Proteome‐wide lysine acetylation profiling to investigate the involvement of histone deacetylase <scp>HDA5</scp> in the salt stress response of Arabidopsis leaves

Tilak, Priyadarshini; Kotnik, Florian; Née, Guillaume; Seidel, Julian; Sindlinger, Julia; Heinkow, Paulina; Eirich, Jürgen; Schwarzer, Dirk; Finkemeier, Iris

doi:10.1111/tpj.16206

Cited by 19 publications

(5 citation statements)

References 93 publications

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“…512 proteins (59%) contained a single K-acetyl site whereas others are more heavily K-acetylated. The acetylated proteins were distributed across multiple subcellular locations and functions supporting recent findings in Arabidopsis (Tilak et al, 2023), but also other plant species , the green algae Chlamydomonas reinhardtii (Fussl et al, 2022)…”

Section: Mapping Biological Ptms; N-terminal and Lysine Acetylation P...supporting

confidence: 82%

Mapping theArabidopsis thalianaproteome in PeptideAtlas and the nature of the unobserved (dark) proteome; strategies towards a complete proteome

van Wijk,

Leppert,

Sun

et al. 2023

Preprint

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This study describes a new release of the Arabidopsis thaliana PeptideAtlas proteomics resource providing protein sequence coverage, matched mass spectrometry (MS) spectra, selected PTMs, and metadata. 70 million MS/MS spectra were matched to the Araport11 annotation, identifying ~0.6 million unique peptides and 18267 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 building 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 certain (e.g. CLE, CEP, IDA, PSY) but not other (e.g. THIONIN, CAP,) signaling peptides families, E3 ligases, TFs, and other proteins with unfavorable physicochemical properties. A machine learning model trained on RNA expression data and protein properties predicts the probability for proteins to be detected. The model aids in discovery of proteins with short-half life (e.g. SIG1,3, ERF-VII TFs) and completing the proteome. PeptideAtlas is linked to TAIR, JBrowse, PPDB, SUBA, UniProtKB and Plant PTM Viewer.

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Section: Mapping Biological Ptms; N-terminal and Lysine Acetylation P...supporting

confidence: 82%

Mapping theArabidopsis thalianaproteome in PeptideAtlas and the nature of the unobserved (dark) proteome; strategies towards a complete proteome

van Wijk,

Leppert,

Sun

et al. 2023

Preprint

View full text Add to dashboard Cite

show abstract

“…512 proteins (59%) contained a single K-acetyl site, whereas others are more heavily K-acetylated. The acetylated proteins were distributed across multiple subcellular locations and functions supporting recent findings in Arabidopsis , but also other plant species, the green algae Chlamydomonas reinhardtii as well as the moss Physcomitrium patens …”

Section: Resultssupporting

confidence: 83%

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

van Wijk,

Leppert,

Sun

et al. 2023

J. Proteome Res.

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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.

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“…Among these genes, the expression levels of PtrHDA906 and PtrHAG3 were the most increased in response to drought stress. It is expected that these genes exert their influence by regulating protein acetylation levels and affecting gene expression, in a manner analogous to their homologous genes [ 42 , 43 ].…”

Section: Discussionmentioning

confidence: 99%

Genome-wide identification and expression analysis of histone deacetylase and histone acetyltransferase genes in response to drought in poplars

Li,

Chen,

Dai

et al. 2024

BMC Genomics

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Background Histone deacetylases (HDACs) and histone acetyltransferases (HATs) are involved in plant growth and development as well as in response to environmental changes, by dynamically regulating gene acetylation levels. Although there have been numerous reports on the identification and function of HDAC and HAT in herbaceous plants, there are fewer report related genes in woody plants under drought stress. Results In this study, we performed a genome-wide analysis of the HDAC and HAT families in Populus trichocarpa, including phylogenetic analysis, gene structure, conserved domains, and expression analysis. A total of 16 PtrHDACs and 12 PtrHATs were identified in P. trichocarpa genome. Analysis of cis-elements in the promoters of PtrHDACs and PtrHATs revealed that both gene families could respond to a variety of environmental signals, including hormones and drought. Furthermore, real time quantitative PCR indicated that PtrHDA906 and PtrHAG3 were significantly responsive to drought. PtrHDA906, PtrHAC1, PtrHAC3, PtrHAG2, PtrHAG6 and PtrHAF1 consistently responded to abscisic acid, methyl jasmonate and salicylic acid under drought conditions. Conclusions Our study demonstrates that PtrHDACs and PtrHATs may respond to drought through hormone signaling pathways, which helps to reveal the hub of acetylation modification in hormone regulation of abiotic stress.

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Proteome‐wide lysine acetylation profiling to investigate the involvement of histone deacetylase HDA5 in the salt stress response of Arabidopsis leaves

Cited by 19 publications

References 93 publications

Mapping theArabidopsis thalianaproteome in PeptideAtlas and the nature of the unobserved (dark) proteome; strategies towards a complete proteome

Mapping theArabidopsis thalianaproteome in PeptideAtlas and the nature of the unobserved (dark) proteome; strategies towards a complete proteome

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

Genome-wide identification and expression analysis of histone deacetylase and histone acetyltransferase genes in response to drought in poplars

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