Impact of the Dimethyl Sulfoxide Reductase Superfamily on the Evolution of Biogeochemical Cycles

Abstract

The dimethyl sulfoxide reductase (or MopB) family is a diverse assemblage of enzymes found throughout Bacteria and Archaea. Many of these enzymes are believed to have been present in the last universal common ancestor (LUCA) of all cellular lineages. However, gaps in knowledge remain about how MopB enzymes evolved and how this diversification of functions impacted global biogeochemical cycles through geologic time. In this study, we perform maximum likelihood phylogenetic analyses on manually curated comparative genomic and metagenomic data sets containing over 47,000 distinct MopB homologs. We demonstrate that these enzymes constitute a catalytically and mechanistically diverse superfamily defined not by the molybdopterin- or tungstopterin-containing [molybdopterin or tungstopterin bis(pyranopterin guanine dinucleotide) (Mo/W-bisPGD)] cofactor but rather by the structural fold that binds it in the protein. Our results suggest that major metabolic innovations were the result of the loss of the metal cofactor or the gain or loss of protein domains. Phylogenetic analyses also demonstrated that formate oxidation and CO₂ reduction were the ancestral functions of the superfamily, traits that have been vertically inherited from the LUCA. Nearly all of the other families, which drive all other biogeochemical cycles mediated by this superfamily, originated in the bacterial domain. Thus, organisms from Bacteria have been the key drivers of catalytic and biogeochemical innovations within the superfamily. The relative ordination of MopB families and their associated catalytic activities emphasize fundamental mechanisms of evolution in this superfamily. Furthermore, it underscores the importance of prokaryotic adaptability in response to the transition from an anoxic to an oxidized atmosphere. IMPORTANCE The MopB superfamily constitutes a repertoire of metalloenzymes that are central to enduring mysteries in microbiology, from the origin of life and how microorganisms and biogeochemical cycles have coevolved over deep time to how anaerobic life adapted to increasing concentrations of O₂ during the transition from an anoxic to an oxic world. Our work emphasizes that phylogenetic analyses can reveal how domain gain or loss events, the acquisition of novel partner subunits, and the loss of metal cofactors can stimulate novel radiations of enzymes that dramatically increase the catalytic versatility of superfamilies. We also contend that the superfamily concept in protein evolution can uncover surprising kinships between enzymes that have remarkably different catalytic and physiological functions.

Keywords: DMSO reductase; MopB; biogeochemical cycles; evolution; molybdopterin.

FIG 1

Maximum likelihood phylogeny of 3,057 MopB domain-containing members constructed using 10,000 ultrafast bootstrap approximations. All sequences came from cultured organisms with sequenced genomes. Branches with blue circles indicate that the MopB homolog was taken from an archaeal genome. The lineages representing MopB families are named in the tree and represented by specific colors. Orange circles at a clade indicate that the lineage has lost the characteristic Mo/W-bisPGD cofactor. Magenta stars indicate that the lineage has acquired novel protein domains not found in other MopB families. Light-green triangles indicate that the MopB homologs in that family lineage no longer have a catalytic function. The light-blue square indicates that the MopB family has lost the N-terminal [4Fe-4S] iron-sulfur cluster.

FIG 2

Superposition of all available crystal structures (of which there are 15) of MopB superfamily members and a single cryo-EM structure. The only portion that is retained is the region where the structural alignment of these structures was found to have significant structural homology. This region corresponds to the MopB domain; a stretch between the N-terminal iron-sulfur cluster, if present; and the PGD moiety of Mo/W-bisPGD proximal to that cluster. The proximal PGD is indicated by a black circle, and the distal PGD (the one furthest away) is indicated by a red circle. The cyan atoms at the intersection of these two circles represent Mo atoms, while the gold atoms represent W atoms. The various iron-sulfur clusters were retained in this image to demonstrate that while the orientation and positioning of the Mo/W-bisPGD cofactor of these diverse enzymes and catalytic subunits are conserved, the positionings of the iron-sulfur clusters differ substantially between different superfamily representatives.

FIG 3

Maximum likelihood phylogeny of 1,570 MopB domain-containing members constructed using 10,000 ultrafast bootstrap approximations. This phylogeny, unlike the others, contains both genomes from cultured isolates and high-quality MAGs taken from metagenomic studies. Branches with blue circles indicate that the MopB homolog was taken from an archaeal genome or MAG. We have overlaid onto the tree topology bootstrap support at crucial nodes. The color scheme for specific MopB families is identical to the one in Fig. 1. Additionally, to emphasize the catalytic versatility of the MopB superfamily, we have highlighted all known biogeochemical cycles that each MopB family is known to mediate. Elements in green boxes are nonmetals, and elements in red boxes represent metalloids.

FIG 4

Subpruned portion of the maximum likelihood phylogeny shown in Fig. 3. This region contains FdhG, the cytoplasmic formate dehydrogenases, and the IdrA/AioA, assimilatory and periplasmic nitrate reductase, and Nqo3 families. Branches with blue circles indicate that the MopB homolog was taken from an archaeal genome or MAG. The color scheme for specific MopB families is identical to the one in Fig. 1. All node supports of ≥70 are provided.

FIG 5

Relative ordination of when MopB superfamily substrates became available over geologic time against the midpoint potential of the conversion of the substrate to the product. This is possible only for oxidation-reduction reactions for which the midpoint potential is known. Nonredox reactions are placed above the y axis (midpoint potential in millivolts). The x axis corresponds to billions of years ago (Gya). Major evolutionary events are also highlighted on the axis. Each dot is accompanied by error bars, indicating the rough estimates for when the substrate might conceivably have been available to life. The colors of both the dots and error bars match the family with which each reaction is associated. When the same reaction evolved in multiple families, we tried to put them in as close spatial proximity as possible. For the conversion of the substrate to the product, normal text indicates that the reaction is a reduction. Boldface type represents oxidase or dehydrogenase reactions, blue text indicates transferases, red text indicates hydration, and pink text indicates hydroxylation reactions. Beside each dot, we also include graphical depictions of cells, again colored by the family from which the reaction evolved. Rod-shaped cells with undotted black borders represent bacterial cells. Rod-shaped cells with dotted black borders represent archaeal cells. If bacterial and archaeal cells are positioned side by side, this indicates that the catalytic function was most likely present in the LUCA. If only one rod-shaped cell is present, this catalytic function is known in only one domain of life. The acquisition of a catalytic subunit by one domain from the other via HGT is depicted using an arrow, indicating the direction of the HGT event. For example, an arrow from a bacterial cell to an archaeal cell indicates that Archaea within this family acquired it from the bacterial domain.