Biology subjects

Ndeh, D.

Publications and source records attributed to Ndeh, D..

3 recordsLinked to original sources

bioRxiv2024

Hybrid xyloglucan utilisation loci are prevalent among plant-associated Bacteroidota

The plant hemicellulose xyloglucan (XyG) is secreted from the roots of numerous plant species, including cereals, and contributes towards soil aggregate formation in terrestrial systems. Whether XyG represents a key nutrient for plant-associated bacteria is unclear. The phylum Bacteroidota are abundant in the plant microbiome and provide several beneficial functions for their host. However, the metabolic and genomic traits underpinning their success remain poorly understood. Here, using proteomics, bacterial genetics, and genomics, we revealed that plant-associated Flavobacterium, a genus within the Bacteroidota, can efficiently utilise XyG through the occurrence of a distinct and conserved gene cluster, referred to as the Xyloglucan Utilisation Loci (XyGUL). Flavobacterium XyGUL is a hybrid of the molecular machinery found in gut Bacteroides spp., Cellvibrio japonicus, and the plant pathogen Xanthomonas. Combining protein biochemistry, computational modelling and phylogenetics, we identified a mutation in the enzyme required for initiating hydrolysis of the XyG polysaccharide, an outer membrane endoxyloglucanase glycoside hydrolase family 5 subfamily 4 (GH5_4), which enhances activity towards XyG. A subclade of GH5_4 homologs carrying this mutation were the dominant form found in soil and plant metagenomes due to their occurrence in Bacteroidota and Proteobacteria. However, only in members of the Bacteroidota spp., particularly Flavobacterium spp. was such a remarkable degree of XyGUL conservation detected. We propose this mechanism enables plant-associated Flavobacterium to specialise in competitive acquisition of XyG exudates and that this hemicellulose may represent an important nutrient source, enabling them to thrive in the plant microbiome, which is typified by intense competition for low molecular weight carbon exudates.

microbiology↗

bioRxiv2024

A platform for the recombinant production of Group A Streptococcus glycoconjugate vaccines

Strep A is a human-exclusive bacterial pathogen killing annually more than 500,000 patients, and no current licensed vaccine exists. Strep A bacteria are highly diverse, but all produce an essential, abundant, and conserved surface carbohydrate, the Group A Carbohydrate, which contains a rhamnose polysaccharide (RhaPS) backbone. RhaPS is a validated universal vaccine candidate in a glycoconjugate prepared by chemical conjugation of the native carbohydrate to a carrier protein. We engineered the Group A Carbohydratte biosynthesis pathway to enable recombinant production using the industry standard route to couple RhaPS to selected carrier proteins within E. coli cells. The structural integrity of the produced recombinant glycoconjugate vaccines was confirmed by NMR spectroscopy and mass spectrometry. Purified RhaPS glycoconjugates elicited carbohydrate-specific antibodies in mice and rabbits and bound to the surface of multiple Strep A strains of diverse M-types, confirming the recombinantly produced RhaPS glycoconjugates as valuable vaccine candidates.

microbiology↗

bioRxiv2024

A genetic locus in the gut microbe Bacteroides thetaiotaomicron encodes activities consistent with mucin-O-glycoprotein processing and plays a critical role in N-acetylgalactosamine metabolism

It is increasingly appreciated that members of the gut microbiota are key modulators of human health and the status of major diseases including cancer, diabetes and inflammatory bowel disease. Central to their survival is the ability to metabolise complex dietary and host-derived glycans including intestinal mucins. The latter are critical components of the gut epithelium glycocalyx and mucus barriers, essential for microbiota-gut homeostasis and protection from infections by pathogens. The prominent and model human gut microbe Bacteroides thetaiotaomicron (B. theta) is a versatile and highly efficient complex glycan degrader thanks to the expansion of gene clusters termed polysaccharide utilisation loci (PULs) in its genome. While the mechanisms for several singular dietary glycan-induced PULs have been elucidated, studies on the 16-18 mucin-induced PULs in B. theta significantly lag behind. A combination of the scale and complexity of B. theta transcriptomic response to mucins and complex glycan configurations of mucins represent major hurdles for the functional characterisation of the mucin induced PULs. As a result, there is very limited knowledge on how mucin metabolism is coordinated in B. theta and what specific PULs, genes and metabolites are critical for mucin-B. theta, and more generally mucin-microbiota interactions and their importance in microbiota-gut homeostasis. Here we show that a mucin inducible PUL BT4240-50, (i) encodes activities consistent with a machinery that couples the processing of mucin-O glycan glycoproteins with the metabolism of N-acetylgalactosamine (GalNAc), an abundant mucin O-glycan sugar; (ii) is important for competitive growth on mucins in-vitro; (iii) encodes a key kinase enzyme (BT4240) that is critical for GalNAc metabolism and (iv) has related PULs encoded by a range of prominent Bacteroides species in the human gut. Furthermore, BT4240 kinase was also critical for glycosaminoglycan metabolism, thus extending the PULs function beyond mucins. Our work advances our understanding of the vital metabolic processes that govern mucosal glycoprotein metabolism and by implication, a key aspect of host-microbiota interactions at mucosal surfaces and highlight GalNAc as a key metabolite targeted for competitive growth.

biochemistry↗