Timing the Evolutionary Advent of Cyanobacteria and the Later Great Oxidation Event Using Gene Phylogenies of a Sunscreen

Abstract

The biosynthesis of the unique cyanobacterial (oxyphotobacterial) indole-phenolic UVA sunscreen, scytonemin, is coded for in a conserved operon that contains both core metabolic genes and accessory, aromatic amino acid biosynthesis genes dedicated to supplying scytonemin's precursors. Comparative genomics shows conservation of this operon in many, but not all, cyanobacterial lineages. Phylogenetic analyses of the operon's aromatic amino acid genes indicate that five of them were recruited into the operon after duplication events of their respective housekeeping cyanobacterial cognates. We combined the fossil record of cyanobacteria and relaxed molecular clock models to obtain multiple estimates of these duplication events, setting a minimum age for the evolutionary advent of scytonemin at 2.1 ± 0.3 billion years. The same analyses were used to estimate the advent of cyanobacteria as a group (and thus the appearance of oxygenic photosynthesis), at 3.6 ± 0.2 billion years before present. Post hoc interpretation of 16S rRNA-based Bayesian analyses was consistent with these estimates. Because of physiological constraints on the use of UVA sunscreens in general, and the biochemical constraints of scytonemin in particular, scytonemin's age must postdate the time when Earth's atmosphere turned oxic, known as the Great Oxidation Event (GOE). Indeed, our biological estimate is in agreement with independent geochemical estimates for the GOE. The difference between the estimated ages of oxygenic photosynthesis and the GOE indicates the long span (on the order of a billion years) of the era of "oxygen oases," when oxygen was available locally but not globally.IMPORTANCE The advent of cyanobacteria, with their invention of oxygenic photosynthesis, and the Great Oxidation Event are arguably among the most important events in the evolutionary history of life on Earth. Oxygen is a significant toxicant to all life, but its accumulation in the atmosphere also enabled the successful development and proliferation of many aerobic organisms, especially metazoans. The currently favored dating of the Great Oxidation Event is based on the geochemical rock record. Similarly, the advent of cyanobacteria is also often drawn from the same estimates because in older rocks paleontological evidence is scarce or has been discredited. Efforts to obtain molecular evolutionary alternatives have offered widely divergent estimates. Our analyses provide a novel means to circumvent these limitations and allow us to estimate the large time gap between the two events.

Keywords: UV photobiology; cyanobacteria; deep evolution; secondary metabolism.

FIG 1

Genomic organization of the cyanobacterial scytonemin operon. Gene nomenclature is based on the annotation of Nostoc punctiforme ATCC 29133. Core biosynthetic genes are shown in yellow. Regulatory genes are shown in blue. Genes shown in black or gray involve a region dedicated to monomer export, and genes shown in various shades of purple/pink code for dedicated aromatic amino acid biosynthetic (AAAB) genes that supply biosynthetic precursors.

FIG 2

Phylogeny derived from BEAST analyses of TrpD amino acid sequences supports an origin of a scytonemin-associated clade in a single internal duplication of housekeeping genes, shown as exemplary of the two phylogenies (TrpB and TrpC) supporting such an origin. The corresponding phylogeny for TrpC is in Fig. S8. Entries in blue type correspond to homologs found within full scytonemin operons. Those marked by a blue arrow were found in remnant scytonemin operons or correspond to supernumerary homologs. Bayesian posterior probabilities (BPP) at the nodes are color coded as follows: red for BPP ≥ 0.8, pink for 0.8 ≥ BPP ≥ 0.5, and white for BPP ≤ 0.5. The red arrow marks the node corresponding to the most recent common ancestor of the oldest clade containing scytonemin-associated homologs.

FIG 3

Phylogeny derived from BEAST analyses of TyrA amino acid sequences supports an origin by lateral transfer from bacterial phyla other than cyanobacteria of the homologs in the scytonemin operon. It is shown as exemplary of the three phylogenies (AAAB loci trpE, aroB, and tyrA) supporting such an origin. Phylogenies for the other genes are found in Fig. S5 and S9. Entries in blue type correspond to homologs found within full scytonemin operons. Those marked by a blue arrow were found in remnant scytonemin operons or correspond to supernumerary homologs. Bayesian posterior probabilities (BPP) at the nodes are color coded as follows: red for BPP ≥ 0.8, pink for 0.8 ≥ BPP ≥ 0.5, and white for BPP ≤ 0.5.

FIG 4

Phylogeny derived from BEAST analyses of TrpB amino acid sequences supports an origin of scytonemin-associated homologs by more than one internal duplication of housekeeping genes, shown as exemplary of the three phylogenies (trpB, trpA, and aroG) supporting such an origin. Phylogenies for the other genes are found in Fig. S6 and S7). Entries in blue type correspond to homologs found within full scytonemin operons. Those marked by a blue arrow were found in remnant scytonemin operons or correspond to supernumerary homologs. Bayesian posterior probabilities (BPP) at the nodes are color coded as follows: red for BPP ≥ 0.8, pink for 0.8 ≥ BPP ≥ 0.5, and white for BPP ≤ 0.5. The red arrow marks the node corresponding to the most recent common ancestor of the oldest clade containing scytonemin-associated homologs.

FIG 5

Time estimates for the origin of cyanobacteria (blue-green) and scytonemin (orange) derived from relaxed molecular clock models applied to the phylogeny of gene products associated with the scytonemin operon. Each of the lower 5 boxes corresponds to a gene product as marked. In each of these boxes, the upper estimates used an age of 0.9 billion years for the common ancestor of all heterocystous cyanobacteria, whereas the lower estimates used an age of 2.1 billion years. Error bars are 95% CI for each estimate. The two uppermost boxes include averages of single-gene estimates for each of the two age scenarios (Means) or for all estimates (Grand Means).

FIG 6

Phylogeny derived from BEAST analyses of full 16S rRNA sequences of cyanobacteria. Bayesian posterior probabilities (BPP) at the nodes are color coded as follows: red for BPP ≥ 0.8, pink for 0.8 ≥ BPP ≥ 0.5, and white for BPP ≤ 0.5. The red arrow marks the node corresponding to the most recent common ancestor of the clades encompassing scytonemin-operon containing genomes.