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1.
Fluorine biocatalysis.
Wu, L, Maglangit, F, Deng, H
Current opinion in chemical biology. 2020;:119-126
Abstract
The introduction of fluorine atoms into organic molecules has received considerable attention as these organofluorines have often found widespread applications in bioorganic chemistry, medicinal chemistry and biomaterial science. Despite innovation of synthetic C-F forming methodologies, selective fluorination is still extremely challenging. Therefore, a biotransformation approach using fluorine biocatalysts is needed to selectively introduce fluorine into structurally diverse molecules. Yet, there are few ways that enable incorporation of fluorine into structurally complex bioactive molecules. One is to extend the substrate scope of the existing enzyme inventory. Another is to expand the biosynthetic pathways to accept fluorinated precursors for producing fluorinated bioactive molecules. Finally, an understanding of the physiological roles of fluorometabolites in the producing microorganisms will advance our ability to engineer a microorganism to produce novel fluorinated commodities. Here, we review the fluorinase biotechnology and fluorine biocatalysts that incorporate fluorine motifs to generate fluorinated molecules, and highlight areas for future developments.
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2.
Redox Imbalance in CD4+ T Cells of Relapsing-Remitting Multiple Sclerosis Patients.
Tavassolifar, MJ, Moghadasi, AN, Esmaeili, B, Sadatpour, O, Vodjgani, M, Izad, M
Oxidative medicine and cellular longevity. 2020;:8860813
Abstract
As a prevalent autoimmune disease of the central nervous system in young adults, multiple sclerosis (MS) is mediated by T cells, particularly CD4+ subsets. Given the evidence that the perturbation in reactive oxygen species (ROS) production has a pivotal role in the onset and progression of MS, its regulation through the antioxidant molecules is too important. Here, we investigated the level of the redox system components in lymphocytes and CD4+ T cells of MS patients. The study was performed on relapsing-remitting MS (RRMS) patients (n = 29) and age- and sex-matched healthy controls (n = 15). Peripheral blood mononuclear cells (PBMCs) were cultured and stimulated by anti-CD3/CD28. The level of ROS, anion superoxide (O2 -), and L-𝛾-glutamyl-Lcysteinylglycine (GSH) was measured by flow cytometry in lymphocytes/CD4+ T cells. The gene expression level of gp91phox, catalase, superoxide dismutase 1/2 (SOD), and nuclear factor-E2-related factor (Nrf2) was also measured by real-time PCR. We found that lymphocytes/CD4+ T cells of RRMS patients at the relapse phase significantly produced higher levels of ROS and O2 - compared to patients at the remission phase (P value < 0.001) and healthy controls (P value < 0.001 and P value < 0.05, respectively). Interestingly, the gene expression level of gp91phox, known as the catalytic subunit of the NADPH oxidase, significantly increased in MS patients at the relapse phase (P value < 0.05). Furthermore, the catalase expression augmented in patients at the acute phase (P value < 0.05), while an increased expression of SOD1 and Nrf2 was found in RRMS patients at relapse and remission phases (P value < 0.05). The increased production of ROS in CD4+ T cells of RRMS patients highlights the importance of amplifying antioxidant components as an efficient approach to ameliorate disease activity in MS patients.
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3.
Cytokinin dehydrogenase: a genetic target for yield improvement in wheat.
Chen, L, Zhao, J, Song, J, Jameson, PE
Plant biotechnology journal. 2020;(3):614-630
Abstract
The plant hormone group, the cytokinins, is implicated in both qualitative and quantitative components of yield. Cytokinins have opposing actions in shoot and root growth-actions shown to involve cytokinin dehydrogenase (CKX), the enzyme that inactivates cytokinin. We revise and provide unambiguous names for the CKX gene family members in wheat, based on the most recently released wheat genome database, IWGSC RefSeq v1.0 & v2.0. We review expression data of CKX gene family members in wheat, revealing tissue-specific gene family member expression as well as sub-genome-specific expression. Manipulation of CKX in cereals shows clear impacts on yield, root growth and orientation, and Zn nutrition, but this also emphasizes the necessity to unlink promotive effects on grain yield from negative effects of cytokinin on root growth and uptake of mineral nutrients, particularly Zn and Fe. Wheat is the most widely grown cereal crop globally, yet is under-research compared with rice and maize. We highlight gaps in our knowledge of the involvement of CKX for wheat. We also highlight the necessity for accurate analysis of endogenous cytokinins, acknowledging why this is challenging, and provide examples where inadequate analyses of endogenous cytokinins have led to unjustified conclusions. We acknowledge that the allohexaploid nature of bread wheat poses challenges in terms of uncovering useful mutations. However, we predict TILLING followed by whole-exome sequencing will uncover informative mutations and we indicate the potential for stacking mutations within the three genomes to modify yield components. We model a wheat ideotype based on CKX manipulation.
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4.
An enzymatic method for precise oxygen affinity measurements over nanomolar-to-millimolar concentration regime.
Sanyal, R, Bhagi-Damodaran, A
Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry. 2020;(2):181-186
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Abstract
Oxygen affinity is an important property of metalloproteins that helps elucidate their reactivity profile and mechanism. Heretofore, oxygen affinity values were determined either using flash photolysis and polarography techniques that require expensive instrumentation, or using oxygen titration methods which are erroneous at low nanomolar and at high millimolar oxygen concentrations. Here, we describe an inexpensive, easy-to-setup, and a one-pot method for oxygen affinity measurements that uses the enzyme chlorite dismutase (Cld) as a precise in situ oxygen source. Using this method, we measure thermodynamic and kinetic oxygen affinities (Kd and KM) of different classes of heme and non-heme metalloproteins involved in oxygen transport, sensing, and catalysis. The method enables oxygen affinity measurements over a wide concentration range from 10 nM to 5 mM which is unattainable by simply diluting oxygen-saturated buffers. In turn, we were able to precisely measure oxygen affinities of a model set of eight different metalloproteins with affinities ranging from 48 ± 3 nM to 1.18 ± 0.03 mM. Overall, the Cld method is easy and inexpensive to set up, requires significantly lower quantities of protein, enables precise oxygen affinity measurements, and is applicable for proteins exhibiting nanomolar-to-millimolar affinity values.
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5.
In Vivo Metabolic Regulation of Alternative Oxidase under Nutrient Deficiency-Interaction with Arbuscular Mycorrhizal Fungi and Rhizobium Bacteria.
Ortíz, J, Sanhueza, C, Romero-Munar, A, Hidalgo-Castellanos, J, Castro, C, Bascuñán-Godoy, L, Coba de la Peña, T, López-Gómez, M, Florez-Sarasa, I, Del-Saz, NF
International journal of molecular sciences. 2020;(12)
Abstract
The interaction of the alternative oxidase (AOX) pathway with nutrient metabolism is important for understanding how respiration modulates ATP synthesis and carbon economy in plants under nutrient deficiency. Although AOX activity reduces the energy yield of respiration, this enzymatic activity is upregulated under stress conditions to maintain the functioning of primary metabolism. The in vivo metabolic regulation of AOX activity by phosphorus (P) and nitrogen (N) and during plant symbioses with Arbuscular mycorrhizal fungi (AMF) and Rhizobium bacteria is still not fully understood. We highlight several findings and open questions concerning the in vivo regulation of AOX activity and its impact on plant metabolism during P deficiency and symbiosis with AMF. We also highlight the need for the identification of which metabolic regulatory factors of AOX activity are related to N availability and nitrogen-fixing legume-rhizobia symbiosis in order to improve our understanding of N assimilation and biological nitrogen fixation.
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6.
A Homozygotic Mutation in KDSR may Cause Keratinization Disorders and Thrombocytopenia: A Case Report.
Liu, C, Chen, XY, Wu, WQ, Zhu, XF
Chinese medical sciences journal = Chung-kuo i hsueh k'o hsueh tsa chih. 2020;(3):278-282
Abstract
Pathogenic mutations in 3-keto-dihydrosphingosine reductase (KDSR) gene are associated with keratinization disorders and impaired platelet function. However, no case with both homozygotic mutation of KDSR and hepatic hemangioendothelioma has ever been reported due to its low prevalence. Here we report a seven months old Chinese boy with a homozygotic missense mutation in KDSR and both of his parents carry a same heterozygous mutation. He was born with thick plate-like scales overlying erythrodermic skin, but the skin symptoms were resolved spontaneously over the first month of his birth. He was also diagnosed with hepatic hemangioendothelioma at birth and accepted a resection surgery at 2 months old. At birth, his platelet count was severely low (10-20×109/L) with recurrent skin and gingival bleeding. Meanwhile, he suffered a mild normocytic, normochromic anemia with normal iron and hematinic levels. The anemia spontaneously recovered over the first 6 months, while the platelet count keeped at a low level (4-20×109/L). Treatment with corticosteroids, immunoglobulin or thrombopoietin was all suboptimal.
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7.
How superoxide reductases and flavodiiron proteins combat oxidative stress in anaerobes.
Martins, MC, Romão, CV, Folgosa, F, Borges, PT, Frazão, C, Teixeira, M
Free radical biology & medicine. 2019;:36-60
Abstract
Microbial anaerobes are exposed in the natural environment and in their hosts, even if transiently, to fluctuating concentrations of oxygen and its derived reactive species, which pose a considerable threat to their anoxygenic lifestyle. To counteract these stressful conditions, they contain a multifaceted array of detoxifying systems that, in conjugation with cellular repairing mechanisms and in close crosstalk with metal homeostasis, allow them to survive in the presence of O2 and reactive oxygen species. Some of these systems are shared with aerobes, but two families of enzymes emerged more recently that, although not restricted to anaerobes, are predominant in anaerobic microbes. These are the iron-containing superoxide reductases, and the flavodiiron proteins, endowed with O2 and/or NO reductase activities, which are the subject of this Review. A detailed account of their physicochemical, physiological and molecular mechanisms will be presented, highlighting their unique properties in allowing survival of anaerobes in oxidative stress conditions, and comparing their properties with the most well-known detoxifying systems.
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8.
Comparative review of the recent enzymatic methods used for selective assay of l-lysine.
Isobe, K, Matsui, D, Asano, Y
Analytical biochemistry. 2019;:113335
Abstract
l-Lysine is an essential amino acid important for maintaining human health. To date, many enzymatic methods for assay of l-lysine have been developed. The first method has been developed using l-lysine α-oxidase (l-LysOα). However, low specificity towards l-lysine of l-LysOα is a disadvantage inherent in this method. Recently, methods more specific to l-lysine were developed using newly discovered enzymes such as l-lysine ε-oxidase (l-LysOε), l-amino acid oxidase/monooxygenase (l-AAO/MOG) and l-lysine decarboxylase/oxidase (l-Lys-DC/OD). The present paper reviews recent enzymatic methods used for assay of l-lysine. These l-lysine selective assays rely on detecting and quantifying hydrogen peroxide, a product generated by the oxidase reaction of these enzymes. l-LysOε catalyzes the oxidative deamination of the ε-amino group of l-lysine, thus assays using this enzyme are more specific towards l-lysine than the ones using l-LysOα. The l-AAO/MOG has high substrate specificity towards l-lysine; however it exhibits l-lysine oxidase and monooxygenase activities. The sensitivity of l-AAO/MOG method was improved either by using its mutant, which has reduced monooxygenase activity, or by coupling with an aminoamide-oxidizing enzyme. The l-Lys-DC/OD exhibits both l-lysine decarboxylase and oxidase activities. The sensitivity of the l-Lys-DC/OD method was improved by using putrescine oxidase to oxidize the decarboxylation product of l-lysine.
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9.
Identification of 4-methyl-5-oxo-octane-1,8-dioic acid and the derivatives as metabolites of steroidal C,D-ring degradation in Comamonas testosteroni TA441.
Horinouchi, M, Malon, M, Hirota, H, Hayashi, T
The Journal of steroid biochemistry and molecular biology. 2019;:277-286
Abstract
Comamonas testosteroni TA441 degrades steroids via 9,17-dioxo-1,2,3,4,10,19-hexanorandrostan-5-oic acid, which is presumed to be further degraded by β-oxidation. In the β-oxidation process, Coenzyme A (CoA)-ester of 9-oxo-1,2,3,4,5,6,10,19-octanor-13,17-secoandrost-8(14)-ene-7,17-dioic acid is produced and converted by β-ketoacyl-CoA-transferase encoded by ORF1 and ORF2 (scdL1L2) to cleave the remaining C-ring. In this study, we isolated and identified 4-methyl-5-oxo-octane-1,8-dioic acid and 4-methyl-5-oxo-3-octene-1,8-dioic acid from the culture of the ORF3 (scdN)-null mutant as metabolites of steroid degradation (ADD and cholic acid analogues; cholic acid, chenodeoxycholic acid, deoxycholic acid, and lithocholic acid). In addition of these compounds, UHPLC/MS analysis of the culture of the scdN-null mutant revealed significant accumulation of another compound, which was detected as a dominant peak of m/z 155 ([M-CO2]-) accompanied by a small peak of parental ion (m/z 199 [M-]). On the bases of experimental data, this compound was presumed to be 4-methyl-5-oxo-2-octene-1,8-dioic acid, whose CoA-ester was indicated to be converted by scdN-encoded CoA-hydratase into the CoA-ester of 3-hydroxy-4-methyl-5-oxooctan-1,7-carboxylic acid.
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10.
Investigation of quaternary structure of aggregating 3-ketosteroid dehydrogenase from Sterolibacterium denitrificans: In the pursuit of consensus of various biophysical techniques.
Sofińska, K, Wojtkiewicz, AM, Wójcik, P, Zastawny, O, Guzik, M, Winiarska, A, Waligórski, P, Cieśla, M, Barbasz, J, Szaleniec, M
Biochimica et biophysica acta. General subjects. 2019;(6):1027-1039
Abstract
In this work we analyzed the quaternary structure of FAD-dependent 3-ketosteroid dehydrogenase (AcmB) from Sterolibacterium denitrificans, the protein that in solution forms massive aggregates (>600 kDa). Using size-excursion chromatography (SEC), dynamic light scattering (DLS), native-PAGE and atomic force microscopy (AFM) we studied the nature of enzyme aggregation. Partial protein de-aggregation was facilitated by the presence of non-ionic detergent such as Tween 20 or by a high degree of protein dilution but not by addition of a reducing agent or an increase of ionic strength. De-aggregating influence of Tween 20 had no impact on either enzyme's specific activity or FAD reconstitution to recombinant AcmB. The joint experimental (DLS, isoelectric focusing) and theoretical investigations demonstrated gradual shift of enzyme's isoelectric point upon aggregation from 8.6 for a monomeric form to even 5.0. The AFM imaging on mica or highly oriented pyrolytic graphite (HOPG) surface enabled observation of individual protein monomers deposited from a highly diluted solution (0.2 μg/ml). Such approach revealed that native AcmB can indeed be monomeric. AFM imaging supported by theoretical random sequential adsorption (RSA) kinetics allowed estimation of distribution enzyme forms in the bulk solution: 5%, monomer, 11.4% dimer and 12% trimer. Finally, based on results of AFM as well as analysis of the surface of AcmB homology models we have observed that aggregation is most probably initiated by hydrophobic forces and then assisted by electrostatic attraction between negatively charged aggregates and positively charged monomers.