Dear Dr. Sun,

Thank you very much for submitting your manuscript "The Correlation Between Cell and Nucleus Size is Explained by an Eukaryotic Cell Growth Model" for consideration at PLOS Computational Biology.

As with all papers reviewed by the journal, your manuscript was reviewed by members of the editorial board and by several independent reviewers. In light of the reviews (below this email), we would like to invite the resubmission of a significantly-revised version that takes into account the reviewers' comments.

We cannot make any decision about publication until we have seen the revised manuscript and your response to the reviewers' comments. Your revised manuscript is also likely to be sent to reviewers for further evaluation.

When you are ready to resubmit, please upload the following:

[1] A letter containing a detailed list of your responses to the 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.

Please prepare and submit your revised manuscript within 60 days. If you anticipate any delay, please let us know the expected resubmission date by replying to this email. Please note that revised manuscripts received after the 60-day due date may require evaluation and peer review similar to newly submitted manuscripts.

Thank you again for your submission. 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,

Oleg A Igoshin

Associate Editor

PLOS Computational Biology

Jason Haugh

Deputy Editor

PLOS Computational Biology

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Reviewer's Responses to Questions

Comments to the Authors:

Please note here if the review is uploaded as an attachment.

Reviewer #1: The work "The Correlation Between Cell and Nucleus Size is Explained by a Eukaryotic Cell Growth Model" used a computational model to quantify factors influencing the cell volume to nuclear volume ratio (C/N ratio). While the regulatory mechanism of C/N ratio is of scientific importance and this work exhibit how simple models could explain complex biological phenomena, several major issues should be resolved before publishing this work as a formal academic paper.

Major issue:

This work heavily relies on simulation, while more quantitative insights on C/N ratio could be obtained by analytical approximations.

The major component of this work, Eq. 23-29. is in the unit of [number per cell], instead of concentration. Once they are changed in to the unit of concentration, one can work towards the steady-state solution. This could be done by dividing a "number" quantity X by their corresponding volumes V, changing into a concentration quantity x:

if dX/dt=F(X),

d(X/V)/dt=(1/V)*dX/dt-(X/V)*(1/V)*dV/dt

as the increasing speed of volume relative to the current volume, (1/V)*dV/dt, can be viewed as the growth rate g, one could obtain a differential equation of the concentration x, with an growth-induced dilution term:

d(X/V)/dt=dx/dt=(1/V)*F(X)-x*g;

for nucleus-related term, it is g_N; for cytoplasm-related term, it is g_C;

b. With the growth-induced dilution term, Eq. 23-29, when changed into the concentration format, should yield a steady-state solution about the concentration of proteins and ribosomes in the nucleus and the cytoplasm. Under this work's assumption of "cell volume is proportional to the protein and macromolecular number" (which itself needs more support from previous researches), a constant C/N ratio would be an intuitive result of "equilibrium between in/out nucleus transportation and diffusion". Then one can investigate how parameters influencing transportation and diffusion influence the relation between g_C and g_N, and the stability of C/N ratio.

2. The current manuscript lacks a clear emphasis on "which scientific questions were solved by this work". While C/N ratio is a field of interest by many researchers (which is also not yet sufficiently reviewed in this current manuscript), is the current manuscript focusing on how a constant C/N ratio can be maintained, or which biological processes may influence this ratio? What are the model results that are supported by previous observations, and what are the unexpected findings that inspire further investigation? For example, this work suggested "for the nutrient-limited cell, the C/N ratio fluctuates periodically", and " s1 and s1r have opposite effects on the C/N ratio" has that been observed in previous experiments?

3. Other than how different parameters influences C/N ratio, the format of equations should also be discussed: Which of the three processes, synthesis/transport/degradation, or subprocesses, plays essential roles in keeping the C/N ratio stable? It seems that the transportation and diffusion between the nucleus and cytoplasm are sufficient to maintain the C/N ratio stable, then what are the roles played by ribosome and protein synthesis? Is the degradation part necessary in this model?

Also, does the assumed format of equations influence the modeling results? Some assumptions in this manuscript are different from previous works: This work assumes a linear relationship between protein synthesis rate and the amino acid concentration, both in nutrient-rich and nutrient-limited conditions, which are different from the Michaelis–Menten format in Scott's 2014 work about the growth law; Also, the square relationship between protein number and its degradation rate is different from the linear degradation term in most modeling works. These differences should be supported, and whether they influence the modeling results should be discussed.

4. While this work focuses on C/N ratio in eukaryotes, the size of the nucleoid in bacterias also scales with the cell size (Gray, William T., et al. "Nucleoid size scaling and intracellular organization of translation across bacteria." Cell 177.6 (2019): 1632-1648.; Cantwell, Helena, and Paul Nurse. "Unravelling nuclear size control." Current genetics 65.6 (2019): 1281-1285). Yet, there is no distinction between the two forms of ribosomes in bacteria, as the size control mechanism proposed in this manuscript. In discussion, a comparison between the size control in eukaryotes and prokaryotes should be meaningful.

Other issues include:

Formating: Eq 22-23 extends outside of the page limit. Eq. 23-29 has no labeling.

In line 285, "ribosome disassembly and protein degradation rates in rapidly growing cells are 1/10 of the synthesis rate" is pretty arbitrary. The degradation rate can be estimated by the protein synthesis rate and the cell mass.

In Fig.4 C, the decrease of cell volume in quiescent status into near-zero value within 2 hours is not very realistic. Is that due to the assumed form of degradation?

Reviewer #2: See attachment

Reviewer #3: The review is uploaded as an attachment.

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Have the authors made all data and (if applicable) computational code underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data and code 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 and code 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 or code —e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

Reviewer #2: No: To be useful, the simulation model should be presented as a code that can be downloaded and the parameters presented in Tables in the supporting Information or as input files for the program.

Reviewer #3: None

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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.

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Reviewer #1: No

Reviewer #2: Yes: Zaida Luthey-Schulten

Reviewer #3: No

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.

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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

Attachments

Attachment

Submitted filename: Review PCOMPBIO-D-21-01529.pdf

Attachment

Submitted filename: rep.pdf

Dear Dr. Sun,

Thank you very much for submitting your manuscript "The Correlation Between Cell and Nucleus Size is Explained by an Eukaryotic Cell Growth Model" for consideration at PLOS Computational Biology. 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,

Oleg A Igoshin

Associate Editor

PLOS Computational Biology

Jason Haugh

Deputy Editor

PLOS Computational Biology

***********************

A link appears below if there are any accompanying review attachments. If you believe any reviews to be missing, please contact ploscompbiol@plos.org immediately:

[LINK]

Reviewer's Responses to Questions

Comments to the Authors:

Please note here if the review is uploaded as an attachment.

Reviewer #1: In the revised version of "The Correlation Between Cell and Nucleus Size is Explained by an Eukaryotic Cell Growth Model", most of the concerns from reviewers were appropriately addressed. Current, I think it is a nice scientific story that aims at solving fundamental questions in cell biology by computational methods with clear logic. However, I still have some concerns about the stability of the C/N ratio.

In the reply for comment 1, the author states that "we can express growth rate as _ = _ = ", which would already lead to a proportional C/N volume, as a result of the exponential growth with the same exponents. From the current concentration equations the authors listed in the reply, can the Jacobian be calculated to prove the stability of the fixed point solution?

In the line "689", there is an "?" that should not be there.

Reviewer #3: The authors have satisfactorily responded to most of my concerns and suggestions. The manuscript reads better now and is more informative. However, we seem to disagree on how to model cellular volume. The authors seem convinced that the cell is a dilute media whose volume is solely determined by its osmolarity, i.e., the cellular volume is proportional to the number of molecules of proteins and ribosomes and is independent of their sizes. This assumption contradicts the modern lore of the cell being a crowded environment and the fact that ribosomes and DNA are significantly large molecules. I should mention that I am mainly aware of the literature on Prokaryotes. I do not know if the authors' assumptions are indeed accurate for Eukaryotes. Also, as there is no experimental evidence of the predicted dependence of cell/nucleus volume on the various parameters studied, it is difficult to assess the correctness of the model. However, I will still recommend acceptance. As the saying goes - all models are wrong, but some are useful. Hopefully, this work will encourage further research on this topic. It will be interesting to see if different modelling approaches predict different outcomes and if experimental observations can differentiate between them.

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Have the authors made all data and (if applicable) computational code underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data and code 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 and code 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 or code —e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

Reviewer #3: Yes

**********

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 #3: No

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 in PLOS Biology 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:

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.

Dear Dr. Sun,

We are pleased to inform you that your manuscript 'The Correlation Between Cell and Nucleus Size is Explained by an Eukaryotic Cell Growth Model' has been provisionally accepted for publication in PLOS Computational Biology.

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 Computational Biology. 

Best regards,

Oleg A Igoshin

Associate Editor

PLOS Computational Biology

Jason Haugh

Deputy Editor

PLOS Computational Biology

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