Bacterial chromosome segregation by the ParABS system

Proper chromosome segregation during cell division is essential in all domains of life. In the majority of bacterial species, faithful chromosome segregation is mediated by the tripartite ParABS system, consisting of an ATPase protein ParA, a CTPase and DNA-binding protein ParB, and a centromere-like parS site. The parS site is most often located near the origin of replication and is segregated first after chromosome replication. ParB nucleates on parS before binding to adjacent non-specific DNA to form a multimeric nucleoprotein complex. ParA interacts with ParB to drive the higher-order ParB–DNA complex, and hence the replicating chromosomes, to each daughter cell. Here, we review the various models for the formation of the ParABS complex and describe its role in segregating the origin-proximal region of the chromosome. Additionally, we discuss outstanding questions and challenges in understanding bacterial chromosome segregation.


Review form: Reviewer 2
Recommendation Accept with minor revision (please list in comments)

Do you have any ethical concerns with this paper? No
Comments to the Author This review is very well written. It clearly summarizes the current literature on the ParABS system, which is broadly conserved in bacteria and is involved in plasmid and chromosome segregation. The review first discusses the current models for the formation and the role of the ParB-parS nucleoprotein complex. The authors describe each model and raise the concerns and remaining investigations for each one. In the following sections, the authors describe the role of the ParA protein in chromosome segregation, the link between chromosome segregation and chromosome organization (through the SMC protein) and finally discuss a few divergent ParABS system. In each section of this review, the models described by the authors are more centered on the general mechanisms shared between different species than on species-specific details. I think this review is a very good ressource that, in my opinion, is valuable to a broad scientific community.
Comments: lines 159-160: I would specify that the structure is lacking the C-terminal domain, especially because at lines 102-104 the authors state that no full length structure of ParB has been resolved yet.
line 204-206: this sentence has no verb: "A co-crystal structure showing CDP binding to the arginine-rich patch at the NTD of B. subtilis ParB (CTP was hydrolyzed to CDP during crystallization)" line 211-212: "The B. subtilis ParB clamp can self-load at parS, without the need of a dedicated loading factor, and spreads by sliding to the neighboring DNA while still entrapping DNA". This sentence is a bit misleading. The sentence before this one states that CTP binding induces a clamp-like ParB. I think that the fact that CTP binding reduces ParB affinity for parS and induces the spreading along the DNA is not clear in this sentence and confuses the reader through the following paragraph.
line 238: in this section 2.6, it remained a little unclear to me if the different models described are totally disconnected or can be integrated together. It seems like the models are discussed here from the simplest 1D model to the most complex caging/CTP-binding model. Based on Figure 1, it also seems like the model are strongly connected but it's not really discussed in this section. line 271: segregation "OF" the origin-proximal lines 333-335: "mutations at the CTP-binding pocket of a ParB-like protein PadC were shown to impair PadC-ParA binding in vitro and gave rise to aberrant ParA localization patterns in vivo [51]." Maybe the authors could make it clearer here that CTP-bound PadC has more affinity to ParA or ParA preferentially binds to PadC-CTP. line 416-417: "A mutational event that resulting in the grafting of an amphipathic helix", replace "that resulting" with "that resulted" Decision letter (RSOB-20-0097.R0)

18-May-2020
Dear Dr Le We are pleased to inform you that your manuscript RSOB-20-0097 entitled "Bacterial chromosome segregation by the ParABS system" has been accepted by the Editor for publication in Open Biology. The reviewer(s) have recommended publication, but also suggest some minor revisions to your manuscript. Therefore, we invite you to respond to the reviewer(s)' comments and revise your manuscript.
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Reviewer(s)' Comments to Author:
Referee: 1 Comments to the Author(s) Review by Jalal and Le comprehensively discusses current models of bacterial chromosome segregation. The manuscript is clearly organised and well written. I appreciate recalling the experimental data that support discussed models. However, since now manuscript is most focused on ParB I would suggest adding some additional information concerning ParA and SMC. Information on ParA structure and more details on the interactions with DNA would be useful. The mention of the current model of SMC action could be included. Finally, the short description of ParA homologues and their varied function would fit nicely in the chapter on the evolution of ParAB system. Referee: 2 Comments to the Author(s) This review is very well written. It clearly summarizes the current literature on the ParABS system, which is broadly conserved in bacteria and is involved in plasmid and chromosome segregation. The review first discusses the current models for the formation and the role of the ParB-parS nucleoprotein complex. The authors describe each model and raise the concerns and remaining investigations for each one. In the following sections, the authors describe the role of the ParA protein in chromosome segregation, the link between chromosome segregation and chromosome organization (through the SMC protein) and finally discuss a few divergent ParABS system. In each section of this review, the models described by the authors are more centered on the general mechanisms shared between different species than on species-specific details. I think this review is a very good ressource that, in my opinion, is valuable to a broad scientific community.
Comments: lines 159-160: I would specify that the structure is lacking the C-terminal domain, especially because at lines 102-104 the authors state that no full length structure of ParB has been resolved yet.
line 204-206: this sentence has no verb: "A co-crystal structure showing CDP binding to the arginine-rich patch at the NTD of B. subtilis ParB (CTP was hydrolyzed to CDP during crystallization)" line 211-212: "The B. subtilis ParB clamp can self-load at parS, without the need of a dedicated loading factor, and spreads by sliding to the neighboring DNA while still entrapping DNA". This sentence is a bit misleading. The sentence before this one states that CTP binding induces a clamp-like ParB. I think that the fact that CTP binding reduces ParB affinity for parS and induces the spreading along the DNA is not clear in this sentence and confuses the reader through the following paragraph.
line 238: in this section 2.6, it remained a little unclear to me if the different models described are totally disconnected or can be integrated together. It seems like the models are discussed here from the simplest 1D model to the most complex caging/CTP-binding model. Based on Figure 1, it also seems like the model are strongly connected but it's not really discussed in this section.
line 271: segregation "OF" the origin-proximal lines 333-335: "mutations at the CTP-binding pocket of a ParB-like protein PadC were shown to impair PadC-ParA binding in vitro and gave rise to aberrant ParA localization patterns in vivo [51]." Maybe the authors could make it clearer here that CTP-bound PadC has more affinity to ParA or ParA preferentially binds to PadC-CTP. line 416-417: "A mutational event that resulting in the grafting of an amphipathic helix", replace "that resulting" with "that resulted" Author's Response to Decision Letter for (RSOB-20-0097.R0)

21-May-2020
Dear Dr Le We are pleased to inform you that your manuscript entitled "Bacterial chromosome segregation by the ParABS system" has been accepted by the Editor for publication in Open Biology.
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Thank you for your fine contribution. On behalf of the Editors of Open Biology, we look forward to your continued contributions to the journal.
Sincerely, The Open Biology Team mailto: openbiology@royalsociety.org Thank you very much for the comments on our manuscript. We are very grateful to the editor and all reviewers for their critical and supportive comments. We have now revised the manuscript accordingly. Detailed responses to the specific points that reviewers have raised are given in the "response to referees" file.

Referee: 2
This review is very well written. It clearly summarizes the current literature on the ParABS system, which is broadly conserved in bacteria and is involved in plasmid and chromosome segregation. The review first discusses the current models for the formation and the role of the ParB-parS nucleoprotein complex. The authors describe each model and raise the concerns and remaining investigations for each one. In the following sections, the authors describe the role of the ParA protein in chromosome segregation, the link between chromosome segregation and chromosome organization (through the SMC protein) and finally discuss a few divergent ParABS system. In each section of this review, the models described by the authors are more centered on the general mechanisms shared between different species than on species-specific details. I think this review is a very good resource that, in my opinion, is valuable to a broad scientific community.
Comments: lines 159-160: I would specify that the structure is lacking the C-terminal domain, especially because at lines 102-104 the authors state that no full-length structure of ParB has been resolved yet. We thank the reviewer for pointing this out and we have now corrected this sentence.
line 204-206: this sentence has no verb: "A co-crystal structure showing CDP binding to the arginine-rich patch at the NTD of B. subtilis ParB (CTP was hydrolyzed to CDP during crystallization)" We have now corrected this sentence to: "A co-crystal structure showed CDP binding to the arginine-rich patch at the NTD of B. subtilis ParB (CTP was hydrolyzed to CDP during crystallization)" line 211-212: "The B. subtilis ParB clamp can self-load at parS, without the need of a dedicated loading factor, and spreads by sliding to the neighboring DNA while still entrapping DNA". This sentence is a bit misleading. The sentence before this one states that CTP binding induces a clamp-like ParB. I think that the fact that CTP binding reduces ParB affinity for parS and induces the spreading along the DNA is not clear in this sentence and confuses the reader through the following paragraph. We thank the reviewer for pointing this out. We have now re-arranged sentences to make the order of facts/observations more logical.
line 238: in this section 2.6, it remained a little unclear to me if the different models described are totally disconnected or can be integrated together. It seems like the models are discussed here from the simplest 1D model to the most complex caging/CTP-binding model. Based on Figure 1, it also seems like the model are strongly connected but it's not really discussed in this section. We refrained from suggesting whether different models are totally disconnected or can be integrated together. Instead, we suggested in our original manuscript that "It is too early to answer this question adequately, given that many mechanistic details are still missing." The main purpose of section 2.6 was to raise a few important questions for the field, if answered, they have the potential to reconcile all models.
line 271: segregation "OF" the origin-proximal Corrected