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.二甲基亚砜还原酶（Dimethyl Sulfoxide Reductase，简称MopB）家族是一类广泛分布于细菌与古菌中的多样化酶类。诸多这类酶被认为起源于所有细胞谱系的最后共同祖先（last universal common ancestor, LUCA）。然而，当前学界对MopB酶的演化路径，以及其功能多样化如何在地质时间尺度上影响全球生物地球化学循环的认知仍存在诸多空白。本研究针对经人工手动整理的比较基因组学与宏基因组学数据集开展了最大似然法系统发育分析，这些数据集包含超过47000个独立的MopB同源蛋白。本研究证实，这类酶构成了一个在催化活性与作用机制层面均具多样性的超家族，其分类依据并非含有钼或钨蝶呤的蝶呤（Mo/W-bisPGD）辅因子，而是蛋白质中结合该辅因子的结构折叠模式。研究结果表明，主要的代谢创新源于金属辅因子的丢失，或是蛋白质结构域的获得或丢失。 基因组数据集通过NCBI的DELTA-BLAST工具获取。分析范围限定于《整合微生物基因组细菌与古菌百科全书》（Integrated Microbial Genomes Encyclopedia of Bacteria and Archaea）所收录的菌门。宏基因组数据集源自GTDB-TK。所有宏基因组数据集的分析均依托计算集群完成。使用BLASTx在GTDB-TK数据集中筛选潜在的MopB超家族成员。 所有序列均通过在线版MAFFT完成多序列比对。宏基因组数据集的系统发育分析采用CDHIT程序生成的精简数据集，本研究使用了CDHIT的50%相似度参数。所有系统发育树构建及氨基酸替换模型测试均通过IQTree完成，所有系统发育树的生成均依托计算集群。 所有数据文件均可通过标准文本编辑器查看。序列比对结果与系统发育树可通过任意标准开源序列及树状可视化软件打开。