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Pentose Phosphate Pathway

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https://www.readbyqxmd.com/read/28221022/quantitative-13c-traces-of-glucose-fate-in-hepatitis-b-virus-infected-hepatocytes
#1
Qianfen Wan, Yulan Wang, Huiru Tang
Quantitative characterization of 13C-labeled metabolites is an important part of the stable isotope tracing method widely used in metabolic flux analysis. Due to long relaxation time and low sensitivity of 13C nuclei, direct measurement of 13C labeled metabolites using one dimensional 13C NMR often fails to meet the demand of metabolomics studies especially with large number of samples and metabolites having low abundance. Although HSQC-based 2D NMR methods have improved sensitivity with inversion detection, they are time-consuming thus unsuitable for high-throughput absolute quantification of 13C-labeled metabolites...
February 21, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28212815/systematic-testing-of-enzyme-perturbation-sensitivities-via-graded-dcas9-modulation-in-saccharomyces-cerevisiae
#2
Matthew Deaner, Hal S Alper
Dissecting genotype-phenotype relationships in a high-throughput and scalable manner is still an unresolved problem facing metabolic engineers. While the RNA-guided nuclease Cas9 has been repurposed as a programmable transcription regulator, its application has typically been limited to binary on/off regulation and thus misses informative and potentially optimal intermediate levels of gene expression. In this work, we establish a rapid method for fine-tuned, graded expression of pathway enzymes via dCas9 regulation by varying sgRNA target location as the dominant parameter...
February 14, 2017: Metabolic Engineering
https://www.readbyqxmd.com/read/28212376/the-legionella-pneumophila-genome-evolved-to-accommodate-multiple-regulatory-mechanisms-controlled-by-the-csra-system
#3
Tobias Sahr, Christophe Rusniok, Francis Impens, Giulia Oliva, Odile Sismeiro, Jean-Yves Coppée, Carmen Buchrieser
The carbon storage regulator protein CsrA regulates cellular processes post-transcriptionally by binding to target-RNAs altering translation efficiency and/or their stability. Here we identified and analyzed the direct targets of CsrA in the human pathogen Legionella pneumophila. Genome wide transcriptome, proteome and RNA-Co-immunoprecipitaion followed by deep sequencing of a wild type and a csrA mutant strain identified 479 RNAs with potential CsrA interaction sites located in the untranslated and/or coding regions of mRNAs or of known non-coding sRNAs...
February 17, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28212285/transcriptomic-analysis-reveals-selective-metabolic-adaptation-of-streptococcus-suis-to-porcine-blood-and-cerebrospinal-fluid
#4
Anna Koczula, Michael Jarek, Christian Visscher, Peter Valentin-Weigand, Ralph Goethe, Jörg Willenborg
Streptococcus suis is a zoonotic pathogen that can cause severe pathologies such as septicemia and meningitis in its natural porcine host as well as in humans. Establishment of disease requires not only virulence of the infecting strain but also an appropriate metabolic activity of the pathogen in its host environment. However, it is yet largely unknown how the streptococcal metabolism adapts to the different host niches encountered during infection. Our previous isotopologue profiling studies on S. suis grown in porcine blood and cerebrospinal fluid (CSF) revealed conserved activities of central carbon metabolism in both body fluids...
February 15, 2017: Pathogens
https://www.readbyqxmd.com/read/28209896/hawkmoths-use-nectar-sugar-to-reduce-oxidative-damage-from-flight
#5
E Levin, G Lopez-Martinez, B Fane, G Davidowitz
Nectar-feeding animals have among the highest recorded metabolic rates. High aerobic performance is linked to oxidative damage in muscles. Antioxidants in nectar are scarce to nonexistent. We propose that nectarivores use nectar sugar to mitigate the oxidative damage caused by the muscular demands of flight. We found that sugar-fed moths had lower oxidative damage to their flight muscle membranes than unfed moths. Using respirometry coupled with δ(13)C analyses, we showed that moths generate antioxidant potential by shunting nectar glucose to the pentose phosphate pathway (PPP), resulting in a reduction in oxidative damage to the flight muscles...
February 17, 2017: Science
https://www.readbyqxmd.com/read/28209202/erratum-to-inflammation-glucose-and-vascular-cell-damage-the-role-of-the-pentose-phosphate-pathway
#6
Concepción Peiró, Tania Romacho, Verónica Azcutia, Laura Villalobos, Emilio Fernández, Juan P Bolaños, Salvador Moncada, Carlos F Sánchez-Ferrer
No abstract text is available yet for this article.
February 16, 2017: Cardiovascular Diabetology
https://www.readbyqxmd.com/read/28209124/rna-seq-and-metabolomic-analyses-of-akt1-mediated-muscle-growth-reveals-regulation-of-regenerative-pathways-and-changes-in-the-muscle-secretome
#7
Chia-Ling Wu, Yoshinori Satomi, Kenneth Walsh
BACKGROUND: Skeletal muscle is a major regulator of systemic metabolism as it serves as the major site for glucose disposal and the main reservoir for amino acids. With aging, cachexia, starvation, and myositis, there is a preferential loss of fast glycolytic muscle fibers. We previously reported a mouse model in which a constitutively-active Akt transgene is induced to express in a subset of muscle groups leading to the hypertrophy of type IIb myofibers with an accompanying increase in strength...
February 16, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28207833/structure-kinetic-characterization-and-subcellular-localization-of-the-two-ribulose-5-phosphate-epimerase-isoenzymes-from-trypanosoma-cruzi
#8
Soledad Natalia Gonzalez, Wanda Mariela Valsecchi, Dante Maugeri, José María Delfino, Juan José Cazzulo
The enzyme of the pentose phosphate pathway (PPP) ribulose-5-phosphate-epimerase (RPE) is encoded by two genes present in the genome of Trypanosoma cruzi CL Brener clone: TcRPE1 and TcRPE2. Despite high sequence similarity at the amino acid residue level, the recombinant isoenzymes show a strikingly different kinetics. Whereas TcRPE2 follows a typical michaelian behavior, TcRPE1 shows a complex kinetic pattern, displaying a biphasic curve, suggesting the coexistence of -at least- two kinetically different molecular forms...
2017: PloS One
https://www.readbyqxmd.com/read/28202838/role-of-ad4-binding-protein-steroidogenic-factor-1-in-regulating-nadph-production-in-adrenocortical-y-1-cells
#9
Bing Li, Takashi Baba, Kanako Miyabayashi, Tetsuya Sato, Yuichi Shima, Tomomi Ichinose, Daisuke Miura, Yasuyuki Ohkawa, Mikita Suyama, Ken-Ichirou Morohashi
Ad4-binding protein/steroidogenic factor 1 (Ad4BP/SF-1), a member of the nuclear receptor superfamily, is expressed in steroidogenic cells and regulates all steroidogenic gene expression. We recently employed mRNA and chromatin immunoprecipitation sequence (ChIP-seq) to demonstrate that Ad4BP/SF-1 directly regulates the expression of nearly all glycolytic genes. The pentose phosphate pathway (PPP) contributes to the production of nicotinamide adenine dinucleotide phosphate (NADPH). Although the expression of PPP genes and intracellular NADPH were decreased by Ad4BP/SF-1 knockdown, these genes were not the direct targets of Ad4BP/SF-1...
February 14, 2017: Endocrine Journal
https://www.readbyqxmd.com/read/28192232/real-time-quantification-of-subcellular-h2o2-and-glutathione-redox-potential-in-living-cardiovascular-tissues
#10
Emiliano Panieri, Carlo Millia, Massimo M Santoro
Detecting and measuring the dynamic redox events that occur in vivo is a prerequisite for understanding the impact of oxidants and redox events in normal and pathological conditions. These aspects are particularly relevant in cardiovascular tissues wherein alterations of the redox balance are associated with stroke, aging, and pharmacological intervention. An ambiguous aspect of redox biology is how redox events occur in subcellular organelles including mitochondria, and nuclei. Genetically-encoded Rogfp2 fluorescent probes have become powerful tools for real-time detection of redox events...
February 10, 2017: Free Radical Biology & Medicine
https://www.readbyqxmd.com/read/28181081/genetic-improvement-of-xylose-metabolism-by-enhancing-the-expression-of-pentose-phosphate-pathway-genes-in-saccharomyces-cerevisiae-ir-2-for-high-temperature-ethanol-production
#11
Yosuke Kobayashi, Takehiko Sahara, Toshihiro Suzuki, Saori Kamachi, Akinori Matsushika, Tamotsu Hoshino, Satoru Ohgiya, Yoichi Kamagata, Kazuhiro E Fujimori
The pentose phosphate pathway (PPP) plays an important role in the efficiency of xylose fermentation during cellulosic ethanol production. In simultaneous saccharification and co-fermentation (SSCF), the optimal temperature for cellulase hydrolysis of lignocellulose is much higher than that of fermentation. Successful use of SSCF requires optimization of the expression of PPP genes at elevated temperatures. This study examined the combinatorial expression of PPP genes at high temperature. The results revealed that over-expression of TAL1 and TKL1 in Saccharomyces cerevisiae (S...
February 8, 2017: Journal of Industrial Microbiology & Biotechnology
https://www.readbyqxmd.com/read/28177519/methionine-35-sulfoxide-reduces-toxicity-of-a%C3%AE-in-red-blood-cell
#12
Cristiana Carelli-Alinovi, Francesco Misiti
The oxidation of Methionine residue in position 35 of Aβ to sulfoxide (Aβ-sulfoxide) has the ability to deeply modify wild type Aβ 1-42 (Aβ) neurotoxic action. Our previous studies suggest that in nucleated cells lower toxicity of Aβ-sulfoxide might result not from structural alteration, but from elevation of Methionine sulfoxide reductase A (MsrA) activity and mRNA levels. On these basis, we hypothesised that red blood cell (RBC), a cell devoid almost completely of MsrA activity, share with nucleated cells an antioxidant system induced by methionine 35 sulfoxide, responsible for the lower toxicity of Aβ-sulfoxide in RBC...
February 8, 2017: European Journal of Clinical Investigation
https://www.readbyqxmd.com/read/28176759/snail-reprograms-glucose-metabolism-by-repressing-phosphofructokinase-pfkp-allowing-cancer-cell-survival-under-metabolic-stress
#13
Nam Hee Kim, Yong Hoon Cha, Jueun Lee, Seon-Hyeong Lee, Ji Hye Yang, Jun Seop Yun, Eunae Sandra Cho, Xianglan Zhang, Miso Nam, Nami Kim, Young-Su Yuk, So Young Cha, Yoonmi Lee, Joo Kyung Ryu, Sunghyouk Park, Jae-Ho Cheong, Sang Won Kang, Soo-Youl Kim, Geum-Sook Hwang, Jong In Yook, Hyun Sil Kim
Dynamic regulation of glucose flux between aerobic glycolysis and the pentose phosphate pathway (PPP) during epithelial-mesenchymal transition (EMT) is not well-understood. Here we show that Snail (SNAI1), a key transcriptional repressor of EMT, regulates glucose flux toward PPP, allowing cancer cell survival under metabolic stress. Mechanistically, Snail regulates glycolytic activity via repression of phosphofructokinase, platelet (PFKP), a major isoform of cancer-specific phosphofructokinase-1 (PFK-1), an enzyme involving the first rate-limiting step of glycolysis...
February 8, 2017: Nature Communications
https://www.readbyqxmd.com/read/28166632/metabolomics-based-elucidation-of-active-metabolic-pathways-in-erythrocytes-and-hsc-derived-reticulocytes
#14
Anubhav Srivastava, Krystal J Evans, Anna Elizabeth Sexton, Louis Schofield, Darren John Creek
A detailed analysis of the metabolic state of human stem cell derived erythrocytes allowed us to characterize the existence of active metabolic pathways in younger reticulocytes and compare them to mature erythrocytes. Using high resolution LC-MS based, untargeted metabolomics, we found that reticulocytes had a comparatively much richer repertoire of metabolites, which spanned a range of metabolite classes. An untargeted metabolomics analysis using stable isotope-labelled glucose showed that only glycolysis and the pentose phosphate pathway actively contributed to the biosynthesis of metabolites in erythrocytes, and these pathways were upregulated in reticulocytes...
February 7, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28165029/quantitative-global-proteome-and-lysine-succinylome-analyses-provide-insights-into-metabolic-regulation-and-lymph-node-metastasis-in-gastric-cancer
#15
Yongxi Song, Jun Wang, Zhongyi Cheng, Peng Gao, Jingxu Sun, Xiaowan Chen, Chen Chen, Yunlong Wang, Zhenning Wang
With the rapid development of high-throughput quantitative proteomic and transcriptomic approaches, the molecular mechanisms of cancers have been comprehensively explored. However, cancer is a multi-dimensional disease with sophisticated regulations, and few studies focus on the crosstalk among multiomics. In order to explore the molecular mechanisms of gastric cancer (GC), particularly in the process of lymph node metastasis (LNM), we investigated dynamic profiling changes as well as crosstalk between long non-coding RNAs (lncRNAs), the proteome, and the lysine succinylome...
February 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28163219/probing-the-metabolic-phenotype-of-breast-cancer-cells-by-multiple-tracer-stable-isotope-resolved-metabolomics
#16
Andrew N Lane, Julie Tan, Yali Wang, Jun Yan, Richard M Higashi, Teresa W-M Fan
Breast cancers vary by their origin and specific set of genetic lesions, which gives rise to distinct phenotypes and differential response to targeted and untargeted chemotherapies. To explore the functional differences of different breast cell types, we performed Stable Isotope Resolved Metabolomics (SIRM) studies of one primary breast (HMEC) and three breast cancer cells (MCF-7, MDAMB-231, and ZR75-1) having distinct genotypes and growth characteristics, using (13)C6-glucose, (13)C-1+2-glucose, (13)C5,(15)N2-Gln, (13)C3-glycerol, and (13)C8-octanoate as tracers...
February 2, 2017: Metabolic Engineering
https://www.readbyqxmd.com/read/28157187/soil-microorganisms-can-overcome-respiration-inhibition-by-coupling-intra-and-extracellular-metabolism-13-c-metabolic-tracing-reveals-the-mechanisms
#17
Ezekiel K Bore, Carolin Apostel, Sara Halicki, Yakov Kuzyakov, Michaela A Dippold
CO2 release from soil is commonly used to estimate toxicity of various substances on microorganisms. However, the mechanisms underlying persistent CO2 release from soil exposed to toxicants inhibiting microbial respiration, for example, sodium azide (NaN3) or heavy metals (Cd, Hg, Cu), remain unclear. To unravel these mechanisms, NaN3-amended soil was incubated with position-specifically (13)C-labeled glucose and (13)C was quantified in CO2, bulk soil, microbial biomass and phospholipid fatty acids (PLFAs)...
February 3, 2017: ISME Journal
https://www.readbyqxmd.com/read/28154945/metabolomics-analysis-of-the-effect-of-dissolved-oxygen-on-spinosad-production-by-saccharopolyspora-spinosa
#18
Chunzhe Lu, Jing Yin, Fanglong Zhao, Feng Li, Wenyu Lu
Spinosad, a universal bio-pesticide, is obtained from the soil actinomycete Saccharopolyspora spinosa. Dissolved oxygen, an important contributing factor in aerobic microbial fermentation, however, is not always available in sufficient amounts. To alleviate oxygen limitation in spinosad production, three different oxygen vectors, namely oleic acid, toluene, and n-dodecane, were added into early fermentation. Results indicated that n-dodecane was the optimal oxygen vector. Spinosad yield was increased by 44...
February 2, 2017: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/28153765/modular-pathway-engineering-of-corynebacterium-glutamicum-to-improve-xylose-utilization-and-succinate-production
#19
Suah Jo, Jinkyung Yoon, Sun-Mi Lee, Youngsoon Um, Sung Ok Han, Han Min Woo
Xylose-negative Corynebacterium glutamicum has been engineered to utilize xylose as the sole carbon source via either the xylose isomerase (XI) pathway or the Weimberg pathway. Heterologous expression of xylose isomerase and overexpression of a gene encoding for xylulose kinase enabled efficient xylose utilization. In this study, we show that two functionally-redundant transcriptional regulators (GntR1 and GntR2) present on xylose repress the pentose phosphate pathway genes. For efficient xylose utilization, pentose phosphate pathway genes and a phosphoketolase gene were overexpressed through - with the XI pathway in C...
January 30, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28153010/targeting-muc1-c-inhibits-the-akt-s6k1-elf4a-pathway-regulating-tigar-translation-in-colorectal-cancer
#20
Rehan Ahmad, Maroof Alam, Masanori Hasegawa, Yasumitsu Uchida, Omar Al-Obaid, Surender Kharbanda, Donald Kufe
BACKGROUND: Colorectal cancer is third most common malignancy and is the second most common cause of cancer-related death. The MUC1 heterodimeric protein is aberrantly overexpressed in colorectal cancer and has been linked to poor outcomes in this disease. Here, we investigate the effects of the MUC1-C subunit inhibitor (GO-203), which disrupts MUC1-C homo-oligomerization, on human colorectal cancer cells. METHODS: TIGAR mRNA level was determined using qRT-PCR. Western blotting was used to measure TIGAR protein level and AKT-mTOR-S6K1 pathways...
February 2, 2017: Molecular Cancer
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