Comparative iTRAQ proteomic profiling of sweet orange fruit on sensitive and tolerant rootstocks infected by ‘Candidatus Liberibacter asiaticus’

Lixiao Yao; Qibin Yu; Ming Huang; Zhen Song; Jude Grosser; Shanchun Chen; Yu Wang; Frederick G. Gmitter Jr.

doi:10.1371/journal.pone.0228876

Peer Review History

Original SubmissionDecember 5, 2019
2 Jan 2020 Decision Letter - Yuan Huang, Editor PONE-D-19-33708 Comparative iTRAQ proteomic profiling of sweet orange fruit on sensitive and tolerant rootstocks infected by ‘Candidatus Liberibacter asiaticus’ PLOS ONE Dear Dr. Yao, 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. We would appreciate receiving your revised manuscript by Feb 16 2020 11:59PM. When you are 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. If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. 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Please ensure that you have an ORCID iD and that it is validated in Editorial Manager. To do this, go to ‘Update my Information’ (in the upper left-hand corner of the main menu), and click on the Fetch/Validate link next to the ORCID field. This will take you to the ORCID site and allow you to create a new iD or authenticate a pre-existing iD in Editorial Manager. Please see the following video for instructions on linking an ORCID iD to your Editorial Manager account: https://www.youtube.com/watch?v=_xcclfuvtxQ [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: Through comparing proteomics of citrus fruit from cLas infected and uninfected Valencia sweet orange scions grafted on Huanglongbing susceptible and tolerant rootstocks, this study identified different proteomic alterations after cLas infection in a same scion grafted on two different types of rootstocks, which could possibly explain the better quality and yield of fruit grafted on tolerant rootstocks. The design of this study and selection of materials were reasonable, and the methods applied should be robust enough for publication. But there were still some small problems including imprecise description and grammar mistakes in the manuscript, so I suggest minor revision. Line 24 ‘incurable’ is not accurate. In some studies and reports HLB affected trees could be cured by applying antibiotics or high temperature treatment. The main challenge of HLB is that there has not been any robust controlling method that could solve the problem once for all. Line 36 and 39 should be ‘jasmonate signaling’ Line 47 delete ‘economically’ Line 49 ‘non-culturable’ is controversial and should be deleted, some study has reported the culture of the bacteria though at very low titer Line 54 What does ‘non-specific’ mean? Do other disease have similar symptoms? If yes why it was still ‘readily distinguishable’? Should be explained or modified. Line 55-56 Do symptomatic fruits always abscise prematurely? If not, ‘often’ should be added in front of abscise Line 62-63 ‘fruit contains lower percentage of soluble solid content and has lower soluble solid content to titratable acidity ratio’ Line 63 ‘amount of’ should not followed by non-countable noun Line 64, lack an ‘and’ Line 71 ‘most of them’ Line 78 delete ‘phenomena’ and ‘even’, and use past form ‘showed’ Line 82 “yet they have not yet been” Line 85 delete ‘even’, should denote whether the HLB-sensitive scion/rootstock is CaLas-infected Line 89 ‘tolerant and sensitive citrus rootstocks’ Line 91 Better modified to be ‘are unevenly distributed’ and ‘could induce similar or different’ Line 93 ‘Due to spreading quickly and the difficulties to control HLB’ should be rewritten Line 95-97, ‘Because’ and ‘therefore’ used together. There seemed to be no strong causal relationship here, and sentence had better be re-structured Line 163 ‘characteristics’ Line 176 Has statistical analysis been done to test the size and weight different? Are there any DE proteins related with fruit quality alteration? There is no discussion on this area at all, then why choosing fruit rather than leaves or other tissues as experimental material. Line 178 ‘proteomic profile’ Line 182-183 Different numbers of DE proteins from that described in Abstract Line 263 ‘serious destructive’ has grammar error. ‘uncured disease’ not appropriate here Fig 1. The go terms had better be put in the graph instead of the number IDs which would make the graph easier to read. There are still a few other grammar mistakes should be revised. Reviewer #2: Huanglongbing is the most serious citrus disease in the world. The manuscript entitled “Comparative iTRAQ proteomic profiling of sweet orange fruit on sensitive and tolerant rootstocks infected by ‘Candidatus Liberibacter asiaticus’” is an interesting article. The authors found a very interesting phenomenon that fruit of susceptible citrus scions can gain the ability of HLB tolerance from their rootstocks. To figure out the underlying mechanism, the authors employed strategy of comparative proteomic analysis and finally found out some potential factors and pathways. In my opinion, this manuscript is well written and provide some novelty results to this research field. However, some questions should be clarified to reader before publication. Minor revision: As shown, the current tables in the manuscript only presented a small part of the differentially expressed proteins, and all other data were enclosed in the supplementary, that restrict the readers to get a full view of the result. A table is fine to present a small number of proteins, but quite limited for hundreds of proteins. Since abundant of differentially expressed proteins were obtained from the comparative proteomic analysis, a more convenient and intuitive interface is quite necessary to present your data, such as pathways combined with hot-map. It is better to use only the name of rootstock instead of “HLB tolerant” or “HLB sensitive” throughout the manuscript after the first introduction of material background. Line 28-31: Confused long sentence. Short sentence can be more understandable, e.g. "same materials without CaLas infection were used as controls”. After revision, this manuscript could be publish in this journal. ****** 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: No [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 to be viewed.] 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 us at figures@plos.org. Please note that Supporting Information files do not need this step. https://doi.org/10.1371/journal.pone.0228876.r001
Revision 1
23 Jan 2020 Author Response For Reviewer #1 Suggestion Line 24 ‘incurable’ is not accurate. In some studies and reports HLB affected trees could be cured by applying antibiotics or high temperature treatment. The main challenge of HLB is that there has not been any robust controlling method that could solve the problem once for all. Reply: We replaced “incurable’ with ‘destructive’ in line 23 of “Manuscript_PONE-D-19-33708”. Suggestion Line 36 and 39 should be ‘jasmonate signaling’; Line 47 delete ‘economically’; Line 49 ‘non-culturable’ is controversial and should be deleted, some study has reported the culture of the bacteria though at very low titer. Reply: Have done in lines 35, 37, and 44 of “Manuscript_PONE-D-19-33708”; ‘non-culturable’ was replaced with more commonly recognized terminology ‘fastidious’ in line 46. Suggestion Line 54 What does ‘non-specific’ mean? Do other disease have similar symptoms? If yes why it was still ‘readily distinguishable’? Should be explained or modified. Reply: We deleted the “non-specific” sentence, for the following sentences described the characteristics of symptomatic fruit. Suggestion Line 55-56 Do symptomatic fruits always abscise prematurely? If not, ‘often’ should be added in front of abscise; Line 62-63 ‘fruit contains lower percentage of soluble solid content and has lower soluble solid content to titratable acidity ratio’. Reply: Have done. Suggestion Line 63 ‘amount of’ should not followed by non-countable noun Reply: Change ‘amount of’ to ‘concentration of’. Suggestion Line 64, lack an ‘and’; Line 71 ‘most of them’; Line 78 delete ‘phenomena’ and ‘even’, and use past form ‘showed’; Line 82 “yet they have not yet been”; Line 85 delete ‘even’, should denote whether the HLB-sensitive scion/rootstock is CaLas-infected; Line 89 ‘tolerant and sensitive citrus rootstocks’; Line 91 Better modified to be ‘are unevenly distributed’ and ‘could induce similar or different’ Reply: Have done. Suggestion Line 93 ‘Due to spreading quickly and the difficulties to control HLB’ should be rewritten; Line 95-97, ‘Because’ and ‘therefore’ used together. There seemed to be no strong causal relationship here, and sentence had better be re-structured Reply: We rewrote it. Suggestion Line 163 ‘characteristics’ Reply: Have done in line 156 of “Manuscript_PONE-D-19-33708”. Suggestion Line 176 Has statistical analysis been done to test the size and weight different? Are there any DE proteins related with fruit quality alteration? There is no discussion on this area at all, then why choosing fruit rather than leaves or other tissues as experimental material. Reply: We did perform statistical analyses to test the size and weight differences; the results are mentioned in lines 165-170 of “Manuscript_PONE-D-19-33708”. Just like the leaves and roots, the development and maturity of fruit is under the HLB stress. Many studies have shown the differentially expressed genes or proteins in leaves and roots. However, we did not know if there are CaLas-sensitive or –tolerant pathways involved in fruits. This is the reason for choosing fruit as the experimental material. We added this sentence to the introduction: “There is very little known about the proteomic differences in fruit pulp tissues as a consequence of HLB, and nothing is known on the impact of using more tolerant rootstocks on the fruit proteome”. Suggestion Line 178 ‘proteomic profile’ Reply: Have done in line 171 of “Manuscript_PONE-D-19-33708”. Suggestion Line 182-183 Different numbers of DE proteins from that described in Abstract Reply: We checked the data carefully and corrected the numbers of DE proteins. For example, we said 573 DE proteins in the symptomatic fruit on ‘Swingle’ in Abstract part, which equaled with 495 DE fruit proteins found only in the symptomatic fruit on ‘Swingle’ and 78 DE proteins shared in fruit on both rootstocks in Results part. Suggestion Line 263 ‘serious destructive’ has grammar error. ‘uncured disease’ not appropriate here Reply: We rewrote it. Suggestion Fig 1. The go terms had better be put in the graph instead of the number IDs which would make the graph easier to read. Reply: Have done. Suggestion There are still a few other grammar mistakes should be revised. Reply: We did our best to correct the other grammar mistakes. For Reviewer #2 Suggestion As shown, the current tables in the manuscript only presented a small part of the differentially expressed proteins, and all other data were enclosed in the supplementary, that restrict the readers to get a full view of the result. A table is fine to present a small number of proteins, but quite limited for hundreds of proteins. Since abundant of differentially expressed proteins were obtained from the comparative proteomic analysis, a more convenient and intuitive interface is quite necessary to present your data, such as pathways combined with hot-map. Reply: We used MapMan to analyze the differentially expressed proteins in biotic stress. The new figure (Figure 1A) provides a more comprehensive view of the results. Suggestion It is better to use only the name of rootstock instead of “HLB tolerant” or “HLB sensitive” throughout the manuscript after the first introduction of material background. Reply: Have done in most places, though kept this designation in the Conclusion section for clarity. Suggestion Line 28-31: Confused long sentence. Short sentence can be more understandable, e.g. "same materials without CaLas infection were used as controls”. Reply: Have done. Attachments Attachment Submitted filename: Response to Reviewers.pdf https://doi.org/10.1371/journal.pone.0228876.r002
27 Jan 2020 Decision Letter - Yuan Huang, Editor Comparative iTRAQ proteomic profiling of sweet orange fruit on sensitive and tolerant rootstocks infected by ‘Candidatus Liberibacter asiaticus’ PONE-D-19-33708R1 Dear Dr. Yao, We are pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it complies with all outstanding technical requirements. Within one week, you will receive an e-mail containing information on the amendments required prior to publication. When all required modifications have been addressed, you will receive a formal acceptance letter and your manuscript will proceed to our production department and be scheduled for publication. Shortly after the formal acceptance letter is sent, an invoice for payment will follow. To ensure an efficient production and billing process, please log into Editorial Manager at https://www.editorialmanager.com/pone/, click the "Update My Information" link at the top of the page, and update your user information. 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 enable them to help maximize its impact. If they will be preparing press materials for this manuscript, you must inform our press team as soon as possible and 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. With kind regards, Yuan Huang Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0228876.r003
Formally Accepted
5 Feb 2020 Acceptance Letter - Yuan Huang, Editor PONE-D-19-33708R1 Comparative iTRAQ proteomic profiling of sweet orange fruit on sensitive and tolerant rootstocks infected by ‘<I>Candidatus</I> Liberibacter asiaticus’ Dear Dr. Yao: I am 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 notify them about your upcoming paper at this point, to enable them to help maximize its impact. If they will be preparing press materials for this manuscript, 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. For any other questions or concerns, please email plosone@plos.org. Thank you for submitting your work to PLOS ONE. With kind regards, PLOS ONE Editorial Office Staff on behalf of Dr. Yuan Huang Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0228876.r004

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