POLD3 as Controller of Replicative DNA Repair
Round 1
Reviewer 1 Report
Comments and Suggestions for AuthorsGeneral remark: I suggest rewriting certain sentences for clarity. Additionally, the usage of capital letters in the abbreviation expansions seems to distract the reader from the context of the manuscript. Therefore, I suggest changing them to small letters. These also appear mixed in the main text and Figure descriptions. The same is true for the blend of present and past tenses. Accordingly, moderate English editing is required.
Minor remarks:
Line 9-10: I suggest rewriting the sentence from “DNA synthesis by Polδ and Polζ is mutagenic, but is needed to survive the DNA breaks” to “DNA synthesis by Polδ and Polζ is mutagenic, but is needed for the survival of cells in the presence of DNA strand breaks”.
Line 12: Please rewrite the sentence “We provide the background to POLD3 discovery and survey POLD3 structure and function in vitro and in cells” to “We provide the background to POLD3 discovery, investigate its structure as well as function in cells”.
Line 24: Please clarify what the authors mean by “disordered regions”
Line 27-29: Please rewrite “There are several uncharacterised motifs of POLD3 that are important for maintaining genome stability and human health, including mutations associated with familial hearing impairment (11) and Omenn Syndrome (12).” to “There are several uncharacterized motifs of POLD3 that are important for maintaining genome stability and human health, preventing mutations associated with familial hearing impairment (11) and Omenn Syndrome (12).”
Line 29-33: Please rewrite: “The significance of POLD3 in mammalian health is clear in adverse effects on genome stability and fertility from deletions and knock-downs of POLD3…..” to “The significance of POLD3 in mammalian health is clear as knock-downs and deletions of POLD3 were associated with genomic instability implicated in the infertility based on Cancer Dependency mapping (DepMap). Additionally, hyperactive DNA synthesis associated with POLD3 was shown to be involved in tumorigenesis and spermatogenesis”.
Line 53: Please remove the capital letters for the abbreviations in the text and remove the red semi-colon.
Line 57-58: Please rewrite the sentence for clarity. What do authors mean by genetic threat?
Line 71-74: Please rewrite the sentence for clarity “We also refer to a timeline for DNA polymerases more generally is provided by the Woodgate group: https://www.nichd.nih.gov/research/atNICHD/Investigators/woodgate/research/DNA-polymerases.” Do the authors mean: “We also refer to a timeline for DNA polymerases discovery and studies previously provided by the Woodgate group”?
Line 103-107: Please rewrite the sentence for clarity.
Lines 123-124/129-132: Please rewrite the sentences as they are not easily understandable.
Line 132-133: Please rewrite the sentence for clarity “It indicates the synergistic presence of POLD3 with POLD1 and POLD2 to protect the integrity of the Polδ complex” Should it be “It indicates that the presence of POLD3 with POLD1 and POLD2 protects the integrity of the Polδ complex”
Line 134-138: Divide the sentence in two for clarity.
Line 142: Please remove the red question mark from the manuscript.
Line 143: Please rewrite the sentence: “More detail about the experimental data is in Section 4 of the text” to “More details about the experimental data can be found in Section 4.”
Line 147. Start with “The completely resolved…”
Line 157: “Conserved IDPR regions of POLD3 are summarised in Figure 4” I think that may be some kind of mistake that should be removed.
Line 167: Remove the (—) and separate into two sentences.
Line 169-70: Please replace the sentence with: “More details about POLD3 post-translational modifications were provided in Section 6.”
Line 186-187: Should “Also shown is the wHTH fold within the Alphafold3 prediction for the majority IDPR of POLD3.” be the continuation of the previous sentences?
Lines 188-196: Start with “Homo sapiens”….and finish the thought with “were used for the sequence alignment”
Line 192: Replace B to “B: Summary of the motifs of POLD3 proteins…”
Lines 198-201: Please rewrite sentences for clarity.
Line 202: replace “identifies” with ”identified”
Lines 206-207: Please rewrite: “The patient’s fibroblast levels of POLD1, POLD2 and POLD3 proteins were unimpaired, indicating conserved physical integrity of the Polδ complex” to “The protein expression of POLD1, POLD2, and POLD3 were unaltered in patient’s fibroblast indicating conserved physical integrity of the Polδ complex”
Line 227-229: Paraphrase the sentence for clarity.
Line 237: Replace “it” with “the binding with DNA”
Line 238: Replace: “POLD3 also facilitates Polδ to bypass DNA lesions such as abasic sites (23), especially if the proofreading function of POLD1 was also compromised, further indicating regulatory effects of POLD3 on DNA synthesis.” with “POLD3 also facilitates the bypass of DNA lesions such as abasic sites by Polδ (23), especially if the proofreading function of POLD1 is compromised, further indicating regulatory effects of POLD3 on DNA synthesis”
Lines 272-273: Replace “recent reviews of homologous recombination pathways are in (95,96)” with “homologous recombination pathways were reviewed by other authors (95,96)”
The description of Figure 5 should be rewritten for clarity.
Line 294: Is “4.3. Mutagenesis caused by POLD3-dependent BIR (17,20,22,100-106)” an error? Should it be somewhere in the main text of the manuscript?
Line 303-308: The information provided here is not clear. Please re-arrange the sentences and rewrite them for clarity.
Line 318-319: “Polζ is reviewed in (127,128)” I think that the authors mean that its structure/function was reviewed by the other authors. Please specify.
Line 327: Please remove red (–).
Line 441. Replace “Cas9 DNA cutting” with “Cas9-mediated DNA cutting”
Comments on the Quality of English LanguageModerate editing of English language required.
Author Response
Please see the attachment.
Author Response File: 
Author Response.pdf
Reviewer 2 Report
Comments and Suggestions for AuthorsThis manuscript reviews the latest findings on POLD3. It seems well written and I would like to point out a few concerns I noticed.
Specific points)
1. Figure 3 is somewhat confusing. For example, how about unifying the colors of each component (POLD3, etc.) in Figure 3A-E? Also, it would be easier to understand Figure 3F if it were shown where it corresponds to in Figure 3C as much as possible.
2. The subheadings below should be changed more appropriately (page 5, lines 157-158; page 9, line 294; page 12, line 405).
3. Page 6, line 184; Is NLS a nuclear localization sequence?
Author Response
Please see the attachment.
Author Response File: Author Response.pdf
Reviewer 3 Report
Comments and Suggestions for AuthorsThere are a number of minor grammatical issues that are listed below, apart from that the review is well organized and written.
Comments on the Quality of English LanguageThere are some minor grammatical issues, following are typical examples but this may not be a complete list.
93-94 The verb is unclear in this sentence, perhaps better: "Follw-up studies indicated Pold is comprised of..."
123-124 The word "With" can be removed for clarity.
131-132 This sentence is unclear.
174 should read "caused a loss of interaction with"
186 Should it be "two hydrophobic phenylalanines"?
200 Second half of the sentence is unclear.
202 Verb tense changes from previous sentence.
209 should be "...an unknown mechanism"
240 verb tense changed from present to past tense here, rest of sentence and paragraph is in present tense.
272-273 Unclear what "recent reviews of homologous recombination are in" means
307 Is the spiral sign correct?
345-346 "catalytical" should be "catalytic" and unclear what "see main text such" means.
423 author's or authors'
Author Response
Please see the attachment.
Author Response File: Author Response.pdf
