Peer Review History
| Original SubmissionFebruary 11, 2025 |
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Dear Dr. Zakataeva, 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. Authors are required to address all feedback provided by the reviewers, with particular emphasis on the need for revisions in the Introduction section. Additionally, any problematic aspects of the methodology must be rectified, along with the parameters selected for discussion. It is imperative to consider the statistical components, as this was frequently highlighted by the reviewers. Furthermore, considerations regarding the zymogram, which is crucial for the publication of the article, must also be duly acknowledged. Please submit your revised manuscript by Apr 17 2025 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.
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, Marcos Pileggi, 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 2. 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. 3. PLOS ONE now requires that authors provide the original uncropped and unadjusted images underlying all blot or gel results reported in a submission’s figures or Supporting Information files. This policy and the journal’s other requirements for blot/gel reporting and figure preparation are described in detail at https://journals.plos.org/plosone/s/figures#loc-blot-and-gel-reporting-requirements and https://journals.plos.org/plosone/s/figures#loc-preparing-figures-from-image-files. When you submit your revised manuscript, please ensure that your figures adhere fully to these guidelines and provide the original underlying images for all blot or gel data reported in your submission. See the following link for instructions on providing the original image data: https://journals.plos.org/plosone/s/figures#loc-original-images-for-blots-and-gels. In your cover letter, please note whether your blot/gel image data are in Supporting Information or posted at a public data repository, provide the repository URL if relevant, and provide specific details as to which raw blot/gel images, if any, are not available. Email us at plosone@plos.org if you have any questions. [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: Yes Reviewer #2: Yes ********** 2. Has the statistical analysis been performed appropriately and rigorously? -->?> Reviewer #1: I Don't Know Reviewer #2: No ********** 3. Have the authors made all data underlying the findings in their manuscript fully available??> The PLOS Data policy Reviewer #1: No Reviewer #2: Yes ********** 4. Is the manuscript presented in an intelligible fashion and written in standard English??> Reviewer #1: No Reviewer #2: No ********** Reviewer #1: The study provides a novel characterization of a glutamate dehydrogenase (GDH) from Pantoea ananatis, a bacterium with biotechnological relevance. The dual coenzyme specificity of GdhPa (NADH/NADPH in reductive amination and NAD+/NADP+ in oxidative deamination) is a rare feature among bacterial GDHs. Find my comments, -The manuscript is mostly clear but contains minor grammatical errors and awkward phrasing. -Introduction section should present importance of NAD(P) dependence for dehydrogenases. A comparison to other DHs in a table would strengthen this section. Here some references for review; "Cloning and expression heterologous alanine dehydrogenase genes: Investigation reductive amination potential of L-alanine dehydrogenases for green synthesis of alanine derivatives", Heliyon, 1(5), 2024, e26899. "Application of reductive amination by heterologously expressed Thermomicrobium roseum L-alanine dehydrogenase to synthesize L-alanine derivatives, Enzyme and Microbial Technology, 2023, 169, 110265. "NADP+ dependent formate dehydrogenase: A Review" Biocatalysis and Biotransformation, 2020, 39(4), 260-268. -The selection of buffers (MES, imidazole, Tris-HCl, CHES) is appropriate, but the rationale for using pH 6.0 for NADP+ and pH 9.5 for NAD+ in oxidative deamination should be explicitly discussed. -It would be helpful to compare kinetic parameters to a broader set of bacterial GDHs, emphasizing how GdhPa's properties differ functionally. - The mechanistic insights into dual coenzyme specificity could be explored further, possibly through structural analysis or computational modeling. tructural modeling of GdhPa using Alphafold2 or SWISS-MODEL would provide deeper insights into coenzyme binding and active site interactions. Here a reference for reviewing, "Structural insights into the NAD+-dependent formate dehydrogenase mechanism revealed from the NADH complex and the formate NAD+ ternary complex of the Chaetomium thermophilum enzyme" Structural Biology, 2020, 212(3),107657. -The statistical significance of differences should be clearly indicated (p-values, error bars clarification, etc.). Reviewer #2: An English language revision is required. The Introduction, as well as the literature, require improvement: mention of plant GDHs and their evolution must be included (see for reference: Kwinta, J., Bielawski, W. Glutamate dehydrogenase in higher plants. Acta Physiol Plant 20, 453–463 (1998). https://doi.org/10.1007/s11738-998-0033-1. Tercé-Laforgue et al. Resolving the role of plant glutamate dehydrogenase: II. Physiological characterization of plants overexpressing the two enzyme subunits individually or simultaneously. Plant Cell Physiol. 2013 Oct;54(10):1635-47. doi: 10.1093/pcp/pct108. Brambilla et al. Glutamate dehydrogenase in “Liverworld”—A study in selected species to explore a key enzyme of plant primary metabolism in Marchantiophyta. Physiologia Plantarum 2023, 175, doi: 10.1111/ppl.14071) Results: 1) statistical analysis and significance must be performed -and provided - for the enzyme activity results 2) a more detailed discussion about the conserved aminoacids in functionally critical positions must be provided 3) in 2025, no newly characterized GDHs can lack an in gel activity characterization, as zymogram is the only way to reveal and assess the distribution of GDH isoenzymes in their active form. This is my major point, and it's not questionable.... Please fix "Mechaelis constants" with "Mechaelis-Menten constant" Figure 4 and 5: please delete "additives" Figure S1: please provide a less slovenly image Figure S2: data are presented without standard deviation bars and statistically significance marks. Please provide a more scientific graph. Figure S3: standard deviation bars curiously seem too homogenous among each others.... My feeling is that bars do not represent the real deviation from means, as the statistical analysis is apparently lacking. Please provide the relative test applied and the significance Figure S5: in my opinion. it should be embedded in the main text Supporting Table S1: primer's names are quite weird, as normally they are not marked with + o - symbols rather than with F o Fw (for forward) and R o Rev (for Reverse) ********** 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. |
| Revision 1 |
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Dear Dr. Zakataeva, 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. Certain critical details, as indicated by the reviewers, must be addressed prior to the acceptance of the manuscript. Please submit your revised manuscript by Jul 20 2025 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.
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, Marcos Pileggi, Ph.D Academic Editor PLOS ONE Journal Requirements: Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice. [Note: HTML markup is below. Please do not edit.] Reviewers' comments: Reviewer's Responses to Questions Comments to the Author Reviewer #1: (No Response) Reviewer #2: (No Response) ********** 2. Is the manuscript technically sound, and do the data support the conclusions??> Reviewer #1: (No Response) Reviewer #2: Yes ********** 3. Has the statistical analysis been performed appropriately and rigorously? -->?> Reviewer #1: (No Response) Reviewer #2: Yes ********** 4. Have the authors made all data underlying the findings in their manuscript fully available??> The PLOS Data policy Reviewer #1: (No Response) Reviewer #2: No ********** 5. Is the manuscript presented in an intelligible fashion and written in standard English??> Reviewer #1: (No Response) Reviewer #2: Yes ********** Reviewer #1: (No Response) Reviewer #2: Overall, the Authors responded to the comments, and the manuscript has improved significantly as a result. However, they missed to address one of my major concerns. In fact, given the complexity of the functional role of GDH enzyme, which is still to be clarified, it is necessary that the authors provide at least a glimpse into its evolutionary features. That's why I suggested to improve the literature by mentioning thre of the most relevant and complete publications (Kwinta, J., Bielawski, W. Glutamate dehydrogenase in higher plants. Acta Physiol Plant 20, 453–463 (1998). https://doi.org/10.1007/s11738-998-0033-1. Tercé-Laforgue et al. Resolving the role of plant glutamate dehydrogenase: II. Physiological characterization of plants overexpressing the two enzyme subunits individually or simultaneously. Plant Cell Physiol. 2013 Oct;54(10):1635-47. doi: 10.1093/pcp/pct108. Brambilla et al. Glutamate dehydrogenase in “Liverworld”—A study in selected species to explore a key enzyme of plant primary metabolism in Marchantiophyta. Physiologia Plantarum 2023, 175, doi: 10.1111/ppl.14071). Despite that, Authors only add one of the suggestions, completely ignoring the sense of the comment itself. Thus, the introduction and the discussion about the conserved aminoacids in functionally critical positions are not adequately informative. ********** 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 |
| Revision 2 |
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Glutamate dehydrogenase from Pantoea ananatis: A new bacterial enzyme with dual coenzyme specificity PONE-D-25-07402R2 Dear Dr. Zakataeva, 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. If you have any questions relating to publication charges, 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, Marcos Pileggi, Ph.D Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: Reviewer's Responses to Questions Comments to the Author Reviewer #2: All comments have been addressed ********** 2. Is the manuscript technically sound, and do the data support the conclusions??> Reviewer #2: Yes ********** 3. Has the statistical analysis been performed appropriately and rigorously? -->?> Reviewer #2: Yes ********** 4. Have the authors made all data underlying the findings in their manuscript fully available??> The PLOS Data policy Reviewer #2: Yes ********** 5. Is the manuscript presented in an intelligible fashion and written in standard English??> Reviewer #2: Yes ********** Reviewer #2: (No Response) ********** 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 #2: No ********** |
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