Structural Insights into the Regulation of <i>Staphylococcus aureus</i> Phosphofructokinase by Tetramer–Dimer Conversion

Tian, Tian; Wang, Chengliang; Wu, Mingzai; Zhang, Xuan; Zang, Jianye

doi:10.1021/acs.biochem.8b00028

Cited by 10 publications

(7 citation statements)

References 24 publications

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“…This study showed that SprC could impact PTS by regulating mtlA (SAOUHSC_02402) encoding one PTS enzyme. ATP-dependent 6-phosphofructokinase encoded by SAOUHSC_01807 ( pfkA ) is the key enzyme in the first committing step of glycolysis ( Tian et al, 2018 ). However, whether SprC has the function of regulating the expression of this enzyme remains to be confirmed, because in this study there were inconclusive results on the expression of pfkA ( Figure 4 ).…”

Section: Discussionmentioning

confidence: 99%

Insights Into the Impact of Small RNA SprC on the Metabolism and Virulence of Staphylococcus aureus

Zhou

Zhao

et al. 2022

Front. Cell. Infect. Microbiol.

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AimOur previous proteomic analysis showed that small RNA SprC (one of the small pathogenicity island RNAs) of Staphylococcus aureus possesses the ability to regulate the expression of multiple bacterial proteins. In this study, our objective was to further provide insights into the regulatory role of SprC in gene transcription and metabolism of S. aureus.MethodsGene expression profiles were obtained from S. aureus N315 wild-type and its sprC deletion mutant strains by RNA-sequencing (RNA-seq), and differentially expressed genes (DEGs) were screened by R language with a |log2(fold change)| ≥1 and a false discovery rate (FDR) ≤ 0.05. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were carried out to understand the significance of the DEGs. The quality of RNA-seq was further verified by quantitative real-time PCR (qRT-PCR), mRNA target prediction, metabolomics analysis and transcript-level expression analysis of genes of sprC complementation strain.ResultsA total of 2497 transcripts were identified, of which 60 transcripts expressions in sprC knockout strain were significantly different (37 up-regulated and 23 down-regulated DEGs). GO analysis showed that the functions of these DEGs were mainly concentrated in the biological process and molecular function related to metabolism and pathogenesis, and a higher number of genes were involved in the oxidation-reduction process, catalytic activity and binding. KEGG pathways enrichment analysis demonstrated that metabolism and pathogenesis were the most affected pathways, such as metabolic pathways, biosynthesis of secondary metabolites, purine metabolism, fructose and mannose metabolism and S. aureus infection. The qRT-PCR results of the DEGs with defined functions in the sprC deletion and complementation strains were in general agreement with those obtained by RNA-seq. Metabolomics analysis revealed 77 specific pathways involving metabolic pathways. Among them, many, such as metabolic pathways, biosynthesis of secondary metabolites and purine metabolism, were consistent with those enriched in the RNA-seq analysis.ConclusionThis study offered valuable and reliable information about the regulatory roles of SprC in S. aureus biology through transcriptomics and metabolomics analysis. These results may provide clues for new potential targets for anti-virulence adjuvant therapy on S. aureus infection.

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Section: Discussionmentioning

confidence: 99%

Insights Into the Impact of Small RNA SprC on the Metabolism and Virulence of Staphylococcus aureus

Zhou

Zhao

et al. 2022

Front. Cell. Infect. Microbiol.

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“…Because few bacterial PFK-1 structures have been experimentally solved [41][42][43][44][45] , we instead compiled a diverse set of sequences from the Uniprot database as inputs for structural prediction using AlphaFold2 46 , and subsequently modeled PEP into the allosteric pocket of each model by structural alignment with the previously solved mutant Geobacillus stearothermophilus PFK-1-PEP (PDB: 4I4I) complex (Figure 5A) (all-atom RMSD of the binding pocket = 0.371 Å; global RMSD = 0.493 Å). 41 We optimized each ortholog's PFK-1 model to a stable, energetically favorable conformation without steric clashes in the pocket using the relax application in the Rosetta macromolecular modeling software.…”

Section: Case Study 3: Trends In Inhibitor Binding For An Evolutionar...mentioning

confidence: 99%

MAGPIE: an interactive tool for visualizing and analyzing protein-ligand interactions

Rodriguez,

Weber,

Sundberg

et al. 2023

Preprint

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We present MAGPIE, a tool for analyzing thousands of protein-ligand interactions at once. MAGPIE generates an interactive 3D visualization from a set of protein complex structures that share a target ligand, as well as sequence logo-style frequency graphs that show all the amino acids from the set of protein binders that interact with user-selected target ligand positions. MAGPIE is compatible with small molecule or protein ligands. Availability and implementation: MAGPIE is implemented in Python 3 and is freely available with two dataset/usage examples and a helper script to prepare MAGPIE inputs at https://github.com/glasgowlab/MAGPIE. Additional documentation is in the Supplementary data online.

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“…Several X-ray crystallographic structures deposited at the Protein Data Bank for three glycolytic enzymes phosphofructokinase (PFK), glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and pyruvate kinase (PK) were extracted for species of Homo sapiens (H. sapiens) (Kung et al, 2012;Kloos et al, 2015;White et al, 2015), Staphylococcus aureus (S. aureus) (Mukherjee et al, 2010;Axerio-Cilies et al, 2012;Tian et al, 2018) and three parasites, Trypanosoma cruzi for GADPH (T. cruzi) (Guido et al, 2009), Trypanosoma brucei (T. brucei) for PFK (McNae et al, 2009) and Leishmania mexicana (L. mexicana) for PK (Rigden et al, 1999) and the selected ones were listed in…”

Section: System Preparationmentioning

confidence: 99%

“…The proposed druggable site encircled in the left figures clearly indicate the active tetramer form displaying a lower degree of frequency shift compared to dimer form. Consequently, the number of druggable sites which satisfied the frequency (Kloos et al, 2015;Tian et al, 2018). ATP and F6P were illustrated with orange and yellow sticks.…”

Section: S Aureus Phosphofructokinase (Sapfk) Indicated An Alternative Allosteric Region In Addition To Well-known Allosteric and Catalytmentioning

confidence: 99%

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Identification of Alternative Allosteric Sites in Glycolytic Enzymes for Potential Use as Species-Specific Drug Targets

Ayyildiz

Celiker

Ozhelvaci

et al. 2020

Front. Mol. Biosci.

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Three allosteric glycolytic enzymes, phosphofructokinase, glyceraldehyde-3 phosphate dehydrogenase and pyruvate kinase, associated with bacterial, parasitic and human species, were explored to identify potential allosteric sites that would be used as prime targets for species-specific drug design purposes using a newly developed approach which incorporates solvent mapping, elastic network modeling, sequence and structural alignments. The majority of binding sites detected by solvent mapping overlapped with the interface regions connecting the subunits, thus appeared as promising target sites for allosteric regulation. Each binding site was then evaluated by its ability to alter the global dynamics of the receptor defined by the percentage change in the frequencies of the lowest-frequency modes most significantly and as anticipated, the most effective ones were detected in the vicinity of the well-reported catalytic and allosteric sites. Furthermore, some of our proposed regions intersected with experimentally resolved sites which are known to be critical for activity regulation, which further validated our approach. Despite the high degree of structural conservation encountered between bacterial/parasitic and human glycolytic enzymes, the majority of the newly presented allosteric sites exhibited a low degree of sequence conservation which further increased their likelihood to be used as species-specific target regions for drug design studies.

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Structural Insights into the Regulation of Staphylococcus aureus Phosphofructokinase by Tetramer–Dimer Conversion

Cited by 10 publications

References 24 publications

Insights Into the Impact of Small RNA SprC on the Metabolism and Virulence of Staphylococcus aureus

Insights Into the Impact of Small RNA SprC on the Metabolism and Virulence of Staphylococcus aureus

MAGPIE: an interactive tool for visualizing and analyzing protein-ligand interactions

Identification of Alternative Allosteric Sites in Glycolytic Enzymes for Potential Use as Species-Specific Drug Targets

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