Articles | Volume 2, issue 1
© Author(s) 2021. This work is distributed underthe Creative Commons Attribution 4.0 License.
Structural polymorphism and substrate promiscuity of a ribosome-associated molecular chaperone
- Final revised paper (published on 04 Jun 2021)
- Supplement to the final revised paper
- Preprint (discussion started on 25 Jan 2021)
- Supplement to the preprint
Comment types: AC – author | RC – referee | CC – community | EC – editor | CEC – chief editor |
: Report abuse
RC1: 'Comment on mr-2021-9', Anonymous Referee #1, 11 Feb 2021
- AC1: 'Reply on RC1', Shang-Te Danny Hsu, 12 Apr 2021
- AC4: 'Reply on RC1', Shang-Te Danny Hsu, 12 Apr 2021
RC2: 'Comment on mr-2021-9', Anonymous Referee #2, 03 Mar 2021
- AC2: 'Reply on RC2', Shang-Te Danny Hsu, 12 Apr 2021
RC3: 'Comment on mr-2021-9', Anonymous Referee #3, 03 Mar 2021
- AC3: 'Reply on RC3', Shang-Te Danny Hsu, 12 Apr 2021
Peer review completion
AR: Author's response | RR: Referee report | ED: Editor decision
AR by Shang-Te Danny Hsu on behalf of the Authors (12 Apr 2021)  Author's response Author's tracked changes Manuscript
ED: Referee Nomination & Report Request started (21 Apr 2021) by Hashim Al-Hashimi
RR by Anonymous Referee #3 (02 May 2021)
ED: Publish subject to corrections (02 May 2021) by Hashim Al-Hashimi
In the present manuscripts the authors aim at characterising the chaperone trigger factor (TF) regarding the dimerisation of TF and its implication on interaction with substrates. If the topic is interesting and trying to answer biologically relevant questions, the overall quality of the paper appears poor and too preliminary for publication.
1. There is a lengthy discussion about TF assignments. As presented here, RDB and PPI domains were assigned previously by the authors, SBD and TF113-432 by Dyson’s group and the full length by Kalodimos and Hiller groups. It thus seems to me that all this constructs were assigned before. Please clarify this section and state explicitly your contribution to the field.
2. For characterising the dimer interface and dynamics, the authors use a combination of NMR line-widths analysis and EPR. This is an interesting approach, however the obtained data remain low resolution and do not allow for a clear description of the dimer properties. This section is thus not very conclusive and as the authors have all the tools in hand to label with MTSL each domain of TF, I am wondering why they do not prepare mixture of isotopically labelled TF with each of the MTSL constructs successively to answer which domains of TF are in fact interacting or in close proximity. Extra EPR measurements could be used to derive informations about the domain even if more distant than the PRE distance range.
3. In the section regarding interaction with peptides, the authors aims at verifying the quality of a theoretical model model regarding TF-target interactions. This is an interesting question however the current approach lack rigorous testing. In fact the selection of the 5 constructs remains unclear to me. For exemple why is the site around 290 not chosen? It seems from the figure to be a potentially better site than 5. Also no testing on a site which is predicted to not or poorly interact is done.
4. In the comparison of the interaction between IcdH2 and IcdH3, in the actual format it is almost impossible to assess the quality and relevance of the data and analysis. The PRE figures are extremely hard to read. Please adjust those figures, possibly with a multiple panel organisation so that the data readable and easily comparable between the different considered systems/probes. Please also indicate where each domain is in the sequence. For exemple, when the authors indicate that “the loss of PRE was much more pronounced for IcdH3 compared to that of IcdH2”, I couldn’t find any quantitative comparison or direct comparison of the experimental data. The conclusion of this section regarding TF dimerisation seems to me quite speculative regarding the current data. It might be possible however to better reach those conclusions if the data where more adequately presented.
5. In the cross-linking section, the authors aims at distinguishing the effect of TF dimerisation on substrate recognition. In Fig 6, the gel used to control the cross-linking data show a band at 50kDa for TF in absence of BS3, while in the presence of BS3 the band is a blurry broad band at very high molecular weight (>130kDa and much higher). This indicate that the form obtained by cross-linking is not a dimer but probably a set of oligomers of TF (with 3, 4 or more TF units). To test the role of dimerisation in the interaction process the cross-linking should have given a dimer and not an oligomer. To me, this render this part of the study inconclusive.
Considering the points above, I consider it difficult to obtain strong conclusions from this study. In the current state I do not see the added value of the current study for the state of the art of the research in the field. The last figure is quite striking to me, only the (b) part seems to be a novel contribution from the group which I believe is lagging behind current structural studies of TF already existing. I would thus not recommend this paper for publication.
Additional extra minor points
1. For readability I would strongly encourage the authors to homogenise the nomenclature regarding TF constructs and domains.
2. Figure S3 is missing in the file I could download
3. Figure 3 could be moved to the SI
4. Some references are incomplete regarding, e.g. doi numbers