MBE Advance Access originally published online on December 5, 2003
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Mol. Biol. Evol. 21(2):364-373. 2004
DOI: 10.1093/molbev/msh024
© 2004 by the Society for Molecular Biology and Evolution. ISSN: 0737-4038
Using Quaternary Structures to Assess the Evolutionary History of Proteins: The Case of the Aspartate Carbamoyltransferase
* Institut de Génétique et Microbiologie, Université Paris-Sud, Orsay, France
Microbiology, Free University of Brussels (VUB) and J. M. Wiame Research Institute1, Brussels, Belgium
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 that allows ascertainment of such questionable scenarios by taking into account quaternary structures: 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 uniquely made up of trimers of PyrB. The PyrB phylogenetic tree is not congruent with the tree of life, but it became coherent when we recognized the existence of two families of ATCases, ATC I and ATC II. Remarkably, a very strong correlation was found between the pattern of PyrB phylogenetic clustering and the different classes of quaternary structures of ATCases. All class B ATCases form a clade in family ATC II, which also contains all eukaryotic sequences. In contrast, family ATC I is made up of classes A and C. These results suggest unexpected common ancestry for prokaryotic B and eukaryotic ATCases on the one hand, and for A and C on the other. Thus, the emergence of specific quaternary structures appears to have been a more recent event than the separation into the 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. The 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 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
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  D. Shi, V. Sagar, Z. Jin, X. Yu, L. Caldovic, H. Morizono, N. M. Allewell, and M. Tuchman The Crystal Structure of N-Acetyl-L-glutamate Synthase from Neisseria gonorrhoeae Provides Insights into Mechanisms of Catalysis and Regulation J. Biol. Chem., March 14, 2008; 283(11): 7176 - 7184. [Abstract] [Full Text] [PDF]
|
|