Bacteria from Poorly Studied Phyla as a Potential Source of New Enzymes: β-Galactosidases from Planctomycetes and Verrucomicrobia

Abstract

Here, we present a phylogenetic analysis of a large group of the nearest homologues of a β-galactosidase, recently cloned from a soil metagenome and representing a new family of glycoside hydrolases. These proteins form an independent subfamily of hypothetical β-galactosidases and are almost exclusively represented in bacteria of the poorly studied phyla Planctomycetes and Verrucomicrobia, as well as Bacteroidetes. The phylogenetic tree of this subfamily consists of eleven highly stable clusters of branches, probably resulting from a series of gene duplications. An analysis of the tree topology suggested that the corresponding genes first evolved in Planctomycetes and most gene duplications occurred within this phylum. Later, these genes spread to several other bacterial phyla through horizontal transfers, the most numerous being transfers to Verrucomicrobia. The genomes of most Planctomycetes contain multiple paralogues of these genes of a different origin: in some cases, the horizontal transfers played a key role, while in other cases gene duplications played a key role. The importance of poorly studied groups of prokaryotes as a source of novel glycoside hydrolases is discussed.