Exploring the lipoproteome of Parageobacillus thermoglucosidasius
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Parageobacillus thermoglucosidasius is a thermophilic endospore-forming Bacillales of considerable biotechnological interest. Bacterial lipoproteins are a significant class of cell envelope components, influencing multiple aspects of the interactions of bacteria with their environments. We have therefore used a bioinformatic approach to identify the lipoproteins encoded in the P. thermoglucosidasius DSM 2542 type strain genome. 89 putative lipoproteins were found, representing ~2.3% of the P. thermoglucosidasius reference proteome; 84% (75) of these were also found in the predicted proteome of P. thermoglucosidasius strain Y4.1MC1. Just over half of the 89 putative lipoproteins are predicted to be substrate binding proteins in ABC importer systems; others function in signalling pathways, protein translocation, in redox processes including the respiratory chain, and as enzymes. At least 10 lipoproteins are predicted to be involved in P. thermoglucosidasius spore cycle, whilst 15 are lipoproteins of unknown function. Proteomic analysis of P. thermoglucosidasius grown to exponential phase in LB medium detected the expression of nearly 60% (52/89) of the predicted lipoproteome, with the notable exception of those functionally linked to sporulation. These data contribute to understanding of the P. thermoglucosidasius cell envelope and so should be of use of those studying the physiology, metabolism and biotechnological utility of this bacterium.
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Thank you for your revised manuscript, which has now been accepted for publication in Access Microbiology.
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This is a study that would be of interest to the field and community. The reviewers have highlighted minor concerns with the work presented. Please ensure that you address their comments.
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Comments to Author
This is an interesting descriptive analysis on the prediction of lipoproteins in P. thermoglucosidasius. A strength is that it uses multiple prediction tools, and that it provides a resource for others working with this bacterium. However, I do think some improvements could increase clarity. One issue that I have with this is that it is rather long with a lot of detail - making this hard to read and many readers will lose the big picture. Perhaps move some of the commentary on individual genes to supplementary files and keep the main text more conceptual? Towards the end, I would like to see a clear statement on the limitations of the study, in that there was no experimental validation of predicted function, which always introduces an element of uncertainty in bioinformatic studies like this. …
Comments to Author
This is an interesting descriptive analysis on the prediction of lipoproteins in P. thermoglucosidasius. A strength is that it uses multiple prediction tools, and that it provides a resource for others working with this bacterium. However, I do think some improvements could increase clarity. One issue that I have with this is that it is rather long with a lot of detail - making this hard to read and many readers will lose the big picture. Perhaps move some of the commentary on individual genes to supplementary files and keep the main text more conceptual? Towards the end, I would like to see a clear statement on the limitations of the study, in that there was no experimental validation of predicted function, which always introduces an element of uncertainty in bioinformatic studies like this. Sometimes it feels that there a bit too much confidence in sequence similarity, while that does not always equate to functional similarity. Finally, I'd like to see something in the conclusion section on how this compares with lipoproteomes from related species; are there any notable similarities or differences? For instance, B. subtilis has been well annotated - is there anything that is unique in the lipoproteome of a thermophile compared to a mesophile?
Please confirm that no generative AI tools or large language models have been used to generate this peer review report or to assist with any part of the peer review process.
I confirm no generative AI tools were used in preparation of this review.
Please rate the manuscript for methodological rigour
Good
Please rate the quality of the presentation and structure of the manuscript
Good
To what extent are the conclusions supported by the data?
Partially support
Do you have any concerns of possible image manipulation, plagiarism or any other unethical practices?
No
Is there a potential financial or other conflict of interest between yourself and the author(s)?
No
If this manuscript involves human and/or animal work, have the subjects been treated in an ethical manner and the authors complied with the appropriate guidelines?
Yes
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Comments to Author
This paper reports a bioinformatic prediction of lipoproteins encoded by P. thermoglucosidasius DSM2542 and predicts that ~2.3% of the proteome is exported and lipidated, presumably by Lgt? It would be useful for the authors to comment briefly on the predicted lipoprotein biogenesis pathway in this organism, e.g., are Lsp and Lgt in single copy? Do they encode Lnt homologues like some other monoderm Gram positive bacteria? The authors also report a proteomic study of P. thermoglucosidasius where they attempt to selectively isolate lipoproteins using a detergent extraction method. This is less successful, as evidenced by the presence of nearly 1000 proteins, which is about a quarter of the predicted proteome (10-fold more than the predicted lipoproteome). It would be useful to include a Table or pie …
Comments to Author
This paper reports a bioinformatic prediction of lipoproteins encoded by P. thermoglucosidasius DSM2542 and predicts that ~2.3% of the proteome is exported and lipidated, presumably by Lgt? It would be useful for the authors to comment briefly on the predicted lipoprotein biogenesis pathway in this organism, e.g., are Lsp and Lgt in single copy? Do they encode Lnt homologues like some other monoderm Gram positive bacteria? The authors also report a proteomic study of P. thermoglucosidasius where they attempt to selectively isolate lipoproteins using a detergent extraction method. This is less successful, as evidenced by the presence of nearly 1000 proteins, which is about a quarter of the predicted proteome (10-fold more than the predicted lipoproteome). It would be useful to include a Table or pie chart here showing the types of proteins extracted and their relative proportions (e.g., cytoplasmic, secreted, integral membrane, peripheral membrane, lipoproteins). Overall I think this is a well executed study and should be accepted for publication subject to some minor amendments (see suggestions above and below). Minor comments: Line 149. Proteomic analysis. How were the overnight cultures inoculated and grown? Line 517: i.e. expression of nearly 60% (52/89) of the predicted lipoproteome. Should be production not expression.
Please confirm that no generative AI tools or large language models have been used to generate this peer review report or to assist with any part of the peer review process.
I confirm no generative AI tools were used in preparation of this review.
Please rate the manuscript for methodological rigour
Very good
Please rate the quality of the presentation and structure of the manuscript
Very good
To what extent are the conclusions supported by the data?
Strongly support
Do you have any concerns of possible image manipulation, plagiarism or any other unethical practices?
No
Is there a potential financial or other conflict of interest between yourself and the author(s)?
No
If this manuscript involves human and/or animal work, have the subjects been treated in an ethical manner and the authors complied with the appropriate guidelines?
Yes
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