Structural insights into xyloglucan recognition by an ABC transporter from a Gram-positive, thermophilic bacterium.

Cell-Surface and Periplasmic Deconstruction of Xylan by Oligotrophic Bacterium Caulobacter vibrioides.

Bacterial species that inhabit diverse nutritional niches, such as plants, the human gut, and aquatic environments, exhibit common and unique molecular mechanisms for acquiring nutrients from plant polysaccharides like xylan. The oligotrophic bacterium Caulobacter vibrioides (Syn. Caulobacter crescentus) shows unique adaptations for growth in low-nutrient conditions and codes for a repertoire of genes that facilitate xylan utilisation as a carbon source. Investigation of xylan and xylan-derivative utilisation by C. vibrioides shows membrane-bound xylanase-mediated xylan deconstruction on the cell surface and further deconstruction of the xylo-oligosaccharides in the periplasm by xylosidases and other accessory enzymes. Proton motive force disruption studies suggest involvement of TonB-dependent transporters, Major Facilitator Superfamily transporters, or ATP-Binding Cassette transporters in the transport of xylo-oligosaccharides and other xylan-derivatives across the membranes of C. vibrioides. Results from our studies using enzyme assays and chromatographic analyses suggest that bacteria deconstruct xylan in a surface-bound manner leading to efficient uptake of xylo-oligosaccharides across the outer membrane, without loss of nutrients to the environment. This proposed model for C. vibrioides xylan utilisation highlights both unique and similar mechanistic features found in gut and plant pathogenic bacteria, advancing the molecular understanding of nutrient acquisition in oligotrophic Gram-negative bacteria.

Comparative genomic analysis of hemicellulose-degrading potential in bacterial isolates from the anterior intestine of Eisenia andrei (Bouché, 1972)

In Silico Insights into Carbohydrate-Active Enzymes (CAZymes) of Bacillus subtilis T7: Lignin and Polysaccharide Degradation Mechanisms

Overall structural integrity for both proteins was confirmed and dynamic dynamics were more variable—xylotetraose remained bound within the Abhydrolase_1 active site for approximately 75 ns before partial displacement, whereas cellotetraose exhibited dynamic association along the GH9 catalytic channel, consistent with processive substrate translocation in endoglucanases.

Cyanochelin uptake reveals an exclusively cyanobacterial class of AMIN-domain TonB-dependent transporters

This study functionally characterise the import system of cyanochelin B, a photolytic β-hydroxy aspartate siderophore produced by several filamentous cyanobacteria, and reports the first functional heterologous expression of a cyanobacterial TonB-dependent transporter and establishes Synechocystis as a promising platform for cyanobacterial xenosiderophore-uptake studies.

Multiomics Identification and Structural Dynamics of PeXyn1: A Novel GH11 Xylanase from Pleurotus eryngii for Substrate Utilization.

This work offers the first molecular insight into P. eryngii xylanases, highlighting PeXyn1 for agro-waste valorization and multiivalent interactions at the CBM1-catalytic interface restrict structural fluctuations, promoting a stable conformation.

AlphaFold-driven structural proteomics reveals extensive cellulosome machinery in human ruminococcal symbionts

ABSTRACT Cellulosomes are large, surface-displayed enzyme complexes that enable anaerobic bacteria to degrade recalcitrant plant polysaccharides, yet cellulosome-expressing bacteria are thought to be rare in the human gut. Here, we show that extensive sequence divergence obscures the detection of many ruminococcal cellulosomes by conventional sequence homology-based methods. Using proteome-scale AlphaFold2 structural predictions, we uncovered a substantially expanded set of putative cellulosome-producing Ruminococcus species, including six previously unrecognized human symbionts. Structure-based clustering identifies several novel cohesin families that retain conserved folds despite extreme sequence divergence and define distinct, phylogenetically conserved cellulosome architectures. The analysis reveals R. callidus and related human symbionts encode elaborate cellulosomes that are invisible to sequence-based annotation. Similarly, R. difficilis, a human gut symbiont, has been found to possess genes for an atypical cohesin-based assembly enriched in amylases and related starch-binding proteins, which may enable this microbe to degrade resistant starches that evade digestion in the upper gastrointestinal tract. Together, these findings reveal that ruminococcal cellulosomes are far more prevalent and diverse than previously appreciated and demonstrate the power of structural proteomics to uncover deeply divergent functional systems in the gut microbiome. IMPORTANCE Plant cell wall polysaccharides are a major dietary carbon source, yet their degradation relies on rare, highly specialized microbial enzyme assemblies known as cellulosomes, which have long been considered uncommon in the human gut. Using proteome-scale structure prediction combined with experimental validation, we show that cellulosomes are far more widespread and structurally diverse in human-associated Ruminococcus species than previously appreciated. We identify multiple new cohesin families and reveal distinct cellulosome architectures likely adapted to degrade different dietary substrates. Together, these findings redefine the distribution and evolution of cellulosomes in gut microbes and demonstrate the power of structural proteomics to uncover deeply diverged biological systems. Plant cell wall polysaccharides are a major dietary carbon source, yet their degradation relies on rare, highly specialized microbial enzyme assemblies known as cellulosomes, which have long been considered uncommon in the human gut. Using proteome-scale structure prediction combined with experimental validation, we show that cellulosomes are far more widespread and structurally diverse in human-associated Ruminococcus species than previously appreciated. We identify multiple new cohesin families and reveal distinct cellulosome architectures likely adapted to degrade different dietary substrates. Together, these findings redefine the distribution and evolution of cellulosomes in gut microbes and demonstrate the power of structural proteomics to uncover deeply diverged biological systems.