Evolution towards simplicity in bacterial small heat shock protein system

Reviewer #1 (Public Review):

The work in this paper is in general done carefully. Reconstructions are done appropriately and the effects of statistical uncertainty are quantified properly. My only slight complaint is that I couldn't find statistics about posterior probabilities anywhere and that the sequences and trees do not seem to be deposited. I would also have preferred to have the actual phylogeny in the main text. This is a crucial piece of data that the reader needs to see to understand what exactly is being reconstructed.
The paper identifies which mutations are crucial for the functional differences between the ancestors tested. This is done quite carefully - the authors even show that the same substitutions also work in extant proteins. My only slight concern was the authors' explanation of what these substitutions do. They show that these substitutions lower the affinity of the C-terminal peptide to the alpha-crystallin domain - a key oligomeric interaction. But the difference is very small - from 4.5 to 7 uM. That seems so small that I find it a bit implausible that this effect alone explains the differences in hydrodynamic radius shown in Figure S8. From my visual inspection, it seems that there is also a noticeable change in the cooperativity of the binding interaction. The binding model the authors use is a fairly simple logarithmic curve that doesn't appear to consider the number of binding sites or potential cooperativity. I think this would have been nice to see here.

Lastly, the authors use likelihood methods to test for signatures of selection. This reviewer is not a fan of these methods, as they are easily misled by common biological processes (see PMID 37395787 for a recent critique). Perhaps these pitfalls could simply be acknowledged, as I don't think the selection analysis is very important to the impact of the work.

Reviewer #2 (Public Review):

This was an interesting study, and I enjoyed seeing different experimental approaches used to compare the properties of the different native proteins, the ancestral reconstructions, and the other mutants. I think it provides convincing mechanistic evidence as to how these small heat shock proteins have evolved. Thus, I think it represents a valuable contribution to the field. However, to a certain extent, I think the authors have at times over-interpeted their results, and over-simplified their explanations, as the differences between the ancestral proteins, and the changes induced by the two mutations, only partially explain the differences between IbpA proteins from the two different species. Furthermore, in some places, I found this difficult to follow and figures were not properly explained or labelled. If these issues were addressed, I think the paper would be considerably more accessible to readers.

Reviewer #3 (Public Review):

Summary:
The study by Karaś et al. reveals how multi-protein systems can evolve into single-protein equivalents, shedding light on the molecular events enabling gene loss during evolution. This work is valuable for researchers in evolutionary fields and offers potential applications in protein and organism engineering. While the findings lack broader appeal and societal implications, the evidence presented supports the proposed molecular mechanism. Using computational methods and biochemical analysis, the authors traced the evolutionary simplification of bacterial small heat shock proteins, linking specific mutations to functional changes. The study's strength lies in its vertical approach, identifying functional residues, but it does not introduce new techniques, limiting its novelty and significance.

Strengths:

1. Experimental Approach
   The research question was clearly outlined and the author's approach to answering it was systematic. In particular, their model system was highly suitable to address the research question. The authors employed appropriate experimental and computational techniques, and their 'vertical approach' was beneficial in that it allowed them to discover functional residues in the sHsp system which may not have been possible otherwise. Overall, their approach to this study was solid.

2. Reproducibility
   The results were presented well. The number of experimental repeats was suitable, as well as their analysis of the data. The values for standard deviation were reasonable, and their results using the alternative ancestors for the substrate aggregation assays helped support the robustness of their observations.

Weaknesses:
During the mutational experiments, the authors examined seven potential substitutions identified through ASR and measured their impact on protein disaggregation activity. Positions 66 and 109 exhibited a significant decrease in luciferase refolding stimulation. To explore the combined effect of these mutations, the authors created the double mutant AncA0. However, predicting the most impactful combination of mutations due to epistatic effects is challenging. A more effective strategy would be to test various combinations of mutations to identify the double mutant with the greatest decrease in luciferase refolding stimulation and/or alternatively perform a co-evolutionary study to try to understand any epistatic effects between the mutations.