On the evolution of chlorophyll synthesis, methanogenesis, and nitrogen fixation. Was the ancestor of Bacteria photosynthetic?

Weiss et al. recently attempted to reconstruct the proteome of the Last Universal Common Ancestor (Weiss et al. 2016). One of the aspects that puzzled me the most about that work is that they suggested the LUCA was methanogenic and a nitrogen fixer, but there was absolutely no mention of photosynthesis.

There are three major groups of nitrogenase-like enzymes known. 1) The ones used for the synthesis of Ni-tetrapyrroles in methanogenic Archaea, 2) the ones used in Mg-tetrapyrroles in photosynthetic bacteria, and 3) proper nitrogenases. It is also likely that there are many uncharacterized enzymes belonging to this superfamily of proteins with unknown functions.

Under orthodox views on the evolution of photosynthesis it can be argued that those used in photosynthesis evolved from nitrogenases or those used in methanogenesis, but the phylogeny of these enzymes is inconsistent with that. It is inconsistent in such a way that the chlorophyll-synthesis enzymes do not seem to emerge from nitroegnases or those used in methanogenesis. What it is actually seen in their phylogeny is a deep divergence between the methanogenesis enzymes and those in photosynthesis: with nitrogenases being closer to the methanogenesis Ni-tetrapyrrole-synthesis enzymes. Therefore, there is a deep split between Bacteria/photosynthesis and Archaea/methanogenesis.

This is the thing, that if nitrogenase and the Ni-tetrapyrrole enzyme share a more recent common ancestor, and these were found in the LUCA, then the LUCA must have had also protochlorophyllide reductase. This may be hard to grasp, but it derives from the phylogenetic relationships of these enzymes. Phylogenetics 101. This is because the branch leading to protochlorophyllide reductase, in this case ChlL, should have diverged before the nitrogenase homolog (NifH) and the Ni-tetrapyrrole one (CbfC) had time to split.

The other way we can see this is that LUCA had the ancestral enzyme to these, and that their specialization occurred later. But there is no evidence that actually suggests the ancestor of these enzymes was more likely to be involved in methanogenesis or nitrogen fixation than photosynthesis.

What is more, I know that these enzymes have enough sequence identity to make it to the threshold of their analysis. And that is why I was puzzled, because I expected some of the chlorophyll synthesis enzymes to show up in their analysis, but apparently didn't...

As I was browsing through all 355 trees from the Weiss et al. work, I found this little gem! See image or the attached newick tree file.

That is indeed protochlorophyllide reductase subunit L splitting away from a NifH-like enzyme in methanogenic Archaea, which is probably a misannotated CbfC. Exactly as it should have been, and so it confirms that my puzzlement was not due to my lack of understanding of the evolution of these proteins.

The phylogeney on the bacteria part of the tree (red) matches perfectly that of ChlL and contains only phototrophs. It is indisputably ChlL and does not represent bacterial nitrogenases.

What does this mean? Well, if the authors work is informative in any way, it would mean that the split of the CbfC and ChlL is a Bacteria/Archaea split, which would make the ancestor to all bacteria photosynthetic. Nevertheless, that photosynthesis originated in the most recent common ancestor of all bacteria, or soon after that, is supported by the evolution of the photosynthetic reaction centres, as I concluded in my first review on the subject (Cardona 2015).

The reason this is not more widely understood or accepted is simply due to prevalent ideas on the evolution of photosynthesis, which are somewhat outdated and are now based more on speculation and personal opinions than on any real data... Something that I am working really hard to change.

If you want to have a look at the data by Weiss et al., have a look at this: https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1007518#sec011

The tree in the image is numbered 2020 in the supplements.

References:

Cardona, T. (2015). "A fresh look at the evolution and diversification of photochemical reaction centers." Photosynthesis research 126(1): 111-134. DOI: 10.1007/s11120-014-0065-x.

Weiss, M. C., F. L. Sousa, N. Mrnjavac, S. Neukirchen, M. Roettger, S. Nelson-Sathi and W. F. Martin (2016). "The physiology and habitat of the last universal common ancestor." Nat Microbiol 1(9): 16116. DOI: 10.1038/nmicrobiol.2016.116.