Systematic analysis of the lysine malonylome in common wheat

- Systematic analysis of the lysine malonylome in common wheat.
- Here, a global analysis of lysine malonylation was performed in wheat..
- The malonylated proteins were located in multiple subcellular compartments, especially in the cytosol (45%) and chloroplast (30.
- Protein interaction network analysis revealed eight highly interconnected clusters of malonylated proteins, and 137 malonylated proteins were mapped to the protein network database.
- 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..
- Although Malonyl-CoA is considered to be one of the most common donors of malo- nyl group, the enzymes controlling the malonylation status of proteins are largely unknown [7, 8].
- Sirt5, a member of the lysine deacetylases (KDACs), was found to be able to catalyze lysine demalonylation reaction in mammalian cells [7, 8].
- Similar to lysine acetylation, many malonylated proteins localized in the nucleus, cytoplasm, mitochondria and chloroplast have been identified indicating that a wide variety of biological processes are potentially regulated by lysine malonylation..
- Full list of author information is available at the end of the article.
- 2018 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0.
- Common wheat (Triticum aestivum L.) is one of the most important cereal crops in the world.
- Systematic analysis of the lysine acetylated [2] and succinylated proteins [3] in common wheat revealed that they were involved in a variety of signaling pathways in development and metabolism.
- To test this hypothesis, we performed the first proteomics study of lysine malonylation in common wheat.
- The malonylated proteins were associated with diversified biological processes and were distributed in multiple compartments, including the cytosol, chloroplast, nucleus, mitochondria, plasma membrane, cytoskeleton, extracellular space and peroxisome.
- Importantly, we found that 30% of the malonylated proteins were located to the chloroplast, and further studies showed that these proteins play an important role in photosynthetic carbon fixation in common wheat.
- Protein extraction from common wheat.
- Qing Mai 6, a common wheat variety (T.
- LC-MS/MS analysis of the malonylation peptides was carried out as described [15–18].
- overfilling of the orbitrap [16].
- The malonylated proteins were analyzed by Gene Ontology (GO) annotation derived from the UniProt- GOA database (http://www.ebi.ac.uk/GOA/) based on biological process, cellular component and molecular function [13].
- A two-tailed Fisher’s exact test was employed to test the enrichment of the malonylated proteins and a corrected p-value <.
- Subcellular localization of the modified proteins was predicated with WoLF PSORT (version PSORT/PSORT II) [22].
- Only predic- tions with a minimum probability of 0.5 for one of the different secondary structures (coil, α-helix, β-strand) were considered for analysis.
- The mean secondary structure probabilities of the malonylated lysine residues were compared with the mean secondary structure probabilities of a control dataset containing all the lysine residues of all the malonylated proteins identified in this study.
- software was employed to analyze the protein-protein interactions for the malonylated proteins and the protein- protein interaction network was obtained from the STRING database [24, 25].
- BLASTP was carried out to determine the conservation of lysine malonylated proteins between common wheat and other organisms..
- Identification of lysine malonylated proteins in common wheat.
- To validate the MS data, the mass error of all the identified peptides was checked, and the total distribution of the mass error was less than 5 ppm, indicating that the mass accuracy of the MS data fit the requirement (Additional file 1: Figure S1b).
- We further checked the distribution of all the peptides, and the results showed that the length of most of the peptides was between 8 and 20 (Additional file 1: Figure S1c), which demonstrated that the sample preparation met the standard [15, 17].
- Three representative MS/MS spectra of the malonylated peptides were showed in Additional file 1: Figure S2.
- The number of malonylated proteins in common wheat was higher than that in S.
- Dehydroascorbate reductase (DHAR), a protein involved in redox homeostasis under biotic and abiotic stresses and a key component of the.
- Thus, the number of malonylated sites in the identified proteins was calculated in common wheat.
- As shown in Additional file 1: Figure S of malonylated proteins had only one malony- lated lysine site, whereas 25% (58) were modified on multiple lysine residues.
- To our knowledge, these findings represent the first report of lysine malonylome in common wheat..
- In accordance with the heat map of the amino acid compositions of the malonylation sites (Fig.
- We further evaluated the surface accessibility of the lysine malonylation sites.
- Conservation of lysine malonylated proteins.
- To date, a large number of lysine malonylated proteins have been identified in several prokaryotes and eukary- otes .
- However, the conservation of lysine malonylation in these organisms is unknown.
- As such, we searched the orthologs of lysine malonylated proteins in common wheat by a protein BLAST search against seven organisms with determined malonylomes: B.
- Totally, 458 orthologs of the malonylproteins in.
- 1 Properties of the lysine malonylation peptides in common wheat.
- a Heat map of the amino acid compositions of the malonylation sites showing the frequency of different amino acids around the modified lysine.
- c Probabilities of lysine malonylation in the structures of alpha-helix, beta-strand and coli.
- 2a, 161 malonylated proteins have orthologs in M.
- amyloliquefaciens (44 proteins), which account for proteins) of the total malonylproteins in common wheat..
- We further classified the malonylated proteins of common wheat depending on the number of their orthologous proteins in other organisms.
- 233 proteins) of the malonylated proteins in common wheat was grouped as novel proteins since no orthologs were identified in other organisms (Fig.
- These observations suggest that although lysine malonylation is largely con- served in prokaryotes and eukaryotes, different organisms contain unique malonylated proteins with specific functions..
- Functional annotation of malonylated proteins.
- Consistent with these observations, a large pro- portion of the malonylated proteins were associated with catalytic (44%) and binding (43%) activities based on.
- Cellular component analysis showed that most of the malonylated proteins were located in the cell (38.
- We further predicted the subcellular localizations of the identified proteins using WoLF PSORT [22].
- 3d showed that most of the malonylated proteins in wheat were located in the cytosol (45%) and chloroplast (30.
- Interestingly, 11% of the malonylated proteins were localized in the nucleus, including histone H4, histone H2B, histone H2A, and histone H3 (Fig.
- Furthermore, other malonylated proteins were predicted to be located to the mitochondria (6.
- These findings indicate that the lysine-malonylated proteins have a broad range of biological functions in common wheat..
- Functional enrichment analysis of malonylated proteins To evaluate the nature of malonylated proteins in wheat, we performed functional enrichment analyses of the GO, KEGG pathway and protein domain.
- In agreement with these observations, most of the malonylated proteins were found to be involved in enzymatic activities and binding according to the enrichment analysis of molecular function (Additional file 1: Figure S5 and Add- itional file 2: Table S4).
- 2 Conservation analysis of lysine malonylated proteins.
- and DNA bending complex were more likely to be malony- lated based on the enrichment analysis of the cellular component (Additional file 1: Figure S5 and Additional file 2:.
- Protein interaction network of malonylated proteins To investigate the cellular processes regulated by lysine malonylation in wheat, a protein interaction network was established with the STRING database using Cytoscape soft- ware [24].
- 5 and Additional file 2: Table S7, 137 malonylated proteins were mapped to the protein.
- 3 Functional classification of lysine malonylated proteins in common wheat.
- a Classification of malonylated proteins according to biological process.
- b Classification of malonylated proteins according to cellular component.
- c Classification of malonylated proteins according to molecular function.
- d Subcellular localization of the malonylated proteins.
- 4 KEGG pathway-based enrichment analysis of the malonylation proteins in common wheat.
- The complicated interaction networks of malonylated proteins indicate that a variety of pathways are putatively modulated by lysine malonylation in common wheat..
- Analysis of malonylated proteins involved in the Calvin cycle In wheat, the Calvin cycle is one of the most important metabolic processes.
- We found that 30% of the malonylated proteins were located in the chloroplast in common wheat (Fig.
- Functional enrichment analysis of the KEGG pathway revealed that the proteins associated.
- These results suggested that lysine malonylation may play an important role in the Calvin cycle in common wheat.
- To confirm these observations, we fur- ther analyzed the malonylated proteins involved in the Calvin cycle.
- 5 Protein interaction networks of the malonylation proteins in common wheat.
- Comparison among the malonylome, acetylome and succinylome in common wheat.
- 6 Identified malonylation proteins in Calvin cycle in common wheat.
- a Working scheme of lysine malonylation events involved in Calvin cycle in common wheat.
- The malonylated proteins were highlighted in red.
- 7 Overlap among lysine malonylation, lysine succinylation and lysine acetylation in common wheat.
- W5GYX5), which is one of the key enzymes involved in the Calvin cycle [29, 30].
- 7b, 2.3 and 5.6% of the malonylation sites could also be acetylated and succinylated, respectively.
- In this study, a total of 233 malonylated proteins with 342 unique modification sites were identified in common wheat.
- The identified malonylated proteins are localized in diverse compartments and are involved in multiple bio- logical processes, especially in the Calvin cycle.
- Systematic analysis of lysine malonylation sites in common wheat.
- Three representative MS/MS spectra of the malonylated peptides.
- Validation of lysine malonylation of DHAR by Western blot analysis.
- Number of malonylation sites per protein in common wheat.
- Domain-based enrichment analysis of malonylated proteins.
- Interaction network of malonylated proteins associated with ribosome.
- The identified lysine malonylation sites in wheat.
- Table S2 Conservation of lysine malonylated proteins.
- None of these funding sources were involved in the design of the study and collection, analysis, and interpretation of data and in writing the manuscript..
- Proteome-wide post-translational modification statistics: frequency analysis and curation of the swiss-prot database.
- Comprehensive profiling of lysine acetylproteome analysis reveals diverse functions of lysine acetylation in common wheat.
- Global analysis of protein lysine succinylation profiles in common wheat.
- Lysine succinylation and lysine malonylation in histones.
- Systematic analysis of the lysine acetylome in Fusarium graminearum

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