine in the presented data sets, it is obvious that it still remains speculative how abundant phosphotyrosine phosphorylation in plants actually is (48,49). Furthermore, the inhibitors of tyrosine phosphorylation (phenylarsine oxide and genistein) applied to the lily cultivated pollen strongly affected its growth rate, likely influencing the dynamics of actin cytoskeleton (50).…”

Section: Discussionmentioning

confidence: 92%

Phosphoproteomics Profiling of Tobacco Mature Pollen and Pollen Activated in vitro

Fíla

Radau

Matros

et al. 2016

Molecular & Cellular Proteomics

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Tobacco mature pollen has extremely desiccated cytoplasm, and is metabolically quiescent. Upon re-hydration it becomes metabolically active and that results in later emergence of rapidly growing pollen tube. These changes in cytoplasm hydration and metabolic activity are accompanied by protein phosphorylation. In this study, we subjected mature pollen, 5-min-activated pollen, and 30-min-activated pollen to TCA/acetone protein extraction, trypsin digestion and phosphopeptide enrichment by titanium dioxide. The enriched fraction was subjected to nLC-MS/MS. We identified 471 phosphopeptides that carried 432 phosphorylation sites, position of which was exactly matched by mass spectrometry. These 471 phosphopeptides were assigned to 301 phosphoproteins, because some proteins carried more phosphorylation sites. Of the 13 functional groups, the majority of proteins were put into these categories: transcription, protein synthesis, protein destination and storage, and signal transduction. Many proteins were of unknown function, reflecting the fact that male gametophyte contains many specific proteins that have not been fully functionally annotated. The quantitative data highlighted the dynamics of protein phosphorylation during pollen activation; the identified phosphopeptides were divided into seven groups based on the regulatory trends. The major group comprised mature pollen-specific phosphopeptides that were dephosphorylated during pollen activation. Several phosphopeptides representing the same phosphoprotein had different regulation, which pinpointed the complexity of protein phosphorylation and its clear functional context. Collectively, we showed the first phosphoproteomics data on activated pollen where the position of phosphorylation sites was clearly demonstrated and regulatory kinetics was resolved. Molecular & Cellular

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Phosphoproteomics perspective on plant signal transduction and tyrosine phosphorylation

Cited by 43 publications

References 84 publications

Meta-Analysis of Arabidopsis thaliana Phospho-Proteomics Data Reveals Compartmentalization of Phosphorylation Motifs

Meta-Analysis of Arabidopsis thaliana Phospho-Proteomics Data Reveals Compartmentalization of Phosphorylation Motifs

Quantitative Phosphoproteomics after Auxin-stimulated Lateral Root Induction Identifies an SNX1 Protein Phosphorylation Site Required for Growth

Phosphoproteomics Profiling of Tobacco Mature Pollen and Pollen Activated in vitro

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