A minimal cellulosome‐like system in Cellulosilyticum lentocellum

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.

Discovery of a multifunctional chitinase-cellulase from Thermococcus chitonophagus with expanded polysaccharide specificity.

BACKGROUND The discovery of novel biocatalysts for the sustainable valorization of complex biomass feedstocks remains a significant challenge. Domain-centric exploration of characterized CAZyme families offers a promising but underexplored strategy for identifying enzymes with unusual architectures and potentially expanded substrate specificities. RESULTS Systematic analysis of archaeal glycoside hydrolase family 18 (GH18) chitinases using the CANDy domain annotation pipeline led to the identification of TcChi from Thermococcus chitonophagus, a multidomain enzyme combining a GH12 and a GH18 catalytic domain alongside two carbohydrate-binding modules. Given that T. chitonophagus also encodes dedicated standalone cellulases and chitinases, we hypothesized that this multidomain assembly may have evolved a broader functional range than either composing domain alone. Biochemical assays of truncated constructs confirmed this hypothesis: the GH18 domain hydrolyzed chitin, chitosan, and β-1,3-glucan, marking the first report of β-1,3-glucanase activity (EC 3.2.1.58) in a GH18 chitinase, while the GH12 domain exhibited strong cellulase activity alongside unexpected chitosanase activity (EC 3.2.1.132), extending the known functional range of this family. Both domains demonstrated high thermostability consistent with the hyperthermophilic origin of T. chitonophagus. CONCLUSIONS TcChi is a thermostable, multifunctional biocatalyst capable of degrading chitin, chitosan, cellulose, and β-1,3-glucan from a single protein scaffold, making it a promising candidate for consolidated biomass deconstruction and waste valorization. These findings also demonstrate that domain-centric analysis of CAZyme families is an effective strategy for uncovering hidden functional diversity in well-characterized enzyme families.

Site-specific processing of phosphoethanolamine cellulose by the BcsZ cellulase reveals stochastic biofilm cellulose modification

Cellulose is a common component of bacterial biofilms where it interacts with other biopolymers to form a 3-dimensional matrix enclosing the bacteria. Synthesized and secreted by the synthase-dependent biosynthesis pathway common to many bacterial exopolysaccharides, its surface exposure depends on the presence of the periplasmic cellulase BcsZ. During export across the periplasm, E. coli and other Enterobacteriaceae modify cellulose with lipid-derived phosphoethanolamine (pEtN). How BcsZ hydrolyzes pEtN-cellulose in the periplasm is unknown and so is the native distribution pattern of pEtN on cellulose. Here, we used carbohydrate synthesis, X-ray crystallography, native mass spectrometry, and super-resolution MINFLUX nanoscopy to delineate BcsZ’s role during cellulose biosynthesis. Crystal structures of BcsZ bound to chemically synthesized pEtN cello-oligosaccharides identify how the enzyme recognizes pEtN-modified glucosyl units. Comparing mono and double substituted cellohexaoses, we identify varying binding poses that are determined by two pEtN coordination sites within BcsZ’s catalytic pocket. Combined, our structural analyses reveal an ideal BcsZ cellohexaose ligand containing two pEtN modified units separated by an unmodified cellotriosyl unit. The enzyme binds and hydrolyzes this compound with substantially increased affinity and efficiency. Further, BcsZ digestion of native pEtN cellulose combined with native mass spectrometry analyses reveals the stochastic distribution of pEtN on biofilm cellulose. Additionally, MINFLUX co-localization of BcsZ with other components of the biosynthetic complex demonstrates BcsZ’s random distribution across the periplasm. Our data suggest BcsZ functions independently of the biosynthetic complex to clear mislocalized pEtN cellulose from the periplasm. Significance Statement Biofilms are an abundant form of bacterial growth and responsible for the majority of hospital-derived infections. Uropathogenic E. coli produces phosphoethanolamine cellulose as a stabilizing extracellular polysaccharide. Surprisingly, the periplasmic cellulase BcsZ, encoded in the cellulose biosynthesis operon, is necessary for efficient bacterial cellulose production. Crystal structures of BcsZ bound to chemically synthesized phosphoethanolamine cellulose fragments reveal how the enzyme recognizes and cleaves its unique substrate. Further, super-resolution fluorescence microscopy shows that BcsZ does not form a stable complex with other cellulose synthase components and likely diffuses in the E. coli periplasm. Finally, mass spectrometry of oligosaccharides released by BcsZ from biofilm E. coli indicates the stochastic modification of cellulose with phosphoethanolamine groups in vivo.

Bacterial Geosmin Biosynthesis is Compartmentalized Inside a Two-Component Protein Shell

Cellulosome engineering as biological macromolecular assembly for lignocellulose deconstruction: Structure, interactions, and functional design.

Lignocellulosic biomass is a heterogeneous solid matrix whose biological deconstruction is limited by cellulose accessibility, lignin exposure, pore-scale transport, and enzyme stability at solid-liquid interfaces. Although bacterial cellulosomes provide a natural strategy for organizing multiple enzymes through scaffoldin-mediated cohesin-dockerin interactions, their engineering value depends on more than enzyme colocalization. This review frames cellulosome engineering as a process-aware macromolecular assembly problem, in which catalytic balance, substrate targeting, assembly size, inter-domain spacing, and environmental robustness must be optimized together. Natural cellulosome architecture is discussed in terms of its roles in enzyme recruitment and catalytic synergy. In addition, cellulosomal systems are compared with industrial fungal enzyme cocktails regarding production, scalability, and substrate accessibility. Rather than viewing engineered cellulosomes as universally superior multienzyme complexes, we evaluate how their performance is constrained by lignin adsorption, steric exclusion, diffusion limitations, high-solids conditions, host burden, catalyst recovery, AI-guided design validation, and the mismatch between model substrates and industrial feedstocks. Future progress will require experimentally validated, substrate-specific, and process-compatible cellulosome designs that balance catalytic diversity with assembly stability, production feasibility, and techno-economic performance.

A novel family of fungal protein biosurfactants: Discovery and sustainable production.

Protein-based biosurfactants remain underexplored compared to glycolipids and lipopeptides, despite their unique interfacial properties and self-assembly behavior. PAC3, a surface-active protein produced by the marine fungus Acremonium sclerotigenum, exhibits dual behavior as both a biosurfactant and bioemulsifier. For this reason, it can be seen as a high molecular weight proteinaceous compound, able to efficiently reduce surface tension. Here, we identify PAC3 as the first member of a previously unrecognized family of fungal protein biosurfactants. The complete amino acid sequence of PAC3 was determined through a combined de novo transcriptomic and mass spectrometry approach, revealing an 83-residue protein that lacks the canonical eight-cysteine motif typical of hydrophobins, the most surface-active proteins known. Sequence, phylogenetic, and structural analyses revealed a distinct fold and amphipathic architecture, with a negatively charged surface and a hydrophobic planar region, providing a molecular basis for its strong interfacial activity. The identification of homologous sequences across fungi supports the existence of a novel protein family. Notably, we show through spectroscopy and confocal microscopy that PAC3 fibrils exhibit deep-blue intrinsic fluorescence, a property recently associated with amyloid architecture. To support industrial application, we developed a simplified downstream process based on methanol/chloroform extraction, reducing costs while preserving functionality. In parallel, the use of waste frying oil enhanced fungal biomass production and supported efficient PAC3 synthesis, demonstrating a sustainable production strategy. Overall, this study introduces a new class of fungal biosurfactant proteins and provides a foundation for their biotechnological exploitation.