Gene family analysis suggests new evolutionary scenario for sterol and hopanoid biomarkers
The Eukaryotic Last Common Ancestor Was Bifunctional for Hopanoid and Sterol Production
Recommendation: posted 18 July 2022, validated 11 October 2022
Irisarri, I. (2022) Gene family analysis suggests new evolutionary scenario for sterol and hopanoid biomarkers. Peer Community in Evolutionary Biology, 100144. https://doi.org/10.24072/pci.evolbiol.100144
Sterols and hopanoids are sometimes used as biomarkers to infer the origin of certain groups of organisms. Traditionally, hopanoid-derived products in ancient rocks have been considered to indicate the presence of bacteria, whereas sterol derivatives have been considered to be exclusive to eukaryotes. However, a closer look at the topic reveals a rather complex distribution of either compound in both bacteria and eukaryotes. (1). The known biosynthetic pathways for sterols and hopanoids are similar but diverge at a critical step where two different enzymes are used: squalene-hopene cyclase (SHC) and oxidosqualene cyclase (OSC), the latter requiring oxygen. These two enzymes belong to the same gene family, whose complex evolutionary history is difficult to reconcile with the known species phylogeny.
In this study (2), Dr. Warren R. Francis revisits the evolution of this gene family using an extended dataset with a broader taxonomic representation. In contrast to the traditional representation of the tree rooted between SHC and OSC paralogs (i.e., based on function), the author proposes that rooting the tree within bacterial SHCs and assuming a secondary origin of OSC is more parsimonious. This postulates SHC to be the ancestral function –retained in many extant bacteria and some eukaryotes– and OSC to have emerged later within bacteria –currently being mostly present in eukaryotes–. The reconstructed evolutionary history is arguably complex and can only be reconciled with the species' phylogeny by invoking many secondary losses. These losses are considered likely because many extant species acquire sterols and hopanoids by diet and lack one or both enzymes. Some cases of recent horizontal gene transfer are also proposed.
In contrast to the dichotomy between bacterial SHCs and eukaryote OSCs, the new proposed scenario suggests that the eukaryote ancestor likely inherited both enzymes from bacteria and thus could be able to synthesize both sterols and hopanoids. Under this hypothesis, not only bacteria but also eukaryotes could be responsible for the hopane found in old rocks. This agrees with eukaryote fossils dating back to more than 1 billion years ago (3). Also, the observed increase of sterane levels in rocks ~600-700 million years old cannot be associated with the origin of eukaryotes, which is a much older event, but could rather reflect changes in atmospheric oxygen levels because oxygen is required for the synthesis of sterols by OSC.
1. Santana-Molina C, Rivas-Marin E, Rojas AM, Devos DP (2020) Origin and Evolution of Polycyclic Triterpene Synthesis. Molecular Biology and Evolution, 37, 1925–1941. https://doi.org/10.1093/molbev/msaa054
2. Francis WR (2022) The Eukaryotic Last Common Ancestor Was Bifunctional for Hopanoid and Sterol Production. Preprints, 2020040186, ver. 5 peer-reviewed and recommended by Peer Community in Evolutionary Biology. https://doi.org/10.20944/preprints202004.0186.v5
3. Butterfield NJ (2000) Bangiomorpha pubescens n. gen., n. sp.: implications for the evolution of sex, multicellularity, and the Mesoproterozoic/Neoproterozoic radiation of eukaryotes. Paleobiology, 26, 386–404. https://doi.org/10.1666/0094-8373(2000)026<0386:BPNGNS>2.0.CO;2
The recommender in charge of the evaluation of the article and the reviewers declared that they have no conflict of interest (as defined in the code of conduct of PCI) with the authors or with the content of the article. The authors declared that they comply with the PCI rule of having no financial conflicts of interest in relation to the content of the article.
Evaluation round #3
DOI or URL of the preprint: https://https://doi.org/10.20944/202004.0186/v3
Version of the preprint: 3
Author's Reply, 07 Jul 2022
Decision by Iker Irisarri, posted 12 Nov 2021
Dear Dr. Francis,
Thank you for submitting your new revised manuscript. I agree with the reviewers that this new version is much improved after most of the previous concerns were addressed. Reviewers have provided some additional comments that still require clarification, but these are rather specific and therefore easy to address.
One of the reviewers suggest some methods for tree rooting, which you might want to explore. This might provide information on the specific bacterial branch where the root might be and thus could strengthen your study, but I do not think this is a requirement. I would urge you, however, to double check your writing is always as careful as it should, especially when explaining your evolutionary hypothesis, which relies on a tree root that makes sense but has basically no support from data. For example, in the abstract “suggests” might be better than “indicates” and “is easier explained” would be better than “is best explained”. Caption of figure 2 and page 5: “SHC probably was the ancestral enzyme” rather than “SHC was the original enzyme”.
Minor comments: In page 3, “The latter three of these make sense with respect to the tree.” You refer to the known species phylogeny and not to Fig 1, right? Please, also check the text throughout for small typos, I found a few but was difficult to note without line numbers.
Reviewed by Denis Baurain, 17 Oct 2021
Reviewed by Samuel Abalde, 01 Nov 2021
Reviewed by Jose Ramon Pardos-Blas, 12 Oct 2021
Evaluation round #2
DOI or URL of the preprint: https://doi.org/10.20944/preprints202004.0186.v2
Version of the preprint: 2
Author's Reply, 08 Sep 2021
Decision by Iker Irisarri, posted 07 Sep 2021
Dear Dr. Francis,
Thank you very much for submitting your revised manuscript. It might seem like the responses to the third reviewer's comments are missing from the uploaded point-by-point letter, could you please check this before we consider your preprint?
Thank you very much for your time. Sincerely,
Evaluation round #1
DOI or URL of the preprint: https://doi.org/10.20944/preprints202004.0186.v1
Version of the preprint: 1
Author's Reply, 07 Sep 2021
Decision by Iker Irisarri, posted 09 Mar 2021
Dear Dr. Francis,
Thank you for your submission and apologies for the delay in our response; it took some time to collect all the reviews.
You will see from the Reviewers’ comments and my own that we definitely think there is merit in your work, but before this preprint can be recommended some revisions would be needed.
As noted by one of the reviewers, one key publication in MBE covers several important aspects that are directly relevant to this preprint. It puts the evolution of sterol/hopanoid pathways in a broader context and tackles several points that are of relevance for your work, and therefore should be appropriately discussed.
A recurrent concern seems to be tree rooting, which is neither trivial nor arbitrary. One of the Reviewers suggests an interesting reference and the MBE paper by Santana-Molina et al. discusses also this topic. Could the presence of SHC/OSC homologs in Archaea help in this task? This possibility is not mentioned by the author, but I assume archaean homologs are unlikely based on what is said in Santana-Molina et al.? Regarding the hypothesis in Fig 1B, I also agree that the bacterial root probably makes most sense. However, the hypothesized evolutionary history of these enzymes rests on this particular rooting for which evidence seems to be scarce besides the phylogenetic distribution of paralogs that seem quite complex anyway. As pointed out by the Reviewers, this assumption should be made explicit and the real uncertainty of the hypothesized scenario better reflected by revising the tone of the relevant sections. The uncertainty could also be better reflected in other sections of the manuscript as well, such as when discussing biomarkers in fossils.
From my viewpoint, the manuscript contains too many expressions that e.g., personalize molecules, assign “choices” to organisms, or claim “bizarre” loss events. Such expressions fit very well into what has been called the “night science” language (Yanai & Lercher 2019; https://doi.org/10.1186/s13059-019-1800-6) but should be avoided in scientific publications. Note also Reviewers’ comments on specific sections where the writing could be improved for clarity and correctness. Finally, there are a few demonstrative pronouns without an object following them (“this”), which sometimes make it difficult to follow the argumentation (e.g. point 2.3).
Regarding the general structure of the paper, I think the current “narrative” structure helps transmitting the Author’s view, but the data behind the claims are not always clear. For example, when laying out the evolutionary history in points 2.2.1 to 2.2.6, it could help to refer to specific parts of the tree that back up each claim, thereby better connecting the phylogenetic hypothesis and the biological interpretation.
I appreciate the transparency of centrally depositing alignments and trees in Bitbucket. It might be good to add a fully annotated tree as a supplement, given that the current taxon names in the tree short and not very informative, and only a cartoon of the tree is presented in the manuscript. Fig. 1 needs support values (at least for the key nodes) and perhaps a rewrite of the caption because the current one “Recreated tree from [Takishita et al., 2012]” might sound like the tree correspond to the old tree by Takishita et al. Note also the comment that asks about how the new added sequenced improved our view on the story. Could the data of Santana-Molina et al. MBE paper change that? Please, take into account the considerations on phylogenetic methodology raised by two of the Reviewers. I wondered whether using HMM or psiBLAST could help identify more distant homologs that might be relevant. For BLAST searches, significance thresholds should be provided.
Lastly, one of the Reviewers suggests adding a schematic figure setting up the stage for the evolutionary questions. This might clarify one doubt I had: Fig 1 of Santana-Molina et al. depicts SQMO as a step in the sterol but not in the hopanoid synthesis, whereas in the preprint I understand that this oxygen-dependent step of SQMO is common to both hopanoid and sterol production: “Following the oxygen-dependent step, one of two enzymes then forms the multi-ring structure, either squalene-hopene cyclase (SHC) for hopanoids or oxidosqualene cyclase (OSC) for sterols.” Which one is right or am I missing something here?