Figure 2

Phylogenetic trees of the Alba and YhbY superfamilies and an evolutionary scheme of the various superfamilies within the IF3-C fold. (a) Phylogenetic tree of the Alba superfamily. The tree shown here was constructed using the maximum-likelihood optimization as described in the Materials and methods section. The black circles indicate nodes with Rell-BP support of 80% or greater. The proteins are named as described in the legend to Figure 1. The divergent versions of Sso10b from the archaeal family of the Alba superfamily are indicated by a red circle. (b) Phylogenetic tree of the YhbY superfamily. Species abbreviations are as in the legend to Figure 1; additional species abbreviations are as follows: Blo, Bifidobacterium longum; Cau, Chloroflexus aurantiacus; Fnu, Fusobacterium nucleatum; Gme, Geobacter metallireducens; Hi, Haemophilus influenzae; Hsp, Halobacterium sp.; Lla, Lactococcus lactis; Pae, Pseudomonas aeruginosa; Spy, Streptococcus pyogenes; Vch, Vibrio cholerae; Xfa, Xylella fastidiosa. (c) An evolutionary scheme of the various superfamilies within the IF3-C fold. The horizontal lines indicate temporal epochs corresponding to certain major transitions in evolution, such as the last common ancestor of extant cellular life forms (LUCA), the divergence between the archaeo-eukaryotic lineage and the bacterial lineage and, finally, the emergence of the extant eukaryotes. The known or clearly predicted biochemical functions of the various superfamilies of this fold and their phyletic patterns have been indicated along with their names. R stands for RNA binding and D for DNA binding. The '>' as in B>E in the phyletic patterns, indicates an ancient transfer from bacteria to eukaryotes. The overall topology of the phylogram was derived using clustering based on DALI Z-scores, and specific shared derived characters. The YhhP family was first identified and predicted to function as a redox regulator in reference [52]. The red lineages are those which can be confidently traced to the LUCA, the black lineages are exclusively archaeo-eukaryotic and the green lineages are mainly bacterial with transfers to eukaryotes.