Construction and Optimization of Malonyl-CoA Sensors in Saccharomyces cerevisiae by Combining Promoter Engineering Strategies

Round 1

Reviewer 1 Report

The authors have constructed an optimized malonyl-CoA biosensor with the FapO/FapR system in Saccharomyces cerevisiae via various engineering techniques. Analysis of operator insertion sites, promoter combinations, intron insertions, and transcription factor modifications resulted in the sensor H-pCCW12(TFBS)-Cti6~fapR. Based on the results provided, the authors claim the sensor had the lowest background noise, doubled response range, and higher response sensitivity than the original sensor.

Major suggestions/ Corrections: 

 

1. I think it is difficult to agree that the results presented in Figure 2a “proves that the fapo/fapr system worked in the strain”. What exactly is being compared to reach this conclusion? is a t test done on that data to establish the statistical significance? Additionally, “the overall pENO2 group was less sensitive to Malonyl-CoA “ however there is no significant difference after addition of cerulenin with FapR present. Please elaborate on how that conclusion was determined instead of concluding the pENO2 (up or down) promoter was not a viable sensor for mCoA detection?

2. Page 6/ Figure 3. Can you comment on the exclusion of constructs with 12 bp downstream of the TATA-Box from analysis and engineered combination sites? It seems based on the data provided, that sites 12 and 22 have very similar outputs and 12 produced a much better response than 32 and 17 bp. Additionally, based on the results provided, the 12 bp downstream site produced similar GFP intensity to the p(FapO) control which would seem to indicate a more powerful sensor compared to 22 bp downstream. It is suggested to add additional experiments where 12bp downstream is further analyzed alone and in combination with the other sites chosen.

3. Please discuss why the sensor H-pCCW12(TFBS)-fapR was chosen for Cti6 and Gal80 fusion over the H-pCCW12(22/32/17)-fapR sensor? Page 7 line 279-281 stated “After adding cerulenin, the promoter 279 strength was only 3.26-fold that before addition, which was lower than H- 280 pCCW12(22/32/17)-fapR strain (3.63-fold).” Thus, why wouldn't the better performing sensor,pCCW12(22/32/17)-fapR, strain be chosen for further optimization?  Was the pCCW12(22/32/17)-fapR strain also fused with Cti6 and Gal80? If not, further elaborate on that decision or consider adding those experiments.

4. Is there a quantitative method to compare the dose-response curves in Figure 2b? pCCW12 was selected for sensor optimization, but other sensors might have a better linear range of detection.

 

Minor suggestions/ Corrections:

1. Page 4, Line 168: “pTEF1-directed fapR expression 168 module were simultaneously expressed”. However, when discussing Figure S2, Lines 145-153, the pTEF1 promoter was never analyzed. It is suggested to further explain why the pTEF1 promoter was chosen for fapR expression. 

 

2. Page 5/Figure 3a and Figure S4: Consider combining the sites (-27, -22, -17 and -12 and 37 and 42) on one figure and the sites which had significant results on one figure to make it easier for the reader to analyze the data, respectively.

 

3. Page 5, Figure 2b: Can you comment on the concentrations of cerulenin chosen for these experiments. Is it possible the increased concentration of cerulenin was resulting in cell death which could also explain the decrease in fluorescence? Please also add the error bars for figure 2b if they are not already there and consider making the legend font more legible. 

 

4. Double check citations 22 and 33. Could not locate either source which made it difficult to review the results presented in section 3.3. Were other introns tested or just the one from the apparent article cited? As stated on page 7, line 248 “It is speculated that the effect of introns on different promoters is not the same, and 284 RPL23A may hurt pCCW12.” As such, it could be beneficial to experiment with different introns for more optimal results. 

 

5. Page 8, Line 320 “At the highest point of responsive- 319 ness, the response fold of the H-pCCW12(TFBS)-Cti6~fapR strain increased to 4.29 times”. Please explain where that value was reported/derived from because on page 8, line 305, it was reported “Overall, H-pCCW12(TFBS)-fapR~Cti6 had a 3.95-fold re- 305 sponse after adding 4 mg/L cerulenin”. Please fix the discrepancies in reported values. 

 

6. How do the results presented in figure 4d compare to those presented in figure 2b? Why was the concentration range of cerulenin lowered? The highest GFP intensity (gfp range of the sensor) had decreased after the engineering compared to some of the sensors tested in figure 2b. While the background noise was much lower with the sensors tested in figure 4d, the highest GFP fluorescence intensities were much lower, please discuss if this was the desired response. 

 

7. Page 8, line 338: “....​​some studies 338 have used heterologous…”. Please provide sources for this statement. 

 

1. Page 4, line 155-157: “Since previous studies have shown that the sites near…”. Please provided sources

Author Response

Dear reviewer:

We sincerely appreciate the great comments and critical evaluation of our paper. Indeed, we have embraced your advice and have implemented the feedback to strengthen this manuscript. We thus made the point-by-point replies to the questions. Please see the attachment.

Yours Sincerely,

Prof. Wenyu Lu

Author Response File: Author Response.pdf

Reviewer 2 Report

What is the novelty of this manuscript according to previous works (ACS Synth Biol. 2015;4(12):1308-15;  Microbial Cell Factories 2020;19:146)?
The manuscript would be edited by a native English speaker.
The quantitative measurement (amount) of Malonyl-CoA by biosensor should be mentioned in the abstract.

Author Response

Dear reviewer:

We sincerely appreciate the great comments and critical evaluation of our paper. Indeed, we have embraced your advice and have implemented the feedback to strengthen this manuscript. We thus made the point-by-point replies to the questions as follows. The comments are in blue font and the revised section in the manuscript was in red font.

Yours Sincerely,

Prof. Wenyu Lu

 

1) What is the novelty of this manuscript according to previous works (ACS Synth Biol. 2015;4(12):1308-15;  Microbial Cell Factories 2020;19:146)?

Response:

In this manuscript, we discussed the effect of different fapO insertion sites on the sensor more systematically, and then targeted improved sensor characteristics by combining different promoter engineering strategies, such as hybridization, intron insertion and transcription factor modification.

 

2) The manuscript would be edited by a native English speaker.

Response:

Thanks to your kind suggestion! The revised manuscript has been revised by English native speaker.

 

3) The quantitative measurement (amount) of Malonyl-CoA by biosensor should be mentioned in the abstract.

Response:

Thank you for your kind suggestion! Based on the previous study [1-3], we chose to draw response curves with the addition of different concentrations of cerulenin. In this manuscript, we focus on ways to improve sensors. If continued with sensor-specific applications, such as dynamic modulation of a particular biosynthetic process, the intracellular Malonyl-CoA concentration could be determined more precisely in real time for the corresponding studies.

[1] Li, S., Si, T., Wang, M., & Zhao, H. (2015). Development of a Synthetic Malonyl-CoA Sensor in Saccharomyces cerevisiae for Intracellular Metabolite Monitoring and Genetic Screening. ACS Synth Biol, 4(12), 1308-1315. https://doi.org/10.1021/acssynbio.5b00069

[2] David, F., Nielsen, J., & Siewers, V. (2016). Flux Control at the Malonyl-CoA Node through Hierarchical Dynamic Pathway Regulation in Saccharomyces cerevisiae. ACS Synth Biol, 5(3), 224-233. https://doi.org/10.1021/acssynbio.5b00161

[3] Chen, X., Yang, X., Shen, Y., Hou, J., & Bao, X. (2018). Screening Phosphorylation Site Mutations in Yeast Acetyl-CoA Carboxylase Using Malonyl-CoA Sensor to Improve Malonyl-CoA-Derived Product. Front Microbiol, 9, 47. https://doi.org/10.3389/fmicb.2018.00047

 

Reviewer 3 Report

To achieve the regulation of application and pathway monitoring of malonyl-CoA, this study proposes a strategy to construct a biosensor using the fapO/fapR system and further optimizing it by combining promoter hybridization, intron insertion, and transcription factor modification, to construct a biosensor with low background noise and high response sensitivity. In general, the work described was well structured and the paper is probably publishable. However, some questions need to be responded and some experiments need to be supplemented before the manuscript can be considered for publication.

 

1.        Line 45-45, Please indicate the source of the reference.

2.        Line 59-69, Please note where the references are inserted.

3.        Line 65-69, What is the difference between the research content of the literature and this study? What are the advantages of this study?

4.        Line 97-100, Please explain why not take the overall high response as a reference for the high response intensity in this study.

5.        Line 155-157, Please insert appropriate references.

6.        Line 171-172, Does the strain itself affect the fapO/fapR system? Does it respond specifically to malonyl-CoA?

7.        Line 208-211, You can put the schematic diagram here.

8.        Line 211-215, What was the concentration of the experiment?

9.        Line 235-241, It is recommended to display relevant data charts.

10.    Line 249-250, Please explain why the response sensitivity of 22 bp downstream of the TATA-box is not the most promising, but the 22/32/17 group.

Author Response

Dear reviewer:

We sincerely appreciate the great comments and critical evaluation of our paper. Indeed, we have embraced your advice and have implemented the feedback to strengthen this manuscript. We thus made the point-by-point replies to the questions. Please see the attachment.

Yours Sincerely,

Prof. Wenyu Lu

Author Response File: Author Response.pdf

Round 2

Reviewer 1 Report

The authors have addressed the concerns and comments of this reviewer.

Reviewer 2 Report

The authors did not properly address my concerns!