MTSviewer: A database to visualize mitochondrial targeting sequences, cleavage sites, and mutations on protein structures

Andrew N. Bayne; Jing Dong; Saeid Amiri; Sali M. K. Farhan; Jean-François Trempe

doi:10.1371/journal.pone.0284541

Peer Review History

Original SubmissionNovember 16, 2022
31 Jan 2023 Decision Letter - Vivek Kumar, Editor PONE-D-22-31504MTSviewer: a database to visualize mitochondrial targeting sequences, cleavage sites, and mutations on protein structuresPLOS ONE Dear Dr. Trempe, 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 Mar 17 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. 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 you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter. 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, Vivek Kumar, Ph. D. 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. 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. Additional Editor Comments: In this manuscript, the authors present MTSViewer, a database for the study of mitochondrial proteins that integrates a number of features such as cleavage predictions, pathogenicity predictions, N-terminomics, genetic variants, and structural visualization using AlphaFold models. They have integrated a number of tools and algorithms into an intuitive, user-friendly, online platform and the capabilities of the database including the workflow, user interface, and an example case study have been mostly described satisfactorily. While the code and data are currently accessible from the public GitHub link shared by the authors, the contents on GitHub link can be revised or removed anytime. We would like to ensure that there is persistent access to them for PLOS ONE readers. Fortunately, there are numerous options available to facilitate this, which authors can exercise as per their convenience. The authors can preferably make the GitHub repository archivable using tools such as Zenodo. They can alternatively consider uploading the archived repository as a DOI artifact on a site like Mendeley and share the DOI in their revised submission. Or, they can also upload these files in a compressed/zipped file format as a supplement to this submission on PLOS ONE site. Eitherway, the authors should revise the submission with additional links based on the options discussed. Also, an examination of the online repository suggests that some of the PDB files were omitted because of the directory size limit of 1000 files with the following message “Sorry, we had to truncate this directory to 1,000 files. 1,026 entries were omitted from the list.” https://github.com/neurobioinfo/MTSvieweR/tree/main/MTSvieweR/PDBs/PDB_original https://github.com/neurobioinfo/MTSvieweR/tree/main/MTSvieweR/PDBs/PDB_extracted The authors can address this issue in a few different ways including archiving the PDB files into one or more zipped files to overcome the file count limit. In addition, the authors are advised to address the valuable feedback below shared by the reviewer. Bayne et al developed and present a novel database (MTSViewer) to consolidate predictions of MTS using multiple predictors, genetic variations, and predicted protein structures by AlphaFold. As described by authors, mitochondria play important roles in eukaryotic cells, and disturbance of targeting signal by genetic variants could potentially lead to dysfunction of this organelle. MTSViewer server is working well, and this platform could potentially be a useful resource for the community. I haven't seen any engineering or technical issues in the server. I feel however the authors should clarify some important aspects. 1. I understand that MTSViewer focuses on MTS (N-MTS and iMTS), however, it should be stated and argued in the context of mitochondrial protein database construction. The introduction section lacks referring to the other mitochondrial protein databases (only slightly mentioned in line 79), and it would be helpful if the currently existing databases are discussed in the section. 2. Comparison to similar databases section mainly discusses the novelty of MTSViewer, emphasizing integrating recent MTS predictors to connect variant information with such predictions. To my best knowledge, a similar approach was taken by another database MitoMiner (http://mitominer.mrc-mbu.cam.ac.uk/). Unfortunately, the database seems to be down for now, but MitoMiner collected genetic variants, pathogenicity information from OMIM, and MTS prediction results for mitochondrial genes. Indeed, MitoMiner was cited by the authors and incorporated into MTSViewer as described in line 105. The advantages and disadvantages of MTSViewer in comparison to MitoMiner (or another similar database) should be discussed as well rather than citing the database as one of the data sources. 3. The utilization of a predicted protein structure in MTSViewer is a bit unclear. As discussed in the main text, N-terminal MTS tends to have a low confidence score of AlphaFold and be shown as unstructured. Indeed, the region doesn’t have a high degree of conservation basically, inferring weaker evolutionary constraint for structuring than at least that for the main body. In contrast, it seems that showing the structure would be more important in the context of iMTS. Although the authors introduced Pink1 as a use case for N-terminal MTS and some iMTS, it would be helpful to discuss other interesting cases in the iMTS context and why structure information is important in this new database in addition to Pink1 case for N-MTS. I understand the C-terminal of Pink1 has a moderate iMLP score, however, it would convince more with an example having a higher score if it’s available. [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: Partly ******** 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? 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 ****** 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 ****** 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: Bayne et al developed and present a novel database (MTSViewer) to consolidate predictions of MTS using multiple predictors, genetic variations, and predicted protein structures by AlphaFold. As described by authors, mitochondria play important roles in eukaryotic cells, and disturbance of targeting signal by genetic variants could potentially lead to dysfunction of this organelle. MTSViewer server is working well, and this platform could potentially be a useful resource for the community. I haven't seen any engineering or technical issues in the server. I feel however the authors should clarify some important aspects. 1. I understand that MTSViewer focuses on MTS (N-MTS and iMTS), however, it should be stated and argued in the context of mitochondrial protein database construction. The introduction section lacks referring to the other mitochondrial protein databases (only slightly mentioned in line 79), and it would be helpful if the currently existing databases are discussed in the section. 2. Comparison to similar databases section mainly discusses the novelty of MTSViewer, emphasizing integrating recent MTS predictors to connect variant information with such predictions. To my best knowledge, a similar approach was taken by another database MitoMiner (http://mitominer.mrc-mbu.cam.ac.uk/). Unfortunately, the database seems to be down for now, but MitoMiner collected genetic variants, pathogenicity information from OMIM, and MTS prediction results for mitochondrial genes. Indeed, MitoMiner was cited by the authors and incorporated into MTSViewer as described in line 105. The advantages and disadvantages of MTSViewer in comparison to MitoMiner (or another similar database) should be discussed as well rather than citing the database as one of the data sources. 3. The utilization of a predicted protein structure in MTSViewer is a bit unclear. As discussed in the main text, N-terminal MTS tends to have a low confidence score of AlphaFold and be shown as unstructured. Indeed, the region doesn’t have a high degree of conservation basically, inferring weaker evolutionary constraint for structuring than at least that for the main body. In contrast, it seems that showing the structure would be more important in the context of iMTS. Although the authors introduced Pink1 as a use case for N-terminal MTS and some iMTS, it would be helpful to discuss other interesting cases in the iMTS context and why structure information is important in this new database in addition to Pink1 case for N-MTS. I understand the C-terminal of Pink1 has a moderate iMLP score, however, it would convince more with an example having a higher score if it’s available. ****** 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 ******** [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.0284541.r001
Revision 1
24 Mar 2023 Author Response Editor comments and author response In this manuscript, the authors present MTSViewer, a database for the study of mitochondrial proteins that integrates a number of features such as cleavage predictions, pathogenicity predictions, N-terminomics, genetic variants, and structural visualization using AlphaFold models. They have integrated a number of tools and algorithms into an intuitive, user-friendly, online platform and the capabilities of the database including the workflow, user interface, and an example case study have been mostly described satisfactorily. While the code and data are currently accessible from the public GitHub link shared by the authors, the contents on GitHub link can be revised or removed anytime. We would like to ensure that there is persistent access to them for PLOS ONE readers. Fortunately, there are numerous options available to facilitate this, which authors can exercise as per their convenience. The authors can preferably make the GitHub repository archivable using tools such as Zenodo. They can alternatively consider uploading the archived repository as a DOI artifact on a site like Mendeley and share the DOI in their revised submission. Or, they can also upload these files in a compressed/zipped file format as a supplement to this submission on PLOS ONE site. Eitherway, the authors should revise the submission with additional links based on the options discussed. We thank the editor for their comments and agree that persistent access to MTSviewer is essential. As suggested, we have archived the GitHub repository with Zenodo (DOI: 10.5281/zenodo.7768427). We have added the Zenodo DOI to the manuscript under the section “Availability of data and materials”. Also, an examination of the online repository suggests that some of the PDB files were omitted because of the directory size limit of 1000 files with the following message “Sorry, we had to truncate this directory to 1,000 files. 1,026 entries were omitted from the list.” https://github.com/neurobioinfo/MTSvieweR/tree/main/MTSvieweR/PDBs/PDB_original https://github.com/neurobioinfo/MTSvieweR/tree/main/MTSvieweR/PDBs/PDB_extracted The authors can address this issue in a few different ways including archiving the PDB files into one or more zipped files to overcome the file count limit. We have tested the offline download from GitHub and can confirm that all 2,000+ PDB files are downloaded correctly and work as intended. The directory size truncation is only a visual warning on the GitHub website and does not remove any of the files when the package is downloaded as a ZIP or pulled directly from GitHub. Still, we have uploaded an “AllPDBs.zip” in the PDB folder using GitHub Large File Storage. Reviewer comments and author response Bayne et al developed and present a novel database (MTSViewer) to consolidate predictions of MTS using multiple predictors, genetic variations, and predicted protein structures by AlphaFold. As described by authors, mitochondria play important roles in eukaryotic cells, and disturbance of targeting signal by genetic variants could potentially lead to dysfunction of this organelle. MTSViewer server is working well, and this platform could potentially be a useful resource for the community. I haven't seen any engineering or technical issues in the server. I feel however the authors should clarify some important aspects. 1. I understand that MTSViewer focuses on MTS (N-MTS and iMTS), however, it should be stated and argued in the context of mitochondrial protein database construction. The introduction section lacks referring to the other mitochondrial protein databases (only slightly mentioned in line 79), and it would be helpful if the currently existing databases are discussed in the section. We agree with the reviewer. We have added new examples of other mitochondrial databases for comparison and have merged the “Comparison to other databases” section (previously at the end of the text) directly into the introduction. These changes are now seen at lines 93-114. 2. Comparison to similar databases section mainly discusses the novelty of MTSViewer, emphasizing integrating recent MTS predictors to connect variant information with such predictions. To my best knowledge, a similar approach was taken by another database MitoMiner (http://mitominer.mrc-mbu.cam.ac.uk/). Unfortunately, the database seems to be down for now, but MitoMiner collected genetic variants, pathogenicity information from OMIM, and MTS prediction results for mitochondrial genes. Indeed, MitoMiner was cited by the authors and incorporated into MTSViewer as described in line 105. The advantages and disadvantages of MTSViewer in comparison to MitoMiner (or another similar database) should be discussed as well rather than citing the database as one of the data sources. We thank the reviewer for this comment and agree it is critical to compare the utility of MTSviewer directly to MitoMiner. While the MitoMiner database is unfortunately still inaccessible, we used an archived version of the web page to access it. As in point #1, this direct comparison has also been included in the new introduction paragraph (commentary on MitoMiner can be found in lines 93-100 as well as 130-135). We also believe that our addition of new MTS profiling data and specific case studies (see question #3 below) implicitly highlights the utility of MTSviewer compared to MitoMiner and other pre-existing databases. 3. The utilization of a predicted protein structure in MTSViewer is a bit unclear. As discussed in the main text, N-terminal MTS tends to have a low confidence score of AlphaFold and be shown as unstructured. Indeed, the region doesn’t have a high degree of conservation basically, inferring weaker evolutionary constraint for structuring than at least that for the main body. In contrast, it seems that showing the structure would be more important in the context of iMTS. Although the authors introduced Pink1 as a use case for N-terminal MTS and some iMTS, it would be helpful to discuss other interesting cases in the iMTS context and why structure information is important in this new database in addition to Pink1 case for N-MTS. I understand the C-terminal of Pink1 has a moderate iMLP score, however, it would convince more with an example having a higher score if it’s available. We thank the reviewer for this comment and have adjusted the text substantially to address this. We added two new sections titled “Global profiling of MTS in human proteins” (line 245-282) and “Structural analysis of iMTS-containing proteins” (line 283-376). In this section: A. We generated new data that directly shows the relationship between MTS score and AlphaFold confidence across the human mitoproteome (Fig 3), providing quantitative evidence to show that while N-MTS’s are mostly unstructured, there are also a significant amount of iMTS’s which exist in high-confidence regions of the AlphaFold predictions. B. We created a new supplemental dataset that counts the number of MTS’s and their location in each protein (across both human and yeast mitoproteomes), both as a resource for the community and to identify new case studies to address this point. In the text, we use this dataset to highlight other human MTS-containing proteins (eg. POLRMT, MAVS, KMO, PUSL1) (line 307-376) and discuss the benefit of considering structural context when investigating MTS’s and mitochondrial import. C. We specifically highlight the structural context of KMO and PUSL1 MTS’s (Fig 4) and discuss the broader utility of MTSviewer, both in the context of previous work in yeast/TOM70 studies and as a resource for studying iMTS-containing proteins in humans. To accurately address all of these comments, we have added new references to the revised version of the manuscript: within the “Global profiling of MTS’s and other case studies” section (references #56-62) and within the introduction (references #13-15 and #24-29). Overall, we believe that the reviewer highlighted key shortcomings in our article that we have sought to address with these new additions. We believe that we have substantially improved our manuscript thanks to the reviewer’s insightful commentary. Thank you for your consideration. Attachments Attachment Submitted filename: Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0284541.r002
3 Apr 2023 Decision Letter - Vivek Kumar, Editor MTSviewer: a database to visualize mitochondrial targeting sequences, cleavage sites, and mutations on protein structures PONE-D-22-31504R1 Dear Dr. Trempe, 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, Vivek Kumar, Ph. D. Academic Editor PLOS ONE Additional Editor Comments (optional): The authors have made significant revisions in response to the the last round of review. Here are the key revisions: They have included references to and comparison with other mitochondrial data sources and tools including MitoMiner. They have also included robust examples and use-cases to highlight the utilization of predicted protein structure in MTSViewer and have added new datasets, two figures and two sections in support of this. They have uploaded additional PDB files to ensure that they are accessible. Also, they have persisted the raw data and supporting Python scripts used in the MTSviewer at GitHub using Zenodo. The authors have also updated the organization and the format of the sections to improve the readability of the manuscript and have uploaded the figures as tiff instead of eps for improved cross-platform access. The manuscript is being recommended for publication in the PLOS ONE. Congratulations! https://doi.org/10.1371/journal.pone.0284541.r003
Formally Accepted
13 Apr 2023 Acceptance Letter - Vivek Kumar, Editor PONE-D-22-31504R1 MTSviewer: a database to visualize mitochondrial targeting sequences, cleavage sites, and mutations on protein structures Dear Dr. Trempe: 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. Vivek Kumar Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0284541.r004

Open letter on the publication of peer review reports

PLOS recognizes the benefits of transparency in the peer review process. Therefore, we enable the publication of all of the content of peer review and author responses alongside final, published articles. Reviewers remain anonymous, unless they choose to reveal their names.

We encourage other journals to join us in this initiative. We hope that our action inspires the community, including researchers, research funders, and research institutions, to recognize the benefits of published peer review reports for all parts of the research system.

Learn more at ASAPbio .