Lysine acetylome profiling uncovers novel histone deacetylase substrate proteins in
            <i>Arabidopsis</i>

Hartl, Markus; Füßl, Magdalena; Boersema, Paul J.; Jost, Jan Oliver; Kramer, Katharina; Bakirbas, Ahmet; Sindlinger, Julia; Plöchinger, Magdalena; Leister, Dario; Uhrig, R. Glen; Moorhead, Greg B. G.; Cox, Jürgen; Salvucci, Michael E.; Schwarzer, Dirk; Mann, Matthias; Finkemeier, Iris

doi:10.15252/msb.20177819

Cited by 128 publications

(162 citation statements)

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“…Twenty of the 134 proteins modified by both phosphorylation and acetylation (15%) are related to light harvesting and photosynthesis (Figure ). 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 ., ).…”

Section: Resultsmentioning

confidence: 97%

“…Data S11–S16 reveal AcK motifs with both conserved and unique chemical properties and to have significant changes between organs and seedlings, ED and EN, and between subcellular locations. Consistent with motif analyses in both photosynthetic (Konig et al ., ; Smith‐Hammond et al ., ,b; Xiong et al ., ; Zhang et al ., ; Zhen et al ., ; Hartl et al ., ) and non‐photosynthetic (Weinert et al ., ; Henriksen et al ., ; Lundby et al ., ) eukaryotic systems, +1 or −2 phenylalanine/tyrosine‐containing acetylated motifs are found in proteins from all organs and seedlings, whereas the motif with aspartate in the −2 position is unique to seedlings (Figure S5). Diurnal changes in organ and seedling‐specific AcK motifs with a −1 glutamine and a +1 tyrosine were found (Data S11 and S12), in addition to 3× ED‐ and 3× EN‐specific AcK motifs (Data S13 and S14).…”

Section: Resultsmentioning

confidence: 99%

“…In particular, plastid proteins with AcKY and [I/L]AcK motifs form large association networks covering a wide range of chloroplast processes (Figure S6; Data S20). With only a few KATs (AtGNATa/AtCBPc) and KDACs (AtHDA14) either predicted (Uhrig et al ., ) or verified (Hartl et al ., ) to be localized to the chloroplast, it is likely that each forms multiple protein complexes to target the diversity of proteins with these motifs. Currently there is little known about these motifs, and there have been few specific studies connecting these protein acetylation motifs with the activities of specific acetyltransferases or deacetylases.…”

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%

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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“…Another well characterized plant PTM is lysine acetylation, which, in addition to other lysine modifications, is available for Arabidopsis and other species in the Protein Lysine Modification (PLM) database (Xu et al ., ). Several studies have highlighted the functional importance of lysine acetylation not only in Arabidopsis (Finkemeier et al ., ; Wu et al ., ; Hartl et al ., ) but also, for example, in rice ( Oryza sativa ) seed development (Wang et al ., ). Although lysine acetylation is reversible, acetylation of the α‐amino group at the protein N‐termini is not and happens either cotranslationally or post‐translationally after protein cleavage events (Bienvenut et al ., ; Drazic et al ., ).…”

Section: Introductionmentioning

confidence: 99%

The Plant PTM Viewer, a central resource for exploring plant protein modifications

et al. 2019

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Summary Post‐translational modifications (PTMs) of proteins are central in any kind of cellular signaling. Modern mass spectrometry technologies enable comprehensive identification and quantification of various PTMs. Given the increased numbers and types of mapped protein modifications, a database is necessary that simultaneously integrates and compares site‐specific information for different PTMs, especially in plants for which the available PTM data are poorly catalogued. Here, we present the Plant PTM Viewer (http://www.psb.ugent.be/PlantPTMViewer), an integrative PTM resource that comprises approximately 370 000 PTM sites for 19 types of protein modifications in plant proteins from five different species. The Plant PTM Viewer provides the user with a protein sequence overview in which the experimentally evidenced PTMs are highlighted together with an estimate of the confidence by which the modified peptides and, if possible, the actual modification sites were identified and with functional protein domains or active site residues. The PTM sequence search tool can query PTM combinations in specific protein sequences, whereas the PTM BLAST tool searches for modified protein sequences to detect conserved PTMs in homologous sequences. Taken together, these tools help to assume the role and potential interplay of PTMs in specific proteins or within a broader systems biology context. The Plant PTM Viewer is an open repository that allows the submission of mass spectrometry‐based PTM data to remain at pace with future PTM plant studies.

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“…N). Protein acetylation motifs vary depending on species, developmental stage and subcellular localization (Hartl et al ). Surprisingly, although most of these motifs have previously been reported in different species, we identified 12 motifs containing two lysine residues in which either lysine could be modified.…”

Section: Resultsmentioning

confidence: 99%

Comparative acetylomic analysis reveals differentially acetylated proteins regulating anther and pollen development in kenaf cytoplasmic male sterility line

Chen

Fan

et al. 2019

Physiologia Plantarum

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Cytoplasmic male sterility (CMS) is widely used in plant breeding and represents a perfect model to understand cyto‐nuclear interactions and pollen development research. Lysine acetylation in proteins is a dynamic and reversible posttranslational modification (PTM) that plays an important roles in diverse cell processes and signaling. However, studies addressing acetylation PTM regarding to anther and pollen development in CMS background are largely lacking. To reveal the possible mechanism of kenaf (Hibiscus cannabinus L.) CMS and pollen development, we performed a label‐free‐based comparative acetylome analysis in kenaf anther of a CMS line and wild‐type (Wt). Using whole transcriptome unigenes of kenaf as the reference genome, we identified a total of 1204 Kac (lysin acetylation) sites on 1110 peptides corresponding to 672 unique proteins. Futher analysis showed 56 out of 672 proteins were differentially acetylated between CMS and Wt line, with 13 and 43 of those characterized up‐ and downregulated, respectively. Thirty‐eight and 82 proteins were detected distinctively acetylated in CMS and Wt lines, respectively. And evaluation of the acetylomic and proteomic results indicated that the most significantly acetylated proteins were not associated with abundant changes at the protein level. Bioinformatics analysis demonstrated that many of these proteins were involved in various biological processes which may play key roles in pollen development, inculding tricarboxylic acid (TCA) cycle and energy metabolism, protein folding, protein metabolism, cell signaling, gene expression regulation. Taken together, our results provide insight into the CMS molecular mechanism and pollen development in kenaf from a protein acetylation perspective.

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Lysine acetylome profiling uncovers novel histone deacetylase substrate proteins in Arabidopsis

Cited by 128 publications

References 76 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

The Plant PTM Viewer, a central resource for exploring plant protein modifications

Comparative acetylomic analysis reveals differentially acetylated proteins regulating anther and pollen development in kenaf cytoplasmic male sterility line

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