Chloroplast Acetyltransferase NSI Is Required for State Transitions in <i>Arabidopsis thaliana</i>

Koskela, Minna M.; Brünje, Annika; Ivanauskaite, Aiste; Grabsztunowicz, Magda; Lassowskat, Ines; Neumann, Ulla; Dinh, Trinh V.; Sindlinger, Julia; Schwarzer, Dirk; Wirtz, Markus; Tyystjärvi, Esa; Finkemeier, Iris; Mulo, Paula

doi:10.1105/tpc.18.00155

Cited by 66 publications

(101 citation statements)

References 74 publications

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“…GO enrichment of biological processes involved in light harvesting and photosynthesis (Data S9) further supports the known role of protein phosphorylation and acetylation in the regulation of photosynthesis (Reiland et al ., ; Finkemeier et al ., ; Hartl et al ., ). Previous studies have reported that light‐harvesting and photosynthesis proteins are regulated by either phosphorylation (Longoni et al ., ; Baginsky, ; Allen, ) or acetylation (Hartl et al ., ; Koskela et al ., ). Our data show when, and on which proteins, these PTMs intersect (Figure ).…”

Section: Resultsmentioning

confidence: 97%

“…The diurnal fluctuations in the abundance that we find for both protein phosphorylation and acetylation events on light‐harvesting and photosystems proteins suggest that these proteins represent key intersecting nodes of signaling and metabolism. Only a single lysine deacetylase (AtHDA14, At4g33470) and three acetyltransferases (AtGNATa, At3g54610; AtCBPc, At1g55970; and NSI1, At1g32070) have been identified as plastidial (Hartl et al ., ; Uhrig et al ., ; Koskela et al ., ), suggesting that substrate specificity for these enzymes must be achieved through the formation of specific but currently unknown protein complexes similar to phosphoprotein phosphatase (PPP)‐family phosphatases (Uhrig et al ., ).…”

Section: Resultsmentioning

confidence: 99%

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Diurnal changes in concerted plant protein phosphorylation and acetylation in Arabidopsis organs and seedlings

et al. 2019

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Summary Protein phosphorylation and acetylation are the two most abundant post‐translational modifications (PTMs) that regulate protein functions in eukaryotes. In plants, these PTMs have been investigated individually; however, their co‐occurrence and dynamics on proteins is currently unknown. Using Arabidopsis thaliana, we quantified changes in protein phosphorylation, acetylation and protein abundance in leaf rosettes, roots, flowers, siliques and seedlings at the end of day (ED) and at the end of night (EN). This identified 2549 phosphorylated and 909 acetylated proteins, of which 1724 phosphorylated and 536 acetylated proteins were also quantified for changes in PTM abundance between ED and EN. Using a sequential dual‐PTM workflow, we identified significant PTM changes and intersections in these organs and plant developmental stages. In particular, cellular process‐, pathway‐ and protein‐level analyses reveal that the phosphoproteome and acetylome predominantly intersect at the pathway‐ and cellular process‐level at ED versus EN. We found 134 proteins involved in core plant cell processes, such as light harvesting and photosynthesis, translation, metabolism and cellular transport, that were both phosphorylated and acetylated. Our results establish connections between PTM motifs, PTM catalyzing enzymes and putative substrate networks. We also identified PTM motifs for further characterization of the regulatory mechanisms that control cellular processes during the diurnal cycle in different Arabidopsis organs and seedlings. The sequential dual‐PTM analysis expands our understanding of diurnal plant cell regulation by PTMs and provides a useful resource for future analyses, while emphasizing the importance of analyzing multiple PTMs simultaneously to elucidate when, where and how they are involved in plant cell regulation.

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Section: Resultsmentioning

confidence: 97%

Section: Resultsmentioning

confidence: 99%

Diurnal changes in concerted plant protein phosphorylation and acetylation in Arabidopsis organs and seedlings

et al. 2019

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“…Interestingly, acetylation of the PsaH protein, in very close proximity to this additional dimer, was found to be essential for state transitions. The loss of this acetylation, though, induced the loss of the classic, well known PSI–LHCII supercomplex, suggesting instead a role in LHCII binding (Koskela et al , ).…”

Section: Discussionmentioning

confidence: 99%

Isolation and characterization of a large photosystem I–light‐harvesting complex II supercomplex with an additional Lhca1–a4 dimer in Arabidopsis

et al. 2020

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The biological conversion of light energy into chemical energy is performed by a flexible photosynthetic machinery located in the thylakoid membranes. Photosystems I and II (PSI and PSII) are the two complexes able to harvest light. PSI is the last complex of the electron transport chain and is composed of multiple subunits: the proteins building the catalytic core complex that are well conserved between oxygenic photosynthetic organisms, and, in green organisms, the membrane light-harvesting complexes (Lhc) necessary to increase light absorption. In plants, four Lhca proteins (Lhca1-4) make up the antenna system of PSI, which can be further extended to optimize photosynthesis by reversible binding of LHCII, the main antenna complex of photosystem II. Here, we used biochemistry and electron microscopy in Arabidopsis to reveal a previously unknown supercomplex of PSI with LHCII that contains an additional Lhca1-a4 dimer bound on the PsaB-PsaI-PsaH side of the complex. This finding contradicts recent structural studies suggesting that the presence of an Lhca dimer at this position is an exclusive feature of algal PSI. We discuss the features of the additional Lhca dimer in the large plant PSI-LHCII supercomplex and the differences with the algal PSI. Our work provides further insights into the intricate structural plasticity of photosystems.

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“…When forming the experimental data for use in FAT‐PTM from PhosPhAt 4.0, phosphorylation site predictions were omitted due to a lack of spectral support by only accounting for modified peptide sequences that had precisely mapped phosphorylation events indicated by (pS), (pT) and (pY). The additional data encompassed in FAT‐PTM, including modification type, localization site and total number of spectral observations supporting each PTM site, were collected from published studies in the literature (Miller et al ., , ; Hemsley et al ., ; Kim et al ., ; Svozil et al ., ; Hu et al ., ; Johnson and Vert, ; Walton et al ., ; Xu et al ., , ; Koskela et al ., ; Liu et al ., ; Majeran et al ., ; Rytz et al ., ; Zeng et al ., ). For quantitative phosphoproteomics studies, abundance fold‐change information for phosphopeptides based on ratiometric quantification of isobaric tag or stable isotope reporters was also collected from supplemental files in the following references (Benschop et al ., ; Nühse et al ., ; Mithoe et al ., ; Zhang et al ., , ; Chen and Hoehenwarter, ; Minkoff et al ., ; Roitinger et al ., ; Cho et al ., ; Bhaskara et al ., ; Wang et al ., ).…”

Section: Methodsmentioning

confidence: 99%

Functional analysis tools for post‐translational modification: a post‐translational modification database for analysis of proteins and metabolic pathways

Cruz

Nguyen

et al. 2019

The Plant Journal

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Summary Post‐translational modifications (PTMs) are critical regulators of protein function, and nearly 200 different types of PTM have been identified. Advances in high‐resolution mass spectrometry have led to the identification of an unprecedented number of PTM sites in numerous organisms, potentially facilitating a more complete understanding of how PTMs regulate cellular behavior. While databases have been created to house the resulting data, most of these resources focus on individual types of PTM, do not consider quantitative PTM analyses or do not provide tools for the visualization and analysis of PTM data. Here, we describe the Functional Analysis Tools for Post‐Translational Modifications (FAT‐PTM) database (https://bioinformatics.cse.unr.edu/fat-ptm/), which currently supports eight different types of PTM and over 49 000 PTM sites identified in large‐scale proteomic surveys of the model organism Arabidopsis thaliana. The FAT‐PTM database currently supports tools to visualize protein‐centric PTM networks, quantitative phosphorylation site data from over 10 different quantitative phosphoproteomic studies, PTM information displayed in protein‐centric metabolic pathways and groups of proteins that are co‐modified by multiple PTMs. Overall, the FAT‐PTM database provides users with a robust platform to share and visualize experimentally supported PTM data, develop hypotheses related to target proteins or identify emergent patterns in PTM data for signaling and metabolic pathways.

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Chloroplast Acetyltransferase NSI Is Required for State Transitions in Arabidopsis thaliana

Cited by 66 publications

References 74 publications

Diurnal changes in concerted plant protein phosphorylation and acetylation in Arabidopsis organs and seedlings

Diurnal changes in concerted plant protein phosphorylation and acetylation in Arabidopsis organs and seedlings

Isolation and characterization of a large photosystem I–light‐harvesting complex II supercomplex with an additional Lhca1–a4 dimer in Arabidopsis

Functional analysis tools for post‐translational modification: a post‐translational modification database for analysis of proteins and metabolic pathways

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