Dear Dr Hamel,

Thank you for submitting the revision of your Review Commons manuscript entitled "The connecting cilium inner scaffold provides a structural foundation that protects against retinal degeneration" for consideration as a Research Article by PLOS Biology.

Your manuscript has now been evaluated by the PLOS Biology editorial staff as well as by an academic editor with relevant expertise and I am writing to let you know that we would like to send the revision back to the original reviewers. However, we need you first to complete your submission by providing the metadata that is required for full assessment. To this end, please login to Editorial Manager where you will find the paper in the 'Submissions Needing Revisions' folder on your homepage. Please click 'Revise Submission' from the Action Links and complete all additional questions in the submission questionnaire.

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Kind regards,

Ines

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Ines Alvarez-Garcia, PhD

Senior Editor

PLOS Biology

ialvarez-garcia@plos.org

Dear Dr Hamel,

Thank you for submitting your revised Research Article entitled "The connecting cilium inner scaffold provides a structural foundation that protects against retinal degeneration" via Review Commons for publication in PLOS Biology. Thank you also for your patience as we completed our editorial process, and please accept my apologies for the delay in providing you with our decision. I have now obtained advice from the three original reviewers and have discussed their comments with the Academic Editor. 

Based on the reviews (attached below), we will probably accept this manuscript for publication, provided you satisfactorily address the remaining minor points raised by the reviewers. Please also make sure to address the data and other policy-related requests stated below my signature.

As you address these items, please take this last chance to 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 If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references.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 cover letter that accompanies your revised manuscript.

We expect to receive your revised manuscript within two weeks.

To submit your revision, please go to https://www.editorialmanager.com/pbiology/ and log in as an Author. Click the link labelled 'Submissions Needing Revision' to find your submission record. Your revised submission must include the following:

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https://journals.plos.org/plosbiology/s/supporting-information  

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Please do not hesitate to contact me should you have any questions.

Sincerely,

Ines

--

Ines Alvarez-Garcia, PhD,

Senior Editor

PLOS Biology

ialvarez-garcia@plos.org

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DATA POLICY: IMPORTANT - PLEASE READ

You may be aware of the PLOS Data Policy, which requires that all data be made available without restriction: http://journals.plos.org/plosbiology/s/data-availability. For more information, please also see this editorial: http://dx.doi.org/10.1371/journal.pbio.1001797 

Note that we do not require all raw data. Rather, we ask that all individual quantitative observations that underlie the data summarized in the figures and results of your paper be made available in one of the following forms:

1) Supplementary files (e.g., excel). Please ensure that all data files are uploaded as 'Supporting Information' and are invariably referred to (in the manuscript, figure legends, and the Description field when uploading your files) using the following format verbatim: S1 Data, S2 Data, etc. Multiple panels of a single or even several figures can be included as multiple sheets in one excel file that is saved using exactly the following convention: S1_Data.xlsx (using an underscore).

2) Deposition in a publicly available repository. Please also provide the accession code or a reviewer link so that we may view your data before publication. 

Regardless of the method selected, please ensure that you provide the individual numerical values that underlie the summary data displayed in the following figure panels as they are essential for readers to assess your analysis and to reproduce it:

Fig. 1J; Fig. 2E-K; Fig. 3B, D, F, G; Fig. 4E-I, L; Fig. S1D, E, F; Fig. S2C, D; Fig. S4B, D; Fig. S5A, B; Fig. S7C and Fig. S8B-D

NOTE: the numerical data provided should include all replicates AND the way in which the plotted mean and errors were derived (it should not present only the mean/average values).

Please also ensure that figure legends in your manuscript include information on WHERE THE UNDERLYDING DATA CAN BE FOUND, and ensure your supplemental data file/s has a legend.

Please ensure that your Data Statement in the submission system accurately describes where your data can be found.

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BLURB

Please also provide a blurb which (if accepted) will be included in our weekly and monthly Electronic Table of Contents, sent out to readers of PLOS Biology, and may be used to promote your article in social media. The blurb should be about 30-40 words long and is subject to editorial changes. It should, without exaggeration, entice people to read your manuscript. It should not be redundant with the title and should not contain acronyms or abbreviations. For examples, view our author guidelines: https://journals.plos.org/plosbiology/s/revising-your-manuscript#loc-blurb

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Reviewers' comments

Rev. 1: Michael Housset and Michel Cayouette

The authors have addressed the major points that were raised in the initial review and their answers/additional data improve the manuscript. This is a very nice study with beautiful and convincing data that will be of great interest to the field. However, one of the authors' responses is debatable:

On page 17 of the revised manuscript, the authors corrected the reference of the Cep290 mutant to support their point of a potential independence between the Y-link structure and the CC-inner scaffold: "Consistently, Rachel and colleagues showed that Cep290ko/ko photoreceptors still possess the CC-inner scaffold, confirming the independence of these two structures".

In their paper, Rachel and colleagues show that connecting cilia fail to dock at the inner segment membrane in photoreceptors of Cep290ko/ko mice at P14 (Figure 4), but they also show that a 9+0 microtubule ring still assembles. As Rachel et al. did not stain for proteins specific of the CC-Inner segment (which was not known at the time) and considering the suboptimal resolution of their en-face EM sections, this data cannot be used to conclude about the presence or absence of a CC-inner scaffold in Cep290 KO mice. Additionally, in contrast to the Rachel et al study, nascent CC were shown to form in Cep290 KO photoreceptors at P10 by Potter and colleagues (2021). In this study, centrin was shown to decorate the nascent CC of Cep290ko/ko photoreceptors (Potter et al, 2021, Figure 6h).

Thus, the authors can only speculate on the interdependence of the Y-link and CC-inner segment scaffold as their presence has not been carefully investigated in Cep290 KO photoreceptors and should modify the text to that effect.

Minor comment on the revised manuscript:

Page 17 "While we found LCA5 mostly enriched at the bulge region, we also found some weak localization that might explain the reported interaction between LCA5 and FAM161A". Which localization are you referring to? The CC-inner scaffold? This is not clear.

Congratulations on this beautiful work.

Rev. 2:

The authors addressed all the points raised by this reviewer. The manuscript was satisfactory revised. This reviewer agrees with publication of this manuscript for PLOS Biology.

Rev. 3:

The authors have adequately addressed all of my previous comments submitted to Review Commons, both textually and experimentally, and have done a commendable and accurate job revising the manuscript accordingly. One minor comment: The titles of Table 1 and Table 2 are mentioned in the revised Supplementary material, but the tables are included in the main manuscript text. If this is supplementary information, they should be included there.

Dear Dr Hamel,

On behalf of my colleagues and the Academic Editor, Renata Basto, I am happy to say that we can in principle accept your Research Article entitled "The connecting cilium inner scaffold provides a structural foundation that protects against retinal degeneration" for publication in PLOS Biology, provided you address any remaining formatting and reporting issues. These will be detailed in an email that will follow this letter and that you will usually receive within 2-3 business days, during which time no action is required from you. Please note that we will not be able to formally accept your manuscript and schedule it for publication until you have completed any requested changes.

Please take a minute to log into Editorial Manager at http://www.editorialmanager.com/pbiology/, click the "Update My Information" link at the top of the page, and update your user information to ensure an efficient production process.

PRESS

We frequently collaborate with press offices. If your institution or institutions have a press office, please notify them about your upcoming paper at this point, to enable them to help maximise its impact. If the press office is planning to promote your findings, we would be grateful if they could coordinate with biologypress@plos.org. If you have previously opted in to the early version process, we ask that you notify us immediately of any press plans so that we may opt out on your behalf.

We also ask that you take this opportunity to read our Embargo Policy regarding the discussion, promotion and media coverage of work that is yet to be published by PLOS. As your manuscript is not yet published, it is bound by the conditions of our Embargo Policy. Please be aware that this policy is in place both to ensure that any press coverage of your article is fully substantiated and to provide a direct link between such coverage and the published work. For full details of our Embargo Policy, please visit http://www.plos.org/about/media-inquiries/embargo-policy/.

Many congratulations and thanks again for choosing PLOS Biology for publication and supporting Open Access publishing. We look forward to publishing your study. 

Sincerely, 

Ines

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Ines Alvarez-Garcia, PhD 

Senior Editor 

PLOS Biology

ialvarez-garcia@plos.org