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Kate E R Hollinshead, Haydn Munford, Katherine L Eales, Chiara Bardella, Chunjie Li, Cristina Escribano-Gonzalez, Alpesh Thakker, Yannic Nonnenmacher, Katarina Kluckova, Mark Jeeves, Robert Murren, Federica Cuozzo, Dan Ye, Giulio Laurenti, Wei Zhu, Karsten Hiller, David J Hodson, Wei Hua, Ian P Tomlinson, Christian Ludwig, Ying Mao, Daniel A Tennant
Since the discovery of mutations in isocitrate dehydrogenase 1 (IDH1) in gliomas and other tumors, significant efforts have been made to gain a deeper understanding of the consequences of this oncogenic mutation. One aspect of the neomorphic function of the IDH1 R132H enzyme that has received less attention is the perturbation of cellular redox homeostasis. Here, we describe a biosynthetic pathway exhibited by cells expressing mutant IDH1. By virtue of a change in cellular redox homeostasis, IDH1-mutated cells synthesize excess glutamine-derived proline through enhanced activity of pyrroline 5-carboxylate reductase 1 (PYCR1), coupled to NADH oxidation...
March 20, 2018: Cell Reports
Wolfgang Buckel, Rudolf K Thauer
There are two types of electron bifurcation (EB), either quinone- or flavin-based (QBEB/FBEB), that involve reduction of a quinone or flavin by a two-electron transfer and two reoxidations by a high- and low-potential one-electron acceptor with a reactive semiquinone intermediate. In QBEB, the reduced low-potential acceptor (cytochrome b) is exclusively used to generate ΔμH+ . In FBEB, the "energy-rich" low-potential reduced ferredoxin or flavodoxin has dual function. It can give rise to ΔμH+ /Na+ via a ferredoxin:NAD reductase (Rnf) or ferredoxin:proton reductase (Ech) or conducts difficult reductions such as CO2 to CO...
March 21, 2018: Chemical Reviews
Erika Salavarría, Sujay Paul, Patricia Gil-Kodaka, Gretty K Villena
To understand the physiological responses of the brown macroalga Macrocystis integrifolia during the marine tidal cycle, two RNA libraries were prepared from algal frond samples collected in the intertidal zone (0 m depth) and subtidal zone (10 m depth). Samples collected from intertidal zone during low tide was considered as abiotic stressed (MI0), while samples collected from subtidal zone was considered as control (MI10). Both RNA libraries were sequenced on Illumina NextSeq 500 which generated approx...
April 2018: 3 Biotech
Karen Nørgaard Nielsen, Julia Peics, Tao Ma, Iuliia Karavaeva, Morten Dall, Sabina Chubanava, Astrid L Basse, Oksana Dmytriyeva, Jonas T Treebak, Zachary Gerhart-Hines
OBJECTIVE: The ability of adipose tissue to expand and contract in response to fluctuations in nutrient availability is essential for the maintenance of whole-body metabolic homeostasis. Given the nutrient scarcity that mammals faced for millions of years, programs involved in this adipose plasticity were likely evolved to be highly efficient in promoting lipid storage. Ironically, this previously advantageous feature may now represent a metabolic liability given the caloric excess of modern society...
March 7, 2018: Molecular Metabolism
Min-Hui Tang, Nan Gao, Jiao Zhou, Yan Zhao, Jing-Sheng Cheng, Wen-Kun Su, Ying-Jin Yuan
Sulfamethoxazole (SMX) has frequently been detected in aquatic environments. In natural environment, not only individual microorganism but also microbial consortia are involved in some biotransformation of pollutants. The competition for space under consortia causing cell-cell contact inhibition changes the cellular behaviors. Herein, the membrane bioreactor system (MBRS) was applied to improve SMX elimination thorough exchanging the cell-free broths (CFB). The removal efficiency of SMX was increased by more than 24% whether under the pure culture of A...
March 15, 2018: Biodegradation
Nanako Kanno, Katsumi Matsuura, Shin Haruta
Purple photosynthetic bacteria utilize light energy for growth. We previously demonstrated that light energy contributed to prolonging the survival of multiple purple bacteria under carbon-starved conditions. In order to clarify the effects of illumination on metabolic states under carbon-starved, non-growing conditions, we herein compared the metabolic profiles of starved cells in the light and dark using the purple bacterium, Rhodopseudomonas palustris. The metabolic profiles of starved cells in the light were markedly different from those in the dark...
March 13, 2018: Microbes and Environments
Katsuaki Kobayashi, Take-Aki Koizumi, Debashis Ghosh, Takashi Kajiwara, Susumu Kitagawa, Koji Tanaka
A RhCp* (Cp* = pentamethylcyclopentadienyl) complex bearing an NAD+ /NADH-functionalized ligand, [RhCp*(pbn)Cl]Cl ([1]Cl, pbn = (2-(2-pyridyl)benzo[b]-1,5-naphthyridine)), was synthesized. The cyclic voltammogram of [1]Cl in CH3 CN shows two reversible redox waves at E1/2 = -0.58 and -1.53 V (vs. the saturated calomel electrode (SCE)), which correspond to the RhIII /RhI and pbn/pbn˙- redox couples, respectively. The addition of acetic acid to the solution afforded the proton-coupled two-electron reduction of [1]Cl at -0...
March 14, 2018: Dalton Transactions: An International Journal of Inorganic Chemistry
Mingming Pu, Lili Sheng, Sooyeon Song, Ting Gong, Thomas K Wood
Pseudomonas aeruginosa causes many biofilm infections, and the rugose small-colony variants (RSCVs) of this bacterium are important for infection. We found here that inactivation of PA2444, which we determined to be a serine hydroxymethyltransferase (SHMT), leads to the RSCV phenotype of P. aeruginosa PA14. In addition, loss of PA2444 increases biofilm formation by two orders of magnitude, increases exopolysaccharide by 45-fold, and abolishes swarming. The RSCV phenotype is related to higher cyclic diguanylate concentrations due to increased activity of the Wsp chemosensory system, including diguanylate cyclase WspR...
2018: Frontiers in Microbiology
Taofeek O Ajiboye, Evelyn Skiebe, Gottfried Wilharm
Phenolic acids with catechol groups are good prooxidants because of their low redox potential. In this study, we provided data showing that phenolic acids, caffeic acid, gallic acid and protocatechuic acid, enhanced colistin-mediated bacterial death by inducing redox imbalance. The minimum inhibitory concentrations of these phenolic acids against Acinetobacter baumannii AB5075 were considerably lowered for ΔsodB and ΔkatG mutants. Checkerboard assay shows synergistic interactions between colistin and phenolic acids...
March 7, 2018: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
Filipa V Sena, Filipe M Sousa, A Sofia F Oliveira, Cláudio M Soares, Teresa Catarino, Manuela M Pereira
Type-II NADH:quinone oxidoreductases (NDH-2s) are membrane proteins involved in respiratory chains and the only enzymes with NADH:quinone oxidoreductase activity expressed in Staphylococcus aureus (S. aureus), one of the most common causes of clinical infections. NDH-2s are members of the two-Dinucleotide Binding Domains Flavoprotein (tDBDF) superfamily, having a flavin adenine dinucleotide, FAD, as prosthetic group and NAD(P)H as substrate. The establishment of a Charge-Transfer Complex (CTC) between the isoalloxazine ring of the reduced flavin and the nicotinamide ring of NAD+ in NDH-2 was described, and in this work we explored its role in the kinetic mechanism using different electron donors and electron acceptors...
February 17, 2018: Redox Biology
Russell P Goodman, Sarah Calvo, Vamsi K Mootha
Compartmentalization is a fundamental design principle of eukaryotic metabolism.  Here, we review the compartmentalization of NAD+/NADH and NADP+/NADPH with a focus on the liver, an organ that experiences the extremes of biochemical physiology each day.  Historical studies of the liver, using classical biochemical  measurements of redox-coupled metabolites, have given rise to the view that mitochondrial NAD(H) pools tend to be oxidized and important for energy homeostasis, whereas cytosolic NADP(H) pools tend to be highly reduced for reductive biosynthesis...
March 7, 2018: Journal of Biological Chemistry
Taewoong Ha, Mi Kyoung Kim, Kwang-Su Park, Woong Jung, Hyunah Choo, Youhoon Chong
(-)-Epigallocatechin-3-gallate (EGCG) is known as a mitochondria-targeted molecule that can prevent mitochondrial deterioration and induce mitochondrial biogenesis by modulating key regulators of mitochondrial metabolism. In this study, we tackled whether derivatization of EGCG could result in enhancement of its effects on mitochondrial biogenesis. EGCG, EGCG peracetate (AcEGCG), and its 4″- O-alkyl substituted congeners prepared by previously reported procedures were biologically evaluated. Interestingly, EGCG and AcEGCG were only marginally effective in inducing mitochondrial biogenesis, while AcEGCG congeners with an alkyl group at the 4″- O position showed significantly increased biological activity compared to their parent compound...
March 8, 2018: Journal of Agricultural and Food Chemistry
Fei-Long Li, Ying Shi, Jiu-Xun Zhang, Jian Gao, Ye-Wang Zhang
A novel nicotinamide adenine dinucleotide (NADH) oxidase from Streptococcus mutans ATCC 25175 (SmNox) was cloned and overexpressed in Escherichia coli BL21 (DE3). Sequence analysis revealed an open reading frame of 1374 bp, capable of encoding a polypeptide of 457 amino acid residues. The molecular mass of the purified SmNox was estimated to be ∼49.9 kDa by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The purified SmNox had the highest specific activity of 281.2 U·mg-1 at optimal pH and temperature of 7...
March 4, 2018: International Journal of Biological Macromolecules
Sen Lin, Shiyong Sun, Ke Wang, Kexuan Shen, Biaobiao Ma, Yuquan Ren, Xiaoyu Fan
The bioinspired design and construction of enzyme@capsule microreactors with specific cell-like functionality has generated tremendous interest in recent years. Inspired by their fascinating complexity, scientists have endeavored to understand the essential aspects of a natural cell and create biomimicking microreactors so as to immobilize enzymes within the hierarchical structure of a microcapsule. In this study, simultaneous encapsulation of alcohol dehydrogenase (ADH) was achieved during the preparation of microcapsules by the Pickering emulsion method using amphiphilic modified TiO₂ nanoparticles (NPs) as building blocks for assembling the photocatalytic microcapsule membrane...
February 24, 2018: Nanomaterials
Gregory A Grant
The equilibrium of the reaction catalyzed by D-3-Phosphoglycerate Dehydrogenase (PGDH), the first enzyme in the l-serine biosynthetic pathway, is far in the direction away from serine synthesis. As such, the enzyme is usually assayed in this direction. In order to easily assay it in the direction of l-serine synthesis, it can be coupled to the next enzyme in the pathway, phosphoserine aminotransferase (PSAT), with the activity monitored by the conversion of NAD+ to NADH by PGDH. However, when PGDH from several different species were coupled to PSAT, it was found that one of them, ecPGDH, conserves coenzyme in the production of l-serine by utilizing an intrinsic cycle of NAD+/NADH interconversion coupled with the conversion of -ketoglutarate (KG) to -hydroxyglutarate (HG)...
March 1, 2018: Biochemistry
Shabir Ahmad Bhat, Iram Khan Iqbal, Ashwani Kumar
NADH/NAD+ levels are an indicator of the bacterial metabolic state. NAD(H) levels are maintained through coordination of pathways involved in NAD(H) synthesis and its catabolic utilization. Conventional methods of estimating NADH/NAD+ require cell disruption and suffer from low specificity and sensitivity and are inadequate in providing spatiotemporal resolution. Recently, genetically encoded biosensors of the NADH/NAD+ ratio have been developed. One of these sensors, Peredox-mCherry, was adapted for the measurement of cellular levels of NADH/NAD+ in the slow-growing Mycobacterium tuberculosis (Mtb) and the fast-growing Mycobacterium smegmatis...
2018: Methods in Molecular Biology
Juan Camilo Molano-Arevalo, Walter Gonzalez, Kevin Jeanne Dit Fouque, Jaroslava Miksovska, Philippe Maitre, Francisco Fernandez-Lima
Nicotinamide adenine dinucleotide (NAD) is found in all living cells where the oxidized (NAD+ ) and reduced (NADH) forms play important roles in many enzymatic reactions. However, little is known about NAD+ and NADH conformational changes and kinetics as a function of the cell environment. In the present work, an analytical workflow is utilized to study NAD+ and NADH dynamics as a function of the organic content in solution using fluorescence lifetime spectroscopy and in the gas-phase using trapped ion mobility spectrometry coupled to mass spectrometry (TIMS-MS) and infrared multiple photon dissociation (IRMPD) spectroscopy...
February 23, 2018: Physical Chemistry Chemical Physics: PCCP
Shanshan Zhang, Shuang Liu, Nan Wu, Youhua Yuan, Wenhong Zhang, Ying Zhang
As dormant phenotypic variants of bacteria, persisters account for many chronic infections affecting human health. Despite numerous studies, the role of small non-coding RNA (sRNA) in bacterial persistence has not been reported. To investigate the role of Hfq-interacting sRNA in persistence, we constructed the deletion mutants of 20 Hfq-interacting sRNAs (RyhB, GcvB, MgrR, RybB, MicF, SgrS, RprA, DicF, SsrS, FnrS, GadY, DsrA, OmrB, ArcZ, RyeB, RydC, OmrA, MicA, MicC, and ChiX) to assess their persistence capacity in uropathogenic Escherichia coli strain UTI89 and identified a new sRNA RyhB being involved in persister formation...
2018: Frontiers in Microbiology
Ana Carolina B Sant'Anna-Silva, Gilson C Santos, Samir P Costa Campos, André Marco Oliveira Gomes, Juan Alberto Pérez-Valencia, Franklin David Rumjanek
Tumor cells are subjected to a broad range of selective pressures. As a result of the imposed stress, subpopulations of surviving cells exhibit individual biochemical phenotypes that reflect metabolic reprograming. The present work aimed at investigating metabolic parameters of cells displaying increasing degrees of metastatic potential. The metabolites present in cell extracts fraction of tongue fibroblasts and of cell lines derived from human tongue squamous cell carcinoma lineages displaying increasing metastatic potential (SCC9 ZsG, LN1 and LN2) were analyzed by1 H NMR (nuclear magnetic resonance) spectroscopy...
2018: Frontiers in Oncology
Yabing Liu, Lejia Hu, Tengfei Ma, Jun Yang, Jianping Ding
Human NAD-dependent isocitrate dehydrogenase (NAD-IDH) catalyzes the oxidative decarboxylation of isocitrate in the citric acid cycle. In the α 2 βγ heterotetramer of NAD-IDH, the γ subunit plays the regulatory role and the β subunit the structural role. Previous biochemical data have shown that mammalian NAD-IDHs can be inhibited by NADH; however, the molecular mechanism is unclear. In this work, we show that the αβ, αγ and α 2 βγ enzymes of human NAD-IDH can be inhibited by NADH, and further determine the crystal structure of the αγ heterodimer bound with an Mg 2+ and an NADH at the active site and an NADH at the allosteric site, which resembles that of the inactive α Mg γ heterodimer...
February 16, 2018: Scientific Reports
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