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Although the PCT domain is characteristic of PYC and is not shared by any other biotin-dependent carboxylase, the oxaloacetate decarboxylase (ODC; E.C. 4.1.1.3, which takes part in Na + transport in some bacteria) is also known to use an α-subunit homologous to the PCT domain [ 48]. Consequently, ODC α-subunit sequences were incorporated into our phylogenetic analyses. In addition, some extremely divergent bacterial homologues showed similarity to transcarboxylases, but we will not treat them here because of their very poor sequence conservation. c) D. R. Nelson, T. Kamataki, D. J. Waxman, F. P. Guengerich, R. W. Estabrook, R. Feyereisen, F. J. Gonzalez, M. J. Coon, I. C. Gunsalus, O. Gotoh, K. Okuda and D. W. Nebert, DNA Cell Biol., 1993, 12, 1–51 CrossRef CAS PubMed. G. Layer, M. Jahn, J. Moser and D. Jahn, ACS Bio Med Chem Au, 2022, 2, 196–204, DOI: 10.1021/acsbiomedchemau.1c00061.

O. T. Magnusson, H. Toyama, M. Saeki, R. Schwarzenbacher and J. P. Klinman, J. Am. Chem. Soc., 2004, 126, 5342–5343 CrossRef CAS PubMed. c) B. Gakière, J. Hao, L. de Bont, P. Pétriacq, A. Nunes-Nesi and A. R. Fernie, Crit. Rev. Plant Sci., 2018, 37, 259–307 CrossRef; S. Gambarelli, F. Luttringer, D. Padovani, E. Mulliez and M. Fontecave, ChemBioChem, 2005, 6, 1960–1962 CrossRef CAS PubMed. a) S. Hwang, B. Cordova, N. Chavarria, D. Elbanna, S. McHugh, J. Rojas, F. Pfeiffer and J. A. Maupin-Furlow, BMC Microbiol., 2014, 14, 260 CrossRef PubMed;

Targeting sequences seem to be absent from eukaryotic PYC and ACC. Both BC- and PCT-domain phylogenies strongly support the branching of eukaryotic PYC sequences among their bacterial homologues, what indicates a bacterial origin even though the vector of this HGT cannot be specified. Surprisingly, concerning the eukaryotic ACCs, the phylogenetic reconstructions are at odds with protein domain comparison. On the one hand, eukaryotic ACCs branch among bacterial ACC sequences in preliminary CCT and accurate BC phylogenies (additional file 1 and Figure 3, respectively), suggesting that bacterial donors are at the origin to these sequences. However, eukaryotic ACC sequences form extremely divergent groups in both BC and CTT phylogenies, probably as a consequence of rapid evolution subsequent to the fusion of these domains to generate the eukaryotic ACC polypeptide. Thus, reconstruction artifacts are likely and little confidence can be given to the position of eukaryotic sequences in these phylogenies. On the other hand, protein domain composition of eukaryotic ACC is very different from those of PYCs and bacterial ACCs, but shares strong similarity with that of XCC (Figure 2). Huang et al. proposed that the most likely way to explain the unique domain composition of eukaryotic ACC is a fusion event between the α- and β-subunits of XCC on both sides of a central linker [ 27]. The elucidation of the function of the BT/PT domain of eukaryotic ACCs will be necessary to decide between the XCC and the bacterial ACC origin for the eukaryotic ACC polypeptides. a) M. Zhang, L. Wang and D. Zhong, Arch. Biochem. Biophys., 2017, 632, 158–174 CrossRef CAS PubMed; e) M. Fischer, W. Romisch, S. Schiffmann, M. Kelly, H. Oschkinat, S. Steinbacher, R. Huber, W. Eisenreich, G. Richter and A. Bacher, J. Biol. Chem., 2002, 277, 41410–41416 CrossRef CAS PubMed; Review: S. Chatterjee, S. Gatreddi, S. Gupta, J. L. Nevarez, J. A. Rankin, A. Turmo, J. Hu and R. P. Hausinger, Biochem. Soc. Trans., 2022, 50, 1187–1196, DOI: 10.1042/BST20220490.55. Bramwell H, Hunter IS, Coggins JR, Nimmo HG: Propionyl-CoA carboxylase from Streptomyces coelicolor A3(2): cloning of the gene encoding the biotin-containing subunit. Microbiology. 1996, 142: 649-655. 10.1099/13500872-142-3-649.

Finally, the BC phylogeny indicates that UCA genes were acquired recently and independently by fungi and green algae from bacteria. Whereas eukaryotes have maintained the same domain structure than their bacterial counterparts for PYC, MCC, PCC and bacterial-type ACC, the components of eukaryotic ACC and UCA have fused to generate large polypeptides. Biotin-dependent carboxylases in Archaea Rodriguez E, Banchio C, Diacovich L, Bibb MJ, Gramajo H: Role of an essential acyl coenzyme A carboxylase in the primary and secondary metabolism of Streptomyces coelicolor A3(2). Applied Environ Microbiol. 2001, 67: 4166-4176. 10.1128/AEM.67.9.4166-4176.2001.

b) A. M. Gobe, R. Toro, X. Li, A. Ornelas, H. Fan, S. Eswaramoorthy, Y. Patskovsky, B. Hillerich, R. Seidel, A. Sali, B. K. Shoichet, S. C. Almo, S. Swaminathan, M. E. Tanner and F. M. Raushel, Biochemistry, 2013, 52, 6525–6536 CrossRef PubMed; Aguilar JA, Zavala AN, Diaz-Perez C, Cervantes C, Diaz-Perez AL, Campos-Garcia J: The atu and liu clusters are involved in the catabolic pathways for acyclic monoterpenes and leucine in Pseudomonas aeruginosa. Applied Environ Microbiol. 2006, 72: 2070-2079. 10.1128/AEM.72.3.2070-2079.2006. a) A. Volbeda, C. Darnault and J.-C. Fontecilla-Camps, J. Am. Chem. Soc., 2016, 138, 11802–11809 CrossRef CAS PubMed;