Never Fold to Fold Continuously: A Conundrum in Ubiquitin–Proteasome System (UPS)-Mediated Protein Quality Control (PQC)
Round 1
Reviewer 1 Report
Comments and Suggestions for AuthorsThe Ms is a timely and very good review by Stefano Magnati and Enrico Bracco on the protein foolding questions arising on the Ubq-Proteasome pathwway.
The only issues I would like to signal are:
- the title is too long and complicated
- the list of references should include work on Ubq by the
Fushman and Assfalg groups and work by Felli and Blackledge
on the methods.
In Figure 2, intrinsically disordered regions (IDR's) should be depicted differently to clearly distinguish them from misfolded proteins.
On the left side of the figure 'Chaperon'-->'Chaperone'
", and" --"and"
Why not write 'Proteasome', as well, in the figure?
In the 'Outlook':
- phrases are long and acronyms too abundant.
- a few suggestions:
"do IDRs might be suitable"-->"could IDRs be suitable"
or "might IDRs be suitable"
"their role is restricted...?" --> "is their role restricted..?"
Writing down a few experimental techniques/approaches that could address
each of the outstanding questions, in addition to raising these questions,
would be great.
Comments on the Quality of English Language
Minor corrections suggested, especially regarding the style.
Author Response
To the reviewer #1
We are delighted that the manuscript has been appreciated and we deeply thank the reviewer for the suggestions and comments given. The manuscript has now been revised according to your suggestions and we bring to your attention the revised form. We hope that the amendments produced have improved the manuscript and thus be reconsidered as suitable for publication in Biophysica.
In the revised version, all the modifications to the manuscript have been marked using the MS Word tracking function (red labeled).
Please find below enclosed our comments to the reviewer (R: Reviewer; A: Authors reply in italics)
R: The Ms is a timely and very good review by Stefano Magnati and Enrico Bracco on the protein foolding questions arising on the Ubq-Proteasome pathway.
The only issues I would like to signal are:
- the title is too long and complicated
A: We deeply appreciate your suggestion; thus, the title of the revised version has been changed and shortened as follows “Never Fold to Fold Continuously: A Conundrum in Ubiquitin-Proteasome System (UPS)-Mediated Protein Quality Control (PQC)”
R: - the list of references should include work on Ubq by the Fushman and Assfalg groups and work by Felli and Blackledge on the methods.
A: In the revised version of the manuscript references from Fushman and Felli and Blackledge have been added (ref. 43 “Pickart C.M., Fushman D. Polyubiquitin chains: polymeric protein signals Curr Opin Chem Biol 2004 8(6):610-6. doi: 10.1016/j.cbpa.2004.09.009.”; ref. 66 “Davey N.E., Babu M.M., Blackledge M., Bridge A., Capella-Gutierrez S. et al. An intrinsically disordered proteins community for ELIXIR F1000Res 2019 Oct 15:8:ELIXIR-1753. doi: 10.12688/f1000research.20136.1.”)
R: In Figure 2, intrinsically disordered regions (IDR's) should be depicted differently to clearly distinguish them from misfolded proteins.
On the left side of the figure 'Chaperon'-->'Chaperone'
", and" --"and"
Why not write 'Proteasome', as well, in the figure?
A: We thank the reviewer for the suggestions and accordingly, the Figure has been fully redrawn.
R: In the 'Outlook':
- phrases are long and acronyms too abundant.
- a few suggestions:
"do IDRs might be suitable"-->"could IDRs be suitable" or "might IDRs be suitable"
"their role is restricted...?" --> "is their role restricted..?"
Writing down a few experimental techniques/approaches that could address each of the outstanding questions, in addition to raising these questions, would be great.
A: We are very grateful for the helpful suggestions received from the reviewer. In the revised version we attempted to edit the language and implement a little bit the approaches/techniques that might help address the open question as follows “Genetic approaches aimed to dissect the IDRs context-specific role/s (i.e., by chimerically combining them, knock-in approach, mutagenesis) would be of great benefit to unraveling their functional behavior. Furthermore, proteomics would enable to improve our current, but so far still rather scant, knowledge on their binding promiscuity. Ultimately, based on the existing scientific community projects (i.e., ELIXIR) [66] and with the freshly developed deep- and machine-learning approaches [67] the prediction of IDRs would be greatly facilitated and boosted.”. An additional, a very recent paper just released, reference (#67) has been added.
Reviewer 2 Report
Comments and Suggestions for AuthorsIn this manuscript, Magnati et al. reviewed the recent progress in understanding the roles of intrinsically disordered regions (IDRs) in protein quality control, with a focus on the ubiquitin proteasome system (UPS). The UPS plays a central role in degrading misfolded protein species to maintain proper protein homeostasis. While the mechanisms of the UPS are well-studied, how the IDRs of UPS component proteins contribute to their innate function remains less understood. This is a timely mini-review complementing many existing summaries of IDRs in other aspects of cell biology. This topic is well-suited for the scope of Biophysica. I support the publication of this manuscript if the following concerns are fully addressed.
1. In section 2, the authors did a good job summarizing the known functions of IDRs. Given the audience of this journal, mostly biophysicists, it would be helpful to introduce some common structural features and biophysical norms of IDRs. For example, in addition to their transient structures, IDRs are distinguishable by their biased amino acid composition; low hydrophobicity and high dipole and net charges; high degree of chain movement; involvement in biomolecular condensates via multivalent interaction, etc.
2. The authors mentioned a few works on IDRs reported in molecular chaperones, where the structural plasticity of IDRs promotes chaperone-substrate recognition. These are sound examples signifying the role of IDRs. While molecular chaperones play an important role in facilitating protein folding and improving protein homeostasis robustness, they are NOT part of the UPS. The authors should list them separately to make the manuscript scientifically sound.
3. In Figure 2 and the associated main text, the authors showed that "IDRs are present in each component of the UPS" and "there is a steep increase in IDRs from E1 to E2, and a further raise from E2 to E3". It would be tremendously helpful if the authors could list the IDR regions (size, position, structural feature, etc.) for the symbolic UPS-associated proteins in a table or the supplementary information. Additionally, what is the average percentage of IDRs in the sequences of human E1, E2, and E3? These are crucial pieces of evidence to support the claim that the increase in IDRs from E1 to E2 to E3 is significant.
Comments on the Quality of English Language
The manuscript would benefit from some careful proofreading. Here, I list a few issues I picked up, but there are more. Line 77: Based on their functionality (missing comma); line 201: Up to a dozen years ago (rarely used in scientific writing).
Author Response
To the reviewer #2
We are delighted that the manuscript has been appreciated. Your kind comments and useful recommendations have been carefully considered. We have revised the manuscript according to your suggestions and bring the revised form to your attention. We would be delighted if you reconsider our revised manuscript for publication in the Biophysica.
In the revised version, all the modifications to the manuscript have been marked using the MS Word tracking function (red labeled).
Annotations to the page number and lines refer to the revised version of the manuscript.
Please find below enclosed our comments to the reviewer (R: Reviewer; A: Authors reply in italics)
R: In this manuscript, Magnati et al. reviewed the recent progress in understanding the roles of intrinsically disordered regions (IDRs) in protein quality control, with a focus on the ubiquitin proteasome system (UPS). The UPS plays a central role in degrading misfolded protein species to maintain proper protein homeostasis. While the mechanisms of the UPS are well-studied, how the IDRs of UPS component proteins contribute to their innate function remains less understood. This is a timely mini-review complementing many existing summaries of IDRs in other aspects of cell biology. This topic is well-suited for the scope of Biophysica. I support the publication of this manuscript if the following concerns are fully addressed.
R:1. In section 2, the authors did a good job summarizing the known functions of IDRs. Given the audience of this journal, mostly biophysicists, it would be helpful to introduce some common structural features and biophysical norms of IDRs. For example, in addition to their transient structures, IDRs are distinguishable by their biased amino acid composition; low hydrophobicity and high dipole and net charges; high degree of chain movement; involvement in biomolecular condensates via multivalent interaction, etc.
A: We are grateful to the reviewer for the suggestion. Consistently, in the revised version we implemented this issue by adding “In addition, IDPRs are characterized by peculiar biophysical and structural properties, namely their aminoacid (aa) composition heterogeneity, low content of hydrophobic aa residues, high net charges associated with the lack of significant ordered secondary structures, flat energy landscapes, involvement in biomolecular condensates, remarkable binding promiscuity, and ability to gain different structures upon binding to different partners. Eventually, they are featured by keeping an essential amount of disorder even in their bound form [7].” A new reference has also been added “Vladimir N Uversky V.N. Unusual biophysics of intrinsically disordered proteins Biochim Biophys Acta 2013 1834(5):932-51. doi: 10.1016/j.bbapap.2012.12.008.”
R: 2. The authors mentioned a few works on IDRs reported in molecular chaperones, where the structural plasticity of IDRs promotes chaperone-substrate recognition. These are sound examples signifying the role of IDRs. While molecular chaperones play an important role in facilitating protein folding and improving protein homeostasis robustness, they are NOT part of the UPS. The authors should list them separately to make the manuscript scientifically sound.
A: We carefully considered the reviewer's suggestion and to avoid misinterpretation we have slightly modified the text (line 230), the paragraph title has been changed too and Figure 2 re-drawn.
R: 3. In Figure 2 and the associated main text, the authors showed that "IDRs are present in each component of the UPS" and "there is a steep increase in IDRs from E1 to E2, and a further raise from E2 to E3". It would be tremendously helpful if the authors could list the IDR regions (size, position, structural feature, etc.) for the symbolic UPS-associated proteins in a table or the supplementary information. Additionally, what is the average percentage of IDRs in the sequences of human E1, E2, and E3? These are crucial pieces of evidence to support the claim that the increase in IDRs from E1 to E2 to E3 is significant.
A: We thank the reviewer for the insightful suggestion. Unfortunately listing position, structural features, and size of IDRs in UPS members is quite hard in such a short time given for the revision, keeping into account that they are approximately 600 members. However, we have provided as Supplementary Material a table (Table S1) in which the average percentage of the IDRs of the human E1, E2 and E3 is summarized.
R: Comments on the Quality of English Language
The manuscript would benefit from some careful proofreading. Here, I list a few issues I picked up, but there are more. Line 77: Based on their functionality (missing comma); line 201: Up to a dozen years ago (rarely used in scientific writing).
A: Thank you very much for pointing out that. The revised version has been edited accordingly.
