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a) C. J. Schwartz, O. Djaman, J. A. Imlay and P. J. Kiley, Proc. Natl. Acad. Sci., 2000, 97, 9009–9014 CrossRef CAS PubMed; b) S. O.-de Choudens, L. Loiseau, Y. Sanakis, F. Barras and M. Fontecave, FEBS Lett., 2005, 79, 3737–3743 CrossRef; f) G. L. Holliday, E. Akiva, E. C.Meng, S. D. Brown, S. Calhoun, U. Pieper, A. Sali, S. J. Booker and P. C. Babbitt, Methods Enzymol., 2018, 606, 1–71 CAS; Chapman-Smith A, Cronan JE: In vivo enzymatic protein biotinylation. Biomol Engineering. 1999, 16: 119-125. 10.1016/S1050-3862(99)00046-7. Since eukaryotes obtained their biotin-dependent carboxylases from bacteria, we ignore them for the discussion concerning the cenancestor complement and we focus specifically on the respective ancestors of Archaea and Bacteria as intermediate steps between present-day species and the cenancestor. The components of biotin-dependent carboxylases have been duplicated, recombined and fused many times across evolution and, thus, many different evolutionary scenarios can be proposed. As it would be too long to discuss all of them, we will focus only on the one that we consider to be the most parsimonious (for examples of other scenarios see additional file 3).

The report provides a broad approach to deciphering the evolution of coenzyme biosynthetic pathways. Here, these various pathways are analyzed with respect to the coenzymes required for this purpose. Coenzymes whose biosynthesis relies on a large number of coenzyme-mediated reactions probably appeared on the scene at a later stage of biological evolution, whereas the biosyntheses of pyridoxal phosphate (PLP) and nicotinamide (NAD +) require little additional coenzymatic support and are therefore most likely very ancient biosynthetic pathways. From the analysis compiled in Scheme 5, it is clear that the appearance of the cofactor encountered in [NiFe]-hydrogenases should be ranked earlier. And ideas about early metabolisms suggest the same as these hydrogenases have links to ancient forms of metabolism, utilizing hydrogen as the original source of reductant on Earth. 97 It has not (yet) been chemically verified whether, from the iron–sulfur clusters very likely present in the “prebiotic” world, chemical accesses to catalytically active clusters mixed with other metals did exist. c) B. M. Hover, N. K. Tonthat, M. A. Schumacher and K. Yokoyama, Proc. Natl. Acad. Sci., 2015, 112, 6347–6352 CrossRef CAS PubMed; The group of 5-deazaflavins includes coenzymes F 0 and F 420 21a and 21b, which are thought to be truly ancient redox factors. 19 Functionally, 5-deazaflavin F 420 21b facilitates various two-electron redox reactions in methanogenic, sulfate-reducing, and probably methanotrophic archaea. In addition to its role in methanogenesis, coenzyme F 420 is also involved in antibiotic biosynthesis and DNA repair. 20 Both structurally and chemically, coenzymes F 0 and F 420 21a and 21b are more closely related to nicotinamide than to flavins, which is why they have occasionally been referred to as “nicotinamide in a flavin's clothing”. 21

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b) C. Bonfio, L. Valer, S. Scintilla, S. Shah, D. J. Evans, L. Jin, J. W. Szostak, D. D. Sasselov, J. D. Sutherland and S. S. Mansy, Nat. Chem., 2017, 9, 1229–1234 CrossRef CAS PubMed; A strong point of this scenario is its relative simplicity, relying on the general assumption of aggregative peptide domain architecture as a major force in protein evolution [ 63]. Noteworthy, this hypothesis assumes the independent emergence of the PT (ancient PYC) domain and the BT (bacterial XCC) domain. Thus, a convergent evolution has to be invoked to explain BT and PT structural resemblances. Despite that little is known concerning the characteristics and conservation of the BT/PT domains, their shared structure consisting of a conserved helix and several β-strands seems simple enough to hypothesize that it could have emerged twice independently and their conserved position between the BC and the BCCP domains could be the result of structural constraints related to their common subunit-interaction roles. b) S. Kumar, X. Cheng, S. Klimasauskas, S. Mi, J. Posfai, R. J. Roberts and G. G. Wilson, Nucleic Acids Res., 1994, 22, 1–10 CrossRef CAS PubMed;

Once iron–sulfur clusters were available they could have rearranged themselves to form the different clusters that are now found in (Fe–S) proteins. These also include more complex metal clusters in which iron is exchanged for other metals. As a consequence, this evolution led to enzyme classes such as nitrogenases and hydrogenases, both key enzymes in the evolution of life. Here, based on the concept of determining the coenzymes required for their biosynthetic generation, an evolutionary relationship can be proposed ( Scheme 5). Noteworthy, four of the five clusters mentioned (the [FeFe], [MoFe], and [VFe] cofactors in nitrogenases and the [FeFe] ‘H-cluster’ found in the corresponding hydrogenase) alone had to wait for SAM 17 to appear ( Scheme 4) before they could step onto the stage. c) E. Smith and H. J. Morowitz, Proc. Natl. Acad. Sci., 2004, 101, 13168–13173 CrossRef CAS PubMed; As previously mentioned, the BCCP domain is characteristic of all the biotin enzyme family, including the decarboxylases and transcarboxylases, whereas the BC domain is limited to the carboxylases. The CT domain gives its substrate specificity to each biotin-dependent carboxylase. Although all biotin-dependent carboxylases bear these three types of protein domains, their arrangement is unequal among different carboxylases and from one domain of life to another. This arrangement will be briefly summarized below (Figure 2B). Menendez C, Bauer Z, Huber H, Gad'on N, Stetter KO, Fuchs G: Presence of acetyl coenzyme A (CoA) carboxylase and propionyl-CoA carboxylase in autotrophic Crenarchaeota and indication for operation of a 3-hydroxypropionate cycle in autotrophic carbon fixation. J Bacteriol. 1999, 181: 1088-1098.A. Pagnier, L. Martin, L. Zeppieri, Y. Nicolet and J. C. Fontecilla-Camps, Proc. Natl. Acad. Sci. U. S. A., 2016, 113, 104–109 CrossRef CAS. Bagautdinov B, Matsuura Y, Bagautdinova S, Kunishima N: Protein biotinylation visualized by a complex structure of biotin protein ligase with a substrate. J Biol Chem. 2008, 283: 14739-14750. 10.1074/jbc.M709116200. G. Layer, J. Reichelt, D. Jahn and D. W. Heinz, Protein Sci., 2010, 19, 1137–1161 CrossRef CAS PubMed. M. R. Challand, F. T. Martins and P. L. Roach, J. Biol. Chem., 2010, 285, 5240–5248 CrossRef CAS PubMed.