Chitin Prevalence and Function in Bacteria, Fungi and Protists

Direct laser infrared microscopy for the monitoring of microplastics in Holothuria poli and sediments of the Mar Menor coastal lagoon

Plastics represent a major threat to marine and terrestrial ecosystems if they are not recycled or disposed properly. Plastics undergo processes of physical erosion and chemical degradation, generating one of the most worrying emerging pollutants: microplastics (MPs), which may be incorporated into the food chain through ingestion by the different organisms that live in that habitat. This study investigates the possible accumulation of MPs in the gut content and integument of deposit feeder sea cucumbers, Holothuria poli Delle Chiaje, 1824 from the Mar Menor lagoon, as well as in the sediments of the areas they inhabit, using laser direct infrared microscopy (LDIR) technique. LDIR is a novel methodology based on illuminating samples with a mid-infrared quantum cascade laser, which was applied to analyse the chemical composition of MPs, as well as their size and shape. This technique offers high sensitivity and selectivity in the measurement of MPs. The most effective sample procedures involved the addition of 3 mL of HNO3 for 48 h at 65 ºC for integument samples (1 g) and 4 mL of H2O2 for 2 h at 65 ºC for sediment and gut content samples (1 g), with subsequent density flotation process for these two last matrices. The presence of MPs in all analysed samples was confirmed through the proposed methodology, especially polyamide and polyethylene particles, confirming the accumulation of these materials in the marine organism and the sediments. These results are key to understand MPs pollution in marine ecosystems and its possible impact on marine fauna.

Proteomic insights into nematode-trapping fungi Arthrobotrys oligospora after their response to chitin

Introduction

Nematode-trapping fungi (NTFs) can produce various chitinases to degrade nematode body wall and eggshell chitin during predation. However, the regulatory mechanisms of their expression of chitinases still remain unclear. The primary objective of this study was to elucidate the differential protein profile of A. oligospora, an NTF, in response to chitin.

Material and Methods

Colloidal chitin was added to induce the culture of A. oligospora, and the phenotypic differences before and after induction were observed under inverted microscope. The differential proteins before and after mycelium induction were screened by liquid chromatography-tandem mass spectrometry. The differentially expressed chitinase was expressed in Pichia yeast, and the recombinant enzyme was incubated with Caenorhabditis elegans and its egg suspension to explore its biological activity.

Results

It was found that there was a significant acceleration in the mycelial growth post chitin interaction in A. oligospora. A total of 1,124 differentially expressed proteins (DEPs) were identified between the control group (AO-c) and the experimental group (AO-e), with 183 upregulated and 941 downregulated. Gene Ontology analysis revealed that the DEPs acted in various metabolic processes with catalysis and binding functions. Kyoto Encyclopedia of Genes and Genomes analysis associated these proteins primarily with signalling pathways related to glucose metabolism. Three chitinases were significantly modulated among DEPs. Moreover, enzymatic activity assays demonstrated that one of them effectively degraded C. elegans and its eggs.

Conclusion

These findings suggest that A. oligospora can significantly alter its protein expression profile in response to chitin, thereby facilitating its sugar metabolism and mycelial development. Our study provided new insights into the regulatory mechanisms of nematode predation in A. oligospora.

Decoding the Nature of the Peritrich Stalk: A Distinctive Organelle in a Large Group of Ciliated Unicellular Eukaryotes

Ciliates represent a diverse assemblage of ancient single-celled eukaryotes characterized by diverse morphological features. Among certain sessilid peritrich ciliates, an exceptional morphological structure known as the stalk has been documented since the pioneering work of Antonie van Leeuwenhoek in the 17th century. This study conducts a comparative genomic analysis of three sessile peritrich species-Epistylis sp., Vorticella campanula, and Zoothamnium arbuscula-and two free-swimming species, Tetrahymena thermophila and Paramecium tetraurelia, within the class Oligohymenophorea. We find that carbohydrate-related components are consistently associated with diverse stalk substructures. Evidence suggests that the branched stalks of colonial E. hentscheli are supported by chitin-based ring-like structures. Through proteomic analysis of the Epistylis stalk, we found peritrich-specific genes, including coiled-coil domain-containing (CCDC) proteins and epidermal growth factor-like (EGF-like) proteins, as key stalk components. CCDC proteins are part of the stalk sheath, and their N-glycosylation may enhance adhesion between the cell body and stalk through lectin interactions. This study sheds light on the genetic innovations behind the stalk in peritrichs, which support their sessile and colonial lifestyles, and identifies peritrich-specific CCDC proteins as potential targets for disrupting the attachment of sessilids to aquaculture animals, addressing issues related to epibiotic burden.

Mining, Identification, and Fermentation Optimization of Chitin Deacetylase from a Novel Strain Enterobacter sp. ZCDA27

Chitin, a natural organic compound with content slightly lower than cellulose, is also known for chitosan, a substance derived from chitin through deacetylation. In this experiment, preliminary screening was conducted using the plate discoloration circle method, leading to the selection of a high-yield CDA-producing strain from 28 candidates through rescreening. Morphological characteristics and 16S rDNA sequence analysis revealed 99.93% homology with Enterobacter sichuanensis strain N24, thus naming this strain Enterobacter strain ZCDA27. Initial fermentation of the strain yielded CDA activity of 9.29 U/mL. Single-factor optimization was then performed, followed by a PB test to screen for significant factors affecting enzyme production. The response surface method was used to further optimize the fermentation conditions. The optimal fermentation conditions for the carbon source, nitrogen source, metal ion, fermentation temperature, time, liquid volume, and initial pH were explored. Significant factors affecting enzyme production, including MgSO4, initial medium pH, and fructose levels, were identified using the PB test. Finally, the fermentation conditions of ZCDA27 were optimized using the Box-Behnken design combined with RSM, which comprised fructose at 1.020%, magnesium sulfate at 0.016%, and peptone at 1%. The fermentation conditions included a temperature of 37, initial pH of 7.1, rotation speed of 140 × g, fermentation time of 28 h, inoculation amount of 2%, and liquid volume of 40%. Under these conditions, the enzyme activity of ZCDA27 reached 14.52 U/mL, a 1.6-fold increase from the pre-optimization levels. In summary, this study provides an experimental foundation for further development and application of Enterobacter spp. ZCDA27 CDA.

Affinity molecular assay for detecting Candida albicans using chitin affinity and RPA-CRISPR/Cas12a

Invasive fungal infections (IFIs) pose a significant threat to immunocompromised individuals, leading to considerable morbidity and mortality. Prompt and accurate diagnosis is essential for effective treatment. Here we develop a rapid molecular diagnostic method that involves three steps: fungal enrichment using affinity-magnetic separation (AMS), genomic DNA extraction with silicon hydroxyl magnetic beads, and detection through a one-pot system. This method, optimized to detect 30 CFU/mL of C. albicans in blood and bronchoalveolar lavage (BAL) samples within 2.5 h, is approximately 100 times more sensitive than microscopy-based staining. Initial validation using clinical samples showed 93.93% sensitivity, 100% specificity, and high predictive values, while simulated tests demonstrated 95% sensitivity and 100% specificity. This cost-effective, highly sensitive technique offers potential for use in resource-limited clinical settings and can be easily adapted to differentiate between fungal species and detect drug resistance.

Polymer degrading marine Microbulbifer bacteria: an un(der)utilized source of chemical and biocatalytic novelty

Microbulbifer is a genus of halophilic bacteria that are commonly detected in the commensal marine microbiomes. These bacteria have been recognized for their ability to degrade polysaccharides and other polymeric materials. Increasingly, Microbulbifer genomes indicate these bacteria to be an untapped reservoir for novel natural product discovery and biosynthetic novelty. In this review, we summarize the distribution of Microbulbifer bacteria, activities of the various polymer degrading enzymes that these bacteria produce, and an up-to-date summary of the natural products that have been isolated from Microbulbifer strains. We argue that these bacteria have been hiding in plain sight, and contemporary efforts into their genome and metabolome mining are going to lead to a proliferation of Microbulbifer-derived natural products in the future. We also describe, where possible, the ecological interactions of these bacteria in marine microbiomes.

Electrolysis as a Universal Approach for Isolation of Diverse Chitin Scaffolds from Selected Marine Demosponges

Three-dimensional chitinous scaffolds often used in regenerative medicine, tissue engineering, biomimetics and technology are mostly isolated from marine organisms, such as marine sponges (Porifera). In this work, we report the results of the electrochemical isolation of the ready to use chitinous matrices from three species of verongiid demosponges (Aplysina archeri, Ianthella basta and Suberea clavata) as a perfect example of possible morphological and chemical dimorphism in the case of the marine chitin sources. The electrolysis of concentrated Na2SO4 aqueous solution showed its superiority over the chemical chitin isolation method in terms of the treatment time reduction: only 5.5 h for A. archeri, 16.5 h for I. basta and 20 h for the S. clavata sample. Further investigation of the isolated scaffolds by digital microscopy and SEM showed that the electrolysis-supported isolation process obtains chitinous scaffolds with well-preserved spatial structure and it can be competitive to other alternative chitin isolation techniques that use external accelerating factors such as microwave irradiation or atmospheric plasma. Moreover, the infrared spectroscopy (ATR-FTIR) proved that with the applied electrochemical conditions, the transformation into chitosan does not take place.

Structural basis for inhibition and regulation of a chitin synthase from Candida albicans

Chitin is an essential component of the fungal cell wall. Chitin synthases (Chss) catalyze chitin formation and translocation across the membrane and are targets of antifungal agents, including nikkomycin Z and polyoxin D. Lack of structural insights into the action of these inhibitors on Chs has hampered their further development to the clinic. We present the cryo-EM structures of Chs2 from Candida albicans (CaChs2) in the apo, substrate-bound, nikkomycin Z-bound, and polyoxin D-bound states. CaChs2 adopts a unique domain-swapped dimer configuration where a conserved motif in the domain-swapped region controls enzyme activity. CaChs2 has a dual regulation mechanism where the chitin translocation tunnel is closed by the extracellular gate and plugged by a lipid molecule in the apo state to prevent non-specific leak. Analyses of substrate and inhibitor binding provide insights into the chemical logic of Chs inhibition, which can guide Chs-targeted antifungal development.

Differentiation and classification of bacterial endotoxins based on surface enhanced Raman scattering and advanced machine learning

Bacterial endotoxin, a major component of the Gram-negative bacterial outer membrane leaflet, is a lipopolysaccharide shed from bacteria during their growth and infection and can be utilized as a biomarker for bacterial detection. Here, the surface enhanced Raman scattering (SERS) spectra of eleven bacterial endotoxins with an average detection amount of 8.75 pg per measurement have been obtained based on silver nanorod array substrates, and the characteristic SERS peaks have been identified. With appropriate spectral pre-processing procedures, different classical machine learning algorithms, including support vector machine, k-nearest neighbor, random forest, etc., and a modified deep learning algorithm, RamanNet, have been applied to differentiate and classify these endotoxins. It has been found that most conventional machine learning algorithms can attain a differentiation accuracy of >99%, while RamanNet can achieve 100% accuracy. Such an approach has the potential for precise classification of endotoxins and could be used for rapid medical diagnoses and therapeutic decisions for pathogenic infections.

Influence of ultrasonic pretreatments on microwave hot-air flow rolling drying mechanism, thermal characteristics and rehydration dynamics of Pleurotus eryngii

BACKGROUND

In order to improve the drying efficiency and reduce the drying energy consumption of Pleurotus eryngii, microwave hot-air flow rolling drying (MHARD) coupled with ultrasonic pretreating time (0, 20, 40, and 60 min) was used to investigate the drying profile, thermal characteristics, water migration, microstructure and rehydration dynamics of P. eryngii using differential scanning calorimetry (DSC), low-field nuclear magnetic resonance (LF-NMR) analysis and scanning electron microscopy (SEM).

RESULTS

Results showed that the drying time of P. eryngii was 80, 70, 60 and 50 min, accordingly. Energy consumption was significantly reduced by ultrasonic pretreatment, and moisture effective diffusivity (D_eff ) was increased with the increase of ultrasonic pretreating time. DSC curves showed that the drying process was accelerated by ultrasonic pretreatment significantly by enhancing the heat transfer. Meanwhile, SEM images showed that the cell was broken and numbers of irregular holes appeared in the ultrasound-pretreated samples. In terms of rehydration dynamics, Page model could well model the rehydration kinetics of dried P. eryngii with R²  > 0.99.

CONCLUSION

The findings indicate that ultrasonic pretreatment is a promising method for MHARD of P. eryngii as it can enhance the drying process, and show potential for industrial application. © 2021 Society of Chemical Industry.

The Under-explored Extracellular Proteome of Aero-Terrestrial Microalgae Provides Clues on Different Mechanisms of Desiccation Tolerance in Non-Model Organisms

Trebouxia sp. (TR9) and Coccomyxa simplex (Csol) are desiccation-tolerant lichen microalgae with different adaptive strategies in accordance with the prevailing conditions of their habitats. The remodelling of cell wall and extracellular polysaccharides depending on water availability are key elements in the tolerance to desiccation of both microalgae. Currently, there is no information about the extracellular proteins of these algae and other aero-terrestrial microalgae in response to limited water availability. To our knowledge, this is the first report on the proteins associated with the extracellular polymeric substances (EPS) of aero-terrestrial microalgae subjected to cyclic desiccation/rehydration. LC-MS/MS and bioinformatic analyses of the EPS-associated proteins in the two lichen microalgae submitted to four desiccation/rehydration cycles allowed the compilation of 111 and 121 identified proteins for TR9 and Csol, respectively. Both sets of EPS-associated proteins shared a variety of predicted biological functions but showed a constitutive expression in Csol and partially inducible in TR9. In both algae, the EPS-associated proteins included a number of proteins of unknown functions, some of which could be considered as small intrinsically disordered proteins related with desiccation-tolerant organisms. Differences in the composition and the expression pattern between the studied EPS-associated proteins would be oriented to preserve the biochemical and biophysical properties of the extracellular structures under the different conditions of water availability in which each alga thrives.

Intestinal Population in Host with Metabolic Syndrome during Administration of Chitosan and Its Derivatives

Chitosan and its derivatives can alleviate metabolic syndrome by different regulation mechanisms, phosphorylation of AMPK (AMP-activated kinase) and Akt (also known as protein kinase B), suppression of PPAR-γ (peroxisome proliferator-activated receptor-γ) and SREBP-1c (sterol regulatory element–binding proteins), and translocation of GLUT4 (glucose transporter-4), and also the downregulation of fatty-acid-transport proteins, fatty-acid-binding proteins, fatty acid synthetase (FAS), acetyl-CoA carboxylase (acetyl coenzyme A carboxylase), and HMG-CoA reductase (hydroxy methylglutaryl coenzyme A reductase). The improved microbial profiles in the gastrointestinal tract were positively correlated with the improved glucose and lipid profiles in hosts with metabolic syndrome. Hence, this review will summarize the current literature illustrating positive correlations between the alleviated conditions in metabolic syndrome hosts and the normalized gut microbiota in hosts with metabolic syndrome after treatment with chitosan and its derivatives, implying that the possibility of chitosan and its derivatives to serve as therapeutic application will be consolidated. Chitosan has been shown to modulate cardiometabolic symptoms (e.g., lipid and glycemic levels, blood pressure) as well as gut microbiota. However, the literature that summarizes the relationship between such metabolic modulation of chitosan and prebiotic-like effects is limited. This review will discuss the connection among their structures, biological properties, and prebiotic effects for the treatment of metabolic syndrome. Our hope is that future researchers will consider the prebiotic effects as significant contributors to the mitigation of metabolic syndrome.

A thermophilic chitinase 1602 from the marine bacterium Microbulbifer sp. BN3 and its high-level expression in Pichia pastoris

Chitinases play an important role in many industrial processes, including the preparation of oligosaccharides with potential applications. In the present study, a 1,713 bp gene of Chi1602, derived from a marine bacterium Microbulbifer sp. BN3, encoding a GH18 family chitinase, was expressed at high levels in Pichia pastoris. Distinct from most of the marine chitinases, the recombinant chitinase 1602 exhibited maximal activity at 60 °C and over a broad pH range between 5.0 and 9.0, and was stable at 50 °C and over the pH range 4.0-9.0. The hydrolytic products derived from colloidal chitins comprised mainly (GlcNAc)₂ and GlcNAc, indicating that rChi1602 is a GH18 processive chitinase in conformity with its hypothetical structure. However, rChi1602 showed traces of β-N-acetylglucosaminidase activity on substrates such as powder chitin, chitosan, and ethylene glycol chitin. The thermophilic rChi1602, which manifests adaptation to a wide pH range and can be expressed at a high level in P. pastoris, is advantageous for applications in industrial processes.