MBE Advance Access published online on December 5, 2003
Molecular Biology and Evolution, doi:10.1093/molbev/msh024
Molecular Biology and Evolution © Society for Molecular Biology and Evolution 2003; all rights reserved
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1 Institut de Génétique et Microbiologie, CNRS UMR 8621, Université Paris Sud, Bâtiment 409, 91405 Orsay Cedex, France
* To whom correspondence should be addressed. E-mail: labedan{at}igmors.u-psud.fr.
Many evolutionary scenarios describing the history of proteins are based solely on phylogenetic studies. We have designed a new approach allowing to ascertain such questionable scenarios by taking into account quaternary structures and we used aspartate carbamoyltransferase (ATCase) as a case study. Prokaryotic ATCases correspond to different classes of quaternary structures according to the mode of association of the catalytic PyrB subunit with other polypeptides: either the PyrI regulatory subunit (class B) or a dihydroorotase (class A), which may be active (PyrC, subclass A1) or inactive (PyrC', subclass A2). Class C is made uniquely of trimers of PyrB. The PyrB phylogenetic tree is not congruent with the tree of life but became coherent when we recognized the existence of two families of ATCases, ATC I and ATC II. Remarkably, a very strong correlation was now found between the pattern of PyrB phylogenetic clustering and the different classes of quaternary structures of ATCases. All class B ATCases are forming a clade in family ATC II which contains also all eukaryotic sequences whereas family ATC I is made of classes A and C. These results suggest unexpected common ancestry for prokaryotic B and eukaryotic ATCases on one side and for A and C on the other side. Thus, the emergence of specific quaternary structures appears to have been a more recent event than the separation in ATC I and ATC II families. We propose that different evolutionary constraints, depending on the identity of the partners interacting in the different kinds of holoenzymes, operated in a concerted way on the ancestral pyrB genes and the respective associated genes pyrI or pyrC, so as to maintain appropriate inter-polypeptides interactions at the level of quaternary structure. Such a process of coevolution of genes encoding proteins interacting in various holoenzymes has been assessed by calculating the correlation coefficient between their respective phylogenetic trees. Our approach integrating data obtained from the separate fields 2 of structural biology and molecular evolution could be useful in other cases where pure statistical data need to receive independent confirmation. Key Words:
aspartate carbamoyltransferase, catalytic PyrB subunit, regulatory PyrI subunit, dihydroorotase, protein - protein interactions, coevolution process, linear correlation coefficient
© 2003 Society for Molecular Biology and Evolution
Original Articles
Using Quaternary Structures to Assess the Evolutionary History of Proteins: The Case of the Aspartate Carbamoyltransferase
2 Microbiology, Free University of Brussels (VUB) and J.M. Wiame Research Institute 1, ave E. Gryzon, B-1070, Brussels, Belgium
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