Aromatic amino acids in the cellulose binding domain of Penicillium crustosum endoglucanase EGL1 differentially contribute to the cellulose affinity of the enzyme

Genome-wide analysis of Flavobacterium strain YJ01 demonstrates abundant enzymes synergistically degrade diverse nature carbohydrates

AIMS

Flavobacterium strains are widely distributed in various environments and generally exhibit specialized roles in the degradation of complex organic substrates. To obtain a deeper understanding of their enzyme profiles, patterns of action on natural carbohydrates degradation, and to mine gene resources for biomass conversion.

METHODS AND RESULTS

We sequenced the whole genome of a novel carbohydrate-degrading Flavobacterium sp. strain YJ01. The genome size of strain YJ01 was 5.48 Mb and encoded 4674 predicted genes. Comparative genomic analysis revealed Flavobacterium strains were characterized by the presence of abundant genes associated with catalytic activity and metabolic processes, especially carbohydrate metabolism. About 9% of genes of strain YJ01 encoded carbohydrate-active enzymes. These enzymes can act on various complex natural and cellular carbohydrates. The synergistic effect of the enzymes on the hydrolysis of complex natural polysaccharides was further experimentally evidenced by using starch and xylan as substrates, in which the degradation rate of an enzyme combination was ~10-fold higher than that of the single enzyme.

CONCLUSIONS

Flavobacterium sp. strain YJ01 has a high degree of catalytic and metabolic activity toward carbohydrates, and it harbors abundant, complete, and efficient enzymes for mediating complex polysaccharide degradation. These enzymes, acting synergistically on complex substrates, greatly improved the efficiency of digestion, which may be associated with the extensive ecological adaptability of Flavobacterium, which genetically heterologous divergent from extremely environments origin Flavobacterium strains.

A dual-sensing strategy for the early diagnosis of urinary tract infections via detecting biofilm cellulose using aromatic amino acid-capped Au and Ag nanoparticles

Currently, urinary tract infection (UTI) diagnosis focuses on planktonic cell detection rather than biofilm detection, but the facile identification of UPEC bacterial biofilms is crucial in UTI diagnosis as the biofilm formed by bacteria is the causative agent of recurrent and chronic UTIs. Therefore, in this work, we developed a simple, cost-effective, colorimetric, and electrochemical-based strategy for the detection of cellulose in urine. Cellulose, a biofilm matrix component, was detected using tyrosine-capped gold and silver nanoparticles through a visible colorimetric change with a decrease in the absorbance intensity and a decrease in current response in the case of cyclic voltammetry. The sensor displayed a linear detection range of 10-70 mg mL-1 for colorimetry and 10-300 μg mL-1 for cyclic voltammetry with a good selectivity of <2.8% and a recovery rate of 95-100% in real-time sample analysis. Moreover, the binding affinity of cellulose with tyrosine was investigated using molecular docking studies to validate the sensing mechanism. We anticipate that our work will aid clinicians in the implementation of rapid, cost-effective, and definitive diagnosis of UTIs.

Role of Natural Binding Proteins in Therapy and Diagnostics

This review systematically investigates the critical role of natural binding proteins (NBPs), encompassing DNA-, RNA-, carbohydrate-, fatty acid-, and chitin-binding proteins, in the realms of oncology and diagnostics. In an era where cancer continues to pose significant challenges to healthcare systems worldwide, the innovative exploration of NBPs offers a promising frontier for advancing both the diagnostic accuracy and therapeutic efficacy of cancer management strategies. This manuscript provides an in-depth examination of the unique mechanisms by which NBPs interact with specific molecular targets, highlighting their potential to revolutionize cancer diagnostics and therapy. Furthermore, it discusses the burgeoning research on aptamers, demonstrating their utility as 'nucleic acid antibodies' for targeted therapy and precision diagnostics. Despite the promising applications of NBPs and aptamers in enhancing early cancer detection and developing personalized treatment protocols, this review identifies a critical knowledge gap: the need for comprehensive studies to understand the diverse functionalities and therapeutic potentials of NBPs across different cancer types and diagnostic scenarios. By bridging this gap, this manuscript underscores the importance of NBPs and aptamers in paving the way for next-generation diagnostics and targeted cancer treatments.

Deconstruction and Reassembly of Renewable Polymers and Biocolloids into Next Generation Structured Materials

This review considers the most recent developments in supramolecular and supraparticle structures obtained from natural, renewable biopolymers as well as their disassembly and reassembly into engineered materials. We introduce the main interactions that control bottom-up synthesis and top-down design at different length scales, highlighting the promise of natural biopolymers and associated building blocks. The latter have become main actors in the recent surge of the scientific and patent literature related to the subject. Such developments make prominent use of multicomponent and hierarchical polymeric assemblies and structures that contain polysaccharides (cellulose, chitin, and others), polyphenols (lignins, tannins), and proteins (soy, whey, silk, and other proteins). We offer a comprehensive discussion about the interactions that exist in their native architectures (including multicomponent and composite forms), the chemical modification of polysaccharides and their deconstruction into high axial aspect nanofibers and nanorods. We reflect on the availability and suitability of the latter types of building blocks to enable superstructures and colloidal associations. As far as processing, we describe the most relevant transitions, from the solution to the gel state and the routes that can be used to arrive to consolidated materials with prescribed properties. We highlight the implementation of supramolecular and superstructures in different technological fields that exploit the synergies exhibited by renewable polymers and biocolloids integrated in structured materials.

Analysis of the phosphorylome of trichoderma reesei cultivated on sugarcane bagasse suggests post-translational regulation of the secreted glycosyl hydrolase Cel7A

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Phosphorylome of Trichoderma reesei reveals phosphosites in some glycosyl hydrolases.

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Phosphoserine and phosphothreonine is the major phosphosites identified.

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Protein Kinase C is the most frequently predicted kinase in phosphorylome.

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The cellulase Cel7A activity is affected by dephosphorylation.

Trichoderma reesei is one of the major producers of holocellulases. It is known that in T. reesei, protein production patterns can change in a carbon source-dependent manner. Here, we performed a phosphorylome analysis of T. reesei grown in the presence of sugarcane bagasse and glucose as carbon source. In presence of sugarcane bagasse, a total of 114 phosphorylated proteins were identified. Phosphoserine and phosphothreonine corresponded to 89.6% of the phosphosites and 10.4% were related to phosphotyrosine. Among the identified proteins, 65% were singly phosphorylated, 19% were doubly phosphorylated, 12% were triply phosphorylated, and 4% displayed even higher phosphorylation. Seventy-five kinases were predicted to phosphorylate the sites identified in this work, and the most frequently predicted serine/threonine kinase was PKC1. Among phosphorylated proteins, four glycosyl hydrolases were predicted to be secreted. Interestingly, Cel7A activity, the most secreted protein, was reduced to approximately 60% after in vitro dephosphorylation, suggesting that phosphorylation might alter Cel7A structure, substrate affinity, and targeting of the substrate to its carbohydrate-binding domain. These results suggest a novel post-translational regulation of Cel7A.

Immobilization and enzymatic properties of glutamate decarboxylase from Enterococcus faecium by affinity adsorption on regenerated chitin

Glutamate decarboxylase (GAD, EC 4.1.1.15) is an important enzyme in gamma-aminobutyric acid biosynthesis and DL-glutamic acid resolution. In this study, the Enterococcus faecium-derived GAD was successfully immobilized by regenerated chitin (RC) via specific adsorption of cellulose-binding domain (CBD). The optimal binding buffer was 20 mmol/L phosphate buffer saline (pH 8.0), and the RC binding capacity was 1.77 ± 0.11 mg_cbd-gad/g_rc under this condition. The ratio of wet RC and crude enzyme solution used for immobilization was recommended to 3:50 (g/mL). To evaluate the effect of RC immobilization on GAD, properties of the immobilize GAD (RC-CBD-GAD) were investigated. Results indicated RC-CBD-GAD was relatively stable at pH 4.4-5.6 and temperature - 20-40 °C, and the optimal reaction pH value and temperature were pH 4.8 and 50 °C, respectively. When it was reacted with 5 mmol/L of follow chemical reagents respectively, the activity of RC-CBD-GAD was hardly affected by EDTA, KCl, and NaCl, and significantly inactivated by AgNO₃, MnSO₄, MgSO₄, CuSO₄, ZnSO₄, FeCl₂, FeCl₃, AlCl₃, CaCl_2, and Pb(CH₃COO)₂. The apparent K_m and V_max were 28.35 mmol/L and 147.06 μmol/(g_RC-CBD-GAD·min), respectively. The optimum time for a batch of catalytic reaction without exogenous pH control was 2 h. Under this reaction time, RC-CBD-GAD had a good reusability with a half-life of 23 cycles, indicating that it was very attractive for GABA industry. As a novel, efficient, and green CBD binding carrier, RC provides an alternative way to protein immobilization.