Differing structures of galactoglucomannan in eudicots and non-eudicot angiosperms

Konan Ishida; Yusuke Ohba; Yoshihisa Yoshimi; Louis F. L. Wilson; Alberto Echevarría-Poza; Li Yu; Hiroaki Iwai; Paul Dupree

doi:10.1371/journal.pone.0289581

Peer Review History

Original SubmissionJuly 17, 2023
13 Aug 2023 Decision Letter - Olga A. Zabotina, Editor PONE-D-23-22384Differing structures of galactoglucomannan in eudicots and non-eudicot angiospermsPLOS ONE Dear Dr. Dupree, 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. One of the reviewers has also offered his suggestions to improve the text (see his attached file). Please submit your revised manuscript by Sep 27 2023 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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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 If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references.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 If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice.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: I Don't Know ****** 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: This rigorous study builds on the Dupree lab's recent and exciting discovery about the structure of patterned beta-galactosylated glucomannans (abbreviated β-GGM) in multiple eudicot species, including Arabidopsis and tomato. Here, the authors investigated the occurrence of β-GGM in 17 monocot species and four basal angiosperm species. Using a series of enzymatic digestions for polysaccharide analysis by gel electrophoresis, the non-eudicot plant tissues did not show any of the carbohydrate bands diagnostic of β-Gal-decorated mannan structures in tomato fruits. While α-Gal mannan substitutions were present, sequential enzyme treatments did not reveal any conserved glycosyl residue patterns in Austrobaileya scandens glucomannan. β-Galactosidase treatments did not alter the GH5 mannanase-released oligosaccharide patterns for the non-eudicot species. Consistent with this observation, putative orthologs of the AtMBGT1 β-galactosyltransferase from Amborella trichopoda and rice (Oryza sativa) did not complement the chemotype of the Arabidopsis mbgt1 mutant. Instead, mutations in the rice gene OsGT47A-VII and its overexpression in Arabidopsis mur3 xlt2 double mutant showed phenotypes consistent with MUR3-like β-Gal addition to the xyloglucan backbone. Altogether, this study indicates that MAGT1 substrate specificity and β-GGM presence are likely eudicot-specific. This manuscript is excellent, so I only have a couple of minor suggestions: line 284 – “manifested growth defects” – the text does not indicate what was decreased lines 314-315 “AcGGM (CSLA9 mannan)” this brief phrase should be re-worded or expanded to assist readers since AcGGM biosynthesis would require multiple activities beyond CSLA9 Fig. 4A the legend includes sugars that are not displayed elsewhere in the figure Reviewer #2: This manuscript presents an investigation of mannan structures among diverse plant species conducted using PACE with various glycanases and glycosidases. In previous work, the authors identified beta-GGM in Arabidopsis, and in this study they aimed to determine the phylogenetic distribution in plants. In this study, PACE analysis revealed no evidence of beta-GGM in the tissues of species tested. The authors acknowledge that while they found no evidence of beta-GGM among the tested plants that this structure might still be present in non-tested tissues, etc. Complementary to PACE analyses, the authors also investigated the functions of homologs of AtMBGT1. Rice and Amborella MBGT-like sequences did not complement the atmbgt1 mutant. Rice mutants containing lesions in the OsGT47A-VII gene exhibited defects consistent with deficits in xyloglucan galactosyltransferase activity. Overall, the experiments seem to have been conducted well and the results are fairly clear. The reviewer's most consequential concern is that some of the patterns on the PACE gels were very faint, making them difficult to interpret (e.g., Fig 3 C & D). What if, for example, the quantity of beta-GGM is low in the sample, might analyzing more sample provide a more convincing result? Could the authors show more heavily loaded PACE gels? It could also be helpful to have an estimate of how small a quantity of beta-GGM is needed for detection (i.e., detection limit). In this way, the authors could further qualify their inability to detect this carbohydrate and present an upper limit for the amount that might be present. Aside from this, I have provided a marked up version of the manuscript with many comments where revisions might improve the clarity of presentation, flow and conventional use of the language. There were a number of spots in the Materials and Methods section where more details would be needed to replicate the experiments - this should be addressed. I hope my writing is legible and the feedback helpful for implementing revisions. ****** 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: Catalin Voiniciuc Reviewer #2: Yes: Aaron Liepman ******** [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. Attachments Attachment Submitted filename: MarkedMS_Ishida_PlosOne2023.pdf https://doi.org/10.1371/journal.pone.0289581.r001
Revision 1
28 Sep 2023 Author Response manuscript: PONE-D-23-22384 Dear Dr Zabotina, Thank you for handling our revised manuscript “Differing structures of galactoglucomannan in eudicots and non-eudicot angiosperms” for publication in PLOS ONE. We appreciate the time and effort that you and the reviewers dedicated to providing feedback on our manuscript. We have incorporated the suggestions made by the reviewers as much as possible. Yours sincerely, Paul Dupree Detailed Response to reviewers Reviewer #1: This manuscript is excellent, so I only have a couple of minor suggestions: line 284 – “manifested growth defects” – the text does not indicate what was decreased. We appreciate your high regard for the manuscript. We corrected the sentence as below. “In the root, both mutants manifested shorter seminal roots (23% and 31% decrease in mean) (Fig 6B).” lines 314-315 “AcGGM (CSLA9 mannan)” this brief phrase should be re-worded or expanded to assist readers since AcGGM biosynthesis would require multiple activities beyond CSLA9. We removed “(CSLA9 mannan)” from the sentence. Fig. 4A the legend includes sugars that are not displayed elsewhere in the figure. We removed the sugars that are not used in the figure from the legend. Reviewer #2: Overall, the experiments seem to have been conducted well and the results are fairly clear. The reviewer's most consequential concern is that some of the patterns on the PACE gels were very faint, making them difficult to interpret (e.g., Fig 3 C & D). What if, for example, the quantity of beta-GGM is low in the sample, might analyzing more sample provide a more convincing result? Could the authors show more heavily loaded PACE gels? It could also be helpful to have an estimate of how small a quantity of beta-GGM is needed for detection (i.e., detection limit). In this way, the authors could further qualify their inability to detect this carbohydrate and present an upper limit for the amount that might be present. We appreciate your detailed reading of the manuscript and feedback. We understand the concern about the intensity of the bands. All forms of glucomannan are relatively low abundance in monocots compared with other plants, meaning that the signals were often scarcely above background. Loading more sample is not necessarily a good idea as it increases the background intensity. The strength of the observation of absence of bands lies in the large number of samples- replicates and different species and tissues analysed, many of which are shown here to illustrate the observation. Had any sample shown clear beta-GGM bands as we find in all eudicots we studied, then this would be apparent we believe. Since beta-GGM is only a few percent of cell walls (Yu et al. 2022) this means our detection method is sensitive. Regarding Fig 3, the experimental setting is designed to discriminate the qualitative phenomenon of the presence or absence of a shift from the band containing the B side chain to the band containing the A side chain. The band intensities are not high (saturated) to make the increase in band intensity clear after galactosidase treatment. Aside from this, I have provided a marked up version of the manuscript with many comments where revisions might improve the clarity of presentation, flow and conventional use of the language. There were a number of spots in the Materials and Methods section where more details would be needed to replicate the experiments - this should be addressed. I hope my writing is legible and the feedback helpful for implementing revisions. Thank you for these helpful suggestions. According to your suggestions, we corrected our manuscript as much as possible. However, some points were not changed. The reasons for these are explained below. ・About the enzyme unit We couldn’t write specific enzyme unit because some of the enzymes are made on a non-commercial collaboration basis and we did not calculate an enzyme unit. We optimised with each enzyme the reaction conditions (amount of enzyme, reaction temperature, and reaction time) for the complete digestion of glucomannan- so the enzyme is in great excess. ・Regarding the schematic diagrams in Fig 1 and Fig 6 For Fig 1, a legend for the constituent sugars has been added. For the structure of xyloglucan in Fig. 6, we did not add a model diagram of the structure, as we believe that the nomenclature is well established in the field. https://doi.org/10.1371/journal.pone.0289581.r002
30 Oct 2023 Decision Letter - Olga A. Zabotina, Editor Differing structures of galactoglucomannan in eudicots and non-eudicot angiosperms PONE-D-23-22384R1 Dear Dr. Dupree, 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, Olga A. Zabotina, PhD Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0289581.r003
Formally Accepted
7 Nov 2023 Acceptance Letter - Olga A. Zabotina, Editor PONE-D-23-22384R1 Differing structures of galactoglucomannan in eudicots and non-eudicot angiosperms Dear Dr. Dupree: 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. Olga A. Zabotina Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0289581.r004

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