ADAR Family Proteins: A Structural Review

Round 1

Reviewer 1 Report

Overall, this is a well-organized review that summarizes the structural features of the ADAR family, which can serve as a very good book chapter for those who are interested in ADARs.

The authors provided sufficient background information about three members of ADARs, from the domain characterization of dsRBD and CDD to the physiological functions involved in cancer progression, neurological disorders, and innate immune diseases/metabolic disorders. The authors also analyzed the evolution of the ADAR family, and the potential reasons why ADAR3 is inactive have been annotated as well. Like most other enzymes, ADARs also have conserved substrate binding sites and catalytic structures, and the structure and length of RNA substrates would affect ADAR editing. However, interestingly, ADARs can be influenced by the nearest neighbor preference and dimerization processes. The dimerization is also well discussed including the factors that would contribute to the process and the interfaces involved in the dimerization. Finally, the specific structures of each ADAR family member are included, such as the Z-DNA binding domains of ADAR1 and the Arg-rich domain of ADAR3. Thus, I do recommend this manuscript to be published.

Although the structural features and functions of ADAR are well-addressed, it lacks information about the upstream regulatory mechanisms of ADARs. For example, how is the expression/activity of the ADAR family regulated? Are there any upstream mediators?

On the other hand, ADARs consist of multiple dsRBDs. Are there any allosteric regulatory mechanisms identified for this family?

Author Response

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Reviewer 2 Report

In the manuscript " ADAR Family Proteins: A Structural Review" by Ashley et al presents a structural analysis of ADAR proteins, highlighting their crucial roles in RNA editing and their impact on human health. RNA editing is a valuable method for increasing the complexity of proteins by way of insertions, deletions, or base conversions that occur posttranscriptionally. One of the key enzymes for RNA editing is ADAR. The authors discussed the structure, function, and implications of ADAR proteins. This report is well written, interesting, and useful for further medical applications. Accordingly, this reviewer recommends publication.

The term ADAR, adenosine deaminase acting on RNA, should be mentioned.

Line 3, 1,2 should be in the same word type.

Figure legend should be provided as words, not in figure.

Please check if figure resolutions do not reach the publication level.

Figure 3 how about the sequence conservation (%)?

Line 177, Is this sentence a subsection?

Please check refs. 26, 49

Please consider providing a table for summarizing the differences in structure and functional characteristics

It is useful if drug structure can be provided for the readers in “5. Future Explorations for Therapeutics and Drug Design”

Author Response

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Reviewer 3 Report

Based on the abstract, the review seems interesting and relevant. But unfortunately the fairly wide scope of problems stated in the abstract is not always resolved.

The first problem is the lack of any clear review plan.

What's the point of calling the first chapter an introduction when it addresses specific issues, such as a general characterization of the family, which in turn lacks a clear definition of what ADAR is and the hydrolytic reaction scheme. The following describes the family composition, localization and functional significance and demonstrates the main drawback of this chapter, as well as subsequent chapters, which is - the review is purely descriptive rather than analytical, which significantly reduces its value, and in some places, completely devalues it.

For example, in lines 71-78, the authors write about the intracellular and tissue-specific localization of the protein, citing different and apparently contradictory data from different works. As a result, it turns out that the protein seems to have a specific localization, but at the same time it is ubiquitously expressed. How can a reader figure this out without re-reading all of the cited works?

In fact, this happens because the authors do not analyze the primary data from the articles, what it is about the protein itself or its RNA and from what source.

The best way to solve the problem is to make a table where information is given about where (an organism, cells and tissues) a protein/RNA was detected. And from this draw the appropriate conclusions.

The situation is approximately the same in the part where the functional role of the protein and its participation in cellular signaling pathways are described.

For example, it is written that “The effects of A-I editing in coding regions have been well, documented, but the vast majority of A-I editing in humans occurs in noncoding regions”, but no references are given that indicates the role of ADAR in both processes.

 Fig. 2 presents a set of not very clear pictures and texts. The caption to Fig. 2 is completely incomprehensible and does not contain all the necessary information. Where in the picture is ADAR itself? Captions for Fig. here and in other Figs. are not text, which makes them difficult to read.

Chapter 2. ADAR Relatives and Evolution. definitely requires a competent evolutionary tree, which shows at what stage of evolution the first ADAR appeared and when further duplications began.

Fig. 3, not informative

Fig. 4, the table is not readable and must be presented separately.

Subsequent chapters are better but still, they have the already indicated lack of comparative analysis of the data presented in the review.

In all Figures of the subsequent chapters there are a lot of problems.

1. Unacceptably low quality of protein aligments.

2. Tables are not readable and must be given separately from the Figures.

3. Figure legends must be in text form.

Unfortunately, the citation report was not available, which does not allow to evaluate the originality.

No major problems

Author Response

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Reviewer 4 Report

The manuscript provided an overview on ADAR functions and discussed their roles in therapeutic strategies. The article is well-written, but some figures are not fully described. Minor revision is suggested. 

1.        Some texts in Figure 2 are not clear. Please consider change the figure with one in a better resolution. 

2.        I would suggest the authors to describe Figure 2 in a better way in the manuscript. Since the authors mentioned Figure 2 several times,  it is difficult for readers to locate the description of Figure 2 (a) and Figure 2 (b). 

3.        In line 186-189, the author wrote that “…residue E488 surrounded by G487 and G489…”. It is not clear the sentence describes which sub-figure in Figure 4. I would suggest the authors to add more details. 

4.        In Section 5. Future explorations for therapeutics and drug design, the authors discussed potential therapeutic strategies. Could the authors also discuss the limitations of using ADAR in theopathic approaches? I think it will be beneficial for readers who are not familiar with the field. 

5.        Also, I’m curious that whether ADAR strategies have been used clinically in human? Could the authors make a list and summarize the recent work (ADAR strategies) with published time included? I believe it can be useful as a reference. 

Author Response

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Round 2

Reviewer 3 Report

The authors have corrected the identified problems. And the article can be published after minor problems are corrected. Table titles should be written at the top. Panels in figure captions must have the same markings. The legends to Figures 4 and 5 are poorly written.

The legends to Figures 4 and 5 are poorly written.

Author Response

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