PONE-D-23-16802Comparative genomics of the proteostasis network in extreme acidophilesPLOS ONE

Dear Dr. Levicán,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.

Please submit your revised manuscript by Aug 09 2023 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.

Please include the following items when submitting your revised manuscript:

• A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'.
• A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'.
• An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'.

If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter.

If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols. Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols.

We look forward to receiving your revised manuscript.

Kind regards,

RAJA AADIL HUSSAIN BHAT

Academic Editor

PLOS ONE

Journal Requirements:

When submitting your revision, we need you to address these additional requirements.

1. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The PLOS ONE style templates can be found at 

https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and 

https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf

2. Thank you for stating the following financial disclosure: 

"This study was funded by Fondo Nacional de Desarrollo Científico y Tecnológico (Fondecyt) from the government of Chile (grants 1211386 and 3200487) and Dicyt-USACH from University of Santiago, Chile. K.I.F was funded by a Conicyt Doctoral Fellowship (N°21210134)."

Please state what role the funders took in the study.  If the funders had no role, please state: "The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript." 

If this statement is not correct you must amend it as needed. 

Please include this amended Role of Funder statement in your cover letter; we will change the online submission form on your behalf.

3. Please expand the acronym “Dicyt” (as indicated in your financial disclosure) so that it states the name of your funders in full.

This information should be included in your cover letter; we will change the online submission form on your behalf.

4. Thank you for stating the following in your Competing Interests section:  

"The authors declare that there are no competing interests."

Please complete your Competing Interests on the online submission form to state any Competing Interests. If you have no competing interests, please state "The authors have declared that no competing interests exist.", as detailed online in our guide for authors at http://journals.plos.org/plosone/s/submit-now 

 This information should be included in your cover letter; we will change the online submission form on your behalf.

5. We note that you have stated that you will provide repository information for your data at acceptance. Should your manuscript be accepted for publication, we will hold it until you provide the relevant accession numbers or DOIs necessary to access your data. If you wish to make changes to your Data Availability statement, please describe these changes in your cover letter and we will update your Data Availability statement to reflect the information you provide.

6. We note that you have included the phrase “data not shown” in your manuscript. Unfortunately, this does not meet our data sharing requirements. PLOS does not permit references to inaccessible data. We require that authors provide all relevant data within the paper, Supporting Information files, or in an acceptable, public repository. Please add a citation to support this phrase or upload the data that corresponds with these findings to a stable repository (such as Figshare or Dryad) and provide and URLs, DOIs, or accession numbers that may be used to access these data. Or, if the data are not a core part of the research being presented in your study, we ask that you remove the phrase that refers to these data.

Additional Editor Comments:

Dear Dr. Gloria Levicán

Thank you for submitting your manuscript to Plos One.

I have completed my evaluation of your manuscript. The reviewers recommend reconsideration of your manuscript following major revision. I invite you to resubmit your manuscript after addressing the comments below. Moreover, you are advised to Improve the DPI of images.

When revising your manuscript, please consider all issues mentioned in the reviewers comments carefully: please outline every change made in response to their comments and provide suitable rebuttals for any comments not addressed. Please note that your revised submission may need to be re-reviewed.

[Note: HTML markup is below. Please do not edit.]

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Partly

Reviewer #2: Yes

**********

2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: N/A

Reviewer #2: Yes

**********

3. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

Reviewer #2: Yes

**********

4. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: Yes

Reviewer #2: Yes

**********

5. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: In this research, a comparative genomic analysis of the genes encoding classical, periplasmic and stress chaperones, and the protease systems was carried out. The research provides valuable information about the diversity and significance of proteostasis mechanisms in bacteria.

Major issues:

Many of the analyzed genomes do not belong even to moderately acidophilic microorganisms, while the authors state that these bacteria are extreme acidophiles. There are also incorrect statements about some autotrophic, mixotrophic, or heterotrophic bacteria. For instance, Mariprofundus ferroxydans is an obligate chemolithoautotroph that oxidizes reduced Fe from a variety of substrates at pH 5.5–7.2 (Singer et al., 2011) https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0025386 . Therefore, it is not an acidophile but a neutrophile and not a mixotroph but an autotroph.

Gallionella capsiferriformans is not an acidophile (grows at circumneutral pH) (Fabisch et al., 2015) https://onlinelibrary.wiley.com/doi/10.1111/gbi.12162 .

Metallibacterium scheffleri is acid-tolerant (optimum pH for growth is 5.5), it inhabits acidic and some neutral environments. It grows with casein as the only carbon and energy source. The strain DKE6(T) was not able to oxidize iron or thiosulfate. Iron reduction was detected. Therefore, it is not obligately autotrophic. https://www.microbiologyresearch.org/content/journal/ijsem/10.1099/ijs.0.042986-0#tab2

https://academic.oup.com/femsec/article/93/3/fix011/2962728 .

Sulfurimonas autotrophica is neutrophilic; it grows at 4·5–9·0 (optimum pH 6·5) https://www.microbiologyresearch.org/content/journal/ijsem/10.1099/ijs.0.02682-0

Alicyclobacillus acidocaldarius subsp. acidocaldarius Tc-4-1 and Alicyclobacillus tengchongensis are heterotrophic microorganisms, not autotrophic.

Acidimicrobium ferrooxidans oxidizes ferrous iron and, therefore, should not be characterized as heterotroph.

Please check relevant information about all bacteria used in this analysis and revise the text throughout the manuscript, including l. 274–275 and Table S1. If this research is focused on extreme acidophiles, only bacterial genomes of acidophilic microorganisms should be included. Otherwise, the concept and focus of this research should be changed.

Reviewer #2: It would be beneficial to begin the introduction with references to the influence of acidic pH, high concentrations of dissolved metals and high osmolarity on proteostasis Network in order to enhance the value of the study. This article can be included after some revisions.

1. The resolution of most Figures are too low to print for publisher.

2. Why did authors choose the 40 acidophilic bacteria mentioned in the manuscript as the research object, and what are the unique features of these bacteria.

3. The content is plentiful, but some part of the reference literatures is kind of obsolete (in 5 years). Key publications should be cited as completed as possible.

**********

6. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files.

If you choose “no”, your identity will remain anonymous but your review may still be made public.

Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy.

Reviewer #1: No

Reviewer #2: No

**********

[NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.]

While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. Please note that Supporting Information files do not need this step.

Attachments

Attachment

Submitted filename: Reviewer Attachments.docx

Comparative genomics of the proteostasis network in extreme acidophiles

PONE-D-23-16802R1

Dear Dr. Levicán,

We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements.

Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication.

An invoice for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. If you have any billing related questions, please contact our Author Billing department directly at authorbilling@plos.org.

If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they’ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org.

Kind regards,

RAJA AADIL HUSSAIN BHAT

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Reviewers' comments: