A Physiogenomic Study of the Tolerance of Saccharomyces cerevisiae to Isoamyl Alcohol

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

1) I assume that ref1 deals with isoamyl salicylate but not isoamyl alcohol.

2) The authors should explain what GO means. They should also describe the tools to analyze GO enrichment.

3)Genotypes should be described in italics including text and figures. However, "WT BY4741" should not be italics in Fig. 3.

4) The authors should add GO numbers to prevent any confusion.

 

 

Author Response

Please refer to the attachment

Author Response File: Author Response.pdf

Reviewer 2 Report

Comments and Suggestions for Authors

In this study, S. cerevisiae was cultured under different concentrations of isoamyl alcohol stress to determine whether isoamyl alcohol has toxicity to S. cerevisiae and the magnitude of toxicit. In addition, transcriptome analysis was used to determine the functional genes that play a key role under isoamyl alcohol pressure, and the knockout strains of related genes were further cultured and verified to prove whether these key genes play important roles under isoamyl alcohol stress. The manuscript is well-structured and well-discussed. However, some points should be checked and corrected before it's accepted in this journal. 

Therefore, according to my comments, I recommended the publication of the paper after major revision

1)      The abstract provides valuable insights into the molecular responses of Saccharomyces cerevisiae to isoamyl alcohol stress. However, it could benefit from a sentence summarizing the key challenges in overcoming isoamyl alcohol toxicity for industrial fermentation processes."

2)      How do the down-regulation of cell wall and membrane-related genes correlate with the observed effects on cell wall stability and membrane fluidity in the presence of isoamyl alcohol?

3)      Were there any unexpected or counterintuitive gene expression patterns observed in the study that may warrant further investigation or explanation?

4)      Can you elaborate on the rationale behind selecting the identified key genes (CCW12, BGL2, NCW2, SUN4, ELO1, ERG2, FAA1, OPI3, ZWF1, PMC1) for knockout experiments and how their absence influenced the response to isoamyl alcohol stress?

5)      How generalizable are the findings from Saccharomyces cerevisiae to other microbial fermentation systems, and what implications might this have for the broader field of industrial fermentation?

6)      Were there any specific challenges or limitations encountered during the RNA-Seq analysis, and how were these addressed to ensure the reliability of the results?

7)      Considering the potential use of isoamyl alcohol as a fuel, could you discuss the practical applications of these findings in terms of engineering yeast strains for improved tolerance and enhanced biofuel production?

8)      Were there any indications of long-term adaptive changes in gene expression or physiological responses when Saccharomyces cerevisiae was continuously exposed to isoamyl alcohol, and how might this impact its potential for industrial-scale fermentation?

9)      In the context of the study's focus on energy production-related genes, how might the up-regulation of ATP biosynthesis and NADPH biosynthesis genes contribute to the overall cellular response to isoamyl alcohol stress?

10)  Can you provide insights into how the identified molecular responses to isoamyl alcohol stress align with existing knowledge on stress responses in Saccharomyces cerevisiae and other yeast species?

Conclusions: It would be beneficial to include a brief statement on the potential practical applications of the study findings, particularly in the context of engineering yeast strains for improved isoamyl alcohol tolerance in industrial settings

Comments on the Quality of English Language

In this study, S. cerevisiae was cultured under different concentrations of isoamyl alcohol stress to determine whether isoamyl alcohol has toxicity to S. cerevisiae and the magnitude of toxicit. In addition, transcriptome analysis was used to determine the functional genes that play a key role under isoamyl alcohol pressure, and the knockout strains of related genes were further cultured and verified to prove whether these key genes play important roles under isoamyl alcohol stress. The manuscript is well-structured and well-discussed. However, some points should be checked and corrected before it's accepted in this journal. 

Therefore, according to my comments, I recommended the publication of the paper after major revision

1)      The abstract provides valuable insights into the molecular responses of Saccharomyces cerevisiae to isoamyl alcohol stress. However, it could benefit from a sentence summarizing the key challenges in overcoming isoamyl alcohol toxicity for industrial fermentation processes."

2)      How do the down-regulation of cell wall and membrane-related genes correlate with the observed effects on cell wall stability and membrane fluidity in the presence of isoamyl alcohol?

3)      Were there any unexpected or counterintuitive gene expression patterns observed in the study that may warrant further investigation or explanation?

4)      Can you elaborate on the rationale behind selecting the identified key genes (CCW12, BGL2, NCW2, SUN4, ELO1, ERG2, FAA1, OPI3, ZWF1, PMC1) for knockout experiments and how their absence influenced the response to isoamyl alcohol stress?

5)      How generalizable are the findings from Saccharomyces cerevisiae to other microbial fermentation systems, and what implications might this have for the broader field of industrial fermentation?

6)      Were there any specific challenges or limitations encountered during the RNA-Seq analysis, and how were these addressed to ensure the reliability of the results?

7)      Considering the potential use of isoamyl alcohol as a fuel, could you discuss the practical applications of these findings in terms of engineering yeast strains for improved tolerance and enhanced biofuel production?

8)      Were there any indications of long-term adaptive changes in gene expression or physiological responses when Saccharomyces cerevisiae was continuously exposed to isoamyl alcohol, and how might this impact its potential for industrial-scale fermentation?

9)      In the context of the study's focus on energy production-related genes, how might the up-regulation of ATP biosynthesis and NADPH biosynthesis genes contribute to the overall cellular response to isoamyl alcohol stress?

10)  Can you provide insights into how the identified molecular responses to isoamyl alcohol stress align with existing knowledge on stress responses in Saccharomyces cerevisiae and other yeast species?

Conclusions: It would be beneficial to include a brief statement on the potential practical applications of the study findings, particularly in the context of engineering yeast strains for improved isoamyl alcohol tolerance in industrial settings

Author Response

Please refer to the attachment

Author Response File: Author Response.pdf

Round 2

Reviewer 2 Report

Comments and Suggestions for Authors

Requested corrections were completed.

Comments on the Quality of English Language

Requested corrections were completed.