Module function analysis of a full-length κ-carrageenase from Pseudoalteromonas sp. ZDY3

Systematic review on carrageenolytic enzymes: From metabolic pathways to applications in biotechnology

Carrageenan, the major carbohydrate component of some red algae, is an important renewable bioresource with very large annual outputs. Different types of carrageenolytic enzymes in the carrageenan metabolic pathway are potentially valuable for the production of carrageenan oligosaccharides, biofuel, and other chemicals obtained from carrageenan. However, these enzymes are not well-developed for oligosaccharide or biofuel production. For further application, comprehensive knowledge of carrageenolytic enzymes is essential. Therefore, in this review, we first summarize various carrageenolytic enzymes, including the recently discovered β-carrageenase, carrageenan-specific sulfatase, exo-α-3,6-anhydro-D-galactosidase (D-ADAGase), and exo-β-galactosidase (BGase), and describe their enzymatic characteristics. Subsequently, the carrageenan metabolic pathways are systematically presented and applications of carrageenases and carrageenan oligosaccharides are illustrated with examples. Finally, this paper discusses critical aspects that can aid researchers in constructing cascade catalytic systems and engineered microorganisms to efficiently produce carrageenan oligosaccharides or other value-added chemicals through the degradation of carrageenan. Overall, this paper offers a comprehensive overview of carrageenolytic enzymes, providing valuable insights for further exploration and application of these enzymes.

Biochemical Characterization of a Heat-Resistant κ-Carrageenase Capable of Tolerating High Temperatures up to 100 °C

κ-Carrageenase plays a crucial role in the high-value utilization of carrageenan. Heat resistance is a key factor in the practical application of κ-carrageenase, as carrageenan exhibits gel-like properties. Previous studies have shown that the C-terminal noncatalytic domains (nonCDs) can affect the thermostability of κ-carrageenases. In this study, we expressed and characterized a κ-carrageenase, MtKC16A, which contains three nonCDs, from Microbulbifer thermotolerans. MtKC16A has the highest activity at 80 °C and pH 7.0. Surprisingly, it exhibits excellent heat resistance, with 71.58% relative activity at 100 °C and still retains over 50% residual activity after incubation at 100 °C for 60 min. Additionally, MtKC16A has been shown to have a dual substrate hydrolysis activity. It can degrade κ-carrageenan to produce highly single Nκ4 and degrade β/κ-carrageenan to produce Nκ2 and desulfated Nκ4 DA-G-DA-G4S, suggesting its potential in producing κ- and β/κ-hybrid oligosaccharides. Furthermore, we found that the unknown function domain (UNFD) in MtKC16A plays the most vital role among the three nonCDs. When this UNFD is truncated, the resulting mutants completely lose their catalytic ability at 100 °C. Finally, by introducing this UNFD to the C-terminal of another κ-carrageenase CaKC16B, we were able to improve its heat resistance at 100 °C.

Expanding the application range of the κ‑carrageenase OUC-FaKC16A when preparing oligosaccharides from κ-carrageenan and furcellaran

Carrageenan oligosaccharides are important products that have demonstrated numerous bioactivities useful in the food, medicine, and cosmetics industries. However, the specific structure-function relationships of carrageenan oligosaccharides are not clearly described due to the deficiency of high specific carrageenases. Here, a truncated mutant OUC-FaKC16Q based on the reported κ-neocarratetrose (Nκ4)-producing κ-carrageenase OUC-FaKC16A from Flavobacterium algicola was constructed and further studied. After truncating the C-terminal Por_Secre_tail (PorS) domain (responsible for substrate binding), the catalytic efficiency and temperature stability decreased to a certain extent. Surprisingly, this truncation also enabled OUC-FaKC16Q to hydrolyze Nκ4 into κ-neocarrabiose (Nκ2). The offset of Arg265 residue in OUC-FaKC16Q may explain this change. Moreover, the high catalytic abilities, the main products, and the degradation modes of OUC-FaKC16A and OUC-FaKC16Q toward furcellaran were also demonstrated. Data suggested OUC-FaKC16A and OUC-FaKC16Q could hydrolyze furcellaran to produce mainly the desulfated oligosaccharides DA-G-(DA-G4S)2 and DA-G-DA-G4S, respectively. As a result, the spectrum of products of κ-carrageenase OUC-FaKC16A has been fully expanded in this study, indicating its promising potential for application in the biomanufacturing of carrageenan oligosaccharides with specific structures.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-023-00181-2.

Salting-out extraction of recombinant κ-carrageenase and phage T7 released from Escherichia coli cells

Traditional technology of cell disruption has become one of the bottlenecks restricting the industrialization of genetic engineering products due to its high cost and low efficiency. In this study, a novel bioprocess of phage lysis coupled with salting-out extraction (SOE) was evaluated. The lysis effect of T7 phage on genetically engineered Escherichia coli expressing κ-carrageenase was investigated at different multiplicity of infection (MOI), meanwhile the phage and enzyme released into the lysate were separated by SOE. It was found that T7 phage could lyse 99.9% of host cells at MOI = 1 and release more than 90.0% of enzyme within 90 min. After phage lysis, 87.1% of T7 phage and 71.2% of κ-carrageenase could be distributed at the middle phase and the bottom phase, respectively, in the SOE system composed of 16% ammonium sulfate and 20% ethyl acetate (w/w). Furthermore, κ-carrageenase in the bottom phase could be salted out by ammonium sulfate with a yield of 40.1%. Phage lysis exhibits some advantages, such as mild operation conditions and low cost. While SOE can efficiently separate phage and intracellular products. Therefore, phage lysis coupled with SOE is expected to become a viable alternative to the classical cell disruption and intracellular product recovery.

Enzymatic Verification and Comparative Analysis of Carrageenan Metabolism Pathways in Marine Bacterium Flavobacterium algicola

Marine bacteria usually contain polysaccharide utilization loci (PUL) for metabolizing red algae polysaccharides. They are of great significance in the carbon cycle of the marine ecosystem, as well as in supporting marine heterotrophic bacterial growth. Here, we described the whole κ-carrageenan (KC), ι-carrageenan (IC), and partial λ-carrageenan (LC) catabolic pathways in a marine Gram-negative bacterium, Flavobacterium algicola, which is involved carrageenan polysaccharide hydrolases, oligosaccharide sulfatases, oligosaccharide glycosidases, and the 3,6-anhydro-d-galactose (d-AHG) utilization-related enzymes harbored in the carrageenan-specific PUL. In the pathways, the KC and IC were hydrolyzed into 4-sugar-unit oligomers by specific glycoside hydrolases. Then, the multifunctional G4S sulfatases would remove their nonreducing ends' G4S sulfate groups, while the ι-neocarratetrose (Nι4) product would further lose the nonreducing end of its DA2S group. Furthermore, the neocarrageenan oligosaccharides (NCOSs) with no G4S and DA2S groups in their nonreducing ends would completely be decomposed into d-Gal and d-AHG. Finally, the released d-AHG would enter the cytoplasmic four-step enzymatic process, and an l-rhamnose-H⁺ transporter (RhaT) was preliminarily verified for the function for transportation of d-AHG. Moreover, comparative analysis with the reported carrageenan metabolism pathways further implied the diversity of microbial systems for utilizing the red algae carrageenan. IMPORTANCE Carrageenan is the main polysaccharide of red macroalgae and is composed of d-AHG and d-Gal. The carrageenan PUL (CarPUL)-encoded enzymes exist in many marine bacteria for decomposing carrageenan to provide self-growth. Here, the related enzymes in Flavobacterium algicola for metabolizing carrageenan were characterized for describing the catabolic pathways, notably, although the specific polysaccharide hydrolases existed that were like previous studies. A multifunctional G4S sulfatase also existed, which was devoted to the removal of G4S or G2S sulfate groups from three kinds of NCOSs. Additionally, the transformation of three types of carrageenans into two monomers, d-Gal and d-AHG, occurred outside the cell with no periplasmic reactions that existed in previously reported pathways. These results help to clarify the diversity of marine bacteria using macroalgae polysaccharides.

Self-assembled κ-carrageenase-inorganic hybrid nanoflowers exerting high catalytic efficiency with stable and recyclable properties

κ-Carrageenan oligosaccharides from κ-carrageenan hydrolysis are important biochemicals with more bioactivity. Enzyme engineering plays a key role in improving κ-carrageenase catalytic efficiency for production of κ-carrageenan oligosaccharides. Effect of metal ions on enzyme activity, especially stability and efficiency, is main factor in catalytic process, but metal ions addition leads to gelation of κ-carrageenan solution. In this study, molecular dynamics simulation was used to explore the interaction between κ-carrageenase CgkPZ and Ca²⁺, and Ca²⁺ bonded to D164 and E167 in the catalytic center resulting in the catalytic efficiency increase. Circular dichroism analysis indicated that the secondary structure of κ-carrageenase could change in the presence of Ca²⁺. Therefore, a novel self-assembly κ-carrageenase-inorganic hybrid nanoflowers CaNF@CgkPZ was synthesized and systematically characterized. The catalytic efficiency (k_cat/K_m) of CaNF@CgkPZ was 382.1 mL·mg^-1·s^-1, increased by 292% compared with free κ-carrageenase. Notably, the enzyme activity of CaNF@CgkPZ was not reduced significantly after 19 cycles use, and 70-100% relative activity was still retained when stored at 4-25 ℃ for 15 days. This work provides an efficient approach for κ-carrageenase immobilization with good storage stability, reusability and enhanced catalytic efficiency, which is of great significance in practical applications.