Plant Synthetic Promoters: Advancement and Prospective

Round 1

Reviewer 1 Report

This review by Khan et al intends to elaborate in detail on the necessity of synthetic promoters in the new era of plant biology. They focus on two major approaches for developing plant-based synthetic promoters: the conventional approach by utilizing the basic knowledge of promoter structure and cis-trans interaction and the new advancement in gene editing technology. The review could be published, but some revisions are needed.

 

Main comments:

-Figure 2: please redraw the picture; Don’t use weapons to show the TFs. Also, more details should be labeled in the image and described in the main text.

-Figure 3: legend A. In vitro assembly of desired cis-elements from the cis-elements pockets over the proximal promoter through deletion (yellow), addition (red), substitution (blue)…

The flowchart shows that the substitutions are marked in purple instead of blue. Moreover, is there any special significance for patterns of different shapes? Please indicate in the legend.

 

-3.3. Chemical-responsive synthetic promoters

-3.7. Bidirectional promoters

The above two parts are not detailed enough

 

Minor comments:

-There are some font or punctuation errors in the text. Here are just some of the tips:

-P114: ‘other…’ the first letter should be capitalized.

-P142-143, P255: some extra punctuation needs to be removed.

-P208: genetic recombination. Pay attention to correct fonts and underlines.

 

-P284: figure 2 should be changed to Figure 2.

Author Response

We would like to thank and express our gratitude to the editor and the reviewer 1 for their time and positive criticism in order to improve the manuscript quality. We have tried to address each of the points raised by the academic editor and reviewer. We believe that the manuscript is now more readable, instructive, and beneficial to the broad audience.

 

Author Response File: Author Response.docx

Reviewer 2 Report

The manuscript entitled "Plant synthetic promoters: advancement and prospective " by Khan et al., was reviewed for publication in agriculture (agriculture-2156039). The manuscript is a review of the advances related to the use of plant synthetic promoters and their potential uses. The subjects covered include a general introduction to gene regulation, followed information about currently available synthetic promoters, and both conventional and CRISPR technology based approaches to develop synthetic promoters. In general, the manuscript contains a good quantity of pertinent information related to the topic, but the writing and organization of the manuscript is not optimal, and is sometimes very wordy. There are some confused sections and some unclear tables that need particular revision. I outlined some problems and possible corrections below. In addition, some English editing is advised to improve the overall quality of the manuscript.  

 

Comments

 

Lines 71-75, The sentence is long and complex, may be better rewritten into two sentences.

 

Line 92 should be “transcription start site (TSS)”, it is not plural.

 

Line 97, should be “DNA motifs”, plural

 

Figure 1 could be cited earlier in the first paragraph of section 2, somewhere in lines 85-91.

 

Line 109, “The resultant color”, it could be indicated that this refers to the colored oval associated with the transcriptional regulation.

 

Line 109, not sure that “equal” is correct here, given that the result of each input “color” may be different, depending on the circumstance.

 

Table 1, the title of this table is a bit odd and I have a problem to understand the information provided. What is meant by “protein elements”? What is the heading “S1” above the first column? The heading for the second column “Promoter elements” does not seem appropriate, given that TFIIA and others listed are transcription factors, and not promoter elements. Promoter elements are DNA sequences. Transcription factors are proteins. The third column “Function” is not well aligned with the first column, so it is hard to read. For example, the MTE is not well aligned with the text in the next column “Motif Ten Element; functions cooperatively with the Inr and is a recognition site for”. So, this table needs to be reorganized and corrected.

 

Lines 137-139, This starts out to be a general sentence about plants, but then the point is actually about the potential of transgenes to be used to combat biotic and abiotic stresses. Endogenous promoters also control the plant response to stress, so this response does not only include transgenes. The point is, promoters are important for proper expression of transgenes in response to stresses.

 

Line 173, what is “+plants”, is that correct?

 

Line 179, ABA already defined above

 

Line 187, “active”, is that correct?

 

Line 208, “genetic recombination” is underlined, and is an active URL. Please check.

 

Table 2, as with Table 1, the horizontal alignment between the columns is mixed, making it hard to read the table. In particular, the text in column 3, and the corresponding synthetic promoter in column 2, is not well aligned horizontally, and is difficult to match up and read. This table as the previous one needs to be corrected.

 

Line 282, promoters are not expressed, they are active and control gene expression.

 

Lines 295-296, Studies show this, but no references are given. Why is the proximal promoter the best option for driving gene expression? What studies show that? Define clearly what is meant here by “proximal” promoter, and include schematically in the Figure 1. Term is first used on line 88, so it should be clearly defined there.

I highlighted questionable vocabulary and other minor problems directly on the pdf I uploaded with the review.

 

There is a recent review entitled “Synthetic biology approaches in regulation of targeted gene expression”, which probably should be cited, given it also examines and includes a table of synthetic promoters. (Huang D, Kosentka PZ, Liu W (2021) Synthetic biology approaches in regulation of targeted gene expression. Curr Opin Plant Biol 63:102036. doi:10.1016/j.pbi.2021.102036)

 

 

 

 

 

 

  

 

 

 

 

Author Response

We would like to thank and express our gratitude to the editor and the reviewer 2 for their time and positive criticism in order to improve the manuscript quality. We have tried to address each of the points raised by the academic editor and reviewer. We believe that the manuscript is now more readable, instructive, and beneficial to the broad audience.

Author Response File: Author Response.docx

Reviewer 3 Report

In this review, the authors intend to discuss basic promoter structure and function, synthetic promoter generation, cis-engineering to increase the transcriptional activity of synthetic promoters, and conventional and advanced approaches to designing synthetic promoters that are efficient and useful. Researchers in this field will benefit greatly from this review, which provides enriched information about advancements in synthetic promoters in plant biotechnology.

I encourage authors to check the references appropriately. Reference citation NO. 50 line 566 is incomplete. I think it is typing mistake

Comments for author File: Comments.pdf

Author Response

We would like to thank and express our gratitude to the editor and the reviewer 3 for their time and positive criticism in order to improve the manuscript quality. We have tried to address each of the points raised by the academic editor and reviewer. We believe that the manuscript is now more readable, instructive, and beneficial to the broad audience.

Author Response File: Author Response.docx

Round 2

Reviewer 2 Report

 

The revised version of the manuscript entitled "Plant synthetic promoters: advancement and prospective" by Khan et al., was reviewed for publication in agriculture (agriculture-2156039). The revised as advised, but there were some suggestions I made directly on the pdf file I uploaded in my first review, so I suggest again and upload another pdf for the authors to make the corrections. In addition, unless I am mistaken, the authors did not explain what the header (S. No.) in column 1 of Tables 1 and 2 means. I do not need to see another version of this manuscript.  

 

 

Comments for author File: Comments.pdf

Author Response

We would like to thank and express our gratitude to the editor and the reviewer 2 for their time and positive criticism in order to improve the manuscript quality. We have tried to address each of the points raised by the academic editor and reviewer. We believe that the manuscript is now more readable, instructive, and beneficial to the broad audience.

Author Response File: Author Response.docx