PLMD: An updated data resource of protein lysine modifications

Xu, Haodong; Zhou, Jiaqi; Lin, Shaofeng; Deng, Wankun; Zhang, Ying; Xue, Yu

doi:10.1016/j.jgg.2017.03.007

Cited by 184 publications

(138 citation statements)

References 44 publications

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“…However, based on the lysine acetylation database, there are a total of 18 putative acetylation sites in E. coli TyrRS (K8, K67, K85, K90, K103, K144, K154, K230, K235, K238, K249, K250, K255, K321, K377, K390, K399, and K416). [25] This might be caused by different E. coli strains, growth conditions, and mass spectrometry methods. It could also imply that the lysine acetylation at other sites in TyrRS might need additional cofactors, coenzymes, or unknown KATs.…”

Section: Resultsmentioning

confidence: 99%

Biochemical Characterization of the Lysine Acetylation of Tyrosyl‐tRNA Synthetase in Escherichia coli

et al. 2017

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Aminoacyl-tRNA synthetases (aaRSs) play essential roles in protein synthesis. As a member of the aaRS family, the tyrosyl-tRNA synthetase (TyrRS) in Escherichia coli has been shown in proteomic studies to be acetylated at multiple lysine residues. However, these putative acetylation targets have not yet been biochemically characterized. In this study, we applied a genetic-code-expansion strategy to site-specifically incorporate Nε-acetyl-L-lysine into selected positions of TyrRS for in vitro characterization. Enzyme assays demonstrated that acetylation at K85, K235, and K238 could impair the enzyme activity. In vitro deacetylation experiments showed that most acetylated lysine residues in TyrRS were sensitive to the E. coli deacetylase CobB but not YcgC. In vitro acetylation assays indicated that 25 members of the Gcn5-related N-acetyltransferase family in E. coli, including YfiQ, could not acetylate TyrRS efficiently, whereas TyrRS could be acetylated chemically by acetyl-CoA or acetyl-phosphate (AcP) only. Our in vitro characterization experiments indicated that lysine acetylation could be a possible mechanism for modulating aaRS enzyme activities, thus affecting translation.

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Section: Resultsmentioning

confidence: 99%

Biochemical Characterization of the Lysine Acetylation of Tyrosyl‐tRNA Synthetase in Escherichia coli

et al. 2017

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“…For example, for Arabidopsis thaliana (Arabidopsis), approximately 57 000 and 48 000 phosphorylation sites are available in PhosPhAt 4.0 (Heazlewood et al, 2008) and the Plant Protein Phosphorylation database (Yao et al, 2014), respectively. 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, 2017b). Several studies have highlighted the functional importance of lysine acetylation not only in Arabidopsis (Finkemeier et al, 2011;Wu et al, 2011;Hartl et al, 2017) but also, for example, in rice (Oryza sativa) seed development .…”

Section: Introductionmentioning

confidence: 99%

“…Given the high quantity of identified PTMs, (species-specific) databases are needed that compile PTM data for further exploration. Examples of such databases are the PLM database (Xu et al, 2017b), dbPTM (Lee et al, 2006), PTMcode (Minguez et al, 2015) and iPTMnet (Huang et al, 2018b). As such, databases often integrate various PTM types, facilitating the exploration of PTM interplays and leading to unexplored hypotheses and experiments.…”

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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“…This method could be coupled with proteomics for the global profiling of cellular crotonylation in the future. It has been reported that up to 20 types of PTMs occur at protein lysine residues, including acetylation, methylation, succinylation, malonylation, glutarylation, butyrylation, propionylation, crotonylation, and pupylation, which are various short‐chain lysine acylations. It seems that the more complex the modification is, the easier it is to design specific chemical probes to detect that modification.…”

Section: Approaches For Ptm Identificationmentioning

confidence: 99%

Advances of Proteomics in Novel PTM Discovery: Applications in Cancer Therapy

Wang

Zhang

et al. 2019

Small Methods

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Protein posttranslational modification (PTM) is a critical mechanism to enhance the diversity of protein species and functions in organisms. Currently, many different PTMs are discovered and found to be involved in a wide range of cellular processes. The aberrant regulation of PTM dynamics is reported to contribute to cancer development. Phosphorylation and acetylation are the best studied PTMs, and the application of high‐resolution mass spectrometry‐based proteomics and specific antibody‐based enrichment technologies significantly promotes novel PTM discovery. This review discusses methods for global PTM identification, including antibody‐based enrichment and chemical probe‐based identification. Several acylations, such as propionylation, butyrylation, succinylation, malonylation, and crotonylation, are recently found to influence both histone and nonhistone proteins and to be intimately linked with the progression of cancer. It is proposed that targeting novel PTM dynamics by pharmacological inhibitors has great potential for cancer therapy.

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PLMD: An updated data resource of protein lysine modifications

Cited by 184 publications

References 44 publications

Biochemical Characterization of the Lysine Acetylation of Tyrosyl‐tRNA Synthetase in Escherichia coli

Biochemical Characterization of the Lysine Acetylation of Tyrosyl‐tRNA Synthetase in Escherichia coli

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

Advances of Proteomics in Novel PTM Discovery: Applications in Cancer Therapy

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