Interaction hierarchy among Cdv proteins drives recruitment to membrane necks

Reviewer #1 (Public review):

Summary:

The authors aimed to elucidate the recruitment order and assembly of the Cdv proteins during Sulfolobus acidocaldarius archaeal cell division using a bottom-up reconstitution approach. They employed liposome-binding assays, EM, and fluorescence microscopy with in vitro reconstitution in dumbbell-shaped liposomes to explore how CdvA, CdvB, and the homologues of ESCRT-III proteins (CdvB, CdvB1, and CdvB2) interact to form membrane remodeling complexes.
The study sought to reconstitute the Cdv machinery by first analyzing their assembly as two sub-complexes: CdvA:CdvB and CdvB1:CdvB2ΔC. The authors report that CdvA binds lipid membranes only in the presence of CdvB and localizes preferentially to membrane necks. Similarly, the findings on CdvB1:CdvB2ΔC indicate that truncation of CdvB2 facilitates filament formation and enhances curvature sensitivity in interaction with CdvB1. Finally, while the authors reconstitute a quaternary CdvA:CdvB:CdvB1:CdvB2 complex and demonstrate its enrichment at membrane necks, the mechanistic details of how these complexes drive membrane remodeling by subcomplexes removal by the proteasome and/or CdvC remain speculative.
Although the work highlights intriguing similarities with eukaryotic ESCRT-III systems and explores unique archaeal adaptations, the conclusions drawn would benefit from stronger experimental validation and a more comprehensive mechanistic framework.

Strengths:

The study of machinery assembly and its involvement in membrane remodeling, particularly using bottom-up reconstituted in vitro systems, presents significant challenges. This is particularly true for systems like the ESCRT-III complex, which localizes uniquely at the lumen of membrane necks prior to scission. The use of dumbbell-shaped liposomes in this study provides a promising experimental model to investigate ESCRT-III and ESCRT-III-like protein activity at membrane necks.
The authors present intriguing evidence regarding the sequential recruitment of ESCRT-III proteins in crenarchaea-a close relative of eukaryotes. This finding suggests that the hierarchical recruitment characteristic of eukaryotic systems may predate eukaryogenesis, which is a significant and exciting contribution. However, the broader implications of these findings for membrane remodeling mechanisms remain speculative, and the study would benefit from stronger experimental validation and expanded contextualization within the field.

Weaknesses:

This manuscript presents several methodological inconsistencies and lacks key controls to validate its claims. Additionally, there is insufficient information about the number of experimental repetitions, statistical analyses, and a broader discussion of the major findings in the context of open questions in the field.

Reviewer #2 (Public review):

Summary:

The Crenarchaeal Cdv division system represents a reduced form of the universal and ubiquitous ESCRT membrane reverse-topology scission machinery, and therefore a prime candidate for synthetic and reconstitution studies. The work here represents a solid extension of previous work in the field, clarifying the order of recruitment of Cdv proteins to curved membranes.

Strengths:

The use of a recently developed approach to produce dumbbell-shaped liposomes (De Franceschi et al. 2022), which allowed the authors to assess recruitment of various Cdv assemblies to curved membranes or membrane necks; reconstitution of a quaternary Cdv complex at a membrane neck.

Weaknesses:

The manuscript is a bit light on quantitative detail, across the various figures, and several key controls are missing (CdvA, B alone to better interpret the co-polymerisation phenotypes and establish the true order of recruitment, for example) - addressing this would make the paper much stronger. The authors could also include in the discussion a short paragraph on implications for our understanding of ESCRT function in other contexts and/or in archaeal evolution, as well as a brief exploration of the possible reasons for the discrepancy between the foci observed in their liposome assays and the large rings observed in cells - to better serve the interests of a broad audience.

Reviewer #3 (Public review):

Summary:

In this report, De Franceschi et al. purify components of the Cdv machinery in archaeon M. sedula and probe their interactions with membrane and with one-another in vitro using two main assays - liposome flotation and fluorescent imaging of encapsulated proteins. This has the potential to add to the field by showing how the order of protein recruitment seen in cells is related to the differential capacity of individual proteins to bind membranes when alone or when combined.

Strengths:

Using the floatation assay, they demonstrate that CdvA and CdvB bind liposomes when combined. While CdvB1 also binds liposomes under these conditions, in the floatation assay, CdvB2 lacking its C-terminus is not efficiently recruited to membranes unless CdvAB or CdvB1 are present. The authors then employ a clever liposome assay that generates chained spherical liposomes connected by thin membrane necks, which allows them to accurately control the buffer composition inside and outside of the liposome. With this, they show that all four proteins accumulate in necks of dumbbell-shaped liposomes that mimic the shape of constricting necks in cell division. Taken altogether, these data lead them to propose that Cdv proteins are sequentially recruited to the membrane as has also been suggested by in vivo studies of ESCRT-III dependent cell division in crenarchaea.

Weaknesses:

These experiments provide a good starting point for the in vitro study the interaction of Cdv system components with the membrane and their consecutive recruitment. However, several experimental controls are missing that complicate their ability to draw strong conclusions. Moreover, some results are inconsistent across the two main assays which make the findings difficult to interpret.

(1) Missing controls.

Various protein mixtures are assessed for their membrane-binding properties in different ways. However, it is difficult to interpret the effect of any specific protein combination, when the same experiment is not presented in a way that includes separate tests for all individual components. In this sense, the paper lacks important controls.

For example, Fig 1C is missing the CdvB-only control. The authors remark that CdvB did not polymerise (data not shown) but do not comment on whether it binds membrane in their assays. In the introduction, Samson et al., 2011 is cited as a reference to show that CdvB does not bind membrane. However, here the authors are working with protein from a different organism in a different buffer, using a different membrane composition and a different assay. Given that so many variables are changing, it would be good to present how M. sedula CdvB behaves under these conditions.

Similarly, there is no data showing how CdvB alone or CdvA alone behave in the dumbbell liposome assay. Without these controls, it's impossible to say whether CdvA recruits CdvB or the other way around.

The manuscript would be much stronger if such data could be added.

(2) Some of the discrepancies in the data generated using different assays are not discussed.

The authors show that CdvB2∆C binds membrane and localizes to membrane necks in the dumbbell liposome assay, but no membrane binding is detected in the flotation assay. The discrepancy between these results further highlights the need for CdvB-only and CdvA-only controls.

(3) Validation of the liposome assay.

The experimental setup to create dumbbell-shaped liposomes seems great and is a clever novel approach pioneered by the team. Not only can the authors manipulate liposome shape, they also state that this allows them to accurately control the species present on the inside and outside of the liposome. Interpreting the results of the liposome assay, however, depends on the geometry being correct. To make this clearer, it would seem important to include controls to prove that all the protein imaged at membrane necks lie on the inside of liposomes. In the images in SFig3 there appears to be protein outside of the liposome. It would also be helpful to present data to show test whether the necks are open, as suggested in the paper, by using FRAP or some other related technique.

(4) Quantification of results from the liposome assay.

The paper would be strengthened by the inclusion of more quantitative data relating to the liposome assay. Firstly, only a single field of view is shown for each condition. Because of this, the reader cannot know whether this is a representative image, or an outlier? Can the authors do some quantification of the data to demonstrate this? The line scan profiles in the supplemental figures would be an example of this, but again in these Figures only a single image is analyzed.

We would recommend that the authors present quantitative data to show the extent of co-localization at the necks in each case. They also need a metric to report instances in which protein is not seen at the neck, e.g. CdvB2 but not CdvB1 in Fig2I, which rules out a simple curvature preference for CdvB2 as stated in line 182.

Secondly, the authors state that they see CdvB2∆C recruited to the membrane by CdvB1 (lines 184-187, Fig 2I). However, this simple conclusion is not borne out in the data. Inspecting the CdvB2∆C panels of Fig 2I, Fig3C, and Fig3D, CdvB2∆C signal can be seen at positions which don't colocalize with other proteins. The authors also observe CdvB2∆C localizing to membrane necks by itself (Fig 2E). Therefore, while CdvB1 and CdvB2∆C colocalize in the flotation assay, there is no strong evidence for CdvB2∆C recruitment by CdvB1 in dumbbells. This is further underscored by the observation that in the presented data, all Cdv proteins always appear to localize at dumbbell necks, irrespective of what other components are present inside the liposome. Although one nice control is presented (ZipA), this suggests that more work is required to be sure that the proteins are behaving properly in this assay. For example, if membrane binding surfaces of Cdv proteins are mutated, does this lead to the accumulation of proteins in the bulk of the liposome as expected?

(5) Rings.

The authors should comment on why they never observe large Cdv rings in their experiments. In crenarchaeal cell division, CdvA and CdvB have been observed to form large rings in the middle of the 1 micron cell, before constriction. Only in the later stages of division are the ESCRTs localized to the constricting neck, at a time when CdvA is no longer present in the ring. Therefore, if the in vitro assay used by the authors really recapitulated the biology, one would expect to see large CdvAB rings in Figs 1EF. This is ignored in the model. In the proposed model of ring assembly (line 252), CdvAB ring formation is mentioned, but authors do not discuss the fact that they do not observe CdvAB rings - only foci at membrane necks. The discussion section would benefit from the authors commenting on this.

(6) Stoichiometry

It is not clear why 100% of the visible CdvA and 100% of the the visible CdvB are shifted to the lipid fraction in 1C. Perhaps this is a matter of quantification. Can the authors comment on the stoichiometry here?

(7) Significance of quantification of MBP-tagged filaments.

Authors use tagging and removal of MBP as a convenient, controllable system to trigger polymerisation of various Cdv proteins. However, it is unclear what is the value and significance of reporting the width and length of the short linear filaments that are formed by the MBP-tagged proteins. Presumably they are artefactual assemblies generated by the presence of the tag? Similar Figure 2C doesn't seem a useful addition to the paper.

Author response:

We thank the three Reviewers for the extensive evaluation of our work, which was largely positive and constructive. Prompted by their reviews and the many suggestions, we plan to do additional control experiments to add further data in a revised manuscript in order to improve the statistics and quantitation. Furthermore, we plan to expand the discussion. We agree that a more comprehensive mechanistic framework would be welcome but note that the system is a complex multicomponent system which is challenging. We plan to expand the work in future follow-up research.