Statistical optimization for production of chitin deacetylase from Rhodococcus erythropolis HG05

A new strain of Rhodococcus indonesiensis T22.7.1T and its functional potential for deacetylation of chitin and chitooligsaccharides

Introduction

Chitin, abundant in marine environments, presents significant challenges in terms of transformation and utilization. A strain, T22.7.1T, with notable chitin deacetylation capabilities, was isolated from the rhizosphere of Acanthus ebracteatus in the North Sea of China. Comparative 16S rDNA sequence analysis showed that the new isolate had the highest sequence similarity (99.79%) with Rhodococcus indonesiensis CSLK01-03T, followed by R. ruber DSM 43338T, R. electrodiphilus JC435T, and R. aetherivorans 10bc312T (98.97%, 98.81%, and 98.83%, respectively). Subsequent genome sequencing and phylogenetic analysis confirmed that strain T22.7.1T belongs to the R. indonesiensis species. However, additional taxonomic characterization identified strain T22.7.1T as a novel type strain of R. indonesiensis distinct from CSLK01-03T.

Methods

This study refines the taxonomic description of R. indonesiensis and investigates its application in converting chitin into chitosan. The chitin deacetylase (RiCDA) activity of strain T22.7.1T was optimized, and the enzyme was isolated and purified from the fermentation products.

Results

Through optimization, the RiCDA activity of strain T22.7.1T reached 287.02 U/mL, which is 34.88 times greater than the original enzyme's activity (8.0 U/mL). The natural CDA enzyme was purified with a purification factor of 31.83, and the specific activity of the enzyme solution reached 1200.33 U/mg. RiCDA exhibited good pH and temperature adaptability and stability, along with a wide range of substrate adaptabilities, effectively deacetylating chitin, chitooligosaccharides, N-acetylglucosamine, and other substrates.

Discussion

Product analysis revealed that RiCDA treatment increased the deacetylation degree (DD) of natural chitin to 83%, surpassing that of commercial chitosan. Therefore, RiCDA demonstrates significant potential as an efficient deacetylation tool for natural chitin and chitooligosaccharides, highlighting its applicability in the biorefining of natural polysaccharides.

Extraction of chitosan from biologically-derived chitin by bacterial chitin deacetylase: Process optimization and product quality assessment

Commercial chitosan manufacturing process relies on strong chemical treatment on chitin that generates chitosan with undesirable properties and leads to environmental pollution. To overcome the adverse consequences, enzymatic chitosan preparation from chitin was undertaken in the current study. A potent chitin deacetylase (CDA) producing bacterial strain was screened and subsequently identified as Alcaligens faecalis CS4. After optimization 40.69 U/ml of CDA production was achieved. By treating the organically extracted chitin with partially purified CDA chitosan yield of 19.04 % was attained having 71 % solubility, 74.9 % degree of deacetylation, 21.16 % crystallinity index, 246.4 kDa molecular weight and 298 °C highest-decomposition temperature. FTIR and XRD analysis revealed characteristics peaks respectively within 870-3425 cm^-1 wavenumber and 10°-20°, for enzymatically and chemically extracted (commercial) chitosan that endorses their structural similarity which validated through electron microscopic study. At 10 mg/ml chitosan concentration 65.49 % DPPH radical scavenging activity endorsed its antioxidant potential. Minimum inhibitory concentration of chitosan was 0.675, 1.75, 0.33 and 0.75 mg/ml for Streptococcus mutans, Enterococcus faecalis, Escherichia coli and Vibrio sp., respectively. Mucoadhesiveness and cholesterol binding properties were also exhibited by extracted chitosan. The present study opens a new vista for eco-friendly extraction of chitosan from chitin that is proficient and sustainable in environmental perspective.

Disruption of peritrophic matrix chitin metabolism and gut immune by chlorantraniliprole results in pathogenic bacterial infection in Bombyx mori

Chlorantraniliprole (CAP) is widely used in pest control, and its environmental residues affect the disease resistance of non-target insect silkworms. Studies have demonstrated that changes in gut microbial communities of insects are associated with susceptibility to pathogens. In the present study, we examined the effects of CAP exposure on the immune system and gut microbial community structure of silkworms. The results showed that after 96 h of exposure to low-concentration CAP, the peritrophic matrix (PM) of silkworm larvae was disrupted, and pathogenic bacteria invaded hemolymph. The trehalase activity in the midgut was significantly decreased, while the activities of chitinase, β-N-acetylglucosaminidase, and chitin deacetylase were increased considerably, resulting in decreased chitin content in PM. In addition, exposure to CAP reduced the expressions of key genes in the Toll, IMD, and JAK/STAT pathways, ultimately leading to the downregulation of antimicrobial peptides (AMPs) genes and alterations in the structure of the gut microbial community. Therefore, after infection with the conditional pathogen Enterobacter cloacae (E. cloacae), CAP-exposed individuals exhibited significantly lower body weight and higher mortality. These findings showed that exposure to low-concentration CAP impacted the biological defense system of silkworms, changed the gut microbial community structure, and increased silkworms' susceptibility to bacterial diseases. Collectively, these findings provided a new perspective for the safety evaluation of low-concentration CAP exposure in sericulture.

Chitin/chitosan extraction from shrimp shell waste by a completely biotechnological process

Two lactic bacteria were used in sequential co-cultures to demineralize (DM) and deproteinize (DP) shrimp shells (SS) to obtain chitin. During the first 24 h, Lactobacillus delbrueckii performed the DM in a minimal medium containing 100 g/L SS and 50 g/L glucose. Then, three different conditions were assayed to complete DM and perform the DP stage: 1) Bifidobacterium lactis was added with 35 g/L of glucose (Ld-G → Bl-G); 2) only B. lactis was added (Ld-G → Bl); and 3) a 35 g/L pulse of glucose was added, and at 48 h, B. lactis was inoculated (Ld-G → G → Bl). The highest DM (98.63 %) and DP (88 %) were obtained using a glucose pulse in the DM step and controlling the pH value above 6.0 in the DP step. Finally, a deacetylases cocktail produced by Aspergillus niger catalyzed the deacetylation of the resulting chitin. The chitosan samples had a deacetylation degree higher than 78 % and a solubility of 25 % in 1.0 N acetic acid. The deacetylation yield was 74 % after a mild chemical treatment, with a molecular weight of 71.31 KDa. This work reports an entirely biological process to get chitin and chitosan from SS with high yields.

Exploring new marine bacterial species, Alcaligenes faecalis Alca F2018 valued for bioconversion of shrimp chitin to chitosan for concomitant biotechnological applications

The exploitation of chitinous materials seems to be an infinite treasure. To this end, using shellfish waste as the sole carbon/nitrogen source solves environmental challenges while lowering microbial chitinase production costs. Bioconversion of shellfish chitin wastes such as shrimp shells has recently been investigated for the production of enzymes and bioactive materials in order to maximize the utilization of chitin-containing seafood processing wastes. In this study, the bioconversion of chitin to chitosan by Alcaligenes faecalis Alca F2018 revealed the highest chitin deacetylase (CDA) activity of 40.6 U/μg. The resulted low K_m and high V_max values explain the high affinity of the purified CDA to the p-nitroacetanilide substrate. CDA with a molecular weight of 66 KDa was purified from F2018 strain, with a 14.5% yield. FT-IR revealed distinct chitosan peaks and XRD revealed that chitosan samples had lower crystallinity than chitin. TGA analysis revealed that the recovered chitosan samples were more thermally stable. The deacetylation degree percentages of the produced chitosan are in the same range as that of the commercial chitosan, suggesting the promising potential of A. faecalis Alca F2018 to utilize shrimp shells in their raw form in the fermentation media based on its CDA enzyme activity.

Enhanced Chitin Deacetylase Production Ability of Rhodococcus equi CGMCC14861 by Co-culture Fermentation With Staphylococcus sp. MC7

Chitin deacetylase (CDA) can hydrolyze the acetamido group of chitin polymers and its deacetylated derivatives to produce chitosan, an industrially important biopolymer. Compared with traditional chemical methods, biocatalysis by CDA is more environment-friendly and easy to control. However, most reported CDA-producing microbial strains show low CDA producing capabilities. Thus, the enhancement of CDA production has always been a challenge. In this study, we report co-culture fermentation to significantly promote the CDA production of Rhodococcus equi CGMCC14861 chitin deacetylase (ReCDA). Due to co-culture fermentation with Staphylococcus sp. MC7, ReCDA yield increased to 21.74 times that of pure culture of R. equi. Additionally, the enhancement was demonstrated to be cell-independent by adding cell-free extracts and the filtrate obtained by 10 kDa ultrafiltration of Staphylococcus sp. MC7. By preliminary characterization, we found extracellular, thermosensitive signal substances produced by Staphylococcus that were less than 10 kDa. We investigated the mechanism of promotion of ReCDA production by transcriptomic analysis. The data showed that 328 genes were upregulated and 1,258 genes were downregulated. The transcription level of the gene encoding ReCDA increased 2.3-fold. These findings provide new insights into the research of co-culture fermentation for the production of CDA and quorum sensing regulation.

Development and Analysis of a Stable, Reduced Complexity Model Soil Microbiome

The soil microbiome is central to the cycling of carbon and other nutrients and to the promotion of plant growth. Despite its importance, analysis of the soil microbiome is difficult due to its sheer complexity, with thousands of interacting species. Here, we reduced this complexity by developing model soil microbial consortia that are simpler and more amenable to experimental analysis but still represent important microbial functions of the native soil ecosystem. Samples were collected from an arid grassland soil and microbial communities (consisting mainly of bacterial species) were enriched on agar plates containing chitin as the main carbon source. Chitin was chosen because it is an abundant carbon and nitrogen polymer in soil that often requires the coordinated action of several microorganisms for complete metabolic degradation. Several soil consortia were derived that had tractable richness (30–50 OTUs) with diverse phyla representative of the native soil, including Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria, and Verrucomicrobia. The resulting consortia could be stored as glycerol or lyophilized stocks at −80°C and revived while retaining community composition, greatly increasing their use as tools for the research community at large. One of the consortia that was particularly stable was chosen as a model soil consortium (MSC-1) for further analysis. MSC-1 species interactions were studied using both pairwise co-cultivation in liquid media and during growth in soil under several perturbations. Co-abundance analyses highlighted interspecies interactions and helped to define keystone species, including Mycobacterium, Rhodococcus, and Rhizobiales taxa. These experiments demonstrate the success of an approach based on naturally enriching a community of interacting species that can be stored, revived, and shared. The knowledge gained from querying these communities and their interactions will enable better understanding of the soil microbiome and the roles these interactions play in this environment.

Isolation, characterisation, and genome sequencing of Rhodococcus equi: a novel strain producing chitin deacetylase

Chitin deacetylase (CDA) can hydrolyse the acetamido group of chitin polymers to produce chitosans, which are used in various fields including the biomedical and pharmaceutical industries, food production, agriculture, and water treatment. CDA represents a more environmentally-friendly and easier to control alternative to the chemical methods currently utilised to produce chitosans from chitin; however, the majority of identified CDAs display activity toward low-molecular-weight oligomers and are essentially inactive toward polymeric chitin or chitosans. Therefore, it is important to identify novel CDAs with activity toward polymeric chitin and chitosans. In this study, we isolated the bacterium Rhodococcus equi F6 from a soil sample and showed that it expresses a novel CDA (ReCDA), whose activity toward 4-nitroacetanilide reached 19.20 U/mL/h during fermentation and was able to deacetylate polymeric chitin, colloidal chitin, glycol-chitin, and chitosan. Whole genome sequencing revealed that ReCDA is unique to the R. equi F6 genome, while phylogenetic analysis indicated that ReCDA is evolutionarily distant from other CDAs. In conclusion, ReCDA isolated from the R. equi F6 strain expands the known repertoire of CDAs and could be used to deacetylate polymeric chitosans and chitin in industrial applications.

Immune function against bacteria of chitin deacetylase 1 (EcCDA1) from Exopalaemon carinicauda

Chitin deacetylase (CDA, EC 3.5.1.41), belonging to a family of extracellular chitin-modifying enzymes, can catalyze the deacetylation of chitin. In this study, the full-length cDNA sequence encoding chitin deacetylase 1 (EcCDA1) was obtained fromExopalaemon carinicauda. The complete nucleotide sequence of EcCDA1 contained a 1611 bp open reading frame (ORF) encoding EcCDA1 precursor of 536 amino acids. The domain architecture of the deduced EcCDA1 protein contained a signal peptide, a chitin-binding peritrophin-A domain (ChtBD2), a low-density lipoprotein receptor class A domain (LDLa) and a Polysacc_deac_1 domain. EcCDA1 mRNA was predominantly expressed in the gills. The expression of EcCDA1 in the prawns challenged with Vibrio parahaemolyticus and Aeromonas hydrophila changed in a time-dependent manner. The expression of EcCDA1 in the prawns challenged with V. parahaemolyticus was up-regulated at 12 h (p < 0.05), and significantly up-regulated at 24 h and 48 h (p < 0.01), and then returned to the control levels at 96 h post-challenge (p > 0.05). At the same time, the expression in Aeromonas-challenged group was significantly up-regulated at 12, 24 and 48 h (p < 0.01) and returned to the control levels at 120 h post-challenge (p > 0.05). Then, EcCDA1 was recombinantly expressed in Pichia pastoris and the purified recombinant EcCDA1 could not inhibit the growth of V. parahaemolyticus or A. hydrophila, which indicated that the CDA1 may play its biological activity in immune defense by deacetylation from chitin.

Production of chitin deacetylase by Aspergillus flavus in submerged conditions

Chitosan is a biopolymer obtained by deacetylation of chitin and has been proven to have various applications in industry and biomedicine. Deacetylation of chitin using the enzyme chitin deacetylase (CDA) is favorable in comparison to the hazardous chemical method involving strong alkali and high temperature. A fungal strain producing CDA was isolated from environmental samples collected from coastal regions of South Kerala, India. It was identified as Aspergillus flavus by morphological characteristics and ITS DNA analysis. Nutritional requirement for maximum production of CDA under submerged condition was optimized using statistical methods including Plackett-Burman and response surface methodology central composite design. A 5.98-fold enhancement in CDA production was attained in shake flasks when the fermentation process parameters were used at their optimum levels. The highest CDA activity was 57.69 ± 1.68 U under optimized bioprocess conditions that included 30 g L(-1) glucose, 40 g L(-1) yeast extract, 15 g L(-1) peptone, and 7 g L(-1) MgCl2 at initial media pH of 7 and incubation temperature of 32°C after 48 hr of incubation, while the unoptimized basal medium yielded 9.64 ± 2.04 U.