ABC system for dietary oligosaccharides: a weapon of Bifidobacterium sp. in the ‘metabolic’ war of the gut

By: Constantinos Drousiotis

Twitter: @Ecolinnit

The human gut microbiota (HGM) is the community of microbes that thrive in the gastrointestinal tract. Lately, it has become evident that HGM has a profound impact on human health which has now attracted a great interest from the scientific community. Current research is aiming to understand the complicated metabolic interactions that exist in the microbiota which can reveal the type of imbalances in diet that could potentially lead to disease.

A rich diet in legumes and seeds leads to an increased population of Bifidobacteria in the HGM. This is ought to the fact that the latter can metabolise raffinose family oligosaccharides (RFO) as opposed to the human gut cells which are unable to. The specialised transport machinery enabling these bacteria to transport and utilise RFOs hasn’t been characterised previously.

The study carried out by Morten et al. aimed to characterise the substrate binding protein (SBP) of the ABC transport system that was expressed in response to growth on RFOs, ie. BlG16BP. The group solved the structure of the BlG16BP and showed that the binding pocket of the protein accommodates oligosaccharides with a glucosyl or galactosyl C4-OH at position 1(non-reducing glycosyl unit) and an α-glycosidic bond to a glucosyl moiety at position 2. Additionally, they showed that the fructosyl or glucosyl groups are tolerated well at position 3 because of the lack of direct polar contacts of the protein with the sugar at this position and additionally, the cleft’s open architecture. These are all features of the sugar structures of raffinose and panose.

Crystal structure of BlG16BP in complex with panose (A) and raffinose (B). The SBPs consist of an N-terminal domain (Domain 1, brown) and a larger C-terminal domain (Domain 2, green). The two domains are linked by hinge regions shown in light blue. Shown on right-hand side, is a close-up of the binding sites of BlG16BP in complex with panose (D) and raffinose (E). The non-reducing end glycosyl unit of both ligands (galactosyl in raffinose and glucosyl in panose) stacks onto Phe-392 (defined as position 1) and makes polar contacts to Asp-394, Asn-109, and His-395. Asp-394 is able to form hydrogen bonds to both the equatorial C4-OH of the non-reducing end glucosyl in panose and the axial C4-OH of the galactosyl in raffinose. The glucosyl moiety of raffinose and panose at position 2 stacks onto Tyr-291 and makes polar contacts to Lys-58, Glu-60, and Asp-326. The position 3 is tolerated well, as the glucosyl moiety of panose stacks onto Trp-216 with almost parallel planes of the sugar rings as opposed to the fructosyl group of raffinose which sits orthogonal against Trp216 due to a smaller area of Van der Walls contacts. As a point of reference, the oligosaccharide structures are provided on the bottom of the figure.


Growth assays with a mixture of RFOs as the carbon source revealed that raffinose and melibiose were utilised first in order throughout the course of growth assays of B. animalis subsp. lactis Bl-04, indicating that are preferentially recognised over tetra- and pentasaccharides. The group suggests that the preferential binding by this transporter could potentially reflect the levels of the respective sugars in the gut or reveal the ability of bifidobacteria to further process the tetra- and pentasaccharides extracellularly. Nonetheless, BlG16BP SBP has a lower affinity to the only two previously characterised oligosaccharide binding proteins from bifidobacteria; the lower affinity could indicate that RFOs are found in higher concentrations than the ligands of the other two oligosaccharide binding proteins.  Also, it could point out to the low level of competition for RFOs which would be agreeable with the fact that this ABC system is not phylogenetically diverse.

Notably, phylogenetic analysis showed, that as far as Lactobacillus species are concerned, this α-galactoside transporter is only found in the human-gut adapted clade of thereof. The lack of this system in Lactobacillus which thrive in other ecological niches suggests that the transporter was acquired by horizontal gene transfer as a survival strategy in response to the fierce microbial competition in the gut. This is in accordance with previous studies which point towards horizontal gene transfer viewed as an adaptation strategy to gut niche.

The study reports the first biochemical and structural insight into an ABC-associated glycoside transport protein and provides evidence that ABC-mediated uptake may confer a competitive edge in the fierce competition for metabolic resources in the human gut niche. Altogether, the findings improved our understanding of the impact of oligosaccharide uptake in preferential glycan utilization.


Source: Morten et. al., (2016) , An ATP Binding Cassette Transporter Mediates the Uptake of α-(1,6)-Linked Dietary Oligosaccharides in Bifidobacterium and Correlates with Competitive Growth on These Substrates. The Journal of Biological Chemistry, 291(38), 20220-231.