Comparison of the Proteome of Staphylococcus aureus Planktonic Culture and 3-Day Biofilm Reveals Potential Role of Key Proteins in Biofilm

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

Rahman et al. performed a proteomic analysis of S. aureus biofilm and planktonic cultures to identify the key proteins involve in virulence. Authors used high end techniques like TMT labelling and LCMS for proteome quantification. To validate the results they performed qPCR. However there are many studies like this studying the total proteome. What is the significance of this current manuscript? If the authors used any clinically isolated strains for this study means it would have been interesting! Why the biofilm of the S. aureus is not shown? Why there are no characterization studies done for the nature of the biofilm? Why authors chose 3 day biofilm compared to other days? 

Introduction is not written well. Authors failed to discuss about previously published biofilm proteomic articles. The differentially regulated proteins can be depicted as heat map and venn diagram in the main text for easy understanding of the readers.

 

Author Response

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Reviewer 2 Report

Comments and Suggestions for Authors

Dear Authors,

I find your paper " Comparison of the proteome of Staphylococcus aureus planktonic culture and 3-day biofilm reveals potential role of key proteins in biofilm " very interesting and I consider that it can bring an important contribution to the research in this field.

Please find below some observations that could help to the further improvement of the manuscript.

-in the Introduction section: please add study hypothesis

-in the Results section: Figure 1 - " # of Proteins " - is it the percentage represented on the vertical axis? Because the values on some of the columns does nor correspond to the value on the axis.

-in the Discussion section: please add verification/not of study hypothesis

-if possible, please use more recent References.

Comments on the Quality of English Language

The paper needs minor English correction.

Author Response

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Author Response File: Author Response.docx

Reviewer 3 Report

Comments and Suggestions for Authors

The paper by Md Arifur Rahman et al. addresses an exciting subject. I express my sincere gratitude for the opportunity to review your manuscript. The effort of the author is appreciated. The manuscript is well written, and the review protocols and data are reported scientifically and presented clearly. Congratulations on your results. 

 

The study aimed to construct a comprehensive reference map of the proteome of S. aureus biofilm grown for 3 days compared to a 24-hour planktonic culture. This was achieved using high-resolution tandem mass tag (TMT)-based mass spectrometry followed by significant pathway analysis.

 

Key Findings:

 

Upregulated Proteins in 3-day Biofilm:

Secondary Metabolites: Proteins involved in the biosynthesis of secondary metabolites were significantly upregulated.

ABC Transporters: These proteins, crucial for the transport of various molecules across cellular membranes, showed significant upregulation.

Amino Acids Biosynthesis: Proteins associated with the biosynthesis of amino acids were upregulated.

Response to Stress: Proteins involved in stress responses were significantly increased.

Amino Sugar and Nucleotide Sugar Metabolism: Metabolic pathways involving amino sugars and nucleotide sugars were upregulated.

 

Downregulated Proteins in 3-day Biofilm:

Virulence Factors: Proteins related to virulence were significantly downregulated.

Microbial Metabolism in Diverse Environments: Proteins involved in microbial metabolism across various environments were downregulated.

Secondary Metabolites: Some proteins associated with secondary metabolite pathways were downregulated.

Translation and Energy Metabolism: Proteins involved in translation and energy metabolism showed significant downregulation.

 

Significantly Dysregulated Proteins:

Hyaluronidase (hysA): This protein, along with chitinase, may play a significant role in preventing or eliminating biofilm development.

Implications: This study advances the understanding of the S. aureus subproteome, identifying potential pathways significant to biofilm biology. The insights gained may aid in developing new therapeutic strategies, including antibiofilm agents, for treating biofilm-related infections associated with implantable medical devices.

 

By shedding light on the complex proteomic changes during biofilm formation, this research highlights critical areas for future therapeutic intervention and enhances the understanding of S. aureus biofilm pathogenicity.

Author Response

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Author Response File: Author Response.docx

Round 2

Reviewer 1 Report

Comments and Suggestions for Authors

In venn diagram fig 1B it is surprising to see why there are no commonly regulated proteins? Please check for it.

Author Response

Comment 1: In venn diagram fig 1B it is surprising to see why there are no commonly regulated proteins? Please check for it.

Response 1: As in this study, we have given particular emphasis on 3-day biofilm, so this Venn diagram represents identified proteins dysregulated (>2-fold, p < 0.05) in the 3-day biofilm only. We identified 273 proteins, and it shows the dispersion of 273 upregulated and downregulated proteins in which 82 upregulated and 191 downregulated proteins in 3-day biofilm only. Therefore, we don't have any common proteins and the Venn diagram is correct in this regard. We will remove zero from common proteins area to avoid any confusion and 3-day biofilm had 313 commonly regulated proteins with planktonic (results not shown).