Integrating Structural, Biochemical, and Cellular Perspectives on the TFIIH Helicases XPB and XPD
Round 1
Reviewer 1 Report
Comments and Suggestions for AuthorsThe review of XPB and XPD TFIIH factors is detailed and well-assembled. The presentation can be improved, e.g., by enhancing the clarity of the Figures and Tables and avoiding too long paragraphs. Some examples are listed below.
Specific points to consider:
1. Line 46. "as a ATP-driven translocase" - should it be "an ATP-"?
2. Line 51. Figures 2 and 3 are mentioned before Figure 1.
3. Lines 66-91. This paragraph is useful, although too long. Splitting it into smaller parts would make reading easier.
4. Figure 1. Too much text, and the font is too small. Reading would be an issue. One option is to reduce the text in the Figure and move it into the Figure legend. The Figure can also be rearranged vertically to allow more space for the remaining text.
5. Lines 104-162. This paragraph is too long. For readers, 10-15 lines is a good enough size of the paragraph. Maximum 20 if really needed.
6. Lines 201-235. Too long a paragraph.
7. Lines 246-282. Too long a paragraph.
8. Also lines 284-306.
9. Figure 3. It has too much text, and the fonts are too small. One option is to divide Figure 3 into two Figures or two clear panels (vertically) to allow more space and larger fonts. Optionally, some text can be moved into the main text or Figure legend. Moreover, this Figure, due to high level of text and no pictures, could be re-made as Tables.
10. Lines 328-354. Too long a paragraph.
11. Also lines 355-397.
12. Text in the Table 1 could be aligned slightly better, making borders between the columns clearer.
13. Lines 434-456. Too long a paragraph.
14. Also lines 467-495.
15. Also lines 496-520.
16. And lines 521-551.
17. And lines 552-584.
18. Table 2. Refs. column can be narrower if sometimes two lines are used. Then it would allow more space for the text columns, improving the presentation.
19. The abbreviations list is useful. And it is mainly alphabetically organized. Kindly check, especially line 874 (NOP2), which seems to be in the wrong place.
Author Response
Comment 1: Line 46. "as a ATP-driven translocase" - should it be "an ATP-"?
Response1: corrected to ""an ATP-." An instead of a should be used when used begore a vowel.
Comment 2: Line 51. Figures 2 and 3 are mentioned before Figure 1.
Response 2: Figure 1 is now only mentioned at Line 51 as the figure demonstrates XPB and XPD and the interacting proteins.
Comment 3: Lines 66-91. This paragraph is useful, although too long. Splitting it into smaller parts would make reading easier.
Response 3: Thank you for this constructive suggestion. We agree that the original paragraph was overly dense and could impact readability. In response, we have reorganized Lines 66–91 into three focused paragraphs separating (i) XP genetic classification and core biological function, (ii) structural organization and regulatory features, and (iii) plant-specific diversification. This restructuring improves logical flow and clarity while preserving all content and citations.
Comment 4: Figure 1. Too much text, and the font is too small. Reading would be an issue. One option is to reduce the text in the Figure and move it into the Figure legend. The Figure can also be rearranged vertically to allow more space for the remaining text.
Response 4: We thank the reviewer for this feedback The figure has been greatly revised. The small text was removed and the figure legend has been updated. The figure was also arranged vertically as suggested. All text was also increased in font size
Comment 5: Lines 104-162. This paragraph is too long. For readers, 10-15 lines is a good enough size of the paragraph. Maximum 20 if really needed.
Response 5: Thank you for this helpful suggestion. We agree that the original paragraph was overly long and difficult to follow. In response, we have reorganized Lines 104–162 into multiple focused paragraphs separating biochemical and genetic analyses, yeast PIC structural organization, mammalian mechanistic insights, TFIIH core architecture, and regulatory mutational studies. No content was removed, and all citations were preserved. This restructuring improves readability and logical progression while maintaining the original scope and detail.
Comment 6: Lines 201-235. Too long a paragraph.
Response 6: Thank you for this helpful comment. We agree that the original paragraph was excessively long and difficult to follow. In response, we have reorganized this section into three focused paragraphs separating (i) experimental and mutational evidence defining XPB’s ATPase-dependent function in NER, (ii) regulatory control by p52, p8, and XPA within the TFIIH core, and (iii) molecular dynamics–based mechanistic models of XPB-driven DNA opening. No content was removed and all citations were preserved. This restructuring improves readability and logical flow while maintaining the original level of detail.
Comment 7: Lines 246-282. Too long a paragraph
Response 7: Thank you for pointing this out. We agree with this comment. Therefore, we have reorganized the originally long paragraph into multiple focused paragraphs to improve readability and logical flow. Specifically, the section has been divided to separately address (i) kinetic and electrochemical analyses defining distinct XPB unwinding modes, (ii) archaeal XPB–Bax1 complex formation and ATPase modulation, and (iii) structural characterization of XPB–Bax1 interactions at DNA junctions. No content was removed and all citations were preserved.
Comment 8: Also lines 284-306.
Response 8: Thank you for pointing this out. We agree with this comment. Therefore, we have reorganized the originally long paragraph into three focused paragraphs to improve readability and clarity. The revised section now separates (i) clinical associations and genotype–phenotype correlations, (ii) TFIIH stability and essentiality of XPB, and (iii) mechanistic consequences of ATP-binding mutations and transcriptional defects. No content was removed and all citations were preserved.
Comment 9: Figure 3. It has too much text, and the fonts are too small. One option is to divide Figure 3 into two Figures or two clear panels (vertically) to allow more space and larger fonts. Optionally, some text can be moved into the main text or Figure legend. Moreover, this Figure, due to high level of text and no pictures, could be re-made as Tables.
Response 9: We thank the reviewer for this feedback. The fonts for figure 3 and now figure 5 have been increased significantly. Figure 4 was divided into two figures so now it is figure 3 for XPB and figure 5 for XPD. I believe this helps with the presentation of the figure and justifies keeping it as a flow/chart instead of a table.
Comment 10: Lines 328-354. Too long a paragraph.
Response 10: Thank you for this comment. We agree that the original paragraph was overly long. Therefore, we have reorganized this section into three focused paragraphs separating (i) triptolide-mediated XPB inhibition and transcriptional suppression, (ii) development and validation of minnelide as a refined XPB-targeting strategy, and (iii) identification of pelitinib as a second-generation XPB inhibitor. No content was removed and all citations were preserved. This revision improves readability and structural clarity.
Comment 11: Also lines 355-397.
Response 11: Thank you for this comment. We agree that the original paragraph was overly long. Therefore, we have reorganized this section into four focused paragraphs separating (i) XPB depletion and UV-sensitization studies, (ii) mechanistic pathways of spironolactone-induced XPB degradation, (iii) viral transcription dependence in EBV models, and (iv) HIV latency and therapeutic combination studies. No content was removed and all citations were preserved. This restructuring improves readability and logical organization.
Comment 12: Text in the Table 1 could be aligned slightly better, making borders between the columns clearer.
Response 12:
Comment 13: Lines 434-456. Too long a paragraph.
Response 13: Thank you for this comment. We agree that the original paragraph was overly long. Therefore, we have reorganized this section into three focused paragraphs separating (i) MAT1-mediated repression of XPD helicase activity, (ii) the regulatory XPD–p44 interface and disease-associated mutations, and (iii) structural positioning of XPD within the yeast PIC during transcription. No content was removed and all citations were preserved. This restructuring improves readability and logical organization
Comment 14: Also lines 467-495
Response 14: Thank you for this comment. We agree that the original paragraph was overly long. Therefore, we have reorganized this section into three focused paragraphs separating (i) CAK-mediated repression and conformational switching of XPD, (ii) early recruitment and inactive configuration during transcription-coupled repair, and (iii) XPA/XPG-driven remodeling and helicase activation during NER. No content was removed and all citations were preserved. This restructuring improves readability and logical clarity.
Comment 15: Also lines 496-520.
Response 15: Thank you for this comment. We agree that the original paragraph was overly long. Therefore, we have reorganized this section into three focused paragraphs separating (i) XPA/XPG-mediated activation of XPD helicase activity, (ii) lesion stalling and the scanning-to-incision transition, and (iii) additional modulators of XPD activity and its mitochondrial localization. No content was removed and all citations were preserved. This restructuring improves readability and logical clarity.
Comment 16: And lines 521-551.
Response 16: Thank you for this comment. We agree that the original paragraph was overly long. Therefore, we have reorganized this section into three focused paragraphs separating (i) lesion-type–specific structural responses of XPD, (ii) cryo-EM visualization of lesion-induced stalling within the helicase channel, and (iii) mutational and biochemical analyses defining XPD as a structural and kinetic checkpoint in NER. No content was removed and all citations were preserved. This restructuring improves readability and logical clarity.
Comment 17: And lines 552-584.
Response 17: Thank you for this comment. We agree that the original paragraph was overly long. Therefore, we have reorganized this section into three focused paragraphs separating (i) biochemical stimulation of XPD by p44/p62, (ii) structural modeling explaining p62-dependent regulation, and (iii) single-molecule analysis demonstrating intrinsically low catalytic activity in the absence of cofactors. No content was removed and all citations were preserved. This restructuring improves readability and logical organization.
Comment 19: 19. The abbreviations list is useful. And it is mainly alphabetically organized. Kindly check, especially line 874 (NOP2), which seems to be in the wrong place.
Response 19: Thank you for pointing this out, NOP2 was moved to the correct alphabetical place in the list of abbreviations
Reviewer 2 Report
Comments and Suggestions for AuthorsSummary: The authors have provided a comprehensive and up-to-date assessment of the structural, molecular, biochemical, and cell biological aspects of the XPB and XPD helicase subunits of the general transcription factor TFIIH. Given the linkage of mutations in the XPB and XPD genes to hereditary diseases, the review will be widely useful to researchers and clinicians as a go-to source for relevant information in this highly relevant area of genome biology and genetic disorders.
General Comments:
There is a lot of valuable information being communicated in this review. However, in some cases there could be improvements stylistically to make it not so daunting to access the information.
- Sometime there is a line space between paragraphs, which is very helpful. See lines 354-355 for example. However, in most cases there is not line space. So the lines keep running from paragraph to paragraph, which can be quite intimidating to the reader who naturally wants to compartmentalize concepts and manuscript text flow. Please insert spaces between paragraphs, assuming the journal accommodates that formatting.
- Related to the point above, a number of the paragraphs are quire long—see examples below in my Specific Comments. Please try to break overly long paragraphs into 2 or 3 paragraphs, making delineations that are logical.
- The text in Figures is often too many works and not legible, even on a large computer screen. See comments for Figures 1 and 3 below.
Specific Comments:
Figure 1 figure legend: Insert space between Figure and 1. Correct “Figure1”
Figure 1: The font is very small and difficult to read. This needs to be revised and made more readable. This issue also applies to Figure 3—see my comment below. Revise significantly.
Section 2.1: Can this section be broken into two paragraphs to make it more approachable for the reader?
Section 2.1: Provide a reference(s) to support the following statement: “XPB levels are tightly regulated in vivo, with each cell type maintaining a character-164 istic and highly uniform XPB concentration.”
Section 2.2: Can the first paragraph of this section be broken into two paragraphs to make it more approachable for the reader?
Figure 3: The font is very small and difficult to read in the various boxes, even when it is enlarged on my computer screen. As currently constructed, the poor legibility and long text within the boxes seriously compromises the utility and value of the figure. Moreover, as currently presented it is my strong impression that the appearance discourages the reader from actually trying to read and interpret what is attempt to be communicated. Revise significantly.
Line 563: Subscript “cat” in “kcat”
An area of growing interest is that of mutations in helicase genes and other DNA repair genes in somatic cancers of various types. This might have been addressed, as it pertains to XPB and XPD, to better appreciate how the knowledge of somatic mutations in XPB and XPD for certain cancers, may aid in diagnosis or possibly treatment strategies. If the frequencies of somatic mutations in XPB and XPD are known, this would be useful information. See the following references for examples of such papers:
Widespread genomic/molecular alterations of DNA helicases and their clinical/therapeutic implications across human cancer - PubMed
RecQ Helicase Somatic Alterations in Cancer - PubMed
Author Response
General Comment 1:
- Sometime there is a line space between paragraphs, which is very helpful. See lines 354-355 for example. However, in most cases there is not line space. So the lines keep running from paragraph to paragraph, which can be quite intimidating to the reader who naturally wants to compartmentalize concepts and manuscript text flow. Please insert spaces between paragraphs, assuming the journal accommodates that formatting.
- Related to the point above, a number of the paragraphs are quire long—see examples below in my Specific Comments. Please try to break overly long paragraphs into 2 or 3 paragraphs, making delineations that are logical.
General Response 1: We thank the reviewer for the excellent feedback. The spaces between paragraph was not intentional and a glance at other review papers from this journal do not typically have spaces between paragraphs. However, The long paragraphs have been logically broken into smaller paragraphs as suggested by another reviewer as well. The paragraphs were split by starting a new line followed by an indentation prior to the first word of the sentence as this journal typically presents paragraphs. I believe this should address the intimidation that was originally presented.
General Comment 2:
- The text in Figures is often too many works and not legible, even on a large computer screen. See comments for Figures 1 and 3 below.
General Response 2: please see response 6 for how this as addressed. This has been fixed.
Comment 1: Figure 1 figure legend: Insert space between Figure and 1. Correct “Figure1”
Response 1: Thank you for catching this typo, the space was added to Figure 1.
Comment 2: Figure 1: The font is very small and difficult to read. This needs to be revised and made more readable. This issue also applies to Figure 3—see my comment below. Revise significantly.
Comment 2: The Figures was revised significantly and the small text was removed and split vertically, the figure legend was updates. Figure 3 was also split into two figures instead.
Comment 3: Section 2.1: Can this section be broken into two paragraphs to make it more approachable for the reader?
Response 3: Thank you for this helpful suggestion. We agree that the original paragraph was overly long and difficult to follow. In response, we have reorganized Lines 104–162 (section 2.1)into multiple focused paragraphs separating biochemical and genetic analyses, yeast PIC structural organization, mammalian mechanistic insights, TFIIH core architecture, and regulatory mutational studies. No content was removed, and all citations were preserved. This restructuring improves readability and logical progression while maintaining the original scope and detail.
Comment 4: Section 2.1: Provide a reference(s) to support the following statement: “XPB levels are tightly regulated in vivo, with each cell type maintaining a character-164 istic and highly uniform XPB concentration.”
Response 4: We thank the reviewer for pointing this out and the correct reference has been added to this statement in section 2.1.
Comment 5: Can the first paragraph of this section be broken into two paragraphs to make it more approachable for the reader
Response 5: Thank you for this helpful comment. We agree that the original paragraph was excessively long and difficult to follow. In response, we have reorganized this section into three focused paragraphs separating (i) experimental and mutational evidence defining XPB’s ATPase-dependent function in NER, (ii) regulatory control by p52, p8, and XPA within the TFIIH core, and (iii) molecular dynamics–based mechanistic models of XPB-driven DNA opening. No content was removed and all citations were preserved. This restructuring improves readability and logical flow while maintaining the original level of detail.
Comment 6: Figure 3: The font is very small and difficult to read in the various boxes, even when it is enlarged on my computer screen. As currently constructed, the poor legibility and long text within the boxes seriously compromises the utility and value of the figure. Moreover, as currently presented it is my strong impression that the appearance discourages the reader from actually trying to read and interpret what is attempt to be communicated. Revise significantly.
Response 6: We appreciate this comment. The small text has been removed and added to the figure legend particularly for figure 1. Figure 3 was been split into two figures now figure 3 and figure 5 for XPB and XPD respectively. Additionally any remaining text in the figures should now be more legible as the figures are bigger and the font has been made larger.
Comment 7: Line 563: Subscript “cat” in “kcat”
Comment 7: We thank the reviewer for pointinh this out and the cat in Kcat was been placed in subscript.
Comment 8: An area of growing interest is that of mutations in helicase genes and other DNA repair genes in somatic cancers of various types. This might have been addressed, as it pertains to XPB and XPD, to better appreciate how the knowledge of somatic mutations in XPB and XPD for certain cancers, may aid in diagnosis or possibly treatment strategies. If the frequencies of somatic mutations in XPB and XPD are known, this would be useful information. See the following references for examples of such papers:
Response 8: We thank the reviewer for this helpful suggestion. As recommended, we have incorporated data from the study cited by the reviewer (“Widespread genomic/molecular alterations of DNA helicases and their clinical/therapeutic implications across human cancer”) to summarize the frequency and distribution of somatic XPB alterations across TCGA cancers. In Section 2.3, we now report that XPB exhibits an approximate 2% mutation frequency across 10,245 tumors spanning 33 cancer types and is not characterized by recurrent amplification or deep deletion events in this dataset. These additions provide quantitative context regarding the relative rarity of somatic XPB alterations in sporadic malignancies and directly address the reviewer’s request to include mutation frequency information. We thank the reviewer for highlighting the importance of somatic helicase mutations in cancer. In response, we have incorporated data addressing somatic alterations of XPD in muscle-invasive urothelial carcinoma. Specifically, whole-exome sequencing of patients treated with neoadjuvant cisplatin-based chemotherapy demonstrated that XPD was the only gene significantly enriched in cisplatin responders, with all identified non-synonymous mutations occurring exclusively in sensitive tumors and a mutation frequency of 36% within the responder cohort. Functional analyses further showed that representative XPD mutants failed to restore cisplatin resistance in deficient cells, supporting a mechanistic link between XPD loss-of-function and enhanced platinum sensitivity. These findings clarify the frequency, tumor specificity, and therapeutic relevance of somatic XPD mutations and directly address the reviewer’s comment regarding their potential diagnostic and treatment implications.
Reviewer 3 Report
Comments and Suggestions for AuthorsThis review by Dr. Li and colleague summarizes the structure, mechanism, evolution, disease relevance, and therapeutic targeting of the XPB and XPD helicases, key components of the TFIIH complex that function in transcription initiation and nucleotide excision repair (NER). The manuscript is comprehensive and largely up to date, providing a timely overview of these important helicases.
I have several major and minor comments:
Major comments:
- References: I suggest placing reference citations at the end of the first sentence that introduces specific findings. In several instances, references appear multiple sentences later, making it difficult to follow which studies support which statements.
- Recent literature: The authors may wish to discuss the recent publication (PMID: 41673165), which may have appeared during the submission process. This study provides important insights directly relevant to Sections 2.2 and 3.2 and would strengthen the review’s coverage of the topic.
Minor comments:
- Line 67 states that XPB exists “across organisms from archaea to humans,” while line 75 states that “XPB exists within all three domains of life.” These statements appear repetitive and somewhat inconsistent. Is XPB present in bacteria?
- Lines 86–91: This sentence is quite long and difficult to follow. Please consider rewriting for clarity.
- Line 110: The phrase “is essential for open complex formation and promoter escape” would benefit from clarification. What is the meaning by “open complex” and “promoter escape” in this context? Please also provide an appropriate reference.
- The first paragraph of Section 2.1 is lengthy and dense. Dividing it into two or three shorter paragraphs may improve readability.
- Line 180: The analogy of the “build-in-block” model is not clearly explained and could be elaborated.
- Line 230: The sentence “on NER mechanism no longer constrained to static biological structures” is unclear and may benefit from rewriting.
- Line 231: XPB is described as a dsDNA translocase. Can it also unwind dsDNA during NER? Clarification would be helpful.
- XPB is referred to consistently as “XPB” throughout most of the manuscript, but in lines 321–327 it is referred to as ERCC3. If there is no specific reason for this change, I suggest using “XPB” consistently to improve readability.
- Lines 355–356: A reference appears to be missing.
- I suggest moving Section 2.5 ahead of Section 2.4. Section 2.5 discusses XPB in antiviral therapy, but the biological context is only described afterward, which disrupts the logical flow.
- Line 460: In the phrase “whereas XPB binds but does not…,” is the word “unwind” missing?
- Line 701: There are two instances of the word “currently.”
- Lines 738–750: Additional discussion on why the K751Q mutation fails to predict chemotherapy outcomes would strengthen this section.
- Line 762: “It’s NOP2, Nucleolar Protein 2 It” appears to contain typo.
Author Response
Major Comment 1: References: I suggest placing reference citations at the end of the first sentence that introduces specific findings. In several instances, references appear multiple sentences later, making it difficult to follow which studies support which statements
Major Response 1: We thank the reviewer for this comment and citations were added to the first sentence that introduces specific findings throughout the entire manuscript.
Major Comment 2: Recent literature: The authors may wish to discuss the recent publication (PMID: 41673165), which may have appeared during the submission process. This study provides important insights directly relevant to Sections 2.2 and 3.2 and would strengthen the review’s coverage of the topic.
Major Response 2: We thank the reviewer for highlighting this recent publication. We have now incorporated the study (PMID: 41673165) into Sections 2.2 and 3.2. Specifically, we added a paragraph in Section 2.2 describing the cryo-EM visualization of XPB HD1–HD2 conformational cycling and the ATP-coupled duplex translocation mechanism (“waddling mechanism”) observed in the fully reconstituted pre-incision complex. In Section 3.2, we incorporated the structural definition of ATP-dependent DNA bubble formation and the resolved engagement of 4–9 nucleotides of the unpaired lesion strand by XPD within the assembled dual-incision complex. These additions strengthen the mechanistic discussion of both XPB and XPD during NER and align the review with the most recent structural insights.
Minor Comment 1: Line 67 states that XPB exists “across organisms from archaea to humans,” while line 75 states that “XPB exists within all three domains of life.” These statements appear repetitive and somewhat inconsistent. Is XPB present in bacteria?
Minor Response 1: The repetition was removed and the wording was adjusted to just state that XPB exists within all three domains of life.
Minor Comment 2: Lines 6–91: This sentence is quite long and difficult to follow. Please consider rewriting for clarity.
Minor Response 2: Thank you for this comment. We agree that the original sentence was overly long and difficult to follow. We have revised this section by separating the structural comparison from the regulatory features of the C-terminal extension to improve clarity while preserving all original content.
Minor Comment 3: Line 110: The phrase “is essential for open complex formation and promoter escape” would benefit from clarification. What is the meaning by “open complex” and “promoter escape” in this context? Please also provide an appropriate reference.
Minor Response 3: Thank you for this suggestion. We have clarified the meaning of “open complex” and “promoter escape” in the revised manuscript by explicitly defining these terms in the context of RNA polymerase II transcription initiation and have retained reference [23] to support this description
Minor Comment 4: The first paragraph of Section 2.1 is lengthy and dense. Dividing it into two or three shorter paragraphs may improve readability.
Minor Response 4:
Thank you for this helpful suggestion. We agree that the original paragraph was overly long and difficult to follow. In response, we have reorganized Lines 104–162 into multiple focused paragraphs separating biochemical and genetic analyses, yeast PIC structural organization, mammalian mechanistic insights, TFIIH core architecture, and regulatory mutational studies. No content was removed, and all citations were preserved. This restructuring improves readability and logical progression while maintaining the original scope and detail.
Minor Comment 5: Line 180: The analogy of the “build-in-block” model is not clearly explained and could be elaborated.
Minor Response 5: We thank the reviewer for noting that the “built-in block” model required clearer explanation. We have revised the text to explicitly describe the mechanism proposed in the cited study. Specifically, we now clarify that XPB intrinsically imposes a block to promoter melting within the pre-initiation complex, and that its ATPase activity functions to relieve this inhibitory constraint. We further explain that transcription can proceed in the absence of XPB because the block is removed, whereas inhibition of XPB’s ATPase activity in the presence of XPB maintains the block and impairs initiation. This clarification better defines the helicase-independent regulatory role of XPB during promoter opening
Minor Comment 6: Line 230: The sentence “on NER mechanism no longer constrained to static biological structures” is unclear and may benefit from rewriting.
Minor Response 6: We thank the reviewer for this comment. The sentence has been revised for clarity to better convey that molecular dynamics simulations provide dynamic insight into NER mechanisms beyond static structural models.
Minor Comment 7: Line 231: XPB is described as a dsDNA translocase. Can it also unwind dsDNA during NER? Clarification would be helpful.
Minor Response 7: We thank the reviewer for requesting clarification regarding whether XPB can unwind dsDNA during NER. We have revised the text to explicitly state that XPB does not function as a conventional helicase during DNA repair. Instead, consistent with the cited study, XPB promotes DNA opening through ATP-dependent dsDNA translocation within fully assembled core TFIIH, generating torsional strain that contributes to initial duplex destabilization. We further clarified that XPA enhances the processivity of this complex without altering XPB’s ATPase rate. The revised sentence now clearly distinguishes XPB’s translocase-driven DNA opening mechanism from canonical helicase-mediated strand separation.
Minor Comment 8: XPB is referred to consistently as “XPB” throughout most of the manuscript, but in lines 321–327 it is referred to as ERCC3. If there is no specific reason for this change, I suggest using “XPB” consistently to improve readability.
Minor Response 8: All instance of ERCC3 were replaced with XPB throughout the manuscript. We thank the reviewer for making this suggestion to improve consistency.
Minor Comment 9: Lines 355–356: A reference appears to be missing
Minor Response 9: The reference was added to support section pertaining to minnelide.
Minor Comment 10: I suggest moving Section 2.5 ahead of Section 2.4. Section 2.5 discusses XPB in antiviral therapy, but the biological context is only described afterward, which disrupts the logical flow.
Minor Response 10: We thank the reviewer for this helpful suggestion. In response, we have moved Section 2.5 ahead of Section 2.4 to improve the logical progression of the manuscript. The revised structure now introduces the relevant biological context before discussing XPB in antiviral therapy, resulting in a clearer and more coherent narrative flow.
Minor Comment 11: Line 460: In the phrase “whereas XPB binds but does not…,” is the word “unwind” missing?
Minor Response 11: Unwind as added to this sentence. We thank the reviewer for bringing this error to our attention
Minor Comment 12: Line 701: There are two instances of the word “currently.”
Minor Response 12: We thank the reviewer for finding this error, the second instance of currently was removed.
Minor Comment 13: Lines 738–750: Additional discussion on why the K751Q mutation fails to predict chemotherapy outcomes would strengthen this section.
Minor Response 13: Thank you for this valuable suggestion. We have revised the Discussion section (Lines 738–750) to further clarify potential reasons for the lack of association between the Lys751Gln polymorphism and oxaliplatin-related toxicities. Specifically, we expanded the text to address factors such as the relatively small sample size, single-center recruitment, limited follow-up duration, and differences in oxaliplatin regimens and ethnic background across studies, which may contribute to inconsistent findings.
Minor Comment 14: Line 762: “It’s NOP2, Nucleolar Protein 2 It” appears to contain typo.
Minor Response 14: We thank the reviewer for finding this typo, this was fixed to state the abbreviation after Nucleolar Protein 2
Reviewer 4 Report
Comments and Suggestions for AuthorsThis manuscript by Bravo and Fan provides a comprehensive and complete review of XPB and XPD.
Some points could be made clearer.
-In line 203, XPB is described in the context of NER as acting as a translocase rather than a canonical helicase. However, it is mentioned later that XPB acts as the primary helicase (line 253). Although this represents a distinct functional variant, a clearer distinction could be made to improve the organization of the manuscript.
-In Figure 1, p8 could be added to the TFIIH schematic.
-Line 762: “It’s NOP2…”. This sentence could be rephrased more clearly.
Author Response
Comment 1: In line 203, XPB is described in the context of NER as acting as a translocase rather than a canonical helicase. However, it is mentioned later that XPB acts as the primary helicase (line 253). Although this represents a distinct functional variant, a clearer distinction could be made to improve the organization of the manuscript.
Response1 :
We thank the reviewer for pointing out the potential inconsistency in terminology. We have revised the manuscript to clarify the functional distinction. The text now avoids referring to XPB as a “primary helicase” and instead specifies that XPB initiates DNA duplex opening through an unconventional molecular wrench mechanism followed by a slower unzipping process. This revision better distinguishes XPB’s mechanistic role in NER from that of a classical processive helicase and improves the overall clarity and organization of the section.
Comment 2: Figure 1, p8 could be added to the TFIIH schematic.
Response 2: We thank the reviewer for suggesting P8 be added, the P8 protein was already added but referred to as TTDA which its alternate name, it is now called p8 in the schematic.
Comment 3: Line 762 It’s NOP2…”. This sentence could be rephrased more clearly.
Response 3: This sentences was fixed and the correct abbreviation was fixed. It was a typo we thank the reviewer for noticing this typo
Round 2
Reviewer 1 Report
Comments and Suggestions for AuthorsThe authors have revised the manuscript according to the comments.
Reviewer 2 Report
Comments and Suggestions for AuthorsThe authors have addressed my critical comments and improved the figures. This paper should be a nice addition to the literature and be resourceful for specialists and non-specialists alike.
Reviewer 3 Report
Comments and Suggestions for AuthorsThe authors addressed all my comments
