Exploring the sequence diversity in glycoside hydrolase family 13_18 reveals a novel glucosylglycerol phosphorylase

Structural basis of the bifunctionality of Marinobacter salinexigens ZYF650T glucosylglycerol phosphorylase in glucosylglycerol catabolism

2-O-α-Glucosylglycerol (GG) is a natural heteroside synthesized by many cyanobacteria and a few heterotrophic bacteria under salt stress conditions. Bacteria produce GG in response to stimuli and degrade it once the stimulus diminishes. Heterotrophic bacteria utilize GG phosphorylase (GGP), a member of the GH13_18 family, via a two-step process consisting of phosphorolysis and hydrolysis for GG catabolism. However, the precise mechanism by which GGP degrades GG remains elusive. We determined the 3D structure of a recently identified GGP (MsGGP) of the deep-sea bacterium Marinobacter salinexigens ZYF650T, in complex with glucose and glycerol, α-d-glucose-1-phosphate (αGlc1-P), and orthophosphate (inorganic phosphate) at resolutions of 2.5, 2.7, and 2.7 Å, respectively. Notably, the first αGlc1-P complex structure in the GH13_18 family, the complex of MsGGP and αGlc1-P, validates that GGP catalyzes GG decomposition through consecutive phosphorolysis and hydrolysis. In addition, the structure reveals the mechanism of high stereoselectivity on αGlc1-P. Glu231 and Asp190 were identified as the catalytic residues. Interestingly, these structures closely resemble each other, indicating minimal conformational changes upon binding end-product glucose and glycerol, or the intermediate αGlc1-P. The structures also indicate that the substrates may follow a specific trajectory and a precise order toward the active center in close proximity and in a geometrically favorable orientation for catalysis in a double displacement mechanism.

High-yield synthesis of 2-O-α-D-glucosyl-D-glycerate by a bifunctional glycoside phosphorylase

Osmolytes are produced by various microorganisms as a defense mechanism to protect cells and macromolecules from damage caused by external stresses in harsh environments. Due to their useful stabilizing properties, these molecules are applied as active ingredients in a wide range of cosmetics and healthcare products. The metabolic pathways and biocatalytic syntheses of glycosidic osmolytes such as 2-O-α-D-glucosyl-D-glycerate often involve the action of a glycoside phosphorylase. Here, we report the discovery of a glucosylglycerate phosphorylase from carbohydrate-active enzyme family GH13 that is also active on sucrose, which contrasts the strict specificity of known glucosylglycerate phosphorylases that can only use α-D-glucose 1-phosphate as glycosyl donor in transglycosylation reactions. The novel enzyme can be distinguished from other phosphorylases from the same family by the presence of an atypical conserved sequence motif at specificity-determining positions in the active site. The promiscuity of the sucrose-active glucosylglycerate phosphorylase can be exploited for the high-yielding and rapid synthesis of 2-O-α-D-glucosyl-D-glycerate from sucrose and D-glycerate. KEY POINTS: • A Xylanimonas protaetiae glycoside phosphorylase can use both d-glycerate and fructose as glucosyl acceptor with high catalytic efficiency • Biocatalytic synthesis of the osmolyte 2-O-α-d-glucosyl-d-glycerate • Positions in the active site of GH13 phosphorylases act as convenient specificity fingerprints.

The many functions of carbohydrate-active enzymes in family GH65: diversity and application

Glycoside Hydrolase family 65 (GH65) is a unique family of carbohydrate-active enzymes. It is the first protein family to bring together glycoside hydrolases, glycoside phosphorylases and glycosyltransferases, thereby spanning a broad range of reaction types. These enzymes catalyze the hydrolysis, reversible phosphorolysis or synthesis of various α-glucosides, typically α-glucobioses or their derivatives. In this review, we present a comprehensive overview of the diverse reaction types and substrate specificities found in family GH65. We describe the determinants that control this remarkable diversity, as well as the applications of GH65 enzymes for carbohydrate synthesis.

Glucosylglycerol phosphorylase, a potential novel pathway of microbial glucosylglycerol catabolism

Glucosylglycerol (GG) is a natural compatible solute that can be synthesized by many cyanobacteria and a few heterotrophic bacteria under high salinity conditions. In cyanobacteria, GG is synthesized by GG-phosphate synthase and GG-phosphate phosphatase, and a hydrolase GGHA catalyzes its degradation. In heterotrophic bacteria (such as some Marinobacter species), a fused form of GG-phosphate phosphatase and GG-phosphate synthase is present, but the cyanobacteria-like degradation pathway is not available. Instead, a phosphorylase GGP, of which the coding gene is located adjacent to the gene that encodes the GG-synthesizing enzyme, is supposed to perform the GG degradation function. In the present study, a GGP homolog from the salt-tolerant M. salinexigens ZYF650T was characterized. The recombinant GGP catalyzed GG decomposition via a two-step process of phosphorolysis and hydrolysis in vitro and exhibited high substrate specificity toward GG. The activity of GGP was enhanced by inorganic salts at low concentrations but significantly inhibited by increasing salt concentrations. While the investigation on the physiological role of GGP in M. salinexigens ZYF650T was limited due to the failed induction of GG production, the heterologous expression of ggp in the living cells of the GG-producing cyanobacterium Synechocystis sp. PCC 6803 significantly reduced the salt-induced GG accumulation. Together, these data suggested that GGP may represent a novel pathway of microbial GG catabolism. KEY POINTS: • GGP catalyzes GG degradation by a process of phosphorolysis and hydrolysis • GGP-catalyzed GG degradation is different from GGHA-based GG degradation • GGP represents a potential novel pathway of microbial GG catabolism.

Self-assembled multienzyme complex facilitates synthesis of glucosylglycerol from maltodextrin and glycerol

BACKGROUND

Compound 2-O-α-d-glucosylglycerol (2αGG) naturally serves as a compatible osmolyte in acclimation to environmental stresses, such as high osmolarity, dryness, and extreme temperature. It presents several bioactivities and has been used in the food, agriculture, and cosmetics areas.

RESULTS

In the present study, we attempted to synthesize the 2αGG from low-cost maltodextrin and glycerol by constructing an in vitro multi-enzyme system. The system contained two core enzymes, namely glucan phosphorylases (GPs) and glucosylglycerol phosphorylases (GGPs), and two auxiliary enzymes, namely isoamylase and 4-α-glucanotransferase. Several new GGPs from different organisms were characterized with the function of converting α-G1P and glycerol to sole stereo-configuration product 2αGG. Then, polypeptide SpyTag-SpyCatcher was employed to construct a self-assembled multienzyme complex, and different combinations between enzymes and peptides were constructed and tested. The best self-assembled multienzyme complex exhibited three-fold higher productivity compared to that of free enzyme. This reaction system also produced 240 mm (61 g L-1 ) 2αGG under high substrate concentration, with a conversion yield of 86%.

CONCLUSION

The present study provides an efficient approach for producing 2αGG. It also demonstrates that the SpyTag-SpyCatcher system could be applied to construct other multienzyme complexes for increased productivity and product titer. © 2023 Society of Chemical Industry.

Biological sources, metabolism, and production of glucosylglycerols, a group of natural glucosides of biotechnological interest

Glucosylglycerols (GGs) are a group of functional heterosides comprising glycerol and glucose. In nature, they are mainly produced by many moderately salt-tolerant cyanobacteria as compatible solutes in a salt-dependent manner and synthesized in a few higher plants and fermentation processes. Because of their many interesting physicochemical properties and biological activities, such as low sweetness, low hygroscopicity, high water-holding capacity, excellent biocompatibility, favorable performance in protecting macromolecules, and antitumor activity, GGs exhibit large application potential in the fields of cosmetics, health care, food service, enzyme production, and pharmaceuticals. Many in vitro systems using different members of the GH (glycoside hydrolase) family have been established for the enzymatic synthesis of GGs, and a few of them are in use for commercial production. Based on a good understanding of the genetic bases, biochemical processes, and regulatory mechanisms of GG metabolism in microorganisms (mainly cyanobacteria), in recent years GG production technologies with in vivo systems have also been developed by applying metabolic and bioprocess engineering to a few native or heterologous microbial cell factories. This successfully provides the market GG products with an alternative source. With the further elucidation of details about the biological functions of GGs and related mechanisms, the application scope of GGs will be greatly expanded. In the present review, the biological sources and physiological roles of GGs, the molecular bases and regulation of GG metabolism, and the recent progress in GG production and application are systematically summarized. A few new questions that have arisen in the basic research of GGs and perspectives on GG application are also discussed.

Discovery and Biotechnological Exploitation of Glycoside-Phosphorylases

Among carbohydrate active enzymes, glycoside phosphorylases (GPs) are valuable catalysts for white biotechnologies, due to their exquisite capacity to efficiently re-modulate oligo- and poly-saccharides, without the need for costly activated sugars as substrates. The reversibility of the phosphorolysis reaction, indeed, makes them attractive tools for glycodiversification. However, discovery of new GP functions is hindered by the difficulty in identifying them in sequence databases, and, rather, relies on extensive and tedious biochemical characterization studies. Nevertheless, recent advances in automated tools have led to major improvements in GP mining, activity predictions, and functional screening. Implementation of GPs into innovative in vitro and in cellulo bioproduction strategies has also made substantial advances. Herein, we propose to discuss the latest developments in the strategies employed to efficiently discover GPs and make the best use of their exceptional catalytic properties for glycoside bioproduction.

Exploration of GH94 Sequence Space for Enzyme Discovery Reveals a Novel Glucosylgalactose Phosphorylase Specificity

The substantial increase in DNA sequencing efforts has led to a rapid expansion of available sequences in glycoside hydrolase families. The ever-increasing sequence space presents considerable opportunities for the search for enzymes with novel functionalities. In this work, the sequence-function space of glycoside hydrolase family 94 (GH94) was explored in detail, using a combined approach of phylogenetic analysis and sequence similarity networks. The identification and experimental screening of unknown clusters led to the discovery of an enzyme from the soil bacterium Paenibacillus polymyxa that acts as a 4-O-β-d-glucosyl-d-galactose phosphorylase (GGalP), a specificity that has not been reported to date. Detailed characterization of GGalP revealed that its kinetic parameters were consistent with those of other known phosphorylases. Furthermore, the enzyme could be used for production of the rare disaccharides 4-O-β-d-glucosyl-d-galactose and 4-O-β-d-glucosyl-l-arabinose. Our current work highlights the power of rational sequence space exploration in the search for novel enzyme specificities, as well as the potential of phosphorylases for rare disaccharide synthesis.

Discovery of a Kojibiose Hydrolase by Analysis of Specificity-Determining Correlated Positions in Glycoside Hydrolase Family 65

The Glycoside Hydrolase Family 65 (GH65) is an enzyme family of inverting α-glucoside phosphorylases and hydrolases that currently contains 10 characterized enzyme specificities. However, its sequence diversity has never been studied in detail. Here, an in-silico analysis of correlated mutations was performed, revealing specificity-determining positions that facilitate annotation of the family’s phylogenetic tree. By searching these positions for amino acid motifs that do not match those found in previously characterized enzymes from GH65, several clades that may harbor new functions could be identified. Three enzymes from across these regions were expressed in E. coli and their substrate profile was mapped. One of those enzymes, originating from the bacterium Mucilaginibacter mallensis, was found to hydrolyze kojibiose and α-1,2-oligoglucans with high specificity. We propose kojibiose glucohydrolase as the systematic name and kojibiose hydrolase or kojibiase as the short name for this new enzyme. This work illustrates a convenient strategy for mapping the natural diversity of enzyme families and smartly mining the ever-growing number of available sequences in the quest for novel specificities.

Engineering of a Thermostable Biocatalyst for the Synthesis of 2-O-Glucosylglycerol

2‐O‐Glucosylglycerol is accumulated by various bacteria and plants in response to environmental stress. It is widely applied as a bioactive moisturising ingredient in skin care products, for which it is manufactured via enzymatic glucosylation of glycerol by the sucrose phosphorylase from Leuconostoc mesenteroides. This industrial process is operated at room temperature due to the mediocre stability of the biocatalyst, often leading to microbial contamination. The highly thermostable sucrose phosphorylase from Bifidobacterium adolescentis could be a better alternative in that regard, but this enzyme is not fit for production of 2‐O‐glucosylglycerol due to its low regioselectivity and poor affinity for glycerol. In this work, the thermostable phosphorylase was engineered to alleviate these problems. Several engineering approaches were explored, ranging from site‐directed mutagenesis to conventional, binary, iterative or combinatorial randomisation of the active site, resulting in the screening of ∼3,900 variants. Variant P134Q displayed a 21‐fold increase in catalytic efficiency for glycerol, as well as a threefold improvement in regioselectivity towards the 2‐position of the substrate, while retaining its activity for several days at elevated temperatures.

Whole cell-based catalyst for enzymatic production of the osmolyte 2-O-α-glucosylglycerol

Background

Glucosylglycerol (2-O-α-d-glucosyl-sn-glycerol; GG) is a natural osmolyte from bacteria and plants. It has promising applications as cosmetic and food-and-feed ingredient. Due to its natural scarcity, GG must be prepared through dedicated synthesis, and an industrial bioprocess for GG production has been implemented. This process uses sucrose phosphorylase (SucP)-catalyzed glycosylation of glycerol from sucrose, applying the isolated enzyme in immobilized form. A whole cell-based enzyme formulation might constitute an advanced catalyst for GG production. Here, recombinant production in Escherichia coli BL21(DE3) was compared systematically for the SucPs from Leuconostoc mesenteroides (LmSucP) and Bifidobacterium adolescentis (BaSucP) with the purpose of whole cell catalyst development.

Results

Expression from pQE30 and pET21 plasmids in E. coli BL21(DE3) gave recombinant protein at 40–50% share of total intracellular protein, with the monomeric LmSucP mostly soluble (≥ 80%) and the homodimeric BaSucP more prominently insoluble (~ 40%). The cell lysate specific activity of LmSucP was 2.8-fold (pET21; 70 ± 24 U/mg; N = 5) and 1.4-fold (pQE30; 54 ± 9 U/mg, N = 5) higher than that of BaSucP. Synthesis reactions revealed LmSucP was more regio-selective for glycerol glycosylation (~ 88%; position O2 compared to O1) than BaSucP (~ 66%), thus identifying LmSucP as the enzyme of choice for GG production. Fed-batch bioreactor cultivations at controlled low specific growth rate (µ = 0.05 h⁻¹; 28 °C) for LmSucP production (pET21) yielded ~ 40 g cell dry mass (CDM)/L with an activity of 2.0 × 10⁴ U/g CDM, corresponding to 39 U/mg protein. The same production from the pQE30 plasmid gave a lower yield of 6.5 × 10³ U/g CDM, equivalent to 13 U/mg. A single freeze–thaw cycle exposed ~ 70% of the intracellular enzyme activity for GG production (~ 65 g/L, ~ 90% yield from sucrose), without releasing it from the cells during the reaction.

Conclusions

Compared to BaSucP, LmSucP is preferred for regio-selective GG production. Expression from pET21 and pQE30 plasmids enables high-yield bioreactor production of the enzyme as a whole cell catalyst. The freeze–thaw treated cells represent a highly active, solid formulation of the LmSucP for practical synthesis.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12934-021-01569-4.

High-Yield Biosynthesis of Glucosylglycerol through Coupling Phosphorolysis and Transglycosylation Reactions

Glucosylglycerol is a powerful osmolyte that has attracted attention as a useful moisturizing ingredient in the cosmetic industry. This study demonstrates two artificially designed synthetic routes for manufacturing glucosylglycerol by combining phosphorolysis and transglycosylation reactions. The overall Gibbs energy change of the synthetic routes was negative, indicating that they are thermodynamically favorable. In vitro biosystems were constructed through combining the phosphorolysis ability of sucrose/maltose phosphorylase and the transglycosylation capacity of glucosylglycerol phosphorylases from different organisms. A near-stoichiometric conversion of sucrose and glycerol with a high product yield of 98% was achieved under optimal reaction conditions. The large-scale glucosylglycerol production of this biosystem was investigated under a high concentration of substrates (2 mol/L sucrose and 2.4 mol/L glycerol), and the titer reached 1.78 mol/L (452 g/L) with a productivity of 24.3 g/L/h. To the best of our knowledge, this value presented the highest glucosylglycerol production level until now, which indicated a great industrial application potential for glucosylglycerol manufacturing.

Sucrose Phosphorylase and Related Enzymes in Glycoside Hydrolase Family 13: Discovery, Application and Engineering

Sucrose phosphorylases are carbohydrate-active enzymes with outstanding potential for the biocatalytic conversion of common table sugar into products with attractive properties. They belong to the glycoside hydrolase family GH13, where they are found in subfamily 18. In bacteria, these enzymes catalyse the phosphorolysis of sucrose to yield α-glucose 1-phosphate and fructose. However, sucrose phosphorylases can also be applied as versatile transglucosylases for the synthesis of valuable glycosides and sugars because their broad promiscuity allows them to transfer the glucosyl group of sucrose to a diverse collection of compounds other than phosphate. Numerous process and enzyme engineering studies have expanded the range of possible applications of sucrose phosphorylases ever further. Moreover, it has recently been discovered that family GH13 also contains a few novel phosphorylases that are specialised in the phosphorolysis of sucrose 6F-phosphate, glucosylglycerol or glucosylglycerate. In this review, we provide an overview of the progress that has been made in our understanding and exploitation of sucrose phosphorylases and related enzymes over the past ten years.

Structural Comparison of a Promiscuous and a Highly Specific Sucrose 6F-Phosphate Phosphorylase

In family GH13 of the carbohydrate-active enzyme database, subfamily 18 contains glycoside phosphorylases that act on α-sugars and glucosides. Because their phosphorolysis reactions are effectively reversible, these enzymes are of interest for the biocatalytic synthesis of various glycosidic compounds. Sucrose 6^F-phosphate phosphorylases (SPPs) constitute one of the known substrate specificities. Here, we report the characterization of an SPP from Ilumatobacter coccineus with a far stricter specificity than the previously described promiscuous SPP from Thermoanaerobacterium thermosaccharolyticum. Crystal structures of both SPPs were determined to provide insight into their similarities and differences. The residues responsible for binding the fructose 6-phosphate group in subsite +1 were found to differ considerably between the two enzymes. Furthermore, several variants that introduce a higher degree of substrate promiscuity in the strict SPP from I. coccineus were designed. These results contribute to an expanded structural knowledge of enzymes in subfamily GH13_18 and facilitate their rational engineering.

Sucrose 6F-phosphate phosphorylase: a novel insight in the human gut microbiome

The human gut microbiome plays an essential role in maintaining human health including in degradation of dietary fibres and carbohydrates further used as nutrients by both the host and the gut bacteria. Previously, we identified a polysaccharide utilization loci (PUL) involved in sucrose and raffinose family oligosaccharide (RFO) metabolism from one of the most common Firmicutes present in individuals, Ruminococcus gnavus E1. One of the enzymes encoded by this PUL was annotated as a putative sucrose phosphate phosphorylase (RgSPP). In the present study, we have in-depth characterized the heterologously expressed RgSPP as sucrose 6^F-phosphate phosphorylase (SPP), expanding our knowledge of the glycoside hydrolase GH13_18 subfamily. Specifically, the enzymatic characterization showed a selective activity on sucrose 6^F-phosphate (S6^FP) acting both in phosphorolysis releasing alpha-d-glucose-1-phosphate (G1P) and alpha-d-fructose-6-phosphate (F6P), and in reverse phosphorolysis from G1P and F6P to S6^FP. Interestingly, such a SPP activity had never been observed in gut bacteria before. In addition, a phylogenetic and synteny analysis showed a clustering and a strictly conserved PUL organization specific to gut bacteria. However, a wide prevalence and abundance study with a human metagenomic library showed a correlation between SPP activity and the geographical origin of the individuals and, thus, most likely linked to diet. Rgspp gene overexpression has been observed in mice fed with a high-fat diet suggesting, as observed for humans, that intestine lipid and carbohydrate microbial metabolisms are intertwined. Finally, based on the genomic environment analysis, in vitro and in vivo studies, results provide new insights into the gut microbiota catabolism of sucrose, RFOs and S6^FP.