Identification of lysine succinylome and acetylome in vancomycin-intermediate Staphylococcus aureus XN108
Ontology highlight
ABSTRACT:
INSTRUMENT(S): timsTOF Pro
ORGANISM(S): Staphylococcus Aureus
TISSUE(S): Whole Body
SUBMITTER: 
Li Tan
LAB HEAD: Li Tan
PROVIDER: PXD033341 | Pride | 2022-11-09
REPOSITORIES: Pride
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Project description:In this study, we detected the first lysine succinylome and acetylome in a vancomycin-intermediate S. aureus (VISA) strain, XN108.Furthermore,Comparative analysis of the protein succinylation and acetylation between XN108-ΔcobB and XN108-WT strain was conducted on the basis of quantitative detection of both protein expression and protein modification
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Project description:Lysine succinylation has been recognized as a post-translational modification (PTM) in recent years. It is plausible that succinylation may have a vaster functional impact than acetylation due to bulkier structural changes and greater charge differences on the modified lysine residue. Currently, however, the quantity of identified succinylated proteins and their corresponding functions in cereal plants remain largely unknown. In this study, 854 lysine succinylation sites on 347 proteins have been identified by a thorough investigation in developing rice seeds. Six motifs were revealed as preferred amino-acid sequence arrangements for succinylation sites, and a noteworthy motif preference was discovered in proteins associated with different biological processes, molecular functions, pathways, and domains. Remarkably, heavy succinylation was detected on major seed storage proteins, in conjunction with key enzymes involved in central carbon metabolism and starch biosynthetic pathways for rice seed development. Conserved succinylated proteins were identified amongst varying organisms. Rice proteins with co-modifications of succinylation, acetylation, malonylation, crotonylation, and 2-hydroxyisobutyrylation were identified through a comprehensive comparison analysis. A striking number of highly conserved succinyl-proteins and multi-modified proteins were shown to be involved in vital metabolic events. Our study delivers a platform for expansive investigation of molecular networks administrating cereal seed development via PTMs.
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Project description:Aspergillus fumigatus is the main culprit of invasive aspergillosis, which has a high mortality rate in immunocompromised patients. Lysine 2-hydroxyisobutyrylation is a highly conserved posttranslational modification found in a wide variety of organisms. In this study, we survey the biological impact of 2-hydroxyisobutyrylation on lysine residuals (Khib) in A. fumigatus. Using an antibody-enrichment approach along with the traditional LC-MS/MS method, the pattern of Khib-modified proteins and sites were analyzed in one wild type strain of A. fumigatus. We identified 3494 Khib-modified proteins with 18091 modified sites in this strain, and a more detailed bioinformatics analysis indicated that the Khib-modified proteins are involved in a wide range of cellular functions with diverse subcellular locations. Functional enrichment analysis featured several prominent functional pathways, including ribosome, biosynthesis of amino acids and nucleocytoplasmic transport – of which the ribosome pathway is the most affected pathway. When compared with other reported Khib eukaryotes, both Khib-modified sites and Khib-modified proteins also remained the highest. It proves that this modification is of great importance in A. fumigatus. At the same time, several enzymes in the fungal ergosterol synthesis pathway are modified with Khib. These bioinformatic results suggest that 2-hydroxyisobutyrylation may play an indispensable role in the regulation of the ribosomal biogenesis and the process of fungal resistance. Findings in this study may provide new insights for studying PTM-associated mechanisms in fungal development and antifungal drug development.
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Project description:Toxoplasma gondii is a protozoan parasite which can infect a wide range of animals, including humans. According to virulence, it is generally divided into three different strains, namely type I (RH strain), type II (PRU strain) and type III (VEG strain). Lysine malonylation (Kmal) is a new type of post-translational modification (PTM), which has been reported to regulate diverse biological pathways in various organisms, including T. gondii. However, there is no knowledge about whether lysine malonylation regulates the virulence of different strains in T. gondii. In this study, for the first time, we identified and quantified lysine malonylation level in three strains of T. gondii. In total, 111 proteins and 152 sites were up-regulated, 17 proteins and sites were down-regulated in RH compared with PRU strains, respectively; 50 proteins and 59 sites were up-regulated, 50 proteins and 53 sites were down-regulated in RH strain compared with VEG strains; 72 proteins and 90 sites were up-regulated, 7 proteins and 8 sites were down-regulated in VEG strain compared with PRU strains. Further analysis indicates that these proteins are involved in many important biological processes and regulating virulence-related functions of T. gondii. These findings provide novel and important resource for the role of lysine malonytion in virulence of T. gondii and provide a new direction for the research of vaccine in T. gondii.
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Project description:Proteins undergo acetylation at the Nε-amino group of lysine residues and the Nα-amino group of the N-terminus in Archaea as in Bacteria and Eukarya. However, the extent, pattern and roles of the modifications in Archaea remain poorly understood. Here we report the proteomic analyses of a wild-type Sulfolobus islandicus strain and its mutant derivative strains lacking either a homologue of the protein acetyltransferase Pat (SisPat) or a homologue of the Nt-acetyltransferase Ard1 (ΔSisArd1). A total of 1,708 Nε-acetylated lysine residues in 684 proteins (26% of the total proteins), and 158 Nt-acetylated proteins (44% of the identified proteins) were found in S. islandicus. ΔSisArd1 grew more slowly than the parental strain, whereas ΔSisPat showed no significant growth defects. Only 24 out of the 1,503 quantifiable Nε-acetylated lysine residues were differentially acetylated, and all but one of the 24 residues were less acetylated, by >1.3 fold in ΔSisPat than in the parental strain, indicating the narrow substrate specificity of the enzyme. Six acyl-CoA synthetases were the preferred substrates of SisPat in vivo, suggesting that Nε-acetylation by the acetyltransferase is involved in maintaining metabolic balance in the cell. Acetylation of acyl-CoA synthetases by SisPat occurred at a sequence motif conserved among all three domains of life. On the other hand, 92% of the identified N-termini were acetylated by SisArd1 in the cell. The enzyme exhibited broad substrate specificity and was capable of modifying nearly all types of the target N-termini of human NatA-NatF. The deletion of the SisArd1 gene altered the cellular levels of 18% of the quantifiable proteins (1,518) by >1.5 fold. Consistent with the growth phenotype of ΔSisArd1, the cellular levels of proteins involved in cell division and cell cycle control, DNA replication, and purine synthesis were significantly lowered in the mutant than those in the parental strain.
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Project description:Candida albicans is the most common human fungal pathogen, causing diseases ranging from mucosal to systemic infections for both immunocompetent and immunocompromised individuals. Lysine 2-hydroxyisobutyrylation is a highly conserved posttranslational modification found in a wide variety of organisms. In this study, we survey the biological impact of 2-hydroxyisobutyrylation on lysine residuals (Khib) in C. albicans. Using an antibody-enrichment approach along with the traditional LC-MS/MS method, the pattern of Khib-modified proteins and sites were analyzed in one wild type strain of C. albicans. We identified 1438 Khib-modified proteins with 6659 modified sites in this strain, and a more detailed bioinformatics analysis indicated that the Khib-modified proteins are involved in a wide range of cellular functions with diverse subcellular locations. Functional enrichment analysis featured several prominent functional pathways, including ribosome, biosynthesis of antibiotics, biosynthesis of secondary metabolites, biosynthesis of amino acids and carbon metabolism – of which the ribosome pathway is the most affected pathway. Even when compared with the reported lysine acetylation (Kac) and succinylation (Ksuc), the Khib-modified sites on ribosomal proteins remained the highest for C. albicans. These bioinformatic results suggest that 2-hydroxyisobutyrylation may play an indispensable role in the regulation of the ribosomal biogenesis and protein translation. Confirmation at the biochemical level would enable us to resolve physiological and pathogenic roles of PTM in C. albicans.
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Project description:Protein posttranslational modifications (PTMs) has been shown to regulate biological processes of human diseases via expanding the genetic code and for regulating cellular pathophysiology, however, the system-wide changes at the PTMs levels in ICH brain remains little known. Given that succinylation is one of the important PTMs in regulating many biological processes. Therefore, in this study, we used a high-resolution mass spectrometry-based, quantitative succinyllysine proteomics approach to firstly investigated the ICH-associated brain protein succinyllysine modifications. We totally identified the concentration of approximately 6000 succinylation events and quantified approximately 3500 sites. Among them, 25 succinyllysine sites on 23 proteins were increased, while 13 succinyllysine sites on 12 proteins were downregulated after ICH. Additionally, the subcellular localization analysis of these significantly changed succinylproteins showed that 58.3% hyposuccinylated proteins were located in the mitochondria, while the percentage of succinylproteins located in mitochondria was decreased to about 35% in ICH brains with concomitant increasing in the percentage of cytoplasm to 30.4%. Further bioinformatic analysis showed that the succinylated proteins were mostly located in mitochondria and synapse-related subcellular spaces, and participate in many pathophysiological processes, such as metabolism, cytoskeleton organization, synapse working and ferroptosis, etc.. Moreover, we performed a combination analysis of our succinylproteomics data with previously published transcriptome data and found that most of the differentially succinylated proteins were distributed into neurons, endothelial cells and astrocytes. In conclusion, our analyses uncover a number of succinylation-affected processes and pathways in ICH brains and provide new insights for understanding ICH pathophysiological processes.
2021-10-29 | PXD025621 | Pride