Abstract
Eukaryogenesis, the origin of the eukaryotes, is still poorly understood. Herein, we show how a detailed all-kingdom phylogenetic analysis overlaid with a map of key biochemical features can provide valuable clues. The photolyase/cryptochrome family of proteins are well known to repair DNA in response to potentially harmful effects of sunlight and to entrain circadian rhythms. Phylogenetic analysis of photolyase/cryptochrome protein sequences from a wide range of prokaryotes and eukaryotes points to a number of horizontal gene transfer events between ancestral bacteria and ancestral eukaryotes. Previous experimental research has characterised patterns of tryptophan residues in these proteins that are important for photoreception, specifically a tryptophan dyad, a canonical tryptophan triad, an alternative tryptophan triad, a tryptophan tetrad and an alternative tetrad. Our results suggest that the spread of the different triad and tetrad motifs across the kingdoms of life accompanied the putative horizontal gene transfers and is consistent with multiple bacterial contributions to eukaryogenesis.
Highlights
It is widely accepted that eukaryogenesis involved an endosymbiosis between at least one archaeon, probably from the Asgard lineage, and at least one bacterium, most likely an ancestral α-proteobacterium (López-García and Moreira 2019)
We present here a phylogenetic analysis of cryptochrome and photolyase proteins that includes an array of prokaryotic sequences
Similar to our previous research on retinoic acid biosynthesis (Miles et al 2019; Millard et al 2014), we find that inclusion of photolyase/cryptochrome sequences and candidate orthologues from across the kingdoms of life brings to the fore phylogenetic relationships that are relevant to eukaryogenesis, in particular with respect to the placement of animal and bacterial orthologues
Summary
It is widely accepted that eukaryogenesis involved an endosymbiosis between at least one archaeon, probably from the Asgard lineage, and at least one bacterium, most likely an ancestral α-proteobacterium (López-García and Moreira 2019). Researchers are finding surprising similarities in chemical signalling-related proteins between animals and groups of complex bacteria, including cyanobacteria (Brash et al 2014; Magnani et al 2017; Miles et al 2019; Millard et al 2014; Picciano and Crane 2019; Ponting et al 1999; Rawlings 2015) that pose some important questions about horizontal gene transfer (HGT) in the origin of animals. This offers an alternative perspective from which to view the major transitions in eukaryogenesis. A good object of study would be a family of proteins found in many major kingdoms and taxa, including animals, and that possesses a highly distinctive biochemical motif or motifs that would allow us to further refine phylogenetic analyses
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