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Polymerase substrate specificity

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https://www.readbyqxmd.com/read/28528003/acinetobacter-baumannii-k11-and-k83-capsular-polysaccharides-have-the-same-6-deoxy-l-talose-containing-pentasaccharide-k-units-but-different-linkages-between-the-k-units
#1
Johanna J Kenyon, Alexander S Shashkov, Sof'ya N Senchenkova, Mikhail M Shneider, Bin Liu, Anastasiya V Popova, Nikolay P Arbatsky, Konstantin A Miroshnikov, Lei Wang, Yuriy A Knirel, Ruth M Hall
Acinetobacter baumannii produces a variety of capsular polysaccharides (CPS) via genes located at the chromosomal K locus and some KL gene clusters include genes for the synthesis of specific sugars. The structures of K11 and K83 CPS produced by isolates LUH5545 and LUH5538, which carry related KL11a and KL83 gene clusters, respectively, were established by sugar analysis and one- and two-dimensional (1)H and (13)C NMR spectroscopy. Both CPS contain L-rhamnose (L-Rha) and 6-deoxy-L-talose (L-6dTal), and both KL gene clusters include genes for dTDP-L-Rhap synthesis and a tle (talose epimerase) gene encoding an epimerase that converts dTDP-L-Rhap to dTDP-L-6dTalp...
May 17, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/28524231/comparison-of-pre-ribosomal-rna-processing-pathways-in-yeast-plant-and-human-cells-focus-on-coordinated-action-of-endo-and-exoribonucleases
#2
REVIEW
Rafal Tomecki, Pawel J Sikorski, Monika Zakrzewska-Placzek
Proper regulation of ribosome biosynthesis is mandatory for cellular adaptation, growth and proliferation. Ribosome biogenesis is the most energetically demanding cellular process, which requires tight control. Abnormalities in ribosome production have severe consequences, including developmental defects in plants and genetic diseases (ribosomopathies) in humans. One of the processes occurring during eukaryotic ribosome biogenesis is processing of the ribosomal RNA precursor molecule (pre-rRNA), synthesized by RNA polymerase I, into mature rRNAs...
May 19, 2017: FEBS Letters
https://www.readbyqxmd.com/read/28514164/the-non-bulky-dna-lesions-spiroiminodihydantoin-and-5-guanidinohydantoin-significantly-block-human-rna-polymerase-ii-elongation-in-vitro
#3
Marina Kolbanovskiy, Moinuddin A Chowdhury, Aditi Nadkarni, Suse Broyde, Nicholas E Geacintov, David A Scicchitano, Vladimir Shafirovich
The most common, oxidatively generated lesion in cellular DNA is 8-oxo-7,8-dihydroguanine, which can be oxidized further to yield highly mutagenic spiroiminodihydantoin (Sp) and 5-guanidinohydantoin (Gh) in DNA. In human cell-free extracts, both lesions can be excised by base excision repair and global genomic nucleotide excision repair. However, it is not known if these lesions can be removed by transcription-coupled DNA repair (TCR), a pathway that clears lesions from DNA that impede RNA synthesis. To determine if Sp or Gh impede transcription, which could make them viable substrates for TCR, either an Sp or a Gh lesion was positioned on the transcribed strand of DNA under the control of a promoter that supports transcription by human RNA polymerase II...
May 17, 2017: Biochemistry
https://www.readbyqxmd.com/read/28502712/ligation-mediated-pcr-with-a-back-to-back-adapter-reduces-amplification-bias-resulting-from-variations-in-gc-content
#4
Satoru Ishihara, Naoe Kotomura, Naoki Yamamoto, Hiroshi Ochiai
Ligation-mediated polymerase chain reaction (LM-PCR) is a common technique for amplification of a pool of DNA fragments. Here, a double-stranded oligonucleotide consisting of two primer sequences in back-to-back orientation was designed as an adapter for LM-PCR. When DNA fragments were ligated with this adapter, the fragments were sandwiched between two adapters in random orientations. In the ensuing PCR, ligation products linked at each end to an opposite side of the adapter, i.e. to a distinct primer sequence, were preferentially amplified compared with products linked at each end to an identical primer sequence...
May 11, 2017: Analytical Biochemistry
https://www.readbyqxmd.com/read/28474789/functional-characterization-and-tissue-expression-of-marmoset-cytochrome-p450-2e1
#5
Shotaro Uehara, Yasuhiro Uno, Etsuko Tomioka, Takashi Inoue, Erika Sasaki, Hiroshi Yamazaki
Common marmosets (Callithrix jacchus) have attracted increasing attention as a useful small non-human primate model in preclinical research. However, studies on marmoset cytochrome P450 (P450) 2E enzyme have scarcely been conducted. In this study, the full-length cDNA encoding P450 2E1 enzyme was isolated from marmoset livers by reverse transcription (RT)-polymerase chain reaction (PCR). Marmoset P450 2E1 amino acid sequences were highly identical (>88%) to those of cynomolgus monkey and human P450 2E1 enzymes...
May 5, 2017: Biopharmaceutics & Drug Disposition
https://www.readbyqxmd.com/read/28469419/an-insight-into-structure-function-and-expression-analysis-of-3-hydroxy-3-methylglutaryl-coa-reductase-of-cymbopogon-winterianus
#6
Kamalakshi Devi, Lochana Patar, Mahendra K Modi, Priyabrata Sen
Citronella (Cymbopogon winterianus) is one of the richest sources of high-value isoprenoid aromatic compounds used as flavour, fragrance, and therapeutic elements. These isoprenoid compounds are synthesized by 2 independent pathways: mevalonate pathway and 2-C-methyl-d-erythritol-4-phosphate pathway. Evidence suggests that 3-hydroxy-3-methylglutaryl-CoA reductase (HMGR) is a rate-controlling enzyme for the synthesis of variety of isoprenoids. This study reports the isolation, characterization, and tissue-specific expression analysis of HMGR from citronella...
2017: Bioinformatics and Biology Insights
https://www.readbyqxmd.com/read/28463692/synergy-of-substrate-conductivity-and-intermittent-electrical-stimulation-towards-osteogenic-differentiation-of-human-mesenchymal-stem-cells
#7
K Ravikumar, Sunil Kumar Boda, Bikramjit Basu
Human Mesenchymal Stem cells (hMSCs) have the unique potential to differentiate into multiple cell types. Depending on the cellular microenvironment (physical and biochemical cues), hMSCs can be directed to differentiate into osteogenic, chondrogenic, myogenic and adipogenic lineages. Among the strategies available to direct stem cell fate processes, electrical stimulation based approach has been extensively investigated in recent studies. In the present study, the conducting Hydroxyapatite-CaTiO3 (HA-CT) composites are used as electroconductive platforms to support the differentiation of hMSCs, in vitro...
March 30, 2017: Bioelectrochemistry
https://www.readbyqxmd.com/read/28450579/quantitative-polymerase-chain-reaction-analysis-of-the-mouse-cyp2c-subfamily-and-characterization-of-their-tissue-distribution
#8
Joan P Graves, Artiom Gruzdev, J Alyce Bradbury, Laura M DeGraff, Matthew L Edin, Darryl C Zeldin
The cytochrome P450 superfamily encompasses a diverse group of enzymes that catalyze the oxidation of various substrates. CYP2C proteins detoxify xenobiotics and metabolize endogenous lipids such as arachidonic acid to bioactive eicosanoids. We report new methods and results for the quantitative polymerase reaction (qPCR) analysis for the 15 members of the mouse Cyp2c subfamily (Cyp2c29, Cyp2c37, Cyp2c38, Cyp2c39, Cyp2c40, Cyp2c44, Cyp2c50, Cyp2c54, Cyp2c55, Cyp2c65, Cyp2c66, Cyp2c67, Cyp2c68, Cyp2c69 and Cyp2c70)...
April 27, 2017: Drug Metabolism and Disposition: the Biological Fate of Chemicals
https://www.readbyqxmd.com/read/28395772/an-electrochemical-aptasensor-for-multiplex-antibiotics-detection-using-y-shaped-dna-based-metal-ions-encoded-probes-with-nmof-substrate-and-csrp-target-triggered-amplification-strategy
#9
Meng Chen, Ning Gan, Tianhua Li, Ye Wang, Qing Xu, Yinji Chen
An effective electrochemical aptasensor has been developed for the detection of multiplex antibiotics using Y-shaped DNA probes. These probes-based metal ions encoded the nanoscale metal-organic frameworks (NMOF) as a substrate, and circular strand-replacement DNA polymerization (CSRP) target triggered the amplification strategy. The Y-DNA probes (Y-DNA) were assembled using an assisted DNA probe (assisted DNA labeled with magnetic gold nanoparticles) which can hybridize to the captured DNA probe (consisting of aptamer and primer recognition region), and signal tags (NMOF encapsulating signal DNAs and different metal ions such as Pb(2+) or Cd(2+))...
May 22, 2017: Analytica Chimica Acta
https://www.readbyqxmd.com/read/28377494/arabidopsis-fructokinase-like-protein-associations-are-regulated-by-atp
#10
John W Riggs, Judy Callis
The Arabidopsis thaliana fructokinase-like proteins FLN1 and FLN2 are required for the differentiation of plastids into photosynthetically competent chloroplasts. However, their specific roles are unknown. FLN1 and FLN2 localize in a multisubunit prokaryotic-type polymerase (plastid-encoded RNA polymerase) complex that transcribes genes encoding components of photosynthesis-related assemblies. Despite sequence identity with fructokinases, which are members of the pfkB (phosphofructokinase B) family of enzymes, kinase activity of FLN1 and FLN2 has not been demonstrated...
May 10, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28349355/polymerase-spiral-reaction-psr-a-novel-visual-isothermal-amplification-method-for-detection-of-canine-parvovirus-2-genomic-dna
#11
Vikas Gupta, Soumendu Chakravarti, Vishal Chander, Saurabh Majumder, Shabir Ahmad Bhat, Vivek Kumar Gupta, Sukdeb Nandi
Canine parvovirus-2 (CPV-2), which is ubiquitously distributed worldwide, causes severe and often fatal gastroenteritis in dogs. Accurate, differential and rapid diagnosis of canine parvoviral enteritis remains a challenge for clinicians. A recently developed isothermal amplification technique, polymerase spiral reaction (PSR), was optimized for the first time for a viral pathogen with reference recombinant plasmid standards from different CPV-2 antigenic variants (CPV-2, CPV-2a, CPV-2b and CPV-2c) and subsequently validated using clinical samples...
March 27, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28347953/maximum-specific-growth-rate-of-anammox-bacteria-revisited
#12
Lei Zhang, Yuko Narita, Lin Gao, Muhammad Ali, Mamoru Oshiki, Satoshi Okabe
Anammox bacteria have long been considered to be slow-growing bacteria. However, it has recently been reported that they could grow much faster than previously thought when they were cultivated in a membrane bioreactor (MBR) with a step-wise decrease in the solid retention time (SRT). Here, we reevaluated the maximum specific growth rates (μmax) of three phylogenetically distant anammox bacterial species (i.e. "Ca. Brocadia sinica", "Ca. Jettenia caeni" and "Ca. Scalindua sp.") by directly measuring 16S rRNA gene copy numbers using newly developed quantitative polymerase chain reaction (qPCR) assays...
June 1, 2017: Water Research
https://www.readbyqxmd.com/read/28345603/pja2-ubiquitinates-the-hiv-1-tat-protein-with-atypical-chain-linkages-to-activate-viral-transcription
#13
Tyler B Faust, Yang Li, Gwendolyn M Jang, Jeffrey R Johnson, Shumin Yang, Amit Weiss, Nevan J Krogan, Alan D Frankel
Transcription complexes that assemble at the HIV-1 promoter efficiently initiate transcription but generate paused RNA polymerase II downstream from the start site. The virally encoded Tat protein hijacks positive transcription elongation factor b (P-TEFb) to phosphorylate and activate this paused polymerase. In addition, Tat undergoes a series of reversible post-translational modifications that regulate distinct steps of the transcription cycle. To identify additional functionally important Tat cofactors, we performed RNAi knockdowns of sixteen previously identified Tat interactors and found that a novel E3 ligase, PJA2, ubiquitinates Tat in a non-degradative manner and specifically regulates the step of HIV transcription elongation...
March 27, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28282871/factors%C3%A2-that%C3%A2-shape%C3%A2-eukaryotic%C3%A2-trnaomes-%C3%A2-processing-%C3%A2-modification%C3%A2-and%C3%A2-anticodon-codon%C3%A2-use
#14
REVIEW
Richard J Maraia, Aneeshkumar G Arimbasseri
Transfer RNAs (tRNAs) contain sequence diversity beyond their anticodons and the large variety of nucleotide modifications found in all kingdoms of life. Some modifications stabilize structure and fit in the ribosome whereas those to the anticodon loop modulate messenger RNA (mRNA) decoding activity more directly. The identities of tRNAs with some universal anticodon loop modifications vary among distant and parallel species, likely to accommodate fine tuning for their translation systems. This plasticity in positions 34 (wobble) and 37 is reflected in codon use bias...
March 8, 2017: Biomolecules
https://www.readbyqxmd.com/read/28258142/activation-mechanism-and-cellular-localization-of-membrane-anchored-alginate-polymerase-in-pseudomonas-aeruginosa
#15
M Fata Moradali, Shirin Ghods, Bernd H A Rehm
The exopolysaccharide alginate, produced by the opportunistic human pathogen Pseudomonas aeruginosa, confers a survival advantage to the bacterium by contributing to the formation of characteristic biofilms during infection. Membrane-anchored proteins Alg8 (catalytic subunit) and Alg44 (copolymerase) constitute the alginate polymerase that is being activated by the second messenger molecule bis-(3', 5')-cyclic dimeric GMP (c-di-GMP), but the mechanism of activation remains elusive. To shed light on the c-di-GMP-mediated activation of alginate polymerization in vivo, an in silico structural model of Alg8 fused to the c-di-GMP binding PilZ domain informed by the structure of cellulose synthase, BcsA, was developed...
May 1, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28202539/parps-and-adp-ribosylation-recent-advances-linking-molecular-functions-to-biological-outcomes
#16
REVIEW
Rebecca Gupte, Ziying Liu, W Lee Kraus
The discovery of poly(ADP-ribose) >50 years ago opened a new field, leading the way for the discovery of the poly(ADP-ribose) polymerase (PARP) family of enzymes and the ADP-ribosylation reactions that they catalyze. Although the field was initially focused primarily on the biochemistry and molecular biology of PARP-1 in DNA damage detection and repair, the mechanistic and functional understanding of the role of PARPs in different biological processes has grown considerably of late. This has been accompanied by a shift of focus from enzymology to a search for substrates as well as the first attempts to determine the functional consequences of site-specific ADP-ribosylation on those substrates...
January 15, 2017: Genes & Development
https://www.readbyqxmd.com/read/28167562/tenofovir-disoproxil-fumarate-is-a-new-substrate-of-atp-binding-cassette-subfamily-c-member-11
#17
Wisith Tun-Yhong, Chatchai Chinpaisal, Perayot Pamonsinlapatham, Sindchai Kaewkitichai
Tenofovir disoproxil fumarate (TDF), a nucleotide reverse transcriptase inhibitor, after conversion to tenofovir (TFV), is mainly eliminated by glomerular filtration and active tubular secretion. The major adverse effect of tenofovir is nephrotoxicity; however, the exact mechanism remains poorly understood. In this study, the ATP-binding cassette subfamily C member 11 (ABCC11; multidrug resistance protein 8 [MRP8]) transporter, which is abundant in proximal tubular cells, was demonstrated to act as an efflux transporter of tenofovir...
April 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28159788/revisiting-the-regulation-of-the-primary-scaffoldin-gene-in-clostridium-thermocellum
#18
Lizett Ortiz de Ora, Iván Muñoz-Gutiérrez, Edward A Bayer, Yuval Shoham, Raphael Lamed, Ilya Borovok
Cellulosomes are considered to be one of the most efficient systems for the degradation of plant cell wall polysaccharides. The central cellulosome component comprises a large, noncatalytic protein subunit called scaffoldin. Multiple saccharolytic enzymes are incorporated into the scaffoldins via specific high-affinity cohesin-dockerin interactions. Recently, the regulation of genes encoding certain cellulosomal components by multiple RNA polymerase alternative σ(I) factors has been demonstrated in Clostridium (Ruminiclostridium) thermocellum In the present report, we provide experimental evidence demonstrating that the C...
April 15, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28152506/detection-fidelity-of-ar-mutations-in-plasma-derived-cell-free-dna
#19
Alexa Goldstein, Patricia Valda Toro, Justin Lee, John L Silberstein, Mary Nakazawa, Ian Waters, Karen Cravero, David Chu, Rory L Cochran, Minsoo Kim, Daniel Shinn, Samantha Torquato, Robert M Hughes, Aparna Pallavajjala, Michael A Carducci, Channing J Paller, Samuel R Denmeade, Bruce Kressel, Bruce J Trock, Mario A Eisenberger, Emmanuel S Antonarakis, Ben H Park, Paula J Hurley
Somatic genetic alterations including copy number and point mutations in the androgen receptor (AR) are associated with resistance to therapies targeting the androgen/AR axis in patients with metastatic castration resistant prostate cancer (mCRPC). Due to limitations associated with biopsying metastatic lesions, plasma derived cell-free DNA (cfDNA) is increasingly being used as substrate for genetic testing. AR mutations detected by deep next generation sequencing (NGS) of cfDNA from patients with mCRPC have been reported at allelic fractions ranging from over 25% to below 1%...
February 28, 2017: Oncotarget
https://www.readbyqxmd.com/read/28140505/n-2-substituted-2-deoxyguanosine-triphosphate-derivatives-as-selective-substrates-for-human-dna-polymerase-%C3%AE%C2%BA
#20
A S Prakasha Gowda, Marietta Lee, Thomas E Spratt
N(2) -Alkyl-2'-deoxyguanosine triphosphate (N(2) -alkyl-dGTP) derivatives with methyl, butyl, benzyl, or 4-ethynylbenzyl substituents were prepared and tested as substrates for human DNA polymerases. N(2) -Benzyl-dGTP was equal to dGTP as a substrate for DNA polymerase κ (pol κ), but was a poor substrate for pols β, δ, η, ι, or ν. In vivo reactivity was evaluated through incubation of N(2) -4-ethynylbenzyl-dG with wild-type and pol κ deficient mouse embryonic fibroblasts. CuAAC reaction with 5(6)-FAM-azide demonstrated that only cells containing pol κ were able to incorporate N(2) -4-ethynylbenzyl-dG into the nucleus...
March 1, 2017: Angewandte Chemie
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