Review Reports

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

The review manuscript titled "Phosphodegrons in Health and Disease: From Cellular Homeostasis to Therapeutic Targets" provides valuable insights into the future directions and challenges in phosphodegron research, highlighting their crucial role in cellular regulation and disease pathology. While compelling, the manuscript would benefit from several improvements to enhance its clarity, structure, and overall impact for publication:

1. The title suggests a focus on phosphodegrons as therapeutic targets, yet specific details on therapeutic applications are absent in the manuscript. Authors should reconsider the title to accurately reflect the content.

2. Do phosphodegrons solely rely on β-TrCP for mediation, or are there β-TrCP-independent mechanisms or involvement of other ubiquitin ligases? If so, authors should dedicate a section to highlight these alternative regulatory pathways.

3. The manuscript broadly discusses the functions of phosphodegrons but lacks a clear definition of what phosphodegrons are exactly. Clarifying this foundational information is necessary.

4. Figure 2 requires more detailed illustration. Currently, it is overly generalized and difficult to interpret.

5. Table 1 lists substrates, kinases, and ubiquitin ligases discussed in the manuscript but lacks a column detailing the significance of these interactions in cellular physiology and disease contexts. Adding this information would enhance the table's relevance and utility.

6. The manuscript could benefit from a concise overview of phosphodegron-based therapeutic targets and approaches for various diseases and pathologies, which is currently missing.

7. Authors should also discuss the advantages and potential limitations of phosphodegron-based therapies to provide a balanced perspective.

8. Minor point: Some paragraphs are too short (eg. 89, 186). Authors are advised to maintain consistency for streamline reading of manuscript.

Author Response

Response to Reviewer #1:
We sincerely appreciate your thorough and insightful review of our manuscript. Your comments have been instrumental in refining the clarity, structure, and overall quality of our work. Below, we provide detailed responses and outline the corresponding revisions, which are highlighted in the resubmitted files.

 

Comment:

“The review manuscript titled Phosphodegrons in Health and Disease: From Cellular Homeostasis to Therapeutic Targets provides valuable insights into the future directions and challenges in phosphodegron research, highlighting their crucial role in cellular regulation and disease pathology. While compelling, the manuscript would benefit from several improvements to enhance its clarity, structure, and overall impact for publication.”

 

Response:

We greatly appreciate your positive and constructive feedback.

 

Comment:

“The title suggests a focus on phosphodegrons as therapeutic targets, yet specific details on therapeutic applications are absent in the manuscript. Authors should reconsider the title to accurately reflect the content.”

 

Response:

We have revised the title by replacing “therapeutic targets” with “therapeutic potential” to more accurately reflect the scope and content of the manuscript.

 

Comment:

“Do phosphodegrons solely rely on β-TrCP for mediation, or are there β-TrCP-independent mechanisms or involvement of other ubiquitin ligases? If so, authors should dedicate a section to highlight these alternative regulatory pathways.”

 

Response:

Phosphodegrons are recognized not only by β-TrCP but also by other ubiquitin ligases or their substrate receptor subunits. We have detailed the specific ubiquitin ligases responsible for corresponding phosphodegrons and summarized these in the newly added Figures 2-8 and revised Table 1. As these additions clarify the issue comprehensively, we have opted not to include a separate section on ubiquitin ligases other than β-TrCP.

 

Comment:

“The manuscript broadly discusses the functions of phosphodegrons but lacks a clear definition of what phosphodegrons are exactly. Clarifying this foundational information is necessary.”

 

Response:

We have provided a more precise definition of phosphodegrons, emphasizing that not all phosphorylated protein motifs function as phosphodegrons. These motifs require specific surrounding sequences recognized by cognate ubiquitin ligases and must include ubiquitylatable lysine residues (lines 37-39).

 

Comment:

“Figure 2 requires more detailed illustration. Currently, it is overly generalized and difficult to interpret.”

 

Response:

We have removed Figure 2 and included representative illustrations of phosphodegron-regulated proteins, highlighting ubiquitin ligases and substrates in each section (new Figures 2-8). We believe these updates enhance the comprehensibility of the manuscript.

 

Comment:

“Table 1 lists substrates, kinases, and ubiquitin ligases discussed in the manuscript but lacks a column detailing the significance of these interactions in cellular physiology and disease contexts. Adding this information would enhance the table's relevance and utility.”

 

Response:

We have added a new column to Table 1 that outlines the functions of phosphodegrons in cellular physiology and disease contexts. These aspects are further clarified in the newly added Figures 2-8.

 

Comment:

“The manuscript could benefit from a concise overview of phosphodegron-based therapeutic targets and approaches for various diseases and pathologies, which is currently missing.”

 

Response:

We have included a new section, “8. Potential and Limitations of Phosphodegron-based Therapeutics,” which provides an overview of phosphodegron-based therapeutic targets and approaches for various diseases and pathologies.

 

Comment:

“Authors should also discuss the advantages and potential limitations of phosphodegron-based therapies to provide a balanced perspective.”

 

Response:

The advantages and potential limitations of phosphodegron-based therapies are now discussed in the newly added section, “8. Potential and Limitations of Phosphodegron-based Therapeutics.”

 

Comment:

“Minor point: Some paragraphs are too short (e.g., 89, 186). Authors are advised to maintain consistency for streamlined reading of the manuscript.”

 

Response:

We have carefully revised the manuscript to ensure that all paragraphs are appropriately structured and consistent in length for improved readability.

 

Additional Revisions:

During the revision process, we identified and addressed the omission of a discussion on phosphodegron-regulated p27 degradation by the SKP2 ubiquitin ligase, which is one of the most well-studied mechanisms with significant implications in cancer development. This has been included in lines 102-107. Additionally, we incorporated recent findings that TRIM21 has been identified as an ubiquitin ligase for PLIN2, now discussed in lines 260-262.

 

We hope these revisions and our detailed responses adequately address the reviewers’ concerns and significantly enhance the clarity, structure, and quality of our manuscript.

Reviewer 2 Report

Comments and Suggestions for Authors

This manuscript reviews four classes of proteins (cell cycle and growth, DNA damage and apoptosis, homeostasis and metabolism, and immune) that are regulated by phosphodegrons. For each class, they give examples of proteins that contain phosphodegrons, list the FBox proteins that bind each degron, and discuss the phenotypic consequences of misregulation of the phosphodegrons. They also discuss the roles of phosphodegrons in cancer progression and neurodegenerative diseases.

Though the level of data reviewed is somewhat superficial and repetitive, the article is scientifically sound. I recommend it for publication after addressing the following minor comments.

1.     Please provide a more detailed description of the phosphodegron. It is described as a motif where a serine, threonine, or tyrosine within it is phosphorylated. However, not all serine, threonines, or tyrosines are phosphorylated, so some discussion of what makes phosphodegrons unique (surrounding amino acids? 3D domain structures?) would be helpful to understand how some S,T, Y are phosphodegrons and some are not.

2.     References are often not appropriately placed. In many paragraphs, there are no references given for the first 2-4 sentences, then all references are given together after the next sentence. This makes it hard to discern exactly what point being referenced goes to which paper. Often the last sentence of the paragraph also needs a reference, but this is rarely done.  Some examples of these problems are lines 94-101 and lines 204-213.

3.     It seems one rate-limiting factor for growth of this field is predicting potential functional phosphodegron motifs. There is some very vague mention of this in the “Future Directions” section. However, the explanation of how this could be done is mostly meaningless jargon (lines 351-355). A more thorough explanation of what the current barriers are to degron prediction and specifics on how they could be overcome would be useful for convincing that prediction may be possible.

Author Response

Response to Reviewer #2:

We sincerely thank you for your constructive comments, which have greatly contributed to the refinement of our manuscript. Detailed responses to your suggestions are provided below, with corresponding revisions highlighted in the resubmitted files.

 

Comment:

“This manuscript reviews four classes of proteins (cell cycle and growth, DNA damage and apoptosis, homeostasis and metabolism, and immune) that are regulated by phosphodegrons. For each class, they give examples of proteins that contain phosphodegrons, list the FBox proteins that bind each degron, and discuss the phenotypic consequences of misregulation of the phosphodegrons. They also discuss the roles of phosphodegrons in cancer progression and neurodegenerative diseases. Though the level of data reviewed is somewhat superficial and repetitive, the article is scientifically sound. I recommend it for publication after addressing the following minor comments.”

 

Response:

We greatly appreciate your positive and constructive feedback.

 

Comment:

“Please provide a more detailed description of the phosphodegron. It is described as a motif where a serine, threonine, or tyrosine within it is phosphorylated. However, not all serine, threonines, or tyrosines are phosphorylated, so some discussion of what makes phosphodegrons unique (surrounding amino acids? 3D domain structures?) would be helpful to understand how some S, T, Y are phosphodegrons and some are not.”

 

Response:

We have provided a more precise definition of phosphodegrons, emphasizing that not all phosphorylated motifs function as phosphodegrons. These motifs require specific surrounding sequences recognized by cognate ubiquitin ligases and must include ubiquitylatable lysine residues (lines 37-39).

 

Comment:

“References are often not appropriately placed. In many paragraphs, there are no references given for the first 2-4 sentences, then all references are given together after the next sentence. This makes it hard to discern exactly what point being referenced goes to which paper. Often the last sentence of the paragraph also needs a reference, but this is rarely done. Some examples of these problems are lines 94-101 and lines 204-213.”

 

Response:

We have revised the placement of references to clearly associate each reference with the specific point it supports. Additional references were added where they were previously missing.

 

Comment:

“It seems one rate-limiting factor for growth of this field is predicting potential functional phosphodegron motifs. There is some very vague mention of this in the “Future Directions” section. However, the explanation of how this could be done is mostly meaningless jargon (lines 351-355). A more thorough explanation of what the current barriers are to degron prediction and specifics on how they could be overcome would be useful for convincing that prediction may be possible.”

 

Response:

We have expanded the discussion on predicting potential functional phosphodegron motifs in the section “9. Future Directions” (lines 479-496). This now includes a more detailed explanation of the current barriers to degron prediction and specific strategies to address these challenges.

 

Additional Revisions:

During the revision process, we identified and addressed the omission of a discussion on phosphodegron-regulated p27 degradation by the SKP2 ubiquitin ligase, which is one of the most well-studied mechanisms with significant implications in cancer development. This has been included in lines 102-107. Additionally, we incorporated recent findings that TRIM21 has been identified as an ubiquitin ligase for PLIN2, now discussed in lines 260-262.

 

We hope these revisions and our detailed responses adequately address the reviewers’ concerns and significantly enhance the clarity, structure, and quality of our manuscript.