Global Profiling of Protein Lysine Malonylation in <i>Escherichia coli</i> Reveals Its Role in Energy Metabolism

Qian, Lili; Nie, Litong; Chen, Ming; Liu, Ping; Zhu, Jun; Zhai, Linhui; Tao, Sheng-Ce; Cheng, Zhongyi; Zhao, Yingming; Tan, Minjia

doi:10.1021/acs.jproteome.6b00264

Cited by 64 publications

(75 citation statements)

References 35 publications

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“…Simulation of Substrate and Enzyme Docking-Recent study demonstrated that lysine modifications such succinylation and malonylation suppressed enzymatic activity (15,37). In this study, we identified much K hib on metabolic enzymes, and therefore we would like to know if the modification has a potential effect on their activities too?…”

Section: Resultsmentioning

confidence: 88%

Systematic Identification of Lysine 2-hydroxyisobutyrylated Proteins in Proteus mirabilis

Dong

Guo

Wei

et al. 2018

Molecular & Cellular Proteomics

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Lysine 2-hydroxyisobutyrylation (K hib) is a novel posttranslational modification (PTM), which was thought to play a role in active gene transcription and cellular proliferation. Here we report a comprehensive identification of K hib in Proteus mirabilis (P. mirabilis). By combining affinity enrichment with two-dimensional liquid chromatography and high-resolution mass spectrometry, 4735 2-hydroxyisobutyrylation sites were identified on 1051 proteins in P. mirabilis. These proteins bearing modifications were further characterized in abundance, distribution and functions. The interaction networks and domain architectures of these proteins with high confidence were revealed using bioinformatic tools. Our data demonstrate that many 2-hydroxyisobutyrylated proteins are involved in metabolic pathways, such as purine metabolism, pentose phosphate pathway and glycolysis/gluconeogenesis. The extensive distribution of K hib also indicates that the modification may play important influence to bacterial metabolism. The speculation is further supported by the observation that carbon sources can influence the occurrence of K hib. Furthermore, we demonstrate that 2-hy-droxyisobutyrylation on K343 was a negative regulatory modification on Enolase (ENO) activity, and molecular docking results indicate the regulatory mechanism that K hib may change the binding formation of ENO and its substrate 2-phospho-D-glycerate (2PG) and cause the substrate far from the active sites of enzyme. We hope this first comprehensive analysis of nonhistone K hib in prokaryotes is valuable for further functional investigation of this modification.

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Section: Resultsmentioning

confidence: 88%

Systematic Identification of Lysine 2-hydroxyisobutyrylated Proteins in Proteus mirabilis

Dong

Guo

Wei

et al. 2018

Molecular & Cellular Proteomics

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“…tuberculosis and V . parahemolyticus 19 – 23 . These indicate a possible function of lysine modifications in coordinating protein biosynthesis and processing.…”

Section: Resultsmentioning

confidence: 99%

Proteome-wide Analysis of Lysine 2-hydroxyisobutyrylation in Developing Rice (Oryza sativa) Seeds

Meng

Xing

Perez

et al. 2017

Sci Rep

108

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Lysine 2-hydroxyisobutyrylation is a recently identified protein post-translational modification that is known to affect the association between histone and DNA. However, non-histone protein lysine 2-hydroxyisobutyrylation remains largely unexplored. Utilizing antibody-based affinity enrichment and nano-HPLC/MS/MS analyses of 2-hydroxyisobutyrylation peptides, we efficaciously identified 9,916 2-hydroxyisobutyryl lysine sites on 2,512 proteins in developing rice seeds, representing the first lysine 2-hydroxyisobutyrylome dataset in plants. Functional annotation analyses indicated that a wide variety of vital biological processes were preferably targeted by lysine 2-hydroxyisobutyrylation, including glycolysis/gluconeogenesis, TCA cycle, starch biosynthesis, lipid metabolism, protein biosynthesis and processing. Our finding showed that 2-hydroxyisobutyrylated histone sites were conserved across plants, human, and mouse. A number of 2-hydroxyisobutyryl sites were shared with other lysine acylations in both histone and non-histone proteins. Comprehensive analysis of the lysine 2-hydroxyisobutyrylation sites illustrated that the modification sites were highly sequence specific with distinct motifs, and they had less surface accessibility than other lysine residues in the protein. Overall, our study provides the first systematic analysis of lysine 2-hydroxyisobutyrylation proteome in plants, and it serves as an important resource for future investigations of the regulatory mechanisms and functions of lysine 2-hydroxyisobutyrylation.

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“…Therefore, it is speculated that both protein acetylation and malonylation are reversibly regulated by lysine acetyltransferases (KATs) and KDACs, which are located to diverse cell compartments [ 7 – 9 ]. Similar to lysine acetylation, many malonylated proteins localized in the nucleus, cytoplasm, mitochondria and chloroplast have been identified [ 5 , 8 , 10 – 13 ], indicating that a wide variety of biological processes are potentially regulated by lysine malonylation.…”

Section: Introductionmentioning

confidence: 99%

Systematic analysis of the lysine malonylome in common wheat

et al. 2018

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BackgroundProtein lysine malonylation, a newly discovered post-translational modification (PTM), plays an important role in diverse metabolic processes in both eukaryotes and prokaryotes. Common wheat is a major global cereal crop. However, the functions of lysine malonylation are relatively unknown in this crop. Here, a global analysis of lysine malonylation was performed in wheat.ResultsIn total, 342 lysine malonylated sites were identified in 233 proteins. Bioinformatics analysis showed that the frequency of arginine (R) in position + 1 was highest, and a modification motif, KmaR, was identified. The malonylated proteins were located in multiple subcellular compartments, especially in the cytosol (45%) and chloroplast (30%). The identified proteins were found to be involved in diverse pathways, such as carbon metabolism, the Calvin cycle, and the biosynthesis of amino acids, suggesting an important role for lysine malonylation in these processes. Protein interaction network analysis revealed eight highly interconnected clusters of malonylated proteins, and 137 malonylated proteins were mapped to the protein network database. Moreover, five proteins were simultaneously modified by lysine malonylation, acetylation and succinylation, suggesting that these three PTMs may coordinately regulate the function of many proteins in common wheat.ConclusionsOur results suggest that lysine malonylation is involved in a variety of biological processes, especially carbon fixation in photosynthetic organisms. These data represent the first report of the lysine malonylome in common wheat and provide an important dataset for further exploring the physiological role of lysine malonylation in wheat and likely all plants.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4535-y) contains supplementary material, which is available to authorized users.

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Global Profiling of Protein Lysine Malonylation in Escherichia coli Reveals Its Role in Energy Metabolism

Cited by 64 publications

References 35 publications

Systematic Identification of Lysine 2-hydroxyisobutyrylated Proteins in Proteus mirabilis

Systematic Identification of Lysine 2-hydroxyisobutyrylated Proteins in Proteus mirabilis

Proteome-wide Analysis of Lysine 2-hydroxyisobutyrylation in Developing Rice (Oryza sativa) Seeds

Systematic analysis of the lysine malonylome in common wheat

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