Protein sumoylation and phosphorylation intersect in Arabidopsis signaling

Nukarinen, Ella; Tomanov, Konstantin; Ziba, Ionida; Weckwerth, Wolfram; Bachmair, Andreas

doi:10.1111/tpj.13575

Cited by 27 publications

(20 citation statements)

References 55 publications

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“…Previous studies in plants have uncovered many phosphoproteins and their phosphorylation sites [ 44 ]. The phospho-proteome of organs (e.g., roots or shoots), cells, or subcellular components (e.g., plasma membranes) was investigated under different growth and culture conditions [ 45 , 46 , 47 , 48 , 49 , 50 , 51 , 52 , 53 , 54 , 55 , 56 , 57 , 58 ]. The data are available in public databases such as PhosPhAt [ 59 ] or Plant Protein Phosphorylation Database (P3DB) [ 60 ].…”

Section: Introductionmentioning

confidence: 99%

Global Quantitative Proteomics Studies Revealed Tissue-Preferential Expression and Phosphorylation of Regulatory Proteins in Arabidopsis

Lu¹,

Fu²,

Li³

et al. 2020

IJMS

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Organogenesis in plants occurs across all stages of the life cycle. Although previous studies have identified many genes as important for either vegetative or reproductive development at the RNA level, global information on translational and post-translational levels remains limited. In this study, six Arabidopsis stages/organs were analyzed using quantitative proteomics and phosphoproteomics, identifying 2187 non-redundant proteins and evidence for 1194 phosphoproteins. Compared to the expression observed in cauline leaves, the expression of 1445, 1644, and 1377 proteins showed greater than 1.5-fold alterations in stage 1–9 flowers, stage 10–12 flowers, and open flowers, respectively. Among these, 294 phosphoproteins with 472 phosphorylation sites were newly uncovered, including 275 phosphoproteins showing differential expression patterns, providing molecular markers and possible candidates for functional studies. Proteins encoded by genes preferentially expressed in anther (15), meiocyte (4), or pollen (15) were enriched in reproductive organs, and mutants of two anther-preferentially expressed proteins, acos5 and mee48, showed obviously reduced male fertility with abnormally organized pollen exine. In addition, more phosphorylated proteins were identified in reproductive stages (1149) than in the vegetative organs (995). The floral organ-preferential phosphorylation of GRP17, CDC2/CDKA.1, and ATSK11 was confirmed with western blot analysis. Moreover, phosphorylation levels of CDPK6 and MAPK6 and their interacting proteins were elevated in reproductive tissues. Overall, our study yielded extensive data on protein expression and phosphorylation at six stages/organs and provides an important resource for future studies investigating the regulatory mechanisms governing plant development.

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Section: Introductionmentioning

confidence: 99%

Global Quantitative Proteomics Studies Revealed Tissue-Preferential Expression and Phosphorylation of Regulatory Proteins in Arabidopsis

Lu¹,

Fu²,

Li³

et al. 2020

IJMS

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“…Furthermore our data show that the broad and deep phosphoproteome coverage was facilitated by high enrichment selectivity of our improved tandem MOAC protocol with more than 75% of peptides identified in each sample being phosphopeptides. By contrast, other previous studies in Arabidopsis required three times more measurement time while identifying only one‐third of the quantified sites (Chen and Hoehenwarter, ; Nukarinen et al ., ). By optimizing the enrichment procedure, we achieved similar coverage to published large‐scale phosphoproteomics studies in tissue, despite using less starting material and analysis time (Lan et al ., ).…”

Section: Resultsmentioning

confidence: 97%

Rapid and reproducible phosphopeptide enrichment by tandem metal oxide affinity chromatography: application to boron deficiency induced phosphoproteomics

Chen

Hoehenwarter

2019

The Plant Journal

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Mass spectrometry has been instrumental in enabling the study of molecular signaling on a cellular scale by way of site-specific quantification of protein post-translational modifications, in particular phosphorylation. Here we describe an updated tandem metal oxide affinity chromatography (MOAC) combined phosphoprotein/phosphopeptide enrichment strategy, a scalable phosphoproteomics approach that allows rapid identification of thousands of phosphopeptides in plant materials. We implemented modifications to several steps of the original tandem MOAC procedure to increase the amount of quantified phosphopeptides and hence site-specific phosphorylation of proteins in a sample beginning with the less amounts of tissue and a substantially smaller amount of extracted protein. We applied this technology to generate time-resolved maps of boron signaling in Arabidopsis roots. We show that the successive enrichment of phosphoproteins in a first and phosphopeptide extraction in a second step using our optimized procedure strongly enriched the root phosphoproteome. Our results reveal that boron deficiency affects over 20% of the measured root phosphoproteome and that many phosphorylation sites with known biological function, and an even larger number of previously undescribed sites, are modified during the time course of boron deficiency. We identify transcription factors as key regulators of hormone signaling pathways that modulate gene expression in boron deprived plants. Furthermore, our phosphorylation kinetics data demonstrate that mitogen-activated protein kinase (MAPK) cascades mediate polarized transport of boron in Arabidopsis roots. Taken together, we establish and validate a robust approach for proteome-wide phosphorylation analysis in plant biology research.

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“…In conclusion, we report the dynamic modulation of the Arabidopsis SUMOylome occurring in defense responses. Undoubtedly, phosphorylation, ubiquitination, acetylation and other PTMs that crosstalk with or modulate the efficacy of SUMOylation influence our data (Nukarinen et al 2017). To further explore these avenues, use of PTM-specific inhibitors and their relative effects on SUMOylome changes are warranted.…”

Section: Discussionmentioning

confidence: 99%

Proteomic analysis of SUMO1-SUMOylome changes during defense elicitation inArabidopsis

Ingole

Dahale

Bhattacharjee

2020

Preprint

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Rapid adaptation of plants to developmental or physiological cues is facilitated by specific receptors that transduce the signals mostly via post-translational modification (PTM) cascades of downstream partners. Reversible covalent attachment of SMALL UBIQUITIN-LIKE MODIFIER (SUMO), a process termed as SUMOylation, influence growth, development and adaptation of plants to various stresses. Strong regulatory mechanisms maintain the steady-state SUMOylome and mutants with SUMOylation disturbances display mis-primed immunity often with growth consequences. Identity of the SUMO-substrates undergoing SUMOylation changes during defences however remain largely unknown. Here we exploit either the auto-immune property of an Arabidopsis mutant or defense responses induced in wild-type plants against Pseudomonas syringae pv tomato (PstDC3000) to enrich and identify SUMO1-substrates. Our results demonstrate massive enhancement of SUMO1-conjugates due to increased SUMOylation efficiencies during defense responses. Of the 261 proteins we identify, 29 have been previously implicated in immune-associated processes. Role of others expand to diverse cellular roles indicating massive readjustments the SUMOylome alterations may cause during induction of immunity. Overall, our study highlights the complexities of a plant immune network and identifies multiple SUMO-substrates that may orchestrate the signalling.

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Protein sumoylation and phosphorylation intersect in Arabidopsis signaling

Cited by 27 publications

References 55 publications

Global Quantitative Proteomics Studies Revealed Tissue-Preferential Expression and Phosphorylation of Regulatory Proteins in Arabidopsis

Global Quantitative Proteomics Studies Revealed Tissue-Preferential Expression and Phosphorylation of Regulatory Proteins in Arabidopsis

Rapid and reproducible phosphopeptide enrichment by tandem metal oxide affinity chromatography: application to boron deficiency induced phosphoproteomics

Proteomic analysis of SUMO1-SUMOylome changes during defense elicitation inArabidopsis

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