keyword
MENU ▼
Read by QxMD icon Read
search

Polymerase substrate specificity

keyword
https://www.readbyqxmd.com/read/27913570/revisiting-the-human-polypeptide-galnac-t1-and-t13-paralogs
#1
María Florencia Festari, Felipe Trajtenberg, Nora Berois, Sergio Pantano, Leslie Revoredo, Yun Kong, Patricia Solari-Saquieres, Yoshiki Narimatsu, Teresa Freire, Sylvie Bay, Carlos Robello, Jean Bénard, Thomas A Gerken, Henrik Clausen, Eduardo Osinaga
Polypeptide GalNAc-transferases (GalNAc-Ts) constitute a family of 20 human glycosyltransferases (comprising 9 subfamilies), which initiate mucin-type O-glycosylation. The O-glycoproteome is thought to be differentially regulated via the different substrate specificities and expression patterns of each GalNAc-T isoforms. Here, we present a comprehensive in vitro analysis of the peptide substrate specificity of GalNAc-T13, showing that it essentially overlaps with the ubiquitous expressed GalNAc-T1 isoform found in the same subfamily as T13...
November 22, 2016: Glycobiology
https://www.readbyqxmd.com/read/27898685/high-resolution-phenotypic-landscape-of-the-rna-polymerase-ii-trigger-loop
#2
Chenxi Qiu, Olivia C Erinne, Jui M Dave, Ping Cui, Huiyan Jin, Nandhini Muthukrishnan, Leung K Tang, Sabareesh Ganesh Babu, Kenny C Lam, Paul J Vandeventer, Ralf Strohner, Jan Van den Brulle, Sing-Hoi Sze, Craig D Kaplan
The active sites of multisubunit RNA polymerases have a "trigger loop" (TL) that multitasks in substrate selection, catalysis, and translocation. To dissect the Saccharomyces cerevisiae RNA polymerase II TL at individual-residue resolution, we quantitatively phenotyped nearly all TL single variants en masse. Three mutant classes, revealed by phenotypes linked to transcription defects or various stresses, have distinct distributions among TL residues. We find that mutations disrupting an intra-TL hydrophobic pocket, proposed to provide a mechanism for substrate-triggered TL folding through destabilization of a catalytically inactive TL state, confer phenotypes consistent with pocket disruption and increased catalysis...
November 2016: PLoS Genetics
https://www.readbyqxmd.com/read/27885504/plant-dicer-like-proteins-double-stranded-rna-cleaving-enzymes-for-small-rna-biogenesis
#3
Akihito Fukudome, Toshiyuki Fukuhara
Dicer, a double-stranded RNA (dsRNA)-specific endoribonuclease, plays an essential role in triggering both transcriptional and post-transcriptional gene silencing in eukaryotes by cleaving dsRNAs or single-stranded RNAs bearing stem-loop structures such as microRNA precursor transcripts into 21- to 24-nt small RNAs. Unlike animals, plants have evolved to utilize at least four Dicer-like (DCL) proteins. Extensive genetic studies have revealed that each DCL protein participates in a specific gene silencing pathway, with some redundancy...
November 24, 2016: Journal of Plant Research
https://www.readbyqxmd.com/read/27881682/stabilization-of-luciferase-from-renilla-reniformis-using-random-mutations
#4
Megumi Shigehisa, Norie Amaba, Shigeki Arai, Chisato Higashi, Ryo Kawanabe, Ayano Matsunaga, Fina Amreta Laksmi, Masao Tokunaga, Matsujiro Ishibashi
We expressed luciferase (RLuc) from Renilla reniformis in Escherichia coli RLuc was purified using a Ni-NTA column and subsequently characterized. It was unstable in acidic solutions and at 30°C. To increase the stability of RLuc, the Rluc gene was randomly mutated using error-prone polymerase chain reaction. E. coli harboring the mutated gene was screened by detecting luminescence on a plate containing the substrate coelenterazine at 34°C. Three mutants, i.e. N264SS287P, N178D and F116LI137V, were obtained...
November 23, 2016: Protein Engineering, Design & Selection: PEDS
https://www.readbyqxmd.com/read/27833949/the-emerging-picture-of-cdk9-p-tefb-more-than-20-years-of-advances-since-pitalre
#5
REVIEW
Nikolas Ferreira Dos Santos Paparidis, Maxwell Castro Durvale, Fernanda Canduri
CDK9 is a prominent member of the transcriptional CDKs subfamily, a group of kinases whose function is to control the primary steps of mRNA synthesis and processing by eukaryotic RNA polymerase II. As a cyclin-dependent kinase, CDK9 activation in vivo depends upon its association with T-type cyclins to assemble the positive transcription elongation factor (P-TEFb). Although CDK9/P-TEFb phosphorylates the C-terminal domain of RNAP II in the same positions targeted by CDK7 (TFIIH) and CDK8 (Mediator), the former does not participate in the transcription initiation, but rather plays a unique role by driving the polymerase to productive elongation...
November 11, 2016: Molecular BioSystems
https://www.readbyqxmd.com/read/27817742/parg-inhibitors-and-functional-parg-inhibition-models
#6
Yuka Sasaki, Miyuki Hozumi, Hiroaki Fujimori, Yasufumi Murakami, Fumiaki Koizumi, Kengo Inoue, Mitsuko Masutani
Poly(ADP-ribose) polymerases (PARPs) family proteins catalyze poly(ADP-ribosylation) (PARylation) by conjugating ADP-ribose residues repeatedly on amino acid residues using nicotinamide adenine dinucleotide as a substrate. The inhibitors of PARP widely block DNA repair processes and are currently examined in clinical trials of cancer therapy. Poly(ADP-ribose) glycohydrolase (PARG) is the main nuclear enzyme, which digests poly(ADP-ribose) into ADP-ribose. PARG inhibitor could also be considered as a chemotherapeutic agent for cancer, because of its involvement in DNA repair...
2016: Current Protein & Peptide Science
https://www.readbyqxmd.com/read/27808482/crystal-structure-of-ralstonia-eutropha-polyhydroxyalkanoate-synthase-c-terminal-domain-and-reaction-mechanisms
#7
Jieun Kim, Yeo-Jin Kim, So Young Choi, Sang Yup Lee, Kyung-Jin Kim
Polyhydroxyalkanoates (PHAs) are natural polyesters synthesized by numerous microorganisms as energy and reducing power storage materials, and have attracted much attention as substitutes for petroleum-based plastics. Here, we report the first crystal structure of Ralstonia eutropha PHA synthase at 1.8 Å resolution and structure-based mechanisms for PHA polymerization. RePhaC1 contains two distinct domains, the N-terminal (RePhaC1ND ) and C-terminal domains (RePhaC1CD ), and exists as a dimer. RePhaC1CD catalyzes polymerization via non-processive ping-pong mechanism using a Cys-His-Asp catalytic triad...
November 3, 2016: Biotechnology Journal
https://www.readbyqxmd.com/read/27754888/regulation-of-transcription-initiation-by-gfh-factors-from-deinococcus-radiodurans
#8
Aleksei Agapov, Daria Esyunina, Danil Pupov, Andrey Kulbachinskiy
The Gre-family transcription factors bind within the secondary channel of bacterial RNA polymerase (RNAP) directly modulating its catalytic activities. Universally conserved Gre factors activate RNA cleavage by RNAP, by chelating catalytic metal ions in the RNAP active site, and facilitate both promoter escape and transcription elongation. Gfh factors are Deinococcus/Thermus -specific homologues of Gre factors whose transcription functions remain poorly understood. Recently, we found that Gfh1 and Gfh2 proteins from Deinococcus radiodurans dramatically stimulate RNAP pausing during transcription elongation in the presence of Mn(2+) but not Mg(2+) ions...
October 17, 2016: Biochemical Journal
https://www.readbyqxmd.com/read/27744351/rna-editing-tutase-1-structural-foundation-of-substrate-recognition-complex-interactions-and-drug-targeting
#9
Lional Rajappa-Titu, Takuma Suematsu, Paola Munoz-Tello, Marius Long, Özlem Demir, Kevin J Cheng, Jason R Stagno, Hartmut Luecke, Rommie E Amaro, Inna Aphasizheva, Ruslan Aphasizhev, Stéphane Thore
Terminal uridyltransferases (TUTases) execute 3' RNA uridylation across protists, fungi, metazoan and plant species. Uridylation plays a particularly prominent role in RNA processing pathways of kinetoplastid protists typified by the causative agent of African sleeping sickness, Trypanosoma brucei In mitochondria of this pathogen, most mRNAs are internally modified by U-insertion/deletion editing while guide RNAs and rRNAs are U-tailed. The founding member of TUTase family, RNA editing TUTase 1 (RET1), functions as a subunit of the 3' processome in uridylation of gRNA precursors and mature guide RNAs...
October 15, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27742790/matrix-mechanics-controls-fhl2-movement-to-the-nucleus-to-activate-p21-expression
#10
Naotaka Nakazawa, Aneesh R Sathe, G V Shivashankar, Michael P Sheetz
Substrate rigidity affects many physiological processes through mechanochemical signals from focal adhesion (FA) complexes that subsequently modulate gene expression. We find that shuttling of the LIM domain (domain discovered in the proteins, Lin11, Isl-1, and Mec-3) protein four-and-a-half LIM domains 2 (FHL2) between FAs and the nucleus depends on matrix mechanics. In particular, on soft surfaces or after the loss of force, FHL2 moves from FAs into the nucleus and concentrates at RNA polymerase (Pol) II sites, where it acts as a transcriptional cofactor, causing an increase in p21 gene expression that will inhibit growth on soft surfaces...
November 1, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27739412/induction-of-apoptosis-in-tnf-treated-l929-cells-in-the-presence-of-necrostatin-1
#11
Hirofumi Sawai
It has been shown that necroptosis-caspase-independent programmed necrotic cell death-can be induced by treatment with tumor necrosis factor (TNF) in the L929 murine fibrosarcoma cell line, even in the absence of a caspase inhibitor. Although it was reported that necrostatin-1-a specific inhibitor of necroptosis-inhibited TNF-induced necroptosis in L929 cells, it has not been elucidated whether the cells eventually die by apoptosis in the presence of necrostatin-1. In this paper, induction of apoptosis was demonstrated in TNF-treated L929 cells in the presence of necrostatin-1...
October 7, 2016: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/27690041/colorimetric-integrated-pcr-protocol-for-rapid-detection-of-vibrio-parahaemolyticus
#12
Kewen Cheng, Daodong Pan, Jun Teng, Li Yao, Yingwang Ye, Feng Xue, Fan Xia, Wei Chen
Rapid detection of pathogens is of great significance for food safety and disease diagnosis. A new colorimetric method for rapid and easy detection of Vibrio parahaemolyticus (V. parahaemolyticus or Vp) has been developed in this research. A specific sequence was designed and integrated with the forward primer for molecular detection of Vp. This specific sequence was tested and treated as the horseradish peroxidase (HRP)-mimicking DNAzyme and could be amplified during the polymerase chain reaction (PCR) process...
2016: Sensors
https://www.readbyqxmd.com/read/27660069/molecular-mechanisms-of-xeroderma-pigmentosum-xp-proteins
#13
Sandra C Koch, Nina Simon, Charlotte Ebert, Thomas Carell
Nucleotide excision repair (NER) is a highly versatile and efficient DNA repair process, which is responsible for the removal of a large number of structurally diverse DNA lesions. Its extreme broad substrate specificity ranges from DNA damages formed upon exposure to ultraviolet radiation to numerous bulky DNA adducts induced by mutagenic environmental chemicals and cytotoxic drugs used in chemotherapy. Defective NER leads to serious diseases, such as xeroderma pigmentosum (XP). Eight XP complementation groups are known of which seven (XPA-XPG) are caused by mutations in genes involved in the NER process...
January 2016: Quarterly Reviews of Biophysics
https://www.readbyqxmd.com/read/27617498/cyp2c9-and-cyp2c19-allele-and-haplotype-distributions-in-four-mestizo-populations-from-western-mexico-an-interethnic-comparative-study
#14
Ana Miriam Saldaña-Cruz, Lilia Carolina León-Moreno, José Sánchez-Corona, Daniel Alejandro Márquez-de Santiago, Francisco Mendoza-Carrera, Xochitl Helga Castro-Martínez, Alejandra Guadalupe García-Zapién, María Cristina Morán-Moguel, Silvia Esperanza Flores-Martínez
AIMS: Polymorphisms in the CYP2C9 and CYP2C19 genes confer potential risk for specific adverse drug reactions and therapeutic effect failure. Their frequencies differ among ethnic groups. This study was aimed to describe the distribution of CYP2C9 and CYP2C19 alleles and haplotypes in four Mestizo populations from Western Mexico and their comparison with the reported data from other ethnic groups. METHODS: The CYP2C alleles (CYP2C9*2, CYP2C9*3, CYP2C19*2, and CYP2C19*3) were genotyped using polymerase chain reaction-restriction fragment length polymorphisms analyses using DNA samples from 477 healthy Mestizo individuals of Colima (n = 100), Jalisco (n = 147), Michoacán (n = 117), and Nayarit (n = 113)...
September 12, 2016: Genetic Testing and Molecular Biomarkers
https://www.readbyqxmd.com/read/27583302/a-microchip-platform-for-structural-oncology-applications
#15
Carly E Winton, Brian L Gilmore, Andrew C Demmert, Vasilea Karageorge, Zhi Sheng, Deborah F Kelly
Recent advances in the development of functional materials offer new tools to dissect human health and disease mechanisms. The use of tunable surfaces is especially appealing as substrates can be tailored to fit applications involving specific cell types or tissues. Here we use tunable materials to facilitate the three-dimensional (3D) analysis of BRCA1 gene regulatory complexes derived from human cancer cells. We employed a recently developed microchip platform to isolate BRCA1 protein assemblies natively formed in breast cancer cells with and without BRCA1 mutations...
2016: NPJ Breast Cancer
https://www.readbyqxmd.com/read/27577607/bis-three-way-junction-nanostructure-and-dna-machineries-for-ultrasensitive-and-specific-detection-of-bcr-abl-fusion-gene-by-chemiluminescence-imaging
#16
Yongjie Xu, Xintong Bian, Ye Sang, Yujian Li, Dandan Li, Wei Cheng, Yibing Yin, Huangxian Ju, Shijia Ding
A novel G-quadruplex DNAzyme-driven chemiluminescence (CL) imaging method has been developed for ultrasensitive and specific detection of BCR/ABL fusion gene based on bis-three-way junction (bis-3WJ) nanostructure and cascade DNA machineries. Bis-3WJ probes are designed logically to recognize BCR/ABL fusion gene, which forms the stable bis-3WJ nanostructure for the activation of polymerase/nicking enzyme machineries in cascade, resulting in synthesis of DNAzyme subunits. These DNAzyme subunits can form integrated DNAzyme by self-assembly to catalyze CL substrate, thus providing an amplified signal for the sensing events or outputs for AND logic operation...
2016: Scientific Reports
https://www.readbyqxmd.com/read/27576714/preparation-of-chromatin-templates-to-study-rna-polymerase-i-transcription-in-vitro
#17
Gernot Längst
Cellular DNA is packaged into chromatin, which is the substrate of all DNA-dependent processes in eukaryotes. The regulation of chromatin requires specialized enzyme activities to allow the access of sequence-specific binding proteins and RNA polymerases. In order to dissect chromatin-dependent features of transcription regulation in detail, in vitro systems to generate defined chromatin templates for transcription are required. I present a protocol that allows the assembly of nucleosomes on ribosomal RNA (rRNA) minigenes by salt gradient dialysis and subsequent sucrose gradient centrifugation...
2016: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27573382/understanding-how-mismatch-repair-proteins-participate-in-the-repair-anti-recombination-decision
#18
Ujani Chakraborty, Eric Alani
Mismatch repair (MMR) systems correct DNA mismatches that result from DNA polymerase misincorporation errors. Mismatches also appear in heteroduplex DNA intermediates formed during recombination between nearly identical sequences, and can be corrected by MMR or removed through an unwinding mechanism, known as anti-recombination or heteroduplex rejection. We review studies, primarily in baker's yeast, which support how specific factors can regulate the MMR/anti-recombination decision. Based on recent advances, we present models for how DNA structure, relative amounts of key repair proteins, the timely localization of repair proteins to DNA substrates and epigenetic marks can modulate this critical decision...
September 2016: FEMS Yeast Research
https://www.readbyqxmd.com/read/27548700/comprehensive-in-vitro-analysis-of-acyltransferase-domain-exchanges-in-modular-polyketide-synthases-and-its-application-for-short-chain-ketone-production
#19
Satoshi Yuzawa, Kai Deng, George Wang, Edward E K Baidoo, Trent R Northen, Paul D Adams, Leonard Katz, Jay D Keasling
Type I modular polyketide synthases (PKSs) are polymerases that utilize acyl-CoAs as substrates. Each polyketide elongation reaction is catalyzed by a set of protein domains called a module. Each module usually contains an acyltransferase (AT) domain, which determines the specific acyl-CoA incorporated into each condensation reaction. Although successful exchange of individual AT domains can lead to the biosynthesis of a large variety of novel compounds, hybrid PKS modules often show significantly decreased activities...
August 22, 2016: ACS Synthetic Biology
https://www.readbyqxmd.com/read/27530537/a-self-activated-mechanism-for-nucleic-acid-polymerization-catalyzed-by-dna-rna-polymerases
#20
Vito Genna, Pietro Vidossich, Emiliano Ippoliti, Paolo Carloni, Marco De Vivo
The enzymatic polymerization of DNA and RNA is the basis for genetic inheritance for all living organisms. It is catalyzed by the DNA/RNA polymerase (Pol) superfamily. Here, bioinformatics analysis reveals that the incoming nucleotide substrate always forms an H-bond between its 3'-OH and β-phosphate moieties upon formation of the Michaelis complex. This previously unrecognized H-bond implies a novel self-activated mechanism (SAM), which synergistically connects the in situ nucleophile formation with subsequent nucleotide addition and, importantly, nucleic acid translocation...
August 31, 2016: Journal of the American Chemical Society
keyword
keyword
77441
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"