Bacterial Transcriptional Regulators: A Road Map for Functional, Structural, and Biophysical Characterization
, Maria Juliana Juncos †, Matias Villarruel Dujovne †and Daiana A. Capdevila *Round 1
Reviewer 1 Report
The manuscript "Bacterial transcriptional regulators: A road map for functional, structural and biophysical characterization" by Pis Diez, Juncos, Villaruel Dujovne, and Capdevila is a well-written and well-organized review about experimental techniques for investigating transcriptional regulators. Different types of experiments are treated in separate chapters, and most chapter include a large Figure which summarizes the chapter and provides a wealth of information. The manuscript also features a brief general introduction into TRs. I think the manuscript is of value for a broad readership at different levels of expertise who work in the field and I think that it ca be published basically in its current state. The few typos that I found and some very minor comments are included in the marked PDF, which is attached.
Kind regards
Comments for author File: 
Comments.pdf
Author Response
Point 1: The manuscript "Bacterial transcriptional regulators: A road map for functional, structural and biophysical characterization" by Pis Diez, Juncos, Villaruel Dujovne, and Capdevila is a well-written and well-organized review about experimental techniques for investigating transcriptional regulators. Different types of experiments are treated in separate chapters, and most chapter include a large Figure which summarizes the chapter and provides a wealth of information. The manuscript also features a brief general introduction into TRs. I think the manuscript is of value for a broad readership at different levels of expertise who work in the field and I think that it ca be published basically in its current state.
The few typos that I found and some very minor comments are included in the marked PDF, which is attached.
Response 1: We thank the reviewer for the positive comments on our manuscript and the precise suggestions he made to improve the language and clarity. We have incorporated all the edits and comments that he or she suggested. Namely:
- we have corrected the spelling of "promotor" to "promoter",
- we have corrected the typos in figure 1,
- we have added a sentence in line 369 to clarify the figure call out: “The different traces (from green to blue) define relative Kds with respect to the competitor, while in the case of direct titrations the Kd can be directly modeled by the 50% occupancy of the labeled ligand (blue)”,
- we have clarified in line 459 the relevance and the opportunity of the increment in CryoEM structure deposition,
- we have corrected the spelling of overexpression and Post-translationally and we have checked the whole document for spelling and grammar mistakes like the one that the reviewer points out.
Reviewer 2 Report
The manuscript "Bacterial transcriptional regulators: A road map for functional, structural, and biophysical characterization" by Cristian Manuel Pis Diez et al is a comprehensive review of bacterial TRs with a focus on their structural and biophysical characterization.
Overall the review is well-organized, with nice illustrations of a biological characterization workflow, the biophysical methods used for binding, the structural data available for several TR families and the timescales of protein dynamics. The writting is good albeit several parts need revision by a native english speakerm while others can be revised by the authors (e.g. the repetitions in the abstract l. 32-33 and 38-39). Some other minor issues can be revised throughout the whole manuscript, such as Kd which should be given as Kd in Figures and legends too (e.g. Figure 2). In addition panel D of figure 3 need revision too, as there can be no crossing between the open and closed states in the μs-ms scale (the purple line should be deleted). At this figure the use of greek μ sympol should be revised to match the font appearence of seconds. Finally, the use of "that" or "which" should be revised too, as in many parts is not used appropriately.
Considering the relevance of this review to the Special Issue submitted, the overal good quality of the manuscript, the adequate number of references and its good organization, I can suggest its publication to IJMS after the authors revise the minor issues mentioned above, as well as several grammatical issues throughout the whole text, which probably requires the aid of a native speaker.
Author Response
Response to Reviewer 2 Comments
Point 1: The manuscript "Bacterial transcriptional regulators: A road map for functional, structural, and biophysical characterization" by Cristian Manuel Pis Diez et al is a comprehensive review of bacterial TRs with a focus on their structural and biophysical characterization.
Overall the review is well-organized, with nice illustrations of a biological characterization workflow, the biophysical methods used for binding, the structural data available for several TR families, and the timescales of protein dynamics. The writing is good albeit several parts need revision by a native English speaker while others can be revised by the authors (e.g. the repetitions in the abstract l. 32-33 and 38-39).
Response 1: We thank the reviewer for the positive comment on our manuscript and for the suggestion to make a more thorough language revision. The manuscript has been revised extensively for repetition like the one the reviewer exemplified by all the authors as well as native English speakers colleagues that have kindly agreed to revise our manuscript.
Point 2: Some other minor issues can be revised throughout the whole manuscript, such as Kd which should be given as Kd in Figures and legends too (e.g. Figure 2).
Response 2: We have corrected this format mistake in figure 2 and checked for similar formatting issues throughout the manuscript.
Point 3: In addition panel, D of figure 3 needs revision too, as there can be no crossing between the open and closed states in the μs-ms scale (the purple line should be deleted). In this figure, the use of the greek μ symbol should be revised to match the font appearance of seconds.
Response 3: We thank the reviewer for pointing out that the free energy surface of the Zn bound state was not clear enough. We have corrected it following the reviewer's suggestion. We have pointed out in the caption that it has been adapted from a previously published work. Also, we have corrected the format inconsistency that the reviewer mentioned.
Point 4: Finally, the use of "that" or "which" should be revised too, as in many parts is not used appropriately. Considering the relevance of this review to the Special Issue submitted, the overall good quality of the manuscript, the adequate number of references, and its good organization, I can suggest its publication to IJMS after the authors revise the minor issues mentioned above, as well as several grammatical issues throughout the whole text, which probably requires the aid of a native speaker.
Response 4: We apologize to the reviewer for the grammar and language issues that were present in the submitted version of the manuscript. We have revised extensively the manuscript for this and other similar grammar errors. All the changes are highlighted in the corrected version of the manuscript that we expect the reviewer finds acceptable for publication. The manuscript has been also revised by a native English speaker who is now acknowledged in the acknowledgment section.
