Browsing by Subject "ENZYMES"

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  • Zhou, Qi-Hang; Qin, Wei-Wei; Finel, Moshe; He, Qing-Qing; Tu, Dong-Zhu; Wang, Chao-Ran; Ge, Guang-Bo (2021)
    Strong inhibition of the human UDP-glucuronosyltransferase enzymes (UGTs) may lead to undesirable effects, including hyperbilirubinaemia and drugiherb-drug interactions. Currently, there is no good way to examine the inhibitory effects and specificities of compounds toward all the important human UGTs, side-by-side and under identical conditions. Herein, we report a new, broad-spectrum substrate for human UGTs and its uses in screening and characterizing of UGT inhibitors. Following screening a variety of phenolic compound(s), we have found that methylophiopogonanone A (MOA) can be readily O-glucuronidated by all tested human UGTs, including the typical N-glucuronidating enzymes UGT1A4 and UGT2B10. MOA-O-glucuronidation yielded a single mono-O-glucuronide that was biosynthesized and purified for structural characterization and for constructing an LC-UV based MOA-O-glucuronidation activity assay, which was then used for investigating MOA-O-glucuronidation kinetics in recombinant human UGTs. The derived K-m values were crucial for selecting the most suitable assay conditions for assessing inhibitory potentials and specificity of test compound(s). Furthermore, the inhibitory effects and specificities of four known UGT inhibitors were reinvestigated by using MOA as the substrate for all tested UGTs. Collectively, MOA is a broad-spectrum substrate for the human UGTs, which offers a new and practical tool for assessing inhibitory effects and specificities of UGT inhibitors. (C) 2021 Elsevier B.V. All rights reserved.
  • Emdin, Connor A.; Haas, Mary E.; Khera, Amit V.; Aragam, Krishna; Chaffin, Mark; Klarin, Derek; Hindy, George; Jiang, Lan; Wei, Wei-Qi; Feng, Qiping; Karjalainen, Juha; Havulinna, Aki; Kiiskinen, Tuomo; Bick, Alexander; Ardissino, Diego; Wilson, James G.; Schunkert, Heribert; McPherson, Ruth; Watkins, Hugh; Elosua, Roberto; Bown, Matthew J.; Samani, Nilesh J.; Baber, Usman; Erdmann, Jeanette; Gupta, Namrata; Danesh, John; Saleheen, Danish; Chang, Kyong-Mi; Vujkovic, Marijana; Voight, Ben; Damrauer, Scott; Lynch, Julie; Kaplan, David; Serper, Marina; Tsao, Philip; Program, Million Veteran; Mercader, Josep; Hanis, Craig; Daly, Mark; Denny, Joshua; Gabriel, Stacey; Kathiresan, Sekar (2020)
    Author summary Cirrhosis is a leading cause of death worldwide. However, the genetic underpinnings of cirrhosis remain poorly understood. In this study, we analyze twelve thousand individuals with cirrhosis and identify a common missense variant in a gene called MARC1 that protects against cirrhosis. Carriers of this missense variant also have lower blood cholesterol levels, lower liver enzyme levels and reduced liver fat. We identify an additional two low-frequency coding variants in MARC1 that are also associated with lower cholesterol levels, lower liver enzyme levels and protection from cirrhosis. Finally, we identify an individual homozygous for a predicted loss-of-function variant in MARC1 who exhibits very low blood LDL cholesterol levels. These genetic findings suggest that MARC1 deficiency may lower blood cholesterol levels and protect against cirrhosis, pointing to MARC1 as a potential therapeutic target for liver disease. Analyzing 12,361 all-cause cirrhosis cases and 790,095 controls from eight cohorts, we identify a common missense variant in the Mitochondrial Amidoxime Reducing Component 1 gene (MARC1 p.A165T) that associates with protection from all-cause cirrhosis (OR 0.91, p = 2.3*10(-11)). This same variant also associates with lower levels of hepatic fat on computed tomographic imaging and lower odds of physician-diagnosed fatty liver as well as lower blood levels of alanine transaminase (-0.025 SD, 3.7*10(-43)), alkaline phosphatase (-0.025 SD, 1.2*10(-37)), total cholesterol (-0.030 SD, p = 1.9*10(-36)) and LDL cholesterol (-0.027 SD, p = 5.1*10(-30)) levels. We identified a series of additional MARC1 alleles (low-frequency missense p.M187K and rare protein-truncating p.R200Ter) that also associated with lower cholesterol levels, liver enzyme levels and reduced risk of cirrhosis (0 cirrhosis cases for 238 R200Ter carriers versus 17,046 cases of cirrhosis among 759,027 non-carriers, p = 0.04) suggesting that deficiency of the MARC1 enzyme may lower blood cholesterol levels and protect against cirrhosis.
  • Semenyuk, Pavel; Tiainen, Tony; Hietala, Sami; Tenhu, Heikki; Aseyev, Vladimir; Muronetz, Vladimir (2019)
    Stabilization of the enzymes under stress conditions is of special interest for modern biochemistry, bioengineering, as well as for formulation and target delivery of protein-based drugs. Aiming to achieve an efficient stabilization at elevated temperature with no influence on the enzyme under normal conditions, we studied chaperone-like activity of thermoresponsive polymers based on poly(dimethylaminoethyl methacrylate) (PDMAEMA) toward two different proteins, glyceraldehyde-3-phosphate dehydrogenase and chicken egg lysozyme. The polymers has been shown to do not interact with the folded protein at room temperature but form a complex upon heating to either protein unfolding or polymer phase transition temperature. A PDMAEMA-PEO block copolymer with a dodecyl end-group (d-PDMAEMA-PEO) as well as PDMAEMA-PEO without the dodecyl groups protected the denatured protein against aggregation in contrast to PDMAEMA homopolymer. No effect of the polymers on the enzymatic activity of the client protein was observed at room temperature. The polymers also partially protected the enzyme against inactivation at high temperature. The results provide a platform for creation of artificial chaperones with unfolded protein recognition which is a major feature of natural chaperones. (C) 2018 Elsevier B.V. All rights reserved.
  • Rahikkala, Elisa; Myllykoski, Matti; Hinttala, Reetta; Vieira, Paivi; Nayebzadeh, Naemeh; Weiss, Simone; Plomp, Astrid S.; Bittner, Reginald E.; Kurki, Mitja I.; Kuismin, Outi; Lewis, Andrea M.; Väisänen, Marja-Leena; Kokkonen, Hannaleena; Westermann, Jonne; Bernert, Gunther; Tuominen, Hannu; Palotie, Aarno; Aaltonen, Lauri; Yang, Yaping; Potocki, Lorraine; Moilanen, Jukka; van Koningsbruggen, Silvana; Wang, Xia; Schmidt, Wolfgang M.; Koivunen, Peppi; Uusimaa, Johanna (2019)
    Purpose: A new syndrome with hypotonia, intellectual disability, and eye abnormalities (HIDEA) was previously described in a large consanguineous family. Linkage analysis identified the recessive disease locus, and genome sequencing yielded three candidate genes with potentially pathogenic biallelic variants: transketolase (TKT), transmembrane prolyl 4-hydroxylase (P4HTM), and ubiquitin specific peptidase 4 (USP4). However, the causative gene remained elusive. Methods: International collaboration and exome sequencing were used to identify new patients with HIDEA and biallelic, potentially pathogenic, P4HTM variants. Segregation analysis was performed using Sanger sequencing. P4H-TM wild-type and variant constructs without the transmembrane region were overexpressed in insect cells and analyzed using sodium dodecyl sulfate-polyacrylamide gel electrophoresis and western blot. Results: Five different homozygous or compound heterozygous pathogenic P4HTM gene variants were identified in six new and six previously published patients presenting with HIDEA. Hypoventilation, obstructive and central sleep apnea, and dysautonomia were identified as novel features associated with the phenotype. Characterization of three of the P4H-TM variants demonstrated yielding insoluble protein products and, thus, loss-of-function. Conclusions: Biallelic loss-of-function P4HTM variants were shown to cause HIDEA syndrome. Our findings enable diagnosis of the condition, and highlight the importance of assessing the need for noninvasive ventilatory support in patients.
  • Arte, Elisa; Huang, Xin; Nordlund, Emilia; Katina, Kati (2019)
    The effect of three combinations of bioprocessing methods by lactic acid fermentation, cell wall hydrolyzing enzymes and phytase on the biochemical (protein, fat, carbohydrate composition) and technofunctional properties (protein solubility, emulsifying and foaming properties) of wheat bran protein isolates were evaluated. The bioprocessing increased the protein (up to 80%) and fat content (up to 22.8%) in the isolates due to the degradation of starch and soluble pentosans. Additional proteins, globulin 3A and 3C, chitinase, beta-amylase and LMW glutenins, were identified from the electrophoretic pattern of the protein isolate bioprocessed with added enzymes. Generally, the bioprocessed protein isolate had lower protein solubility and stronger net charge in pH below 7, when compared to the protein isolate made without bioprocessing. The emulsifying properties of the protein isolates were not affected by bioprocessing. However, the foaming stability of the protein isolates was nearly doubled by bioprocessing with cell wall hydrolyzing enzymes and phytase.
  • Ellilä, Simo; Bromann, Paul; Nyyssönen, Mari; Itävaara, Merja; Koivula, Anu; Paulin, Lars; Kruus, Kristiina (2019)
    Xylanases are in important class of industrial enzymes that are essential for the complete hydrolysis of lignocellulosic biomass into fermentable sugars. In the present study, we report the cloning of novel xylanases with interesting properties from compost metagenomics libraries. Controlled composting of lignocellulosic materials was used to enrich the microbial population in lignocellulolytic organisms. DNA extracted from the compost samples was used to construct metagenomics libraries, which were screened for xylanase activity. In total, 40 clones exhibiting xylanase activity were identified and the thermostability of the discovered xylanases was assayed directly from the library clones. Five genes, including one belonging to the more rare family GH8, were selected for subcloning and the enzymes were expressed in recombinant form in E. coli. Preliminary characterization of the metagenome-derived xylanases revealed interesting properties of the novel enzymes, such as high thermostability and specific activity, and differences in hydrolysis profiles. One enzyme was found to perform better than a standard Trichoderma reesei xylanase in the hydrolysis of lignocellulose at elevated temperatures.
  • Miyauchi, Shingo; Hage, Hayat; Drula, Elodie; Lesage-Meessen, Laurence; Berrin, Jean-Guy; Navarro, David; Favel, Anne; Chaduli, Delphine; Grisel, Sacha; Haon, Mireille; Piumi, Francois; Levasseur, Anthony; Lomascolo, Anne; Ahrendt, Steven; Barry, Kerrie; LaButti, Kurt M.; Chevret, Didier; Daum, Chris; Mariette, Jerome; Klopp, Christophe; Cullen, Daniel; de Vries, Ronald P.; Gathman, Allen C.; Hainaut, Matthieu; Henrissat, Bernard; Hilden, Kristiina S.; Kuees, Ursula; Lilly, Walt; Lipzen, Anna; Maekelae, Miia R.; Martinez, Angel T.; Morel-Rouhier, Melanie; Morin, Emmanuelle; Pangilinan, Jasmyn; Ram, Arthur F. J.; Woesten, Han A. B.; Ruiz-Duenas, Francisco J.; Riley, Robert; Record, Eric; Grigoriev, Igor; Rosso, Marie-Noelle (2020)
    White-rot (WR) fungi are pivotal decomposers of dead organic matter in forest ecosystems and typically use a large array of hydrolytic and oxidative enzymes to deconstruct lignocellulose. However, the extent of lignin and cellulose degradation may vary between species and wood type. Here, we combined comparative genomics, transcriptomics and secretome proteomics to identify conserved enzymatic signatures at the onset of wood-decaying activity within the Basidiomycota genus Pycnoporus. We observed a strong conservation in the genome structures and the repertoires of protein-coding genes across the four Pycnoporus species described to date, despite the species having distinct geographic distributions. We further analysed the early response of P. cinnabarinus, P. coccineus and P. sanguineus to diverse (ligno)-cellulosic substrates. We identified a conserved set of enzymes mobilized by the three species for breaking down cellulose, hemicellulose and pectin. The co-occurrence in the exo-proteomes of H2O2-producing enzymes with H2O2-consuming enzymes was a common feature of the three species, although each enzymatic partner displayed independent transcriptional regulation. Finally, cellobiose dehydrogenase-coding genes were systematically co-regulated with at least one AA9 lytic polysaccharide monooxygenase gene, indicative of enzymatic synergy in vivo. This study highlights a conserved core white-rot fungal enzymatic mechanism behind the wood-decaying process.
  • Mäki, Mari; Mali, Tuulia; Hellén, Heidi; Heinonsalo, Jussi; Lundell, Taina; Bäck, Jaana (2021)
    Wood-decaying fungi in the phylum Basidiomycota play a significant role in the global carbon cycle, as they decompose deadwood effectively. Fungi may compete for utilizable substrate and growth space by producing soluble metabolites and by releasing volatile organic compounds (VOCs). We determined the role of wood substrate (Scots pine or Norway spruce) on the generation of hyphal biomass, secreted metabolites and enzyme activities, wood decomposition rate, and fungal species-species interactions on VOC release. We studied one brown-rot species (Fomitopsis pinicola) and two white-rot species (Phlebia radiata and Trichaptum abietinum) cultivated individually or in combinations. Wood substrate quality influences VOC release by the wood-decaying fungi, with signature differences caused by the decomposition trait (brown rot or white rot) and species-species interactions. VOC release was higher in the cultures of Basidiomycota than in uncolonized sawdust. Fungal biomass, decomposition activity, iron reduction, enzyme activities, oxalate anion content, and oxalic acid production explained VOC release from decaying wood.
  • Ebrahimi, Nashmin; Hartikainen, Helina; Simojoki, Asko; Hajiboland, Roghieh; Seppanen, Mervi (2015)
    The uptake by and subsequent translocation of selenium (Se) within the plant is dependent on its chemical form and soil properties that dictate this trace element's bioavailability. Plant species differ in their tendency to accumulate Se. Se taken-up by plants is returned to soil in plant residues, but the bioavailability of organic Se in those residues is poorly known. We investigated the impact of inorganic (Na2SeO4), organic (Se-enriched stem and leaf residues) Se applications and also soil microbial respiration on the growth and Se concentrations of various plant organs of oilseed rape (Brassica napus L.) during its development from the rosette to the seed filling stage. Both inorganic and organic Se slightly improved plant growth and enhanced plant development. Inorganic Se was more bioavailable than the organic forms and resulted in 3-fold to 6-fold higher Se concentrations in the siliques. Inorganic Se in autoclaved soil tended to elevate the Se concentration in all plant parts and at all growth stages. The organic Se raised Se concentrations in plants much less effectively than the inorganic selenate. Therefore, the use of inorganic Se is still recommended for biofortification.
  • Morais de Carvalho, Danila; Lahtinen, Maarit; Lawoko, Martin; Mikkonen, Kirsi S. (2020)
    Lignin-carbohydrate complexes (LCCs) are hybrid structures containing covalently linked moieties of lignin and carbohydrates. The structure and behavior of LCCs affect both industrial processes and practical applications of lignocellulosic biomass. However, the identification of phenylglycoside, benzylether, and gamma (gamma)-ester LCC bonds in lignocellulosic biomass is limited due to their relatively low abundance compared to plain carbohydrate and lignin structures. Herein, we enriched the LCC bonds in softwood galactoglucomannan (GGM)-rich extract fractionated by (1) a solvent (ethanol), (2) enzymes, and (3) physical techniques. Two-dimensional nuclear magnetic resonance (NMR) spectroscopy analysis was used to identify the LCC bonds. Phenylglycoside and benzylether bonds were concentrated in the ethanol-soluble GGM fractions. A benzylether bond was concentrated into GGM fractions containing larger molecules (>500 Da) through physical techniques. The gamma-ester bond was identified in all studied GGM fractions, which is explained by its stability and possible presence in residual xylan. In summary, we demonstrated the potential of the suggested techniques to enrich LCC bonds in softwood extract and improve LCC identification. Such techniques may also enable further studies on the structure and functionality of LCC bonds and open new prospects in the engineering of biomolecules.
  • Alegre, Sara; Pascual, Jesús; Trotta, Andrea; Angeleri, Martina; Rahikainen, Moona; Brosche, Mikael; Moffatt, Barbara; Kangasjärvi, Saijaliisa (2020)
    Trans-methylation reactions are intrinsic to cellular metabolism in all living organisms. In land plants, a range of substrate-specific methyltransferases catalyze the methylation of DNA, RNA, proteins, cell wall components and numerous species-specific metabolites, thereby providing means for growth and acclimation in various terrestrial habitats. Trans-methylation reactions consume vast amounts of S-adenosyl-L-methionine (SAM) as a methyl donor in several cellular compartments. The inhibitory reaction by-product, S-adenosyl-L-homocysteine (SAH), is continuously removed by SAH hydrolase (SAHH), which essentially maintains trans-methylation reactions in all living cells. Here we report on the evolutionary conservation and post-translational control of SAHH in land plants. We provide evidence suggesting that SAHH forms oligomeric protein complexes in phylogenetically divergent land plants and that the predominant protein complex is composed by a tetramer of the enzyme. Analysis of light-stress-induced adjustments of SAHH in Arabidopsis thaliana and Physcomitrella patens further suggests that regulatory actions may take place on the levels of protein complex formation and phosphorylation of this metabolically central enzyme. Collectively, these data suggest that plant adaptation to terrestrial environments involved evolution of regulatory mechanisms that adjust the trans-methylation machinery in response to environmental cues.
  • Sun, Peicheng; Li, Xinxin; Dilokpimol, Adiphol; Henrissat, Bernard; de Vries, Ronald P.; Kabel, Mirjam A.; Mäkelä, Miia R. (2022)
    Xyloglucan is a prominent matrix heteropolysaccharide binding to cellulose microfibrils in primary plant cellwalls. Hence, the hydrolysis of xyloglucan facilitates the overall lignocellulosic biomass degradation. Xyloglucanases (XEGs) are key enzymes classified in several glycoside hydrolase (GH) families. So far, family GH44 has been shown to contain bacterial XEGs only. Detailed genome analysis revealed GH44 members in fungal species from the phylum Basidiomycota, but not in other fungi, which we hypothesized to also be XEGs. Two GH44 enzymes from Dichomitus squalens and Pleurotus ostreatus were heterologously produced and characterized. They exhibited XEG activity and displayed a hydrolytic cleavage pattern different fromthat observed in fungal XEGs from other GH families. Specifically, the fungal GH44 XEGs were not hindered by substitution of neighboring glucosyl units and generated various," "XXXG- type,'' "GXXX(G)-type,'' and "XXX-type'' oligosaccharides. Overall, these fungal GH44 XEGs represent a novel class of enzymes for plant biomass conversion and valorization.
  • Daly, Paul; Peng, Mao; Di Falco, Marcos; Lipzen, Anna; Wang, Mei; Ng, Vivian; Grigoriev, Igor; Tsang, Adrian; Makela, Miia R.; de Vries, Ronald P. (2019)
    The extent of carbon catabolite repression (CCR) at a global level is unknown in wood-rotting fungi, which are critical to the carbon cycle and are a source of biotechnological enzymes. CCR occurs in the presence of sufficient concentrations of easily metabolizable carbon sources (e.g., glucose) and involves downregulation of the expression of genes encoding enzymes involved in the breakdown of complex carbon sources. We investigated this phenomenon in the white-rot fungus Dichomitus squalens using transcriptomics and exoproteomics. In D. squalens cultures, approximately 7% of genes were repressed in the presence of glucose compared to Avicel or xylan alone. The glucose-repressed genes included the essential components for utilization of plant biomass-carbohydrate-active enzyme (CAZyme) and carbon catabolic genes. The majority of polysaccharide-degrading CAZyme genes were repressed and included activities toward all major carbohydrate polymers present in plant cell walls, while repression of ligninolytic genes also occurred. The transcriptome-level repression of the CAZyme genes observed on the Avicel cultures was strongly supported by exoproteomics. Protease-encoding genes were generally not glucose repressed, indicating their likely dominant role in scavenging for nitrogen rather than carbon. The extent of CCR is surprising, given that D. squalens rarely experiences high free sugar concentrations in its woody environment, and it indicates that biotechnological use of D. squalens for modification of plant biomass would benefit from derepressed or constitutively CAZyme-expressing strains. IMPORTANCE White-rot fungi are critical to the carbon cycle because they can mineralize all wood components using enzymes that also have biotechnological potential. The occurrence of carbon catabolite repression (CCR) in white-rot fungi is poorly understood. Previously, CCR in wood-rotting fungi has only been demonstrated for a small number of genes. We demonstrated widespread glucose-mediated CCR of plant biomass utilization in the white-rot fungus Dichomitus squalens. This indicates that the CCR mechanism has been largely retained even though wood-rotting fungi rarely experience commonly considered CCR conditions in their woody environment. The general lack of repression of genes encoding proteases along with the reduction in secreted CAZymes during CCR suggested that the retention of CCR may be connected with the need to conserve nitrogen use during growth on nitrogen-scarce wood. The widespread repression indicates that derepressed strains could be beneficial for enzyme production.
  • Chroumpi, Tania; Aguilar-Pontes, Maria Victoria; Peng, Mao; Wang, Mei; Lipzen, Anna; Ng, Vivian; Grigoriev, Igor; Makela, Miia R.; de Vries, Ronald P. (2020)
    In fungi, L-rhamnose (Rha) is converted via four enzymatic steps into pyruvate and L-lactaldehyde, which enter central carbon metabolism. In Aspergillus niger, only the genes involved in the first three steps of the Rha catabolic pathway have been identified and characterized, and the inducer of the pathway regulator RhaR remained unknown. In this study, we identified the gene (lkaA) involved in the conversion of L-2-keto-3-deoxyrhamnonate (L-KDR) into pyruvate and L-lactaldehyde, which is the last step of the Rha pathway. Deletion of lkaA resulted in impaired growth on L-rhamnose, and potentially in accumulation of L-KDR. Contrary to Delta lraA, Delta lrlA and Delta lrdA, the expression of the Rha-responsive genes that are under control of RhaR, were at the same levels in Delta lkaA and the reference strain, indicating the role of L-KDR as the inducer of the Rha pathway regulator.
  • Kinnunen, Anu Johanna; Maijala, Pekka Mikael; Järvinen, Päivi Pauliina; Hatakka, Annele Inkeri (2017)
    Background: Wood rotting white-rot and litter-decomposing basidiomycetes form a huge reservoir of oxidative enzymes, needed for applications in the pulp and paper and textile industries and for bioremediation. Objective: The aim was (i) to achieve higher throughput in enzyme screening through miniaturization and automatization of the activity assays, and (ii) to discover fungi which produce efficient oxidoreductases for industrial purposes. Methods: Miniaturized activity assays mostly using dyes as substrate were carried out for lignin peroxidase, versatile peroxidase, manganese peroxidase and laccase. Methods were validated and 53 species of basidiomycetes were screened for lignin modifying enzymes when cultivated in liquid mineral, soy, peptone and solid state oat husk medium. Results: Manganese peroxidases were the most common enzymes produced by 96% of the species. They typically had acidic pH optima, although Hyphodontia sp., Pleurotus pulmonarius and Trametes ochracea produced enzymes highly active at pH 7. Versatile peroxidase was produced by 66% of the fungi with efficient production from Phlebia radiata, P. pulmonarius and Galerina marginata. Novel lignin peroxidase producing fungi Cylindrobasidium evolvens and Daedaleopsis septentrionalis were found among the 26% of the species showing here lignin peroxidase production. Laccase was shown in 92% of the species. Several fungi produced laccase active at pH 7, which is noteworthy because usually laccases of white-rot fungi are efficient and relevant for many industrial applications. Conclusion: Automated screening allowed us to monitor many specific enzyme activities and extend the range of assay conditions from relatively small fungal cultivation sample volumes.
  • Liu, Xin-Yu; Lv, Xia; Wang, Ping; Ai, Chun-Zhi; Zhou, Qi-Hang; Finel, Moshe; Fan, Bin; Cao, Yun-Feng; Tang, Hui; Ge, Guang-Bo (2019)
    Flavonoids are widely distributed phytochemicals in vegetables, fruits and medicinal plants. Recent studies demonstrate that some natural flavonoids are potent inhibitors of the human UDP-glucuronosyltransferase 1A1 (UGT1A1), a key enzyme in detoxification of endogenous harmful compounds such as bilirubin. In this study, the inhibitory effects of 56 natural and synthetic flavonoids on UGT1A1 were assayed, while the structure–inhibition relationships of flavonoids as UGT1A1 inhibitors were investigated. The results demonstrated that the C-3 and C-7 hydroxyl groups on the flavone skeleton would enhance UGT1A1 inhibition, while flavonoid glycosides displayed weaker inhibitory effects than their corresponding aglycones. Further investigation on inhibition kinetics of two strong flavonoid-type UGT1A1 inhibitors, acacetin and kaempferol, yielded interesting results. Both flavonoids were competitive inhibitors against UGT1A1-mediated NHPN-O-glucuronidation, but were mixed and competitive inhibitors toward UGT1A1-mediated NCHN-O-glucuronidation, respectively. Furthermore, docking simulations showed that the binding areas of NHPN, kaempferol and acacetin on UGT1A1 were highly overlapping, and convergence with the binding area of bilirubin within UGT1A1. In summary, detailed structure-inhibition relationships of flavonoids as UGT1A1 inhibitors were investigated carefully and the findings shed new light on the interactions between flavonoids and UGT1A1, and will contribute considerably to the development of flavonoid-type drugs without strong UGT1A1 inhibition.
  • Ribeiro de Barros, Heloise; Garcia, Isabel; Kuttner, Christian; Zeballos, Nicoll; Camargo, Pedro H. C.; Cordoba de Torresi, Susana Ines; Lopez-Gallego, Fernando; Liz-Marzan, Luis M. (2021)
    The use of light as an external stimulus to control the enzyme activity is an emerging strategy that enables accurate, remote, and noninvasive biotransformations. In this context, immobilization of enzymes on plasmonic nanoparticles offers an opportunity to create light-responsive biocatalytic materials. Nevertheless, a fundamental and mechanistic understanding of the effects of localized surface plasmon resonance (LSPR) excitation on enzyme regulation remains elusive. We herein investigate the plasmonic effects on biocatalysis using Au nanospheres (AuNSp) and nanostars (AuNSt) as model plasmonic nanoparticles, lipase from Candida antarctica fraction B (CALB) as a proof-of-concept enzyme, and 808 nm as near-infrared light excitation. Our data show that LSPR excitation enables an enhancement of 58% in the enzyme activity for CALB adsorbed on AuNSt, compared with the dark conditions. This work shows how photothermal heating over the LSPR excitation enhances the CALB activity through favoring product release in the last step of the enzyme mechanism. We propose that the results reported herein shed important mechanistic and kinetic insights into the field of plasmonic biocatalysis and may inspire the rational development of plasmonic nanomaterial-enzyme hybrids with tailored activities under external light irradiation.
  • George, Jack; Tuomela, Tea; Kemppainen, Esko; Nurminen, Antti; Braun, Samuel; Yalgin, Cagri; Jacobs, Howard T. (2019)
    ABSTRACTThe Drosophila bang-sensitive mutant tko25t, manifesting a global deficiency in oxidative phosphorylation due to a mitochondrial protein synthesis defect, exhibits a pronounced delay in larval development. We previously identified a number of metabolic abnormalities in tko25t larvae, including elevated pyruvate and lactate, and found the larval gut to be a crucial tissue for the regulation of larval growth in the mutant. Here we established that expression of wild-type tko in any of several other tissues of tko25t also partially alleviates developmental delay. The effects appeared to be additive, whilst knockdown of tko in a variety of specific tissues phenocopied tko25t, producing developmental delay and bang-sensitivity. These findings imply the existence of a systemic signal regulating growth in response to mitochondrial dysfunction. Drugs and RNAi-targeted on pyruvate metabolism interacted with tko25t in ways that implicated pyruvate or one of its metabolic derivatives in playing a central role in generating such a signal. RNA-seq revealed that dietary pyruvate-induced changes in transcript representation were mostly non-coherent with those produced by tko25t or high-sugar, consistent with the idea that growth regulation operates primarily at the translational and/or metabolic level.
  • Cannata Serio, Magda; Graham, Laurie A.; Ashikov, Angel; Larsen, Lars Elmann; Raymond, Kimiyo; Timal, Sharita; Le Meur, Gwenn; Ryan, Margret; Czarnowska, Elzbieta; Jansen, Jos C.; He, Miao; Ficicioglu, Can; Pichurin, Pavel; Hasadsri, Linda; Minassian, Berge; Rugierri, Alessandra; Kalimo, Hannu; Rios-Ocampo, W. Alfredo; Gilissen, Christian; Rodenburg, Richard; Jonker, Johan W.; Holleboom, Adriaan G.; Morava, Eva; Veltman, Joris A.; Socha, Piotr; Stevens, Tom H.; Simons, Matias; Lefeber, Dirk J. (2020)
    Background and Aims Vacuolar H+-ATP complex (V-ATPase) is a multisubunit protein complex required for acidification of intracellular compartments. At least five different factors are known to be essential for its assembly in the endoplasmic reticulum (ER). Genetic defects in four of these V-ATPase assembly factors show overlapping clinical features, including steatotic liver disease and mild hypercholesterolemia. An exception is the assembly factor vacuolar ATPase assembly integral membrane protein (VMA21), whose X-linked mutations lead to autophagic myopathy. Approach and Results Here, we report pathogenic variants in VMA21 in male patients with abnormal protein glycosylation that result in mild cholestasis, chronic elevation of aminotransferases, elevation of (low-density lipoprotein) cholesterol and steatosis in hepatocytes. We also show that the VMA21 variants lead to V-ATPase misassembly and dysfunction. As a consequence, lysosomal acidification and degradation of phagocytosed materials are impaired, causing lipid droplet (LD) accumulation in autolysosomes. Moreover, VMA21 deficiency triggers ER stress and sequestration of unesterified cholesterol in lysosomes, thereby activating the sterol response element-binding protein-mediated cholesterol synthesis pathways. Conclusions Together, our data suggest that impaired lipophagy, ER stress, and increased cholesterol synthesis lead to LD accumulation and hepatic steatosis. V-ATPase assembly defects are thus a form of hereditary liver disease with implications for the pathogenesis of nonalcoholic fatty liver disease.
  • Munsch-Alatossava, Patricia; Käkelä, Reijo; Ibarra, Dominique; Youbi-Idrissi, Mohammed; Alatossava, Tapani (2018)
    Cold storage aims to preserve the quality and safety of raw milk from farms to dairies; unfortunately, low temperatures also promote the growth of psychrotrophic bacteria, some of which produce heat-stable enzymes that cause spoilage of milk or dairy products. Previously, N-2 gas flushing of raw milk has demonstrated significant potential as a method to hinder bacterial growth at both laboratory and pilot plant scales. Using a mass spectrometry-based lipidomics approach, we examined the impact of cold storage [at 6 degrees C for up to 7 days, the control condition (C)], on the relative amounts of major phospholipids (phosphatidylethanolamine/PE, phosphatidylcholine/PC, phosphatidylserine/PS, phosphatidylinositol/PI, and sphingomyelin/SM) in three bovine raw milk samples, and compared it to the condition that received additional N-2 gas flushing (N). As expected, bacterial growth was hindered by the N-2-based treatment (over 4 log-units lower at day 7) compared to the non-treated control condition. At the end of the cold storage period, the control condition (C7) revealed higher hydrolysis of PC, SM, PE, and PS (the major species reached 27.2, 26.7, 34.6, and 9.9 mu M, respectively), compared to the N-2-flushed samples (N7) (the major species reached 55.6, 35.9, 54.0, and 18.8 mu M, respectively). C7 samples also exhibited a three-fold higher phosphatidic acid (PA) content (6.8 mu M) and a five-fold higher content (17.3 mu M) of lysophospholipids (LPE, LPC, LPS, and LPI) whereas both lysophospholipids and PA remained at their initial levels for 7 days in N7 samples. Taking into consideration the significant phospholipid losses in the controls, the lipid profiling results together with the microbiological data suggest a major role of phospholipase (PLase) C (PLC) in phospholipolysis during cold storage. However, the experimental data also indicate that bacterial sphingomyelinase C, together with PLases PLD and PLA contributed to the degradation of phospholipids present in raw milk as well, and potential contributions from PLB activity cannot be excluded. Altogether, this lipidomics study highlights the beneficial effects of N-2 flushing treatment on the quality and safety of raw milk through its ability to effectively hinder phospholipolysis during cold storage.