Three alginate lyases provide a new gut Bacteroides ovatus isolate with the ability to grow on alginate.

Humans consume alginate in the form of seaweed, food hydrocolloids, and encapsulations, making the digestion of this mannuronic acid (M) and guluronic acid (G) polymer of key interest for human health. To increase knowledge on alginate degradation in the gut, a gene catalog from human feces was mined for potential alginate lyases (ALs). The predicted ALs were present in nine species of the Bacteroidetes phylum, of which two required supplementation of an endo-acting AL, expected to mimic cross-feeding in the gut. However, only a new isolate grew on alginate. Whole-genome sequencing of this alginate-utilizing isolate suggested that it is a new Bacteroides ovatus strain harboring a polysaccharide utilization locus (PUL) containing three ALs of families: PL6, PL17, and PL38. The BoPL6 degraded polyG to oligosaccharides of DP 1-3, and BoPL17 released 4,5-unsaturated monouronate from polyM. BoPL38 degraded both alginates, polyM, polyG, and polyMG, in endo-mode; hence, it was assumed to deliver oligosaccharide substrates for BoPL6 and BoPL17, corresponding well with synergistic action on alginate. BoPL17 and BoPL38 crystal structures, determined at 1.61 and 2.11 Å, respectively, showed (α/α)6-barrel + anti-parallel ß-sheet and (α/α)7-barrel folds, distinctive for these PL families. BoPL17 had a more open active site than the two homologous structures. BoPL38 was very similar to the structure of an uncharacterized PL38, albeit with a different triad of residues possibly interacting with substrate in the presumed active site tunnel. Altogether, the study provides unique functional and structural insights into alginate-degrading lyases of a PUL in a human gut bacterium.IMPORTANCEHuman ingestion of sustainable biopolymers calls for insight into their utilization in our gut. Seaweed is one such resource with alginate, a major cell wall component, used as a food hydrocolloid and for encapsulation of pharmaceuticals and probiotics. Knowledge is sparse on the molecular basis for alginate utilization in the gut. We identified a new Bacteroides ovatus strain from human feces that grew on alginate and encoded three alginate lyases in a gene cluster. BoPL6 and BoPL17 show complementary specificity toward guluronate (G) and mannuronate (M) residues, releasing unsaturated oligosaccharides and monouronic acids. BoPL38 produces oligosaccharides degraded by BoPL6 and BoPL17 from both alginates, G-, M-, and MG-substrates. Enzymatic and structural characterization discloses the mode of action and synergistic degradation of alginate by these alginate lyases. Other bacteria were cross-feeding on alginate oligosaccharides produced by an endo-acting alginate lyase. Hence, there is an interdependent community in our guts that can utilize alginate.

Gut bacterial alginate degrading enzymes.

Alginates are abundant marine anionic polysaccharides consumed by humans. Thus, over the years some understanding has emerged about alginate utilization by human gut microbiota (HGM). However, insights have been obtained only recently at the molecular level with regard to structure and function of alginate degrading and metabolizing enzymes from HGM. Still, numerous studies report on effects of alginates on bacterial communities from digestive tracts of various, predominantly marine organisms feeding on alginate and some of the involved alginate lyases have been characterized. Other studies describe the beneficial impact on gut microbiota elicited by alginates in animal models, for example, high-fat-diet-fed mice addressing obesity or as feed supplements for livestock. Alginates are depolymerized by a ß-elimination reaction catalyzed by polysaccharide lyases (PLs) referred to as alginate lyases (ALs). The ALs are found in 15 of the 42 PL families categorized in the CAZy database. While genome mining has led to prediction of ALs encoded by bacteria of the HGM; currently, only four enzymes from this niche have been characterized biochemically and two crystal structures are reported. Alginates are composed of mannuronate (M) and guluronate (G) residues organized in M-, G-, and MG-blocks, which calls for ALs of complementary specificity to effectively depolymerize alginate to alginate oligosaccharides (AOSs) and monosaccharides. Typically, ALs of different PL families are encoded by genes arranged in clusters denoted as polysaccharide utilization loci. Currently, biochemical and structural analyses of marine bacterial ALs contribute to depicting the mode of action of predicted enzymes from bacteria of the HGM.