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Nucleic Acids Research

Neha Nirwan, Pratima Singh, Gyana Gourab Mishra, Christopher M Johnson, Mark D Szczelkun, Katsuaki Inoue, Kutti R Vinothkumar, Kayarat Saikrishnan
McrBC is one of the three modification-dependent restriction enzymes encoded by the Escherichia coli K12 chromosome. Amongst restriction enzymes, McrBC and its close homologues are unique in employing the AAA+ domain for GTP hydrolysis-dependent activation of DNA cleavage. The GTPase activity of McrB is stimulated by the endonuclease subunit McrC. It had been reported previously that McrB and McrC subunits oligomerise together into a high molecular weight species. Here we conclusively demonstrate using size exclusion chromatography coupled multi-angle light scattering (SEC-MALS) and images obtained by electron cryomicroscopy that McrB exists as a hexamer in solution...
December 6, 2018: Nucleic Acids Research
Sergey V Melnikov, Nelli F Khabibullina, Elisabeth Mairhofer, Oscar Vargas-Rodriguez, Noah M Reynolds, Ronald Micura, Dieter Söll, Yury S Polikanov
During protein synthesis, ribosomes discriminate chirality of amino acids and prevent incorporation of D-amino acids into nascent proteins by slowing down the rate of peptide bond formation. Despite this phenomenon being known for nearly forty years, no structures have ever been reported that would explain the poor reactivity of D-amino acids. Here we report a 3.7Å-resolution crystal structure of a bacterial ribosome in complex with a D-aminoacyl-tRNA analog bound to the A site. Although at this resolution we could not observe individual chemical groups, we could unambiguously define the positions of the D-amino acid side chain and the amino group based on chemical restraints...
December 6, 2018: Nucleic Acids Research
Thalia Salinas, Samira El Farouk-Ameqrane, Elodie Ubrig, Claude Sauter, Anne-Marie Duchêne, Laurence Maréchal-Drouard
No abstract text is available yet for this article.
December 5, 2018: Nucleic Acids Research
Neelanjan Mukherjee, Hans-Hermann Wessels, Svetlana Lebedeva, Marcin Sajek, Mahsa Ghanbari, Aitor Garzia, Alina Munteanu, Dilmurat Yusuf, Thalia Farazi, Jessica I Hoell, Kemal M Akat, Altuna Akalin, Thomas Tuschl, Uwe Ohler
RNA-binding proteins (RBPs) control and coordinate each stage in the life cycle of RNAs. Although in vivo binding sites of RBPs can now be determined genome-wide, most studies typically focused on individual RBPs. Here, we examined a large compendium of 114 high-quality transcriptome-wide in vivo RBP-RNA cross-linking interaction datasets generated by the same protocol in the same cell line and representing 64 distinct RBPs. Comparative analysis of categories of target RNA binding preference, sequence preference, and transcript region specificity was performed, and identified potential posttranscriptional regulatory modules, i...
December 5, 2018: Nucleic Acids Research
Arthur R Gorter de Vries, Lucas G F Couwenberg, Marcel van den Broek, Pilar de la Torre Cortés, Jolanda Ter Horst, Jack T Pronk, Jean-Marc G Daran
Targeted DNA double-strand breaks (DSBs) with CRISPR-Cas9 have revolutionized genetic modification by enabling efficient genome editing in a broad range of eukaryotic systems. Accurate gene editing is possible with near-perfect efficiency in haploid or (predominantly) homozygous genomes. However, genomes exhibiting polyploidy and/or high degrees of heterozygosity are less amenable to genetic modification. Here, we report an up to 99-fold lower gene editing efficiency when editing individual heterozygous loci in the yeast genome...
December 5, 2018: Nucleic Acids Research
François Sieber, Antonio Placido, Samira El Farouk-Ameqrane, Anne-Marie Duchêne, Laurence Maréchal-Drouard
No abstract text is available yet for this article.
December 5, 2018: Nucleic Acids Research
Thea S Lotz, Thomas Halbritter, Christoph Kaiser, Martin M Rudolph, Leon Kraus, Florian Groher, Sabrina Steinwand, Josef Wachtveitl, Alexander Heckel, Beatrix Suess
Regulation of complex biological networks has proven to be a key bottleneck in synthetic biology. Interactions between the structurally flexible RNA and various other molecules in the form of riboswitches have shown a high-regulation specificity and efficiency and synthetic riboswitches have filled the toolbox of devices in many synthetic biology applications. Here we report the development of a novel, small molecule binding RNA aptamer, whose binding is dependent on light-induced change of conformation of its small molecule ligand...
December 5, 2018: Nucleic Acids Research
Lufen Chang, Lei Shen, Hu Zhou, Jing Gao, Hangyi Pan, Li Zheng, Brian Armstrong, Yang Peng, Guang Peng, Binhua P Zhou, Steven T Rosen, Binghui Shen
The downregulation of the DNA damage response (DDR) enables aggressive tumors to achieve uncontrolled proliferation against replication stress, but the mechanisms underlying this process in tumors are relatively complex. Here, we demonstrate a mechanism through which a distinct E3 ubiquitin ligase, ITCH, modulates DDR machinery in triple-negative breast cancer (TNBC). We found that expression of a nuclear form of ITCH was significantly increased in human TNBC cell lines and tumor specimens. Phosphorylation of ITCH at Ser257 by AKT led to the nuclear localization of ITCH and ubiquitination of H1...
December 4, 2018: Nucleic Acids Research
Kathryn L Black, Ammar S Naqvi, Mukta Asnani, Katharina E Hayer, Scarlett Y Yang, Elisabeth Gillespie, Asen Bagashev, Vinodh Pillai, Sarah K Tasian, Matthew R Gazzara, Martin Carroll, Deanne Taylor, Kristen W Lynch, Yoseph Barash, Andrei Thomas-Tikhonenko
No abstract text is available yet for this article.
December 4, 2018: Nucleic Acids Research
Daniel O'Reilly, Zachary J Kartje, Eman A Ageely, Elise Malek-Adamian, Maryam Habibian, Annabelle Schofield, Christopher L Barkau, Kushal J Rohilla, Lauren B DeRossett, Austin T Weigle, Masad J Damha, Keith T Gagnon
CRISPR (clustered regularly interspaced short palindromic repeat) endonucleases are at the forefront of biotechnology, synthetic biology and gene editing. Methods for controlling enzyme properties promise to improve existing applications and enable new technologies. CRISPR enzymes rely on RNA cofactors to guide catalysis. Therefore, chemical modification of the guide RNA can be used to characterize structure-activity relationships within CRISPR ribonucleoprotein (RNP) enzymes and identify compatible chemistries for controlling activity...
December 4, 2018: Nucleic Acids Research
Jun Xiong, Tian-Tian Ye, Cheng-Jie Ma, Qing-Yun Cheng, Bi-Feng Yuan, Yu-Qi Feng
In addition to DNA cytosine methylation (5-methyl-2'-deoxycytidine, m5dC), DNA adenine methylation (N6-methyl-2'-deoxyadenosine, m6dA) is another DNA modification that has been discovered in eukaryotes. Recent studies demonstrated that the content and distribution of m6dA in genomic DNA of vertebrates and mammals exhibit dynamic regulation, indicating m6dA may function as a potential epigenetic mark in DNA of eukaryotes besides m5dC. Whether m6dA undergoes the further oxidation in a similar way to m5dC remains elusive...
December 4, 2018: Nucleic Acids Research
Lijun Zhao, Jianzhong Cao, Kexin Hu, Penghui Wang, Guodong Li, Xiaodong He, Tanjun Tong, Limin Han
Although several studies indicate that RNA-binding proteins (RBPs) contribute to key steps in a variety of physiological processes and cancer, the detailed biological functions and mechanisms remain to be determined. By performing bioinformatics analysis using well-established hepatocellular carcinoma (HCC) datasets, we identified a set of HCC progression-associated RBPs (HPARBPs) and found that the global expression of HPARBPs was significantly correlated with patient prognosis. Among the 42 HPARBPs, human ribosomal protein S3 (RPS3) was one of the most abundant genes whose role remains uncharacterized in HCC...
December 4, 2018: Nucleic Acids Research
Pierre Dupuy, Laurent Sauviac, Claude Bruand
DNA double-strand breaks (DSB) in bacteria can be repaired by non-homologous end-joining (NHEJ), a two-component system relying on Ku and LigD. While performing a genetic characterization of NHEJ in Sinorhizobium meliloti, a representative of bacterial species encoding several Ku and LigD orthologues, we found that at least two distinct functional NHEJ repair pathways co-exist: one is dependent on Ku2 and LigD2, while the other depends on Ku3, Ku4 and LigD4. Whereas Ku2 likely acts as canonical bacterial Ku homodimers, genetic evidences suggest that Ku3-Ku4 form eukaryotic-like heterodimers...
December 4, 2018: Nucleic Acids Research
Marius Gheorghe, Geir Kjetil Sandve, Aziz Khan, Jeanne Chèneby, Benoit Ballester, Anthony Mathelier
Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is the most popular assay to identify genomic regions, called ChIP-seq peaks, that are bound in vivo by transcription factors (TFs). These regions are derived from direct TF-DNA interactions, indirect binding of the TF to the DNA (through a co-binding partner), nonspecific binding to the DNA, and noise/bias/artifacts. Delineating the bona fide direct TF-DNA interactions within the ChIP-seq peaks remains challenging. We developed a dedicated software, ChIP-eat, that combines computational TF binding models and ChIP-seq peaks to automatically predict direct TF-DNA interactions...
December 4, 2018: Nucleic Acids Research
Sara K Young-Baird, Byung-Sik Shin, Thomas E Dever
The heterotrimeric eukaryotic translation initiation factor (eIF) 2 plays critical roles in delivering initiator Met-tRNAiMet to the 40S ribosomal subunit and in selecting the translation initiation site. Genetic analyses of patients with MEHMO syndrome, an X-linked intellectual disability syndrome, have identified several unique mutations in the EIF2S3 gene that encodes the γ subunit of eIF2. To gain insights into the molecular consequences of MEHMO syndrome mutations on eIF2 function, we generated a yeast model of the human eIF2γ-I259M mutant, previously identified in a patient with MEHMO syndrome...
December 4, 2018: Nucleic Acids Research
Weina Ke, Enping Hong, Renata F Saito, Maria Cristina Rangel, Jian Wang, Mathias Viard, Melina Richardson, Emil F Khisamutdinov, Martin Panigaj, Nikolay V Dokholyan, Roger Chammas, Marina A Dobrovolskaia, Kirill A Afonin
Nucleic acid-based assemblies that interact with each other and further communicate with the cellular machinery in a controlled manner represent a new class of reconfigurable materials that can overcome limitations of traditional biochemical approaches and improve the potential therapeutic utility of nucleic acids. This notion enables the development of novel biocompatible 'smart' devices and biosensors with precisely controlled physicochemical and biological properties. We extend this novel concept by designing RNA-DNA fibers and polygons that are able to cooperate in different human cell lines and that have defined immunostimulatory properties confirmed by ex vivo experiments...
December 4, 2018: Nucleic Acids Research
Dmitry Sutormin, Natalia Rubanova, Maria Logacheva, Dmitry Ghilarov, Konstantin Severinov
An important antibiotic target, DNA gyrase is an essential bacterial enzyme that introduces negative supercoils into DNA and relaxes positive supercoils accumulating in front of moving DNA and RNA polymerases. By altering the superhelical density, gyrase may regulate expression of bacterial genes. The information about how gyrase is distributed along genomic DNA and whether its distribution is affected by drugs is scarce. During catalysis, gyrase cleaves both DNA strands forming a covalently bound intermediate...
December 4, 2018: Nucleic Acids Research
Pawel Dabrowski-Tumanski, Pawel Rubach, Dimos Goundaroulis, Julien Dorier, Piotr Sulkowski, Kenneth C Millett, Eric J Rawdon, Andrzej Stasiak, Joanna I Sulkowska
The KnotProt 2.0 database (the updated version of the KnotProt database) collects information about proteins which form knots and other entangled structures. New features in KnotProt 2.0 include the characterization of both probabilistic and deterministic entanglements which can be formed by disulfide bonds and interactions via ions, a refined characterization of entanglement in terms of knotoids, the identification of the so-called cysteine knots, the possibility to analyze all or a non-redundant set of proteins, and various technical updates...
December 1, 2018: Nucleic Acids Research
Xiaohuan Jin, Zhengyi Lv, Junbao Gao, Rui Zhang, Ting Zheng, Ping Yin, Dongqin Li, Liangcai Peng, Xintao Cao, Yan Qin, Staffan Persson, Bo Zheng, Peng Chen
Modified nucleosides on tRNA are critical for decoding processes and protein translation. tRNAs can be modified through 1-methylguanosine (m1G) on position 37; a function mediated by Trm5 homologs. We show that AtTRM5a (At3g56120) is a Trm5 ortholog in Arabidopsis thaliana. AtTrm5a is localized to the nucleus and its function for m1G and m1I methylation was confirmed by mutant analysis, yeast complementation, m1G nucleoside level on single tRNA, and tRNA in vitro methylation. Arabidopsis attrm5a mutants were dwarfed and had short filaments, which led to reduced seed setting...
December 1, 2018: Nucleic Acids Research
Angelo de Vivo, Anthony Sanchez, Jose Yegres, Jeonghyeon Kim, Sylvia Emly, Younghoon Kee
Timely stalling and resumption of RNA polymerases at damaged chromatin are actively regulated processes. Prior work showed an importance of FACT histone chaperone in such process. Here we provide a new role of OTUD5 deubiquitinase in the FACT-dependent process. Through a DUB RNAi screen, we found OTUD5 as a specific stabilizer of the UBR5 E3 ligase. OTUD5 localizes to DNA double strand breaks (DSBs), interacts with UBR5 and represses the RNA Pol II elongation and RNA synthesis. OTUD5 co-localizes and interacts with the FACT component SPT16 and antagonizes the histone H2A deposition at DSB lesions...
December 1, 2018: Nucleic Acids Research
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