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Many bacteria have evolved ways to interact with glycosylation functions of the immune system of their hosts. Streptococcus pyogenes [GAS (group A Streptococcus)] secretes the enzyme EndoS that cleaves glycans on human IgG and impairs the effector functions of the antibody. The ndoS gene, encoding EndoS, has, until now, been thought to be conserved throughout the serotypes. However, in the present study, we identify EndoS₂, an endoglycosidase in serotype M49 GAS strains. We characterized EndoS₂ and the corresponding ndoS2 gene using sequencing, bioinformatics, phylogenetic analysis, recombinant expression and LC–MS analysis of glycosidic activity. This revealed that EndoS₂ is present exclusively, and highly conserved, in serotype M49 of GAS and is only 37% identical with EndoS. EndoS₂ showed endo-β-N-acetylglucosaminidase activity on all N-linked glycans of IgG and on biantennary …