PONE-D-23-28472Antimicrobial Peptides from Solanaceae Plants: Analyzing Their Effect on Phytopathogenic Fungus Rhizoctonia solaniPLOS ONE

Dear Dr. Islam,

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.

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Please review the comments provided by the reviewers and address their feedback. Additionally, we recommend seeking a professional English editor to ensure the manuscript is free of language errors. Once these steps are taken, kindly submit your revised manuscript.

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Please submit your revised manuscript by Nov 18 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.

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We look forward to receiving your revised manuscript.

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Kamal Ahmad Qureshi, PhD

Academic Editor

PLOS ONE

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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: Yes

Reviewer #2: Yes

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

Reviewer #1: Yes

Reviewer #2: Yes

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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

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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: No

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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: The authors of a study have suggested that peptides derived from Solanaceous plants like Solanum tuberosum and Capsicum annum have antifungal properties against R. solani, a fungal pathogen. They have also performed molecular docking studies of these peptides with pathogenicity-related proteins of R. solani. The study did not present any new scientific hypothesis or concept. Therefore, my comments are:

There are some suggestions for improvement. Firstly, the abstract needs to be shortened to only present the silent findings of the research outcome. Secondly, performing q-PCR of blight resistance and sensitivity-related genes from treated and non-treated samples with peptides would validate the findings.

In the material method section, it is suggested to provide the full genus name as the first time appearing in the manuscript for C. annum and S. tuberosum. Additionally, it is unclear if the author quantified the level of peptide and identified any. The extraction buffer used for peptide extraction should be mentioned too.

Barashkova and Rogozhin, 2020 is a review article, so it should be clarified if the author made any modifications or standardized the protocol. Moreover, it is unclear how the author deduced that the extract contains peptides that were used for docking.

Lastly, the author needs to justify why they have selected prp Histone demethylase. The paper needs to be reorganized and proofread before submission.

Reviewer #2: The present article entitled "Antimicrobial Peptides from Solanaceae Plants: Analyzing Their Effect on

Phytopathogenic Fungus Rhizoctonia solani" based on a good theme and authors have briefly discussed all the point. The presenation of the article is also fine.

How ever I have only suggestion to improve the English of the article

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Reviewer #1: Yes: Prashant Kumar Singh

Reviewer #2: No

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PONE-D-23-28472R1Antimicrobial Peptides from Solanaceae Plants: Analyzing Their Effect on Phytopathogenic Fungus Rhizoctonia solaniPLOS ONE

Dear Dr. Islam,

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 Apr 25 2024 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,

Kamal Ahmad Qureshi, PhD

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.

Additional Editor Comments:

Note: Kindly address the comments of our respected reviewers. 

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation.

Reviewer #1: All comments have been addressed

Reviewer #3: (No Response)

Reviewer #4: All comments have been addressed

Reviewer #5: All comments have been addressed

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2. 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: Yes

Reviewer #3: (No Response)

Reviewer #4: No

Reviewer #5: Partly

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

Reviewer #1: Yes

Reviewer #3: (No Response)

Reviewer #4: Yes

Reviewer #5: N/A

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4. 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 #3: (No Response)

Reviewer #4: Yes

Reviewer #5: Yes

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5. 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 #3: (No Response)

Reviewer #4: No

Reviewer #5: Yes

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6. 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: Authors have resolved the all my concern related to MS. Therefore, my decision to accept the ms for publication.

Reviewer #3: The manuscript is of wrathful consideration for plant scientists. This is based upon effective study Antimicrobial Peptides from Solanaceae Plants: Analyzing, Their Effect on Phytopathogenic Fungus Rhizoctonia solan in that region. The write-up of whole manuscript is up to mark. English quality is acceptable but minor revision needed. However, there are some suggestions that need to be incorporated before final acceptance as elaborated below:

- Title of the manuscript should be changed.

- The Abstract needs few details about materials of the experiments.

- Please note the opening paragraph of the introduction could provide stronger context to the paper, and, similarly, the findings at the end could potentially be richer.

- At the end of Introduction section, there should be clear hypothesis and objectives of the designed study.

- Statistical designs and data analysis confusing. It needs to present in a proper way

- Results presentations should be revised profoundly.

- I suggest that the author should provide more justification for your study (specifically, you should expand upon the knowledge gap in the abstract, introduction, and all other sections being filled) which should be improved upon before Acceptance.

- The discussion need to revised and need to make it more focused based on results.

Reviewer #4: (No Response)

Reviewer #5: Reviewer’s comment

The manuscript is written on potential antimicrobial peptides for the control of Rhizoctonia solani, causing rice sheath blight. Corrections are suggested below.

In abstract: A statement need to be included the confirmation of presence of peptides in the extracts.

In materials and method, et al., is written in italics. Should be same throughout the manuscript. The field details (name, district, latitude, longitude etc.) under source of inoculum should be mentioned. Space should be given between 5 mm. 2.3 and 2.4 should be merged. Hour should be written as h. There should be space between ° and C.

How do you know the extract is peptide rich? Include suitable references indicating peptide extraction protocol. Otherwise, characterization needs to be done.

In-vitro should be in italics.

2.11 Once Rhizoctonia solani written in abstract, no need to mention complete name, only write R. solani should be written throughout the manuscript.

What are the names of the peptides present in the peptide rich extract? How do you prepare their structures? Mention the names and structures if someone has already been identified them previously from the plants taken.

2.12. Molecular dynamics studies and MM-PBSA calculations section is very elaborative. It should be written concisely. Use references and avoid detail process.

For statistical analysis, atleast five test concentrations should be taken along with positive and negative control with three or more replications.

What was the positive control. Please mention the name and data in the table 1 and 2.

Table 4. Mention the source (reference from where the sequences of the peptides retrieved). The names of enzymes in Table 4 should be properly written. Write the unit of binding energy (kcal).

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7. 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: Yes: PRASHANT KUMAR Singh

Reviewer #3: No

Reviewer #4: No

Reviewer #5: No

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[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.

In-vitro and In-silico Investigation of Effects of Antimicrobial Peptides from Solanaceae Plants on Rice Sheath Blight Pathogen

PONE-D-23-28472R2

Dear Dr. %Tofazzal Islam%,

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.

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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,

Kamal Ahmad Qureshi, PhD

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation.

Reviewer #1: All comments have been addressed

Reviewer #5: All comments have been addressed

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2. 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: Yes

Reviewer #5: Yes

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

Reviewer #1: I Don't Know

Reviewer #5: N/A

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4. 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 #5: (No Response)

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5. 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 #5: Yes

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6. 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: Authors have already complied my comments and concerns raised. Hence MS is in shape and can be accepted to plos one

Reviewer #5: Since the suggested correction have been incorporated in the revised manuscript thus, the manuscript may be accepted for publication.

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7. 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: Yes: Prashant Kumar Singh

Reviewer #5: No

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