| 1. |
- Aevarsson, Arnthór, et al.
(författare)
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Going to extremes - a metagenomic journey into the dark matter of life
- 2021
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Ingår i: FEMS Microbiology Letters. - : Oxford University Press (OUP). - 1574-6968. ; 368:12
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Forskningsöversikt (refereegranskat)abstract
- The Virus-X-Viral Metagenomics for Innovation Value-project was a scientific expedition to explore and exploit uncharted territory of genetic diversity in extreme natural environments such as geothermal hot springs and deep-sea ocean ecosystems. Specifically, the project was set to analyse and exploit viral metagenomes with the ultimate goal of developing new gene products with high innovation value for applications in biotechnology, pharmaceutical, medical, and the life science sectors. Viral gene pool analysis is also essential to obtain fundamental insight into ecosystem dynamics and to investigate how viruses influence the evolution of microbes and multicellular organisms. The Virus-X Consortium, established in 2016, included experts from eight European countries. The unique approach based on high throughput bioinformatics technologies combined with structural and functional studies resulted in the development of a biodiscovery pipeline of significant capacity and scale. The activities within the Virus-X consortium cover the entire range from bioprospecting and methods development in bioinformatics to protein production and characterisation, with the final goal of translating our results into new products for the bioeconomy. The significant impact the consortium made in all of these areas was possible due to the successful cooperation between expert teams that worked together to solve a complex scientific problem using state-of-the-art technologies as well as developing novel tools to explore the virosphere, widely considered as the last great frontier of life.
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| 2. |
- Ahlqvist, Josefin, et al.
(författare)
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Crystal structure and initial characterization of a novel archaeal-like Holliday junction-resolving enzyme from Thermus thermophilus phage Tth15-6
- 2022
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Ingår i: Acta crystallographica. Section D, Structural biology. - 2059-7983. ; 78:Pt 2, s. 212-227
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Tidskriftsartikel (refereegranskat)abstract
- This study describes the production, characterization and structure determination of a novel Holliday junction-resolving enzyme. The enzyme, termed Hjc_15-6, is encoded in the genome of phage Tth15-6, which infects Thermus thermophilus. Hjc_15-6 was heterologously produced in Escherichia coli and high yields of soluble and biologically active recombinant enzyme were obtained in both complex and defined media. Amino-acid sequence and structure comparison suggested that the enzyme belongs to a group of enzymes classified as archaeal Holliday junction-resolving enzymes, which are typically divalent metal ion-binding dimers that are able to cleave X-shaped dsDNA-Holliday junctions (Hjs). The crystal structure of Hjc_15-6 was determined to 2.5 Å resolution using the selenomethionine single-wavelength anomalous dispersion method. To our knowledge, this is the first crystal structure of an Hj-resolving enzyme originating from a bacteriophage that can be classified as an archaeal type of Hj-resolving enzyme. As such, it represents a new fold for Hj-resolving enzymes from phages. Characterization of the structure of Hjc_15-6 suggests that it may form a dimer, or even a homodimer of dimers, and activity studies show endonuclease activity towards Hjs. Furthermore, based on sequence analysis it is proposed that Hjc_15-6 has a three-part catalytic motif corresponding to E-SD-EVK, and this motif may be common among other Hj-resolving enzymes originating from thermophilic bacteriophages.
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| 3. |
- Ahlqvist, Josefin, et al.
(författare)
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Crystal structure of DNA polymerase I from Thermus phage G20c
- 2022
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Ingår i: Acta crystallographica. Section D, Structural biology. - 2059-7983. ; 78:Pt 11, s. 1384-1398
-
Tidskriftsartikel (refereegranskat)abstract
- This study describes the structure of DNA polymerase I from Thermus phage G20c, termed PolI_G20c. This is the first structure of a DNA polymerase originating from a group of related thermophilic bacteriophages infecting Thermus thermophilus, including phages G20c, TSP4, P74-26, P23-45 and phiFA and the novel phage Tth15-6. Sequence and structural analysis of PolI_G20c revealed a 3'-5' exonuclease domain and a DNA polymerase domain, and activity screening confirmed that both domains were functional. No functional 5'-3' exonuclease domain was present. Structural analysis also revealed a novel specific structure motif, here termed SβαR, that was not previously identified in any polymerase belonging to the DNA polymerases I (or the DNA polymerase A family). The SβαR motif did not show any homology to the sequences or structures of known DNA polymerases. The exception was the sequence conservation of the residues in this motif in putative DNA polymerases encoded in the genomes of a group of thermophilic phages related to Thermus phage G20c. The structure of PolI_G20c was determined with the aid of another structure that was determined in parallel and was used as a model for molecular replacement. This other structure was of a 3'-5' exonuclease termed ExnV1. The cloned and expressed gene encoding ExnV1 was isolated from a thermophilic virus metagenome that was collected from several hot springs in Iceland. The structure of ExnV1, which contains the novel SβαR motif, was first determined to 2.19 Å resolution. With these data at hand, the structure of PolI_G20c was determined to 2.97 Å resolution. The structures of PolI_G20c and ExnV1 are most similar to those of the Klenow fragment of DNA polymerase I (PDB entry 2kzz) from Escherichia coli, DNA polymerase I from Geobacillus stearothermophilus (PDB entry 1knc) and Taq polymerase (PDB entry 1bgx) from Thermus aquaticus.
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| 4. |
- Allahgholi, Leila, et al.
(författare)
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Exploring a novel β-1,3-glucanosyltransglycosylase, MlGH17B, from a marine Muricauda lutaonensis strain for modification of laminari-oligosaccharides
-
Ingår i: Glycobiology. - 1460-2423.
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Tidskriftsartikel (refereegranskat)abstract
- The marine environment, contains plentiful renewable resources, e.g. macroalgae with unique polysaccharides, motivating search for enzymes from marine microorganisms to explore conversion possibilities of the polysaccharides. In this study, the first GH17 glucanosyltransglycosylase, MlGH17B, from a marine bacterium (Muricauda lutaonensis), was characterized. The enzyme was moderately thermostable with Tm at 64.4 °C and 73.2 °C, but an activity optimum at 20 °C, indicating temperature sensitive active site interactions. MlGH17B uses β-1,3 laminari-oligosaccharides with a degree of polymerization (DP) of 4 or higher as donors. Two glucose moieties (bound in the aglycone +1 and + 2 subsites) are cleaved off from the reducing end of the donor while the remaining part (bound in the glycone subsites) is transferred to an incoming β-1,3 glucan acceptor, making a β-1,6-linkage, thereby synthesizing branched or kinked oligosaccharides. Synthesized oligosaccharides up to DP26 were detected by mass spectrometry analysis, showing that repeated transfer reactions occurred, resulting in several β-1,6-linked branches. The modelled structure revealed an active site comprising five subsites: three glycone (-3, -2 and - 1) and two aglycone (+1 and + 2) subsites, with significant conservation of substrate interactions compared to the only crystallized 1,3-β-glucanosyltransferase from GH17 (RmBgt17A from the compost thriving fungus Rhizomucor miehei), suggesting a common catalytic mechanism, despite different phylogenetic origin, growth environment, and natural substrate. Both enzymes lacked the subdomain extending the aglycone subsites, found in GH17 endo-β-glucanases from plants, but this extension was also missing in bacterial endoglucanases (modelled here), showing that this feature does not distinguish transglycosylation from hydrolysis, but may rather relate to phylogeny.
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| 5. |
- Allahgholi, Leila, et al.
(författare)
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Fermentation of the Brown Seaweed Alaria esculenta by a Lactic Acid Bacteria Consortium Able to Utilize Mannitol and Laminari-Oligosaccharides
- 2023
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Ingår i: Fermentation. - 2311-5637. ; 9:6
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Tidskriftsartikel (refereegranskat)abstract
- The brown seaweed Alaria esculenta is the second most cultivated species in Europe, and it is therefore of interest to expand its application by developing food products. In this study, a lactic acid bacteria consortium (LAB consortium) consisting of three Lactiplantibacillus plantarum strains (relative abundance ~94%) and a minor amount of a Levilactobacillus brevis strain (relative abundance ~6%) was investigated for its ability to ferment carbohydrates available in brown seaweed. The consortium demonstrated the ability to ferment glucose, mannitol, galactose, mannose, and xylose, of which glucose and mannitol were the most favored substrates. No growth was observed on fucose, mannuronic and guluronic acid. The consortium used different pathways for carbohydrate utilization and produced lactic acid as the main metabolite. In glucose fermentation, only lactic acid was produced, but using mannitol as a carbohydrate source resulted in the co-production of lactic acid, ethanol, and succinate. Xylose fermentation resulted in acetate production. The consortium was also able to utilize laminari-oligosaccharides (DP2-4), obtained after enzymatic hydrolysis of laminarin, and produced lactic acid as a metabolite. The consortium could grow directly on A. esculenta, resulting in a pH decrease to 3.8 after 7 days of fermentation. Incubation of the same seaweed in corresponding conditions without inoculation resulted in spoilage of the seaweed by endogenous bacteria.
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| 6. |
- Ara, Kazi Zubaida Gulshan, et al.
(författare)
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Characterization and diversity of the complete set of GH family 3 enzymes from Rhodothermus marinus DSM 4253
- 2020
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 10
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Tidskriftsartikel (refereegranskat)abstract
- The genome of Rhodothermus marinus DSM 4253 encodes six glycoside hydrolases (GH) classified under GH family 3 (GH3): RmBgl3A, RmBgl3B, RmBgl3C, RmXyl3A, RmXyl3B and RmNag3. The biochemical function, modelled 3D-structure, gene cluster and evolutionary relationships of each of these enzymes were studied. The six enzymes were clustered into three major evolutionary lineages of GH3: β-N-acetyl-glucosaminidases, β-1,4-glucosidases/β-xylosidases and macrolide β-glucosidases. The RmNag3 with additional β-lactamase domain clustered with the deepest rooted GH3-lineage of β-N-acetyl-glucosaminidases and was active on acetyl-chitooligosaccharides. RmBgl3B displayed β-1,4-glucosidase activity and was the only representative of the lineage clustered with macrolide β-glucosidases from Actinomycetes. The β-xylosidases, RmXyl3A and RmXyl3B, and the β-glucosidases RmBgl3A and RmBgl3C clustered within the major β-glucosidases/β-xylosidases evolutionary lineage. RmXyl3A and RmXyl3B showed β-xylosidase activity with different specificities for para-nitrophenyl (pNP)-linked substrates and xylooligosaccharides. RmBgl3A displayed β-1,4-glucosidase/β-xylosidase activity while RmBgl3C was active on pNP-β-Glc and β-1,3-1,4-linked glucosyl disaccharides. Putative polysaccharide utilization gene clusters were also investigated for both R. marinus DSM 4253 and DSM 4252T (homolog strain). The analysis showed that in the homolog strain DSM 4252T Rmar_1080 (RmXyl3A) and Rmar_1081 (RmXyl3B) are parts of a putative polysaccharide utilization locus (PUL) for xylan utilization.
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| 7. |
- Ara, Kazi Zubaida Gulshan, et al.
(författare)
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Engineering CGTase to improve synthesis of alkyl glycosides
- 2021
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Ingår i: Glycobiology. - : Oxford University Press (OUP). - 1460-2423. ; 31:5, s. 603-612
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Tidskriftsartikel (refereegranskat)abstract
- Alkyl glycoside surfactants with elongated carbohydrate chains are useful in different applications due to their improved biocompatibility. Cyclodextrin glucanotransferases can catalyse the elongation process through the coupling reaction. However, due to the presence of a hydrophobic tail, the interaction between an alkyl glycoside acceptor and the active site residues is weaker than the interaction with maltooligosaccharides at the corresponding site. Here we report the mutations of F197, G263 and E266 near the acceptor subsites in the CGTase CspCGT13 from Carboxydocella sp. The results showed that substitutions of both F197 and G263 were important for the binding of acceptor substrate dodecyl maltoside during coupling reaction. The double mutant F197Y/G263A showed enhanced coupling activity and displayed a 2-fold increase of the primary coupling product using γ-cyclodextrin as donor when compared to wildtype CspCGT13. Disproportionation activity was also reduced, which was also the case for another double mutant (F197Y/E266A) that however not showed the corresponding increase in coupling. A triple mutant F197Y/G263A/E266A maintained the increase in primary coupling product (1.8-fold increase) using dodecyl maltoside as acceptor, but disproportionation was approximately at the same level as in the double mutants. In addition, hydrolysis of starch was slightly increased by the F197Y and G263A substitutions, indicating that interactions at both positions influenced the selectivity between glycosyl and alkyl moieties.
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| 8. |
- Aristizábal-Lanza, Lucía, et al.
(författare)
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Comparison of the enzymatic depolymerization of polyethylene terephthalate and AkestraTM using Humicola insolens cutinase
- 2022
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Ingår i: Frontiers in Chemical Engineering. - : Frontiers Media SA. - 2673-2718. ; 4
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Tidskriftsartikel (refereegranskat)abstract
- The enzymatic depolymerization of synthetic polyesters has become of great interest in recycling plastics. Most of the research in this area focuses on the depolymerization of polyethylene terephthalate (PET) due to its widespread use in various applications. However, the enzymatic activity on other commercial polyesters is less frequently investigated. Therefore, AkestraTM attracted our attention, which is a copolymer derived from PET with a partially biobased spirocyclic acetal structure. In this study, the activity of Humicola insolens cutinase (HiCut) on PET and AkestraTM films and powder was investigated. HiCut showed higher depolymerization activity on amorphous PET films than on Akestra™ films. However, an outstanding performance was achieved on AkestraTM powder, reaching 38% depolymerization in 235h, while only 12% for PET powder. These results are consistent with the dependence of the enzymes on the crystallinity of the polymer since Akestra™ is amorphous while the PET powder has 14% crystallinity. On the other hand, HiCut docking studies and molecular dynamic simulations (MD) suggested that the PET-derived mono (hydroxyethyl)terephthalate dimer (MHET)2 is a hydrolyzable ligand, producing terephthalic acid (TPA), while the Akestra™-derived TPA-spiroglycol ester is not, which is consistent with the depolymerization products determined experimentally. MD studies also suggest ligand-induced local conformational changes in the active site.
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| 9. |
- Aronsson, Anna, et al.
(författare)
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Structural insights of RmXyn10A – A prebiotic-producing GH10 xylanase with a non-conserved aglycone binding region
- 2018
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Ingår i: Biochimica et Biophysica Acta - Proteins and Proteomics. - : Elsevier BV. - 1570-9639. ; 1866:2, s. 292-306
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Tidskriftsartikel (refereegranskat)abstract
- Hydrolysis of arabinoxylan (AX) by glycoside hydrolase family 10 (GH10) xylanases produces xylo- and arabinoxylo-oligosaccharides ((A)XOS) which have shown prebiotic effects. The thermostable GH10 xylanase RmXyn10A has shown great potential to produce (A)XOS. In this study, the structure of RmXyn10A was investigated, the catalytic module by homology modelling and site-directed mutagenesis and the arrangement of its five domains by small-angle X-ray scattering (SAXS). Substrate specificity was explored in silico by manual docking and molecular dynamic simulations. It has been shown in the literature that the glycone subsites of GH10 xylanases are well conserved and our results suggest that RmXyn10A is no exception. The aglycone subsites are less investigated, and the modelled structure of RmXyn10A suggests that loop β6α6 in the aglycone part of the active site contains a non-conserved α-helix, which blocks the otherwise conserved space of subsite +2. This structural feature has only been observed for one other GH10 xylanase. In RmXyn10A, docking revealed two alternative binding regions, one on either side of the α-helix. However, only one was able to accommodate arabinose-substitutions and the mutation study suggests that the same region is responsible for binding XOS. Several non-conserved structural features are most likely to be responsible for providing affinity for arabinose-substitutions in subsites +1 and +2. The SAXS rigid model of the modular arrangement of RmXyn10A displays the catalytic module close to the cell-anchoring domain while the carbohydrate binding modules are further away, likely explaining the observed lack of contribution of the CBMs to activity.
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| 10. |
- Bustos, Atma-Sol, et al.
(författare)
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Interaction between Myricetin Aggregates and Lipase under Simplified Intestinal Conditions
- 2020
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Ingår i: Foods. - : MDPI AG. - 2304-8158. ; 9:6
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Tidskriftsartikel (refereegranskat)abstract
- Myricetin, a flavonoid found in the plant kingdom, has previously been identified as a food molecule with beneficial effects against obesity. This property has been related with its potential to inhibit lipase, the enzyme responsible for fat digestion. In this study, we investigate the interaction between myricetin and lipase under simplified intestinal conditions from a colloidal point of view. The results show that myricetin form aggregates in aqueous medium and under simplified intestinal condition, where it was found that lipase is in its monomeric form. Although lipase inhibition by myricetin at a molecular level has been reported previously, the results of this study suggest that myricetin aggregates inhibit lipase by a sequestering mechanism as well. The size of these aggregates was determined to be in the range of a few nm to >200 nm.
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| 11. |
- Bustos, Atma Sol, et al.
(författare)
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Interaction Between Phenolic Compounds and Lipase : The Influence of Solubility and Presence of Particles in the IC50 Value
- 2018
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Ingår i: Journal of Food Science. - : Wiley. - 0022-1147 .- 1750-3841. ; 83:8, s. 2071-2076
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Tidskriftsartikel (refereegranskat)abstract
- Obesity is one of the principal human health problems and one of the main treatments against it is the inhibition of pancreatic lipase, the main responsible enzyme of lipid digestion. For that purpose, previous studies have tested several phenolic compounds against lipase, without considering their aggregation behavior in aqueous solutions. Because of this, the present study focuses on understanding how the solubility and the presence of particles affect the IC50 value of the interaction between lipase and phenolic compounds present in beverages like fruit juices and teas. Therefore, the inhibitory capacity against pancreatic lipase and the aggregate formation of 9 phenolic compounds (quercetin, rutin, myricetin, catechin, epigallocatechin gallate, cyanidin, caffeic acid, chlorogenic acid, and vanillic acid) were analyzed. The results obtained together with the solubility data from literature were treated by principal component analysis and indicate that the IC50 value does not correlate with the solubility or aggregate formation of the phenolic compounds. However, the IC50 values of phenolic compounds which aggregate during the assay conditions have low reproducibility. This study shows that the aggregate formation of phenolic compounds plays an important role during in vitro assays for pancreatic lipase inhibition and should be considered in future experiments as it can lead to false positive results. In terms of particle formation, the flavonoids investigated in this study are more prone to aggregation compared to the phenolic acids.
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| 12. |
- Bustos, Atma-Sol, et al.
(författare)
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Interaction of quercetin and epigallocatechin gallate (EGCG) aggregates with pancreatic lipase under simplified intestinal conditions
- 2020
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Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 15:4, s. 0224853-0224853
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Tidskriftsartikel (refereegranskat)abstract
- Diets rich in flavonoids have been related with low obesity rates, which could be related with their potential to inhibit pancreatic lipase, the main enzyme of fat assimilation. Some flavonoids can aggregate in aqueous medium suggesting that the inhibition mechanism could occur on both molecular and colloidal levels. This study investigates the interaction of two flavonoid aggregates, quercetin and epigallocatechin gallate (EGCG), with pancreatic lipase under simplified intestinal conditions. The stability and the morphology of these flavonoid aggregates were studied in four different solutions: Control (water), salt, low lipase concentration and high lipase concentration. Particles were found by optical microscopy in almost all the solutions tested, except EGCG-control. The results show that the precipitation rate decreases for quercetin and increases for EGCG in salt solution and that lipase stabilize quercetin aggregates. In addition, both flavonoids were shown to precipitate together with pancreatic lipase resulting in a sequestering of the enzyme.
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| 13. |
- Choi, Jaeyeong, et al.
(författare)
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Study on oligomerization of glutamate decarboxylase from Lactobacillus brevis using asymmetrical flow field-flow fractionation (AF4) with light scattering techniques
- 2018
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Ingår i: Analytical and Bioanalytical Chemistry. - : Springer Science and Business Media LLC. - 1618-2642 .- 1618-2650. ; 410:2, s. 451-458
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Tidskriftsartikel (refereegranskat)abstract
- In this work, asymmetrical flow field-flow fractionation (AF4) coupled with UV/Vis, multi-angle light scattering (MALS), and differential refractive index (dRI) detectors (AF4-UV-MALS-dRI) was employed for analysis of glutamate decarboxylase (LbGadB) from Lactobacillus brevis (L. brevis). AF4 provided molecular weight (MW) (or size)-based separation of dimer, hexamer, and aggregates of LbGadB. The effect of pH on oligomerization of LbGadB was investigated, and then AF4 results were compared to those from molecular modeling. The MWs measured by AF4-UV-MALS-dRI for dimeric and hexameric forms of LbGadB were 110 and 350 kDa, respectively, which are in good agreements with those theoretically calculated (110 and 330 kDa). The molecular sizes determined by AF4-UV-MALS-dRI were also in good agreement with those obtained from molecular modeling (6 and 10 nm, respectively, for dimeric and hexameric from AF4-UV-MALS-dRI and 6.4 × 7.6 and 7.6 × 13.1 nm from molecular modeling). The effects of temperature, salt type, and salt concentration on oligomerization of LbGadB were also investigated using dynamic light scattering (DLS). It was found that the hexameric form of LbGadB was most stable at pH 6 and in presence of NaCl or KCl. The results indicate that AF4, in combination of various online detectors mentioned above, provides an effective tool for monitoring of oligomerization of LbGadB under different conditions, such as temperature, pH, type of salts, and salt concentrations.
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| 14. |
- Curi-Borda, Cecilia K, et al.
(författare)
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Multilayer Bixin Microcapsules: The Impact of Native Carbohydrates on the Microencapsulation Efficiency and Dispersion Stability
- 2019
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Ingår i: Foods. - : MDPI AG. - 2304-8158. ; 8:3
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Tidskriftsartikel (refereegranskat)abstract
- Bixin is a hydrophobic carotenoid present in the integument of the seeds of Bixa orellana. Microencapsulation was applied to obtain water dispersible formulations and protect the colorant against degradation. Microencapsulated systems were obtained by spray-drying a mild alkaline bixin dispersion with different encapsulating materials. The encapsulation trials were performed with and without native carbohydrates of the integument in addition to the main encapsulant. It was possible to dry dispersions with up to 10% bixin counted on total solids. All the studied systems were characterized by colorimetry, UV-vis spectroscopy, Scanning Electron Microscopy, light microscopy, turbidometric sedimentation analyses and laser light diffraction analyses. All the systems showed aqueous dispersibility but displayed differences in their transparency, UV-vis spectra and physical stability at pH 3. The results show that the native carbohydrates enhance the encapsulation efficiency of other encapsulating materials. The chemical composition of this native carbohydrate fraction shows the presence of polysaccharides containing arabinose, galactose and glucose as monomers. Starch was identified enzymatically. The native carbohydrates allowed the encapsulation of bixin in its native microcrystalline form, resulting in a multilayer structure after spray-drying. In addition, the colorant particles displayed dispersibility under acidic aqueous conditions suggesting that they are stabilized by the native carbohydrates after the microcapsules are dissolved.
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| 15. |
- Daugbjerg Christensen, Monica, et al.
(författare)
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Cloning and Characterization of a Novel N-Acetyl-D-galactosamine-4-O-sulfate Sulfatase, SulA1, from a Marine Arthrobacter Strain
- 2024
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Ingår i: Marine Drugs. - 1660-3397. ; 22:3
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Tidskriftsartikel (refereegranskat)abstract
- Sulfation is gaining increased interest due to the role of sulfate in the bioactivity of many polysaccharides of marine origin. Hence, sulfatases, enzymes that control the degree of sulfation, are being more extensively researched. In this work, a novel sulfatase (SulA1) encoded by the gene sulA1 was characterized. The sulA1-gene is located upstream of a chondroitin lyase encoding gene in the genome of the marine Arthrobacter strain (MAT3885). The sulfatase was produced in Escherichia coli. Based on the primary sequence, the enzyme is classified under sulfatase family 1 and the two catalytic residues typical of the sulfatase 1 family—Cys57 (post-translationally modified to formyl glycine for function) and His190—were conserved. The enzyme showed increased activity, but not improved stability, in the presence of Ca2+, and conserved residues for Ca2+ binding were identified (Asp17, Asp18, Asp277, and Asn278) in a structural model of the enzyme. The temperature and pH activity profiles (screened using p-nitrocatechol sulfate) were narrow, with an activity optimum at 40–50 °C and a pH optimum at pH 5.5. The Tm was significantly higher (67 °C) than the activity optimum. Desulfation activity was not detected on polymeric substrates, but was found on GalNAc4S, which is a sulfated monomer in the repeated disaccharide unit (GlcA–GalNAc4S) of, e.g., chondroitin sulfate A. The position of the sulA1 gene upstream of a chondroitin lyase gene and combined with the activity on GalNAc4S suggests that there is an involvement of the enzyme in the chondroitin-degrading cascade reaction, which specifically removes sulfate from monomeric GalNAc4S from chondroitin sulfate degradation products.
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| 16. |
- Din, Salah Ud, et al.
(författare)
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The Purification and Characterization of a Cutinase-like Enzyme with Activity on Polyethylene Terephthalate (PET) from a Newly Isolated Bacterium Stenotrophomonas maltophilia PRS8 at a Mesophilic Temperature
- 2023
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Ingår i: Applied Sciences (Switzerland). - : MDPI AG. - 2076-3417. ; 13:6
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Tidskriftsartikel (refereegranskat)abstract
- A polyethylene terephthalate (PET)-degrading bacterium identified as Stenotrophomonas maltophilia PRS8 was isolated from the soil of a landfill. The degradation of the PET bottle flakes and the PET prepared as a powder were assessed using live cells, an extracellular medium, or a purified cutinase-like enzyme. These treated polymers were analyzed using Fourier transform infrared spectroscopy (FTIR) and scanning electron microscopy (SEM). The depolymerization products, identified using HPLC and LC-MS, were terephthalic acid (TPA), mono(2-hydroxyethyl)-TPA (MHET), and bis(2-hydroxyethyl)-TPA (BHET). Several physicochemical factors were optimized for a better cutinase-like enzyme production by using unique single-factor and multi-factor statistical models (the Plackett–Burman design and the central composite design software). The enzyme was purified for homogeneity through column chromatography using Sephadex G-100 resin. The molecular weight of the enzyme was approximately 58 kDa. The specific activity on para nitrophenyl butyrate was estimated at 450.58 U/mg, with a purification of 6.39 times and a yield of 48.64%. The enzyme was stable at various temperatures (30–40 °C) and pH levels (8.0–10.0). The enzyme activity was significantly improved by the surfactants (Triton X-100 and Tween-40), organic solvent (formaldehyde), and metals (NiCl2 and Na2SO4). The extracellular medium containing the cutinase-type enzyme showed a depolymerization yield of the PET powder comparable to that of Idonella skaiensis IsPETase and significantly higher than that of Humicola insolens thermostable HiCut (HiC) cutinase. This study suggests that S. maltophilia PRS8 is able to degrade PET at a mesophilic temperature and could be further explored for the sustainable management of plastic waste.
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| 17. |
- Dong, Zehui, et al.
(författare)
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Investigation of Structural Features of Two Related Lipases and the Impact on Fatty Acid Specificity in Vegetable Fats
- 2022
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Ingår i: International Journal of Molecular Sciences. - : MDPI AG. - 1422-0067. ; 23:13
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Tidskriftsartikel (refereegranskat)abstract
- One of the indispensable applications of lipases in modification of oils and fats is the possibility to tailor the fatty acid content of triacylglycerols (TAGs), to meet specific requirements from various applications in food, nutrition, and cosmetic industries. Oleic acid (C18:1) and stearic acid (C18:0) are two common long fatty acids in the side chain of triglycerides in plant fats and oils that have similar chemical composition and structures, except for an unsaturated bond between C9 and C10 in oleic acid. Two lipases from Rhizomucor miehei (RML) and Rhizopus oryzae (ROL), show activity in reactions involving oleate and stearate, and share high sequence and structural identity. In this research, the preference for one of these two similar fatty acid side chains was investigated for the two lipases and was related to the respective enzyme structure. From transesterification reactions with 1:1 (molar ratio) mixed ethyl stearate (ES) and ethyl oleate (EO), both RML and ROL showed a higher activity towards EO than ES, but RML showed around 10% higher preference for ES compared with ROL. In silico results showed that stearate has a less stable interaction with the substrate binding crevice in both RML and ROL and higher tendency to freely move out of the substrate binding region, compared with oleate whose structure is more rigid due to the existence of the double bond. However, Trp88 from RML which is an Ala at the identical position in ROL shows a significant stabilization effect in the substrate interaction in RML, especially with stearate as a ligand.
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| 18. |
- Gil-Ramirez, Alicia, et al.
(författare)
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Data on saponins, xylan and cellulose yield obtained from quinoa stalks after pressurized hot water extraction
- 2018
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Ingår i: Data in Brief. - : Elsevier BV. - 2352-3409. ; 20, s. 289-292
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Tidskriftsartikel (refereegranskat)abstract
- The data we present below are linked to our research paper “Integrated process for sequential extraction of saponins, xylan and cellulose from quinoa stalks (Chenopodium quinoa Willd.)” (Gil-Ramírez et al., 2018) [1]. The objective is to provide supplementary information in order to facilitate the comprehension of the central composite experimental design (rotatable 22) used in the integrated process of extractions. Two factors, temperature and time of extraction are considered in the design. The responses are the yield of saponin, xylan and cellulose. First, the desirable linear regression obtained by the observed vs. predicted yields plot for each variable response confirm the validation of the model (Fig. 1). Second, the data presented here through Standardized Pareto Charts (Fig. 2), provides information about the effect of the time and temperature, as well as their interactions, in the yield of saponins, xylan and cellulose obtained in an integrated sequential extraction.
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| 19. |
- Hero, Johan S., et al.
(författare)
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Endo-xylanases from Cohnella sp. AR92 aimed at xylan and arabinoxylan conversion into value-added products
- 2021
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Ingår i: Applied Microbiology and Biotechnology. - : Springer Science and Business Media LLC. - 1432-0614 .- 0175-7598. ; 105:18, s. 6759-6778
-
Tidskriftsartikel (refereegranskat)abstract
- The genus Cohnella belongs to a group of Gram-positive endospore-forming bacteria within the Paenibacillaceae family. Although most species were described as xylanolytic bacteria, the literature still lacks some key information regarding their repertoire of xylan-degrading enzymes. The whole genome sequence of an isolated xylan-degrading bacterium Cohnella sp. strain AR92 was found to contain five genes encoding putative endo-1,4-β-xylanases, of which four were cloned, expressed, and characterized to better understand the contribution of the individual endo-xylanases to the overall xylanolytic properties of strain AR92. Three of the enzymes, CoXyn10A, CoXyn10C, and CoXyn11A, were shown to be effective at hydrolyzing xylans-derived from agro-industrial, producing oligosaccharides with substrate conversion values of 32.5%, 24.7%, and 10.6%, respectively, using sugarcane bagasse glucuronoarabinoxylan and of 29.9%, 19.1%, and 8.0%, respectively, using wheat bran-derived arabinoxylan. The main reaction products from GH10 enzymes were xylobiose and xylotriose, whereas CoXyn11A produced mostly xylooligosaccharides (XOS) with 2 to 5 units of xylose, often substituted, resulting in potentially prebiotic arabinoxylooligosaccharides (AXOS). The endo-xylanases assay displayed operational features (temperature optima from 49.9 to 50.4 °C and pH optima from 6.01 to 6.31) fitting simultaneous xylan utilization. Homology modeling confirmed the typical folds of the GH10 and GH11 enzymes, substrate docking studies allowed the prediction of subsites (- 2 to + 1 in GH10 and - 3 to + 1 in GH11) and identification of residues involved in ligand interactions, supporting the experimental data. Overall, the Cohnella sp. AR92 endo-xylanases presented significant potential for enzymatic conversion of agro-industrial by-products into high-value products.Key points• Cohnella sp. AR92 genome encoded five potential endo-xylanases.• Cohnella sp. AR92 enzymes produced xylooligosaccharides from xylan, with high yields.• GH10 enzymes from Cohnella sp. AR92 are responsible for the production of X2 and X3 oligosaccharides.• GH11 from Cohnella sp. AR92 contributes to the overall xylan degradation by producing substituted oligosaccharides.
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| 20. |
- Hreggvidsson, Gudmundur O, et al.
(författare)
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Biocatalytic refining of polysaccharides from brown seaweeds
- 2020. - 1
-
Ingår i: Sustainable Seaweed Technologies : Cultivation, Biorefinery and Applications - Cultivation, Biorefinery and Applications. - 9780128179437 - 9780128179444 ; , s. 447-504
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Bokkapitel (refereegranskat)abstract
- Brown macroalgae constitute 40% of the global production of seaweed, corresponding to approximately 10 million tonnes annually. Traditionally, seaweeds have been the source of hydrocolloids, food, and feed products. Due to possibilities for large-scale farming, brown macroalgae are a biomass with considerable potential for increased utilization. The main constituent polysaccharides, being alginate, cellulose, laminaran, and fucoidan, are the components of greatest importance for biorefinery usage. The polysaccharides can be extracted and applied for their physical or bioactive properties or used as a carbon source for microbial conversions to biofuels and commodity chemicals. The structural complexity and heterogeneous sugar composition of the polysaccharides make them a challenging biorefinery feedstock. These challenges can be overcome by the increasingly innovative biocatalytic tools, enzymes and microbes, that are being developed and that can be expected to open new opportunities and expand the product portfolio. However, there are still knowledge gaps, and further understanding is required on the molecular level of these interesting polymers, the tools, the refining possibilities, as well as transforming this knowledge to innovations—processes and products.
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| 21. |
- Ibieta, Gabriela, et al.
(författare)
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Molecular characterization of a galactomannan extracted from Tara (Caesalpinia spinosa) seeds
- 2023
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Ingår i: Scientific Reports. - 2045-2322. ; 13
-
Tidskriftsartikel (refereegranskat)abstract
- Tara gum (TG) is a polysaccharide extracted from the seeds of a South American tree called Tara (Caesalpinia spinosa). TG is a galactomannan with many applications in the food industry, mainly as an emulsifier and stabilizer agent. In addition, it is also used in the paper and cosmetic industries. In the present study, we performed a molecular characterization based on chemical composition and physicochemical properties to understand the properties behind TG applications. TG was extracted and purified from Tara seeds distributed in different ecoregions of Bolivia. The monosaccharide composition analysis was determined by high-performance anion-exchange chromatography/pulsed amperometric detection (HPAEC-PAD). At the same time, their molecular characteristics, such as molar mass, root-mean-square radius, hydrodynamic radius, conformation, and densities, were studied by asymmetrical flow field-flow fractionation coupled to multi-angle light scattering refractive index (AF4-MALS-dRI), also the specific refractive index increment (dn/dc) was determined for the first time using AF4 for TG. The results revealed that the gum samples are galactomannans composed of mannose (Man) and galactose (Gal) in a ratio of 3.37 (Man/Gal), with an average molar mass range from 2.460 × 107 to 3.699 × 107 Da, distributed in a single population. The root-mean-square radius range from 260.4 to 281.6 nm, and dn/dc is 0.1454. The Kratky plots based on 14 scattering angles indicated that the conformation of all samples corresponds to random coil monodisperse, while their gyration radius/hydrodynamic radius ratio (ρ) is high. All these results suggest that the chains have a low branched density, consistent with the Gal/Man composition. To the best of our knowledge, we report for the first time an integrated physicochemical study of TG relevant to developing emulsifier and stabilizer formulations.
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| 22. |
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| 23. |
- Khaleghipour, Leila, et al.
(författare)
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Extraction of sugarcane bagasse arabinoxylan, integrated with enzymatic production of xylo-oligosaccharides and separation of cellulose
- 2021
-
Ingår i: Biotechnology for Biofuels. - : Springer Science and Business Media LLC. - 1754-6834. ; 14:1
-
Tidskriftsartikel (refereegranskat)abstract
- Sugarcane processing roughly generates 54 million tonnes sugarcane bagasse (SCB)/year, making SCB an important material for upgrading to value-added molecules. In this study, an integrated scheme was developed for separating xylan, lignin and cellulose, followed by production of xylo-oligosaccharides (XOS) from SCB. Xylan extraction conditions were screened in: (1) single extractions in NaOH (0.25, 0.5, or 1 M), 121 °C (1 bar), 30 and 60 min; (2) 3 × repeated extraction cycles in NaOH (1 or 2 M), 121 °C (1 bar), 30 and 60 min or (3) pressurized liquid extractions (PLE), 100 bar, at low alkalinity (0-0.1 M NaOH) in the time and temperature range 10-30 min and 50-150 °C. Higher concentration of alkali (2 M NaOH) increased the xylan yield and resulted in higher apparent molecular weight of the xylan polymer (212 kDa using 1 and 2 M NaOH, vs 47 kDa using 0.5 M NaOH), but decreased the substituent sugar content. Repeated extraction at 2 M NaOH, 121 °C, 60 min solubilized both xylan (85.6% of the SCB xylan), and lignin (84.1% of the lignin), and left cellulose of high purity (95.8%) in the residuals. Solubilized xylan was separated from lignin by precipitation, and a polymer with β-1,4-linked xylose backbone substituted by arabinose and glucuronic acids was confirmed by FT-IR and monosaccharide analysis. XOS yield in subsequent hydrolysis by endo-xylanases (from glycoside hydrolase family 10 or 11) was dependent on extraction conditions, and was highest using xylan extracted by 0.5 M NaOH, (42.3%, using Xyn10A from Bacillus halodurans), with xylobiose and xylotriose as main products. The present study shows successful separation of SCB xylan, lignin, and cellulose. High concentration of alkali, resulted in xylan with lower degree of substitution (especially reduced arabinosylation), while high pressure (using PLE), released more lignin than xylan. Enzymatic hydrolysis was more efficient using xylan extracted at lower alkaline strength and less efficient using xylan obtained by PLE and 2 M NaOH, which may be a consequence of polymer aggregation, via remaining lignin interactions.
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| 24. |
- Li, Xiaoya, et al.
(författare)
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Synthesis, Enzymatic Degradation, and Polymer-Miscibility Evaluation of Nonionic Antimicrobial Hyperbranched Polyesters with Indole or Isatin Functionalities
- 2021
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Ingår i: Biomacromolecules. - : American Chemical Society (ACS). - 1525-7797 .- 1526-4602. ; 22:5, s. 2256-2271
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Tidskriftsartikel (refereegranskat)abstract
- Most macromolecular antimicrobials are ionic and thus lack miscibility/compatibility with nonionic substrate materials. In this context, nonionic hyperbranched polyesters (HBPs) with indole or isatin functionality were rationally designed, synthesized, and characterized. Antimicrobial disk diffusion assay indicated that these HBPs showed significant antibacterial activity against 8 human pathogenic bacteria compared to small molecules with indole or isatin groups. According to DSC measurements, up to 20% indole-based HBP is miscible with biodegradable polyesters (polyhydroxybutyrate or polycaprolactone), which can be attributed to the favorable hydrogen bonding between the N-H moiety of indole and the C=O of polyesters. HBPs with isatin or methylindole were completely immiscible with the same matrices. None of the HBPs leaked out from plastic matrix after being immersed in water for 5 days. The incorporation of indole into HBPs as well as small molecules facilitated their enzymatic degradation with PETase from Ideonella sakaiensis, while isatin had a complex impact. Molecular docking simulations of monomeric molecules with PETase revealed different orientations of the molecules at the active site due to the presence of indole or isatin groups, which could be related to the observed different enzymatic degradation behavior. Finally, biocompatibility analysis with a mammalian cell line showed the negligible cytotoxic effect of the fabricated HBPs.
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| 25. |
- Linares-Pastén, Javier A., et al.
(författare)
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Modeled 3D-Structures of Proteobacterial Transglycosylases from Glycoside Hydrolase Family 17 Give Insight in Ligand Interactions Explaining Differences in Transglycosylation Products
- 2021
-
Ingår i: Applied Sciences (Switzerland). - : MDPI AG. - 2076-3417. ; 11:9
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Tidskriftsartikel (refereegranskat)abstract
- The structures of glycoside hydrolase family 17 (GH17) catalytic modules from modular proteins in the ndvB loci in Pseudomonas aeruginosa (Glt1), P. putida (Glt3) and Bradyrhizobium diazoefficiens (previously B. japonicum) (Glt20) were modeled to shed light on reported differences between these homologous transglycosylases concerning substrate size, preferred cleavage site (from reducing end (Glt20: DP2 product) or non-reducing end (Glt1, Glt3: DP4 products)), branching (Glt20) and linkage formed (1,3-linkage in Glt1, Glt3 and 1,6-linkage in Glt20). Hybrid models were built and stability of the resulting TIM-barrel structures was supported by molecular dynamics simulations. Catalytic amino acids were identified by superimposition of GH17 structures, and function was verified by mutagenesis using Glt20 as template (i.e., E120 and E209). Ligand docking revealed six putative subsites (−4, −3, −2, −1, +1 and +2), and the conserved interacting residues suggest substrate binding in the same orientation in all three transglycosylases, despite release of the donor oligosaccharide product from either the reducing (Glt20) or non-reducing end (Glt1, Gl3). Subsites +1 and +2 are most conserved and the difference in release is likely due to changes in loop structures, leading to loss of hydrogen bonds in Glt20. Substrate docking in Glt20 indicate that presence of covalently bound donor in glycone subsites −4 to −1 creates space to accommodate acceptor oligosaccharide in alternative subsites in the catalytic cleft, promoting a branching point and formation of a 1,6-linkage. The minimum donor size of DP5, can be explained assuming preferred binding of DP4 substrates in subsite −4 to −1, preventing catalysis.
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| 26. |
- Linares-Pastén, Javier A, et al.
(författare)
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Novel xylan-degrading enzymes from polysaccharide utilizing loci of Prevotella copri DSM18205
- 2021
-
Ingår i: Glycobiology. - : Oxford University Press (OUP). - 1460-2423. ; 31:10, s. 1330-1349
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Tidskriftsartikel (refereegranskat)abstract
- Prevotella copri is a bacterium that can be found in the human gastrointestinal tract (GIT). The role of P. copri in the GIT is unclear, and elevated numbers of the microbe have been reported both in dietary fiber-induced improvement in glucose metabolism but also in conjunction with certain inflammatory conditions. These findings raised our interest in investigating the possibility of P. copri to grow on xylan, and identify the enzyme systems playing a role in digestion of xylan-based dietary fibers. Two xylan degrading polysaccharide utilizing loci (PUL10 and 15) were found in the genome, with three and eight glycoside hydrolase (GH) -encoding genes, respectively. Three of them were successfully produced in Escherichia coli: One extracellular enzyme from GH43 (subfamily 12, in PUL10, 60 kDa) and two enzymes from PUL15, one extracellular GH10 (41 kDa), and one intracellular GH43 (subfamily 137 kDa). Based on our results, we propose that in PUL15, GH10 (1) is an extracellular endo-1,4-β-xylanase, that hydrolazes mainly glucuronosylated xylan polymers to xylooligosaccharides (XOS); while, GH43-1 in the same PUL, is an intracellular β-xylosidase, catalyzing complete hydrolysis of the XOS to xylose. In PUL10, the characterized GH43-12 is an arabinofuranosidase, with a role in degradation of arabinoxylan, catalyzing removal of arabinose-residues on xylan.
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| 27. |
- Linares-Pastén, Javier A., et al.
(författare)
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Three-dimensional structures and functional studies of two GH43 arabinofuranosidases from Weissella sp. strain 142 and Lactobacillus brevis
- 2017
-
Ingår i: The FEBS Journal. - : Wiley. - 1742-464X. ; 284:13, s. 2019-2036
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Tidskriftsartikel (refereegranskat)abstract
- Arabinofuranosidases degrade arabinose-containing oligo and polysaccharides, releasing l-arabinose, which is a potentially useful sugar, shown to reduce glycemic response under certain conditions. Arabinofuranosidases (Arafs) are frequently found in GH43, one of the most common GH-families encoded in genomes in gut microbiota, and hence it is of interest to increase understanding of the function of these enzymes in species occurring in the gut. Here we have produced, characterized and solved the three-dimensional structures, at 1.9 and 2.0 Å resolution respectively, of two homologous GH43 enzymes, classified under subfamily 26, from Lactobacillus brevis DSM1269 (LbAraf43) and Weissella strain 142 (WAraf43), respectively. The enzymes, with 74% sequence identity to each other, are composed of a single catalytic module with a β-propeller structure typical of GH43, and an active-site pocket with three identifiable subsites (−1, +1, and +2). According to size exclusion chromatography, native WAraf43 is a dimer, while LbAraf43 is a tetramer in solution. Both of them show activity with similar catalytic efficiency on 1,5-α-l-arabinooligosaccharides with a degree of polymerization (DP) of 2–3. Activity is restricted to substrates of low DP, and the reason for this is believed to be an extended loop at the entrance to the active site, creating interactions in the +2 subsite. Database: Structural data are available in the PDB under the accession numbers 5M8B (LbAraf43) and 5M8E (WAraf43).
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| 28. |
- Linares-Pastén, Javier, et al.
(författare)
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Efficient poly(3-hydroxypropionate) production from glycerol using Lactobacillus reuteri and recombinant Escherichia coli harboring L. reuteri propionaldehyde dehydrogenase and Chromobacterium sp. PHA synthase genes.
- 2015
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Ingår i: Bioresource Technology. - : Elsevier BV. - 1873-2976 .- 0960-8524. ; 180, s. 172-176
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Tidskriftsartikel (refereegranskat)abstract
- Poly(3-hydroxypropionate), P(3HP), is a polymer combining good biodegradability with favorable material properties. In the present study, a production system for P(3HP) was designed, comprising conversion of glycerol to 3-hydroxypropionaldehyde (3HPA) as equilibrium mixture with 3HPA-hydrate and -dimer in aqueous system (reuterin) using resting cells of native Lactobacillus reuteri in a first stage followed by transformation of the 3HPA to P(3HP) using recombinant Escherichia coli strain co-expressing highly active coenzyme A-acylating propionaldehyde dehydrogenase (PduP) from L. reuteri and polyhydroxyalkanoate synthase (PhaCcs) from Chromobacterium sp. P(3HP) content of up to 40% (w/w) cell dry weight was reached, and the yield with respect to the reuterin consumed by the cells was 78%. Short biotransformation period (4.5h), lack of additives or expensive cofactors, and use of a cheap medium for cultivation of the recombinant strain, provides a new efficient and potentially economical system for P(3HP) production.
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| 29. |
- Manasian, Panagiotis, et al.
(författare)
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First Evidence of Acyl-Hydrolase/Lipase Activity From Human Probiotic Bacteria: Lactobacillus rhamnosus GG and Bifidobacterium longum NCC 2705
- 2020
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Ingår i: Frontiers in Microbiology. - : Frontiers Media SA. - 1664-302X.
-
Tidskriftsartikel (refereegranskat)abstract
- Lactobacillus rhamnosus GG (ATCC 53103) and Bifidobacterium longum NCC 2705 are among the most studied probiotics. However, the first evidence of acyl hydrolase/lipase of two annotated proteins, one in each genome of these strains, is reported in this work. Signal peptide analysis has predicted that these proteins are exported to the extracellular medium. Both proteins were produced in Escherichia coli, purified and characterized. Molecular masses (without signal peptides) were 27 and 52.3 kDa for the proteins of L. rhamnosus and B. longum, respectively. Asymmetrical flow field-flow fractionation analysis has shown that both proteins are present as monomers in their native forms at pH 7. Both have shown enzymatic activity on pNP-laurate at pH 7 and 37°C. The enzyme from L. rhamnosus was characterized deeper, showing preference on pNP-esters with short chain fatty acids. In addition, a computational model of the 3D structure has allowed the prediction of the catalytic amino acids. The enzymatic activities using synthetic substrates were very low for both enzymes. The investigation of natural substrates and biological functions of these enzymes is still open.
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| 30. |
- Mobarec, Hugo, et al.
(författare)
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Microwave-assisted xylanase reaction : impact in the production of prebiotic xylooligosaccharides
- 2021
-
Ingår i: RSC Advances. - 2046-2069. ; 11:20, s. 11882-11888
-
Tidskriftsartikel (refereegranskat)abstract
- The enzymatic production of prebiotic xylooligosaccharides (XOS) has become an attractive way to valorise lignocellulosic biomass. However, despite numerous xylanases reported for potential use in the production of XOS, most of the family GH10 also produce xylose. This monosaccharide can negatively affect the selectivity to stimulate the growth of intestinal microorganisms beneficial to human health. In this work, thermostable alkali-tolerant xylanase (BhXyn10A) from Bacillus halodurans S7 has been used to produce XOS under conventional convective heat transfer and microwave radiation. The microwave-assisted reaction markedly decreases the xylose content in the hydrolysates and significantly increases the yield of XOS, compared to conventional heating. Molecular dynamics simulations of BhXyn10A have shown increased fluctuations of the amino acids of the aglycone subsites suggesting that these subsites can determine the production of xylose. Thus, microwave heating could affect the amino acid fluctuations in the aglycone subsites reducing the xylose formation. These findings open up new avenues in enzyme technology for the production of XOS.
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| 31. |
- Månberger, Anna, et al.
(författare)
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Taxogenomic assessment and genomic characterisation of Weissella cibaria strain 92 able to metabolise oligosaccharides derived from dietary fibres
- 2020
-
Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 10:1
-
Tidskriftsartikel (refereegranskat)abstract
- The importance of the gut microbiota in human health has led to an increased interest to study probiotic bacteria. Fermented food is a source of already established probiotics, but it also offers an opportunity to discover new taxa. Four strains of Weissella sp. isolated from Indian fermented food have been genome sequenced and classified into the species W. cibaria based on whole-genome phylogeny. The genome of W. cibaria strain 92, known to utilise xylooligosaccharides and produce lactate and acetate, was analysed to identify genes for oligosaccharide utilisation. Clusters including genes involved in transportation, hydrolysis and metabolism of xylooligosaccharides, arabinooligosaccharides and β-glucosides were identified. Growth on arabinobiose and laminaribiose was detected. A 6-phospho-β-glucosidase clustered with a phosphotransferase system was found upregulated during growth on laminaribiose, indicating a mechanism for laminaribiose utilisation. The genome of W. cibaria strain 92 harbours genes for utilising the phosphoketolase pathway for the production of both acetate and lactate from pentose and hexose sugars but lacks two genes necessary for utilising the pentose phosphate pathway. The ability of W. cibaria strain 92 to utilise several types of oligosaccharides derived from dietary fibres, and produce lactate and acetate makes it interesting as a probiotic candidate for further evaluation.
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| 32. |
- Najjari, Afef, et al.
(författare)
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Physiological and genomic insights into abiotic stress of halophilic archaeon Natrinema altunense 4.1R isolated from a saline ecosystem of Tunisian desert
- 2023
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Ingår i: Genetica. - : Springer Science and Business Media LLC. - 1573-6857 .- 0016-6707. ; 151:2, s. 133-152
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Tidskriftsartikel (refereegranskat)abstract
- Halophilic archaea are polyextremophiles with the ability to withstand fluctuations in salinity, high levels of ultraviolet radiation, and oxidative stress, allowing them to survive in a wide range of environments and making them an excellent model for astrobiological research. Natrinema altunense 4.1R is a halophilic archaeon isolated from the endorheic saline lake systems, Sebkhas, located in arid and semi-arid regions of Tunisia. It is an ecosystem characterized by periodic flooding from subsurface groundwater and fluctuating salinities. Here, we assess the physiological responses and genomic characterization of N. altunense 4.1R to UV-C radiation, as well as osmotic and oxidative stresses. Results showed that the 4.1R strain is able to survive up to 36% of salinity, up to 180 J/m2 to UV-C radiation, and at 50 mM of H2O2, a resistance profile similar to Halobacterium salinarum, a strain often used as UV-C resistant model. In order to understand the genetic determinants of N. altunense 4.1R survival strategy, we sequenced and analyzed its genome. Results showed multiple gene copies of osmotic stress, oxidative stress, and DNA repair response mechanisms supporting its survivability at extreme salinities and radiations. Indeed, the 3D molecular structures of seven proteins related to responses to UV-C radiation (excinucleases UvrA, UvrB, and UvrC, and photolyase), saline stress (trehalose-6-phosphate synthase OtsA and trehalose-phosphatase OtsB), and oxidative stress (superoxide dismutase SOD) were constructed by homology modeling. This study extends the abiotic stress range for the species N. altunense and adds to the repertoire of UV and oxidative stress resistance genes generally known from haloarchaeon.
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| 33. |
- Ngo, Ngoc T. N., et al.
(författare)
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Synthesis of novel oligomeric anionic alkyl glycosides using laccase/TEMPO oxidation and cyclodextrin glucanotransferase (CGTase)‐catalysed transglycosylation
- 2021
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Ingår i: Biotechnology and Bioengineering. - : Wiley. - 1097-0290 .- 0006-3592. ; 118:7, s. 2548-2558
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Tidskriftsartikel (refereegranskat)abstract
- Modification of alkyl glycosides, to alter their properties and widen the scope of potential applications, is of considerable interest. Here, we report the synthesis of new anionic alkyl glycosides with long carbohydrate chains, using two different approaches: laccase/TEMPO oxidation of a long‐carbohydrate‐chain alkyl glycoside, and cyclodextrin glucanotransferase (CGTase)‐catalysed elongation of anionic alkyl glycosides. The laccase/TEMPO oxidation of dodecyl β‐D‐maltooctaoside proceeded efficiently with the formation of aldehyde and acid products. However, depolymerization occurred to a large extent, limiting the product yield and purity. On the other hand, CGTase‐catalysed coupling/disproportionation reactions with α‐cyclodextrin and dodecyl β‐D‐maltoside diuronic acid (DDM‐2COOH) or octyl β‐D‐glucuronic acid (OG‐COOH) as substrates gave high conversions, especially when the CGTase Toruzyme was used. It was found that pH had a strong influence on both the enzyme activity and the acceptor specificity. With non‐ionic substrates (dodecyl β‐D‐maltoside and octyl β‐D‐glucoside), Toruzyme exhibited high catalytic activity at pH 5‐6, but for the acidic substrates (DDM‐2COOH and OG‐COOH) the activity was highest at pH 4. This is most likely due to the enzyme favoring the protonated forms of DDM‐2COOH and OG‐COOH, which exist at lower pH (pKa about 3).
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| 34. |
- Nordberg Karlsson, Eva, et al.
(författare)
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Endo-xylanases as tools for production of substituted xylooligosaccharides with prebiotic properties
- 2018
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Ingår i: Applied Microbiology and Biotechnology. - : Springer Science and Business Media LLC. - 0175-7598 .- 1432-0614. ; 102:21, s. 9081-9088
-
Forskningsöversikt (refereegranskat)abstract
- Xylan has a main chain consisting of β-1,4-linked xylose residues with diverse substituents. Endoxylanases cleave the xylan chain at cleavage sites determined by the substitution pattern and thus give different oligosaccharide product patterns. Most known endoxylanases belong to glycoside hydrolase (GH) families 10 and 11. These enzymes work well on unsubstituted xylan but accept substituents in certain subsites. The GH11 enzymes are more restricted by substituents, but on the other hand, they are normally more active than the GH10 enzymes on insoluble substrates, because of their smaller size. GH5 endoxylanases accept arabinose substituents in several subsites and require it in the − 1 subsite. This specificity makes the GH5 endoxylanases very useful for degradation of highly arabinose-substituted xylans and for the selective production of arabinoxylooligosaccharides, without formation of unsubstituted xylooligosaccharides. The GH30 endoxylanases have a related type of specificity in that they require a uronic acid substituent in the − 2 subsite, which makes them very useful for the production of uronic acid substituted oligosaccharides. The ability of dietary xylooligosaccharides to function as prebiotics in humans is governed by their substitution patterns. Endoxylanases are thus excellent tools to tailor prebiotic oligosaccharides to stimulate various types of intestinal bacteria and to cause fermentation in different parts of the gastrointestinal tract. Continuously increasing knowledge on the function of the gut microbiota and discoveries of novel endoxylanases increase the possibilities to achieve health-promoting effects.
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| 35. |
- Osorio-Macías, Daniel E., et al.
(författare)
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Characterization on the impact of different clarifiers on the white wine colloids using Asymmetrical Flow Field-Flow Fractionation
- 2022
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Ingår i: Food Chemistry. - : Elsevier BV. - 0308-8146. ; 381
-
Tidskriftsartikel (refereegranskat)abstract
- Clarifiers are substances used during the winemaking process to enhance clarity and stability in the wines. The different clarifiers may alter removal capacities differently. In this study, the removal efficiency of seven common fining agents, divided into three groups (mineral clarifiers, synthetic polymeric clarifiers, and vegetable protein clarifiers), was analyzed with Asymmetrical Flow Field-Flow fractionation (AF4). Besides, the relationship between the removal capacity and different molecular and macromolecular properties has been evaluated. The results showed extensive removal of colloidal and macromolecular matter by the bentonites with potential impact on characteristic properties of the wine. The vegetable clarifiers showed a more profiled reduction, potentially preserving characteristics of the wine. The synthetic polymers showed a more limited removal efficiency but with a high affinity to remove colloidal phenols. The use of AF4-UV-MALS-dRI allowed the characterization of the wines after different clarification treatments, showing to be an analytical technique with a potential impact on the wine industry.
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| 36. |
- Salas-Veizaga, Daniel Martin, et al.
(författare)
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A novel glycoside hydrolase 43-like enzyme from Clostridium boliviensis is an endo-xylanase and a candidate for xylooligosaccharide production from different xylan substrates
- 2024
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Ingår i: Applied and Environmental Microbiology. - 0099-2240. ; 90:4
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Tidskriftsartikel (refereegranskat)abstract
- An uncharacterized gene encoding a glycoside hydrolase family 43-like enzyme from Clostridium boliviensis strain E-1 was identified from genomic sequence data, and the encoded enzyme, CbE1Xyn43-l, was produced in Escherichia coli. CbE1Xyn43-l (52.9 kDa) is a two-domain endo-β-xylanase consisting of a C-terminal CBM6 and a GH43-like catalytic domain. The positions of the catalytic dyad conserved in GH43, the catalytic base (Asp74), and proton donor (Glu240) were identified in alignments including GH43-enzymes of known 3D-structure from different subfamilies. CbE1Xyn43-l is active at pH 7.0–9.0, with optimum temperature at 65°C, and a more than 7 days’ half-life in irreversible deactivation studies at this temperature. The enzyme hydrolyzed birchwood xylan, quinoa stalks glucuronoarabinoxylan, and wheat arabinoxylan with xylotriose and xylotetraose as major hydrolysis products. CbE1Xyn43-l also released xylobiose from pNPX2 with low turnover (kcat of 0.044 s−1) but was inactive on pNPX, showing that a degree of polymerization of three (DP3) was the smallest hydrolyzable substrate. Divalent ions affected the specific activity on xylan substrates, which dependent on the ion could be increased or decreased. In conclusion, CbE1Xyn43-l from C. boliviensis strain E-1 is the first characterized member of a large group of homologous hypothetical proteins annotated as GH43-like and is a thermostable endo-xylanase, producing xylooligosaccharides of high DP (xylotriose and xylotetraose) producer.
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| 37. |
- Schmitz, Eva, et al.
(författare)
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Novel Function of CtXyn5A from Acetivibrio thermocellus: Dual Arabinoxylanase and Feruloyl Esterase Activity Occur in the Same Active Site
- 2022
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Uncharacterized side activities of enzymes can have significant negative effects on reaction products and yields. Hence, their identification and characterization is crucial for the development of successful reaction systems. Here, we report the presence of feruloyl esterase activity in CtXyn5A from Acetivibrio thermocellus besides its well-known arabinoxylanase activity for the first time. Both reaction types appear to be catalysed in the same active site in two subsequential steps. The ferulic acid substituent is cleaved off first, followed by the hydrolysis of the xylan backbone. The esterase activity on complex carbohydrates was found to be higher than the one of a designated ferulic acid esterase (E-FAERU). Therefore, we conclude that the enzyme exhibits a dual function rather than an esterase side activity.
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| 38. |
- Wagner-Egea, Paula, et al.
(författare)
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Assessment of IsPETase-Assisted Depolymerization of Terephthalate Aromatic Polyesters and the Effect of the Thioredoxin Fusion Domain
- 2021
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Ingår i: Applied Sciences (Switzerland). - : MDPI AG. - 2076-3417. ; 11:18
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Tidskriftsartikel (refereegranskat)abstract
- Terephthalate polyesters such as poly(ethylene terephthalate) (PET) have been massively produced over the last few decades due to their attractive properties in multiple applications. However, due to their limited biodegradability, they have accumulated in landfills and oceans, posing an environmental threat. Enzymatic recycling technologies are predicted to generate long-term socioeconomic benefits. In the present work, we compared the IsPETase (from Ideonella sakaiensis 201-F6) activity on a series of polyesters, including poly(butylene) terephthalate (PBT), poly(hexamethylene) terephthalate (PHT) and Akestra™, with PET. The IsPETase showed remarkable activity toward PET (39% degradation of the original polyester) that was higher than that toward Akestra™ (0.13%), PBT (0.25%) and PHT (0.13%) after 72 h. Thus, based on experimental data and computational analysis, we report insights into IsPETase activity on a series of terephthalate-based polyesters. Aside from that, the fusion domain (Trx) effect in the production and activity of a recombinant Trx-IsPETase is reported.
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| 39. |
- Wagner-Egea, Paula, et al.
(författare)
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Marine PET Hydrolase (PET2) : Assessment of Terephthalate- and Indole-Based Polyester Depolymerization
- 2023
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Ingår i: Catalysts. - 2073-4344. ; 13:9
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Tidskriftsartikel (refereegranskat)abstract
- Enzymatic polyethylene terephthalate (PET) recycling processes are gaining interest for their low environmental impact, use of mild conditions, and specificity. Furthermore, PET hydrolase enzymes are continuously being discovered and engineered. In this work, we studied a PET hydrolase (PET2), initially characterized as an alkaline thermostable lipase. PET2 was produced in a fusion form with a 6-histidine tag in the N-terminal. The PET2 activity on aromatic terephthalate and new indole-based polyesters was evaluated using polymers in powder form. Compared with IsPETase, an enzyme derived from Ideonella sakaiensis, PET2 showed a lower PET depolymerization yield. However, interestingly, PET2 produced significantly higher polybutylene terephthalate (PBT) and polyhexylene terephthalate (PHT) depolymerization yields. A clear preference was found for aromatic indole-derived polyesters over non-aromatic ones. No activity was detected on Akestra™, an amorphous copolyester with spiroacetal structures. Docking studies suggest that a narrower and more hydrophobic active site reduces its activity on PET but favors its interaction with PBT and PHT. Understanding the enzyme preferences of polymers will contribute to their effective use to depolymerize different types of polyesters.
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| 40. |
- Zher Neoh, Soon, et al.
(författare)
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Polyhydroxyalkanoate synthase (PhaC) : The key enzyme for biopolyester synthesis
- 2022
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Ingår i: Current Research in Biotechnology. - : Elsevier BV. - 2590-2628. ; 4, s. 87-101
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Forskningsöversikt (refereegranskat)abstract
- Polyhydroxyalkanoates (PHAs) are considered good candidates in replacing commercial petrochemical plastics in certain applications like single-use packaging since they are biodegradable, biocompatible and share similar properties with conventional plastics. PHA synthase (PhaC) is the key enzyme in PHA biosynthesis. There are four classes of PhaC, namely, class I, class II, class III and class IV, each with their distinct characteristics. To date, there are two PhaCs with successfully solved catalytic domain structures. They are PhaC from C. necator (PhaCCn-CAT) (Ser201–Ala589) and PhaC from Chromobacterium sp. USM2 (PhaCCs-CAT) (Phe175–Asn567). Generally, the structure of PhaC consists of an N-terminal domain and a C-terminal catalytic domain. The N-terminal domain is flexible and has not been successfully visualized in any existing structures of PhaC. It is suggested to affect the dimerization and stability of the PhaC dimer, enzymatic activity, substrate specificity, molecular weight of PHA produced, expression of PhaC, and its ability to bind to PHA granules and PHA-related proteins. The C-terminal catalytic domain contains the cap subdomain, substrate entrance channel, active site, and product egress tunnel.
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