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RNA polymerase

Caixia Hou, Tapan Biswas, Oleg Tsodikov
Bacterial primase DnaG is an essential nucleic acid polymerase that generates primers for replication of chromosomal DNA. The mechanism of DnaG remains unclear, due to the paucity of structural information on DnaG in complexes with other replisome components. Here we report the first crystal structures of noncovalent DnaG-DNA complexes, obtained with the RNA polymerase domain of Mycobacterium tuberculosis DnaG and various DNA ligands. One structure, obtained with ds DNA, reveals interactions with DnaG as it slides on ds DNA and suggests how DnaG binds template for primer synthesis...
March 20, 2018: Biochemistry
Daisuke Kobayashi, Katsunori Murota, Ryosuke Fujita, Kentaro Itokawa, Akira Kotaki, Meng Ling Moi, Hiroko Ejiri, Yoshihide Maekawa, Kohei Ogawa, Yoshio Tsuda, Toshinori Sasaki, Mutsuo Kobayashi, Tomohiko Takasaki, Haruhiko Isawa, Kyoko Sawabe
In 2014 in Japan, 162 autochthonous dengue cases were reported for the first time in nearly 70 years. Here, we report the results of the detection and isolation of dengue virus (DENV) from mosquitoes collected in Tokyo Metropolis in 2014 and 2015. The phylogenetic relationship among DENV isolates from mosquitoes and from patients based on both the entire envelope gene and whole coding sequences was evaluated. Herein, 2,298 female and 956 male Aedes albopictus mosquitoes were collected at six suspected locations of DENV infection in Tokyo Metropolis from August to October in 2014 and grouped into 124 and 35 pools, respectively, for viral genome detection and DENV isolation...
March 19, 2018: American Journal of Tropical Medicine and Hygiene
Ivana Mareković, Zrinka Bošnjak, Karla Jurić, Mario Ćorić, Sanja Popović-Grle
Nitroxoline (NTX), 5-nitro-8-hydroxyquinoline is an oral antibiotic with mechanism of bacteriostatic activity that is based on chelation of divalent cations required for bacterial RNA polymerase. Susceptibility to NTX of 100 Escherichia coli urine isolates was determined at the Department of Clinical and Molecular Microbiology, University Hospital Centre Zagreb during September and October 2017. Antimicrobial susceptibility was tested by disc diffusion and the results were interpreted according to the European Committee for Antimicrobial Susceptibility Testing (EUCAST) standards...
March 20, 2018: Journal of Chemotherapy
Choung-Soo Kim, Hyunsu Choi, Ki Cheol Park, Sung Won Kim, Dong-Il Sun
Objective This study investigated the ability of implanted human nasal inferior turbinate-derived mesenchymal stem cells (hTMSCs) to repair injured vocal folds. To this end, we used quantitative real-time polymerase chain reaction (PCR) to analyze the early phase of wound healing and histopathological analysis to explore the late phase of wound healing in xenograft animal models. Study Design Prospective animal study. Setting Research laboratory. Subjects and Methods The right-side lamina propria of the vocal fold was injured in 20 rabbits and 30 rats...
March 1, 2018: Otolaryngology—Head and Neck Surgery
Radhey S Gupta, Sahil Sawnani, Mobolaji Adeolu, Seema Alnajar, Aharon Oren
The genus Mycoplasma, including species earlier classified in the genera Eperythrozoon and Haemobartonella, contains ~ 120 species and constitutes an extensively polyphyletic assemblage of bacteria within the phylum Tenericutes. Due to their small genome sizes and lack of unique characteristics, the relationships among the mycoplasmas/Tenericutes are not reliably discerned. Using genome sequences for 140 Tenericutes, their evolutionary relationships were examined using multiple independent approaches. Phylogenomic trees were constructed for 63 conserved proteins, 45 ribosomal proteins, three main subunits of RNA polymerase and 16S rRNA gene sequences...
March 20, 2018: Antonie Van Leeuwenhoek
Duanyang Zhai, Chunhui Cui, Lang Xie, Lianxu Cai, Jinlong Yu
Metastasis is the primary cause of mortality in colorectal cancer (CRC), the mechanism of which remains unclear. In the present study, by detecting mRNA expression using a reverse transcription-quantitative polymerase chain reaction (qPCR), it was revealed that sterol regulatory element-binding protein 1 (SREBP1) is highly expressed in CRC. Using a cell wound healing assay and a cell invasion assay, a novel metastasis-promoting role for SREBP1 in CRC was identified. Furthermore, snail family transcriptional repressor 1 (SNAIL) was identified as a key downstream effector of SREBP1 in CRC by the use of small interfering RNA against SNAIL...
April 2018: Oncology Letters
Zhiyuan Xing, Fengbo Sun, Wang He, Zhiwei Wang, Xiuqi Song, Fengjuan Zhang
Ubiquitin-specific peptidase 39 (USP39) has been reported to participate in the mitotic spindle checkpoint and the process of cytokinesis. and has been identified as a therapeutic target for various types of cancer. However, the effect of USP39 in colorectal cancer (CRC) has not been investigated. To explore the functional role of USP39 in CRC cell growth, lentivirus-mediated RNA interference was applied to inhibit USP39 expression in SW1116 and HCT116 cells. The relative USP39 mRNA and protein expression levels were significantly reduced in the USP39 knockdown cells, as verified by reverse transcription-quantitative polymerase chain reaction and western blot analysis...
April 2018: Oncology Letters
Yaqiong Liu, Yi Fan, Xiaoyu Wang, Zijian Huang, Kun Shi, Bei Zhou
Cervical cancer is one of the most common gynecological malignancies. Mousasi 2 (Msi2) is a RNA-binding protein that regulates various key cellular functions and has emerged as a crucial regulator of cancer development. However, the clinical significance and biological functions of Msi2 in cervical cancer remain unknown. The current study assessed the expression of Msi2 mRNA using reverse transcription-quantitative polymerase chain reaction. Furthermore, the expression of Msi2 was examined in 162 cervical cancer samples using immunohistochemistry and the association between Msi2 expression and patient clinicopathological features was analyzed...
April 2018: Oncology Letters
Kunyuan Wang, Chenxi Duan, Xuejing Zou, Yang Song, Wenwen Li, Lushan Xiao, Jie Peng, Liheng Yao, Qian Long, Li Liu
Mediator complex subunit 15 (MED15) is a coactivator involved in the regulated transcription of RNA polymerase II-dependent genes and serves an oncogenic role in numerous types of cancer. However, the expression and function of MED15 in hepatocellular carcinoma (HCC) remain unknown. In the present study, the aim was to investigate the expression and clinical significance of MED15 in HCC. Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and immunohistochemical analysis revealed that MED15 mRNA and protein levels were significantly upregulated in HCC tissues compared with those in the corresponding adjacent non-tumor liver tissues...
April 2018: Oncology Letters
Anniina Vihervaara, Fabiana M Duarte, John T Lis
Proteotoxic stress, that is, stress caused by protein misfolding and aggregation, triggers the rapid and global reprogramming of transcription at genes and enhancers. Genome-wide assays that track transcriptionally engaged RNA polymerase II (Pol II) at nucleotide resolution have provided key insights into the underlying molecular mechanisms that regulate transcriptional responses to stress. In addition, recent kinetic analyses of transcriptional control under heat stress have shown how cells 'prewire' and rapidly execute genome-wide changes in transcription while concurrently becoming poised for recovery...
March 19, 2018: Nature Reviews. Genetics
Dai Hatakeyama, Masaki Shoji, Seiya Yamayoshi, Rina Yoh, Naho Ohmi, Shiori Takenaka, Ayaka Saitoh, Yumie Arakaki, Aki Masuda, Tsugunori Komatsu, Rina Nagano, Masahiro Nakano, Takeshi Noda, Yoshihiro Kawaoka, Takashi Kuzuhara
Histone acetylation plays crucial roles in transcriptional regulation and chromatin organization. Viral RNA of the influenza virus interacts with its nucleoprotein (NP), whose function corresponds to that of eukaryotic histones. NP regulates viral replication and has been shown to undergo acetylation by the CREB-binding protein (CBP) from the host. However, whether NP is the target of other host acetyltransferases is unknown. Here, we show that influenza virus NP undergoes acetylation by the two host acetyltransferases GCN5 and P300/CBP-associated factor (PCAF) and that this modification affects viral polymerase activities...
March 19, 2018: Journal of Biological Chemistry
Andrey G Baranovskiy, Vincent N Duong, Nigar D Babayeva, Yinbo Zhang, Youri I Pavlov, Karen S Anderson, Tahir H Tahirov
DNA polymerase α (Polα) plays an important role in genome replication. In a complex with primase, Polα synthesizes chimeric RNA-DNA primers necessary for replication of both chromosomal DNA strands. During RNA primer extension with deoxyribonucleotides, Polα needs to use double-stranded helical substrates having different structures. Here, we provide a detailed structure-function analysis of human Polα's interaction with dNTPs and DNA templates primed with RNA, chimeric RNA-DNA, or DNA. We report the crystal structures of two ternary complexes of the Polα catalytic domain containing dCTP, a DNA template, and either a DNA or an RNA primer...
March 19, 2018: Journal of Biological Chemistry
Hyukho Sheen, K Andrew White
Bacteriophage T7 promoter and RNA polymerase (T7-Pol) are widely used for recombinant protein expression in bacteria. In plants, there exists conflicting results regarding the efficacy of protein expression from T7-Pol-derived mRNAs. To reconcile these contradictory observations, the expression of green fluorescent protein (GFP) from T7 constructs was evaluated in tobacco protoplasts. T7 constructs transcribed by a nuclear-targeted T7-Pol did not express GFP in plant protoplasts, however T7-Pol lacking a nuclear targeting signal was able to translate cytosolic-transcribed mRNAs, but only if the messages contained a viral translation enhancer...
March 16, 2018: Biochemical and Biophysical Research Communications
Seong-Hyun Park, Kyung-Lee Yu, Yu-Mi Jung, Seong-Deok Lee, Ji Chang You
Transcription termination factor-1 (TTF-I) is an RNA polymerase 1-mediated transcription terminator and consisting of a C-terminal DNA-binding domain, central domain, and N-terminal regulatory domain. This protein binds to a so-called 'Sal box' composed of an 11-base pair motif. The interaction of TTF-I with the 'Sal box' is important for many cellular events, including efficient termination of RNA polymerase-1 activity involved in pre-rRNA synthesis and formation of a chromatin loop. To further understand the role of TTF-I in human immunodeficiency virus (HIV)-I virus production, we generated various TTF-I mutant forms...
March 20, 2018: BMB Reports
Maayan Margalit Levi, Yaarit Nachum-Biala, Roni King, Gad Baneth
BACKGROUND: Babesia spp. and Hepatozoon spp. are apicomplexan parasites that infect a variety of animals, including canids. Their life-cycle includes an invertebrate hematophagous vector as a definitive host and vertebrates as intermediate hosts. The aims of this study were to investigate the prevalence and risk factors for Babesia spp. and Hepatozoon spp. infections in wild golden jackals (Canis aureus) and red foxes (Vulpes vulpes) in Israel and to compare spleen with blood sample polymerase chain reaction (PCR) for the detection of infection...
March 20, 2018: Parasites & Vectors
M S da Silva, S Silveira, V S Caron, A C S Mósena, M N Weber, S P Cibulski, A A R Medeiros, G S Silva, L G Corbellini, R Klein, L C Kreutz, R Frandoloso, C W Canal
Background: Hepatitis E virus (HEV) is the causative agent of acute hepatitis worldwide. There is no seroprevalence study in backyard farms, which are characterized by suboptimal hygienic conditions in Brazil. We aimed to determine the seroprevalence and genetic diversity of HEV in backyard pigs in Brazil. Methods: Swine serum samples collected in 2012 (n=731) and 2014 (n=713) were analysed. The presence of anti-HEV immunoglobulin G in pig serum was evaluated by indirect enzyme-linked immunosorbent assay...
March 15, 2018: Transactions of the Royal Society of Tropical Medicine and Hygiene
Tomasz Krzywkowski, Malte Kühnemund, Di Wu, Mats Nilsson
Phi29 (Φ29) DNA polymerase is an enzyme commonly used in DNA amplification methods such as rolling circle amplification (RCA) and multiple strand displacement amplification (MDA), as well as in DNA sequencing methods such as single molecule real time (SMRT) sequencing. Here, we report the ability of phi29 DNA polymerase to amplify RNA-containing circular substrates during RCA. We found that circular substrates with single RNA substitutions are amplified at a similar amplification rate as non-chimeric DNA substrates, and that consecutive RNA pyrimidines were generally preferred over purines...
March 15, 2018: Nucleic Acids Research
Isaac H Solomon, Kristyn M Spera, Sophia L Ryan, Jeffrey Helgager, Juliana Andrici, Sherif R Zaki, Henrikas Vaitkevicius, Kristoffer E Leon, Michael R Wilson, Joseph L DeRisi, Sophia Koo, Stelios M Smirnakis, Umberto De Girolami
Importance: Powassan virus is a rare but increasingly recognized cause of severe neurological disease. Objective: To highlight the diagnostic challenges and neuropathological findings in a fatal case of Powassan encephalitis caused by deer tick virus (lineage II) in a patient with follicular lymphoma receiving rituximab, with nonspecific anti-GAD65 antibodies, who was initially seen with fever and orchiepididymitis. Design, Setting, and Participants: Comparison of clinical, radiological, histological, and laboratory findings, including immunohistochemistry, real-time polymerase chain reaction, antibody detection, and unbiased sequencing assays, in a single case report (first seen in December 2016) at an academic medical center...
March 19, 2018: JAMA Neurology
Xiuguo Yu, Jianpei Zhao, Yaguang He
PURPOSE: Recently, long noncoding RNAs (lncRNAs) have caught more attention for their role in tumor progression. Colon cancer is one of these ordinary malignant tumors. This study aimed to identify how lnc RNA PVT1 affects the progression of colon cancer. METHODS: PVT1 expression of both colon cancer cell tissue and 60 paired cancer and peri-tumoral tissue samples was detected by real-time quantitative polymerase chain reaction (RT-qPCR). The associations between lnc RNA PVT1 expression level and clinicopathological characteristics and patients' disease-free survival rate were evaluated...
January 2018: Journal of B.U.ON.: Official Journal of the Balkan Union of Oncology
Legang Sun, Ling Liu, Tingting Yu, Qiuqin Wang, Honghai Fu
In the present study, RNA interference (RNAi) was used to investigate the effect of vascular cell adhesion molecule 1 ( VCAM1 ) silencing on the proliferation of human oral squamous carcinoma HN12 cells. HN12 cells were divided into three groups: The untreated blank control cell group (CK), the negative control group transfected with non-homologous vector (NC) and the positive group transfected with the target sequence VCAM1 small hairpin RNA (KD). Reverse-transcription polymerase chain reaction and western blot analysis were used to examine the effects of VCAM1 -knockdown on the mRNA expression of VCAM1 and subsequent protein expression...
April 2018: Oncology Letters
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