A new undescribed clade of ancient phototrophic bacteria in metagenomic data

Protochlorophyllide and chlorophyllide reductases, two enzymes required for the synthesis of chlorophyll and bacteriochlorophyll precursors share significant sequence identity with an enzyme required for the synthesis of the Ni-tetrapyrrole, cofactor F430 of Methyl-coenzyme M reductase, a key enzyme in methanogenic and methanotrophic archaea. These enzymes are also closely related to nitrogenases, but the evolutionary relationships among the tetrapyrrole synthesis enzymes and nitrogenases have been difficult to resolve. Recent phylogenomic analysis have suggested that the last universal common ancestor was capable of nitrogen fixation and methanogenesis, raising puzzling questions about the early origin of photosynthesis and the early diversification of the tetrapyrrole biosynthesis enzymes.

I serendipitously stumbled upon two sequences annotated as ChlL subunits while searching for homologs to a subunit of the Ni-tetrapyrrole synthesis enzyme (CfbC) in a BLAST restricted to the domain Archaea.

The ChlL subunits appeared in the recently published genomes of of Candidatus Altiarchaeales archaeon WOR SM1 SCG and Candidatus Altiarchaeales archaeon WOR SM1 86-2, hereafter named Alti_SCG and Alti_86-2, respectively. An investigation of the genomic region surrounding the putative ChlL contained the two additional subunits of protochlorophyllide reductase, ChlB and ChlN, in the genome of Alti_86-2 but not in Alti_SCG1. However, after communication with the authors who sequenced the genomes of this strain it turns out that ChlB and N, in Alti_SCG1 are located in a different region of the genome. Though for some reason, the BLAST could not find them.

http://journal.frontiersin.org/article/10.3389/fmicb.2016.01221/full

The ChL proteins RefSeq Accession are ODS40814.1 and ODS39344.1

The sequence from strain Alti_SCG has 81% sequence identity to that if strain Alti_86-2 This suggests that they are quite a distance apart, but still within “the same phylum”. These strains have 83.1% sequence identity of the 16S rRNA, which suggests that these strains diverged already quite some time ago.

I have performed ML phylogenetic analysis of the sequences that I retrieved and performed a quick molecular clock analysis of ChlL. 

What you can see is that the Archeal sequences branch together with those of photosynthetic bacteria. They are indeed true subunits of protochlorophyllide reductase. This suggest that the proteins were acquired via horizontal gene transfer from a phototrophic bacterium.

Interestingly, the sequences do not branch within any of the known clades of phototrophic bacteria. From the phyllogeny of ChlN and B it would seem plausible that the sequences have some affinity to those in Heliobacteira, which may suggest that the source of the genes is a phototrophic Firmicutes distantly related to Heliobacteria... in fact, predating the divergence of Heliobacteria. This would be my most conservative guess. However, it may as well be a completely new phylum of bacteria.

One thing we can be sure of... the sequences do not match any of the known clades.

The molecular clock analysis, using a relaxed log-normal autocorrelated clock, with the CAT model, suggested that the event of horizontal gene transfer occurred about 1.3 +/- 0.4 billion years ago, as estimated by the divergence time of the ChlL from the two archeal strains.

From the position of the archaeal branches we can conclude that the "new clade" of phototrophic bacteria is an early evolving one... a really early one.

Fascinating stuff. This is a pretty rough and quick analysis though, I'll need some time to study this in more detail... might even need a grant. Any donors? ;) Haha, I wish, right?