Mining the human gut microbiome identifies mycobacterial d-arabinan degrading enzymes

Abstract

Division and degradation of bacterial cell walls requires coordinated action from a myriad of enzymes. This particularly applies to the elaborate cell walls of acid-fast organisms such as Mycobacterium tuberculosis, which consist of a multi-layered cell wall that contains an unusual glycan called arabinogalactan. Enzymes that cleave the D-arabinan core of this structure have not previously been identified in any organism. We have exploited the breadth of carbohydrate active enzymes in the human gut microbiota to identify four families of glycoside hydrolases each with the capability to degrade the D-arabinan or D-galactan components of arabinogalactan. We have discovered novel exo-D-galactofuranosidases from gut bacteria and used them to discover both endo- and exo- acting enzymes that cleave D-arabinan. This includes new members of the DUF2961 family (GH172), and a novel family of glycoside hydrolases (DUF4185) which display endo-ᴅ-arabinofuranase activity. The DUF4185 enzmyes are conserved in mycobacteria and found in many microbes, suggesting that the ability to degrade mycobacterial glycans plays an important role in the biology of diverse organisms. All mycobacteria encode two conserved endo-D-arabinanases that display different preferences for the essential cell wall components arabinogalactan and lipoarabinomannan, suggesting they are important to cell wall modification and/or degradation. Identification of these enzymes will enable isolation and analysis of mycobacterial cell wall components and facilitate the discovery of new therapeutic or diagnostic options for mycobacterial diseases.