Malonyl-proteome profiles of Staphylococcus aureus reveal lysine malonylation modification in enzymes involved in energy metabolism

Abstract Background Protein lysine malonylation, a novel post-translational modification (PTM), has been recently linked with energy metabolism in bacteria. Staphylococcus aureus is the third most important foodborne pathogen worldwide. Nonetheless, substrates and biological roles of malonylation are still poorly understood in this pathogen. Results Using anti-malonyl-lysine antibody enrichment and high-resolution LC-MS/MS analysis, 440 lysine-malonylated sites were identified in 281 proteins of S. aureus strain. The frequency of valine in position − 1 and alanine at + 2 and + 4 positions was high. KEGG pathway analysis showed that six categories were highly enriched, including ribosome, glycolysis/gluconeogenesis, pentose phosphate pathway (PPP), tricarboxylic acid cycle (TCA), valine, leucine, isoleucine degradation, and aminoacyl-tRNA biosynthesis. In total, 31 malonylated sites in S. aureus shared homology with lysine-malonylated sites previously identified in E. coli, indicating malonylated proteins are highly conserved among bacteria. Key rate-limiting enzymes in central carbon metabolic pathways were also found to be malonylated in S. aureus, namely pyruvate kinase (PYK), 6-phosphofructokinase, phosphoglycerate kinase, dihydrolipoyl dehydrogenase, and F1F0-ATP synthase. Notably, malonylation sites were found at or near protein active sites, including KH domain protein, thioredoxin, alanine dehydrogenase (ALD), dihydrolipoyl dehydrogenase (LpdA), pyruvate oxidase CidC, and catabolite control protein A (CcpA), thus suggesting that lysine malonylation may affect the activity of such enzymes. Conclusions Data presented herein expand the current knowledge on lysine malonylation in prokaryotes and indicate the potential roles of protein malonylation in bacterial physiology and metabolism.

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Malonyl-Proteome Profiles of Staphylococcus Aureus Reveal Lysine Malonylation Modification in Enzymes Involved in Energy Metabolism

10.21203/rs.3.rs-95144/v1 ◽

2020 ◽

Author(s):

Yanan Shi ◽

Aixiang HUANG ◽

Jingjing Zhu ◽

Yan Xu ◽

Xiaozhao Tang ◽

...

Keyword(s):

Staphylococcus Aureus ◽

Energy Metabolism ◽

Active Sites ◽

Current Knowledge ◽

Tricarboxylic Acid Cycle ◽

Protein A ◽

Pentose Phosphate ◽

Post Translational Modification ◽

Bacterial Physiology ◽

Dihydrolipoyl Dehydrogenase

Abstract BackgroundProtein lysine malonylation, a novel post-translational modification (PTM), has been recently linked with energy metabolism in bacteria. Staphylococcus aureus is the third most important foodborne pathogen worldwide. Nonetheless, substrates and biological roles of malonylation are still poorly understood in this pathogen. ResultsUsing anti-malonyl-lysine antibody enrichment and high-resolution LC-MS/MS analysis, 440 lysine-malonylated sites were identified in 281 proteins of S. aureus strain. The frequency of valine in position -1 and alanine at +2 and +4 position was high. KEGG pathway analysis showed that six categories were highly enriched: ribosome, glycolysis/gluconeogenesis, pentose phosphate pathway (PPP), tricarboxylic acid cycle (TCA), valine, leucine, isoleucine degradation, and aminoacyl-tRNA biosynthesis. In total, 31 malonylated sites in S. aureus shared homology with lysine-malonylated sites previously identified in E. coli, indicating malonylated proteins are highly conserved among bacteria. Key rate-limiting enzymes in central carbon metabolic pathways were also found to be malonylated in S. aureus, namely pyruvate kinase (PYK), 6-phosphofructokinase, phosphoglycerate kinase, dihydrolipoyl dehydrogenase, and F1F0-ATP synthase. Notably, malonylation sites were found at or near protein active sites, including KH domain, thioredoxin, alanine dehydrogenase (ALD), dihydrolipoyl dehydrogenase (LpdA), pyruvate oxidase CidC and catabolite control protein A (CcpA), thus suggesting that lysine malonylation may affect the activity of such enzymes. ConclusionsData presented herein expand the current knowledge on lysine malonylation in prokaryotes and indicate potential roles of protein malonylation in bacterial physiology and metabolism.

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PSIV-B-34 Late-Breaking: Targeted metabolomics analysis reveals that dietary super-nutritional selenium regulates energy metabolism homeostasis in pig liver

Journal of Animal Science ◽

10.1093/jas/skz258.658 ◽

2019 ◽

Vol 97 (Supplement_3) ◽

pp. 328-329

Author(s):

Junmin Zhang ◽

Chaohua Tang ◽

Kai Zhang

Keyword(s):

Energy Metabolism ◽

Mrna Expression ◽

Redox State ◽

Profile Analysis ◽

Tricarboxylic Acid Cycle ◽

Basal Diet ◽

Metabolite Profile ◽

Pentose Phosphate ◽

Pig Liver ◽

Treatment Groups

Abstract Energy metabolism is a major mechanism of power reduction needed to maintain the redox state in an organism. By using a selenium (Se)-deficiency model we have previously demonstrated that Se can shift glycolysis by regulating the redox state in pig skeletal muscle. How dietary super-nutritional Se affects the energy metabolism in pig liver remains unknown. In the present study, super-nutritional Se supplementation (as selenomethionine) effects on liver selenoprotein expression and energy metabolite profiles in pigs were evaluated. In total, 36 castrated male pigs (Duroc × Landrace × Yorkshire, 62.3 ± 3.3 kg) were randomly assigned to two treatment groups with six replicates of three pigs per replicate. The two treatment groups received the same basal diet supplemented with different levels of selenomethionine: Se adequate (Se-A, 0.25 mg Se/kg) and Se supra-nutritional (2.5 mg Se/kg) for 60 days. Animals were then scarified and their livers were sampled for Se content, selenotranscriptome, and energy-targeted metabolite profile analysis. Super-nutritional Se supplementation increased the levels of serum fasting glucose, insulin, and free fatty acid levels (P < 0.05), as well as elevated the total Se liver content (P < 0.05). Glutathione peroxidase 4 mRNA expression was upregulated, while thioredoxin reductase 1 and selenoprotein W mRNA expression levels were downregulated in the super-nutritional Se group. LC-MS-based target metabolomics showed that high Se supplementation increased the levels of most metabolites involved in glycolysis, pentose phosphate pathway, tricarboxylic acid cycle, and acylcarnitine metabolism. These results indicated that dietary super-nutritional Se can regulate energy metabolism homeostasis in the pig liver.

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Axillary bud outgrowth in rose is controlled by sugar metabolic and signalling pathways

Journal of Experimental Botany ◽

10.1093/jxb/erab046 ◽

2021 ◽

Cited By ~ 1

Author(s):

Ming Wang ◽

Maria-Dolores Pérez-Garcia ◽

Jean-Michel Davière ◽

François Barbier ◽

Laurent Ogé ◽

...

Keyword(s):

Regulatory Networks ◽

Current Knowledge ◽

Tricarboxylic Acid Cycle ◽

Tca Cycle ◽

Tricarboxylic Acid ◽

Pentose Phosphate ◽

Signalling Pathways ◽

Shoot Branching ◽

Endogenous Factors

Abstract Shoot branching is a pivotal process during plant growth and development, antagonistically orchestrated by auxin and sugars. By contrast to extensive investigations on hormonal regulatory networks, our current knowledge on the role of sugar signalling pathways in bud outgrowth is still scarce. Based on a stepwise and comprehensive strategy, we investigated the role of glycolysis/the tricarboxylic acid (TCA) cycle and the oxidative pentose phosphate pathway (OPPP) in the control of bud outgrowth. We demonstrated that these two pathways are necessary for bud outgrowth promotion upon plant decapitation and in response to sugar availability. They are also targets of the antagonistic crosstalk between auxin and sugar availability. These two pathways act synergistically to downregulate the expression of BRC1, a conserved inhibitor of shoot branching. Using Rosa calluses stably transformed with GFP-fused promoter sequences of RhBRC1 (pRhBRC1), glycolysis/TCA-cycle and the OPPP were found to repress the transcriptional activity of pRhBRC1 cooperatively. Glycolysis/TCA-cycle- and OPPP-dependent regulations involve the -1973bp/-1611bp and -1206bp/-709bp regions of pRhBRC1, respectively. Taken together, our findings indicate that glycolysis/the tricarboxylic acid cycle and the OPPP are integrative parts of shoot branching control and can link endogenous factors to the developmental program of bud outgrowth, more likely through two distinct mechanisms.

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Impact of the Histidine-Containing Phosphocarrier Protein HPr on Carbon Metabolism and Virulence in Staphylococcus aureus

Microorganisms ◽

10.3390/microorganisms9030466 ◽

2021 ◽

Vol 9 (3) ◽

pp. 466

Author(s):

Linda Pätzold ◽

Anne-Christine Brausch ◽

Evelyn-Laura Bielefeld ◽

Lisa Zimmer ◽

Greg A. Somerville ◽

...

Keyword(s):

Staphylococcus Aureus ◽

Pathogenic Bacteria ◽

Protein A ◽

Common Mechanism ◽

Central Metabolism ◽

Phosphotransferase System ◽

Reading Frame ◽

Bacterial Physiology ◽

Catabolite Control Protein A ◽

Regulatory Functions

Carbon catabolite repression (CCR) is a common mechanism pathogenic bacteria use to link central metabolism with virulence factor synthesis. In gram-positive bacteria, catabolite control protein A (CcpA) and the histidine-containing phosphocarrier protein HPr (encoded by ptsH) are the predominant mediators of CCR. In addition to modulating CcpA activity, HPr is essential for glucose import via the phosphotransferase system. While the regulatory functions of CcpA in Staphylococcus aureus are largely known, little is known about the function of HPr in CCR and infectivity. To address this knowledge gap, ptsH mutants were created in S. aureus that either lack the open reading frame or harbor a ptsH variant carrying a thymidine to guanosine mutation at position 136, and the effects of these mutations on growth and metabolism were assessed. Inactivation of ptsH altered bacterial physiology and decreased the ability of S. aureus to form a biofilm and cause infections in mice. These data demonstrate that HPr affects central metabolism and virulence in S. aureus independent of its influence on CcpA regulation.

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Staphylococcus aureus and its IgE-inducing enterotoxins in asthma: current knowledge

European Respiratory Journal ◽

10.1183/13993003.01592-2019 ◽

2020 ◽

Vol 55 (4) ◽

pp. 1901592 ◽

Cited By ~ 9

Author(s):

Claus Bachert ◽

Marc Humbert ◽

Nicola A. Hanania ◽

Nan Zhang ◽

Stephen Holgate ◽

...

Keyword(s):

Staphylococcus Aureus ◽

Severe Asthma ◽

Cell Activation ◽

Late Onset ◽

Current Knowledge ◽

Protein A ◽

Lymphoid Cells ◽

Oral Steroid ◽

Future Research ◽

The Impact

While immunoglobulin (Ig) E is a prominent biomarker for early-onset, its levels are often elevated in non-allergic late-onset asthma. However, the pattern of IgE expression in the latter is mostly polyclonal, with specific IgEs low or below detection level albeit with an increased total IgE. In late-onset severe asthma patients, specific IgE to Staphylococcal enterotoxins (se-IgE) can frequently be detected in serum, and has been associated with asthma, with severe asthma defined by hospitalisations, oral steroid use and decrease in lung function. Recently, se-IgE was demonstrated to even predict the development into severe asthma with exacerbations over the next decade. Staphylococcus aureus manipulates the airway mucosal immunology at various levels via its proteins, including superantigens, serine-protease-like proteins (Spls), or protein A (SpA) and possibly others. Release of IL-33 from respiratory epithelium and activation of innate lymphoid cells (ILCs) via its receptor ST2, type 2 cytokine release from those ILCs and T helper (Th) 2 cells, mast cell degranulation, massive local B-cell activation and IgE formation, and finally eosinophil attraction with consequent release of extracellular traps, adding to the epithelial damage and contributing to disease persistence via formation of Charcot–Leyden crystals are the most prominent hallmarks of the manipulation of the mucosal immunity by S. aureus. In summary, S. aureus claims a prominent role in the orchestration of severe airway inflammation and in current and future disease severity. In this review, we discuss current knowledge in this field and outline the needs for future research to fully understand the impact of S. aureus and its proteins on asthma.

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Impact of Antibiotics with Various Target Sites on the Metabolome of Staphylococcus aureus

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.03104-14 ◽

2014 ◽

Vol 58 (12) ◽

pp. 7151-7163 ◽

Cited By ~ 46

Author(s):

Kirsten Dörries ◽

Rabea Schlueter ◽

Michael Lalk

Keyword(s):

Staphylococcus Aureus ◽

Tricarboxylic Acid Cycle ◽

Pentose Phosphate ◽

Outer Cell ◽

Primary Metabolism ◽

Metabolic Profiles ◽

Dependent Manner ◽

Content Type ◽

Morphological Alterations ◽

The Impact

ABSTRACTIn this study, global intra- and extracellular metabolic profiles were exploited to investigate the impact of antibiotic compounds with different cellular targets on the metabolome ofStaphylococcus aureusHG001. Primary metabolism was largely covered, yet uncommon staphylococcal metabolites were detected in the cytosol ofS. aureus, including sedoheptulose-1,7-bisphosphate and the UDP-MurNAc-pentapeptide with an alanine-seryl residue. By comparing the metabolic profiles of unstressed and stressed staphylococcal cells in a time-dependent manner, we found far-ranging effects within the metabolome. For each antibiotic compound, accumulation as well as depletion of metabolites was detected, often comprising whole biosynthetic pathways, such as central carbon and amino acid metabolism and peptidoglycan, purine, and pyrimidine synthesis. Ciprofloxacin altered the pool of (deoxy)nucleotides as well as peptidoglycan precursors, thus linking stalled DNA and cell wall synthesis. Erythromycin tended to increase the amounts of intermediates of the pentose phosphate pathway and lysine. Fosfomycin inhibited the first enzymatic step of peptidoglycan synthesis, which was followed by decreased levels of peptidoglycan precursors but enhanced levels of substrates such as UDP-GlcNAc and alanine-alanine. In contrast, vancomycin and ampicillin inhibited the last stage of peptidoglycan construction on the outer cell surface. As a result, the amounts of UDP-MurNAc-peptides drastically increased, resulting in morphological alterations in the septal region and in an overall decrease in central metabolite levels. Moreover, each antibiotic affected intracellular levels of tricarboxylic acid cycle intermediates.

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Staphylococcus aureus CcpA Affects Biofilm Formation

Infection and Immunity ◽

10.1128/iai.00035-08 ◽

2008 ◽

Vol 76 (5) ◽

pp. 2044-2050 ◽

Cited By ~ 91

Author(s):

Kati Seidl ◽

Christiane Goerke ◽

Christiane Wolz ◽

Dietrich Mack ◽

Brigitte Berger-Bächi ◽

...

Keyword(s):

Staphylococcus Aureus ◽

Biofilm Formation ◽

Tricarboxylic Acid Cycle ◽

Protein A ◽

Growth Conditions ◽

Extracellular Dna ◽

Proteinase K ◽

Growth Media ◽

Sodium Metaperiodate

ABSTRACT Biofilm formation in Staphylococcus aureus under in vitro growth conditions is generally promoted by high concentrations of sugar and/or salts. The addition of glucose to routinely used complex growth media triggered biofilm formation in S. aureus strain SA113. Deletion of ccpA, coding for the catabolite control protein A (CcpA), which regulates gene expression in response to the carbon source, abolished the capacity of SA113 to form a biofilm under static and flow conditions, while still allowing primary attachment to polystyrene surfaces. This suggested that CcpA mainly affects biofilm accumulation and intercellular aggregation. trans-Complementation of the mutant with the wild-type ccpA allele fully restored the biofilm formation. The biofilm produced by SA113 was susceptible to sodium metaperiodate, DNase I, and proteinase K treatment, indicating the presence of polysaccharide intercellular adhesin (PIA), protein factors, and extracellular DNA (eDNA). The investigation of several factors which were reported to influence biofilm formation in S. aureus (arlRS, mgrA, rbf, sarA, atl, ica, citZ, citB, and cidABC) showed that CcpA up-regulated the transcription of cidA, which was recently shown to contribute to eDNA production. Moreover, we showed that CcpA increased icaA expression and PIA production, presumably over the down-regulation of the tricarboxylic acid cycle genes citB and citZ.

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