Molecular cloning, characterization, and heterologous expression of a new κ-carrageenase gene from marine bacterium Zobellia sp. ZM-2

Enzymatic Preparation of Carrageenan Oligosaccharides and Evaluation of the Effects on Growth Performance, Serum Biochemical Parameters and Non-Specific Immunity of Crucian carp

Carrageenan oligosaccharides (COSs) possess versatile activities and have drawn increasing attention in recent years. Due to their unique structures, COSs have been considered to be potential antibacterial agents and immune stimulators. Herein, we aimed to efficiently prepare the COSs by using a novel carrageenase CgkA from Zobellia uliginosa with high activity and further investigate the effects of dietary supplementation with COSs on the growth performance, serum biochemical parameters and non-specific immunity in Carassius auratus gibelio. The results indicated that the CgkA could effectively degrade the carrageenan into oligosaccharides with DPs of 2-6 and the oligosaccharides exhibited promoting effects on growth performance, serum biochemical index and non-specific immune parameters. After a 6-month feeding trial, the SR (Survival Ratio) was significantly higher in fish fed 0.1% (Diet 1), 0.2% (Diet 2), 0.5% (Diet 3) and 1% (Diet 4) COSs diets than that in the control group (p < 0.05). In addition, the supplementation of COSs decreased the malondialdehyde (MDA) content in the serum and increased the activity of lysozyme (LZM), superoxide dismutase (SOD) and catalase (CAT). In conclusion, COSs as a dietary supplement enhance the growth performance and non-specific immunity of crucian carp and their resistance to diseases.

Directed preparation of algal oligosaccharides with specific structures by algal polysaccharide degrading enzymes

Seaweed polysaccharides have a wide range of sources and rich content, with various biological activities such as anti-inflammatory, anti-tumor, anticoagulant, and blood pressure lowering. They can be applied in fields such as food, agriculture, and medicine. However, the poor solubility of macromolecular seaweed polysaccharides limits their further application. Reports have shown that some biological activities of seaweed oligosaccharides are more extensive and superior to that of seaweed polysaccharides. Therefore, reducing the degree of polymerization of polysaccharides will be the key to the high value utilization of seaweed polysaccharide resources. There are three main methods for degrading algal polysaccharides into algal oligosaccharides, physical, chemical and enzymatic degradation. Among them, enzymatic degradation has been a hot research topic in recent years. Various types of algal polysaccharide hydrolases and related glycosidases are powerful tools for the preparation of algal oligosaccharides, including α-agarases, β-agaroses, α-neoagarose hydrolases and β-galactosidases that are related to agar, κ-carrageenases, ι-carrageenases and λ-carrageenases that are related to carrageenan, β-porphyranases that are related to porphyran, funoran hydrolases that are related to funoran, alginate lyases that are related to alginate and ulvan lyases related to ulvan. This paper describes the bioactivities of agar oligosaccharide, carrageenan oligosaccharide, porphyran oligosaccharide, funoran oligosaccharide, alginate oligosaccharide and ulvan oligosaccharide and provides a detailed review of the progress of research on the enzymatic preparation of these six oligosaccharides. At the same time, the problems and challenges faced are presented to guide and improve the preparation and application of algal oligosaccharides in the future.

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.

Biosynthesis of l-histidine from marine biomass-derived galactans in metabolically engineered Corynebacterium glutamicum

l-Histidine plays significant roles in the food and pharmaceutical industries, and its demand has been steadily increasing recently. As demand for l-histidine continues, the development of eco-friendly processes is required. To pursue this goal, D-galactose, a primary component of red algae, was employed as a carbon source for synthesizing l-histidine. To harness this marine biomass, κ-carrageenan was preferentially hydrolyzed to obtain D-galactose using κ-carrageenase (CgkA) and iduronate-2-sulfatase (IdsA3). Subsequently, l-histidine production was enhanced by modifying precursor pathways in Corynebacterium glutamicum. The resulting strain, TDPH6 exhibited a remarkable 2.15-fold increase in l-histidine production compared to TDP. Furthermore, a galactose utilization system was introduced and named TDPH6G2. During fermentation, this strain efficiently consumed 100 % of the D-galactose and synthesized 0.395 g/L of l-histidine. In conclusion, this study presents a sustainable approach to L-histidine synthesis by introducing a galactose utilization system into C. glutamicum.

Biochemical characterization and elucidation of the action mode of a GH16 family κ-carrageenase for efficient preparation of carrageenan oligosaccharides

κ-Carrageenan oligosaccharides have a variety of biological activities. Degradation of κ-carrageenan by κ-carrageenase leads to degradation products with different degrees of polymerization (DPs). A novel gene (CecgkA) encoding a new κ-carrageenase was cloned from Colwellia echini and heterologously expressed in Escherichia coli BL21 (DE3). The enzyme is 1104 bp in length, encodes 367 amino acid residues and has a molecular weight of 41.30 kDa. Multiple alignment analysis showed that CeCgkA belongs to the glycoside hydrolase (GH16) family and has the highest homology with the κ-carrageenase of Rhodopirellula maiorica SM1, with 58% homology. The CeCgkA showed maximum activity (453.15 U/mg) at pH 8.0 and 35 °C. Determination of biochemical properties showed that CeCgkA was a thermal recovery enzyme, and 51.6% of the initial enzyme activity was recovered by immediately placing the sample at 35 °C for 60 min after enzymatic inactivation by boiling for 10 min. K⁺, Na⁺, and EDTA had an activating effect on the enzyme activity, while Ni²⁺, Cu²⁺, and Zn²⁺ inhibited the activity of the enzyme. In addition, TLC and ESI-MS analysis showed that the maximum recognition unit of CecgkA was decasaccharide and that the main degradation products were disaccharides, tetrasaccharides and hexasaccharides, indicating that the enzyme is an endo-type carrageenase.

A Novel κ-Carrageenase from Marine Bacterium Rhodopirellula sallentina SM41: Heterologous Expression, Biochemical Characterization and Salt-Tolerance Mechanism Investigation

κ-carrageenases are members of the glycoside hydrolase family 16 (GH16) that hydrolyze sulfated galactans in red algae, known as κ-carrageenans. In this study, a novel κ-carrageenase gene from the marine bacterium Rhodopirellula sallentina SM41 (RsCgk) was discovered via the genome mining approach. There are currently no reports on κ-carrageenase from the Rhodopirellula genus, and RsCgk shares a low identity (less than 65%) with κ- carrageenase from other genera. The RsCgk was heterologously overexpressed in Escherichia coli BL21 and characterized for its enzymatic properties. RsCgk exhibited maximum activity at pH 7.0 and 40 °C, and 50% of its initial activity was retained after incubating at 30 °C for 2 h. More than 70% of its activity was maintained after incubation at pH 6.0-8.0 and 4 °C for 24 h. As a marine derived enzyme, RsCgk showed excellent salt tolerance, retaining full activity in 1.2 M NaCl, and the addition of NaCl greatly enhanced its thermal stability. Mass spectrometry analysis of the RsCgk hydrolysis products revealed that the enzyme had high degradation specificity and mainly produced κ-carrageenan disaccharide. Comparative molecular dynamics simulations revealed that the conformational changes of tunnel-forming loops under salt environments may cause the deactivation or stabilization of RsCgk. Our results demonstrated that RsCgk could be utilized as a potential tool enzyme for efficient production of κ-carrageenan oligosaccharides under high salt conditions.

Recent Advances in the Heterologous Expression of Biosynthetic Gene Clusters for Marine Natural Products

Marine natural products (MNPs) are an important source of biologically active metabolites, particularly for therapeutic agent development after terrestrial plants and nonmarine microorganisms. Sequencing technologies have revealed that the number of biosynthetic gene clusters (BGCs) in marine microorganisms and the marine environment is much higher than expected. Unfortunately, the majority of them are silent or only weakly expressed under traditional laboratory culture conditions. Furthermore, the large proportion of marine microorganisms are either uncultivable or cannot be genetically manipulated. Efficient heterologous expression systems can activate cryptic BGCs and increase target compound yield, allowing researchers to explore more unknown MNPs. When developing heterologous expression of MNPs, it is critical to consider heterologous host selection as well as genetic manipulations for BGCs. In this review, we summarize current progress on the heterologous expression of MNPs as a reference for future research.

Biochemical Characterization of a Carrageenase, Car1383, Derived From Associated Bacteria of Antarctic Macroalgae

A carrageenase gene, car1383, was obtained from the metagenome of Antarctic macroalgae-associated bacteria. The amino acid sequence of its product showed up to 33% similarity with other carrageenases and contained a GH16-family motif. The recombinant Car1383 was heterologously expressed in Eschericia coli and exhibited maximal activity at 50°C and pH 6.0, with a K_m of 6.51 mg/ml and a V_max of 55.77 U/mg. Its activity was enhanced by some cations (Na⁺, K⁺, and Fe²⁺), but inhibited or inactivated by others (Sr²⁺, Ca²⁺, Ni²⁺, Ba²⁺, Mn²⁺, Cu²⁺, Fe³⁺, and Mg²⁺). Car1383 degraded carrageenan into neocarrabiose and neocarratetraose. Site-directed mutagenesis indicated that putative active sites, E₁₉₀ and E₁₉₅, conserved sites, W₁₈₃ and G₂₅₅, play important roles in Car1383 activity. This study provides a new candidate for the industrial preparation of bioactive algal oligosaccharides.

C-Terminal Bacterial Immunoglobulin-like Domain of κ-Carrageenase Serves as a Multifunctional Module to Promote κ-Carrageenan Hydrolysis

κ-Carrageenase is an important component for κ-carrageenan oligosaccharide production. Generally, noncatalytic domains are appended to carbohydrate-active domains and potentiate catalytic activity. However, studies devoted to κ-carrageenase are relatively few. Here, a C-terminal bacterial immunoglobulin-like domain (Big_2) was identified in κ-carrageenase (PpCgk) from Pseudoalteromonas porphyrae. Biochemical characterization of native PpCgk and its two truncations, PpCgkCD (catalytic domain) and PpBig_2 (Big_2 domain), revealed that the specific activity, catalytic efficiency (k_cat/K_m(app)), specific κ-carrageenan-binding capacity, and thermostability of PpCgk were significantly higher than those of PpCgkCD, suggesting that the noncatalytic PpBig_2 domain is a multifunctional module and essential for maintaining the activity and thermostability of PpCgk. Furthermore, it was found that the mode of action of PpCgk was more processive on both the dissolved and gelled substrates than that of PpCgkCD, indicating that PpBig_2 contributes to the processivity of PpCgk. Interestingly, PpBig_2 can be used as an independent module to enhance the hydrolysis of κ-carrageenan through its disruptive function. In addition, sequence analysis suggests that Big_2 domains are highly conserved in bacterial κ-carrageenases, implying the universality of their noncatalytic functions. These findings reveal the multifunctional role of the noncatalytic PpBig_2 and will guide future functional analyses and biotechnology applications of Big_2 domains.

Marine microbial enzymes for the production of algal oligosaccharides and its bioactive potential for application as nutritional supplements

Marine macroalgae have a very high carbohydrate content due to complex algal polysaccharides (APS) like agar, alginate, and ulvan in their cell wall. Despite numerous reports on their biomedical properties, their hydrocolloid nature limits their applications. Algal oligosaccharides (AOS), which are hydrolyzed forms of complex APS, are gaining importance due to their low molecular weight, biocompatibility, bioactivities, safety, and solubility in water that makes it a lucrative alternative. The AOS produced through enzymatic hydrolysis using microbial enzymes have far-reaching applications because of its stereospecific nature. Identification and characterization of novel microorganisms producing APS hydrolyzing enzymes are the major bottlenecks for the efficient production of AOS. This review will discuss the marine microbial enzymes identified for AOS production and the bioactive potential of enzymatically produced AOS. This can improve our understanding of the biotechnological potential of microbial enzymes for the production of AOS and facilitate the sustainable utilization of algal biomass. Enzymatically produced AOS are shown to have bioactivities such as antioxidant, antiglycemic, prebiotic, immunomodulation, antiobesity or antihypercholesterolemia, anti-inflammatory, anticancer, and antimicrobial activity. The myriad of health benefits provided by the AOS is the need of the hour as there is an alarming increase in physiological disorders among a wide range of the global population.

A multi-functional genetic manipulation system and its use in high-level expression of a β-mannanase mutant with high specific activity in Pichia pastoris

To further extend the practical application of a thermostable and acidic resistance β-mannanase (ManAK) in animal feed additives, an effective strategy that combined directed evolution and metabolic engineering was developed. Four positive mutants (P191M, P194E, S199G and S268Q) with enhanced specific activity (25.5%-60.9%) were obtained. The S199G mutant exhibited 56.7% enhancement of specific activity at 37°C and good thermostability, and this was selected for high-level expression in P. pastoris X33. A multi-functional and scarless genetic manipulation system was proposed and functionally verified (gene deletion, substitution/insertion and point mutation). This was then subjected to Rox1p (an oxygen related transcription regulator) deletion and Vitreoscilla haemoglobin (VHb) co-expression for high enzyme productivity in P. pastoris X33VIIManAKS199G . An excellent strain, named X33VIIManAKS199G ∆rox1::VHb, was achieved by combining these two factors, and then the maximum enzymatic activity was further increased to 3753 U ml-1 , which was nearly twice as much as the maximum production of ManAK in P. pastoris. This work provides a systematic and effective method to improve the enzymatic yield of β-mannanase, promotes the application of ManAK in feed additives, and also demonstrated that a scarless genetic manipulation tool is useful in P. pastoris.

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

κ-Carrageenan oligosaccharides with many excellent biological properties could be produced by κ-carrageenases selectively. In this study, based on the encoding gene of full length κ-carrageenase obtained from Pseudoalteromonas sp. ZDY3 and the reported mature secreted κ-carrageenase composed of 275 amino acid residues (N26-T300), CgkPZ_GH16 was expressed in E. coli, but no soluble active protein could be detected. Fortunately, the signal peptide of wild-type κ-carrageenase was recognized, and cleaved in the soluble and folding form in E. coli, the K_m and k_cat values of CgkPZ_SP_GH16 was 1.007 mg/mL and 362.8 s^-1. By molecular dynamics simulations, it was showed that YjdB domain might affect the activity of κ-carrageenase. Due to the absence of mature processing modification system in E. coli, YjdB was remained in recombinant full length κ-carrageenase, and the lost catalytic efficiency of CgkPZ was compensated by expression level and thermal stability. Interestingly, CgkPZ_GH16_YjdB was expressed soluble without the signal peptide, which indicated that YjdB could contribute to the expression and folding of κ-carrageenase. These results provide new insight into the effects of different modules of κ-carrageenase on the expression and properties of enzyme.

Expression and Characterization of a Thermostable Carrageenase From an Antarctic Polaribacter sp. NJDZ03 Strain

The complete genome of Polaribacter sp. NJDZ03, which was isolated from the surface of Antarctic macroalgae, was analyzed by next-generation sequencing, and a putative carrageenase gene Car3206 was obtained. Car3206 was cloned and expressed in Escherichia coli BL21(DE3). After purification by Ni-NTA chromatography, the recombinant Car3206 protein was characterized and the antioxidant activity of the degraded product was investigated. The results showed that the recombinant plasmid pet-30a-car3206 was highly efficiently expressed in E. coli BL21(DE3). The purified recombinant Car3206 showed a single band on sodium dodecyl sulfate-polyacrylamide gel electrophoresis, with an apparent molecular weight of 45 kDa. The optimum temperature of the recombinant Car3206 was 55°C, and it maintain 60-94% of its initial activity for 4-12 h at 55°C. It also kept almost 70% of the initial activity at 30°C, and more than 40% of the initial activity at 10°C. These results show that recombinant Car3206 had good low temperature resistance and thermal stability properties. The optimum pH of recombinant Car3206 was 7.0. Car3206 was activated by Na+, K+, and Ca2+, but was significantly inhibited by Cu2+ and Cr2+. Thin-layer chromatographic analysis indicated that Car3206 degraded carrageenan generating disaccharides as the only products. The antioxidant capacity of the degraded disaccharides in vitro was investigated and the results showed that different concentrations of the disaccharides had similar scavenging effects as vitamin C on O 2 • - , •OH, and DPPH•. To our knowledge, this is the first report about details of the biochemical characteristics of a carrageenase isolated from an Antarctic Polaribacter strain. The unique characteristics of Car3206, including its low temperature resistance, thermal stability, and product unity, suggest that this enzyme may be an interesting candidate for industrial processes.

Improving the kinetic stability of a hyperthermostable β-mannanase by a rationally combined strategy

Feasible and easily accessible methods for the rational design of enzyme engineering strategies remain to be established. Thus, a new rationally combined strategy based on disulfide bond engineering and HotSpot Wizard 3.0 was proposed and experimentally demonstrated to be effective using a hyperthermostable β-mannanase. Ten of 42 mutants showed prominent enhancement of kinetic stability with 26.4%-39.9% increases in t_1/2 (75 °C) compared with the parent enzyme ManAKH. The best mutant, D273-V308, showed apparent increases in both optimal temperature (5 °C) and T₅₀ (6.8 °C), as well as advanced catalytic efficiency. The low rate of inactive mutants and the high rate of positive mutants indicated that newly introduced screening factors (distance from catalytic residues, Gibbs free energy term, molecular simulation, and visual inspections) greatly enhance the design of thermostable β-mannanase. Moreover, these findings further advance the industrial application of β-mannanase (ManAK) in food and food-related applications.

Purification and characterization of a cold-adapted κ-carrageenase from Pseudoalteromonas sp. ZDY3

κ-Carrageenase (EC3.2.1.83) is a class of glycoside hydrolase, which can be used for hydrolysis of κ-carrageenan to κ-carrageenan oligosaccharides. In this study, a bacterium, identified as Pseudoalteromonas sp. ZDY3 isolated from rotten algae, was capable to degrade κ-carrageenan. The κ-carrageenase produced by Pseudoalteromonas sp. ZDY3 was purified to homogeneity and named as CgkZDY3. The accurate molecular mass of CgkZDY3 was determined through LC-HRMS, and a posttranslational removal of C-terminal end of the protein was discovered. CgkZDY3 had strict hydrolysis specificity to κ-carrageenan, the values of K_m and k_cat/K_m of CgkZDY3 were 3.67 mg mL^-1 and 53.0 mL mg^-1 s^-1, respectively. CgkZDY3 was a cold-adapted κ-carrageenase with excellent storage stability of both the temperature below 35 °C and a wide pH range, and was an endo-type κ-carrageenase with high hydrolysis rate, oligosaccharides with different degrees of polymerization can be obtained by controlling the hydrolysis time, and the final products were κ-neocarrabiose and κ-neocarratetraose. These properties are of great significance for production of κ-carrageenan oligosaccharides with different polymerization degrees under process control.

Production of a thermo-tolerant κ-carrageenase via a food-grade host and anti-oxidant activity of its enzymatic hydrolysate

κ-Carrageenase cleaves the β-(1-4) linkages of κ-carrageenan into κ-carrageenan oligosaccharides (κ-COS), which exhibit various biological activities. In this study, a glycoside hydrolase (GH) family 16 κ-carrageenase gene, cgkA, was cloned from the marine bacterium Vibrio sp. SY01 and secretory expressed in a food-grade host, Yarrowia lipolytica. The specific activity of the purified CgkA was 12.5 U/mg. Determination of biochemical properties showed that CgkA was a thermo-tolerant enzyme, and 59.9% of the initial enzyme activity was recovered by immediately placing the sample at 20 °C for 30 min after enzymatic inactivation by boiling for 5 min. The recombinant CgkA was an endo-type enzyme, the main enzymatic product was κ-carradiaose (accounting for 87.6% of total products), and κ-carratetraose was the minimum substrate. Additionally, in vitro and in vivo analyses indicated that enzymatic κ-carradiaose possesses anti-oxidant activity. These features make CgkA as a promising candidate for biotechnological applications in the production of anti-oxidant κ-COS.

High-efficiency expression of a superior β-mannanase engineered by cooperative substitution method in Pichia pastoris and its application in preparation of prebiotic mannooligosaccharides

β-mannanase with high specific activity is a prerequisite for the industrial preparation of prebiotic mannooligosaccharides. Three mutants, namely MEI, MER, and MEIR, were constructed by cooperative substitution based on three predominant single-point site mutations (K291E, L211I, and Q112R, respectively). Heterologous expression was facilitated in Pichia pastoris and the recombinase was characterized completely. The specific activities of MER (7481.9 U mg^-1) and MEIR (9003.1 U mg^-1) increased by 1.07- and 1.29-fold from the initial activity of ME (6970.2U mg^-1), respectively. MEIR was used for high-cell-density fermentation to further improve enzyme activity, and the expression levels achieved in the 10-L fermenter were significantly high (105,836 U mL^-1). The prebiotic mannooligosaccharides (<2000 Da) were prepared by hydrolyzing konjac gum and locust bean gum with MEIR, with 100% and 76.40% hydrolysis rates, respectively. These characteristics make MEIR highly attractive for prebiotic development in food and related industries.

Marine-polysaccharide degrading enzymes: Status and prospects

Marine-polysaccharide degrading enzymes have recently been studied extensively. They are particularly interesting as they catalyze the cleavage of glycosidic bonds in polysaccharide macromolecules and produce oligosaccharides with low degrees of polymerization. Numerous findings have demonstrated that marine polysaccharides and their biotransformed products possess beneficial properties including antitumor, antiviral, anticoagulant, and anti-inflammatory activities, and they have great value in healthcare, cosmetics, the food industry, and agriculture. Exploitation of enzymes that can degrade marine polysaccharides is in the ascendant, and is important for high-value use of marine biomass resources. In this review, we describe research and prospects regarding the classification, biochemical properties, and catalytic mechanisms of the main types of marine-polysaccharide degrading enzymes, focusing on chitinase, chitosanase, alginate lyase, agarase, and carrageenase, and their product oligosaccharides. The state-of-the-art discussion of marine-polysaccharide degrading enzymes and their properties offers information that might enable more efficient production of marine oligosaccharides. We also highlight current problems in the field of marine-polysaccharide degrading enzymes and trends in their development. Understanding the properties, catalytic mechanisms, and modification of known enzymes will aid the identification of novel enzymes to degrade marine polysaccharides and facilitation of their use in various biotechnological processes.

High-level expression of a thermophilic and acidophilic β-mannanase from Aspergillus kawachii IFO 4308 with significant potential in mannooligosaccharide preparation

An engineered thermophilic and acidophilic β-mannanase (ManAK) from Aspergillus kawachii IFO 4308 was highly expressed in Pichia pastoris. Through high cell density fermentation, the maximum yield reached 11,600 U/mL and 15.5 g/L, which is higher than most extreme β-mannanases. The recombinant ManAK was thermostable with a temperature optimum of 80 °C, and acid tolerant with a pH optimum of 2.0. ManAK could efficiently degrade locust bean gum, konjac gum, and guar gum into small molecular mannooligosaccharide (<2000 Da), even at high initial substrate concentration (10%), and displayed different Mw distributions in their end products. Docking analysis demonstrated that the catalytic pocket of ManAK could only accommodate a galactopyranosyl residue in subsite -1, which might be responsible for the distinct hydrolysis product compositions from locust bean gum and guar gum. These superior properties of ManAK strongly facilitate mannooligosaccharide preparation and application in food and feed area.

Characterization of a thermostable κ-carrageenase from a hot spring bacterium and plant protection activity of the oligosaccharide enzymolysis product

BACKGROUND

Seaweed oligosaccharides are environmentally-friendly natural products and their use for disease control in sustainable agriculture is extremely promising. Enzymatic digestion to prepare seaweed oligosaccharides has drawn considerable interest. However, the study of enzymatically degraded products of carrageenan is still in its infancy compared with that of other hydrocolloids such as agar and alginate. To prepare degraded carrageenan on a commercial scale, it is necessary to select superior producer bacterial strains to improve the yield and thermostability of carrageenases.

RESULTS

The carrageenan-degrading bacterium Bacillus sp. HT19 was isolated from sediment of a hot spring in Indonesia, and a κ-carrageenase with high activity was purified from the culture supernatant. The purified enzyme, named Car19, had maximum activity (538 U mg^-1 ) at 60 °C and pH 7.0. Notably, the enzyme retained >90% of its initial activity after incubation at 60 °C for 24 h. The Ca²⁺ obviously improved the thermostability of Car19 at 70 °C. The K_m and V_max values of purified Car19 were 0.061 mg mL^-1 and 115.13 U mg^-1 , respectively, with κ-carrageenan as substrate. Thin-layer chromatography and electrospray ionization mass-spectrometry analysis of hydrolysates indicated that the enzyme exolytically depolymerized κ-carrageenan to neo-carrabiose. The hydrolysate enhanced the resistance of cucumber to cucumber mosaic virus and increased the activity of antioxidant enzymes in infected plants.

CONCLUSION

To our knowledge, Car19 is the most thermostable κ-carrageenase reported so far. Its high optimal reaction temperature and thermostability, and unitary hydrolysate constituent, makes Car19 a promising candidate for the preparation of carrageenan oligosaccharides with plant protection activity. © 2018 Society of Chemical Industry.

A CAZyme-Rich Genome of a Taxonomically Novel Rhodophyte-Associated Carrageenolytic Marine Bacterium

Carbohydrate-active enzymes (CAZymes) have significant biotechnological potential as agents for degradation or modification of polysaccharides/glycans. As marine macroalgae are known to be rich in various types of polysaccharides, seaweed-associated bacteria are likely to be a good source of these CAZymes. A genomics approach can be used to explore CAZyme abundance and diversity, but it can also provide deep insights into the biology of CAZyme producers and, in particular, into molecular mechanisms that mediate their interaction with their hosts. In this study, a Gram-negative, aerobic, rod-shaped, carrageenolytic, and culturable marine bacterium designated as AOL6 was isolated from a diseased thallus of a carrageenan-producing farmed rhodophyte, Kappaphycus alvarezii (Gigartinales, Rhodophyta). The whole genome of this bacterium was sequenced and characterized. Sequence reads were assembled producing a high-quality genome assembly. The estimated genome size of the bacterium is 4.4 Mb and a G+C content of 52%. Molecular phylogenetic analysis based on a complete sequence of 16S rRNA, rpoB, and a set of 38 single-copy genes suggests that the bacterium is an unknown species and represents a novel genus in the family Cellvibrionaceae that is most closely related to the genera Teredinibacter and Saccharophagus. Genome comparison with T. turnerae T7901 and S. degradans 2-40 reveals several features shared by the three species, including a large number of CAZymes that comprised > 5% of the total number of protein-coding genes. The high proportion of CAZymes found in the AOL6 genome exceeds that of other known carbohydrate degraders, suggesting a significant capacity to degrade a range of polysaccharides including κ-carrageenan; 34% of these CAZymes have signal peptide sequences for secretion. Three putative κ-carrageenase-encoding genes were identified from the genome of the bacterium via in silico analysis, consistent with the results of the zymography assay (with κ-carrageenan as substrate). Genome analysis also indicated that AOL6 relies exclusively on type 2 secretion system (T2SS) for secreting proteins (possibly including glycoside hydrolases). In relation to T2SS, the product of the pilZ gene was predicted to be highly expressed, suggesting specialization for cell adhesion and secretion of virulence factors. The assignment of proteins to clusters of orthologous groups (COGs) revealed a pattern characteristic of r-strategists. Majority of two-component system proteins identified in the AOL6 genome were also predicted to be involved in chemotaxis and surface colonization. These genomic features suggest that AOL6 is an opportunistic pathogen, adapted to colonizing polysaccharide-rich hosts, including carrageenophytes.

High-level expression and characterization of a new κ-carrageenase from marine bacterium Pedobacter hainanensis NJ-02

A novel κ-carrageenase gene (CgkB) has been cloned from Pedobacter hainanensis NJ-02 and expressed heterologously in Escherichia coli BL21 (DE3). It consisted of 1935 bp and encoded 644 amino acid residues with a molecular weight of 71·61 kDa. The recombinant enzyme showed maximal activity of 2458 U mg^-1 at 40°C and pH 8·0. Additionally, it could retain more than 70% of its maximal activity after being incubated at pH of 5·5-10·0 below 40°C. K⁺ and a broad range of NaCl can activate the enzyme. The K_m and V_max of CgkB was 2·4 mg ml^-1 and 126 mmol mg^-1  min^-1 . The ESI-MS analysis of hydrolysates indicated that the enzyme can endolytically depolymerize the carrageenan into tetrasaccharides and hexasaccharides. The results indicated that the enzyme with high activity could be a valuable enzyme tool to produce carrageenan oligosaccharides with various activities.

SIGNIFICANCE AND IMPACT OF THE STUDY

Enzymatic preparation of carrageenan oligosaccharides has drawn increased attention due to their various physiological activities. It is urgent to explore enzyme tools with higher activity and better stability. In this work, a novel κ-carrageenase was identified and characterized from marine bacterium Pedobacter hainanensis NJ-02. The enzyme with high activity could be a valuable tool to produce carrageenan oligosaccharides with various activities.

Structural insights into marine carbohydrate degradation by family GH16 κ-carrageenases

Carrageenans are sulfated α-1,3-β-1,4-galactans found in the cell wall of some red algae that are practically valuable for their gelation and biomimetic properties but also serve as a potential carbon source for marine bacteria. Carbohydrate degradation has been studied extensively for terrestrial plant/bacterial systems, but sulfation is not present in these cases, meaning the marine enzymes used to degrade carrageenans must possess unique features to recognize these modifications. To gain insights into these features, we have focused on κ-carrageenases from two distant bacterial phyla, which belong to glycoside hydrolase family 16 and cleave the β-1,4 linkage of κ-carrageenan. We have solved the crystal structure of the catalytic module of ZgCgkA from Zobellia galactanivorans at 1.66 Å resolution and compared it with the only other structure available, that of PcCgkA from Pseudoalteromonas carrageenovora 9T (ATCC 43555T). We also describe the first substrate complex in the inactivated mutant form of PcCgkA at 1.7 Å resolution. The structural and biochemical comparison of these enzymes suggests key determinants that underlie the functional properties of this subfamily. In particular, we identified several arginine residues that interact with the polyanionic substrate, and confirmed the functional relevance of these amino acids using a targeted mutagenesis strategy. These results give new insight into the diversity of the κ-carrageenase subfamily. The phylogenetic analyses show the presence of several distinct clades of enzymes that relate to differences in modes of action or subtle differences within the same substrate specificity, matching the hybrid character of the κ-carrageenan polymer.

Nonribosomal Peptides from Marine Microbes and Their Antimicrobial and Anticancer Potential

Marine environments are largely unexplored and can be a source of new molecules for the treatment of many diseases such as malaria, cancer, tuberculosis, HIV etc. The Marine environment is one of the untapped bioresource of getting pharmacologically active nonribosomal peptides (NRPs). Bioprospecting of marine microbes have achieved many remarkable milestones in pharmaceutics. Till date, more than 50% of drugs which are in clinical use belong to the nonribosomal peptide or mixed polyketide-nonribosomal peptide families of natural products isolated from marine bacteria, cyanobacteria and fungi. In recent years large numbers of nonribosomal have been discovered from marine microbes using multi-disciplinary approaches. The present review covers the NRPs discovered from marine microbes and their pharmacological potential along with role of genomics, proteomics and bioinformatics in discovery and development of nonribosomal peptides drugs.

Characterization of Full-Length and Truncated Recombinant κ-Carrageenase Expressed in Pichia pastoris

κ-Carrageenase belongs to glycoside hydrolase family 16 and cleaves the β-(1→4) linkages of κ-carrageenan. In this study, genes encoding the full-length (cgkZ), Por secretion tail-truncated (cgkZΔPst) and carbohydrate binding domain-truncated (cgkZΔCBM) κ-carrageenase proteins were expressed in Pichia pastoris. The copy numbers of gene cgkZ, cgkZΔPst and cgkZΔCBM were 7, 7 and 6, respectively. The enzymatic activities of recombinant enzymes cgkZ, cgkZΔPst and cgkZΔCBM reached 4.68, 5.70, and 3.02 U/mL, respectively, after 120 h of shake flask fermentation at 22°C and pH 6 in the presence of 1 % (v/v) methanol. The molecular weights of recombinant cgkZ, cgkZΔPst, and cgkZΔCBM were approximately 65, 45, and 40 kDa; their K_m values were 2.07, 1.85, and 1.04 mg/mL; and they exhibited optimal activity at 45-50°C and pH 6-7. All the recombinant enzymes were stimulated by Na⁺, Mg²⁺, Ca²⁺, and dithiothreitol. The end-products of enzymatic hydrolysis were mainly composed of κ-carrageenan tetrasaccharide and hexasaccharide. The removal of the Por secretion tail of κ-carrageenase promoted the transcription of κ-carrageenase gene, enhancing the specific activity of κ-carrageenase without significantly changing its catalytic properties. Although the transcription level of κ-carrageenase gene after the removal of the carbohydrate binding domain was relatively high, the specific activity of the recombinant enzyme significantly decreased. The comprehensive application of the P. pastoris expression system combined with the rational modification of genes may provide a novel approach for the heterologous expression of various marine enzymes with high activities.

Bacterial carrageenases: an overview of production and biotechnological applications

Carrageenan, one of the phycocolloids is a sulfated galactan made up of linear chains of galactose and 3,6-anhydrogalactose with alternating α-(1 → 3) and β-(1 → 4) linkages and further classified based on the number and the position of sulfated ester(s); κ-, ι- and λ-carrageenan. Enzymes which degrade carrageenans are called k-, ι-, and λ-carrageenases. They all are endohydrolases that cleave the internal β-(1-4) linkages of carrageenans yielding products of the oligo-carrageenans. These enzymes are produced only by bacteria specifically gram negative bacteria. Majority of the marine bacteria produce these enzymes extracellularly and their activity is in wide range of temperature. They have found potential applications in biomedical field, bioethanol production, textile industry, as a detergent additive and for isolation of protoplast of algae etc. A comprehensive information shall be helpful for the effective understanding and application of these enzymes. In this review exhaustive information of bacterial carrageenases reported till date has been done. All the aspects like sources, production conditions, characterization, cloning and- biotechnological applications are summarized.

Efficient extracellular production of κ-carrageenase in Escherichia coli: effects of wild-type signal sequence and process conditions on extracellular secretion

Signal peptides direct proteins to translocate across the bacterial cytoplasmic membrane. This study aimed to improve the level of extracellular secretion of recombinant carrageenase by recombining the gene encoding wild-type signal peptide (OmpZ) of Zobellia sp. ZM-2 κ-carrageenase into the expression vector pProEX-HTa-cgkZ. The recombinant strain BL21-HTa-cgkZ achieved extracellular secretion of κ-carrageenase. The effects of induction, culture conditions, and additives were investigated to further promote the extracellular secretion of the enzyme. Results showed that the wild-type signal sequence secreted recombinant κ-carrageenase out of the cytoplasmic membrane. Low temperature (23 °C) and optimum isopropyl-β-thiogalactoside concentration (0.9 mM) favored soluble protein expression. Moreover, additives such as lactose, glycine, Tween-80, and TritonX-100 promoted the release of intracellular enzymes. The existence of OmpZ resulted in 51% of the total κ-carrageenase accumulation secreted into culture medium, and 33% accumulated in the periplasmic space. High extracellular secretion of recombinant κ-carrageenase under the optimum conditions showed promising applications of the process for extracellular protein production.

Microorganisms living on macroalgae: diversity, interactions, and biotechnological applications

Marine microorganisms play key roles in every marine ecological process, hence the growing interest in studying their populations and functions. Microbial communities on algae remain underexplored, however, despite their huge biodiversity and the fact that they differ markedly from those living freely in seawater. The study of this microbiota and of its relationships with algal hosts should provide crucial information for ecological investigations on algae and aquatic ecosystems. Furthermore, because these microorganisms interact with algae in multiple, complex ways, they constitute an interesting source of novel bioactive compounds with biotechnological potential, such as dehalogenases, antimicrobials, and alga-specific polysaccharidases (e.g., agarases, carrageenases, and alginate lyases). Here, to demonstrate the huge potential of alga-associated organisms and their metabolites in developing future biotechnological applications, we first describe the immense diversity and density of these microbial biofilms. We further describe their complex interactions with algae, leading to the production of specific bioactive compounds and hydrolytic enzymes of biotechnological interest. We end with a glance at their potential use in medical and industrial applications.