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Article
Peer-Review Record

Novel Selectable Marker Sesquiterpenoid Antibiotic Pentalenolactone

Int. J. Mol. Sci. 2024, 25(24), 13328; https://doi.org/10.3390/ijms252413328
by Arina A. Nikandrova 1,2,3, Anna D. Petriakova 2, Anton R. Izzi 1,4, Garegin A. Petrosyan 5, Vadim N. Tashlitsky 6, Vera A. Alferova 3,7, Tatiana V. Panova 6, Maria G. Khrenova 6,8, Mikhail V. Biryukov 2,9, Yuliya V. Zakalyukina 5, Maria I. Zvereva 6, Dmitrii A. Lukianov 1,6,* and Petr V. Sergiev 1,3,6
Reviewer 1: Anonymous
Reviewer 2: Anonymous
Int. J. Mol. Sci. 2024, 25(24), 13328; https://doi.org/10.3390/ijms252413328
Submission received: 1 November 2024 / Revised: 4 December 2024 / Accepted: 6 December 2024 / Published: 12 December 2024
(This article belongs to the Special Issue Antimicrobial Agents and Resistance Mechanisms)

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

The authors create a selectable marker with pentalenolactone sesquiterpenoid antibiotic, and their studies could contribute to the development of more tools for current genetic operations. However, the aims of this manuscript are ambiguous. The opening clues point at antibiotic resistance, whereas the following results turn to provide a genetic tool with new selectable marker. The results sections include many viewpoints from references, and it’s misleading for the readers. The nomination of plasmids and the labeling of figures are inconsistent. The explanations of the images are insufficient. Actually, since 2008, Liebeke has reported that quinone compounds target gapA (Mol Microbiol. 2008, 69:1513-29). Therefore, it’s inappropriate to claim that “it expands the scope of ….molecular biology.” In addition, some other concerns are listed below:

1.         Line 92/93 The species’ name and genes should be written in italics typeface. Correct the same problems throughout the manuscript.

2.         The explanation to each experimental Figure should be expanded. The authors should provide a detailed interpretation of the results, highlighting key findings and their implications.

3.         The quality of Figure 1 is not good enough to recognize its characteristics.

4.         The authors claimed the characteristics of fugal strain only based on the morphology of a single hypha in Figure 3. More proofs or a figure containing more hyphae should be supplied to support this claim.

5.         Converting the results of Table 1 into graphical format would make the data more intuitive and easier to understand.

6.         Line 134-138, Line 201-204, Line 214-222. The tense throughout the entire text should remain consistent, and the description of results should be in the past tense.

7.         The quality of Figure 4 should be enhanced. The resolution of the picture is low, which affects its clarity and detail.

8.         “ug/ml” should be revised to “μg/mL”. Correct it through the whole paper.

9.         Line 230, the sentence of “It had a concentration of 50 ug/ml” is ambiguous.

10.      Figure 9, The labels of “pCDF_PLR” or “pRFPCER” could not be found in this figure.

11.      In Table 3, it’s hard to understand “non-resistant cells”. Does it mean the strain E. coli DH5α with control plasmid pRFPCER without gapA?

12.      The detailed information of all instruments, reagents, especially the strains and the plasmids should be provided.

13.      The section of Statistical Analysis in methods are lacking. The author should provide a detailed description of the statistical methods used in this study.

 

Comments on the Quality of English Language

  The formatting of this manuscript needs significant improvement, especially the units and temperature indications. The English language must be revised. The writing is too colloquial.

Author Response

Thank you very much for getting acquainted with our work and for carefully approaching the process of leaving comments on it. Your comments have helped us improve our work and we are now presenting the revised version. We have also slightly changed the introduction to put more emphasis on the story of resistant markers.

Feedback on the text and our responses.

  1. Line 92/93 The species’ name and genes should be written in italics typeface. Correct the same problems throughout the manuscript.
    1. Response: Thank you for your comment. We have fixed it throughout the text.
  2. The explanation to each experimental Figure should be expanded. The authors should provide a detailed interpretation of the results, highlighting key findings and their implications.
    1. Response: We appreciate your comment and have enhanced the text to ensure that every image has an in-depth description.
  3. The quality of Figure 1 is not good enough to recognize its characteristics.
    1. Response: We appreciate your feedback. We have enhanced the quality of the picture.
  4. The authors claimed the characteristics of fugal strain only based on the morphology of a single hypha in Figure 3. More proofs or a figure containing more hyphae should be supplied to support this claim
    1. Response: We have added pictures with different magnification options.
  5. Converting the results of Table 1 into graphical format would make the data more intuitive and easier to understand.
    1. Response: We are grateful for your comment and have made the table more understandable.
  6. Line 134-138, Line 201-204, Line 214-222. The tense throughout the entire text should remain consistent, and the description of results should be in the past tense.
    1. Response: Thank you for your comment. We have made improvements to these parts of the text and reviewed all others.
  7. The quality of Figure 4 should be enhanced. The resolution of the picture is low, which affects its clarity and detail.
    1. Response: We have improved the picture's quality.
  8. “ug/ml” should be revised to “μg/mL”. Correct it through the whole paper.
    1. Response: We have modified the text.
  9. Line 230, the sentence of “It had a concentration of 50 ug/ml” is ambiguous. 
    1. Response: The fragment of text was reworked
  10. Figure 9, The labels of “pCDF_PLR” or “pRFPCER” could not be found in this figure.
    1. Response: This picture has been improved.
  11. In Table 3, it’s hard to understand “non-resistant cells”. Does it mean the strain coliDH5α with control plasmid pRFPCER without gapA? 
    1. Response: Your comment is much appreciated. To make the text clearer, we added a more detailed explanation of this experiment and changed the names of the constructions to more understandable ones.
  12. The detailed information of all instruments, reagents, especially the strains and the plasmids should be provided.
    1. Response: We have added all the requested information.
  13. The section of Statistical Analysis in methods are lacking. The author should provide a detailed description of the statistical methods used in this study.
    1. Response: Thank you for your comment. In our work, the only place where we present numerical values is the MIC values. The typical procedure for microbiological measurements involves conducting three experiments and obtaining the most frequently encountered result, which does not require statistical processing. A clarification about this feature of MIC measurement has been added to the corresponding section.

Reviewer 2 Report

Comments and Suggestions for Authors

A nice study which can be of impact for biotechnology and molecular biology studying the phenotypic, morphological characteristics of the Streptomyces sp AP22 (that is capable of producing pentalenolactone) and its biological activity, targeting selectable markers, created by genetic constructs including the gene of glyceraldehyde-3-phosphate dehydrogenase with a resistance mutation.

The study could be considered as new and valuable.

Introduction part is well written, but please develop this part by introducing data from main-stream about  the genes which encodes glyceraldehyde-3-phosphate dehydrogenase, that leads to resistance.

Author Response

Thank you for getting acquainted with our work and for your feedback. The important part of the text has been included in the introduction after your suggestion.

Round 2

Reviewer 1 Report

Comments and Suggestions for Authors

Almost all the comments have been adequately taken into account. However, the abstract should be further revised. It’s inappropriate to claim that “it expands the scope of ….molecular biology.”

Author Response

Thank you very much for your impact on improving our work!
The abstract has been improved and we are now uploading a modified version.

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