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RNA metabolism

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https://www.readbyqxmd.com/read/28230109/pentose-sugars-inhibit-metabolism-and-increase-expression-of-an-agrd-type-cyclic-pentapeptide-in-clostridium-thermocellum
#1
Tobin J Verbeke, Richard J Giannone, Dawn M Klingeman, Nancy L Engle, Thomas Rydzak, Adam M Guss, Timothy J Tschaplinski, Steven D Brown, Robert L Hettich, James G Elkins
Clostridium thermocellum could potentially be used as a microbial biocatalyst to produce renewable fuels directly from lignocellulosic biomass due to its ability to rapidly solubilize plant cell walls. While the organism readily ferments sugars derived from cellulose, pentose sugars from xylan are not metabolized. Here, we show that non-fermentable pentoses inhibit growth and end-product formation during fermentation of cellulose-derived sugars. Metabolomic experiments confirmed that xylose is transported intracellularly and reduced to the dead-end metabolite xylitol...
February 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28228764/de-novo-transcriptome-assembly-of-chinese-kale-and-global-expression-analysis-of-genes-involved-in-glucosinolate-metabolism-in-multiple-tissues
#2
Shuanghua Wu, Jianjun Lei, Guoju Chen, Hancai Chen, Bihao Cao, Changming Chen
Chinese kale, a vegetable of the cruciferous family, is a popular crop in southern China and Southeast Asia due to its high glucosinolate content and nutritional qualities. However, there is little research on the molecular genetics and genes involved in glucosinolate metabolism and its regulation in Chinese kale. In this study, we sequenced and characterized the transcriptomes and expression profiles of genes expressed in 11 tissues of Chinese kale. A total of 216 million 150-bp clean reads were generated using RNA-sequencing technology...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28228595/hepatitis-c-virus-specific-t-cell-receptor-mrna-engineered-human-t-cells-impact-of-antigen-specificity-on-functional-properties
#3
Anangi Balasiddaiah, Haleh Davanian, Soo Aleman, Anna Pasetto, Lars Frelin, Matti Sällberg, Volker Lohmann, Sarene Koh, Antonio Bertoletti, Margaret Chen
Therapy with genetically modified autologous T cells has shown great promise in cancer therapy. For an efficient control of hepatitis C virus (HCV) infection, cytotoxic T cells (CTL) are pivotal but persistence of activated T cells may lead to liver toxicity. Here, anti-HCV T cell receptors (TCRs) recognising the HCV non-structural (NS) NS3 or NS5 viral peptide target were examined by mRNA transfection of human peripheral blood lymphocytes (PBL) derived from healthy donors as well as chronically infected HCV patients...
February 22, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28228125/rna-seq-of-life-stages-of-the-oomycete-phytophthora-infestans-reveals-dynamic-changes-in-metabolic-signal-transduction-and-pathogenesis-genes-and-a-major-role-for-calcium-signaling-in-development
#4
Audrey M V Ah-Fong, Kyoung Su Kim, Howard S Judelson
BACKGROUND: The oomycete Phytophthora infestans causes the devastating late blight diseases of potato and tomato. P. infestans uses spores for dissemination and infection, like many other filamentous eukaryotic plant pathogens. The expression of a subset of its genes during spore formation and germination were studied previously, but comprehensive genome-wide data have not been available. RESULTS: RNA-seq was used to profile hyphae, sporangia, sporangia undergoing zoosporogenesis, motile zoospores, and germinated cysts of P...
February 23, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28228093/comparative-profiling-of-hepatopancreas-transcriptomes-in-satiated-and-starving-pomacea-canaliculata
#5
Lei Yang, Tian-Yin Cheng, Fei-Yan Zhao
BACKGROUND: Although Pomacea canaliculata is native to South and Central America, it has become one of the most abundant invasive species worldwide and causes extensive damage to agriculture and horticulture. Conventional physical and chemical techniques have been used to eliminate P. canaliculata, but the effects are not ideal. Therefore, it is important to devise a new method based on a greater understanding of the biology of P. canaliculata. However, the molecular mechanisms underlying digestion and absorption in P...
February 22, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28225081/biomolecular-condensates-organizers-of-cellular-biochemistry
#6
REVIEW
Salman F Banani, Hyun O Lee, Anthony A Hyman, Michael K Rosen
Biomolecular condensates are micron-scale compartments in eukaryotic cells that lack surrounding membranes but function to concentrate proteins and nucleic acids. These condensates are involved in diverse processes, including RNA metabolism, ribosome biogenesis, the DNA damage response and signal transduction. Recent studies have shown that liquid-liquid phase separation driven by multivalent macromolecular interactions is an important organizing principle for biomolecular condensates. With this physical framework, it is now possible to explain how the assembly, composition, physical properties and biochemical and cellular functions of these important structures are regulated...
February 22, 2017: Nature Reviews. Molecular Cell Biology
https://www.readbyqxmd.com/read/28224978/methylated-antibody-affinity-purification-to-improve-proteomic-identification-of-plant-rna-polymerase-pol-v-complex-and-the-interacting-proteins
#7
Guochen Qin, Jun Ma, Xiaomei Chen, Zhaoqing Chu, Yi-Min She
Affinity purification followed by enzymatic digestion and mass spectrometry has been widely utilized for the sensitive detection of interacting proteins and protein complexes in various organisms. In plants, the method is technically challenging due to the low abundance proteins, non-specific binding and difficulties of eluting interacting proteins from antibody beads. In this report, we describe a strategy to modify antibodies by reductive methylation of lysines without affecting their binding properties, followed by on-bead digestion of bound proteins with endoproteinase Lys-C...
February 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28224655/rna-seq-analysis-of-transcriptional-change-in-the-freshwater-mussel-elliptio-complanata-after-environmentally-relevant-sodium-chloride-exposure
#8
Laura S Robertson, Heather S Galbraith, Deborah Iwanowicz, Carrie J Blakeslee, R Scott Cornman
To identify potential biomarkers of salt stress in a freshwater sentinel species, we examined transcriptional responses of the common mussel Elliptio complanata to controlled NaCl exposures. RNA-Seq of mantle tissue identified 481 transcripts differentially expressed in adult mussels exposed to 2 ppt NaCl (1.2 ppt chloride) for seven days, of which 290 had non-overlapping intervals. Differentially expressed gene categories included ion and transmembrane transport, oxidoreductase activity, maintenance of protein folding, and amino acid metabolism...
February 22, 2017: Environmental Toxicology and Chemistry
https://www.readbyqxmd.com/read/28224117/perc-manipulates-metabolism-and-surface-antigens-in-enteropathogenic-escherichia-coli
#9
Jay L Mellies, Amy Platenkamp, Jossef Osborn, Lily Ben-Avi
Enteropathogenic Escherichia coli is an important cause of profuse, watery diarrhea in infants living in developing regions of the world. Typical strains of EPEC (tEPEC) possess a virulence plasmid, while related clinical isolates that lack the pEAF plasmid are termed atypical EPEC (aEPEC). tEPEC and aEPEC tend to cause acute vs. more chronic type infections, respectively. The pEAF plasmid encodes an attachment factor as well as a regulatory operon, perABC. PerC, a poorly understood regulator, was previously shown to regulate expression of the type III secretion system through Ler...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28223972/changes-in-metabolically-active-bacterial-community-during-rumen-development-and-their-alteration-by-rhubarb-root-powder-revealed-by-16s-rrna-amplicon-sequencing
#10
Zuo Wang, Chijioke Elekwachi, Jinzhen Jiao, Min Wang, Shaoxun Tang, Chuanshe Zhou, Zhiliang Tan, Robert J Forster
The objective of this present study was to explore the initial establishment of metabolically active bacteria and subsequent evolution in four fractions: rumen solid-phase (RS), liquid-phase (RL), protozoa-associated (RP), and epithelium-associated (RE) through early weaning and supplementing rhubarb root powder in 7 different age groups (1, 10, 20, 38, 41, 50, and 60 d) during rumen development. Results of the 16S rRNA sequencing based on RNA isolated from the four fractions revealed that the potentially active bacterial microbiota in four fractions were dominated by the phyla Proteobacteria, Firmicutes, and Bacteroidetes regardless of different ages...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28223504/transcriptome-wide-microrna-and-target-dynamics-in-the-fat-body-during-the-gonadotrophic-cycle-of-aedes-aegypti
#11
Xiufeng Zhang, Emre Aksoy, Thomas Girke, Alexander S Raikhel, Fedor V Karginov
The mosquito Aedes aegypti is a major vector of numerous viral diseases, because it requires a blood meal to facilitate egg development. The fat body, a counterpart of mammalian liver and adipose tissues, is the metabolic center, playing a key role in reproduction. Therefore, understanding of regulatory networks controlling its functions is critical, and the role of microRNAs (miRNAs) in the process is largely unknown. We aimed to explore miRNA expression and potential targets in the female fat body of Ae. aegypti, as well as their changes postblood meal (PBM)...
February 21, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28223460/mechanism-of-h2s-oxidation-by-the-dissimilatory-perchlorate-reducing-microorganism-azospira-suillum-ps
#12
Misha G Mehta-Kolte, Dana Loutey, Ouwei Wang, Matthew D Youngblut, Christopher G Hubbard, Kelly M Wetmore, Mark E Conrad, John D Coates
The genetic and biochemical basis of perchlorate-dependent H2S oxidation (PSOX) was investigated in the dissimilatory perchlorate-reducing microorganism (DPRM) Azospira suillum PS (PS). Previously, it was shown that all known DPRMs innately oxidize H2S, producing elemental sulfur (S(o)). Although the process involving PSOX is thermodynamically favorable (ΔG°' = -206 kJ ⋅ mol(-1) H2S), the underlying biochemical and genetic mechanisms are currently unknown. Interestingly, H2S is preferentially utilized over physiological electron donors such as lactate or acetate although no growth benefit is obtained from the metabolism...
February 21, 2017: MBio
https://www.readbyqxmd.com/read/28223366/la-deletion-from-mouse-brain-alters-pre-trna-metabolism-and-accumulation-of-pre-5-8s-rrna-with-neuron-death-and-reactive-astrocytosis
#13
Nathan H Blewett, James R Iben, Sergei Gaidamakov, Richard J Maraia
Human La antigen (Sjögren's syndrome antigen B, SSB) is an abundant multifunctional RNA-binding protein. In the nucleoplasm, La binds to and protects from 3' exonucleases, the ends of precursor-tRNAs and other transcripts synthesized by RNA polymerase III, and facilitates their maturation, while a nucleolar isoform has been implicated in rRNA biogenesis by multiple independent lines of evidence. We showed earlier that conditional La knockout (La cKO) from mouse cortex neurons results in defective tRNA processing although pathway(s) involved in neuronal loss thereafter was unknown...
February 21, 2017: Molecular and Cellular Biology
https://www.readbyqxmd.com/read/28222744/herpes-simplex-virus-1-infection-dampens-the-immediate-early-antiviral-innate-immunity-signaling-from-peroxisomes-by-tegument-protein-vp16
#14
Chunfu Zheng, Chenhe Su
BACKGROUND: Herpes simplex virus 1 (HSV-1) is an archetypal member of the alphaherpesvirus subfamily with a large genome encoding over 80 proteins, many of which play a critical role in virus-host interactions and immune modulation. Upon viral infections, the host cells activate innate immune responses to restrict their replications. Peroxisomes, which have long been defined to regulate metabolic activities, are reported to be important signaling platforms for antiviral innate immunity...
February 21, 2017: Virology Journal
https://www.readbyqxmd.com/read/28221941/the-hap-complex-governs-fumonisin-biosynthesis-and-maize-kernel-pathogenesis-in-fusarium-verticillioides
#15
John B Ridenour, Jonathon E Smith, Burton H Bluhm
Contamination of maize ( Zea mays ) with fumonisins produced by the fungus Fusarium verticillioides is a global concern for food safety. Fumonisins are a group of polyketide-derived secondary metabolites linked to esophageal cancer and neural tube birth defects in humans and numerous toxicoses in livestock. Despite the importance of fumonisins in global maize production, the regulation of fumonisin biosynthesis during kernel pathogenesis is poorly understood. The HAP complex is a conserved, heterotrimeric transcriptional regulator that binds the consensus sequence CCAAT to modulate gene expression...
September 2016: Journal of Food Protection
https://www.readbyqxmd.com/read/28221022/quantitative-13c-traces-of-glucose-fate-in-hepatitis-b-virus-infected-hepatocytes
#16
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/28220845/heterogeneous-nuclear-ribonucleoprotein-a1-regulates-rhythmic-synthesis-of-mouse-nfil3-protein-via-ires-mediated-translation
#17
Hyo-Jin Kim, Hwa-Rim Lee, Ji-Young Seo, Hye Guk Ryu, Kyung-Ha Lee, Do-Yeon Kim, Kyong-Tai Kim
Nuclear factor, interleukin 3, regulated (Nfil3, also known as E4 Promoter-Binding Protein 4 (E4BP4)) protein is a transcription factor that binds to DNA and generally represses target gene expression. In the circadian clock system, Nfil3 binds to a D-box element residing in the promoter of clock genes and contributes to their robust oscillation. Here, we show that the 5'-untranslated region (5'-UTR) of Nfil3 mRNA contains an internal ribosome entry site (IRES) and that IRES-mediated translation occurs in a phase-dependent manner...
February 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28220138/de-novo-transcriptome-assembly-of-phomopsis-liquidambari-provides-insights-into-genes-associated-with-different-lifestyles-in-rice-oryza-sativa-l
#18
Jun Zhou, Xin Li, Yan Chen, Chuan-Chao Dai
The mechanisms that trigger the switch from endophytic fungi to saprophytic fungi are largely unexplored. Broad host range Phomopsis liquidambari is established in endophytic and saprophytic systems with rice (Oryza sativa L.). Endophytic P. liquidambari promotes rice growth, increasing rice yield and improving the efficiency of nitrogen fertilizer. This species's saprophytic counterpart can decompose rice litterfall, promoting litter organic matter cycling and the release of nutrients and improving the soil microbial environment...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28220135/differential-gene-expression-analysis-in-polygonum-minus-leaf-upon-24-h-of-methyl-jasmonate-elicitation
#19
Reyhaneh Rahnamaie-Tajadod, Kok-Keong Loke, Hoe-Han Goh, Normah M Noor
Polygonum minus is an herbal plant that grows in Southeast Asian countries and traditionally used as medicine. This plant produces diverse secondary metabolites such as phenolic compounds and their derivatives, which are known to have roles in plant abiotic and biotic stress responses. Methyl jasmonate (MeJA) is a plant signaling molecule that triggers transcriptional reprogramming in secondary metabolism and activation of defense responses against many biotic and abiotic stresses. However, the effect of MeJA elicitation on the genome-wide expression profile in the leaf tissue of P...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28219744/metabolic-labeling-and-recovery-of-nascent-rna-to-accurately-quantify-mrna-stability
#20
Joseph Russo, Adam M Heck, Jeffrey Wilusz, Carol J Wilusz
Changes in the rate of mRNA decay are closely coordinated with transcriptional changes and together these events have profound effects on gene expression during development and disease. Traditional approaches to assess mRNA decay have relied on inhibition of transcription, which can alter mRNA decay rates and confound interpretation. More recently, metabolic labeling combined with chemical modification and fractionation of labeled RNAs has allowed the isolation of nascent transcripts and the subsequent calculation of mRNA decay rates...
February 17, 2017: Methods: a Companion to Methods in Enzymology
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