Comparing Transcriptome Profiles of Saccharomyces Cerevisiae Cells Exposed to Cadmium Selenide/Zinc Sulfide and Indium Phosphide/Zinc Sulfide
Round 1
Reviewer 1 Report
In this article, Horstmann and Kim have tested the effects of sub lethal doses of quantum dots, CdSe/ZnS and InP/ZnS, on the growth and physiology of budding yeast. They have used different parameters to test the effects of QDs toxicity including growth assay, ROS estimation and RNA Seq analysis and found that both the tested QDs produce mild but different toxicities to the cells. RNA Seq data showed differential expression profiles in CdSe/ZnS and InP/ZnS however I am wondering if the authors have verified these results by qPCR analysis. It would be interesting if they can do some qPCR verification of up- and down regulated genes. Overall, the authors study is reasonably well executed and contributes an important information regarding QD based toxicities in the yeast model.
Suggestions-
-Please do qPCR analysis to verify some up- and down regulated genes in both arms to confirm the results of RNA seq analysis.
-Please add scale bar to fig. 4.
Author Response
This letter is to follow the first revisions of our manuscript “Comparing Transcriptome Profiles Exposed to Cadmium Selenide/Zinc Sulfide and Indium Phosphide/Zinc Sulfide in Saccharomyces cerevisiae”. We appreciate the time and effort put forth by the reviewers to improve the quality of our manuscript. We have reviewed all of the reviewer’s comments and put much effort in to revising each one.
After reading our manuscript, the reviewers believe that our study is reasonably well executed and contributes important information regarding QD-based toxicities in the yeast model. All revisions can be seen in the manuscript due to the use of the track changes function on Microsoft Word. More detailed responses can be found below following the reviewer’s comments, which are red and bolded.
Reviewer 1:
“Please do qPCR analysis to verify some up- and down regulated genes in both arms to confirm the results of RNA seq analysis”
The authors have conducted an RT-qPCR experiment with a gene (YPT53) significantly downregulated in both CdSe/ZnS and InP/ZnS-treated groups. The resulting fold-change results indicated YPT53 was downregulated compared to the reference gene (ALG9) in both CdSe/ZnS and InP/ZnS-treated groups, but the difference in fold-change was not statistically significant in either group.
The authors provided a figure for our RT-qPCR data and inserted it directly after line 415 on page 12. The new RT-qPCR figure replaced Fig. 3, so every figure after Fig. 3 was changed. For example, Fig. 3 before we inserted the new figure was changed to Fig. 4 and so on.
“Please add scale bar to fig. 4”
We added scale bard in the figure, which is now figure 5.
Thank you again for considering publication of the revised MS in your journal.
Dr. Kyoungtae Kim
Missouri State University
Reviewer 2 Report
The article is of interest for understanding of the mechanisms of toxicity of heavy metals. However, by my opinion, revision of the manuscript required .
The article title needs modification
Transcriptome Profiles of Cadmium Selenide/Zinc …
Probably, «under exposure with Cadmium Selenide/Zinc…
“2.2. Growth assay with exposure to CdSe/ZnS and InP/ZnS QDs 104
Wild-type S. cerevisiae S288C cells (MATα SUC2 gal2 mal2 mel flo1 flo8–1 hap1)
The strain is not a wild –type strain.
Results
Fig. 1A It is not clear enough how the authors explain the stimulation of yeast growth in the presence of CdSe/ZnS
Page 6 Table 1, Probably this Table is a technical mistake ?
In the discussion, it would be useful to compare the biological effect of the compounds used by the authors with the effect of cadmium inov on yeast cells. There is a lot of literature data on this issue. For example:
Wysocki R, Tamás MJ. How Saccharomyces cerevisiae copes with toxic metals and metalloids. FEMS Microbiol Rev. 2010 Nov;34(6):925-51. doi: 10.1111/j.1574-6976.2010.00217.x. PMID: 20374295.
Tamás MJ, Fauvet B, Christen P, Goloubinoff P. Misfolding and aggregation of nascent proteins: a novel mode of toxic cadmium action in vivo. Curr Genet. 2018 Feb;64(1):177-181. doi: 10.1007/s00294-017-0748-x. Epub 2017 Sep 21. PMID: 28936749; PMCID: PMC5778182.
Ozturk M, Metin M, Altay V, De Filippis L, Ünal BT, Khursheed A, Gul A, Hasanuzzaman M, Nahar K, Kawano T, Caparrós PG. Molecular Biology of Cadmium Toxicity in Saccharomyces cerevisiae. Biol Trace Elem Res. 2021 Jan 18. doi: 10.1007/s12011-021-02584-7. Epub ahead of print. PMID: 33462792.
Rajakumar S, Abhishek A, Selvam GS, Nachiappan V. Effect of cadmium on essential metals and their impact on lipid metabolism in Saccharomyces cerevisiae. Cell Stress
Author Response
This letter is to follow the first revisions of our manuscript “Comparing Transcriptome Profiles Exposed to Cadmium Selenide/Zinc Sulfide and Indium Phosphide/Zinc Sulfide in Saccharomyces cerevisiae”. We appreciate the time and effort put forth by the reviewers to improve the quality of our manuscript. We have reviewed all of the reviewer’s comments and put much effort in to revising each one.
After reading our manuscript, the reviewers believe that our study is reasonably well executed and contributes important information regarding QD-based toxicities in the yeast model. All revisions can be seen in the manuscript due to the use of the track changes function on Microsoft Word. More detailed responses can be found below following the reviewer’s comments, which are red and bolded.
Reviewer 2:
“The article title needs modification”
The authors have modified the title and changed it from “Comparing Transcriptome Profiles of Cadmium Selenide/Zinc Sulfide in Saccharomyces cerevisiae” to “Comparing Transcriptome Profiles Exposed to Cadmium Selenide/Zinc Sulfide in Saccharomyces cerevisiae”.
“2.2. Growth assay with exposure to CdSe/ZnS and InP/ZnS QDs
Wild-type S. cerevisiae S288C cells (MAT-alpha SUC2 gal2 mal2 mel flo1 flo8-1 hap1)
The strain in not a wild-type strain”
The authors have modified this section on line 121 by removing “Wild-type” so it reads: “S. cerevisiae S288C cells (MATα SUC2 gal2 mal2 mel flo1 flo8–1 hap1) were purchased from…”
“Results
Fig. 1A It is not clear enough how the authors explain the stimulation of yeast growth in the presence of CdSe/ZnS”
The authors recognize that the explanation in the results section over Fig. 1A was not clear. We have revised the section starting on line 259-274. We explained, in greater detail and in easier language, the results of the growth curves in both CdSe/ZnS and InP/ZnS treated samples and the authors also added more details to the endpoints bar-graph data section (Fig. 1 C&D).
“Page 6 Table 1, Probably this Table is a technical mistake?”
The authors recognize that the table that was on page 6 labeled table 1 was a technical mistake where we forgot to delete the example table that was on the manuscript template word document. The authors have deleted the table that was on page 6.
“In the discussion, it would be useful to compare the biological effect of the compounds used by the authors with the effect of cadmium inov on yeast cells.”
The authors recognize that the addition of a section that compares the transcriptomic profile of CdSe/ZnS in yeast to the transcriptomic profile of Cd metal. We inserted this new section at the end of the discussion section starting on page 26 and line 800. The authors titled the section “4.5. Comparing the biological effects of CdSe/ZnS with known biological effects of Cd in Saccharomyces cerevisiae” and we discuss the difference between the transcriptomic profile of CdSe/ZnS QDs that we observed in our RNA-seq data and the common metal-responsive gene response.
Thank you again for considering publication of the revised MS in your journal.
Dr. Kyoungtae Kim
Missouri State University
Round 2
Reviewer 2 Report
My suggestion for the article title is:
Comparing Transcriptome Profiles of Saccharomyces cerevisiae cells
Exposed to Cadmium Selenide/Zinc Sulfide
In this paper, two effects are considered: one (the exposition with InP/ZnS leads to inhibition of growth, and the other ( the exposition with CdSe/ZnS) leads to stimulate yeast growth. The reasons of increase in optical density of yeast culture and decrease in the length of the lag-phase in the case of exposition with CdSe/ZnS needs to be clearly explained in terms of the observed changes in gene expression.
Author Response
This letter is to follow the second revisions of our manuscript “Comparing Transcriptome Profiles of Saccharomyces cerevisiae cells Exposed to Cadmium Selenide/Zinc Sulfide”. We once again appreciate the time spent by the reviewers to help improve our work. We have reviewed the reviewer’s comments again and have revised and responded to each.
After reading our manuscript, the reviewers suggested we slightly alter our title and give an explanation on some of our cellular viability experiment results.
All revisions can be seen in the manuscript with the track changes function. More detailed responses can be found below following the reviewer’s comments, which are red and bolded.
“My suggestion for the article title is: Comparing Transcriptome Profiles of Saccharomyces cerevisiae cells Exposed to Cadmium Selenide/Zinc Sulfide”
The authors have considered the reviewer’s suggestion as a title for the manuscript and cannot change the title to “Comparing Transcriptome Profiles of Saccharomyces cerevisiae cells Exposed to Cadmium Selenide/Zinc Sulfide” because it does not accurately represent the comparison between CdSe/ZnS and InP/ZnS induced changes in yeast’s transcriptome. The authors believe the current title accurately encompasses that comparison, which can be seen on line 2-4.
In this paper, two effects are considered: one (the exposition with InP/ZnS leads to inhibition of growth, and the other (the exposition with CdSe/ZnS) leads to stimulate yeast growth. The reasons of increase in optical density of yeast culture and decrease in the length of the lag-phase in the case of exposition with CdSe/ZnS needs to be clearly explained in terms of the observed changes in gene expression.
The authors have read the reviewer’s request for explaining why CdSe/ZnS stimulates yeast growth and decreases the time spent in lag-phase with observed changes in gene expression. We speculated briefly on the changes with our gene expression data on lines 622-626.
Thank you again for considering publication of the revised MS in your journal.
