Characterization and diversity of the complete set of GH family 3 enzymes from Rhodothermus marinus DSM 4253
Kazi Zubaida Gulshan Ara, Anna Månberger, Marek Gabriško, Javier A. Linares‐Pastén, Andrius Jasilionis, Ólafur H. Friðjónsson, Guðmundur Ó. Hreggviðsson, Ŝtefan Janeĉek, Eva Nordberg Karlsson
Abstract
Abstract The genome of Rhodothermus marinus DSM 4253 encodes six glycoside hydrolases (GH) classified under GH family 3 (GH3): Rm Bgl3A, Rm Bgl3B, Rm Bgl3C, Rm Xyl3A, Rm Xyl3B and Rm Nag3. The biochemical function, modelled 3D-structure, gene cluster and evolutionary relationships of each of these enzymes were studied. The six enzymes were clustered into three major evolutionary lineages of GH3: β- N -acetyl-glucosaminidases, β-1,4-glucosidases/β-xylosidases and macrolide β-glucosidases. The Rm Nag3 with additional β-lactamase domain clustered with the deepest rooted GH3-lineage of β- N -acetyl-glucosaminidases and was active on acetyl-chitooligosaccharides. Rm Bgl3B displayed β-1,4-glucosidase activity and was the only representative of the lineage clustered with macrolide β-glucosidases from Actinomycetes. The β-xylosidases, Rm Xyl3A and Rm Xyl3B, and the β-glucosidases Rm Bgl3A and Rm Bgl3C clustered within the major β-glucosidases/β-xylosidases evolutionary lineage. Rm Xyl3A and Rm Xyl3B showed β-xylosidase activity with different specificities for para -nitrophenyl ( p NP)-linked substrates and xylooligosaccharides. Rm Bgl3A displayed β-1,4-glucosidase/β-xylosidase activity while Rm Bgl3C was active on p NP-β-Glc and β-1,3-1,4-linked glucosyl disaccharides. Putative polysaccharide utilization gene clusters were also investigated for both R. marinus DSM 4253 and DSM 4252 T (homolog strain). The analysis showed that in the homolog strain DSM 4252 T Rmar_1080 ( Rm Xyl3A) and Rmar_1081 ( Rm Xyl3B) are parts of a putative polysaccharide utilization locus (PUL) for xylan utilization.