title: Episodic positive selection during the evolution of naphthalene dioxygenase to nitroarene dioxygenase.
abstract: Using different maximum-likelihood models of adaptive evolution, signatures of natural selective pressure, operating across the naphthalene family of dioxygenases, were examined. A lineage- and branch-site specific combined analysis revealed that purifying selection pressure dominated the evolutionary history of the enzyme family. Specifically, episodic positive Darwinian selection pressure, affecting only a few sites in a subset of lineages, was found to be responsible for the evolution of nitroarene dioxygenases (NArDO) from naphthalene dioxygenase (NDO). Site-specific analysis confirmed the absence of diversifying selection pressure at any particular site. Different sets of positively selected residues, obtained from branch-site specific analysis, were detected for the evolution of each NArDO. They were mainly located around the active site, the catalytic pocket and their adjacent regions, when mapped onto the 3D structure of the α-subunit of NDO. The present analysis enriches the current understanding of adaptive evolution and also broadens the scope for rational alteration of substrate specificity of enzyme by directed evolution.
authors.affiliation: Department of Microbiology, Bose Institute, Kolkata 700054, India.
authors.forename: Arindam
authors.initials: A
authors.lastname: Dutta
authors.forename: Joydeep
authors.initials: J
authors.lastname: Chakraborty
authors.forename: Tapan K
authors.initials: TK
authors.lastname: Dutta
mesh_terms: D001419:Bacteria / Q000737:chemistry / Q000201:enzymology* / Q000235:genetics / Q000378:metabolism; D049308:Dioxygenases / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D019143:Evolution, Molecular; D009097:Multienzyme Complexes / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D009574:Nitro Compounds / Q000378:metabolism; D010802:Phylogeny
chemical_list: D009097:Multienzyme Complexes; D009574:Nitro Compounds; D049308:Dioxygenases; C038703:naphthalene dioxygenase
keywords: Adaptive evolution; Aromatic ring-hydroxylating oxygenase; Episodic positive selection; Naphthalene dioxygenase; Nitroarene dioxygenase