The Evolutionary History of Carbamoyltransferases: A Complex Set of Paralogous Genes Was Already Present in the Last Universal Common Ancestor |
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Authors: | Bernard Labedan Anne Boyen Margot Baetens Daniel Charlier Pingguo Chen Raymond Cunin Virginie Durbeco Nicolas Glansdorff Guy Herve Christianne Legrain Ziyuan Liang Christina Purcarea Martine Roovers Rony Sanchez Thia-Lin Toong Marc Van de Casteele Françoise van Vliet Ying Xu Yuan-Fu Zhang |
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Institution: | (1) Institut de Génétique et de Microbiologie, CNRS UMR 8621, Université Paris-sud, Batiment 409, F-91405 Orsay Cedex, France, FR;(2) Microbiologie, Vrije Universiteit Brussel, 1 ave E. Gryson, B-1070 Brussels, Belgium, BE;(3) Vlaams Interuniversitair Instituut voor Biotechnologie, 1 ave E. Gryson, B-1070 Brussels, Belgium, BE;(4) Research Institute, CERIA-COOVI, 1 ave E. Gryson, B-1070 Brussels, Belgium, BE;(5) Laboratoire de Microbiologie, Universite Libre de Bruxelles, 1 ave E. Gryson, B-1070 Brussels, Belgium, BE;(6) Laboratoire de Biochimie des Signaux Régulateurs Cellulaires et Moléculaires, URA CNRS 1682-Université Pierre et Marie Curie, 96, Bd. Raspail, 75006 Paris, France, FR |
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Abstract: | Forty-four sequences of ornithine carbamoyltransferases (OTCases) and 33 sequences of aspartate carbamoyltransferases (ATCases)
representing the three domains of life were multiply aligned and a phylogenetic tree was inferred from this multiple alignment.
The global topology of the composite rooted tree (each enzyme family being used as an outgroup to root the other one) suggests
that present-day genes are derived from paralogous ancestral genes which were already of the same size and argues against
a mechanism of fusion of independent modules. A closer observation of the detailed topology shows that this tree could not
be used to assess the actual order of organismal descent. Indeed, this tree displays a complex topology for many prokaryotic
sequences, with polyphyly for Bacteria in both enzyme trees and for the Archaea in the OTCase tree. Moreover, representatives
of the two prokaryotic Domains are found to be interspersed in various combinations in both enzyme trees. This complexity
may be explained by assuming the occurrence of two subfamilies in the OTCase tree (OTC α and OTC β) and two other ones in
the ATCase tree (ATC I and ATC II). These subfamilies could have arisen from duplication and selective losses of some differentiated
copies during the successive speciations. We suggest that Archaea and Eukaryotes share a common ancestor in which the ancestral
copies giving the present-day ATC II/OTC β combinations were present, whereas Bacteria comprise two classes: one containing
the ATC II/OTC α combination and the other harboring the ATC I/OTC β combination. Moreover, multiple horizontal gene transfers
could have occurred rather recently amongst prokaryotes. Whichever the actual history of carbamoyltransferases, our data suggest
that the last common ancestor to all extant life possessed differentiated copies of genes coding for both carbamoyltransferases,
indicating it as a rather sophisticated organism. |
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Keywords: | : Carbamoyltransferases — ATCase — OTCase — Protein evolution — Gene duplication — Paralogous proteins — Last universal common ancestor — Molecular phylogeny |
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