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DNA ligase

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https://www.readbyqxmd.com/read/28212551/nrip-dcaf6-stabilizes-the-androgen-receptor-protein-by-displacing-ddb2-from-the-cul4a-ddb1-e3-ligase-complex-in-prostate-cancer
#1
Hsin-Hsiung Chen, Ping Fan, Szu-Wei Chang, Yeou-Ping Tsao, Hsiang-Po Huang, Show-Li Chen
Both nuclear receptor interaction protein (NRIP) and DNA damage binding protein 2 (DDB2) belong to the Cullin 4 (CUL4)-DDB1 binding protein family and are androgen receptor (AR)-interacting proteins. Here, we investigated the expression patterns of the NRIP, DDB2 and AR proteins in human prostate cancer tissues and found that the expression levels of NRIP and AR were higher, but the DDB2 level was lower, in prostate cancer tissues than in non-neoplastic controls, suggesting NRIP as a candidate tumor promoter and DDB2 as a tumor suppressor in prostate cancer...
February 14, 2017: Oncotarget
https://www.readbyqxmd.com/read/28197906/functions-of-sumo-in-the-maintenance-of-genome-stability
#2
Nicola Zilio, Karolin Eifler-Olivi, Helle D Ulrich
Like in most other areas of cellular metabolism, the functions of the ubiquitin-like modifier SUMO in the maintenance of genome stability are manifold and varied. Perturbations of global sumoylation causes a wide spectrum of phenotypes associated with defects in DNA maintenance, such as hypersensitivity to DNA-damaging agents, gross chromosomal rearrangements and loss of entire chromosomes. Consistent with these observations, many key factors involved in various DNA repair pathways have been identified as SUMO substrates...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28194022/multifaceted-roles-of-trim38-in-innate-immune-and-inflammatory-responses
#3
REVIEW
Ming-Ming Hu, Hong-Bing Shu
The tripartite motif-containing (TRIM) proteins represent the largest E3 ubiquitin ligase family. The multifaceted roles of TRIM38 in innate immunity and inflammation have been intensively investigated in recent years. TRIM38 is essential for cytosolic RNA or DNA sensor-mediated innate immune responses to both RNA and DNA viruses, while negatively regulating TLR3/4- and TNF/IL-1β-triggered inflammatory responses. In these processes, TRIM38 acts as an E3 ubiquitin or SUMO ligase, which targets key cellular signaling components, or as an enzymatic activity-independent regulator...
February 13, 2017: Cellular & Molecular Immunology
https://www.readbyqxmd.com/read/28191039/elevated-transcriptional-levels-of-aldolase-a-aldoa-associates-with-cell-cycle-related-genes-in-patients-with-nsclc-and-several-solid-tumors
#4
Fan Zhang, Jie-Diao Lin, Xiao-Yu Zuo, Yi-Xuan Zhuang, Chao-Qun Hong, Guo-Jun Zhang, Xiao-Jiang Cui, Yu-Kun Cui
BACKGROUND: Aldolase A (ALDOA) is one of the glycolytic enzymes primarily found in the developing embryo and adult muscle. Recently, a new role of ALDOA in several cancers has been proposed. However, the underlying mechanism remains obscure and inconsistent. In this study, we tried to investigate ALDOA-associated (AA) genes using available microarray datasets to help elucidating the role of ALDOA in cancer. RESULTS: In the dataset of patients with non-small-cell lung cancer (NSCLC, E-GEOD-19188), 3448 differentially expressed genes (DEGs) including ALDOA were identified, in which 710 AA genes were found to be positively associated with ALDOA...
2017: BioData Mining
https://www.readbyqxmd.com/read/28190841/hairpin-shaped-dna-templated-copper-nanoparticles-for-fluorescence-detection-of-adenosine-triphosphate-based-on-ligation-mediated-exonuclease-cleavage
#5
Wenping Zhu, Liyan Dai, Zengchen Liu, Weijie Yang, Chunxiang Zhao, Yanxia Li, Yahong Chen
DNA-templated copper nanoparticles (CuNPs) have recently received considerable interest as functional fluorescent probes for biochemical analysis. In this work, a novel ATP-dependent ligation reactions (ATP-DLR) based ATP assay strategy was proposed by using hairpin-shaped (HS) DNA templated CuNPs as a fluorescent probe. Nick sealing by T4 DNA ligase leads to the formation of intact HS DNA, which can resist the exonuclease cleavage and be taken as the template for CuNPs formation, resulting in strong fluorescence...
2017: Analytical Sciences: the International Journal of the Japan Society for Analytical Chemistry
https://www.readbyqxmd.com/read/28184006/the-human-dna-ligase-iii%C3%AE-x-ray-repair-cross-complementing-protein-1-complex-performs-dna-nick-repair-after-transient-unwrapping-of-nucleosomal-dna
#6
Wendy J Cannan, Ishtiaque Rashid, Alan E Tomkinson, Susan S Wallace, David S Pederson
Reactive oxygen species generate potentially cytotoxic and mutagenic lesions in DNA, both between and within the nucleosomes that package DNA in chromatin. The vast majority of these lesions are subject to base excision repair (BER). Enzymes that catalyze the first three steps in BER can act at many sites in nucleosomes without the aid of chromatin-remodeling agents, and without irreversibly disrupting the host nucleosome. Here, we show that the same is true is true for a protein complex comprising DNA ligase IIIα and the scaffolding protein X-ray repair cross-complementing protein 1 (XRCC1), which completes the fourth and final step in (short-patch) BER...
February 8, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28181316/an-improved-method-for-purification-and-refolding-of-recombinant-hiv-vif-expressed-in-e-coli
#7
Carlos A Duarte, Mickel Palomino
Virion infectivity factor (Vif) is a 23 KDa protein which protects HIV-1 from deamination of its proviral DNA by APOBEC3G. The active form of Vif is a multimer that interacts simultaneously with CBF-beta, the Elongin B and C subunits, Cullin 5 and APOBEC3G to form a ubiquitin ligase complex targeting the latter for degradation. Vif clearly represents an attractive target for developing novel antiviral drugs for the therapy of HIV/AIDS, and this goal requires a source of well folded, readily available protein...
February 8, 2017: Biotechnology and Applied Biochemistry
https://www.readbyqxmd.com/read/28179534/impaired-sting-pathway-in-the-human-osteosarcoma-u2os-cells-contributes-to-the-growth-of-icp0-null-mutant-herpes-simplex-virus
#8
Thibaut Deschamps, Maria Kalamvoki
Human herpes simplex virus-1 (HSV-1) is a wide spread pathogen with 80% of the population being latently infected. To successfully evade the host the virus has evolved strategies to counteract antiviral responses, including the gene silencing and innate immunity machineries. The immediately early protein of the virus, Infected Cell Protein 0 (ICP0) plays central role in these processes. ICP0 blocks innate immunity and one mechanism is by degrading hostile factors with its intrinsic E3 ligase activity. ICP0 functions also as a promiscuous transactivator and it blocks repressor complexes to enable viral gene transcription...
February 8, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28177129/role-of-parp-activity-in-lung-cancer-induced-cachexia-effects-on-muscle-oxidative-stress-proteolysis-anabolic-markers-and-phenotype
#9
Alba Chacon-Cabrera, Mercè Mateu-Jimenez, Klaus Langohr, Clara Fermoselle, Elena García-Arumí, Antoni L Andreu, Jose Yelamos, Esther Barreiro
Strategies to treat cachexia are still at its infancy. Enhanced muscle protein breakdown and ubiquitin-proteasome system are common features of cachexia associated with chronic conditions including lung cancer (LC). Poly(ADP-ribose) polymerases (PARP), which play a major role in chromatin structure regulation, also underlie maintenance of muscle metabolism and body composition. We hypothesized that protein catabolism, proteolytic markers, muscle fiber phenotype, and muscle anabolism may improve in respiratory and limb muscles of LC-cachectic Parp-1-deficient (Parp-1(-/-) ) and Parp-2(-/-) mice...
February 8, 2017: Journal of Cellular Physiology
https://www.readbyqxmd.com/read/28166483/the-importance-of-regulatory-ubiquitination-in-cancer-and-metastasis
#10
L H Gallo, J Ko, D J Donoghue
Ubiquitination serves as a degradation mechanism of proteins, but is involved in additional cellular processes such as activation of NFκB inflammatory response and DNA damage repair. We highlight the E2 ubiquitin conjugating enzymes, E3 ubiquitin ligases and Deubiquitinases that support the metastasis of a plethora of cancers. E3 ubiquitin ligases also modulate pluripotent cancer stem cells attributed to chemotherapy resistance. We further describe mutations in E3 ubiquitin ligases that support tumor proliferation and adaptation to hypoxia...
February 6, 2017: Cell Cycle
https://www.readbyqxmd.com/read/28166445/mdm2-splice-isoforms-regulate-the-p53-mdm2-mdm4-regulatory-circuit-via-ring-domain-mediated-ubiquitination-of-p53-and-mdm4
#11
Chuandong Fan, Xinjiang Wang
p53 is regulated by heterodimer E3 ligase Mdm2-Mdm4 via RING domain interaction. Mdm2 transcripts undergo alternative splicing, and Mdm2 splice isoforms are increased in cancer and induced by DNA damage. Although two major Mdm2 splice isoforms that do not bind to p53 were reported to impact the p53 pathway, the underlying biochemical mechanisms were not understood. Here, we show that these Mdm2 splice isoforms ubiquitinate Mdm2 and Mdm4 in vitro and regulate the activity of Mdm2-Mdm4 E3 complex in cells. The Mdm2 isoforms are capable of promoting p53 ubiquitination in the absence of Mdm2 or Mdm4...
February 6, 2017: Cell Cycle
https://www.readbyqxmd.com/read/28165732/rapid-timescale-binding-analysis-of-t4-dna-ligase-dna-binding
#12
Robert John Bauer, Thomas J Jurkiw, Thomas C Evans, Gregory J S Lohman
DNA ligases, essential to both in vivo genome integrity and in vitro molecular biology, catalyze phosphodiester bond formation between adjacent 3'-OH and 5'-phosphorylated termini in dsDNA. This reaction requires enzyme self-adenylylation, using ATP or NAD+ as a cofactor, and AMP release concomitant with phosphodiester bond formation. In this study, we present the first fast-timescale binding kinetics of T4 DNA ligase to both nicked substrate DNA (nDNA) and product-equivalent non-nicked dsDNA, as well as binding and release kinetics of AMP...
February 6, 2017: Biochemistry
https://www.readbyqxmd.com/read/28165030/structural-analysis-and-evolution-of-specificity-of-the-sumo-ufd-e1-e2-interactions
#13
Bing Liu, L Maria Lois, David Reverter
SUMO belongs to the ubiquitin-like family (UbL) of protein modifiers. SUMO is conserved among eukaryotes and is essential for the regulation of processes such as DNA damage repair, transcription, DNA replication and mitosis. UbL modification of proteins occurs via a specific enzymatic cascade formed by the crosstalk between the E1-activating enzyme, the E2-conjugating enzyme and the E3-ligase. An essential discrimination step in all UbL modifiers corresponds to the interaction between E1 and E2 enzymes, which is mediated by the recruitment of the E2 to the UFD domain (Ubiquitin-Fold Domain) of the E1 enzyme...
February 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28161170/maternal-supplementation-with-rumen-protected-methionine-increases-prepartal-plasma-methionine-concentration-and-alters-hepatic-mrna-abundance-of-1-carbon-methionine-and-transsulfuration-pathways-in-neonatal-holstein-calves
#14
C B Jacometo, Z Zhou, D Luchini, M N Corrêa, J J Loor
An important mechanism of nutritional "programming" induced by supplementation with methyl donors during pregnancy is the alteration of mRNA abundance in the offspring. We investigated the effects of rumen-protected Met (RPM) on abundance of 17 genes in the 1-carbon, Met, and transsulfuration pathways in calf liver from cows fed the same basal diet without (control, CON) or with RPM at 0.08% of diet dry matter/d (MET) from -21 through +30 d around calving. Biopsies (n = 8 calves per diet) were harvested on d 4, 14, 28, and 50 of age...
February 1, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/28148912/the-e3-ligase-mule-protects-the-heart-against-oxidative-stress-and-mitochondrial-dysfunction-through-myc-dependent-inactivation-of-pgc-1%C3%AE-and-pink1
#15
Keith Dadson, Ludger Hauck, Zhenyue Hao, Daniela Grothe, Vivek Rao, Tak W Mak, Filio Billia
Cardiac homeostasis requires proper control of protein turnover. Protein degradation is principally controlled by the Ubiquitin-Proteasome System. Mule is an E3 ubiquitin ligase that regulates cellular growth, DNA repair and apoptosis to maintain normal tissue architecture. However, Mule's function in the heart has yet to be described. In a screen, we found reduced Mule expression in left ventricular samples from end-stage heart failure patients. Consequently, we generated conditional cardiac-specific Mule knockout (Mule (fl/fl(y));mcm) mice...
February 2, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28143883/fzr1-loss-increases-sensitivity-to-dna-damage-and-consequently-promotes-murine-and-human-b-cell-acute-leukemia
#16
Jo Ishizawa, Eiji Sugihara, Shinji Kuninaka, Kaoru Mogushi, Kensuke Kojima, Christopher B Benton, Ran Zhao, Dhruv Chachad, Norisato Hashimoto, Rodrigo O Jacamo, Yihua Qiu, Suk Young Yoo, Shinichiro Okamoto, Michael Andreeff, Steven M Kornblau, Hideyuki Saya
FZR1 (fizzy-related protein homolog, also called CDH1, cell division cycle 20 related 1) functions in the cell cycle as a specific activator of APC/C (anaphase-promoting complex or cyclosome) ubiquitin ligase, regulating late mitosis, G1 phase and activation of the G2-M checkpoint. FZR1 has been implicated as both a tumor suppressor and oncoprotein, and its precise contribution to carcinogenesis remains unclear. Here, we examined the role of FZR1 in tumorigenesis and cancer therapy by analyzing tumor models and patient specimens...
January 31, 2017: Blood
https://www.readbyqxmd.com/read/28133776/non-homologous-end-joining-common-interaction-sites-and-exchange-of-multiple-factors-in-the-dna-repair-process
#17
Stuart L Rulten, Gabrielle J Grundy
Non-homologous end-joining (NHEJ) is the dominant means of repairing chromosomal DNA double strand breaks (DSBs), and is essential in human cells. Fifteen or more proteins can be involved in the detection, signalling, synapsis, end-processing and ligation events required to repair a DSB, and must be assembled in the confined space around the DNA ends. We review here a number of interaction points between the core NHEJ components (Ku70, Ku80, DNA-PKcs, XRCC4 and Ligase IV) and accessory factors such as kinases, phosphatases, polymerases and structural proteins...
January 30, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/28119419/single-stranded-dna-library-preparation-from-highly-degraded-dna-using-t4-dna-ligase
#18
Marie-Theres Gansauge, Tobias Gerber, Isabelle Glocke, Petra Korlević, Laurin Lippik, Sarah Nagel, Lara Maria Riehl, Anna Schmidt, Matthias Meyer
DNA library preparation for high-throughput sequencing of genomic DNA usually involves ligation of adapters to double-stranded DNA fragments. However, for highly degraded DNA, especially ancient DNA, library preparation has been found to be more efficient if each of the two DNA strands are converted into library molecules separately. We present a new method for single-stranded library preparation, ssDNA2.0, which is based on single-stranded DNA ligation with T4 DNA ligase utilizing a splinter oligonucleotide with a stretch of random bases hybridized to a 3' biotinylated donor oligonucleotide...
January 23, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28118850/humans-from-wuchereria-bancrofti-endemic-area-elicit-substantial-immune-response-to-proteins-of-the-filarial-parasite-brugia-malayi-and-its-endosymbiont-wolbachia
#19
Ruchi Jha, Mamta Gangwar, Dhanvantri Chahar, Anand Setty Balakrishnan, Mahendra Pal Singh Negi, Shailja Misra-Bhattacharya
BACKGROUND: In the past, immune responses to several Brugia malayi immunodominant antigens have been characterized in filaria-infected populations; however, little is known regarding Wolbachia proteins. We earlier cloned and characterized few B. malayi (trehalose-6-phosphate phosphatase, Bm-TPP and heavy chain myosin, BmAF-Myo) and Wolbachia (translation initiation factor-1, Wol Tl IF-1 and NAD(+)-dependent DNA ligase, wBm-LigA) proteins and investigated the immune responses, which they triggered in animal models...
January 24, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/28116145/overexpression-of-pcna-attenuates-oxidative-stress-caused-delay-of-gap-filling-during-repair-of-uv-induced-dna-damage
#20
Yi-Chih Tsai, Yi-Hsiang Wang, Yin-Chang Liu
UVC irradiation-caused DNA lesions are repaired in mammalian cells solely by nucleotide excision repair (NER), which consists of sequential events including initial damage recognition, dual incision of damage site, gap-filling, and ligation. We have previously shown that gap-filling during the repair of UV-induced DNA lesions may be delayed by a subsequent treatment of oxidants or prooxidants such as hydrogen peroxide, flavonoids, and colcemid. We considered the delay as a result of competition for limiting protein/enzyme factor(s) during repair synthesis between NER and base excision repair (BER) induced by the oxidative chemicals...
2017: Journal of Nucleic Acids
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