Advances and Challenges in Biomanufacturing of Glycosylation of Natural Products

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

This manuscript is not well prepared. It consists of obvious statements and narratives like Author et al. (Ref. X) did this and that. In the next sentence the same arrangement: Author et al. (Ref. Y) showed this and this. And such a narrative pattern dominates the entire manuscript. There is no coherent discussion carried out. No critical insight from the authors of the manuscript. I don't see a thought leading in this manuscript. I have provided detailed comments below.

I find the definition of natural products not very fortuitous.

In Table 1, a different symbol is used instead of a comma. In addition, the word "compounds" is unnecessarily moved between lines so that the "s" is on the second line.

We write the configuration series (D and L) in a plain and the same font as the rest of the text, but definitely smaller.

In the case of glycosides, the symbols of atoms, "N" and etc. are written in italics, similarly in the case of names, where the symbol of an atom indicates the place of substitution, as for example for glucosamine. 

The term "sugar groups" (l. 51) is not correct, it should be "sugar moieties".

The term "flavanoid structures" (l. 49) is not correct. I would suggest using "flavonoid compounds". 

The term "glucoside ligand" (l. 51) is incorrect for two reasons. First, glucosides are glucose glycosides, and here it refers to the general case. Second, the non-sugar part in glucosides is called aglycone.

Be careful and do not confuse the terms "glucosides" and "glycosides" (l. 59)

Some drugs are written with a capital letter others are not (l. 55-65), this should be standardized. In my opinion, if they are not trade names, but the common names of APIs, they should be written with a lowercase letter.

Some researchers believe that C-glycosides are not really glycosides. In fact, are the mentioned enzymes able, by analogy with other (proper glycosides) to catalyze the glycosylation process (l. 66-68, Ref. 21)?

References are given in round brackets and should be in square brackets.

Exceptionally, when it is not possible to write in a smaller font, the configuration series (D and L) are written with a lowercase letter. But in the body of the manuscript this is not justified, so the designation of the configuration series in l. 74 for glucosamine should be corrected. 

Table 1 appears under Figure 1 at the end of the introduction, but there is no reference to this table in the text. Any element such as a figure, scheme or table should be mentioned in the text.

The authors stated the source of funding, the person (co-author) responsible for receiving funding. But I don't really understand how a review article can be funding. Unless it is to cover the cost of APC or language correction. Please specify what was funded.

Comments on the Quality of English Language

It would be good if the manuscript was checked and language corrected. 

Author Response

Reviewer #1: This manuscript is not well prepared. It consists of obvious statements and narratives like Author et al. (Ref. X) did this and that. In the next sentence the same arrangement: Author et al. (Ref. Y) showed this and this. And such a narrative pattern dominates the entire manuscript. There is no coherent discussion carried out. No critical insight from the authors of the manuscript. I don't see a thought leading in this manuscript. I have provided detailed comments below.

Response: Thank you very much for your comments and pointing out the current issues. In terms of writing, we have made extensive revisions to the entire manuscript to make it more fluent and logical. In the abstract, introduction, and discussion sections, the latest research progress and challenges in glycosylation of natural products are elaborated, as well as potential application areas in the future.

Comment 1: I find the definition of natural products not very fortuitous.

Response: Thank you for your comments. According to the research of Kurze and others, we have redefined natural products and inserted the reference literature. 

In lines 37-42 on page 1：Natural products (NPs) are a family of compounds that are widely distributed in nature and are produced by any organism using biological catalysts. These include primary and secondary (or specialized) metabolites. However, there is controversy in the classification of these compounds in some cases. This family includes alkaloids, terpenes, phenolic compounds, flavonoids, and lignans, among others.

Comment 2: In Table 1, a different symbol is used instead of a comma. In addition, the word "compounds" is unnecessarily moved between lines so that the "s" is on the second line.

Response: Thank you for your comments. In Table 1, The symbols in Table 1 have been unified and the line spacing has been adjusted.

Comment 3: We write the configuration series (D and L) in a plain and the same font as the rest of the text, but definitely smaller.

Response: Thank you for your comments. We've made changes based on your comments.

Comment 4: In the case of glycosides, the symbols of atoms, "N" and etc. are written in italics, similarly in the case of names, where the symbol of an atom indicates the place of substitution, as for example for glucosamine. 

Response: Thank you for your comments. We have made revisions based on your recommendation.,

In line 22 on page 1 and In line 77 on page 2. The positions O-, C-, S-, and N- have been changed to italics.

Comment 5: The term "sugar groups" (l. 51) is not correct, it should be "sugar moieties".

Response: Thank you for your comments. In line 61 on page 2. "Sugar groups" has been corrected to "sugar moieties".

Comment 6: The term "flavanoid structures" (l. 49) is not correct. I would suggest using "flavonoid compounds". 

Response: Thank you for your comments. In line 59 on page 2. “flavanoid structures” has been corrected to “flavonoid compounds”.

Comment 7: The term "glucoside ligand" (l. 51) is incorrect for two reasons. First, glucosides are glucose glycosides, and here it refers to the general case. Second, the non-sugar part in glucosides is called aglycone.

Response: Thank you for your comments. In line 60 on page 2. " glucoside ligand " has been corrected to "aglycone ".

Comment 8: Be careful and do not confuse the terms "glucosides" and "glycosides" (l. 59)

Response: Thank you for your comments. Based on your suggestion, the corresponding modifications have been made.

Comment 9: Some drugs are written with a capital letter others are not (l. 55-65), this should be standardized. In my opinion, if they are not trade names, but the common names of APIs, they should be written with a lowercase letter.

Response: Thank you for your comments. In lines 64-66 on page 2. Based on your suggestion, the corresponding modifications have been made.

Comment 10: Some researchers believe that C-glycosides are not really glycosides. In fact, are the mentioned enzymes able, by analogy with other (proper glycosides) to catalyze the glycosylation process (l. 66-68, Ref. 21)?

Response: Thank you for your comments. Certainly, the glycosyltransferases mentioned in the study can catalyze the formation of glycosides other than C-glycosides. Li et al. (1) synthesized 3-O-glycosides by enzymatic cleavage with a microbial glycosyltransferase. Wen et al. (2) reported the formation of O-, N-, and S-glycosides by a glycosyltransferase (UGT74AN1) and by showing unprecedented promiscuity towards 53 structurally diverse natural and unnatural compounds.

Comment 11: References are given in round brackets and should be in square brackets.

Response: Thank you for your comments. References have been placed in square brackets.

Comment 12: Exceptionally, when it is not possible to write in a smaller font, the configuration series (D and L) are written with a lowercase letter. But in the body of the manuscript this is not justified, so the designation of the configuration series in l. 74 for glucosamine should be corrected. 

Response: Thank you for your comments. In line 85 on page 2. Based on your comment, glucosamine's conformation series has been corrected.

Comment 13: Table 1 appears under Figure 1 at the end of the introduction, but there is no reference to this table in the text. Any element such as a figure, scheme or table should be mentioned in the text. 

Response: Thank you for your comments. In line 45 page 2. Table 1 has been referred to in the text.

Comment 14: The authors stated the source of funding, the person (co-author) responsible for receiving funding. But I don't really understand how a review article can be funding. Unless it is to cover the cost of APC or language correction. Please specify what was funded.

Response: Thank you for your comments.The journal Fermentation is an open access journal, and the funding stated in this manuscript is to cover the costs of APC and language correction.

Reviewer 2 Report

Comments and Suggestions for Authors

This is an interesting review discussing the progress and challenges in the study of glycosylation of natural products, including the latest research results and potential applications in the biosynthesis of glycosylated derivatives of terpenoids, flavonoids, polyketides, aromatic compounds, and  other compounds.

It is well written and up to date and it provides a comprehensive overview of the advances and challenges in green biomanufacturing of glycosylation modification of natural products.

The structure of manuscript is good and literature used is appropriate.
The information reviewed is abundant and well organized.
The authors themselves examine the limitations of their work in the conclusions stating that research on glycosylation of natural products still faces many challenges such as the production of NP-specific glycosides that depends on the biosynthetic pathway of NP precursors, which are often incomplete.

In my opinion it's a good review and it deserves publication.

Authors should only explain acronyms in full when they first appear in the text.

Author Response

Reviewer #2: This is an interesting review discussing the progress and challenges in the study of glycosylation of natural products, including the latest research results and potential applications in the biosynthesis of glycosylated derivatives of terpenoids, flavonoids, polyketides, aromatic compounds, and other compounds.

It is well written and up to date and it provides a comprehensive overview of the advances and challenges in green biomanufacturing of glycosylation modification of natural products. 

The structure of manuscript is good and literature used is appropriate.

The information reviewed is abundant and well organized. The authors themselves examine the limitations of their work in the conclusions stating that research on glycosylation of natural products still faces many challenges such as the production of NP-specific glycosides that depends on the biosynthetic pathway of NP precursors, which are often incomplete.

In my opinion it's a good review and it deserves publication.

Response: Thank you very much for your comment and affirmation.

Comment 1: Authors should only explain acronyms in full when they first appear in the text.

Response: Thank you for your comments. We have provided a full explanation of the abbreviations where they first appear in the text.

Reviewer 3 Report

Comments and Suggestions for Authors

COMMENTS

-The title is not immediately understood by the audience. Here, use of ‘’green and bio’’ looks like a double positive to me, but also ‘‘Glycosylation Modification’’ should be both grammatically and scientifically wrong. You need to recheck and rephrase the title.

-The abstract does not clearly indicate the purpose of the review, the methods used, key findings and the conclusions/future research directions.

-Keywords used should rather be devoid of unusual abbreviation(s), as well as words which are already embodied in the title.

-Intext citations should be aligned to the journal guidelines.

-L85-89: Several reviews have been done on this subject previously. Please, acknowledge them and show how your current review continues from their reviews.

https://doi.org/10.1016/j.biotechadv.2023.108267

https://doi.org/10.3390/catal13101359

- What is the source of Figure 1? Is it based on published literature?

-Authors need to harmonize the units for titer used in Table 1; this will allow fir comparison between studies.

-The study should provide a short conclusion, highlighting the directions for future research.

-English language need to be rechecked to avoid redundancy and flow of information.

-Other suggestions are in the attached manuscript PDF file

Comments for author File: Comments.pdf

Comments on the Quality of English Language

Needs to be fixed 

Author Response

Reviewer #3: 

Comment 1: The title is not immediately understood by the audience. Here, use of ‘’green and bio’’ looks like a double positive to me, but also ‘‘Glycosylation Modification’’ should be both grammatically and scientifically wrong. You need to recheck and rephrase the title.

Response: Thank you for your comments and suggestions. We have changed the title to: Advances and Challenges in Biomanufacturing of Glycosylation of Natural Products

Comment 2: The abstract does not clearly indicate the purpose of the review, the methods used, key findings and the conclusions/future research directions.

Response: Thank you for your comments. The following changes have been made to the summary section based on your suggestions: This work summarizes the latest progress and challenges in the field of natural product glycosylation, covering the research results and potential applications of glycosylated derivatives of terpenes, flavonoids, polyphenols, aromatic compounds, and other compounds in terms of biogenesis. Looking to the future, research may leverage artificial intelligence-driven synthetic biology techniques to decipher genes related to the synthetic pathway, which is expected to further promote the large-scale synthesis and application of glycosylated NPs  and increase the diversity of NPs in the pharmaceutical, functional food, and cosmetic industries.

Comment 3: Keywords used should rather be devoid of unusual abbreviation(s), as well as words which are already embodied in the title.

Response: Thank you for your comments. The keywords have been changed based on your comments

Comment 4: Intext citations should be aligned to the journal guidelines.

Response: Thank you for your comments. We have made changes to the citation format

Comment 5: Several reviews have been done on this subject previously. Please, acknowledge them and show how your current review continues from their reviews.

Response: Thank you for your comments. In lines 98-102 on page 3. We have made the following changes: The regulation of post-translational mechanisms in microalgae was explored, which are essential for ensuring the proper production and glycosylation of antibodies [32]. Andreu et al. (4) reported on enzymatic glycosylation strategies for the production of bioactive compounds and noted the advantages of enzymatic glycosylation including its high regioselectivity, stereoselectivity, and sustainability, as well as the possibility of incorporating immobilization techniques or chemical or genetic modifications to improve the glycosylation process.

Comment 6: What is the source of Figure 1? Is it based on published literature?

Response: Thank you for your comments. Figure 1 was drawn by ourselves We have referred to some literature, including: "Structure–function relationship of terpenoid

glycosyltransferases from plants", "Structure–function relationships in plant UDP-glycosyltransferases", "UDP-Glycosyltransferases in Edible Fungi: Function, Structure,and Catalytic Mechanism"

Comment 7: Authors need to harmonize the units for titer used in Table 1; this will allow fir comparison between studies.

Response: Thank you for your comments. Units of titer in Table 1 have been standardized to g/L.

Comment 8: The study should provide a short conclusion, highlighting the directions for future research.

Response: Thank you for your comments. In lines 436-440 on page 13. We have completed the following brief discussion: In the future, utilizing artificial intelligence-driven synthetic biology to decipher syn-thesis pathways related genes, rate-limiting steps, co-factor supply, and metabolic flux balance will further promote large-scale synthesis and application of glycosylated NPs, increasing the diversity of NPs glycosides used in pharmaceuticals, functional foods, and cosmetics in industrial production.

Comment 9: English language need to be rechecked to avoid redundancy and flow of information.

Response: Thank you for your comments. Now the language was improved in the revised manuscript..

Comment 10: Other suggestions are in the attached manuscript PDF file.

Response: Thank you for your comments. The manuscript has been revised based on your comments.

Round 2

Reviewer 1 Report

Comments and Suggestions for Authors

The authors have not very accurately corrected the notation of the configuration series (D and L) and the atom to which the substituent is attached. Configuration series are not written in italics, but in smaller font. We write the symbol of the atom to which the substituent is attached in italics (this applies to atoms, for example, N and O and in the name C-glycosides). Please correct this during editorial proofreading. On the other hand, the language has been corrected and other points I raised in the previous review. Although the manuscript is not outstanding in my opinion, I propose to accept it in its present form.

Reviewer 3 Report

Comments and Suggestions for Authors

Authors have addressed all the concerns I had on the previous manuscript version

Comments on the Quality of English Language

Minor fixes required