Conserved sequence motifs in the abiotic stress response protein late embryogenesis abundant 3

Karamjeet K. Singh; Steffen P. Graether

doi:10.1371/journal.pone.0237177

Peer Review History

Original SubmissionMay 15, 2020
6 Jul 2020 Decision Letter - Ruslan Kalendar, Editor PONE-D-20-14558 Conserved Sequence Motifs in the Abiotic Stress Response Protein Late Embryogenesis Abundant 3 PLOS ONE Dear Dr. Graether, 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 Aug 20 2020 11:59PM. 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. 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We require that authors provide all relevant data within the paper, Supporting Information files, or in an acceptable, public repository. Please add a citation to support this phrase or upload the data that corresponds with these findings to a stable repository (such as Figshare or Dryad) and provide and URLs, DOIs, or accession numbers that may be used to access these data. Or, if the data are not a core part of the research being presented in your study, we ask that you remove the phrase that refers to these data. Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. Is the manuscript technically sound, and do the data support the conclusions? . Reviewer #1: Yes ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: N/A ****** 3. Have the authors made all data underlying the findings in their manuscript fully available? Reviewer #1: Yes ****** 4. Is the manuscript presented in an intelligible fashion and written in standard English? Reviewer #1: Yes ****** 5. Review Comments to the Author Reviewer #1: The paper focused on the characterisation and sequencing of LEA3 proteins. For this, the authors performed bioinformatics analyses of these dehydrins using Phytozome database and Pfam LEA3 sequences as sources ultimately creating a LEA3 sequence dataset. The authors separated the data for vascular and non-vascular plants and studied the spread of LEA3 proteins in plant spp. 1. The authors should think about Figs 1, 2A, 5A, 5B in terms of accessibility particularly when accessed by colour blind readers. The figures mentioned have the potential to be completely uninformative if viewed in wrong conditions. 2. I couldn’t access S1 Figure but I think it would be great to have principal components showing some sort of clustering of the LEA3 proteins identified with respect to the plant species 3. Line 469 This is not true. There are reviews and articles that showed that the molecular weight of LEA proteins could be up to 200KDa. See: a) Hanin, M., Brini, F., Ebel, C., Toda, Y., Takeda, S. and Masmoudi, K., 2011. Plant dehydrins and stress tolerance: versatile proteins for complex mechanisms. Plant signaling & behavior, 6(10), pp.1503-1509; b) Graether, S.P. and Boddington, K.F., 2014. Disorder and function: a review of the dehydrin protein family. Frontiers in plant science, 5, p.576; c) Ogbaga, C.C., Stepien, P., Dyson, B.C., Rattray, N.J., Ellis, D.I., Goodacre, R. and Johnson, G.N., 2016. Biochemical analyses of sorghum varieties reveal differential responses to drought. PloS one, 11(5). d) Yu, Z., Wang, X. and Zhang, L., 2018. Structural and functional dynamics of dehydrins: a plant protector protein under abiotic stress. International journal of molecular sciences, 19(11), p.3420. Language Line 15 change containing to contain Line 25 change arose to arisen ****** 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: Yes:** Chukwuma C. Ogbaga [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. https://doi.org/10.1371/journal.pone.0237177.r001
Revision 1
19 Jul 2020 Author Response Dear Editor, Thank-you for the opportunity to submit a revision of our manuscript titled “Conserved Sequence Motifs in the Abiotic Stress Response Protein Late Embryogenesis Abundant 3.” We hope that addressing these issues will allow our manuscript to be published. Response to the Editor 1) We have revised our manuscript to ensure that it follows the PLOS One formatting guidelines. 2) We have removed the “data not shown” statements and rewritten the text to indicate that a) no algae sequences were found so that there is no data shown and b) the data for the lower plant N-terminal sequences are shown in the supplemental data. Response to Reviewer #1 1) We thank the reviewer for pointing out that our figures did not take color vision deficiency into account. We have corrected the Figures 1, 2, and 5 to ensure that the colors and color shades are appropriate now. 2) The suggestion of using PCA to see if there is any clustering of sequences by species is interesting, but one that we feel that the reviewer would not see as necessary if they were able to open Fig. S1. There does not seem to be any significant trend, other than our previously described observation that the M[AS][RK] N-terminal sequence is predominantly found in Commelinids. We are also unclear on what variables or categories would be used for the PCA. We therefore felt that adding a PCA analysis would not significantly improve the manuscript. 3) We corrected the upper MW limit of dehydrins (now Line 566 in the revised with track-changes manuscript). 4) We corrected ‘containing’ to ‘contain’ (now line 18) and ‘arose’ to ‘arisen’ (now line 28). Sincerely, Steffen Graether, Ph.D. Associate Professor Department of Molecular and Cellular Biology University of Guelph Guelph, Ontario Attachments Attachment Submitted filename: Response to reviewers.doc https://doi.org/10.1371/journal.pone.0237177.r002
22 Jul 2020 Decision Letter - Ruslan Kalendar, Editor Conserved Sequence Motifs in the Abiotic Stress Response Protein Late Embryogenesis Abundant 3 PONE-D-20-14558R1 Dear Dr. Graether, 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, Ruslan Kalendar, PhD Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0237177.r003
Formally Accepted
27 Jul 2020 Acceptance Letter - Ruslan Kalendar, Editor PONE-D-20-14558R1 Conserved sequence motifs in the abiotic stress response protein late embryogenesis abundant 3 Dear Dr. Graether: I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department. If your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. 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. If we can help with anything else, please email us at plosone@plos.org. Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staff on behalf of Dr. Ruslan Kalendar Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0237177.r004

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