A novel gene encoding xanthan lyase of Paenibacillus alginolyticus strain XL-1

Xanthan: enzymatic degradation and novel perspectives of applications

The extracellular heteropolysaccharide xanthan, synthesized by bacteria of the genus Xanthomonas, is widely used as a thickening and stabilizing agent across the food, cosmetic, and pharmaceutical sectors. Expanding the scope of its application, current efforts target the use of xanthan to develop innovative functional materials and products, such as edible films, eco-friendly oil surfactants, and biocompatible composites for tissue engineering. Xanthan-derived oligosaccharides are useful as nutritional supplements and plant defense elicitors. Development and processing of such new functional materials and products often necessitate tuning of xanthan properties through targeted structural modification. This task can be effectively carried out with the help of xanthan-specific enzymes. However, the complex molecular structure and intricate conformational behavior of xanthan create problems with its enzymatic hydrolysis or modification. This review summarizes and analyzes data concerning xanthan-degrading enzymes originating from microorganisms and microbial consortia, with a particular focus on the dependence of enzymatic activity on the structure and conformation of xanthan. Through a comparative study of xanthan-degrading pathways found within various bacterial classes, different microbial enzyme systems for xanthan utilization have been identified. The characterization of these new enzymes opens new perspectives for modifying xanthan structure and developing innovative xanthan-based applications. KEY POINTS: • The structure and conformation of xanthan affect enzymatic degradation. • Microorganisms use diverse multienzyme systems for xanthan degradation. • Xanthan-specific enzymes can be used to develop xanthan variants for novel applications.

Dissecting the essential role of N-glycosylation in catalytic performance of xanthan lyase

Modified xanthan produced by xanthan lyase has broad application prospects in the food industry. However, the catalytic performance of xanthan lyase still needs to be improved through rational design. To address this problem, in this work, the glycosylation and its influences on the catalytic performance of a xanthan lyase (EcXly), which was heterologously expressed in Escherichia coli, were reported. Liquid chromatography coupled to tandem mass spectrometry analysis revealed that the N599 site of EcXly was modified by a single N-glycan chain. Based on sequence alignment and three-dimensional structure prediction, it could be deduced that the N599 site was located in the catalytic domain of EcXly and in close proximity to the catalytic residues. After site-directed mutagenesis of N599 with alanine, aspartic acid and glycine, respectively, the EcXly and its mutants were characterized and compared. The results demonstrated that elimination of the N-glycosylation had diminished the specific activity, pH stability, and substrate affinity of EcXly. Fluorescence spectra further revealed that the glycosylation could significantly affect the overall tertiary structure of EcXly. Therefore, in prokaryotic hosts, the N-glycosylation could influence the catalytic performance of the enzyme by changing its structure. To the best of our knowledge, this is the first report about the post-translational modification of xanthan lyase in prokaryotes. Overall, our work enriched research on the role of glycan chains in the functional performance of proteins expressed in prokaryotes and should be valuable for the rational design of xanthan lyase to produce modified xanthan for industrial application.

Novel β-Glucosidase Mibgl3 from Microbacterium sp. XT11 with Oligoxanthan-Hydrolyzing Activity

The enzymatic pathway of xanthan depolymerization has been predicted previously; however, the β-glucosidase and unsaturated glucuronyl hydrolase in this system have not been cloned and characterized. This lack of knowledge hinders rational modification of xanthan and exploration of new applications. In this work, we report on the properties of Mibgl3, a xanthan-degrading enzyme isolated from Microbacterium sp. XT11. Mibgl3 exhibits typical structural features of the GH3 family but shares low sequence identity with reported GH3 enzymes. The activity of Mibgl3 can be inhibited by Cu²⁺, Fe²⁺, Zn²⁺, and glucose. Unlike most β-glucosidases, Mibgl3 can tolerate a wide pH range and is activated by high concentrations of NaCl. This improves the commercial value of Mibgl3. In particular, Mibgl3 exhibits higher substrate specificity toward oligoxanthan than other β-glucosidases. Ion chromatography, ultrahigh-performance liquid chromatography-mass spectrometry (UPLC-MS), and GC-MS results showed that Mibgl3 could effectively hydrolyze oligoxanthan to release glucose and glucuronate. Therefore, Mibgl3 might play an important role in xanthan depolymerization by functioning as hydrolase of both the xanthan backbone and sidechains. This knowledge of the enzymatic properties and hydrolysis mechanism of a β-glucosidase will be beneficial for future applications.

Production and purification of a novel xanthan lyase from a xanthan-degrading Microbacterium sp. strain XT11

A xanthan lyase was produced and purified from the culture supernatant of an excellent xanthan-modifying strain Microbacterium sp. XT11. Xanthan lyase was induced by xanthan but was inhibited by its structural monomer glucose. Its production by strain XT11 is much higher than that by all other reported strains. The purified xanthan lyase has a molecular mass of 110 kDa and a specific activity of 28.2 U/mg that was much higher than that of both Paenibacillus and Bacillus lyases. It was specific on the pyruvated mannosyl residue in the intact xanthan molecule, but about 50% lyase activity remained when xanthan was partially depyruvated. Xanthan lyase was optimally active at pH 6.0–6.5 and 40°C and alkali-tolerant at a high pH value of 11.0. The metal ions including K⁺, Ca²⁺, Na⁺, Mg²⁺, Mn²⁺, and Li⁺ strongly stimulated xanthan lyase activity but ions Zn²⁺ and Cu²⁺ were its inhibitor. Xanthan lyase should be a novel enzyme different from the other xanthan lyases ever reported.

Prebiotic content of bread prepared with flour from immature wheat grain and selected dextran-producing lactic acid bacteria

In the last few years the need to produce food with added value has fueled the search for new ingredients and health-promoting compounds. In particular, to improve the quality of bakery products with distinct nutritional properties, the identification of new raw materials, appropriate technologies, and specific microbial strains is necessary. In this study, different doughs were prepared, with 10% and 20% flour from immature wheat grain blended with type "0 America" wheat flour. Immature flour was obtained from durum wheat grains harvested 1 to 2 weeks after anthesis. Doughs were obtained by both the straight-dough and sourdough processes. Two selected exopolysaccharide-producing strains of lactic acid bacteria (LAB), Leuconostoc lactis A95 and Lactobacillus curvatus 69B2, were used as starters. Immature flour contained 2.21 g/100 g (dry weight) of fructo-oligosaccharides. Twenty percent immature flour in dough resulted in a shorter leavening time (4.23 ± 0.03 h) than with the control and dough with 10% immature flour. The total titratable acidity of sourdough with 20% immature flour was higher (12.75 ± 0.15 ml 0.1 N NaOH) than in the control and sourdough with 10% immature wheat flour (9.20 ml 0.1 N NaOH). Molecular analysis showed that all samples contained three LAB species identified as L. lactis, L. curvatus, and Pediococcus acidilactici. A larger amount of exopolysaccharide was found in sourdough obtained with 20% immature flour (5.33 ± 0.032 g/kg), positively influencing the exopolysaccharide content of the bread prepared by the sourdough process (1.70 ± 0.03 g/kg). The addition of 20% immature flour also led to a greater presence of fructo-oligosaccharides in the bread (900 mg/100 g dry weight), which improved its nutritional characteristics. While bread volume decreased as the concentration of immature wheat flour increased, its mechanical characteristics (stress at a strain of 30%) were the same in all samples obtained with different percentages of fructo-oligosaccharides. These data support the use of immature wheat grain flour, and exopolysaccaride-producing lactic acid bacteria in formulating functional prebiotic baked goods whose nutritional value can be suitably improved.

Deciphering the role of Paenibacillus strain Q8 in the organic matter recycling in the acid mine drainage of Carnoulès

Background

The recycling of the organic matter is a crucial function in any environment, especially in oligotrophic environments such as Acid Mine Drainages (AMDs). Polymer-degrading bacteria might play an important role in such ecosystem, at least by releasing by-products useful for the rest of the community. In this study, physiological, molecular and biochemical experiments were performed to decipher the role of a Paenibacillus strain isolated from the sediment of Carnoulès AMD.

Results

Even though Paenibacillus sp. strain Q8 was isolated from an oligotrophic AMD showing an acidic pH, it developed under both acidic and alkaline conditions and showed a heterotrophic metabolism based on the utilization of a broad range of organic compounds. It resisted to numerous metallic stresses, particularly high arsenite (As(III)) concentrations (> 1,800 mg/L). Q8 was also able to efficiently degrade polymers such as cellulose, xylan and starch. Function-based screening of a Q8 DNA-library allowed the detection of 15 clones with starch-degrading activity and 3 clones with xylan-degrading activity. One clone positive for starch degradation carried a single gene encoding a "protein of unknown function". Amylolytic and xylanolytic activities were measured both in growing cells and with acellular extracts of Q8. The results showed the ability of Q8 to degrade both polymers under a broad pH range and high As(III) and As(V) concentrations. Activity measurements allowed to point out the constitutive expression of the amylase genes and the mainly inducible expression of the xylanase genes. PACE demonstrated the endo-acting activity of the amylases and the exo-acting activity of the xylanases.

Conclusions

AMDs have been studied for years especially with regard to interactions between bacteria and the inorganic compartment hosting them. To date, no study reported the role of microorganisms in the recycling of the organic matter. The present work suggests that the strain Q8 might play an important role in the community by recycling the scarce organic matter (cellulose, hemicellulose, starch...), especially when the conditions change. Furthermore, function-based screening of a Q8 DNA library allowed to assign an amylolytic function to a gene previously unknown. AMDs could be considered as a reservoir of genes with potential biotechnological properties.

Structural and mechanistic classification of uronic acid-containing polysaccharide lyases

Polysaccharide lyases (PLs) have been assigned to 21 families based on their sequences, with ~ 50 singletons awaiting further classification. For 19 of these families, the structure of at least one protein is known. In this review, we have analyzed the available structural information and show that presently known PL families belong to six general folds. Only two general catalytic mechanisms have been observed among these PLs: (1) metal-assisted neutralization of the acidic group of the sugar next to the cleaved bond, with, rather unusually, arginine or lysine playing the role of Brønsted base and (2) neutralization of the acidic group on the sugar by a close approach of an amino or acidic group forcing its protonation and Tyr or Tyr-His acting as the Brønsted base and acid.

Polysaccharide Lyases: Recent Developments as Biotechnological Tools

Polysaccharide lyases, which are polysaccharide cleavage enzymes, act mainly on anionic polysaccharides. Produced by prokaryote and eukaryote organisms, these enzymes degrade (1,4) glycosidic bond by a beta elimination mechanism and have unsaturated oligosaccharides as major products. New polysaccharides are cleaved only by their specific polysaccharide lyases. From anionic polysaccharides controlled degradations, various biotechnological applications were investigated. This review catalogues the degradation of bacterial, plant and animal polysaccharides (neutral and anionic) by this family of carbohydrate acting enzymes.

Polysaccharide lyase: molecular cloning, sequencing, and overexpression of the xanthan lyase gene of Bacillus sp. strain GL1

When grown on xanthan as a carbon source, the bacterium Bacillus sp. strain GL1 produces extracellular xanthan lyase (75 kDa), catalyzing the first step of xanthan depolymerization (H. Nankai, W. Hashimoto, H. Miki, S. Kawai, and K. Murata, Appl. Environ. Microbiol. 65:2520-2526, 1999). A gene for the lyase was cloned, and its nucleotide sequence was determined. The gene contained an open reading frame consisting of 2,793 bp coding for a polypeptide with a molecular weight of 99,308. The polypeptide had a signal peptide (2 kDa) consisting of 25 amino acid residues preceding the N-terminal amino acid sequence of the enzyme and exhibited significant homology with hyaluronidase of Streptomyces griseus (identity score, 37.7%). Escherichia coli transformed with the gene without the signal peptide sequence showed a xanthan lyase activity and produced intracellularly a large amount of the enzyme (400 mg/liter of culture) with a molecular mass of 97 kDa. During storage at 4 degrees C, the purified enzyme (97 kDa) from E. coli was converted to a low-molecular-mass (75-kDa) enzyme with properties closely similar to those of the enzyme (75 kDa) from Bacillus sp. strain GL1, specifically in optimum pH and temperature for activity, substrate specificity, and mode of action. Logarithmically growing cells of Bacillus sp. strain GL1 on the medium with xanthan were also found to secrete not only xanthan lyase (75 kDa) but also a 97-kDa protein with the same N-terminal amino acid sequence as that of xanthan lyase (75 kDa). These results suggest that, in Bacillus sp. strain GL1, xanthan lyase is first synthesized as a preproform (99 kDa), secreted as a precursor (97 kDa) by a signal peptide-dependent mechanism, and then processed into a mature form (75 kDa) through excision of a C-terminal protein fragment with a molecular mass of 22 kDa.