Phylogenetic analyses of the MopB superfamily

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.  P..., 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., 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.