Distinct Short-Term Response of Intracellular Amino Acids in Saccharomyces cerevisiae and Pichia pastoris to Oxidative and Reductive Stress

Round 1

Reviewer 1 Report

The manuscript by Burcu Şirin Kaya & Emrah Nikerel describes the AA-based chemical response to oxidative and reductive stress of two yeast strains. This manuscript has interesting elements and provides relevant information for readers. However, some issues should be addressed before further consideration.

1.    Line 18: A conclusive sentence is missing.

2.    Abstract: Include specific results in the Abstract.

3.    Line 107: The origin of the test yeasts must be provided.

4.    Line 166: There is no information regarding the amino acid identification. I deduced that it was achieved by co-chromatography using commercially-purchased amino acid standards. If yes, the origin, quality, and brand of standard amino acids used for the quantification must be provided. Indeed, the method using external or internal standards is also lacking. If the authors employed external standards, the calibration curve information is missing and must be added.

5.    Line 172: Which units were used to express the quantified amino acid contents? Indeed, the results of individual amino acids must be provided as a Table in the supplementary material to support data availability.

6.    Figures 1 and 2: The resolution and size of these figures must be improved since the information is challenging to visualize.

7.    Figure 2: Indicate the unit of Y-axis in the time-series plots per amino acid.

8.    The discussion is highly descriptive and summarizes the results. In fact, some passages can be confused with result descriptions/explanations. Separating the results from the discussion into separate sections is recommended to visualize this study's contribution better. Therefore, the results can be exploited to provide a more comprehensive discussion, e.g., under comparison with previous studies or theory.

9. The conclusion section employs contextual ideas and summarizes the results. Therefore, it is recommended to rewrite conclusions from the results into conceptual findings from the mechanistic point of view.

There are several issues regarding grammar and style throughout the manuscript, so following the information/ideas is challenging. An editing service is recommended.

Author Response

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Author Response File: Author Response.pdf

Reviewer 2 Report

This article aims to assess the effect of oxidative and reductive stress on different yeasts, especially on intracellular amino acid profiles. Although the aim of this manuscript is reasonable, yet the data is not discussed well. The abstract and conclusion are not descriptive enough. In addition, the introduction does not provide the rationale behind the study. Material methods are unclear, e.g. what is the composition of stocks of vitamins and metals?

How many sample repetition was analyzed for comparison, no standard deviation was reported in the figures. The findings should be clearly highlighted and the significance of the study is also hard to follow.

Author Response

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Author Response File: Author Response.pdf

Reviewer 3 Report

Using conventional model yeast S. cerevisiae and non-conventional model yeast P. pastoris chemostat cultures as materials, the fermentation profiles, intracellular amino acid levels as well as intracellular glutathione levels, were monitored and compared in the manuscript. However, some issues still need to be solved.

1. There is no clear conclusion in the abstract. It should be rewritten.

2. Line 136, how was the concentration of 20 mM Dithiothreitol (DTT) determined? The relative information should be provided.

3. There is no result information of Figure1 in the result section of manuscript. Additionally, panel A, B, C, D in “Response to reductive stress (20 mM DDT)” should be changed into E, F, G, H.

4. It is suggested to separate Results & Discussion into two sections: Results section and Discussion section.

5. In Figure 2, please add the full names of the abbreviations in the metabolic pathway in figure legend. Additionally, please number the top panel as A, and bottom panel as B, for instance.

6. In line 316, “lastly, measured time profiles of glutathione and precursor amino acid profiles allows to point to potential bottlenecks in glutathione production in both yeasts”. But it seems there is no corresponding data presented in the manuscript.

Using conventional model yeast S. cerevisiae and non-conventional model yeast P. pastoris chemostat cultures as materials, the fermentation profiles, intracellular amino acid levels as well as intracellular glutathione levels, were monitored and compared in the manuscript. However, some issues still need to be solved.

1. There is no clear conclusion in the abstract. It should be rewritten.

2. Line 136, how was the concentration of 20 mM Dithiothreitol (DTT) determined? The relative information should be provided.

3. There is no result information of Figure1 in the result section of manuscript. Additionally, panel A, B, C, D in “Response to reductive stress (20 mM DDT)” should be changed into E, F, G, H.

4. It is suggested to separate Results & Discussion into two sections: Results section and Discussion section.

5. In Figure 2, please add the full names of the abbreviations in the metabolic pathway in figure legend. Additionally, please number the top panel as A, and bottom panel as B, for instance.

6. In line 316, “lastly, measured time profiles of glutathione and precursor amino acid profiles allows to point to potential bottlenecks in glutathione production in both yeasts”. But it seems there is no corresponding data presented in the manuscript.

Author Response

Please see the attachment.

Author Response File: Author Response.pdf

Reviewer 4 Report

I congratulate the authors for their work and manuscript. Manuscript ID: fermentation-2797571 "Distinct short-term response of intracellular amino acids in Saccharomyces cerevisiae and Pichia pastoris to oxidative and reductive stress" reports on the investigation of the effects of redox stresses on amino acid levels in two major yeast species of industrial importance. The manuscript is direct, addressing an objective experimental design. The text can be improved by revision by a English native speaker. Methods are described in enough detail for reproduction, including statistical analysis. The results are discussed in light of previous findings, and can be appreciated even by non-specialists. I will recommend acceptance for publication and only have a couple of minor suggestions: the Abstract can be extended by including more details of the major findings and impact of the study. This will improve the overall appreciation of the work that is being presented and might attract more readers to the full article.
In addition:
Figure 1: Define DO% in the legend.
Lines 157-158: Review sentence for clarity.

The text can be improved by revision by a English native speaker.

Author Response

Please see the attachment. 

Author Response File: Author Response.pdf

Round 2

Reviewer 3 Report

As the issues concerned has been revised, I suggest the acceptance of this manuscript.