Structural insights into the RNA interaction with Yam bean Mosaic virus (coat protein) from Pachyrhizus erosus using bioinformatics approach

Varsha Acharya; R. Arutselvan; Kalidas Pati; Ajaya Kumar Rout; Budheswar Dehury; V. B. S. Chauhan; M. Nedunchezhiyan

doi:10.1371/journal.pone.0270534

Peer Review History

Original SubmissionFebruary 10, 2022
16 Mar 2022 Decision Letter - Rajarshi Gaur, Editor PONE-D-22-04164Structural insights into the RNA interaction with Yam bean Mosaic Virus (coat protein) from Pachyrhizus erosus using bioinformatics approachPLOS ONE Dear Dr. Pati, 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 30 2022 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. 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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. We note you have included a table to which you do not refer in the text of your manuscript. Please ensure that you refer to Table 2 in your text; if accepted, production will need this reference to link the reader to the Table. 3. Please include captions for your Supporting Information files at the end of your manuscript, and update any in-text citations to match accordingly. Please see our Supporting Information guidelines for more information: http://journals.plos.org/plosone/s/supporting-information. 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: No ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: N/A ****** 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: No ****** 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: Title; Structural insights into the RNA interaction with Yam bean Mosaic Virus (coat protein) from Pachyrhizus erosus using bioinformatics approach. Comments; 1. Authors have not provided the name of the template used for model generation in the abstract. 2. Authors have suggested to rewrite the results and conclusion part of the abstract based on findings. In addition, the authors have advised adding a brief description of methodology in the abstract. 3. Objective of the study should be clear at the end of the introduction section. 4. Authors have been advised to correct the spelling mistakes throughout the manuscript. For example “formatted”. 5. In the Introduction section the author should refer to the research paper and comment on recent in-silico techniques. It will be good information for the readers. I would like to recommend several papers, among many others, providing further explanation on this topic:PMID: 34717229 PMID: 33465692 PMID: 33749525 PMID: 29380245 PMID: 31933177 PMID: 32353478 PMID: 33993976 6. Provide citations for all the PDB IDs mentioned in the manuscript. 7. Authors should include studies with RNA on the predicted binding site. This could be done by docking and MD simulations. 8. MD simulations should be carried out to identify key structural changes and residues involved in protein-RNA interactions. 9. Clearly mention the aim and objective of the study in the last paragraph of the introduction section. 10. Including limitations of the study in the discussion and conclusions section. 11. Authors have not provided references regarding servers used in the studies. 12. Figure 6 is not visible authors have advised redrawing the figure. 13. Authors have advised to include more rigorous analysis and validate the findings by experimental/computational analyses. 18. Authors have not compared their findings with already present literature based on similar studies. 19. Overall, the manuscript is written in a very confusing and poor way. The writing needs substantial improvement. Need to edit the English language through a native speaker or by other means. In my view, the results obtained in this study are worthy for publication. The manuscript needs major essential revision before publication. I would like to overview the revised version of the manuscript before it accept for publication. Reviewer #2: In this manuscript titled “Structural insights into the RNA interaction with Yam bean Mosaic Virus (coat protein) from Pachyrhizus erosus using bioinformatics approach” authors have modeled the 3D structure of CP and merely predicted the amino acid that is involved in interaction with RNA. There is no experimental evidence for their finding. I recommend the authors plan a wet lab experiment to demonstrate the role of those amino acids in RNA binding. For instance, make mutation of those amino acid residues by SDM and test the ability of mutant proteins to bind RNA by EMSA, fluorescent spectroscopy, etc. The manuscript is not written well. Specific comments: Page 3, Line 15: “Chenopodium amanticolor, Nicotiana megalosiphon and Nicotiana benthamiana”. Scientific name should be italicized. Page 3, Line 80: “Sorensen” since there are more than one author in this study, you should mention as Sorensen et al., Page 3, Line 86: Similar to previous comment. Change “Damayanti” to ““Damayanti et al” Page 4, Line 88: “Afterward in……”. Not scientific. Rephrase this sentence. ****** 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: Yes:** PRABU GNANASEKARAN [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. https://doi.org/10.1371/journal.pone.0270534.r001
Revision 1
20 Apr 2022 Author Response Manuscript Number: PONE-D-22-04164 Point-to-point response to the Reviewers' comments We thank the editor for the positive evaluation of our paper, and the two reviewers for recognizing the merit of our work and for providing very valuable suggestions. As detailed below, we have addressed the Reviewers’ comments carefully and revised the manuscript accordingly. To facilitate the reviewing process, we have copied the Reviewers’ original comments, which are shown in black (italic font) and our responses are then shown in blue. Reviewer #1 Comments 1 Authors have not provided the name of the template used for model generation in the abstract. Authors Response The template used for the model generation is 5ODV. We have added the template name in the abstract section of the Ms. Comments 2 Authors have suggested to rewrite the results and conclusion part of the abstract based on findings. In addition, the authors have advised adding a brief description of methodology in the abstract. Authors Response As per the suggestion, the results, conclusion and methodology part has been revised accordingly in the abstract section of the Ms. Comments 3 Objective of the study should be clear at the end of the introduction section. Authors Response Thank you for your response. We have modified the introduction section as desired by you. Comments 4 Authors have been advised to correct the spelling mistakes throughout the manuscript. For example, “formatted”. Authors Response We have corrected our spelling mistakes throughout the manuscript. Comments 5 In the Introduction section the author should refer to the research paper and comment on recent in-silico techniques. It will be good information for the readers. I would like to recommend several papers, among many others, providing further explanation on this topic: PMID: 34717229 PMID: 33465692 PMID: 33749525 PMID: 29380245 PMID: 31933177 PMID: 32353478 PMID: 33993976 Authors Response Thank you for your valuable comments. These publications are highly useful regarding in silico techniques and we have also cited the same in the Ms accordingly. Comments 6 Provide citations for all the PDB IDs mentioned in the manuscript. Authors Response We have cited all PDB IDs in the Manuscript. Comments 7 Authors should include studies with RNA on the predicted binding site. This could be done by docking and MD simulations. Authors Response Thank you for your suggestion. We have performed an MD simulation of 50ns using Desmond with Optimized Potentials for Liquid Simulations (OPLS) 2005 force field. Comments 8 MD simulations should be carried out to identify key structural changes and residues involved in protein-RNA interactions. Authors Response As suggested, we performed an MD simulation to analyze the key structural changes and residues involved in protein-RNA interaction in the Ms. Comments 9 Clearly mention the aim and objective of the study in the last paragraph of the introduction section. Authors Response The aim and objective of the study have been rectified and explained properly in the introduction section of the Ms. Comments 10 Including limitations of the study in the discussion and conclusions section. Authors Response We have modified the discussion and conclusion section as per your suggestion. Comments 11 Authors have not provided references regarding servers used in the studies. Authors Response Thank you for your recommendation. We have cited some references in the Manuscript. Comments 12 Figure 6 is not visible authors have advised redrawing the figure. Authors Response We have revised figure 6 as per your suggestion. Comments 13 Authors have advised to include more rigorous analysis and validate the findings by experimental/computational analyses. Authors Response We have performed a molecular dynamics simulation to validate more findings in computational bioinformatics techniques. Comments 14 Authors have not compared their findings with already present literature based on similar studies. Authors Response We have revised the Manuscript with recent literature studies. Comments 15 Overall, the manuscript is written in a very confusing and poor way. The writing needs substantial improvement. Need to edit the English language through a native speaker or by other means. Authors Response We apologize for the inconvenience. We have revised the manuscript accordingly. We have used Grammarly software and corrected the spelling and grammatical errors present in the manuscript and rewritten the portion that was confusing for the reviewer. Reviewer #2 Comments 1 There is no experimental evidence for their finding. I recommend the authors plan a wet lab experiment to demonstrate the role of those amino acids in RNA binding. For instance, make mutation of those amino acid residues by SDM and test the ability of mutant proteins to bind RNA by EMSA, fluorescent spectroscopy, etc. Authors Response Thank you very much for your recommendation. We agree with the reviewer on the above remarks that, the findings from the computational study should be validated through an experimental approach. We are a small group of researchers working in computational biology without the support of a wet-lab experimental setup, therefore, we apologize that the suggested experiments by the esteemed reviewer could not be performed at present MS. However, we strongly believe that our computational findings will be helpful for the researchers working in this area to plan and undertake such studies involving site-directed mutagenesis, EMSA and fluorescent spectroscopy studies which will unravel the binding of RNA to the protein. To additionally, support our study, we have performed all-atoms MD simulation for 50 ns to analyze the structural changes and residues involved in protein-RNA interaction and stability of the complex through RMSD, RMSF, Rg and H-bond analysis (Please see in Fig. 7 of the Ms). Comment 2 The manuscript is not written well. Authors Response Thank you for your suggestion. We have revised the manuscript rigorously and rectified the grammatical mistakes throughout the manuscript. Specific comments: Comments 3 Page 3, Line 15: “Chenopodium amanticolor, Nicotiana megalosiphon and Nicotiana benthamiana”. Scientific name should be italicized. Authors Response We have corrected the scientific name in italics. Comments 4 Page 3, Line 80: “Sorensen” since there are more than one author in this study, you should mention as Sorensen et al., Authors Response We have revised the Sorensen as Sorensen et al., in the Ms. Comments 5 Page 3, Line 86: Similar to previous comment. Change “Damayanti” to ““Damayanti et al” Authors Response We have corrected the “Damayanti” to “Damayanti et al” in the introduction section. Comments 6 Page 4, Line 88: “Afterward in……”. Not scientific. Rephrase this sentence. Authors Response As per the reviewer's suggestion, we have rewritten the above line. Attachments Attachment Submitted filename: Response to Reviewer.doc https://doi.org/10.1371/journal.pone.0270534.r002
29 Apr 2022 Decision Letter - Rajarshi Gaur, Editor PONE-D-22-04164R1Structural insights into the RNA interaction with Yam bean Mosaic Virus (coat protein) from Pachyrhizus erosus using bioinformatics approachPLOS ONE Dear Dr. Pati, 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 Jun 13 2022 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, Rajarshi Gaur Academic Editor PLOS ONE [Note: HTML markup is below. Please do not edit.] 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 #2: (No Response) ******** 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 #2: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: I Don't Know Reviewer #2: N/A ****** 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 #2: Yes ****** 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 #2: Yes ****** 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: The authors have responded to all the concerns meticulously and improved the manuscript accordingly. The revised draft is improved significantly. I do not have further comments. Reviewer #2: Authors have addressed the comments partially. Still there is no strong evidence for their conclusion. I recommend authors to perform atleast few more computational analyses to support their conclusion. Specific comments: Still, there is no wet lab experimental evidence for their finding. But authors have performed MD simulation to analyze the structural changes and residues involved in protein-RNA interaction. However, I recommend the authors to add atleast few more computation analysis, such as, Generate simulation of mutant protein structure Determining the wildtype and mutant protein affinity for RNA by Haddock score calculation. Identify the pocket that binds to RNA, and the amino acid residues involved in the interaction in both wild-type and mutant protein. To perform these experiments, I suggest authors to cite and follow the following publications. Gnanasekaran, P., Gupta, N., Ponnusamy, K., and Chakraborty, S. (2021). Betasatellite encoded βC1 protein exhibits novel ATP hydrolysis activity that influences its DNA-binding activity and viral pathogenesis. Journal of Virology, 95 (20): e00475-21. Gnanasekaran, P., Ponnusamy, K., and Chakraborty, S. (2019) A geminivirus betasatellite encoded βC1 protein interacts with PsbP and subverts PsbP-mediated antiviral defense in plants. Molecular Plant Pathology, 20(7): 943-960. ****** 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: No Reviewer #2: Yes:** PRABU GNANASEKARAN [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. https://doi.org/10.1371/journal.pone.0270534.r003
Revision 2
4 Jun 2022 Author Response Manuscript Number: PONE-D-22-04164R2 Point-to-point response to the Reviewers' comments We thank the editor for the positive evaluation of our paper, and the two reviewers for recognizing the merit of our work and for providing very valuable suggestions. As detailed below, we have addressed the Reviewers’ comments carefully and revised the manuscript accordingly. To facilitate the reviewing process, we have copied the Reviewers’ original comments, which are shown in black (italic font) and our responses are then shown in blue. Reviewer #1 Comments The authors have responded to all the concerns meticulously and improved the manuscript accordingly.The revised draft is improved significantly. I do not have further comments. Authors Response Thank you for your possetive response. Reviewer #2 Comments 1 Generate simulation of mutant protein structure Authors Response Thank you very much for your recommendation. As per your suggestion, we have generated the mutant structure of R124A which plays important role in the interaction of YBMV_CP with RNA and maintained stable connection throughout the simulation. All the simulation analysis have been included in the MS. Comment 2 Determining the wildtype and mutant protein affinity for RNA by Haddock score calculation. Authors Response Thank you for your suggestion. We have revised the manuscript accordingly. The HADDOCK score for the wild type and mutant type have been presented in the manuscript. Comments 3 Identify the pocket that binds to RNA, and the amino acid residues involved in the interaction in both wild-type and mutant protein. Authors Response We have identified the pocket that binds to RNA, and the amino acid residues involved in the interaction in both wild-type and mutant type. Comments 4 To perform these experiments, I suggest authors to cite and follow the following publications. Gnanasekaran, P., Gupta, N., Ponnusamy, K., and Chakraborty, S. (2021). Betasatellite encoded βC1 protein exhibitsnovel ATP hydrolysis activity that influences its DNA-binding activity and viral pathogenesis. Journal of Virology, 95(20): e00475-21. Gnanasekaran, P., Ponnusamy, K., and Chakraborty, S. (2019) A geminivirus betasatellite encoded βC1 proteininteracts with PsbP and subverts PsbP-mediated antiviral defense in plants. Molecular Plant Pathology, 20(7): 943-960. Authors Response Thank you for your suggestion. We have cited the two references in the Manuscript. Attachments Attachment Submitted filename: Response to Reviewer.doc https://doi.org/10.1371/journal.pone.0270534.r004
12 Jun 2022 Decision Letter - Rajarshi Gaur, Editor Structural insights into the RNA interaction with Yam bean Mosaic Virus (coat protein) from Pachyrhizus erosus using bioinformatics approach PONE-D-22-04164R2 Dear Dr. Pati, 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, Rajarshi Gaur Academic Editor PLOS ONE 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 #2: All comments have been addressed ******** 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 #2: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: Yes ****** 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 #2: Yes ****** 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 #2: Yes ****** 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: (No Response) Reviewer #2: Authors have addressed all the comments. My recommendation is to accept the manuscript for publication. ****** 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: No Reviewer #2: Yes: PRABU GNANASEKARAN ******** https://doi.org/10.1371/journal.pone.0270534.r005
Formally Accepted
11 Jul 2022 Acceptance Letter - Rajarshi Gaur, Editor PONE-D-22-04164R2 Structural insights into the RNA interaction with Yam bean Mosaic Virus (coat protein) from Pachyrhizus erosus using bioinformatics approach Dear Dr. Pati: I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department. If your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. 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. If we can help with anything else, please email us at plosone@plos.org. Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staff on behalf of Professor Rajarshi Gaur Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0270534.r006

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