Abstract
This study aimed to establish the mode of binding between Quercetin (QEN) and an essential protein called ClfB in forming biofilm in Staphylococcus aureus (S. aureus). In this study, the raw data of GSE163153 were analyzed for quality control, alignment, and gene counts, and the differential analysis detected the key differentially expressed genes (DEGs) assisting in the formation of the S. aureus biofilm. Then, the protein-protein interaction (PPI) and gene function enrichment analyses of the target genes, identified a gene called clfB to be closely related to biofilm formation. ClfB was structurally characterized, molecularly docked, and kinetically simulated to unravel the mode of binding of QEN to ClfB. Meanwhile, the growth curve and transmission electron microscopy methods examined the effect of QEN on the S. aureus growth. Results indicated that the clfB gene was increasingly expressed during biofilm formation and was involved in cell adhesion, pathogenicity, and infection. We identified 5 amino acid sites of ClfB (D272, R331, I379, K391, E490) as potential sites for binding QEN, which would indirectly influence the changes in the functional sites N234, D270, Y273, F328, inhibiting the formation of biofilm. Meanwhile, 128 μg/ml of QEN could significantly inhibit the S. aureus biofilm formation. This manuscript serves as a molecular foundation for QEN as an antibacterial drug providing a new perspective for developing antibacterial drugs.
Highlights
Staphylococcus aureus (S. aureus) is a Gram-positive bacterium infecting humans and animals, existing either as unicellular or sessile aggregates
The results showed that the quality scores of all the positions of clean reads for all the samples were greater than 30, i.e., false discovery rate (FDR) < 0.001, which met the subsequent analysis
The top ten genes were selected as the key candidate genes based on the ranking of the Degree values, arranged in descending order as clfA, clfB, sdrC, isdA, isdB, sdrD, srtA, icaA, sdrE, and ebpS
Summary
Staphylococcus aureus (S. aureus) is a Gram-positive bacterium infecting humans and animals, existing either as unicellular or sessile aggregates (known as biofilms). Almost 60% of S. aureus infections are triggered due to biofilm formation (Costerton, 1999). The establishment of S. aureus biofilm leads to a resistance to antimicrobial therapy and host immune response. As a result, it imparts the pathogen with the ability to trigger recurrent infections, leading to the ineffectiveness of a single antimicrobial drugs administration (Costerton, 1999). Once the biofilm is established, the bacteria within the biofilm require more antibiotics than those required by the planktonic bacteria (Wu et al, 2015; Memariani et al, 2019) As a result, it leaves humans at risk from an ever-increasing number of antibiotics
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