Thermophilic and halophilic β-agarase from a halophilic archaeon Halococcus sp. 197A

Production of extracellular agarase from Priestia megaterium AT7 and evaluation on marine algae hydrolysis

Agar is a common component biosynthesized from various marine algae species that is widely applied in various fields including food and pharmaceutical industries. However, the structural composition of agar is highly resisted against chemical and biological hydrolysis. Therefore, tremendous research is exploring various pretreatment strategies to break down the intrinsic chemical structural of agar linkage (i.e. neutral agarose and highly sulfated agaropectin) prior for its industrial potential usage. In this research work, a novel agar degrading bacterium was screened and isolated from agriculture soils. Molecular identification using nucleotide sequence of 16 s rRNA region comparison has indicated that the isolate belonged to Priestia genus, and was identified as Priestia megaterium AT7. The maximum enzyme activity was 52.85 ± 1.76 U/mL after 96 h of culture with 5% inoculum size and agitation speed of 180 rpm. Results indicated that the optimal condition for the production of agarose was achieved at pH 7 at 50 °C. The effects of metal ions (e.g. Ca2+, Co2+, Cu2+, Mn2+, Mg2+, Zn2+ and Fe2+) and organic solvents (e.g. acetone, ethanol, methanol, hexane and isopropanol) on enzyme activity were also evaluated. Marine algae hydrolysis evaluation at concentration of 0.1% indicated the enzyme produced reducing sugar of 683.94 ± 26.93 µg/g after 24 h of treatment. It was also found that the highest antioxidant activities obtained after 20 h of treatment was able to achieve 81.76 ± 3.90% at marine algae concentration of 0.1%. The findings obtained from this research work shows the promising application of extracellular agarase to saccharify marine algae for the recovery of value-added bioproducts.

Enzymatic preparation and potential applications of agar oligosaccharides: a review

Oligosaccharides derived from agar, that is, agarooligosaccharides and neoagarooligosaccharides, have demonstrated various kinds of bioactivities which have been utilized in a variety of fields. Enzymatic hydrolysis is a feasible approach that principally allows for obtaining specific agar oligosaccharides in a sustainable way at an industrial scale. This review summarizes recent technologies employed to improve the properties of agarase. Additionally, the relationship between the degree of polymerization, bioactivities, and potential applications of agar-derived oligosaccharides for pharmaceutical, food, cosmetic, and agricultural industries are discussed. Engineered agarase exhibited general improvement of enzymatic performance, which is mostly achieved by truncation. Rational and semi-rational design assisted by computational methods present the latest strategy for agarase improvement with greatest potential to satisfy future industrial needs. Agarase immobilized on magnetic Fe3O4 nanoparticles via covalent bond formation showed characteristics well suited for industry. Additionally, albeit with the relationship between the degree of polymerization and versatile bioactivities like anti-oxidants, anti-inflammatory, anti-microbial agents, prebiotics and in skin care of agar-derived oligosaccharides are discussed here, further researches are still needed to unravel the complicated relationship between bioactivity and structure of the different oligosaccharides.

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.

Expression and Characterization of a GH16 Family β-Agarase Derived from the Marine Bacterium Microbulbifer sp. BN3 and Its Efficient Hydrolysis of Agar Using Raw Agar-Producing Red Seaweeds Gracilaria sjoestedtii and Gelidium amansii as Substrates

Agarases catalyze the hydrolysis of agarose to oligosaccharides which display an array of biological and physiological functions with important industrial applications in health-related fields. In this study, the gene encoding agarase (Aga-ms-R) was cloned from Microbulbifer sp. BN3 strain. Sequence alignment indicated that Aga-ms-R belongs to the GH16 family and contains one active domain and two carbohydrate binding module (CBM) domains. The mature Aga-ms-R was expressed successfully by employing the Brevibacillus system. Purified rAga-ms-R was obtained with a specific activity of 100.75 U/mg. rAga-ms-R showed optimal activity at 50 °C and pH 7.0, and the enzyme activity was stable at 50 °C and also over the pH range of 5.0–9.0. After exposure of rAga-ms-R to 70 °C for 30 min, only partial enzyme activity remained. Thin layer chromatographic analysis of the enzymatic hydrolysate of agar obtained using rAga-ms-R disclosed that the hydrolysate comprised, in a long intermediate-stage of the hydrolysis reaction, mainly neoagarotetraose (NA4) and neoagarohexaose (NA6) but ultimately, predominantly neoagarotetraose and trace amounts of neoagarobiose (NA2). Hydrolysates of the raw red seaweeds Gracilaria sjoestedtii and Gelidium amansii, produced by incubation with rAga-ms-R, were mainly composed of neoagarotetraose. The results demonstrate the high efficiency of rAga-ms-R in producing neoagaraoligosaccharide under low-cost conditions.

Implications of agar and agarase in industrial applications of sustainable marine biomass

Agar, a major component of the cell wall of red algae, is an interesting heteropolysaccharide containing an unusual sugar, 3,6-anhydro-L-galactose. It is widely used as a valuable material in various industrial and experimental applications due to its characteristic gelling and stabilizing properties. Agar-derived oligosaccharides or mono-sugars produced by various agarases have become a promising subject for research owing to their unique biological activities, including anti-obesity, anti-diabetic, immunomodulatory, anti-tumor, antioxidant, skin-whitening, skin-moisturizing, anti-fatigue, and anti-cariogenic activities. Agar is also considered as an alternative sustainable source of biomass for chemical feedstock and biofuel production to substitute for the fossil resource. In this review, we summarize various biochemically characterized agarases, which are useful for industrial applications, such as neoagarooligosaccharide or agarooligosaccharide production and saccharification of agar. Additionally, we succinctly discuss various recent studies that have been conducted to investigate the versatile biological activities of agar-derived saccharides and biofuel production from agar biomass. This review provides a basic framework for understanding the importance of agarases and agar-derived saccharides with broad applications in pharmaceutical, cosmetic, food, and bioenergy industries.

Mutagenesis on the surface of a β-agarase from Vibrio sp. ZC-1 increased its thermo-stability

The recombinant rAgaZC-1 was a family GH50 β-agarase from Vibrio sp. ZC-1 (CICC 24670). In this paper, the mutant D622G (i.e., mutate the aspartic acid at position 622 to glycine) had better thermo-stability than rAgaZC-1, showing 1.5℃ higher T₅₀¹⁰ (the temperature at which the half-time is 10 min) and 4-folds of half-time at 41℃, while they had almost same optimum temperature (38.5℃), optimum pH (pH6.0) and catalytic efficiency. Thermal deactivation kinetical analysis showed that D622G had higher activation energy for deactivation, enthalpy and Gibbs free energy than rAgaZC-1, indicating that more energy is required by D622G for deactivation. Substrate can protect agarase against thermal inactivation, especially D622G. Hence the yield of agarose hydrolysis catalyzed by D622G was higher than that by rAgaZC-1. The models of D622G and rAgaZC-1 predicted by homology modeling were compared to find that it is the improved distribution of surface electrostatic potential, great symmetric positive potential and more hydrophobic interactions of D622G that enhance the thermo-stability.

Draft Genome Sequence of Bacillus salarius IM0101, Isolated from Hypersaline Soil in Inner Mongolia, China

Bacillus salarius IM0101 is a halophilic bacterium that was isolated from soil in Inner Mongolia, China. The genome sequence of B. salarius IM0101 contains a biomarker gene for polyhydroxyalkanoate (PHA) synthesis.

Bacillus salarius IM0101 is a halophilic bacterium that was isolated from soil in Inner Mongolia, China. The genome sequence of B. salarius IM0101 contains a biomarker gene for polyhydroxyalkanoate (PHA) synthesis. This 6.9-Mb draft genome sequence of B. salarius IM0101 will provide new insights into the organism’s PHA production machinery.

A novel GH16 beta-agarase isolated from a marine bacterium, Microbulbifer sp. BN3 and its characterization and high-level expression in Pichia pastoris

An agar-degrading bacterium, strain BN3, was isolated from a coastal soil sample collected in Taiwan Strait, China and identified to be a novel species of the genus Microbulbifer. The gene (N3-1) encoding for a novel β-agarase from the isolate was cloned and sequenced. It encoded a mature protein with 274 amino acids and a calculated molecular mass of 34.3 kDa. The deduced amino acid sequence manifested sequence similarity (61-84% identity) to characterized β-agarases in the glycoside hydrolase family 16. The recombinant agarase was hyper-produced extracellularly using Pichia pastoris as the host. After induction in a shake flask for 96 h, the yield of recombinant N3-1 protein reached 0.406 mg/mL, and the enzyme activity attained 502.1 U/mL. The enzyme purified by ion exchange chromatography displayed a specific activity of 6447 U/mg at pH 6.0 and 50 °C. The optimal pH and temperature for agarase activity were approximately 6 and 50 °C, respectively. The pattern of agarose hydrolysis showed that the enzyme was an endo-type β-agarase, capable of hydrolyzing agarose and Gracilaria lemaneiformis, with neoagarobiose and neoagarotetraose as the final main products.

Molecular cloning, expression, and functional characterization of the β-agarase AgaB-4 from Paenibacillus agarexedens

In this study, a β-agarase gene, agaB-4, was isolated for the first time from the agar-degrading bacterium Paenibacillus agarexedens BCRC 17346 by using next-generation sequencing. agaB-4 consists of 2652 bp and encodes an 883-amino acid protein with an 18-amino acid signal peptide. agaB-4 without the signal peptide DNA was cloned and expressed in Escherichia coli BL21(DE3). His-tagged recombinant AgaB-4 (rAgaB-4) was purified from the soluble fraction of E. coli cell lysate through immobilized metal ion affinity chromatography. The optimal temperature and pH of rAgaB-4 were 55 °C and 6.0, respectively. The results of a substrate specificity test showed that rAgaB-4 could degrade agar, high-melting point agarose, and low-melting point agarose. The V_max and K_m of rAgaB-4 for low-melting point agarose were 183.45 U/mg and 3.60 mg/mL versus 874.61 U/mg and 9.29 mg/mL for high-melting point agarose, respectively. The main products of agar and agarose hydrolysis by rAgaB-4 were confirmed to be neoagarotetraose. Purified rAgaB-4 can be used in the recovery of DNA from agarose gels and has potential application in agar degradation for the production of neoagarotetraose.

Extracellular expression of a novel β-agarase from Microbulbifer sp. Q7, isolated from the gut of sea cucumber

A novel endo-type β-agarase was cloned from an agar-degrading bacterium, Microbulbifer sp. Q7 (CGMCC No. 14061), that was isolated from sea cucumber gut. The agarase-encoding gene, ID2563, consisted of 1800 bp that encoded a 599-residue protein with a signal peptide of 19 amino acids. Sequence analysis suggested that the agarase belongs to the GH16 family. The agarase was expressed in Escherichia coli with a total activity of 4.99 U/mL in fermentation medium. The extracellular enzyme activity accounted for 65.73% of the total activity, which indicated that the agarase can be extracellularly secreted using the wild-type signal peptide from Microbulbifer sp. Q7. The agarase exhibited maximal activity at approximately 40 °C and pH 6.0. It was stable between pH 6.0 and pH 9.0, which was a much wider range than most of the reported agarases. The agarase was sensitive to some metal ions (Cu²⁺, Zn²⁺ and Fe³⁺), but was resistant to urea and SDS. The agarase hydrolyzed β-1,4-glycosidic linkages of agarose, primarily yielding neoagarotetraose and neoagarohexaose as the final products. These indicate that this recombinant agarase can be an effective tool for the preparing functional neoagaro-oligosaccharides.

Characterization and overexpression of a glycosyl hydrolase family 16 beta-agarase YM01-1 from marine bacterium Catenovulum agarivorans YM01T

Agar, usually extracted from seaweed, has a wide variety of industrial applications due to its gelling and stabilizing characteristics. Agarases are the enzymes which hydrolyze agar into agar oligosaccharides. The produced agar oligosaccharides have been widely used in cosmetic, food, and medical fields due to their biological functions. A beta-agarase gene, YM01-1, was cloned and expressed from a marine bacterium Catenovulum agarivorans YM01^T. The encoding agarase of YM01-1 consisted of 331 amino acids with an apparent molecular mass of 37.7 kDa and a 23-amino-acids signal peptide. YM01-1 belongs to glycoside hydrolase 16 (GH16) family based on the amino acid sequence homology. The optimum pH and temperature for its activity was 7.0 and 50 °C, respectively. YM01-1 was stable at a pH of pH 6.0-9.0 and temperatures below 45 °C. Thin layer chromatography (TLC) and ion trap mass spectrometer of the YM01-1 hydrolysis products displayed that YM01-1 was an endo-type β-agarase and degrades agarose, neoagarohexaose, neoagarotetraose into neoagarobiose. The K_m, V_max, K_cat and K_cat/K_m values of the YM01-1 for agarose were 8.69 mg/ml, 4.35 × 10³ U/mg, 2.4 × 10³ s^-1 and 2.7 × 10⁶ s^-1 M^-1, respectively. Hence, the enzyme with high agarolytic activity and single end product was different from other GH16 agarases, which has potential applications for the production of oligosaccharides with remarkable activities.

Systematics of haloarchaea and biotechnological potential of their hydrolytic enzymes

Halophilic archaea, also referred to as haloarchaea, dominate hypersaline environments. To survive under such extreme conditions, haloarchaea and their enzymes have evolved to function optimally in environments with high salt concentrations and, sometimes, with extreme pH and temperatures. These features make haloarchaea attractive sources of a wide variety of biotechnological products, such as hydrolytic enzymes, with numerous potential applications in biotechnology. The unique trait of haloarchaeal enzymes, haloenzymes, to sustain activity under hypersaline conditions has extended the range of already-available biocatalysts and industrial processes in which high salt concentrations inhibit the activity of regular enzymes. In addition to their halostable properties, haloenzymes can also withstand other conditions such as extreme pH and temperature. In spite of these benefits, the industrial potential of these natural catalysts remains largely unexplored, with only a few characterized extracellular hydrolases. Because of the applied impact of haloarchaea and their specific ability to live in the presence of high salt concentrations, studies on their systematics have intensified in recent years, identifying many new genera and species. This review summarizes the current status of the haloarchaeal genera and species, and discusses the properties of haloenzymes and their potential industrial applications.

Halococcus agarilyticus sp. nov., an agar-degrading haloarchaeon isolated from commercial salt

Two agar-degrading halophilic archaeal strains, 62ET and 197A, were isolated from commercial salt samples. Cells were non-motile cocci, approximately 1.2–2.0 µm in diameter and stained Gram-negative. Colonies were pink-pigmented. Strain 62ET was able to grow with 24–30 % (w/v) NaCl (optimum, 27 %), at pH 6.5–8.5 (optimum, pH 7.5) and at 22–47 °C (optimum, 42 °C). The 16S rRNA gene sequences of strains 62ET and 197A were identical, and the level of DNA–DNA relatedness between them was 90 and 90 % (reciprocally). The closest relative was Halococcus saccharolyticus JCM 8878T with 99.7 % similarity in 16S rRNA orthologous gene sequences, followed by Halococcus salifodinae JCM 9578T (99.6 %), while similarities with other species of the genus Halococcus were equal to or lower than 95.1 %. The rpoB′ gene tree strongly supported that the two strains were members of the genus Halococcus . Mean DNA–DNA relatedness between strain 62ET and H. saccharolyticus JCM 8878T and H. salifodinae JCM 9578T was 46 and 44 %, respectively. The major polar lipids were archaeol derivatives of phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, derived from both C20C20 and C20C25 archaeol, and sulfated diglycosyl archaeol-1. Several unidentified glycolipids were present. Based on the phenotypic and phylogenetic analyses, the isolates are considered to represent a novel species of the genus Halococcus , for which the name Halococcus agarilyticus sp. nov. is proposed. The type strain is 62ET ( = JCM 19592T = KCTC 4143T).

Extracellular production of a novel endo-β-agarase AgaA from Pseudomonas vesicularis MA103 that cleaves agarose into neoagarotetraose and neoagarohexaose

The gene agaA, of the isolated marine bacterium Pseudomonas vesicularis MA103, comprised 2958-bp nucleotides encoding a putative agarase AgaA of 985 amino acids, which was predicted to contain a signal peptide of 29 amino acids in the N-terminus, a catalytic domain of glycoside hydrolase 16 (GH16) family, a bacterial immunoglobulin group 2 (Big 2), and three carbohydrate binding modules 6 (CBM 6). The gene agaA was cloned and overexpressed in Escherichia coli, and the optimum temperatures for AgaA overexpression were 16, 20 and 24 °C. The agaA was cloned without its signal peptide for cytosolic production overexpression, whereas it was cloned with the heterologous signal peptide PelB and its endogenous signal peptide for periplasmic and extracellular productions, respectively. Extracellular and periplasmic rAgaA showed greater activity than that of cytosolic rAgaA, indicating that membrane translocation of AgaA may encourage proper protein folding. Time-course hydrolysis of agarose by rAgaA was accomplished and the products were analyzed using thin layer chromatography and matrix-assisted laser desorption inoization-time of flight mass spectrometry, indicating that AgaA from P. vesicularis was an endo-type β-1,4 agarase that cleaved agarose into neoagarotetraose and neoagarohexaose as the final products.

Draft genome sequence of the agarolytic haloarchaeon Halobellus rufus type strain CBA1103

The extremely halophilic archaeon Halobellus rufus type strain CBA1103(T) (CECT 8423(T) and JCM 19434(T)) was isolated from non-purified solar salt and characterized as an agarase producer. The draft genome sequence contains 3852 303 bp with a G + C content of 64.1% and includes genomic information on various carbohydrate-active enzymes. This is the first sequenced genome of the genus Halobellus, and is expected to provide general sequence information for halophilic carbohydrate-active enzymes and opportunities for biotechnological applications of novel halophilic enzymes.

Draft genome sequence of Halolamina rubra CBA1107(T), an agarolytic haloarchaeon isolated from solar salt

Halolamina rubra CBA1107(T) (=CECT 8421(T), JCM 19436(T)), an extremely halophilic archaeon, was isolated from non-purified solar salt in the Republic of Korea. H. rubra CBA1107(T) shows agarase activity, and its draft genome contains 2955,064bp with a G+C content of 69.0%. This is the first genome that has been sequenced in the genus Halolamina.