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Table 2 Repertoire of SAM-binding proteins in the Last Universal Common Ancestor

From: Natural history of S-adenosylmethionine-binding proteins

COG Phyletic pattern parsimony1 Tree topology2 Protein product name and function Fold class
    SAM-binding proteins in LUCA – best-supported COGs
COG0030 1/0 + KsgA, Dimethyladenosine transferase (rRNA methylation) Rossmann fold
COG0144 1/0 + Sun, tRNA and rRNA cytosine-C5-methylases Rossmann fold
COG0192 0/1 3 + 3 MetK, S-adenosylmethionine synthetase (releases SAM as product) SAM synthase
COG0421 1/0 + SpeE, Spermidine synthase Rossmann fold
COG0500 1/0 + SmtA, SAM-dependent methyltransferases Rossmann fold
COG0621 1/0 + MiaB, 2-methylthioadenine synthetase Rossmann fold
COG1180 0/1 + PflA, Pyruvate-formate lyase-activating enzyme SAM radical (TIM barrel)
COG1586 0/1 3 + 3 SpeD, S-adenosylmethionine decarboxylase SAM decarboxylase
COG2890 1/0 + PrmC (HemK), Methylase of polypeptide chain release factors Rossmann fold
    SAM-binding proteins in LUCA – tentatively supported COGs
COG0007 1/0 ? CysG, Uroporphyrinogen-III methylase SAM radical (TIM barrel)
COG0220 1/0 ? Predicted S-adenosylmethionine-dependent methyltransferase Rossmann fold
COG0293 0/1 ? FtsJ, 23S rRNA methylase Rossmann fold
COG0320 0/1 ? LipA, Lipoate synthase SAM radical (TIM barrel)
COG0502 0/1 ? BioB, Biotin synthase and related enzymes SAM radical (TIM barrel)
COG0565 0/1 ? LasT, rRNA methylases SPOUT
COG0685 1/0 ? MetF, 5,10-methylenetetrahydrofolate reductase (binds SAM as inhibitor) TIM barrel
COG1189 0/1 ? Predicted rRNA methylase Rossmann fold
COG2226 1/0 ? UbiE, Methylase involved in ubiquinone/menaquinone biosynthesis Rossmann fold
  1. 1 Placement of COGs in LUCA based on weighted parsimony analysis of phyletic patterns [138]. 1/0 indicates that this gene has been tracked back to LUCA genome under all tested conditions; 0/1 indicates tentative placement of gene in LUCA under some but not all conditions.
  2. 2 Phylogenetic analysis of each COG. Plus sign indicates tree topology that is fully consistent with gene presence in LUCA, and the question mark indicates a tentative support for the LUCA hypothesis (see Materials and Methods)
  3. 3 The common ancestry and phylogeny of archaeal, bacterial, and eukaryotic homologs was established in this work (see text for details).