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Phylogenetic analyses of the MopB superfamily


Wells, Michael et al. (2023), Phylogenetic analyses of the MopB superfamily, Dryad, Dataset,


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 on 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 datasets containing over 47,000 distinct MopB homologs.  We demonstrate that these enzymes constitute a catalytically and mechanistically diverse superfamily defined, not by the molybdo- or tungstopterin containing pterin (Mo/W-bisPGD) co-factor, 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 co-factor, 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 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.  Further, it underscores the importance of prokaryotic adaptability in response to the transition from an anoxic to oxidized atmosphere.  


Genomics datasets were obtained using NCBI's DELTA-BLAST tool.  Analyses were restricted to phyla represented in the Integrated Microbial Genomics Encyclopedia of Bacteria and Archaea.  Metagenomic datasets were obtained from GTDB-TK.  All metagenomic dataset analyses were performed using a computing cluster.  BLASTx was used to find putative MopB superfamily members in the GTDB-TK dataset.

All sequences were aligned using the online version of MAFFT.  Phylogenetic analyses of the metagenomic datasets were done using a reduced dataset generated by the CDHIT program.  We utilized the CDHIT 50 setting.  All phylogenies and amino acid substitution model tests were done using IQTree.  All phylogenies were generated using a computing cluster.

Usage notes

All datafiles can be viewed using a standard text editor.  Sequence alignments and phylogenetic trees can be opened using any standard, open-source software programs for sequence and tree visualization.