https://orcid.org/0000-0003-1246-7823
Peer Review History
| Original SubmissionJuly 19, 2022 |
|---|
|
Dear Dr. Spriggs, Thank you very much for submitting your manuscript "Components of the LINC and NPC complexes coordinately target and translocate a virus into the nucleus to promote infection" for consideration at PLOS Pathogens. As with all papers reviewed by the journal, your manuscript was reviewed by members of the editorial board and by several independent reviewers. The reviewers appreciated the attention to an important topic. Based on the reviews, we are likely to accept this manuscript for publication, providing that you modify the manuscript according to the review recommendations. Please prepare and submit your revised manuscript within 30 days. If you anticipate any delay, please let us know the expected resubmission date by replying to this email. When you are ready to resubmit, please upload the following: [1] A letter containing a detailed list of your responses to all review comments, and a description of the changes you have made in the manuscript. Please note while forming your response, if your article is accepted, you may have the opportunity to make the peer review history publicly available. The record will include editor decision letters (with reviews) and your responses to reviewer comments. If eligible, we will contact you to opt in or out [2] Two versions of the revised manuscript: one with either highlights or tracked changes denoting where the text has been changed; the other a clean version (uploaded as the manuscript file). Important additional instructions are given below your reviewer comments. Thank you again for your submission to our journal. We hope that our editorial process has been constructive so far, and we welcome your feedback at any time. Please don't hesitate to contact us if you have any questions or comments. Sincerely, Walter J. Atwood Associate Editor PLOS Pathogens Karl Münger Section Editor PLOS Pathogens Kasturi Haldar Editor-in-Chief PLOS Pathogens orcid.org/0000-0001-5065-158X Michael Malim Editor-in-Chief PLOS Pathogens *********************** Reviewer Comments (if any, and for reference): Reviewer's Responses to Questions Part I - Summary Please use this section to discuss strengths/weaknesses of study, novelty/significance, general execution and scholarship. Reviewer #1: Spriggs et al. report the mechanism of nuclear translocation by SV40, the prototype polyomavirus (PyV), through engagement of nuclear membrane proteins, Nesprin-2 of LINC and NUP188 of the NPC. Additionally, this work demonstrates that virus disassembly steps occur during nuclear entry, and a subcomplex of viral genome and capsid proteins VP1 and VP3 cross the NPC to mediate delivery of the viral genome to the nucleus. This work builds upon previous findings that SV40 PyV is delivered to the nuclear envelope, possibly by a dynein-BICD2 complex. Overall, the findings in this paper significantly advance the field of viral entry and trafficking, the experiments are elegantly designed, the data are compelling, and the paper is well written. Reviewer #2: This excellent paper by Spriggs et al. investigates the biology of SV40 nuclear import, identifying and mapping a novel interaction between SV40 and the motor binding domain of Nesprin-2 for Nup188-dependent nuclear import of VP3/genome. These aspects of SV40 (and polyomavirus) biology were not well defined and using coIPs, MS/proteomics, microscopy, and some customized novel assays, this paper does an excellent job to identify new important interactions that illuminate this area of the SV40 life cycle. The data are very sound and well controlled, the science is solid, and the paper is very well written. Only a few minor concerns are outlined below. ********** Part II – Major Issues: Key Experiments Required for Acceptance Please use this section to detail the key new experiments or modifications of existing experiments that should be absolutely required to validate study conclusions. Generally, there should be no more than 3 such required experiments or major modifications for a "Major Revision" recommendation. If more than 3 experiments are necessary to validate the study conclusions, then you are encouraged to recommend "Reject". Reviewer #1: No major issues Reviewer #2: No major issues. Overall a fantastic paper that advances the field of nuclear entry of viruses. ********** Part III – Minor Issues: Editorial and Data Presentation Modifications Please use this section for editorial suggestions as well as relatively minor modifications of existing data that would enhance clarity. Reviewer #1: - Abstract, Line 26: change to “for most DNA viruses…” - Fig 2 – Is the partial disassembly of the virus by treatment w/ DTT/EGTA established in the literature? Can you provide a reference on line 167? - Figure 2 legend – D is not described. Maybe C on line 491 should be D? Also, the short and long exposure are not described. - The PCR analysis performed in Figure 2 is not described in the M&Ms and should be included. - It’s unclear why Fig. 2E has significantly reduced FLAG-SR51-56 KASH in comparison to the deltaAD or in D? Please provide an explanation or consider adding quantitation of several replicates. - Is it possible that the non-infectious VP1 particles that enter the cell are intentional by-products of replication that have a pro-viral effect on SV40 infection or are the empty particles an effect of using high MOIs in these studies? - Please include more detail on how the images and W blots were quantified in Fiji. - Figure 5G – The input Nup188 protein levels appear to be reduced in Nesprin-2-treated cells. Given that Nup188 interacts with Nesprin-2, is KD of Nesprin-2 reducing Nup188? Can this be quantified to demonstrate if input is not reduced or approached in another way possibly with an additional control KD such as RanBP2 KD? An explanation could be provided in the Discussion. Reviewer #2: Line 280/281. If VP1 enters the nucleus independently of Nesprin-2 and VP3 (as shown in Figure 4D) then why is it described as in complex with VP3/genome? Seems it wouldn’t be in complex right? This was confusing. The disassembly data in 5G- genome was detected but what’s responsible for the change in mobility through the sucrose gradient? Dissociation of VP2 or VP3 from genome? Loss of VP1 pentamers? Loss of histones? Although some blots could clarify the speculation/insight provided in the discussion, this is merely a suggestion to potentially improve the paper- I would not consider this a mandatory requirement for acceptance as it can be addressed in future studies. Nup188 silencing resulted in the strongest inhibition of SV40 infection, but other Nups were close. Do these coIP with the Nestrin-2/SV40 comlex too? Does Nestrin-2 silencing affect the interaction between these Nups and SV40? Again, this could be explored in future work. What component of SV40 actually binds Nestrin-2? VP3? VP1? If this could be easily clarified it would strengthen the paper, if not then can be addressed in future work. The final model figure could be improved to show more details concerning VP1, VP2, VP3, etc. What is the teal aura around the viral genome represent? VP1 pentamers as a capsid? The EdU-labeling methodology of SV40 needs to be better detailed in Materials and Methods. What concentration of EdU was used, when was it added post-infection, etc. ********** 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: Samuel K. Campos Figure 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. 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 us at figures@plos.org. Data Requirements: Please note that, as a condition of publication, PLOS' data policy requires that you make available all data used to draw the conclusions outlined in your manuscript. Data must be deposited in an appropriate repository, included within the body of the manuscript, or uploaded as supporting information. This includes all numerical values that were used to generate graphs, histograms etc.. For an example see here: http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001908#s5. Reproducibility: To enhance the reproducibility of your results, we recommend that you deposit your laboratory protocols in protocols.io, where a protocol can be assigned its own identifier (DOI) such that it can be cited independently in the future. Additionally, PLOS ONE offers an option to publish peer-reviewed clinical study protocols. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols References: 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. |
| Revision 1 |
|
Dear Dr. Spriggs, We are pleased to inform you that your manuscript 'Components of the LINC and NPC complexes coordinately target and translocate a virus into the nucleus to promote infection' has been provisionally accepted for publication in PLOS Pathogens. Before your manuscript can be formally accepted you will need to complete some formatting changes, which you will receive in a follow up email. A member of our team will be in touch with a set of requests. Please note that your manuscript will not be scheduled for publication until you have made the required changes, so a swift response is appreciated. IMPORTANT: The editorial review process is now complete. PLOS will only permit corrections to spelling, formatting or significant scientific errors from this point onwards. Requests for major changes, or any which affect the scientific understanding of your work, will cause delays to the publication date of your manuscript. Should you, your institution's press office or the journal office choose to press release your paper, you will automatically be opted out of early publication. We ask that you notify us now if you or your institution is planning to press release the article. All press must be co-ordinated with PLOS. Thank you again for supporting Open Access publishing; we are looking forward to publishing your work in PLOS Pathogens. Best regards, Walter J. Atwood Associate Editor PLOS Pathogens Karl Münger Section Editor PLOS Pathogens Kasturi Haldar Editor-in-Chief PLOS Pathogens orcid.org/0000-0001-5065-158X Michael Malim Editor-in-Chief PLOS Pathogens *********************************************************** Reviewer Comments (if any, and for reference): |
| Formally Accepted |
|
Dear Dr. Spriggs, We are delighted to inform you that your manuscript, "Components of the LINC and NPC complexes coordinately target and translocate a virus into the nucleus to promote infection," has been formally accepted for publication in PLOS Pathogens. We have now passed your article onto the PLOS Production Department who will complete the rest of the pre-publication process. All authors will receive a confirmation email upon publication. The corresponding author will soon be receiving a typeset proof for review, to ensure errors have not been introduced during production. Please review the PDF proof of your manuscript carefully, as this is the last chance to correct any scientific or type-setting errors. Please note that major changes, or those which affect the scientific understanding of the work, will likely cause delays to the publication date of your manuscript. Note: Proofs for Front Matter articles (Pearls, Reviews, Opinions, etc...) are generated on a different schedule and may not be made available as quickly. Soon after your final files are uploaded, the early version of your manuscript, if you opted to have an early version of your article, will be published online. The date of the early version will be your article's publication date. The final article will be published to the same URL, and all versions of the paper will be accessible to readers. Thank you again for supporting open-access publishing; we are looking forward to publishing your work in PLOS Pathogens. Best regards, Kasturi Haldar Editor-in-Chief PLOS Pathogens orcid.org/0000-0001-5065-158X Michael Malim Editor-in-Chief PLOS Pathogens |
Open letter on the publication of peer review reports
PLOS recognizes the benefits of transparency in the peer review process. Therefore, we enable the publication of all of the content of peer review and author responses alongside final, published articles. Reviewers remain anonymous, unless they choose to reveal their names.
We encourage other journals to join us in this initiative. We hope that our action inspires the community, including researchers, research funders, and research institutions, to recognize the benefits of published peer review reports for all parts of the research system.
Learn more at ASAPbio .