-
1.
Enzymatic cofactor regeneration systems: A new perspective on efficiency assessment.
Bachosz, K, Zdarta, J, Bilal, M, Meyer, AS, Jesionowski, T
The Science of the total environment. 2023;:161630
Abstract
Nowadays, the specificity of enzymatic processes makes them more and more important every year, and their usage on an industrial scale seems to be necessary. Enzymatic cofactors, however, play a crucial part in the prospective applications of enzymes, because they are indispensable for conducting highly effective biocatalytic activities. Due to the relatively high cost of these compounds and their consumption during the processes carried out, it has become crucial to develop systems for cofactor regeneration. Therefore, in this review, an attempt was made to summarize current knowledge on enzymatic regeneration methods, which are characterized by high specificity, non-toxicity and reported to be highly efficient. The regeneration of cofactors, such as nicotinamide dinucleotides, coenzyme A, adenosine 5'-triphosphate and flavin nucleotides, which are necessary for the proper functioning of a large number of enzymes, is discussed, as well as potential directions for further development of these systems are highlighted. This review discusses a range of highly effective cofactor regeneration systems along with the productive synthesis of many useful chemicals, including the simultaneous renewal of several cofactors at the same time. Additionally, the impact of the enzyme immobilization process on improving the stability and the potential for multiple uses of the developed cofactor regeneration systems was also presented. Moreover, an attempt was made to emphasize the importance of the presented research, as well as the identification of research gaps, which mainly result from the lack of available literature on this topic.
-
2.
Feruloylated Arabinoxylan and Oligosaccharides: Chemistry, Nutritional Functions, and Options for Enzymatic Modification.
Lin, S, Agger, JW, Wilkens, C, Meyer, AS
Annual review of food science and technology. 2021;:331-354
Abstract
Cereal brans and grain endosperm cell walls are key dietary sources of different types of arabinoxylan. Arabinoxylan is the main group of hemicellulosic polysaccharides that are present in the cell walls of monocot grass crops and hence in cereal grains. The arabinoxylan polysaccharides consist of a backbone of β-(1→4)-linked xylopyranosyl residues, which carry arabinofuranosyl moieties, hence the term arabinoxylan. Moreover, the xylopyranosyl residues can be acetylated or substituted by 4-O-methyl-d-glucuronic acid. The arabinofuranosyls may be esterified with a feruloyl group. Feruloylated arabinoxylo-oligosaccharides exert beneficial bioactivities via prebiotic, immunomodulatory, and/or antioxidant effects. New knowledge on microbial enzymes that catalyze specific structural modifications of arabinoxylans can help us understand how these complex fibers are converted in the gut and provide a foundation for the production of feruloylated arabinoxylo-oligosaccharides from brans or other cereal grain processing sidestreams as functional food ingredients. There is a gap between the structural knowledge, bioactivity data, and enzymology insight. Our goal with this review is to present an overview of the structures and bioactivities of feruloylated arabinoxylo-oligosaccharides and review the enzyme reactions that catalyze specific changes in differentially substituted arabinoxylans.
-
3.
Conserved unique peptide patterns (CUPP) online platform: peptide-based functional annotation of carbohydrate active enzymes.
Barrett, K, Hunt, CJ, Lange, L, Meyer, AS
Nucleic acids research. 2020;(W1):W110-W115
-
-
Free full text
-
Abstract
The CUPP platform includes a web server for functional annotation and sub-grouping of carbohydrate active enzymes (CAZymes) based on a novel peptide-based similarity assessment algorithm, i.e. protein grouping according to Conserved Unique Peptide Patterns (CUPP). This online platform is open to all users and there is no login requirement. The web server allows the user to perform genome-based annotation of carbohydrate active enzymes to CAZy families, CAZy subfamilies, CUPP groups and EC numbers (function) via assessment of peptide-motifs by CUPP. The web server is intended for functional annotation assessment of the CAZy inventory of prokaryotic and eukaryotic organisms from genomic DNA (up to 30MB compressed) or directly from amino acid sequences (up to 10MB compressed). The custom query sequences are assessed using the CUPP annotation algorithm, and the outcome is displayed in interactive summary result pages of CAZymes. The results displayed allow for inspection of members of the individual CUPP groups and include information about experimentally characterized members. The web server and the other resources on the CUPP platform can be accessed from https://cupp.info.
-
4.
Enzymatic transfucosylation for synthesis of human milk oligosaccharides.
Zeuner, B, Meyer, AS
Carbohydrate research. 2020;:108029
Abstract
Human milk oligosaccharides (HMOs) are a family of structurally distinct carbohydrate oligomers present in human milk. HMOs protect breastfed babies against infection and promote the development of infant health and cognition. In the gut, fucosylated HMOs in particular function as decoy receptors that intercept epithelial attachment of enteric pathogens and hence help reduce infection. Infant formulae made from bovine milk are essentially devoid of HMOs, which creates a large impetus for biosynthetic production of HMOs. Certain microbial α-L-fucosidases (EC 3.2.1.51, EC 3.2.1.111), specifically various retaining α-L-fucosidases of glycoside hydrolase family 29 (GH29), are capable of catalysing transfucosylation. The use of GH29 α-L-fucosidases to promote transfucosylation reactions thus represents a strategy for biocatalytic synthesis of fucosylated HMOs. The purpose of this review is to present the current knowledge on the use of such α-L-fucosidases for synthesis of fucosylated HMOs by enzymatic transfucosylation. We summarize the available data obtained for both wild type and engineered microbial α-L-fucosidases, discuss enzyme and substrate sources, and review factors governing transglycosylation performance, particularly the use of protein engineering. We describe the mechanistic reaction details of α-l-fucosidase transfucosylation, and examine details of enzyme mutation strategies promoting transfucosylation. Finally, we list recommendations for future reaction targets based on currently abundant substrate sources.
-
5.
Synthesis of Human Milk Oligosaccharides: Protein Engineering Strategies for Improved Enzymatic Transglycosylation.
Zeuner, B, Teze, D, Muschiol, J, Meyer, AS
Molecules (Basel, Switzerland). 2019;(11)
Abstract
Human milk oligosaccharides (HMOs) signify a unique group of oligosaccharides in breast milk, which is of major importance for infant health and development. The functional benefits of HMOs create an enormous impetus for biosynthetic production of HMOs for use as additives in infant formula and other products. HMO molecules can be synthesized chemically, via fermentation, and by enzymatic synthesis. This treatise discusses these different techniques, with particular focus on harnessing enzymes for controlled enzymatic synthesis of HMO molecules. In order to foster precise and high-yield enzymatic synthesis, several novel protein engineering approaches have been reported, mainly concerning changing glycoside hydrolases to catalyze relevant transglycosylations. The protein engineering strategies for these enzymes range from rationally modifying specific catalytic residues, over targeted subsite -1 mutations, to unique and novel transplantations of designed peptide sequences near the active site, so-called loop engineering. These strategies have proven useful to foster enhanced transglycosylation to promote different types of HMO synthesis reactions. The rationale of subsite -1 modification, acceptor binding site matching, and loop engineering, including changes that may alter the spatial arrangement of water in the enzyme active site region, may prove useful for novel enzyme-catalyzed carbohydrate design in general.
-
6.
Classification and enzyme kinetics of formate dehydrogenases for biomanufacturing via CO2 utilization.
Nielsen, CF, Lange, L, Meyer, AS
Biotechnology advances. 2019;(7):107408
Abstract
The reversible interconversion of formate (HCOO-) and carbon dioxide (CO2) is catalyzed by formate dehydrogenase (FDH, EC 1.17.1.9). This enzyme can be used as a first step in the utilization of CO2 as carbon substrate for production of high-in-demand chemicals. However, comparison and categorization of the very diverse group of FDH enzymes has received only limited attention. With specific emphasis on FDH catalyzed CO2 reduction to HCOO-, we present a novel classification scheme for FDHs based on protein sequence alignment and gene organization analysis. We show that prokaryotic FDHs can be neatly divided into six meaningful sub-types. These sub-types are discussed in the context of overall structural composition, phylogeny of the gene segment organization, metabolic role, and catalytic properties of the enzymes. Based on the available literature, the influence of electron donor choice on the efficacy of FDH catalyzed CO2 reduction is quantified and compared. This analysis shows that methyl viologen and hydrogen are several times more potent than NADH as electron donors. Hence, the new FDH classification scheme and the electron donor analysis provide an improved base for developing FDH-facilitated CO2 reduction as a viable step in the utilization of CO2 as carbon source for green production of chemicals.
-
7.
Whole grain-rich diet reduces body weight and systemic low-grade inflammation without inducing major changes of the gut microbiome: a randomised cross-over trial.
Roager, HM, Vogt, JK, Kristensen, M, Hansen, LBS, Ibrügger, S, Mærkedahl, RB, Bahl, MI, Lind, MV, Nielsen, RL, Frøkiær, H, et al
Gut. 2019;68(1):83-93
-
-
-
Free full text
-
Plain language summary
Whole grain consumption has been linked with decreased risk of lifestyle-related diseases. While animal studies have shown the gut microbiome to be a mediator of metabolic health, human studies examining the effect of whole grain intake of the gut remain inconclusive. The aim of this study was to investigate the effects of a whole grain diet on the gut microbiome, gut functionality and biomarkers of metabolic health. In this randomised, controlled, crossover study, 50 participants completed two 8-week dietary intervention periods comprising of a whole grain diet and a refined grain diet with a 6-week washout period. Examinations were done at the beginning and end of each intervention period to assess anthropometry and various plasma and gut markers. This study found that a whole grain diet as compared with a refined grain diet reduced energy intake and body weight as well as circulating markers of inflammation. Contrary to the hypothesis, these benefits were all observed independent of changes in the gut microbiome. Based on these results, the authors conclude higher intake of whole grains should be recommended to those at risk of inflammation-related disease.
Abstract
OBJECTIVE To investigate whether a whole grain diet alters the gut microbiome and insulin sensitivity, as well as biomarkers of metabolic health and gut functionality. DESIGN 60 Danish adults at risk of developing metabolic syndrome were included in a randomised cross-over trial with two 8-week dietary intervention periods comprising whole grain diet and refined grain diet, separated by a washout period of ≥6 weeks. The response to the interventions on the gut microbiome composition and insulin sensitivity as well on measures of glucose and lipid metabolism, gut functionality, inflammatory markers, anthropometry and urine metabolomics were assessed. RESULTS 50 participants completed both periods with a whole grain intake of 179±50 g/day and 13±10 g/day in the whole grain and refined grain period, respectively. Compliance was confirmed by a difference in plasma alkylresorcinols (p<0.0001). Compared with refined grain, whole grain did not significantly alter glucose homeostasis and did not induce major changes in the faecal microbiome. Also, breath hydrogen levels, plasma short-chain fatty acids, intestinal integrity and intestinal transit time were not affected. The whole grain diet did, however, compared with the refined grain diet, decrease body weight (p<0.0001), serum inflammatory markers, interleukin (IL)-6 (p=0.009) and C-reactive protein (p=0.003). The reduction in body weight was consistent with a reduction in energy intake, and IL-6 reduction was associated with the amount of whole grain consumed, in particular with intake of rye. CONCLUSION Compared with refined grain diet, whole grain diet did not alter insulin sensitivity and gut microbiome but reduced body weight and systemic low-grade inflammation. TRIAL REGISTRATION NUMBER NCT01731366; Results.
-
8.
A low-gluten diet induces changes in the intestinal microbiome of healthy Danish adults.
Hansen, LBS, Roager, HM, Søndertoft, NB, Gøbel, RJ, Kristensen, M, Vallès-Colomer, M, Vieira-Silva, S, Ibrügger, S, Lind, MV, Mærkedahl, RB, et al
Nature communications. 2018;(1):4630
Abstract
Adherence to a low-gluten diet has become increasingly common in parts of the general population. However, the effects of reducing gluten-rich food items including wheat, barley and rye cereals in healthy adults are unclear. Here, we undertook a randomised, controlled, cross-over trial involving 60 middle-aged Danish adults without known disorders with two 8-week interventions comparing a low-gluten diet (2 g gluten per day) and a high-gluten diet (18 g gluten per day), separated by a washout period of at least six weeks with habitual diet (12 g gluten per day). We find that, in comparison with a high-gluten diet, a low-gluten diet induces moderate changes in the intestinal microbiome, reduces fasting and postprandial hydrogen exhalation, and leads to improvements in self-reported bloating. These observations suggest that most of the effects of a low-gluten diet in non-coeliac adults may be driven by qualitative changes in dietary fibres.
-
9.
Developments in support materials for immobilization of oxidoreductases: A comprehensive review.
Zdarta, J, Meyer, AS, Jesionowski, T, Pinelo, M
Advances in colloid and interface science. 2018;:1-20
Abstract
Bioremediation, a biologically mediated transformation or degradation of persistent chemicals into nonhazardous or less-hazardous substances, has been recognized as a key strategy to control levels of pollutants in water and soils. The use of enzymes, notably oxidoreductases such as laccases, tyrosinases, various oxygenases, aromatic dioxygenases, and different peroxidases (all of EC class 1) is receiving significant research attention in this regard. It should be stated that immobilization is emphasized as a powerful tool for enhancement of enzyme activity and stability as well as for protection of the enzyme proteins against negative effects of harsh reaction conditions. As proper selection of support materials for immobilization and their performance is overlooked when it comes to comparing performance of immobilized enzyme in academic studies, this review summarizes the current state of knowledge regarding the materials used for enzyme immobilization of these oxidoreductase enzymes for environmental applications. In the presented study, thorough physicochemical characteristics of the support materials was presented. Moreover, various types of reactions and notably operational modes of enzymatic processes for biodegradation of harmful pollutants are summarized, and future trends in use of immobilized oxidoreductases for environmental applications are discussed. Our goal is to provide an improved foundation on which new technological advancements can be made to achieve efficient enzyme-assisted bioremediation.
-
10.
A structural-chemical explanation of fungal laccase activity.
Mehra, R, Muschiol, J, Meyer, AS, Kepp, KP
Scientific reports. 2018;(1):17285
Abstract
Fungal laccases (EC 1.10.3.2) are multi-copper oxidases that oxidize a wide variety of substrates. Despite extensive studies, the molecular basis for their diverse activity is unclear. Notably, there is no current way to rationally predict the activity of a laccase toward a given substrate. Such knowledge would greatly facilitate the rational design of new laccases for technological purposes. We report a study of three datasets of experimental Km values and activities for Trametes versicolor and Cerrena unicolor laccase, using a range of protein modeling techniques. We identify diverse binding modes of the various substrates and confirm an important role of Asp-206 and His-458 (T. versicolor laccase numbering) in guiding substrate recognition. Importantly, we demonstrate that experimental Km values correlate with binding affinities computed by MMGBSA. This confirms the common assumption that the protein-substrate affinity is a major contributor to observed Km. From quantitative structure-activity relations (QSAR) we identify physicochemical properties that correlate with observed Km and activities. In particular, the ionization potential, shape, and binding affinity of the substrate largely determine the enzyme's Km for the particular substrate. Our results suggest that Km is not just a binding constant but also contains features of the enzymatic activity. In addition, we identify QSAR models with only a few descriptors showing that phenolic substrates employ optimal hydrophobic packing to reach the T1 site, but then require additional electronic properties to engage in the subsequent electron transfer. Our results advance our ability to model laccase activity and lend promise to future rational optimization of laccases toward phenolic substrates.