Glycobiology Advance Access published online on February 24, 2009
Glycobiology, doi:10.1093/glycob/cwp028
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The family 6 carbohydrate binding modules have co-evolved with their appended catalytic modules towards similar substrate specificity
1 UPMC Univ Paris 06, UMR 7139 Marine Plants and Biomolecules, Station Biologique de Roscoff, F-29682 Roscoff, Bretagne, France
2 CNRS, UMR 7139 Marine Plants and Biomolecules, Station Biologique de Roscoff, F-29682 Roscoff, Bretagne, France
* Corresponding author: Tel (33) 298 29 23 30, Fax (33) 298 29 23 24, E-mail: gurvan{at}sb-roscoff.fr
Received on November 22, 2008; accepted on February 17, 2009
The survey of carbohydrate active enzymes in genomic data uncovered the modular architecture of most of these proteins. Many of the additional modules associated to catalytic modules tightly bind carbohydrates. The primary role of these carbohydrate binding modules (CBMs) is to enhance the enzymatic activity of the ensemble by bringing their appended catalytic module(s) in intimate contact with their substrates. Biochemical and biophysical approaches have unraveled the subtle interplay of the modules and the structural basis for their ligand specificities, but little attention has been paid to the evolutionary mechanisms leading to the appearance of modular architecture in carbohydrate active enzymes. Focusing on the promiscuous family CBM6 modules, we investigated the evolution of substrate specificities in parallel to that of their respectively appended catalytic modules. An extensive phylogenetic analysis of family CBM6 modules indicates that these non-catalytic modules have diverged into clades which coincide with their substrate selectivity. These data as well as the remarkable congruence of the phylogenetic trees inferred from CBM6s on the one hand and their associated catalytic modules on the other hand show that CBM6s and their associated glycoside hydrolases have co-evolved to acquire the same substrate specificity. We also propose an evolutionary scenario explaining the emergence of the modular agarases, by which existent alpha-agarases acquired their agar-binding CBM6 module through a lateral transfer from pre-existing beta-agarases. Altogether, this observed co-evolution between CBM6s and their catalytic modules will facilitate the prediction of the substrate specificity of uncharacterized CBM6 modules present in genomic data.
Key words: CBM6 / glycoside hydrolase / modularity / co-evolution / agarase