Identification of levoglucosan degradation pathways in bacteria and sequence similarity network analysis

Abstract

Levoglucosan is produced in the pyrolysis of cellulose and starch, including from bushfires or the burning of biofuels, and is deposited from the atmosphere across the surface of the earth. We describe two levoglucosan degradingPaenarthrobacterspp. (Paenarthrobacter nitrojuajacolisLG01 andPaenarthrobacter histidinolovoransLG02) that were isolated by metabolic enrichment on levoglucosan as sole carbon source. Genome sequencing and proteomics analysis revealed expression of a series of gene clusters encoding known levoglucosan degrading enzymes, levoglucosan dehydrogenase (LGDH, LgdA), 3-keto-levoglucosan β-eliminase (LgdB1) and glucose 3-dehydrogenase (LgdC), along with an ABC transporter cassette and associated solute binding protein. However, no homologues of 3-ketoglucose dehydratase (LgdB2) were evident, while the expressed gene clusters contained a range of putative sugar phosphate isomerase/xylose isomerases with weak similarity to LgdB2. Sequence similarity network analysis of genome neighbors of LgdA revealed that homologues of LgdB1 and LgdC are generally conserved in a range of bacteria in the phyla Firmicutes, Actinobacteria and Proteobacteria. One sugar phosphate isomerase/xylose isomerase cluster (LgdB3) was identified with limited distribution mutually exclusive with LgdB2 that may fulfil a similar function. LgdB1, LgdB2 and LgdB3 adopt similar predicted 3D folds suggesting overlapping function in processing intermediates in LG metabolism. Our findings highlight the diversity within the LGDH pathway through which bacteria utilize levoglucosan as a nutrient source.

Functional metagenomics reveals an alternative, broad-specificity pathway for metabolism of carbohydrates in human gut commensal bacteria

“…The best studied example was the plant pathogen Agrobacterium tumefaciens, which converts sucrose, among other disaccharides, to 3-keto-sucrose 30,31 . However, the identity of the enzymes responsible was not known and no chemical rationale was provided for the oxidation: the enzymes responsible for breaking the glycosidic bonds were assumed to be regular glycosidases. More recently, ketosugars have been reported as intermediates in the breakdown of anhydrosugars such as levoglucosan 32,33 , as well as C-glycosidecleaving systems that operate via similar oxidation and elimination reactions. [34][35][36][37][38] As mentioned, other glycosidases that transiently oxidize sugar hydroxy groups as part of their mechanism have been reported by us and others 9,[39][40][41] .…”