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Prokaryotes use a wide variety of bioenergetic pathways but the order of emergence of these pathways and their evolutionary relationships are still unresolved issues. In this study we focus on the evolutionary relationships of different families of b-type cytochromes, which form part of a variety of bioenergetic enzymes (the cytochrome b6f complex, ubiquinol and menaquinol reductases, formate dehydrogenase, Ni/Fe-hydrogenase, and succinate dehydrogenase). We use data from 272 species of fully sequenced bacteria and archaea, which represent the full diversity of prokaryotic lineages and multiple bioenergetic modes, to examine the distribution of these cytochromes across lineages, and ask the question of whether sequences from different species cluster by cytochrome-b family, by bioenergetic mode or by taxonomic group. Different cytochrome-b types are found in many lineages of the bacteria and archaea, and form distinct groups in phylogenetic analysis, which indicates an ancient origin for this complex, and diversification of different cytochrome-b types before the diversification of lineages. We find that species do not cluster based on bioenergetic mode. We also re-examine data from previous studies using this expanded sample of organisms spanning the full diversity of prokaryotic lineages. Concerning the b6f complex of photosynthetic organisms, our expanded phylogenies do not show significant bootstrap support for a "green clade" of cytochrome b6; also, the split form of b6 is not monophyletic, indicating that the split form arose independently multiple times. We also present data on the similarities between prokaryotic and eukaryotic cytochrome b561 sequences, in light of the recently reported structure of eukaryotic cytochrome b561.
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