Dear Dr Nahas,

Thank you for submitting your manuscript entitled "A BRC1-modulated switch in auxin transport accounts for the competition between Arabidopsis axillary buds" 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 your submission out for external peer review.

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Feel free to email us at plosbiology@plos.org if you have any queries relating to your submission.

Kind regards,

Ines

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Ines Alvarez-Garcia, PhD

Senior Editor

PLOS Biology

ialvarez-garcia@plos.org

Dear Dr Nahas,

Thank you for your patience while your manuscript entitled "A BRC1-modulated switch in auxin transport accounts for the competition between Arabidopsis axillary buds" went through peer-review at PLOS Biology. Your manuscript has now been evaluated by the PLOS Biology editors, an Academic Editor with relevant expertise, and by two independent reviewers.

The reviews are attached below. As you will see, the reviewers find the results interesting, but they also raise several points that would need to be addressed before we can consider the manuscript for publication. Reviewer 1 mentions that the interpretation of some of the results is confusing and that BRC1 modulates auxin transport is not directly demonstrated. The reviewer also offers an alternative explanation by which BRC1 impacts auxin availability rather than transport itself, and has some doubts regarding the role of BRC2, which is not analysed. Reviewer 2 raises three points that need clarification: s/he notes that in the model there is no parameter that is dependent on the amount of auxin in the system and wonders if sugar could be playing a role; whether or not the effect could be due to boosting the total level of auxin in the system; and if both buds could reach the ‘tipping point’ of canalisation faster, it would be more auxin available. In addition, the reviewer makes suggestions to improve readability and the proposed model.

In light of the reviews, we are pleased to offer you the opportunity to address the comments from the reviewers in a revision that we anticipate should not take you very long. We will then assess your revised manuscript and your response to the reviewers' comments with our Academic Editor aiming to avoid further rounds of peer-review, although we might need to consult with the reviewers, depending on the nature of the revisions.

In addition to these revisions, 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 shortly.

We expect to receive your revised manuscript within 1 month. Please email us (plosbiology@plos.org) if you have any questions or concerns, or would like to request an extension.

At this stage, your manuscript remains formally under active consideration at our journal; please notify us by email if you do not intend to submit a revision so that we withdraw the manuscript.

**IMPORTANT - SUBMITTING YOUR REVISION**

Your revisions should address the specific points made by each reviewer. Please submit the following files along with your revised manuscript:

1. A 'Response to Reviewers' file - this should detail your responses to the editorial requests, present a point-by-point response to all of the reviewers' comments, and indicate the changes made to the manuscript.

*NOTE: In your point-by-point response to the reviewers, please provide the full context of each review. Do not selectively quote paragraphs or sentences to reply to. The entire set of reviewer comments should be present in full and each specific point should be responded to individually.

You should also cite any additional relevant literature that has been published since the original submission and mention any additional citations in your response.

2. In addition to a clean copy of the manuscript, please also upload a 'track-changes' version of your manuscript that specifies the edits made. This should be uploaded as a "Revised Article with Changes Highlighted " file type.

3. Resubmission Checklist

When you are ready to resubmit your revised manuscript, please refer to this resubmission checklist: https://plos.io/Biology_Checklist

To submit a revised version of your manuscript, please go to https://www.editorialmanager.com/pbiology/ and log in as an Author. Click the link labelled 'Submissions Needing Revision' where you will find your submission record.

Please make sure to read the following important policies and guidelines while preparing your revision and fulfil the editorial requests:

a) *PLOS Data Policy*

Please note that as a condition of publication PLOS' data policy (http://journals.plos.org/plosbiology/s/data-availability) requires that you make available all data used to draw the conclusions arrived at in your manuscript. If you have not already done so, you must include any data used in your manuscript either in appropriate repositories, within the body of the manuscript, or as supporting information (N.B. this includes any numerical values that were used to generate graphs, histograms etc.). Please also indicate in each figure legend where the data can be found. For an example see here: http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001908#s5

b) *Published Peer Review*

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. Please see here for more details:

https://blogs.plos.org/plos/2019/05/plos-journals-now-open-for-published-peer-review/

c) *Blot and Gel Data Policy*

Please provide the original, uncropped and minimally adjusted images supporting all blot and gel results reported in an article's figures or Supporting Information files. We will require these files before a manuscript can be accepted so please prepare them now, if you have not already uploaded them. Please carefully read our guidelines for how to prepare and upload this data: https://journals.plos.org/plosbiology/s/figures#loc-blot-and-gel-reporting-requirements

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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

e) *Protocols deposition*

To enhance the reproducibility of your results, we recommend that if applicable 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. For instructions see: https://journals.plos.org/plosbiology/s/submission-guidelines#loc-materials-and-methods

Thank you again for your submission to our journal. We hope that our editorial process has been constructive thus far, and we welcome your feedback at any time. Please don't hesitate to contact us if you have any questions or comments.

Sincerely,

Ines

--

Ines Alvarez-Garcia, PhD

Senior Editor

PLOS Biology

ialvarez-garcia@plos.org

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Reviewers' comments

Rev. 1:

This manuscript studies how auxin transport and the transcription factor BRC1 interact to regulate axillary bud outgrowth. Both responses are controlled by strigolactone (SL) signaling. Using two-node explant bud competition experiments in several genetic backgrounds -brc1brc2, smxl678, and the brc1brc2 smxl678- and in response to GR24 (synthetic SL) treatments the authors investigate in depth how buds compete and respond, and how SL, BRC1 and the auxin. Transporter PIN1 participate in this process. These experiments allow them to generate and validate, also in detail, a mathematical model aimed at understanding the molecular components influencing the lag phase and the rapid outgrowth phase of bud activation. The extensive data, together with previous work from the same group, shows that SL acts through both a BRC1/2-dependent and a BRC1/2-independent pathway during bud outgrowth. In particular, during the rapid outgrowth phase, SL appears to influence auxin transport in a BRC1-independent manner.

The authors also design an elegant experiment, in which a domain of PIN1 is replaced with the corresponding domain of PIN3 to generate a modified PIN1 less responsive to SL (SIP1). The authors show that SIP1 protein is indeed more resistant to SL. However, interpretation of these results becomes confusing due to a partial SL sensitivity of the protein, noticeable in the response of buds to SL, and to impaired auxin transport in the SIP1 lines. This complicates the interpretation of all the experiments performed with this line (eg. Figure 8, Figures S6, S9).

One of the main conclusions of the paper, also featured in the title of the manuscript, is that BRC1 modulates auxin transport. However, this point is not directly demonstrated. It is derived from interpretations of the modeling outputs and the behavior of buds in the competition assays. In the discussion, the authors note this limitation and acknowledge that no auxin transporters are currently known to be transcriptional targets of BRC1. They suggest a possible post-translational mechanism, though this remains speculative. Besides, one known BRC1 target, GH3.5, reduces active IAA levels through conjugation, which could offer an alternative explanation (not considered) by which BRC1 impacts auxin availability rather than transport per se.

It is also worth noting that while all genetic experiments are carried out using the brc1 brc2 double mutant, the qPCR analyses and the modeling (and the title) focus on BRC1. This raises the question of why is BRC2 excluded from these parts of the study.

Rev. 2:

The manuscript by Nahas et al is an elegant integration of computational modeling and experimental validation—both aimed at formalizing a minimal regulatory model for competition between buds. The authors have done a significant amount of work, and it is all thoughtfully designed, appropriately controlled and interpreted with reasonable cautions. The engineering of a largely SL-independent PIN1 was excellent, although more work could be done to enhance interpretability, as the authors describe. Available mutants are used to great effect throughout.

The utility of a model with minimal parameters cannot be overstated, especially for hypothesis generation, and the authors have done an admirable job of capturing decades of findings within a strikingly simple architecture. Essentially, the authors argue that both model and validating experiments point to two significant tuning knobs that together determine whether one or both buds will grow in a 2-node explant: (1) how much auxin efflux transporter is removed from the membrane, and (2) what is the basal rate of auxin efflux. They go on to show that strigolactones primarily control the former, while BRC1 is largely acting on the latter.

I have no major concerns, but a few questions:

1) If I am reading the model correctly, there is no parameter that is dependent on the amount of auxin in the system. If I understand that correctly, I wonder if that partially explains the unexpected behavior of the smxl678 mutant in the 2 node vs 1 node assay. The authors argue that sugar could be playing a role here, and I wonder if that effect could be by boosting the total level of auxin in the system. If there was more overall auxin, perhaps both buds could reach the 'tipping point' of canalization more quickly.

2) It is a personal preference, but in the interest of readability, I would love to see fewer abbreviations used throughout the text. Maximum growth rate is somewhat cumbersome to spell out, but MGR is not really an improvement in my opinion. Similarly, in Figures like S1, it would be wonderful to have the meanings of each parameter being tested spelled out in the titles of each graph or at least in the figure legend to avoid having to flip back and forth.

3) It would be useful to have the authors speculate a bit on how the current model might succeed or struggle in a more complex system of higher numbers of buds, and other considerations that might need to be incorporated to apply the model to other plants (e.g., different shoot architectures).

Dear Dr Nahas,

Thank you for your patience while we considered your revised manuscript entitled "A BRC1-modulated switch in auxin efflux accounts for the competition between Arabidopsis axillary buds" for publication as a Research Article at PLOS Biology. This revised version of your manuscript has been evaluated by the PLOS Biology editors and by the Academic Editor.

Based on our Academic Editor's assessment of your revision, we are likely to accept this manuscript for publication, provided you satisfactorily 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.

In addition to these revisions, you may 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 shortly. If you do not receive a separate email within a few days, please assume that checks have been completed, and no additional changes are required.

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:

- a cover letter that should detail your responses to any editorial requests, if applicable, and whether changes have been made to the reference list

- a Response to Reviewers file that provides a detailed response to the reviewers' comments (if applicable, if not applicable please do not delete your existing 'Response to Reviewers' file.)

- a track-changes file indicating any changes that you have made to the manuscript.

NOTE: If Supporting Information files are included with your article, note that these are not copyedited and will be published as they are submitted. Please ensure that these files are legible and of high quality (at least 300 dpi) in an easily accessible file format. For this reason, please be aware that any references listed in an SI file will not be indexed. For more information, see our Supporting Information guidelines:

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

*Published Peer Review History*

Please note that 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. Please see here for more details:

https://plos.org/published-peer-review-history/

*Press*

Should you, your institution's press office or the journal office choose to press release your paper, please ensure you have opted out of Early Article Posting on the submission form. We ask that you notify us as soon as possible if you or your institution is planning to press release the article.

*Protocols deposition*

To enhance the reproducibility of your results, we recommend that if applicable 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 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

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. 2B-E; Fig. 3C; Fig. 4A; Fig. 5B, C; Fig. 6B, C; Fig. 7A-E; Fig. 8C, E; Fig. 9C, F; Fig. S5B, C; Fig. S6; Fig. S7A, B and Fig. S8A-E

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 UNDERLYING 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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CODE POLICY

Per journal policy, if you have generated any custom code during the course of this investigation, please make it available without restrictions. Please ensure that the code is sufficiently well documented and reusable, and that your Data Statement in the Editorial Manager submission system accurately describes where your code can be found.

Please note that we do need a DOI number for the code, thus we suggest you deposit it also in Zenodo, which will generate a DOI number and you will need to provide in the Data Accessibility Statement

Dear Dr Nahas,

Thank you for the submission of your revised Research Article entitled "A BRC1-modulated switch in auxin efflux accounts for the competition between Arabidopsis axillary buds" for publication in PLOS Biology. On behalf of my colleagues and the Academic Editor, Xinnian Dong, I am delighted to let you know that we can in principle accept your manuscript for publication, provided you address any remaining formatting and reporting issues. These will be detailed in an email you should receive within 2-3 business days from our colleagues in the journal operations team; no action is required from you until then. 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

--

Ines Alvarez-Garcia, PhD

Senior Editor

PLOS Biology

ialvarez-garcia@plos.org