Dear Dr. Long,

Please submit your revised manuscript by Jan 10 2026 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.

• 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,

Katherine A. Borkovich, Ph.D.

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. Please include your tables as part of your main manuscript and remove the individual files. Please note that supplementary tables (should remain/ be uploaded) as separate "supporting information" files.’

3. PLOS requires an ORCID iD for the corresponding author in Editorial Manager on papers submitted after December 6th, 2016. Please ensure that you have an ORCID iD and that it is validated in Editorial Manager. To do this, go to ‘Update my Information’ (in the upper left-hand corner of the main menu), and click on the Fetch/Validate link next to the ORCID field. This will take you to the ORCID site and allow you to create a new iD or authenticate a pre-existing iD in Editorial Manager.

4. Thank you for stating the following financial disclosure:

United Kingdom Medical Research Council (MRC Doctoral Training Program Grant G82144A).

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.

5. Thank you for stating the following in the Acknowledgments Section of your manuscript:

We thank Dr Howard G Wildman from Microbial Management Systems Australia for his advice on yeast isolation during the early stages of this work. This work was supported by the United Kingdom Medical Research Council (MRC Doctoral Training Program Grant G82144A).

We note that you have provided funding information that is not currently declared in your Funding Statement. However, funding information should not appear in the Acknowledgments section or other areas of your manuscript. We will only publish funding information present in the Funding Statement section of the online submission form.

Please remove any funding-related text from the manuscript and let us know how you would like to update your Funding Statement. Currently, your Funding Statement reads as follows:

United Kingdom Medical Research Council (MRC Doctoral Training Program Grant G82144A).

Please include your amended statements within your cover letter; we will change the online submission form on your behalf.

6. We note that your Data Availability Statement is currently as follows: All relevant data are within the manuscript and its Supporting Information files.

Please confirm at this time whether or not your submission contains all raw data required to replicate the results of your study. Authors must share the “minimal data set” for their submission. PLOS defines the minimal data set to consist of the data required to replicate all study findings reported in the article, as well as related metadata and methods (https://journals.plos.org/plosone/s/data-availability#loc-minimal-data-set-definition).

For example, authors should submit the following data:

- The values behind the means, standard deviations and other measures reported;

- The values used to build graphs;

- The points extracted from images for analysis.

Authors do not need to submit their entire data set if only a portion of the data was used in the reported study.

If your submission does not contain these data, please either upload them as Supporting Information files or deposit them to a stable, public repository and provide us with the relevant URLs, DOIs, or accession numbers. For a list of recommended repositories, please see https://journals.plos.org/plosone/s/recommended-repositories.

If there are ethical or legal restrictions on sharing a de-identified data set, please explain them in detail (e.g., data contain potentially sensitive information, data are owned by a third-party organization, etc.) and who has imposed them (e.g., an ethics committee). Please also provide contact information for a data access committee, ethics committee, or other institutional body to which data requests may be sent. If data are owned by a third party, please indicate how others may request data access.

7. 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.

8. If the reviewer comments include a recommendation to cite specific previously published works, please review and evaluate these publications to determine whether they are relevant and should be cited. There is no requirement to cite these works unless the editor has indicated otherwise.

[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?

Reviewer #1: Partly

Reviewer #2: Partly

**********

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

Reviewer #1: Yes

Reviewer #2: Yes

**********

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

The PLOS Data policy

Reviewer #1: Yes

Reviewer #2: Yes

**********

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

Reviewer #1: Yes

Reviewer #2: No

**********

Reviewer #1: The manuscript by Gaseca et al. presents a proteomic analysis of UV-B–induced stress responses in a UV-tolerant Sporobolomyces strain and generates a dataset that is potentially useful, albeit essentially descriptive in nature. In its current form, however, the work remains largely correlative and falls well short of supporting the very strong causal and evolutionary claims made in the title and abstract, particularly the assertion that an Nrf2/Yap1-like bZIP protein “drives” the UV-induced oxidative stress response and exemplifies an evolutionarily conserved mechanism. The experimental design (limited biological replication, lack of direct ROS or oxidative-damage measurements) and the purely observational nature of the proteomic analysis do not allow the authors to move beyond identifying a candidate regulator and associated protein signatures; they certainly do not justify mechanistic language implying necessity, sufficiency, or functional conservation with the animal Nrf2 pathway. Substantial, data-driven revision is therefore required—either by adding targeted functional validation of the candidate bZIP factor (e.g. genetic perturbation, localisation and downstream target analyses) and strengthening the quantitative proteomic/statistical framework, or by significantly toning down the rhetoric throughout and explicitly reframing the manuscript as a descriptive proteomic survey of UV-B responses.

In addition to these substantive issues, the manuscript also contains several basic and rather elementary formatting, nomenclature and focus problems that further detract from its presentation. For example, (1) at line 39, the qualifier “sp.” is incorrectly italicised, whereas standard taxonomic convention requires genus and species names to be in italics but rank qualifiers such as sp./spp. to remain in roman type; (2) the layout of several sections (e.g. lines 183–188, 210–220, 299–330, 357–366, 414–424) is highly unconventional for a scientific article, reading more like bullet-point notes than continuous academic prose; (3) multiple places in the manuscript (e.g. lines 654–657; 764, 771, 798, 815, 863, 871, 872, 875) still display unresolved Word cross-reference errors such as “Error! Reference source not found.”, indicating that the citation and cross-referencing system has not been properly checked prior to submission; (4) the quality, numbering and labelling of the final figures and tables are far below publication standard and severely compromise readability—for instance, only “Figure 1” and “Figure 11” appear, “Figure 1” is reused several times without clear distinction, and one figure is even labelled “Figure Error! No text of specified style in document.”; (5) with respect to species names, Rhodosporidium toruloides has been reclassified as Rhodotorula toruloides and the genus Rhodosporidium is no longer in current use, so the entire manuscript should be carefully checked and updated to reflect the current, accepted taxonomy; (6) an inordinate amount of space is devoted to animal systems and to Saccharomyces cerevisiae—especially the latter—far beyond what would be reasonable as background, whereas the stated subject of the manuscript is UV stress responses in a Sporobolomyces yeast, so the balance of the Introduction and Discussion should be substantially adjusted so that the narrative is clearly centred on UV-B–induced responses and on the Sporobolomyces system actually investigated here; and (7) the use of italics for biological and technical terms is often incorrect or inconsistent—for instance, Latin-derived expressions such as ex vivo (and similarly in vivo, in vitro, in situ, etc.) should consistently appear in italics, while gene/protein symbols and other specialist terminology should follow standard formatting conventions. These issues collectively suggest that the manuscript requires much more careful technical editing and proofreading before it can be considered for publication.

Taken together, while the overall topic and dataset are, in principle, suitable for publication, this can only be contemplated after a thorough major revision—potentially including substantial rewriting of key sections—that carefully and systematically addresses the methodological, interpretative and presentation issues outlined above.

Reviewer #2: The manuscript entitled “An Nrf2/Yap1-like bZIP protein drives UV-induced oxidative stress response in a Sporobolomyces yeast with evolutionary conservation” presents MudPIT-based proteomic data describing global protein-level changes in Sporobolomyces following UV-B irradiation. While the topic is of interest and the dataset itself has potential value, the manuscript in its current form is excessively long and the depth of analysis does not justify a full research article. The work is essentially a descriptive proteomics study, yet the manuscript extends far beyond what is required for a concise presentation of these results. I strongly recommend substantial shortening and restructuring. With a more focused narrative and clearer figures, the work may be appropriate for publication as a short communication, but in its current form it does not meet the expectations for a full research paper.

Major Comments

• Manuscript length and structure

The manuscript is disproportionately long in all sections. The Results section (8 pages) is followed by an extremely lengthy Discussion (over 30 pages), making the manuscript difficult to read. Much of the Discussion resembles a review article rather than an interpretation of the presented data. The Discussion should be rewritten to focus on the authors’ own findings and reduced to approximately 3 pages.

• Introduction

The Introduction is overly detailed. This makes it difficult for the reader to identify the key context needed to understand the study. The authors should significantly shorten the Introduction and ensure that only relevant background information is retained.

• Results

Each subsection of the Results should begin with a short introductory sentence explaining the purpose of the analysis.

All figures in the manuscript are labeled as “Figure 1,” which needs correction.

In Figure 1, the abbreviation “BY” is used but never defined.

The description of MudPIT results is unnecessarily fragmented, with proteins divided into multiple categories, each discussed in separate paragraphs. This part should be condensed substantially to highlight the main trends without excessive repetition.

• Discussion

The Discussion requires a major rewrite. Concerns include:

Excessive length: Over 30 pages is not acceptable for this type of dataset; it should be condensed to a maximum of 3 pages.

Lack of focus: Much of the text provides general literature review rather than discussing the authors’ specific findings.

Methodology included in Discussion (L662–668): Methods should not appear in this section.

Terminology correction: At L676, the term “ROS” should replace “RS.”

Overly long, difficult-to-read sentences: For example, the sentence across lines 674–678 should be rewritten for clarity.

Scope of conclusions: In lines 699–704, conclusions are presented as if they apply only to yeast, although similar UV-B-induced antioxidant responses occur in human cells. The authors should consider whether the described mechanisms are more general.

Chaotic section on stress responses: The discussion of toxic metal responses lacks structure and does not integrate well with the main argument. This section should be reorganized.

Yap transcription factor section (L739–758): The discussion of Yap factors in S. cerevisiae is too extensive, especially given that no homologs were found in Sporobolomyces. This information should be condensed or removed.

Minor Comments

Ensure all abbreviations are defined upon first use.

Carefully check formatting, particularly consistent figure numbering.

Reevaluate which background elements are essential and remove redundant text.

Summary

The authors have generated an interesting proteomic dataset; however, the manuscript requires substantial shortening, restructuring, and improved focus in all major sections. The Discussion must be rewritten to directly address and interpret the results rather than providing an extensive literature review. With these major revisions, the manuscript may become suitable for publication as a shorter contribution.

**********

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.]

To ensure your figures meet our technical requirements, please review our figure guidelines: https://journals.plos.org/plosone/s/figures

You may also use PLOS’s free figure tool, NAAS, to help you prepare publication quality figures: https://journals.plos.org/plosone/s/figures#loc-tools-for-figure-preparation.

NAAS will assess whether your figures meet our technical requirements by comparing each figure against our figure specifications.

Proteomic profiling of a Sporobolomyces yeast reveals global responses to UV-B–induced oxidative stress

PONE-D-25-49810R1

Dear Dr. Long,

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 will be generated when your article is formally accepted. Please note, if your institution has a publishing partnership with PLOS and your article meets the relevant criteria, all or part of your publication costs will be covered. Please make sure your user information is up-to-date by logging into Editorial Manager at Editorial Manager®  and clicking the ‘Update My Information' link at the top of the page. For questions related to billing, please contact billing support .

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,

Katherine A. Borkovich, Ph.D.

Academic Editor

PLOS One

Additional Editor Comments (optional):

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

Reviewer #1: All comments have been addressed

Reviewer #2: All comments have been addressed

**********

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

Reviewer #1: Yes

Reviewer #2: Yes

**********

3. Has the statistical analysis been performed appropriately and rigorously? -->?>

Reviewer #1: I Don't Know

Reviewer #2: Yes

**********

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

The PLOS Data policy

Reviewer #1: Yes

Reviewer #2: Yes

**********

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

Reviewer #1: Yes

Reviewer #2: Yes

**********

Reviewer #1: The authors have satisfactorily addressed the major concerns; I recommend acceptance after minor final formatting adjustments are completed.

Reviewer #2: The authors have addressed all my comments and revised the manuscript in accordance with the suggestions of both reviewers.

**********

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

**********