Probing the molecular determinant for the catalytic efficiency of L-arabinose isomerase from Bacillus licheniformis

Metal-based micro-composite of L-arabinose isomerase and L-ribose isomerase for the sustainable synthesis of L-ribose and D-talose

The biocatalysts are broadly explored in the biological transformation processes. The enzyme cascade catalysis involves various catalytic activities in a sequential process to produce the desired product including the formation of reaction intermediates. Enzyme immobilization is a method in which enzymes are confined within a support or matrix either physically or chemically to enhance their relative stability and catalytic activity in the enzyme cascade catalysis. In view of this, L-arabinose isomerase (L-AI) and L-ribose isomerase (L-RI) were immobilized on zeolite based metal framework as a micro-composite construct (DEMC@L-AI+L-RI) using linker, and metal ions. Such immobilization could be of great significance and provide several advantages like mesoporous surface for enzyme adsorption, desirable functionality in the production of products in enzyme cascade reaction, high storage stability and enhanced recyclability. The developed DEMC@L-AI+L-RI was characterized using SEM, FTIR, CLSM and TGA. The immobilization yield was 32% and loading of enzyme was 22% on the surface of micro-composite. The DEMC@L-AI+L-RI showed relatively stable catalytic activity at pH 5-6 and temperature 40 °C. The catalytic efficiency (k_cat/K_m) of both the enzymes was increased by 1.5-fold after immobilization. With the immobilized biocatalyst, bioconversion of L-arabinose to L-ribose was 22.6% and D-galactose to D-talose was 15.2%. The reusability of developed biocatalyst for more than six cycles was observed for more than 50% yield of the sugars. The conversion of biomass sugars from beetroot and onion waste residues was 20% and 14% to produce ribose and talose, respectively.

Optimization of fermentation conditions for production of l-arabinose isomerase of Lactobacillus plantarum WU14

As a substitute sweetener for sucrose, d-tagatose is widely used in products, such as health drinks, yogurt, fruit juices, baked goods, confectionery, and pharmaceutical preparations. In the fermentation process of l-AI produced by Lactobacillus plantarum, d-tagatose is produced through biotransformation and this study was based on the fermentation process of Lactobacillus plantarum WU14 producing l-AI to further research the biotransformation and separation process of d-tagatose. The kinetics of cell growth, substrate consumption, and l-arabinose isomerase formation were established by nonlinear fitting, and the fitting degrees were 0.996, 0.994, and 0.991, respectively, which could better reflect the change rule of d-tagatose biotransformation in the fermentation process of L. plantarum WU14. The separation process of d-tagatose was identified by decolorization, protein removal, desalination, and freeze drying, initially. Finally, the volume ratio of whole cell catalysts, d-galactose, and borate was 5:1:2 at 60°C, pH 7.17 through borate complexation; then, after 24 hr of conversion, the yield of d-tagatose was 58 g/L.

Characterization of an L-Arabinose Isomerase from Bacillus velezensis and Its Application for L-Ribulose and L-Ribose Biosynthesis

L-Ribulose and L-ribose are two high-value unnatural sugars that can be biosynthesized by sugar isomerases. In this paper, an L-arabinose isomerase (BvAI) from Bacillus velezensis CICC 24777 was cloned and overexpressed in Escherichia coli BL21 (DE3) strain. The maximum activity of recombinant BvAI was observed at 45 °C and pH 8.0, in the presence of 1.0 mM Mn²⁺. Approximately 207.2 g/L L-ribulose was obtained from 300 g/L L-arabinose in 1.5 h by E. coli harboring BvAI. In addition, approximately 74.25 g/L L-ribose was produced from 300 g/L L-arabinose in 7 h by E. coli co-expressing BvAI and L-RI from Actinotalea fermentans ATCC 43279 (AfRI). This study provides a feasible approach for producing L-ribose from L-arabinose using a co-expression system harboring L-Al and L-RI.

Galactose to tagatose isomerization at moderate temperatures with high conversion and productivity

There are many industrially-relevant enzymes that while active, are severely limited by thermodynamic, kinetic, or stability issues (isomerases, lyases, transglycosidases). In this work, we study Lactobacillus sakeil-arabinose isomerase (LsLAI) for d-galactose to d-tagatose isomerization—that is limited by all three reaction parameters. The enzyme demonstrates low catalytic efficiency, low thermostability at temperatures > 40 °C, and equilibrium conversion < 50%. After exploring several strategies to overcome these limitations, we show that encapsulating LsLAI in gram-positive Lactobacillus plantarum that is chemically permeabilized enables reactions at high rates, high conversions, and elevated temperatures. In a batch process, this system enables ~ 50% conversion in 4 h starting with 300 mM galactose (an average productivity of 37 mM h⁻¹), and 85% conversion in 48 h. We suggest that such an approach may be invaluable for other enzymatic processes that are similarly kinetically-, thermodynamically-, and/or stability-limited.

Production of tagatose, a sugar substitute, by isomerization of galactose suffers from unfavorable enzymatic kinetics, low enzyme stability, and low equilibrium constant. Here, the authors simultaneously overcome these limitations by encapsulating l-arabinose isomerase in permeabilized Lactobacillus plantarum.

Construction of genetically engineered Candida tropicalis for conversion of l-arabinose to l-ribulose

For the biological production of l-ribulose, conversion by enzymes or resting cells has been investigated. However, expensive or concentrated substrates, an additional purification step to remove borate and the requirement for cell cultivation and harvest steps before utilization of resting cells make the production process complex and unfavorable. Microbial fermentation may help overcome these limitations. In this study, we constructed a genetically engineered Candida tropicalis strain to produce l-ribulose by fermentation with a glucose/l-arabinose mixture. For the uptake of l-arabinose as a substrate and conversion of l-arabinose to l-ribulose, two heterologous genes coding for l-arabinose transporter and l-arabinose isomerase, were constitutively expressed in C. tropicalis under the GAPDH promoter. The Arabidopsis thaliana-originated l-arabinose transporter gene (STP2)-expressing strain exhibited a high l-arabinose uptake rate of 0.103 g/g cell/h and the expression of l-arabinose isomerase from Lactobacillus sakei 23 K showed 30% of conversion (9 g/L) from 30 g/L of l-arabinose. This genetically engineered strain can be used for l-ribulose production by fermentation using mixed sugars of glucose and l-arabinose.

Rational Design of Bacillus coagulans NL01 l-Arabinose Isomerase and Use of Its F279I Variant in d-Tagatose Production

d-Tagatose is a prospective functional sweetener that can be produced by l-arabinose isomerase (AI) from d-galactose. To improve the activity of AI toward d-galactose, the AI of Bacillus coagulans was rationally designed on the basis of molecular modeling and docking. After alanine scanning and site-saturation mutagenesis, variant F279I that exhibited improved activity toward d-galactose was obtained. The optimal temperature and pH of F279I were determined to be 50 °C and 8.0, respectively. This variant possessed 1.4-fold catalytic efficiency compared with the wild-type (WT) enzyme. The recombinant Escherichia coli overexpressing F279I also showed obvious advantages over the WT in biotransformation. Under optimal conditions, 67.5 and 88.4 g L^-1 d-tagatose could be produced from 150 and 250 g L^-1 d-galactose, respectively, in 15 h. The biocatalyst constructed in this study presents a promising alternative for large-scale d-tagatose production.

Characterization of an L-arabinose isomerase from Bacillus coagulans NL01 and its application for D-tagatose production

Background

L-arabinose isomerase (AI) is a crucial catalyst for the biotransformation of D-galactose to D-tagatose. In previous reports, AIs from thermophilic bacterial strains had been wildly researched, but the browning reaction and by-products formed at high temperatures restricted their applications. By contrast, AIs from mesophilic Bacillus strains have some different features including lower optimal temperatures and lower requirements of metallic cofactors. These characters will be beneficial to the development of a more energy-efficient and safer production process. However, the relevant data about the kinetics and reaction properties of Bacillus AIs in D-tagatose production are still insufficient. Thus, in order to support further applications of these AIs, a comprehensive characterization of a Bacillus AI is needed.

Results

The coding gene (1422 bp) of Bacillus coagulans NL01 AI (BCAI) was cloned and overexpressed in the Escherichia coli BL21 (DE3) strain. The enzymatic property test showed that the optimal temperature and pH of BCAI were 60 °C and 7.5 respectively. The raw purified BCAI originally showed high activity in absence of outsourcing metallic ions and its thermostability did not change in a low concentration (0.5 mM) of Mn²⁺ at temperatures from 70 °C to 90 °C. Besides these, the catalytic efficiencies (k_cat/K_m) for L-arabinose and D-galactose were 8.7 mM^-1 min^-1 and 1.0 mM^-1 min^-1 respectively. Under optimal conditions, the recombinant E. coli cell containing BCAI could convert 150 g L^-1 and 250 g L^-1 D-galactose to D-tagatose with attractive conversion rates of 32 % (32 h) and 27 % (48 h).

Conclusions

In this study, a novel AI from B. coagulans NL01was cloned, purified and characterized. Compared with other reported AIs, this AI could retain high proportions of activity at a broader range of temperatures and was less dependent on metallic cofactors such as Mn²⁺. Its substrate specificity was understood deeply by carrying out molecular modelling and docking studies. When the recombinant E. coli expressing the AI was used as a biocatalyst, D-tagatose could be produced efficiently in a simple one-pot biotransformation system.

Electronic supplementary material

The online version of this article (doi:10.1186/s12896-016-0286-5) contains supplementary material, which is available to authorized users.

The secreted L-arabinose isomerase displays anti-hyperglycemic effects in mice

Background

The l-arabinose isomerase is an intracellular enzyme which converts l-arabinose into l-ribulose in living systems and d-galactose into d-tagatose in industrial processes and at industrial scales. d-tagatose is a natural ketohexose with potential uses in pharmaceutical and food industries. The d-galactose isomerization reaction is thermodynamically equilibrated, and leads to secondary subproducts at high pH. Therefore, an attractive l-arabinose isomerase should be thermoactive and acidotolerant with high catalytic efficiency. While many reports focused on the set out of a low cost process for the industrial production of d-tagatose, these procedures remain costly. When compared to intracellular enzymes, the production of extracellular ones constitutes an interesting strategy to increase the suitability of the biocatalysts.

Results

The l-arabinose isomerase (l-AI) from Lactobacillus sakei was expressed in Lactococcus lactis in fusion with the signal peptide of usp45 (SP_Usp45). The l-AI protein and activity were detected only in the supernatant of the induced cultures of the recombinant L. lactis demonstrating the secretion in the medium of the intracellular L. sakeil-AI in an active form. Moreover, we showed an improvement in the enzyme secretion using either (1) L. lactis strains deficient for their two major proteases, ClpP and HtrA, or (2) an enhancer of protein secretion in L. lactis fused to the recombinant l-AI with the SP_Usp45. Th l-AI enzyme secreted by the recombinant L. lactis strains or produced intracellularly in E. coli, showed the same functional properties than the native enzyme. Furthermore, when mice are fed with the L. lactis strain secreting the l-AI and galactose, tagatose was produced in vivo and reduced the glycemia index.

Conclusions

We report for the first time the secretion of the intracellular l-arabinose isomerase in the supernatant of food grade L. lactis cultures with hardly display other secreted proteins. The secreted l-AI originated from the food grade L. sakei 23 K was active and showed the same catalytic and structural properties as the intracellular enzyme. The L. lactis strains secreting the l-arabinose isomerase has the ability to produce d-tagatose in vivo and conferred an anti-hyperglycemic effect to mice.

L-Arabinose isomerase and its use for biotechnological production of rare sugars

L-Arabinose isomerase (AI), a key enzyme in the microbial pentose phosphate pathway, has been regarded as an important biological catalyst in rare sugar production. This enzyme could isomerize L-arabinose into L-ribulose, as well as D-galactose into D-tagatose. Both the two monosaccharides show excellent commercial values in food and pharmaceutical industries. With the identification of novel AI family members, some of them have exhibited remarkable potential in industrial applications. The biological production processes for D-tagatose and L-ribose (or L-ribulose) using AI have been developed and improved in recent years. Meanwhile, protein engineering techniques involving rational design has effectively enhanced the catalytic properties of various AIs. Moreover, the crystal structure of AI has been disclosed, which sheds light on the understanding of AI structure and catalytic mechanism at molecular levels. This article reports recent developments in (i) novel AI screening, (ii) AI-mediated rare sugar production processes, (iii) molecular modification of AI, and (iv) structural biology study of AI. Based on previous reports, an analysis of the future development has also been initiated.

Probing the molecular determinant of the lipase-specific foldase Lif26 for the interaction with its cognate Lip26

As a steric chaperone, the lipase-specific foldase Lif26 from Acinetobacter sp. XMZ-26 is required for correct folding of the lipase Lip26 in in vivo co-expression and in vitro refolding systems. Lif26 interacts with Lip26 as determined by yeast two hybrid assays in vivo and GST pull-down experiments in vitro. To study the molecular determinants of the interaction between Lif26 and Lip26, a homology model-based screening of residues, molecular dynamics (MD) simulation-based calculation of interaction energies, and site-directed mutagenesis to alter individual screened residues were applied. One conserved amino acid in the C-terminal mini-domain of Lif26, Arg332, was involved in the interaction with Lip26. Arg332 could not be replaced by any other residue, based on saturated site-directed mutagenesis, and it formed a conserved and stable salt bridge with Glu112 of Lip26, which may contribute to binding specificity. The residues surrounding Arg332, such as Trp288 in α9, likely stabilized Arg332 in the proper conformation for the interaction with Lip26.

Carbohydrate force fields

Carbohydrates present a special set of challenges to the generation of force fields. First, the tertiary structures of monosaccharides are complex merely by virtue of their exceptionally high number of chiral centers. In addition, their electronic characteristics lead to molecular geometries and electrostatic landscapes that can be challenging to predict and model. The monosaccharide units can also interconnect in many ways, resulting in a large number of possible oligosaccharides and polysaccharides, both linear and branched. These larger structures contain a number of rotatable bonds, meaning they potentially sample an enormous conformational space. This article briefly reviews the history of carbohydrate force fields, examining and comparing their challenges, forms, philosophies, and development strategies. Then it presents a survey of recent uses of these force fields, noting trends, strengths, deficiencies, and possible directions for future expansion.

Heterologous expression and characterization of Bacillus coagulans L-arabinose isomerase

Bacillus coagulans has been of great commercial interest over the past decade owing to its strong ability of producing optical pure L: -lactic acid from both hexose and pentose sugars including L: -arabinose with high yield, titer and productivity under thermophilic conditions. The L: -arabinose isomerase (L-AI) from Bacillus coagulans was heterologously over-expressed in Escherichia coli. The open reading frame of the L-AI has 1,422 nucleotides encoding a protein with 474 amino acid residues. The recombinant L-AI was purified to homogeneity by one-step His-tag affinity chromatography. The molecular mass of the enzyme was estimated to be 56 kDa by SDS-PAGE. The enzyme was most active at 70°C and pH 7.0. The metal ion Mn(2+) was shown to be the best activator for enzymatic activity and thermostability. The enzyme showed higher activity at acidic pH than at alkaline pH. The kinetic studies showed that the K (m), V (max) and k (cat)/K (m) for the conversion of L: -arabinose were 106 mM, 84 U/mg and 34.5 mM(-1)min(-1), respectively. The equilibrium ratio of L: -arabinose to L: -ribulose was 78:22 under optimal conditions. L: -ribulose (97 g/L) was obtained from 500 g/l of L: -arabinose catalyzed by the enzyme (8.3 U/mL) under the optimal conditions within 1.5 h, giving at a substrate conversion of 19.4% and a production rate of 65 g L(-1) h(-1).

The acid-tolerant L-arabinose isomerase from the mesophilic Shewanella sp. ANA-3 is highly active at low temperatures

Background

L-arabinose isomerases catalyse the isomerization of L-arabinose into L-ribulose at insight biological systems. At industrial scale of this enzyme is used for the bioconversion of D-galactose into D-tagatose which has many applications in pharmaceutical and agro-food industries. The isomerization reaction is thermodynamically equilibrated, and therefore the bioconversion rates is shifted towards tagatose when the temperature is increased. Moreover, to prevent secondary reactions it will be of interest to operate at low pH. The profitability of this D-tagatose production process is mainly related to the use of lactose as cheaper raw material. In many dairy products it will be interesting to produce D-tagatose during storage. This requires an efficient L-arabinose isomerase acting at low temperature and pH values.

Results

The gene encoding the L-arabinose isomerase from Shewanella sp. ANA-3 was cloned and overexpressed in Escherichia coli. The purified protein has a tetrameric arrangement composed by four identical 55 kDa subunits. The biochemical characterization of this enzyme showed that it was distinguishable by its maximal activity at low temperatures comprised between 15-35°C. Interestingly, this biocatalyst preserves more than 85% of its activity in a broad range of temperatures from 4.0 to 45°C. Shewanella sp. ANA-3 L-arabinose isomerase was also optimally active at pH 5.5-6.5 and maintained over 80% of its activity at large pH values from 4.0 to 8.5. Furthermore, this enzyme exhibited a weak requirement for metallic ions for its activity evaluated at 0.6 mM Mn²⁺. Stability studies showed that this protein is highly stable mainly at low temperature and pH values. Remarkably, T268K mutation clearly enhances the enzyme stability at low pH values. Use of this L-arabinose isomerase for D-tagatose production allows the achievement of attractive bioconversion rates of 16% at 4°C and 34% at 35°C.

Conclusions

Here we reported the purification and the biochemical characterization of the novel Shewanella sp. ANA-3 L-arabinose isomerase. Determination of the biochemical properties demonstrated that this enzyme was highly active at low temperatures. The generated T268K mutant displays an increase of the enzyme stability essentially at low pH. These features seem to be very attractive for the bioconversion of D-galactose into D-tagatose at low temperature which is very interesting from industrial point of view.

The acid tolerant L-arabinose isomerase from the food grade Lactobacillus sakei 23K is an attractive D-tagatose producer

The araA gene encoding an L-arabinose isomerase (L-AI) from the psychrotrophic and food grade Lactobacillus sakei 23K was cloned, sequenced and over-expressed in Escherichia coli. The recombinant enzyme has an apparent molecular weight of nearly 220 kDa, suggesting it is a tetramer of four 54 kDa monomers. The enzyme is distinguishable from previously reported L-AIs by its high activity and stability at temperatures from 4 to 40 degrees C, and pH from 3 to 8, and by its low metal requirement of only 0.8 mM Mn(2+) and 0.8 mM Mg(2+) for its maximal activity and thermostability. Enzyme kinetic studies showed that this enzyme displays a high catalytic efficiency allowing D-galactose bioconversion rates of 20% and 36% at 10 and 45 degrees C, respectively, which are useful for commercial production of D-tagatose.