Oxidative adaptations in prokaryotes imply the oxygenic photosynthesis before crown-group Cyanobacteria

Abstract

The metabolic transition from anaerobic to aerobic in prokaryotes reflects adaptations to oxidative stress. Methanogen, one of the earliest life forms on Earth, has evolved into three major groups within the Euryarchaeota, exhibiting different phylogenetic affiliations and metabolic characters. In comparison with other strictly anaerobic methanogenic groups, the Class II methanogens possess a better capability to adapt to limited oxygen pressure. Cyanobacteria is considered the first and only prokaryote evolving oxygenic photosynthesis and is responsible for the Great Oxidation Event on Earth. However, the connection between oxygenic Cyanobacteria and evolutionary adaptations to oxidative stress in prokaryotes remains elusive. Here, through the gene encoding structural maintenance of chromosomes (SMC) protein, which was horizontally transferred from ancient Class II methanogens to the last common ancestor of the crown-group Cyanobacteria, we demonstrate that the origin of extant Cyanobacteria was undoubtedly posterior to the occurrence of oxygen-tolerant Class II methanogens. In addition, we found that certain prokaryotic lineages had evolved the tolerance mechanisms against oxidative stress before the origin of extant Cyanobacteria. The contradiction that oxidative adaptations in Class II methanogens and other prokaryotes predating the crown-group oxygenic Cyanobacteria implies the existence of more ancient biological oxygenesis. We propose that these potential oxygenic organisms might represent the extinct phototrophs and first emerge during the Paleoarchean, contributing to the oxidative adaptations in the prokaryotic tree of life and facilitating the dispersal of reaction centers across the bacterial domain.

Keywords: Cyanobacteria; methanogen; molecular dating; oxidative adaptation; oxygenic photosynthesis.

Fig. 1.

The phylogeny of prokaryotic SMC protein. A) The archaeal and cyanobacterial SMC proteins were identified from the genomes sampled at the genus level in GTDB r207. SMC proteins in Bacteria (excluding Cyanobacteria) were identified from all available genomes in GTDB r207, and highly homologous sequences were removed using CD-HIT v4.8.1 (61) to facilitate tractable phylogenetic inference. The phylogenetic tree was constructed using IQ-TREE 2 (62–64) with the parameters -alrt 1000 -bb 1000 -m LG + F + R10. This analysis supports the HGT of the smc gene from Halobacteriota to Cyanobacteria. B) The genomes from Halobacteriota and Cyanobacteria were carefully selected to ensure even taxon sampling. To pinpoint the exact donor lineage within phylum Halobacteriota, noncyanobacterial bacterial genomes were excluded due to computational limitations. The phylogenetic tree was reconstructed using IQ-TREE 2 (62–64) under parameters -alrt 1000 -bb 1000 -m LG + F + R8. The clades outside of Cyanobacteria and Halobacteriota are collapsed for clarity.

Fig. 2.

Average abundance of oxygen-tolerant enzyme families involved in the elimination of oxygen/ROS and repair of oxidative damages. The COG information was retrieved from the COG database. All available genomes of phyla Cyanobacteria, Margulisbacteria, Halobacteriota, Methanobacteriota, and Methanobacteriota_A in GTDB r207 were collected. Functional annotations were performed using eggNOG-mapper v2 (67–69) with default parameters. For the calculation of enzyme family abundance, only the primary root eggNOG_OGs annotation for each sequence was retained.

Fig. 3.

Hypothesized evolutionary scenarios of oxygen-tolerant enzymes within Class II methanogens. A) The depicted enzymes are posited to have derived from a common ancestral origin shared among Class II methanogens. B) An alternative scenario suggests that these enzymes emerged subsequent to the divergence of the three primary clades observed within Class II methanogens. C) Additionally, it is proposed that certain enzymes might have been acquired through recent HGT into particular lineages following their evolutionary radiation. In each panel, the timeline incorporates schematic representations marked by bars to denote the period during which hypothesized stem-group oxyphototrophs are thought to have emerged, thereby contextualizing the temporal framework of these proposed evolutionary scenarios.

Fig. 4.

Hypothetical evolutionary scenarios of oxygenic photosynthesis in prokaryotes. A) Hypothetical evolutionary pathways of oxygenic photosynthesis. B) Hypothetical single origin of PSs/RCs. C) Hypothetical multiple originations of PSs/RCs. Gene gain, loss, and transfer events are labeled with the capital letters “G,” “L,” and “T,” respectively. The hypothetical extinct lineages are depicted in dashed branches, and the capital letter “X” denotes extinction.

Fig. 5.

Divergence time estimations of Class II methanogens and other Halobacteriota lineages under different root settings. Phylogenomic trees were reconstructed using IQ-TREE 2 (62–64) under parameters -alrt 1000 -bb 1000 -m LG + R10 + C60, based on the concatenated alignments of SMC and 37 conserved proteins (2, 65, 87, 91). Node dates were inferred using MCMCTree in paml v4.8 (89, 90). The substitution rate was calculated using 3.46 Ga (92) as the root node age. The root node, representing the beginning of the archaeal domain radiation, was calibrated to 3.46–4.29 Ga (92, 93). The MRCA of the crown-group oxygenic Cyanobacteria was calibrated to 2.50–3.00 Ga (40, 44). The divergence between families Nostocaceae and Chroococcidiopsidaceae was calibrated to 0.80–2.00 Ga (94–96). The 95% highest posterior density intervals were indicated by flanking horizontal bars. The last common ancestor of Class II methanogens is marked with a star. The geological timescale follows the ICS International Chronostratigraphic Chart (v 2023/06) (97). The visualization was accomplished using the R package ggtree (98). A) The root was set between the superphylum DPANN and the rest of archaeal lineages. B) The root was set between the superphyla DPANN, TACK, Asgard and the rest archaeal lineages. C) The root was set between the superphylum TACK and other archaeal lineages, after excluding DPANN species.