Moushtaq, L. | Search bioRxiv

bioRxiv2026

Outer membrane 'PusCD' complexes coordinate phospho(inositol)lipid utilisation in plant Bacteroidota

Gram-negative bacteria belonging to the phylum Bacteroidota are prominent and ecologically important members of host-associated microbiomes. A feature of Bacteroidota species is the presence of diverse outer membrane TonB-dependent transporter and cognate surface exposed lipoprotein (TBDT-SLP) complexes. Many 'SusCD-like' TBDT-SLPs coordinate complex carbohydrate capture from the environment. Here, we show the model soil Bacteroidota species Flavobacterium johnsoniae synthesises two TBDT-SLP complexes (named PusCD1 and PusCD2) that are essential for growth on phosphatidylinositol, a member of an abundant lipid class within plant plasma membranes, as a phosphorus source. Structural characterisation of ligand-bound PusCD1 complex from F. johnsoniae membranes reveals a new binding mechanism for organophosphorus and broadens the known functional repertoire of this class of transporters. Diverse PusCD-like complexes are widespread among plant associated Bacteroidota, pointing to a major, previously unrecognised route for the recycling of organophosphorus compounds in the rhizosphere, with potential implications for engineering microbial-mediated phosphorus recovery from organic waste streams.

microbiology↗

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↗