PONE-D-22-08232Genome-Wide Exploration of Sugar Transporter (Sweet) Family Proteins In Fabaceae For Sustainable Protein And Carbon SourcePLOS ONE

Dear Dr. Singh,

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 23.04.2022. 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 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,

Pradeep Kumar

Academic Editor

PLOS ONE

Journal Requirements:

When submitting your revision, we need you to address these additional requirements.

1. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. 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 that the grant information you provided in the ‘Funding Information’ and ‘Financial Disclosure’ sections do not match. 

When you resubmit, please ensure that you provide the correct grant numbers for the awards you received for your study in the ‘Funding Information’ section.

3. Thank you for stating the following in the Acknowledgments Section of your manuscript: 

"NS acknowledges the funding from the Department of Science & Technology, Government of India through the DST INSPIRE Faculty Award Grant (DST/INSPIRE/04/2018/003674)."

We note that you have provided funding information that is not currently declared in your Funding Statement. However, funding information should not appear in the Acknowledgments section or other areas of your manuscript. We will only publish funding information present in the Funding Statement section of the online submission form. 

Please remove any funding-related text from the manuscript and let us know how you would like to update your Funding Statement. Currently, your Funding Statement reads as follows: 

"1) Department of Science and Technoogy, Government of India, DST/INSPIRE/04/2018/003674 

2) RMC-UTM, Malaysia for industrial grants No. R.J130000.7609.4C284 and R.J13000.7609.4C187"

Please include your amended statements within your cover letter; we will change the online submission form on your behalf.

4. Please amend your authorship list in your manuscript file to include author Hesham Ali El Enshasy and Ahmed M Kenawy.

5. 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.

6. 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.

[Note: HTML markup is below. Please do not edit.]

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: Yes

**********

2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

Reviewer #2: Yes

**********

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: Yes

**********

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: In the current manuscript, the authors have performed biocomputational analysis of SWEET protein across different Fabaceae species to analyze their cellular, molecular and structure composition in 12 diverse Legume species. Authors findings suggest that SWEETs are rich in polar amino acid i.e., alanine, leucine, serine and phenylalanine while glutamine, tryptophan, cystine and histidine are less abundant. In addition, a detailed domain and motif and structural analysis was conducted to understand the function and regulation of sugar transporters and its metabolic enzymes in legumes will help mitigate the global food security and malnutrition problems because legumes are greater source of essential amino acids.

I have few observations in these manuscripts which Authors needs to address:

1) Why only complete proteome of 12 legumes was taken? Why only the primary sequence of total of 155 STPs were analyzed? What was the basis of selection? Authors needs to incorporate in the manuscript

2) The manuscript is well written. One round of careful editing shall further improve the minor editing issues that were observed at a few places. There is no need to capitalize Legume in sentence case, etc.

3) Authors need to enhance the quality and resolution of figures for publications

4) All references should be thoroughly checked especially Author must confirm only relevant publications should be cited.

5) I am wondering to see the authors contributions because the contribution of two other authors Sapna Langyan and R Z Sayyed has not been stated in the manuscript, also why NKS is mentioned there in the Authors contributions section and not in the list of authors. Authors should check it very critically and provide detailed contributions of other mentioned authors.

6) Also, I am surprised why there are three equal contributors, it will be better to keep two if the authors have not significantly contributed.

7) Authors have performed in-depth bioinformatics analysis on SWEET proteins which provide deeper insights on functional level of these 155 SWEET proteins. This study will be useful to understand the molecular mechanism and pathway analysis on these SWEET proteins involved in both abiotic and biotic stress management in diverse legumes. However, my recommendation would be it required revision to incorporate suggested changes manuscript.

Reviewer #2: The authors have performed bioinformatics analysis of SWEET protein on 12 Fabaceae species. They have identified the genome wide SWEET proteins using similarity search and performed the secondary analysis. This secondary data analysis could be more useful and interesting, to infer their mechanism at structural and functional level which play essential roles in growth, development, and stress responses. This study will be useful to examine photosynthetic productivity, embryo sugar content, seed quality and yield enhancement in Fabaceae for sustainable source of essential amino acids and carbon source.

However, I have few observations in this manuscript:

1) Introduction and Material and methods part is well written; however, Authors should avoid repeated sentence from introduction and Results section.

2) Authors need to check and rephrase this sentence “Many people's diets in poor nations are based on legumes and cereals” in Introduction section line number 60-61.

3) Authors can rephrase this sentence “Other than the nutritional composition of the legumes, epidemiology studies reveal that regular intake of legumes can reduce the incidence of various diseases like HDL, cholesterol, metabolic syndrome, and heart disease”. Like. Beside nutritional composition of the legumes, epidemiology studies reveal that regular intake of legumes can reduce the incidence of various diseases like HDL, cholesterol, metabolic syndrome, and heart disease.

4) Authors need to check line no. 78-79 “The amount of sucrose available for transportation to sink tissue is significant [9,10] for plant development”.

5) In introduction line no. 79 STPs should be expand first and then use STPs in entire manuscript.

6) In some places Authors have written Fabaceae in italics, it should be standard and uniform throughout manuscript.

7) In line number 103 it should be written as profile, secondary structure, phylogenetic relationship, motif identification and homology modeling of sugar transporter proteins.

8) I would recommend Authors need to check typo errors such as Cajanus cajan in some places it is written italics and somewhere non-italic.

9) Authors should include details of parameters used in BLASTp search algorithms, to identifies these STPS.

10) Authors should also discuss why they have selected 12 legumes to identify SWEET proteins

11) Authors needs to pay more attention on the Discussion section and discuss about the role of different amino acids across these 12 legumes.

12) Overall, the manuscript is well written and has great potential in legume research. The manuscript can be considered for publications after addressing above comments.

**********

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: Abdul Gafur

[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.

Genome-Wide Exploration of Sugar Transporter (Sweet) Family Proteins In Fabaceae For Sustainable Protein And Carbon Source

PONE-D-22-08232R1

Dear Dr. Singh,

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,

Pradeep Kumar

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

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: All the queries have been addressed. The manuscript has been revised as per my comments. This revision has improved the manuscript

Reviewer #2: You have addressed all my queries and have revised the manuscript as per my concern. The manuscript is now in a good shape

**********

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: No